diff --git a/.project b/.project
new file mode 100644
index 0000000000000000000000000000000000000000..809d36f60a6ac3bf52f0248047688a372acd94bf
--- /dev/null
+++ b/.project
@@ -0,0 +1,17 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<projectDescription>
+ <name>ih</name>
+ <comment></comment>
+ <projects>
+ </projects>
+ <buildSpec>
+ <buildCommand>
+ <name>org.python.pydev.PyDevBuilder</name>
+ <arguments>
+ </arguments>
+ </buildCommand>
+ </buildSpec>
+ <natures>
+ <nature>org.python.pydev.pythonNature</nature>
+ </natures>
+</projectDescription>
diff --git a/.pydevproject b/.pydevproject
new file mode 100644
index 0000000000000000000000000000000000000000..40e9f40a0ade3a088c757afd454acb9750da90c3
--- /dev/null
+++ b/.pydevproject
@@ -0,0 +1,5 @@
+<?xml version="1.0" encoding="UTF-8" standalone="no"?>
+<?eclipse-pydev version="1.0"?><pydev_project>
+<pydev_property name="org.python.pydev.PYTHON_PROJECT_INTERPRETER">Default</pydev_property>
+<pydev_property name="org.python.pydev.PYTHON_PROJECT_VERSION">python 2.7</pydev_property>
+</pydev_project>
diff --git a/.settings/org.eclipse.core.resources.prefs b/.settings/org.eclipse.core.resources.prefs
new file mode 100644
index 0000000000000000000000000000000000000000..9bf00a264e770c8124b759e1a325e07b7de9a0c9
--- /dev/null
+++ b/.settings/org.eclipse.core.resources.prefs
@@ -0,0 +1,2 @@
+eclipse.preferences.version=1
+encoding//docs/source/conf.py=utf-8
diff --git a/GPL.txt b/GPL.txt
new file mode 100644
index 0000000000000000000000000000000000000000..94a9ed024d3859793618152ea559a168bbcbb5e2
--- /dev/null
+++ b/GPL.txt
@@ -0,0 +1,674 @@
+ GNU GENERAL PUBLIC LICENSE
+ Version 3, 29 June 2007
+
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+by the Free Software Foundation.
+
+ If the Program specifies that a proxy can decide which future
+versions of the GNU General Public License can be used, that proxy's
+public statement of acceptance of a version permanently authorizes you
+to choose that version for the Program.
+
+ Later license versions may give you additional or different
+permissions. However, no additional obligations are imposed on any
+author or copyright holder as a result of your choosing to follow a
+later version.
+
+ 15. Disclaimer of Warranty.
+
+ THERE IS NO WARRANTY FOR THE PROGRAM, TO THE EXTENT PERMITTED BY
+APPLICABLE LAW. EXCEPT WHEN OTHERWISE STATED IN WRITING THE COPYRIGHT
+HOLDERS AND/OR OTHER PARTIES PROVIDE THE PROGRAM "AS IS" WITHOUT WARRANTY
+OF ANY KIND, EITHER EXPRESSED OR IMPLIED, INCLUDING, BUT NOT LIMITED TO,
+THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+PURPOSE. THE ENTIRE RISK AS TO THE QUALITY AND PERFORMANCE OF THE PROGRAM
+IS WITH YOU. SHOULD THE PROGRAM PROVE DEFECTIVE, YOU ASSUME THE COST OF
+ALL NECESSARY SERVICING, REPAIR OR CORRECTION.
+
+ 16. Limitation of Liability.
+
+ IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING
+WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MODIFIES AND/OR CONVEYS
+THE PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES, INCLUDING ANY
+GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING OUT OF THE
+USE OR INABILITY TO USE THE PROGRAM (INCLUDING BUT NOT LIMITED TO LOSS OF
+DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY YOU OR THIRD
+PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER PROGRAMS),
+EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF
+SUCH DAMAGES.
+
+ 17. Interpretation of Sections 15 and 16.
+
+ If the disclaimer of warranty and limitation of liability provided
+above cannot be given local legal effect according to their terms,
+reviewing courts shall apply local law that most closely approximates
+an absolute waiver of all civil liability in connection with the
+Program, unless a warranty or assumption of liability accompanies a
+copy of the Program in return for a fee.
+
+ END OF TERMS AND CONDITIONS
+
+ How to Apply These Terms to Your New Programs
+
+ If you develop a new program, and you want it to be of the greatest
+possible use to the public, the best way to achieve this is to make it
+free software which everyone can redistribute and change under these terms.
+
+ To do so, attach the following notices to the program. It is safest
+to attach them to the start of each source file to most effectively
+state the exclusion of warranty; and each file should have at least
+the "copyright" line and a pointer to where the full notice is found.
+
+ <one line to give the program's name and a brief idea of what it does.>
+ Copyright (C) <year> <name of author>
+
+ This program is free software: you can redistribute it and/or modify
+ it under the terms of the GNU General Public License as published by
+ the Free Software Foundation, either version 3 of the License, or
+ (at your option) any later version.
+
+ This program is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ GNU General Public License for more details.
+
+ You should have received a copy of the GNU General Public License
+ along with this program. If not, see <http://www.gnu.org/licenses/>.
+
+Also add information on how to contact you by electronic and paper mail.
+
+ If the program does terminal interaction, make it output a short
+notice like this when it starts in an interactive mode:
+
+ <program> Copyright (C) <year> <name of author>
+ This program comes with ABSOLUTELY NO WARRANTY; for details type `show w'.
+ This is free software, and you are welcome to redistribute it
+ under certain conditions; type `show c' for details.
+
+The hypothetical commands `show w' and `show c' should show the appropriate
+parts of the General Public License. Of course, your program's commands
+might be different; for a GUI interface, you would use an "about box".
+
+ You should also get your employer (if you work as a programmer) or school,
+if any, to sign a "copyright disclaimer" for the program, if necessary.
+For more information on this, and how to apply and follow the GNU GPL, see
+<http://www.gnu.org/licenses/>.
+
+ The GNU General Public License does not permit incorporating your program
+into proprietary programs. If your program is a subroutine library, you
+may consider it more useful to permit linking proprietary applications with
+the library. If this is what you want to do, use the GNU Lesser General
+Public License instead of this License. But first, please read
+<http://www.gnu.org/philosophy/why-not-lgpl.html>.
diff --git a/README.md b/README.md
index 60ff33b24ca2e5163d8b7dc367b3a4414634d2d8..b61f2e6100204dc3e505b07bb97334d91e366a72 100644
--- a/README.md
+++ b/README.md
@@ -1,2 +1,2 @@
Image Harvest Git Repo!
-Full documentation can be found on the [Project Webiste](http://cropstressgenomics.org/phenomics.php)
+Full documentation can be found on the [Project Website](http://cropstressgenomics.org/phenomics.php)
diff --git a/build/lib/htpia/__init__.py b/build/lib/htpia/__init__.py
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/build/lib/htpia/conf.py b/build/lib/htpia/conf.py
new file mode 100644
index 0000000000000000000000000000000000000000..65ba485c2ad13edddf382b18434e8e60b9be73cb
--- /dev/null
+++ b/build/lib/htpia/conf.py
@@ -0,0 +1,1239 @@
+import cv2
+
+"""
+A dictionary used to map input-output types to a cv2 color code
+"""
+colors = {
+ "bgr": {
+ "gray": [cv2.COLOR_BGR2GRAY],
+ "hsv": [cv2.COLOR_BGR2HSV],
+ "lab": [cv2.COLOR_BGR2LAB],
+ "ycrcb": [cv2.COLOR_BGR2YCR_CB]
+ },
+ "gray": {
+ "bgr": [cv2.COLOR_GRAY2BGR],
+ "hsv": [cv2.COLOR_GRAY2BGR, cv2.COLOR_BGR2HSV],
+ "lab": [cv2.COLOR_GRAY2BGR, cv2.COLOR_BGR2LAB],
+ "ycrcb": [cv2.COLOR_GRAY2BGR, cv2.COLOR_BGR2YCR_CB]
+ },
+ "hsv": {
+ "bgr": [cv2.COLOR_HSV2BGR],
+ "gray": [cv2.COLOR_HSV2BGR, cv2.COLOR_BGR2GRAY],
+ "lab": [cv2.COLOR_YCR_CB2BGR, cv2.COLOR_BGR2LAB],
+ "ycrcb": [cv2.COLOR_YCR_CB2BGR, cv2.COLOR_BGR2YCR_CB]
+ },
+ "lab": {
+ "bgr": [cv2.COLOR_LAB2BGR],
+ "gray": [cv2.COLOR_LAB2BGR, cv2.COLOR_BGR2GRAY],
+ "hsv": [cv2.COLOR_LAB2BGR, cv2.COLOR_BGR2HSV],
+ "ycrcb": [cv2.COLOR_LAB2BGR, cv2.COLOR_BGR2YCR_CB]
+ },
+ "ycrcb": {
+ "bgr": [cv2.COLOR_YCR_CB2BGR],
+ "gray": [cv2.COLOR_YCR_CB2BGR, cv2.COLOR_BGR2GRAY],
+ "hsv": [cv2.COLOR_YCR_CB2BGR, cv2.COLOR_BGR2HSV],
+ "lab": [cv2.COLOR_YCR_CB2BGR, cv2.COLOR_BGR2LAB]
+ }
+}
+
+"""
+A dicitonary used to map threshold-types to cv2 threshold codes
+"""
+thresholds = {
+ "binary": cv2.THRESH_BINARY,
+ "inverse": cv2.THRESH_BINARY_INV,
+ "truncate": cv2.THRESH_TRUNC,
+ "tozero": cv2.THRESH_TOZERO,
+ "otsu": cv2.THRESH_BINARY + cv2.THRESH_OTSU
+}
+
+"""
+A dictionary used to map adaptive-types to cv2 adaptive codes
+"""
+adaptives = {
+ "mean": cv2.ADAPTIVE_THRESH_MEAN_C,
+ "gauss": cv2.ADAPTIVE_THRESH_GAUSSIAN_C,
+ "gaussian": cv2.ADAPTIVE_THRESH_GAUSSIAN_C
+}
+
+"""
+A dictionary used to map border-types to cv2 border codes
+"""
+borders = {
+ "default": cv2.BORDER_DEFAULT,
+ "constant": cv2.BORDER_CONSTANT,
+ "reflect": cv2.BORDER_REFLECT,
+ "replicate": cv2.BORDER_REPLICATE,
+ "transparent": cv2.BORDER_TRANSPARENT,
+ "wrap": cv2.BORDER_WRAP
+}
+
+"""
+A dictionary used to map morphology types to cv2 morphology codes
+"""
+morph = {
+ "dilate": cv2.MORPH_DILATE,
+ "erode": cv2.MORPH_ERODE,
+ "open": cv2.MORPH_OPEN,
+ "close": cv2.MORPH_CLOSE,
+ "gradient": cv2.MORPH_GRADIENT,
+ "tophat": cv2.MORPH_TOPHAT,
+ "blackhat": cv2.MORPH_BLACKHAT
+}
+
+"""
+A dictionary used to map kernel types to cv2 kernel coces
+"""
+kernels = {
+ "rect": cv2.MORPH_RECT,
+ "ellipse": cv2.MORPH_ELLIPSE,
+ "cross": cv2.MORPH_CROSS
+}
+
+"""
+Defines the maximum size of a displayed image in total pixels.
+"""
+maxArea = 360000
+
+"""
+Defines imtype mapping
+"""
+typeMap = {
+ "rgbsv": "rgb",
+ "rgbtv": "rgb",
+ "fluosv": "fluo",
+ "fluotv": "fluo"
+}
+
+"""
+Defines all optional / required keys for all templates.
+"""
+
+templateKeys = {
+ "loading": {
+ "required": ["path", "base", "data", "order"],
+ "optional": ["translations", "filetype"],
+ "data": {
+ "required": ["type"],
+ "type": ["value", "file", "date"],
+ "value": {
+ "required": ["value", "type"],
+ "optional": ["translate"]
+ },
+ "file": {
+ "required": ["type", "value", "key", "keyColumn", "valueColumn"],
+ "optional": ["translate", "separator"]
+ },
+ "date": {
+ "required": ["type", "value", "format"],
+ "optional": []
+ }
+ },
+ "translations": {
+
+ }
+ },
+ "config": {
+ "required": ["installdir", "profile"],
+ "optional": ["cluster", "email"]
+ },
+ "imgproc": {
+ "required": ["workflows", "extract"],
+ "optional": ["options"],
+ "job": {
+ "required": ["executable", "inputs", "outputs", "arguments", "name"],
+ "optional": ["depends"]
+ },
+ "options": {
+ "required": [],
+ "optional": ["save-steps"]
+ },
+ "extract": {
+ "required": ["workflows"],
+ "optional": ["histogram-bin"],
+ "workflows": {
+ "required": [], # imtype are required, handled at run time.
+ "optional": []
+ },
+ "histogram-bin": {
+ "required": ["chunks", "group", "channels"],
+ "optional": []
+ }
+ }
+ },
+ "stats": {
+ "required": ["workflows"],
+ "optional": ["options"],
+ "job": {
+ "required": ["executable", "inputs", "outputs", "arguments", "name"],
+ "optional": ["depends"]
+ }
+ }
+}
+
+"""
+Defines valid date format character
+"""
+dateFormat = ["Y", "y", "M", "m", "d", "B", "b"]
+dateSep = ["/", "-", "_", " "]
+
+"""
+Defines required headers for output
+"""
+outHeaders = ["pegasusid", "experiment", "id", "genotype", "date", "treatment", "imgname", "imtype", "path"]
+
+"""
+Defines ALL possible output headers
+"""
+allHeaders = outHeaders + ["error", "rowNum", "colNum"]
+
+"""
+Defines required files for job checking
+"""
+jobFiles = ["config.json", "imgproc.json", "stats.json", "images.db"]
+imgprocFiles = ["config.json", "imgproc.json", "images.db"]
+statisticsFiles = ["config.json", "stats.json"]
+
+workflowFile = "imgproc.json"
+configFile = "config.json"
+dbFile = "images.db"
+statsFile = "stats.json"
+outputdb = "output.db"
+
+
+"""
+Defines two things for stats functions.
+'Required' columns are the metadata columns a function needs to execute properly.
+'Exclude' columns are the metadata columns that become uninteresting after execution.
+"""
+statsColumns = {
+ "histogramBins": {
+ "ref": False,
+ "add": ["name", "minr", "ming", "minb", "maxr", "maxg", "maxb"],
+ "required": ["pegasusid", "experiment", "id", "date", "imtype", "imgname", "outputPath"],
+ "exclude": ["all"],
+ "overwrite": []
+ },
+ "ttest": {
+ "ref": True,
+ "add": [],
+ "required": ["pegasusid", "date", "imtype"],
+ "exclude": ["pegasusid", "path", "outputPath", "error", "id", "genotype", "treatment"],
+ "overwrite": []
+ },
+ "treatmentComp": {
+ "ref": True,
+ "add": [],
+ "required": ["pegasusid", "id", "genotype", "date", "treatment", "imtype"],
+ "exclude": ["pegasusid", "id", "path", "outputPath", "error"],
+ "overwrite": ["treatment"]
+ },
+ "shootArea": {
+ "ref": True,
+ "add": [],
+ "required": ["pegasusid", "id", "genotype", "date", "treatment", "imtype"],
+ "exclude": ["pegasusid", "imgname", "path", "outputPath", "error", "rowNum", "colNum"],
+ "overwrite": ["imtype"]
+ },
+ "normalize": {
+ "ref": True,
+ "add": [],
+ "required": ["pegasusid"],
+ "exclude": ["pegasusid", "path", "outputPath", "error"],
+ "overwrite": []
+ },
+ "correlation": {
+ "ref": True,
+ "add": [],
+ "required": ["pegasusid", "id", "date"],
+ "exclude": ["pegasusid", "path", "outputPath", "error", "rowNum", "colNum", "date", "imgname"],
+ "overwrite": []
+ },
+ "threshold": {
+ "ref": True,
+ "add": [],
+ "required": ["pegasusid"],
+ "exclude": ["pegasusid", "path", "outputPath", "error"],
+ "overwrite": []
+ },
+ "anova": {
+ "ref": False,
+ "add": ["factors"],
+ "required": ["pegasusid", "treatment", "date", "imtype"],
+ "exclude": ["pegasusid", "experiment", "id", "genotype", "date", "treatment", "imgname", "path", "outputPath", "error"],
+ "overwrite": ["imtype"]
+ }
+}
+
+"""
+Defines allowed image extensions, png is preferred.
+"""
+imageExtensions = [".png", ".jpg", ".jpeg", ".gif"]
+
+"""
+Defines allowed file extensions
+"""
+fileExtensions = {
+ "image": ".png",
+ "roi": ".json",
+ "binfile": ".json",
+ "csv": ".csv",
+}
+
+
+"""
+Defines valid arguments for stats and image processing
+functions.
+"""
+valid = {
+ "pcv-color-filter": {
+ "type": "imgproc",
+ "inputs": ["image", "roi"],
+ "outputs": ["image"],
+ "arguments": {
+ "--input": {
+ "type": "derived",
+ "key": "inputs",
+ "index": 0,
+ "required": "true"
+ },
+ "--output": {
+ "type": "derived",
+ "key": "outputs",
+ "index": 0,
+ "required": "true"
+ },
+ "--outputdir": {
+ "type": "overwrite",
+ "value": "."
+ },
+ "--roi": {
+ "type": "derived",
+ "key": "inputs",
+ "index": 1
+ },
+ "--logic": {
+ "type": "string",
+ "required": "true",
+ "complex": "true"
+ }
+ }
+ },
+ "pcv-edges": {
+ "type": "imgproc",
+ "inputs": ["image"],
+ "outputs": ["image"],
+ "arguments": {
+ "--input": {
+ "type": "derived",
+ "key": "inputs",
+ "index": 0,
+ "required": "true"
+ },
+ "--output": {
+ "type": "derived",
+ "key": "outputs",
+ "index": 0,
+ "required": "true"
+ },
+ "--outputdir": {
+ "type": "overwrite",
+ "value": "."
+ },
+ "--threshold1": {
+ "type": "numeric",
+ "required": "true"
+ },
+ "--threshold2": {
+ "type": "numeric",
+ "required": "true"
+ },
+ "--apertureSize": {
+ "type": "numeric",
+ "validation": "list",
+ "value": range(1, 50)
+ },
+ "--L2gradient": {
+ "type": "exist"
+ }
+ }
+ },
+ "pcv-contour-cut": {
+ "type": "imgproc",
+ "inputs": ["image", "image"],
+ "outputs": ["image", "roi"],
+ "arguments": {
+ "--input": {
+ "type": "derived",
+ "key": "inputs",
+ "index": 0,
+ "required": "true"
+ },
+ "--binary": {
+ "type": "derived",
+ "key": "inputs",
+ "index": 1,
+ "required": "true"
+ },
+ "--output": {
+ "type": "derived",
+ "key": "outputs",
+ "index": 0,
+ "required": "true"
+ },
+ "--outputdir": {
+ "type": "overwrite",
+ "value": "."
+ },
+ "--basemin": {
+ "type": "numeric"
+ },
+ "--padminx": {
+ "type": "numeric"
+ },
+ "--padmaxx": {
+ "type": "numeric"
+ },
+ "--padminy": {
+ "type": "numeric"
+ },
+ "--padmaxy": {
+ "type": "numeric"
+ },
+ "--resize": {
+ "type": "exist"
+ },
+ "--returnBound": {
+ "type": "derived",
+ "key": "outputs",
+ "index": 1,
+ "value": ""
+ },
+ "--roiwrite": {
+ "type": "derived",
+ "key": "outputs",
+ "index": 1
+ }
+ }
+ },
+ "pcv-crop": {
+ "type": "imgproc",
+ "inputs": ["image", "roi"],
+ "outputs": ["image"],
+ "arguments": {
+ "--input": {
+ "type": "derived",
+ "key": "inputs",
+ "index": 0,
+ "required": "true"
+ },
+ "--output": {
+ "type": "derived",
+ "key": "outputs",
+ "index": 0,
+ "required": "true"
+ },
+ "--outputdir": {
+ "type": "overwrite",
+ "value": "."
+ },
+ "--roi": {
+ "type": "derived",
+ "key": "inputs",
+ "index": 1,
+ "required": "true"
+ },
+ "--resize": {
+ "type": "exist"
+ }
+ }
+ },
+ "pcv-morphology": {
+ "type": "imgproc",
+ "inputs": ["image"],
+ "outputs": ["image"],
+ "arguments": {
+ "--input": {
+ "type": "derived",
+ "key": "inputs",
+ "index": 0,
+ "required": "true"
+ },
+ "--output": {
+ "type": "derived",
+ "key": "outputs",
+ "index": 0,
+ "required": "true"
+ },
+ "--outputdir": {
+ "type": "overwrite",
+ "value": "."
+ },
+ "--morphType": {
+ "type": "string",
+ "validation": "dictionary",
+ "value": morph,
+ "required": "true"
+ },
+ "--ktype": {
+ "type": "string",
+ "validation": "dictionary",
+ "value": kernels,
+ "required": "true"
+ },
+ "--kwidth": {
+ "type": "numeric",
+ "validation": "list",
+ "value": range(1, 256, 2),
+ "required": "true"
+ },
+ "--kheight": {
+ "type": "numeric",
+ "validation": "list",
+ "value": range(1, 256, 2),
+ "required": "true"
+ },
+ "--anchorx": {
+ "type": "numeric",
+ "validation": "list",
+ "value": range(-255, 256),
+ },
+ "--anchory": {
+ "type": "numeric",
+ "validation": "list",
+ "value": range(-255, 256),
+ },
+ "--iterations": {
+ "type": "numeric",
+ "validation": "list",
+ "value": range(1, 100)
+ },
+ "--border": {
+ "type": "string",
+ "validation": "dictionary",
+ "value": borders
+ }
+ }
+ },
+ "pcv-normalize-intensity": {
+ "type": "imgproc",
+ "inputs": ["image"],
+ "outputs": ["image"],
+ "arguments": {
+ "--input": {
+ "type": "derived",
+ "key": "inputs",
+ "index": 0,
+ "required": "true"
+ },
+ "--output": {
+ "type": "derived",
+ "key": "outputs",
+ "index": 0,
+ "required": "true"
+ },
+ "--outputdir": {
+ "type": "overwrite",
+ "value": "."
+ }
+ }
+ },
+ "pcv-gaussian-blur": {
+ "type": "imgproc",
+ "inputs": ["image"],
+ "outputs": ["image"],
+ "arguments": {
+ "--input": {
+ "type": "derived",
+ "key": "inputs",
+ "index": 0,
+ "required": "true"
+ },
+ "--output": {
+ "type": "derived",
+ "key": "outputs",
+ "index": 0,
+ "required": "true"
+ },
+ "--outputdir": {
+ "type": "overwrite",
+ "value": "."
+ },
+ "--kwidth": {
+ "type": "numeric",
+ "validation": "list",
+ "value": range(1, 256, 2),
+ "required": "true"
+ },
+ "--kheight": {
+ "type": "numeric",
+ "validation": "list",
+ "value": range(1, 256, 2),
+ "required": "true"
+ },
+ "--sigmax": {
+ "type": "numeric"
+ },
+ "--sigmay": {
+ "type": "numeric"
+ },
+ "--border": {
+ "type": "string",
+ "validation": "dictionary",
+ "value": borders
+ }
+ }
+ },
+ "pcv-median-blur": {
+ "type": "imgproc",
+ "inputs": ["image"],
+ "outputs": ["image"],
+ "arguments": {
+ "--input": {
+ "type": "derived",
+ "key": "inputs",
+ "index": 0,
+ "required": "true"
+ },
+ "--output": {
+ "type": "derived",
+ "key": "outputs",
+ "index": 0,
+ "required": "true"
+ },
+ "--outputdir": {
+ "type": "overwrite",
+ "value": "."
+ },
+ "--ksize": {
+ "type": "numeric",
+ "validation": "list",
+ "value": range(1, 256, 2),
+ "required": "true"
+ }
+ }
+ },
+ "pcv-blur": {
+ "type": "imgproc",
+ "inputs": ["image"],
+ "outputs": ["image"],
+ "arguments": {
+ "--input": {
+ "type": "derived",
+ "key": "inputs",
+ "index": 0,
+ "required": "true"
+ },
+ "--output": {
+ "type": "derived",
+ "key": "outputs",
+ "index": 0,
+ "required": "true"
+ },
+ "--outputdir": {
+ "type": "overwrite",
+ "value": "."
+ },
+ "--kwidth": {
+ "type": "numeric",
+ "validation": "list",
+ "value": range(1, 256, 2),
+ "required": "true"
+ },
+ "--kheight": {
+ "type": "numeric",
+ "validation": "list",
+ "value": range(1, 256, 2),
+ "required": "true"
+ },
+ "--anchorx": {
+ "type": "numeric",
+ "validation": "list",
+ "value": range(-255, 256),
+ },
+ "--anchory": {
+ "type": "numeric",
+ "validation": "list",
+ "value": range(-255, 256),
+ },
+ "--border": {
+ "type": "string",
+ "validation": "dictionary",
+ "value": borders
+ }
+ }
+ },
+ "pcv-adaptive-threshold": {
+ "type": "imgproc",
+ "inputs": ["image"],
+ "outputs": ["image"],
+ "arguments": {
+ "--input": {
+ "type": "derived",
+ "key": "inputs",
+ "index": 0,
+ "required": "true"
+ },
+ "--output": {
+ "type": "derived",
+ "key": "outputs",
+ "index": 0,
+ "required": "true"
+ },
+ "--outputdir": {
+ "type": "overwrite",
+ "value": "."
+ },
+ "--value": {
+ "type": "numeric",
+ "validation": "list",
+ "value": range(0, 256),
+ "required": "true"
+ },
+ "--adaptiveType": {
+ "type": "string",
+ "validation": "dictionary",
+ "value": adaptives,
+ "required": "true"
+ },
+ "--thresholdType": {
+ "type": "string",
+ "validation": "dictionary",
+ "value": {"binary": "", "inverse": ""},
+ "required": "true"
+ },
+ "--blockSize": {
+ "type": "numeric",
+ "validation": "list",
+ "value": range(1, 256, 2),
+ "required": "true"
+ },
+ "--C": {
+ "type": "numeric",
+ "required": "true",
+ }
+ }
+ },
+ "pcv-meanshift": {
+ "type": "imgproc",
+ "inputs": ["image"],
+ "outputs": ["image"],
+ "weight": .3,
+ "arguments": {
+ "--input": {
+ "type": "derived",
+ "key": "inputs",
+ "index": 0,
+ "required": "true"
+ },
+ "--output": {
+ "type": "derived",
+ "key": "outputs",
+ "index": 0,
+ "required": "true"
+ },
+ "--outputdir": {
+ "type": "overwrite",
+ "value": "."
+ },
+ "--spatial_radius": {
+ "type": "numeric",
+ "required": "true"
+ },
+ "--range_radius": {
+ "type": "numeric",
+ "required": "true"
+ },
+ "--min_density": {
+ "type": "numeric",
+ "required": "true"
+ }
+ }
+ },
+ "pcv-convert-color": {
+ "type": "imgproc",
+ "inputs": ["image"],
+ "outputs": ["image"],
+ "arguments": {
+ "--input": {
+ "type": "derived",
+ "key": "inputs",
+ "index": 0,
+ "required": "true"
+ },
+ "--output": {
+ "type": "derived",
+ "key": "outputs",
+ "index": 0,
+ "required": "true"
+ },
+ "--outputdir": {
+ "type": "overwrite",
+ "value": "."
+ },
+ "--intype": {
+ "type": "string",
+ "validation": "dictionary",
+ "value": colors,
+ "required": "true"
+ },
+ "--outtype": {
+ "type": "string",
+ "validation": "dictionary",
+ "key": "--intype",
+ "value": colors,
+ "required": "true"
+ }
+ }
+ },
+ "pcv-threshold": {
+ "type": "imgproc",
+ "inputs": ["image"],
+ "outputs": ["image"],
+ "arguments": {
+ "--input": {
+ "type": "derived",
+ "key": "inputs",
+ "index": 0,
+ "required": "true"
+ },
+ "--output": {
+ "type": "derived",
+ "key": "outputs",
+ "index": 0,
+ "required": "true"
+ },
+ "--outputdir": {
+ "type": "overwrite",
+ "value": "."
+ },
+ "--thresh": {
+ "type": "numeric"
+ },
+ "--max": {
+ "type": "numeric",
+ "validation": "list",
+ "value": range(0, 256)
+ },
+ "--type": {
+ "type": "string",
+ "validation": "list",
+ "value": ["binary", "trunc", "otsu", "tozero"]
+ }
+ }
+ },
+ "pcv-bitwise-or": {
+ "type": "imgproc",
+ "inputs": ["image", "image"],
+ "outputs": ["image"],
+ "arguments": {
+ "--input1": {
+ "type": "derived",
+ "key": "inputs",
+ "index": 0,
+ "required": "true"
+ },
+ "--input2": {
+ "type": "derived",
+ "key": "inputs",
+ "index": 1,
+ "required": "true"
+ },
+ "--output": {
+ "type": "derived",
+ "key": "outputs",
+ "index": 0,
+ "required": "true"
+ },
+ "--outputdir": {
+ "type": "overwrite",
+ "value": "."
+ }
+ }
+ },
+ "pcv-bitwise-xor": {
+ "type": "imgproc",
+ "inputs": ["image", "image"],
+ "outputs": ["image"],
+ "arguments": {
+ "--input1": {
+ "type": "derived",
+ "key": "inputs",
+ "index": 0,
+ "required": "true"
+ },
+ "--input2": {
+ "type": "derived",
+ "key": "inputs",
+ "index": 1,
+ "required": "true"
+ },
+ "--output": {
+ "type": "derived",
+ "key": "outputs",
+ "index": 0,
+ "required": "true"
+ },
+ "--outputdir": {
+ "type": "overwrite",
+ "value": "."
+ }
+ }
+ },
+ "pcv-bitwise-not": {
+ "type": "imgproc",
+ "inputs": ["image"],
+ "outputs": ["image"],
+ "arguments": {
+ "--input": {
+ "type": "derived",
+ "key": "inputs",
+ "index": 0,
+ "required": "true"
+ },
+ "--output": {
+ "type": "derived",
+ "key": "outputs",
+ "index": 0,
+ "required": "true"
+ },
+ "--outputdir": {
+ "type": "overwrite",
+ "value": "."
+ }
+ }
+ },
+ "pcv-bitwise-and": {
+ "type": "imgproc",
+ "inputs": ["image", "image"],
+ "outputs": ["image"],
+ "arguments": {
+ "--input1": {
+ "type": "derived",
+ "key": "inputs",
+ "index": 0,
+ "required": "true"
+ },
+ "--input2": {
+ "type": "derived",
+ "key": "inputs",
+ "index": 1,
+ "required": "true"
+ },
+ "--output": {
+ "type": "derived",
+ "key": "outputs",
+ "index": 0,
+ "required": "true"
+ },
+ "--outputdir": {
+ "type": "overwrite",
+ "value": "."
+ }
+ }
+ },
+ "pcv-extract": {
+ "type": "system",
+ "inputs": ["image", "binfile"],
+ "outputs": ["none"],
+ "arguments": {
+ "--input": {
+ "type": "derived",
+ "key": "inputs",
+ "index": 0,
+ "required": "true"
+ },
+ "--dimensions": {
+ "type": "exist"
+ },
+ "--pixels": {
+ "type": "exist"
+ },
+ "--moments": {
+ "type": "exist"
+ },
+ "--bins": {
+ "type": "string"
+ },
+ "--channels": {
+ "type": "exist"
+ }
+ }
+ },
+ "pcv-error-log": {
+ "type": "imgproc"
+ },
+ "pcv-extract-all": {
+ "type": "system"
+ },
+ "pcv-extract-multi": {
+ "type": "system"
+ },
+ "pcv-sql-aggregate": {
+ "type": "system"
+ },
+ "pcv-stats-export": {
+ "type": "statistics",
+ "inputs": ["table"],
+ "outputs": ["csv"],
+ "arguments": {
+ "--table": {
+ "type": "derived",
+ "key": "inputs",
+ "index": 0,
+ "required": "true"
+ },
+ "--fname": {
+ "type": "derived",
+ "key": "outputs",
+ "index": 0,
+ "required": "true"
+ }
+ }
+ },
+ "pcv-stats-histogram-bin": {
+ "type": "system",
+ "inputs": ["table"],
+ "outputs": ["table"],
+ "arguments": {
+ "--intable": {
+ "type": "derived",
+ "key": "inputs",
+ "index": 0,
+ "required": "true"
+ },
+ "--outtable": {
+ "type": "derived",
+ "key": "outputs",
+ "index": 0,
+ "required": "true"
+ },
+ "--channels": {
+ "type": "dict",
+ "required": "true"
+ },
+ "--group": {
+ "type": "dict",
+ "required": "true"
+ },
+ "--chunks": {
+ "type": "dict",
+ "required": "true"
+ }
+ }
+ },
+ "pcv-stats-ttest": {
+ "type": "statistics",
+ "inputs": ["table"],
+ "outputs": ["table"],
+ "arguments": {
+ "--intable": {
+ "type": "derived",
+ "key": "inputs",
+ "index": 0,
+ "required": "true"
+ },
+ "--outtable": {
+ "type": "derived",
+ "key": "outputs",
+ "index": 0,
+ "required": "true"
+ },
+ "--comp": {
+ "type": "string",
+ "validation": "list",
+ "value": ["imtype", "imgname"],
+ "required": "true"
+ },
+ "--overwrite": {
+ "type": "overwrite",
+ "value": ""
+ }
+ }
+ },
+ "pcv-stats-treatment-comp": {
+ "type": "statistics",
+ "inputs": ["table"],
+ "outputs": ["table"],
+ "arguments": {
+ "--intable": {
+ "type": "derived",
+ "key": "inputs",
+ "index": 0,
+ "required": "true"
+ },
+ "--outtable": {
+ "type": "derived",
+ "key": "outputs",
+ "index": 0,
+ "required": "true"
+ },
+ "--type": {
+ "type": "string",
+ "validation": "list",
+ "value": ["ratio", "difference"],
+ "required": "true"
+ },
+ "--direction": {
+ "type": "string",
+ "validation": "list",
+ "value": ["Control", "Stress"],
+ "required": "true"
+ },
+ "--comp": {
+ "type": "string",
+ "validation": "list",
+ "value": ["imtype", "imgname"],
+ "required": "true"
+ },
+ "--overwrite": {
+ "type": "overwrite",
+ "value": ""
+ }
+ }
+ },
+ "pcv-stats-anova": {
+ "type": "statistics",
+ "inputs": ["table"],
+ "outputs": ["table"],
+ "arguments": {
+ "--group": {
+ "type": "list",
+ "required": "true",
+ "join": " "
+ },
+ "--intable": {
+ "type": "derived",
+ "key": "inputs",
+ "index": 0,
+ "required": "true"
+ },
+ "--outtable": {
+ "type": "derived",
+ "key": "outputs",
+ "index": 0,
+ "required": "true"
+ },
+ "--overwrite": {
+ "type": "overwrite",
+ "value": ""
+ }
+ }
+ },
+ "pcv-stats-shoot-area": {
+ "type": "statistics",
+ "inputs": ["table"],
+ "outputs": ["table"],
+ "arguments": {
+ "--group": {
+ "type": "list",
+ "required": "true",
+ "join": " "
+ },
+ "--intable": {
+ "type": "derived",
+ "key": "inputs",
+ "index": 0,
+ "required": "true"
+ },
+ "--outtable": {
+ "type": "derived",
+ "key": "outputs",
+ "index": 0,
+ "required": "true"
+ },
+ "--overwrite": {
+ "type": "overwrite",
+ "value": ""
+ }
+ }
+ },
+ "pcv-stats-threshold": {
+ "type": "statistics",
+ "inputs": ["table"],
+ "outputs": ["table"],
+ "arguments": {
+ "--thresh": {
+ "type": "numeric",
+ "required": "true"
+ },
+ "--intable": {
+ "type": "derived",
+ "key": "inputs",
+ "index": 0,
+ "required": "true"
+ },
+ "--outtable": {
+ "type": "derived",
+ "key": "outputs",
+ "index": 0,
+ "required": "true"
+ },
+ "--overwrite": {
+ "type": "overwrite",
+ "value": ""
+ }
+ }
+ },
+ "pcv-stats-normalize": {
+ "type": "statistics",
+ "inputs": ["table"],
+ "outputs": ["table"],
+ "arguments": {
+ "--column": {
+ "type": "string"
+ },
+ "--intable": {
+ "type": "derived",
+ "key": "inputs",
+ "index": 0,
+ "required": "true"
+ },
+ "--outtable": {
+ "type": "derived",
+ "key": "outputs",
+ "index": 0,
+ "required": "true"
+ },
+ "--overwrite": {
+ "type": "overwrite",
+ "value": ""
+ }
+ }
+ },
+ "pcv-stats-correlate": {
+ "type": "statistics",
+ "inputs": ["table", "csv", "csv"],
+ "outputs": ["table"],
+ "arguments": {
+ "--intable": {
+ "type": "derived",
+ "key": "inputs",
+ "index": 0,
+ "required": "true"
+ },
+ "--outtable": {
+ "type": "derived",
+ "key": "outputs",
+ "index": 0,
+ "required": "true"
+ },
+ "--datafile": {
+ "type": "derived",
+ "key": "inputs",
+ "index": 1,
+ "required": "true"
+ },
+ "--dataheaders": {
+ "type": "derived",
+ "key": "inputs",
+ "index": 2,
+ "required": "true"
+ },
+ "--overwrite": {
+ "type": "overwrite",
+ "value": ""
+ }
+ }
+ }
+}
diff --git a/build/lib/htpia/imgproc.py b/build/lib/htpia/imgproc.py
new file mode 100644
index 0000000000000000000000000000000000000000..38cd0c4ae215016fc23eb3bacbd281a6505310f7
--- /dev/null
+++ b/build/lib/htpia/imgproc.py
@@ -0,0 +1,940 @@
+"""
+
+.. module:: imgproc
+ :platform: Mac, Linux
+ :synopsis: Image processing function wrappers to opencv.
+
+.. moduleauthor:: Avi Knecht <avi@kurtknecht.com>
+
+"""
+
+import os
+import cv2
+import numpy as np
+import math
+import conf
+import sqlite3
+import pymeanshift as pms
+import traceback
+import json
+
+class ColorFilter(object):
+
+ """
+ Color Filtration logic container.
+ """
+ def __init__(self, filter):
+ self.tokens = {
+ "True": True,
+ "False": False,
+ "and": lambda left, right: np.logical_and(left, right),
+ "or": lambda left, right: np.logical_or(left, right),
+ ">": lambda left, right: left > right,
+ "<": lambda left, right: left < right,
+ ">=": lambda left, right: left >= right,
+ "<=": lambda left, right: left <= right,
+ "=": lambda left, right: left == right,
+ "+": lambda left, right: left + right,
+ "-": lambda left, right: left - right,
+ "*": lambda left, right: left * right,
+ "/": lambda left, right: left / right,
+ "max": lambda left, right: np.maximum(left, right),
+ "min": lambda left, right: np.minimum(left, right),
+ "not": lambda left, right: np.invert(left),
+ "(": "(",
+ ")": ")",
+ }
+ self.filterString = filter
+ self.emptyRes = True
+ return
+
+ def _createArgList(self):
+ s = self.filterString.replace("(", " ( ")
+ s = s.replace(")", " ) ")
+ self.filter = []
+ for item in s.split():
+ if item in self.tokens:
+ self.filter.append(self.tokens[item])
+ else:
+ try:
+ val = int(item)
+ self.filter.append(val)
+ except:
+ raise Exception("Invalid logic string.")
+ #self.filter = [self.tokens[x] if x in self.tokens else int(x) for x in s.split()]
+ return
+
+ def _find(self, what, start = 0):
+ return [i for i,x in enumerate(self.filter) if x == what and i >= start]
+
+ def _parens(self):
+ left_1st = self._find("(")
+ if not left_1st:
+ return False, -1, -1
+ left = left_1st[-1]
+ right = self._find(")", left + 2)[0]
+ return True, left, right
+
+ def _eval(self, filter):
+ return filter[1](filter[0], filter[2])
+
+ def _formattedEval(self, filter):
+ if not filter:
+ return self.emptyRes
+ if len(filter) == 1:
+ return filter[0]
+
+ has_parens, l_paren, r_paren = self._parens()
+
+ if not has_parens:
+ return self._eval(filter)
+
+ filter[l_paren:r_paren + 1] = [self._eval(filter[l_paren+1:r_paren])]
+ self.emptyRes = self._eval
+ return self._formattedEval(filter)
+
+ def apply(self, image, roi):
+ self.tokens["r"] = image[:,:,2].astype(float)
+ self.tokens["g"] = image[:,:,1].astype(float)
+ self.tokens["b"] = image[:,:,0].astype(float)
+ self._createArgList()
+ result = cv2.cvtColor(np.where(self._formattedEval(self.filter), 255, 0).astype(np.uint8), cv2.COLOR_GRAY2BGR)
+ image[roi[0]:roi[1], roi[2]:roi[3]] = cv2.bitwise_and(image[roi[0]:roi[1], roi[2]:roi[3]], result[roi[0]:roi[1], roi[2]:roi[3]])
+ return image
+
+
+
+class Image(object):
+
+ """
+ Each image is instantiated as a class
+ """
+ def __init__(self, input, outputdir = ".", writename = None, dev = False, db = None, dbid = None):
+ """
+ :param input: The input resource, either a path to an image or a raw numpy array.
+ :type resource: numpy.ndarray or str
+ :param outputdir: The directory to write output files
+ :type outputdir: str
+ :param writename: The name to write the output file as, should include extension.
+ :type writename: str
+ :param dev: Dev mode will do something...
+ :type dev: bool
+ """
+ if os.path.isdir(outputdir):
+ self.states = {}
+ self._loadDb(db, dbid)
+ self.input = input
+ self.fname, self.image = self._loadResource(input)
+ self.y = self.image.shape[0]
+ self.x = self.image.shape[1]
+ self.outputdir = os.path.abspath(outputdir)
+ if writename:
+ self.writename = writename
+ elif isinstance(input, np.ndarray):
+ self.writename = "out.png"
+ else:
+ self.writename = os.path.basename(input)
+ self.dev = dev
+ self.window = 1
+ else:
+ raise Exception("Invalid output!")
+ return
+
+ def _loadDb(self, db, dbid):
+ if db:
+ if os.path.isfile(db):
+ if dbid:
+ self.dbid = dbid
+ self.conn = sqlite3.connect(db, check_same_thread = False)
+ self.conn.row_factory = sqlite3.Row
+ result = self.conn.execute("select pegasusid from images where pegasusid=?", (self.dbid,))
+ if not result.fetchone():
+ raise Exception("Invalid pegasusid given!")
+ self._addColumn("error")
+ else:
+ raise Exception("A database id must be provided if you give a database.")
+ else:
+ raise Exception("Invalid database given!")
+ else:
+ self.conn = False
+ return
+
+ def _addColumn(self, column, tablename = "images"):
+ if self.conn:
+ if column not in [row["name"] for row in self.conn.execute("PRAGMA table_info(" + tablename + ");")]:
+ self.conn.execute("alter table " + tablename + " add column " + column + ";")
+ self.conn.commit()
+ return
+
+ def _loadROIArg(self, arg, i):
+ vals = {
+ 0: "0",
+ 1: str(self.y),
+ 2: "0",
+ 3: str(self.x)
+ }
+ arg = str(arg)
+ arg = arg.replace("x", str(self.x)).replace("y", str(self.y)).replace(" ","").replace("-1",vals[i])
+ if "-" in arg:
+ try:
+ left, right = arg.split("-")
+ return int(left) - int(right)
+ except:
+ raise Exception("Could not load roi arg '%s'" % (arg,))
+ elif "+" in arg:
+ try:
+ left, right = arg.split("+")
+ return int(left) + int(right)
+ except:
+ raise Exception("Could not load roi arg '%s'" % (arg,))
+ else:
+ return int(arg)
+
+ def _loadROI(self, roi):
+ """
+ :param roi: The region of interest to load.
+ :type roi: list or file
+ :return: The region of interest of form [ystart, yend, xstart, xend]
+ :rtype: list
+ :raises OSError: if the input path does not exist.
+
+ Loads a region of interest, either a path to an roi or a raw list.
+ """
+ if not roi:
+ roi = [-1, -1, -1, -1]
+ if isinstance(roi, list):
+ return [self._loadROIArg(z, i) for i,z in enumerate(roi)]
+ else:
+ if os.path.isfile(roi):
+ try:
+ with open(roi, "r") as rh:
+ r = json.load(rh)
+ if all(x in r for x in ["xstart", "xend", "ystart", "yend"]):
+ return [self._loadROIArg(r["ystart"], 0), self._loadROIArg(r["yend"], 1), self._loadROIArg(r["xstart"], 2), self._loadROIArg(r["xend"], 3)]
+ else:
+ raise Exception("Input roi file '%s' needs xstart, xend, ystart, and yend definitions!" % (roi,))
+ except Exception as e:
+ print traceback.format_exc()
+ raise Exception("Input roi file '%s' is not valid json!" % (roi,))
+ else:
+ raise Exception("Input path to roi file '%s' does not exist!" % (roi,))
+ return
+
+ def _writeROI(self, roi, output):
+ """
+ :param roi: The region of interest to write.
+ :type roi: list
+ """
+ try:
+ with open(self.outputdir + "/" + output, "w") as wh:
+ wh.write(json.dumps({"ystart": roi[0], "yend": roi[1], "xstart": roi[2], "xend": roi[3]}, indent = 4))
+ except:
+ raise Exception("Could not write roi.")
+ return
+
+ def _loadBins(self, binlist):
+ """
+ :param bin: The bin to load
+ :type bin: list or file
+ """
+
+ if isinstance(binlist, list):
+ return binlist
+ else:
+ if os.path.isfile(binlist):
+ try:
+ with open(binlist, "r") as rh:
+ return json.load(rh)
+ except:
+ raise Exception("Bin list not valid json!")
+ else:
+ raise Exception("Bin file does not exist.")
+ return
+
+ def _loadResource(self, resource):
+ """
+ :param resource: The resource to load.
+ :type resource: numpy.ndarray or file
+ :return: The image
+ :rtype: numpy.ndarray
+ :raises OSError: if the input path does not exist.
+
+ Loads a resource, either a path to an image or a raw numpy array.
+ """
+ if isinstance(resource, np.ndarray):
+ return ("unknown", resource.copy())
+ else:
+ if resource in self.states:
+ return (resource, self.states[resource].copy())
+ elif os.path.isfile(resource):
+ image = cv2.imread(resource)
+ if image is not None:
+ return (os.path.basename(resource), image)
+ else:
+ if self.conn:
+ self.conn.execute("update images set error =? where pegasusid = ?", ("Load Error, input is not an image.", self.dbid))
+ self.conn.commit()
+ raise Exception("Input is not an image.")
+ else:
+ if self.conn:
+ self.conn.execute("update images set error = ? where pegasusid = ?", ("Load Error, input path doesn't exist or specified resource is not a saved state.", self.dbid))
+ self.conn.commit()
+ raise Exception("Input path to resource does not exist.")
+ return
+
+ def _colorHistogram(self):
+ """
+ :return: A list of histograms, corresponding to R, G, B.
+ :rtype: List of numpy arrays.
+
+ Calculates a normalized colorHistogram of the current image.
+ The intensity is normalized between 0 and 255.
+ """
+ returnhist = []
+
+ for ch in range(0, 3):
+ hist_item = cv2.calcHist([self.image], [ch], None, [256], [1,255])
+ cv2.normalize(hist_item, hist_item, 0, 255, cv2.NORM_MINMAX)
+ hist = np.int32(np.around(hist_item))
+ returnhist.append(hist)
+ return returnhist
+
+ def _isColor(self, image = None):
+ image = self.image if image is None else image
+ return len(image.shape) == 3
+
+ def save(self, name):
+ """
+ :param name: The name to save the image under.
+ :type name: str OR any hashable type.
+
+ This function saves the current image in the 'states' variable under
+ the specified name. It can then be reloaded using the :py:meth:`~htpia.imgproc.Image.restore`
+ method.
+ """
+ self.states[name] = self.image.copy()
+ return
+
+ def restore(self, name):
+ """
+ :param name: The name the image is saved under.
+ :type name: str OR any hashable type.
+
+ Reloads a previously saved image from the 'states' variable.
+ """
+ if name in self.states:
+ self.image = self.states[name].copy()
+ else:
+ print "Invalid state specified."
+ return
+
+ def list(self):
+ """
+ Lists all saved states.
+ """
+ for state in self.states:
+ print state
+ return
+
+ def destroy(self):
+ """
+ Destroys all currently open windows.
+ """
+ cv2.destroyAllWindows()
+ return
+
+ def wait(self):
+ """
+ Waits until a key is pressed, then destroys all windows and
+ continues program execution.
+ """
+ cv2.waitKey(0)
+ self.destroy()
+ return
+
+ def show(self, title = None):
+ """
+ :param title: The title to give the display window, if left blank one will be created.
+ :type title: str
+ :return: None
+
+ Displays the image in a window. Utilizes the :py:meth:`~htpia.ImageProcessor.Image.resize` function.
+ If a title is not specified, the window will be named 'windowX' where X is the number of times
+ show has been called.
+
+ """
+ cv2.imshow(title if title else "window " + str(self.window), self.resize())
+ self.window += 1
+ return
+
+ def resize(self):
+ """
+ If the image is large than conf.maxArea, resize its total area down to conf.maxArea.
+ This function is primarily used for viewing purposes, and as such, it does not resize
+ the base image, but creates a copy to resize instead.
+ """
+ if (self.image.shape[0] * self.image.shape[1] > conf.maxArea):
+ scale = 1 / math.sqrt((self.image.shape[1] * self.image.shape[0]) / conf.maxArea)
+ return cv2.resize(self.image.copy(), (int(self.image.shape[1]*scale), int(self.image.shape[0]*scale)))
+ else:
+ return self.image
+
+ def write(self, name = None):
+ """
+ Writes the current image to the given output directory, with the given name.
+ """
+ writename = self.writename if not name else name
+ cv2.imwrite(self.outputdir + "/" + writename, self.image)
+ return
+
+ def convertColor(self, intype, outtype):
+ """
+ :param intype: The input image type
+ :type intype: str
+ :param outtype: The output image type
+ :type outtype: str
+ :return: The converted image.
+ :rtype: numpy.ndarray
+ :raises: KeyError
+
+ Converts the given image between color spaces, based on the given types.
+ Supported types are: rgb, bgr, gray, hsv, lab, and ycrcb
+ """
+ if intype in conf.colors:
+ if outtype in conf.colors[intype]:
+ for code in conf.colors[intype][outtype]:
+ self.image = cv2.cvtColor(self.image, code)
+ else:
+ raise KeyError(outtype + " is not a valid image type.")
+ else:
+ raise KeyError(intype + " is not a valid image type.")
+ return
+
+ def threshold(self, thresh, max = 255, type = "binary"):
+ """
+ :param thresh: Threshold value.
+ :type thresh: int
+ :param max: Write value for binary threshold.
+ :type max: int
+ :param type: Threhsold type.
+ :type type: str
+ :return: The thresholded image.
+ :rtype: numpy.ndarray
+ :raises KeyError: if the specified threshold type doesn't exist.
+
+ Thresholds the image based on the given type.
+ Supported types are: binary, truncate, tozero, and otsu.
+ """
+ if self._isColor():
+ self.convertColor("bgr", "gray")
+ if type in conf.thresholds:
+ self.image = cv2.threshold(self.image, thresh, max, conf.thresholds[type])[1]
+ else:
+ raise KeyError(type + " is not a valid threshold type.")
+ return
+
+ def meanshift(self, spatial_radius, range_radius, min_density):
+ """
+ :param spatial_radius: Spatial Radius
+ :type spatial_radius: float
+ :param range_radius: Range Radius.
+ :type range_radius: float
+ :param min_density: Minimum Density.
+ :type min_density: int
+ :return: The mean-shifted image.
+ :rtype: numpy.ndarray
+
+ Reference to paper HERE: http://dx.doi.org/10.1109/34.1000236
+ Reference to pymeanshift HERE: https://code.google.com/p/pymeanshift/
+ Segments the image into clusters based on nearest neighbors.
+ """
+ (self.image, labels_image, number_regions) = pms.segment(self.image, spatial_radius = spatial_radius, range_radius = range_radius, min_density = min_density)
+ return
+
+ def adaptiveThreshold(self, value, adaptiveType, thresholdType, blockSize, C):
+ """
+ :param value: Write value for the pixels based on the conditions.
+ :type param: int
+ :param adaptiveType: Adaptive algorithm to use, should be either 'mean' or 'gaussian'.
+ :type adaptiveType: str
+ :param thresholdType: Threshold type, should be either 'binary' or 'inverse'.
+ :type thresholdType: str
+ :param blockSize: The window size to consider while thresholding, should only be an odd number.
+ :type blockSize: int
+ :param C: A constant subtracted from the calculated mean in each window.
+ :type C: int
+
+ Thresholds an image by considering the image in several different windows instead of the image
+ as a whole. MATH HERE, REFERENCE OPENCV DOCS.
+ """
+ if self._isColor():
+ self.convertColor("bgr", "gray")
+ if adaptiveType in conf.adaptives:
+ if thresholdType == "binary" or thresholdType == "inverse":
+ self.image = cv2.adaptiveThreshold(self.image, value, conf.adaptives[adaptiveType], conf.thresholds[thresholdType], blockSize, C)
+ else:
+ raise Exception("Threshold type: " + thresholdType + " must be either binary or inverse.")
+ else:
+ raise Exception("Adaptive type: " + adaptiveType + " is not a valid adaptive threshold type, should be either 'mean' or 'gaussian'")
+ return
+
+ def blur(self, ksize, anchor = (-1, -1), borderType = "default"):
+ """
+ :param ksize: The size of the kernel represented by a tuple (width, height). Both numbers should be odd and positive.
+ :type ksize: tuple
+ :param anchor: The anchor point for filtering. Default is (-1, -1) which is the center of the kernel.
+ :type anchor: tuple
+ :param borderType: The type of border mode used to extrapolate pixels outside the image. Literally no information on this.
+ :type borderType: str
+
+ This function smoothes an image using the following kernel: MATH HERE.
+
+ Changing the anchor point changes the location considered by the kernel. If you have
+ the kernel: MATH, when the anchor point is in the center, you consider 1 pixel in each
+ direciton around your target pixel. If you move the anchor point to the top, you consider
+ no pixels above, and more below. MORE MATH.
+ REFERENCE OPENCV DOCS.
+ """
+ if borderType in conf.borders:
+ self.image = cv2.blur(self.image, anchor = anchor, borderType = conf.borders[borderType])
+ else:
+ raise Exception("Invalid border type, should be one of: " + ",".join(conf.borders.keys()) + ".")
+ return
+
+ def medianBlur(self, ksize):
+ """
+ :param ksize: The size of the kernel (ksize x ksize). Should be odd and positive.
+ :type ksize: int
+
+ This function smoothes an image using the median filter. The kernel is set to size (ksize, ksize).
+ The anchor position is assumed to be the center.
+ REFERENCE OPENCV MEDIAN BLUR
+ """
+ self.image = cv2.medianBlur(self.image, ksize)
+ return
+
+ def gaussianBlur(self, ksize, sigmaX = 0, sigmaY = 0, borderType = "default"):
+ """
+ :param ksize: The size of the kernel represented by a tuple (width, height). Both numers should be odd and positive.
+ :type ksize: tuple
+ :param sigmaX: The standard deviation in the x direction. If 0, the value is calculated based on the kernel size.
+ :type sigmaX: float
+ :param sigmaY: The standard deviation in the y direction. If 0, the value is equal to sigmaX.
+ :type sigmaY: float
+ :param borderType: The type of border mode used to extrapolate pixels outside the image. Literally no information on this.
+ :type borderType: str
+
+ This function blurs an image based on a Gaussian kernel -- which is defined as: MATH.
+ REFERENCE to OPENCV GAUSSIAN BLUR
+ REFERENCE OPENCV GAUSSIAN KERNEL
+ """
+ if borderType in conf.borders:
+ sigmaY = sigmaX if sigmaY == 0 else sigmaY
+ self.image = cv2.GaussianBlur(self.image, ksize, sigmaX, sigmaY, borderType = conf.borders[borderType])
+ else:
+ raise Exception("Invalid border type, should be one of: " + ",".join(conf.borders.keys()) + ".")
+ return
+
+ def normalizeByIntensity(self):
+ """
+ Normalizes each channel of by pixel intensity. That is, for each pixel:
+ I = R + G + B
+ newr = R * 255 / I
+ newg = G * 255 / I
+ newb = B * 255 / I
+ """
+ f = self.image.astype(float)
+ combined = np.add(np.add(f[:,:,0], f[:,:,1]), f[:,:,2])
+ scaled = np.multiply(f, [255])
+ self.image = np.divide(scaled, combined[:,:,None]).astype(np.uint8)
+ return
+
+ def morphology(self, morphType, ktype, ksize, anchor = (-1, -1), iterations = 1, borderType = "default"):
+ """
+ :param morphType: The type of morphology to perform. Should be dilate, erode, open, close, gradient, tophat, or blackhat.
+ :type morphType: str
+ :param ktype: the type of the kernel, should be rect, ellipse, or cross.
+ :type ktype: str
+ :param ksize: The size of the kernel represented by a tuple (width, height). Both numbers should be odd and positive.
+ :type ksize: tuple
+ :param anchor: The anchor point for filtering. Default is (-1, -1) which is the center of the kernel.
+ :type anchor: tuple
+ :param iterations: The number of times to perform the specified morphology.
+ :type iterations: int
+ :param borderType: The type of border mode used to extrapolate pixels outside the image. Literally no information on this.
+ :type borderType: str
+
+ This function performs morphological operations based on the inputted values.
+ REFERENCE to OPENCV MORPHOLOGY
+ SHOW MORPHOLOGY EXAMPLES
+ """
+ if morphType in conf.morph:
+ if ktype in conf.kernels:
+ if borderType in conf.borders:
+ kernel = cv2.getStructuringElement(conf.kernels[ktype], ksize, anchor)
+ self.image = cv2.morphologyEx(self.image, conf.morph[morphType], kernel, anchor = anchor, iterations = iterations, borderType = conf.borders[borderType])
+ else:
+ raise Exception("Invalid border type, should be one of: " + ",".join(conf.borders.keys()) + ".")
+ else:
+ raise Exception("Invalid kernel type, should be one of: " + ",".join(conf.kernels.keys()) + ".")
+ else:
+ raise Exception("Invalid morphology type, should be one of: " + ",".join(conf.morph.keys()) + ".")
+
+ def crop(self, roi, resize = False):
+ """
+ :param roi: A list corresponding to the area of the image you want. List should be of the form [ystart, yend, xstart, xend]
+ :type roi: list or roi file
+ :param resize: If True, actually adjusts the size of the image, otherwise just draws over the part of the image not in the roi.
+ :type resize: bool
+
+ This function crops the image based on the given roi [ystart, yend, xstart, xend]. There are two crop options,
+ by default, the function doesn't actually resize the image. Instead, it sets each pixel not in the roi to black.
+ If resize is set to True, the function will actually crop the image down to the roi.
+ """
+ roi = self._loadROI(roi)
+ ystart, yend, xstart, xend = roi
+ if (resize):
+ self.image = self.image[ystart: yend, xstart: xend]
+ self.x = self.image.shape[1]
+ self.y = self.image.shape[0]
+ else:
+ maxx = self.x
+ maxy = self.y
+ off = [0, 0, 0] if self._isColor() else [0]
+ self.image[0:ystart, 0:maxx] = off
+ self.image[yend:maxy, 0:maxx] = off
+ self.image[0:maxy, 0:xstart] = off
+ self.image[0:maxy, xend:maxx] = off
+ return
+
+ def contourCut(self, binary, basemin = 100, padding = [0, 0, 0, 0], resize = False, returnBound = False, roiwrite = "roi.json"):
+ """
+ :param binary: The binary image to find contours of.
+ :type binary: str or np.ndarray
+ :param basemin: The minimum area a contour must have to be consider part of the foreground.
+ :type basemin: int
+ :param padding: Padding add to all sides of the final roi.
+ :type padding: int
+ :param returnBound: If set, instead of cropping the image, simply write the detected roi.
+ :type returnBound: bool
+ :param resize: Whether or not to resize the image.
+ :type resize: bool
+
+ This function crops an image based on the size of detected contours in the image. The
+ image is cropped such that all contours that are greater than the specified area are
+ included in the final output image. If returnBound is set, instead of actually
+ cropping the image, the detected roi is written to a file instead. Otherwise,
+ the detected roi is passed into the :py:meth:`~htpia.imgproc.crop` function,
+ with the given resize value.
+ """
+ bname, binary = self._loadResource(binary)
+ if self._isColor(binary):
+ binary = cv2.cvtColor(binary, cv2.COLOR_BGR2GRAY)
+ contours = cv2.findContours(binary, cv2.RETR_TREE, cv2.CHAIN_APPROX_SIMPLE)[0]
+ minx = binary.shape[1]
+ miny = binary.shape[0]
+ maxx = 0
+ maxy = 0
+ for cnt in contours:
+ x,y,w,h = cv2.boundingRect(cnt)
+ if (basemin < cv2.contourArea(cnt)):
+ if (x < minx):
+ minx = x
+ if (y < miny):
+ miny = y
+ if (x + w > maxx):
+ maxx = x + w
+ if (y + h > maxy):
+ maxy = y + h
+ roi = [0 if miny - padding[0] < 0 else miny - padding[0], binary.shape[0] if maxy + padding[1] > binary.shape[0] else maxy + padding[1], 0 if minx - padding[2] < 0 else minx - padding[2], binary.shape[1] if maxx + padding[3] > binary.shape[1] else maxx + padding[3]]
+ if returnBound:
+ self._writeROI(roi, roiwrite)
+ self.crop(roi, resize)
+ return
+
+ def edges(self, threshold1, threshold2, apertureSize = 3, L2gradient = False):
+ """
+ :param threshold1: First threshold for the hysteresis procedure.
+ :type threshold1: int
+ :param threshold2: Second threshold for the hysteresis procedure.
+ :type threshold2: int
+ :param apertureSize: aperture size used for the Sobel algorithm.
+ :type apertureSize: int
+ :L2gradient: Used to calculate Image gradient magnitude, if true then :math:`L = \sqrt{(dI/dx)^2 + (dI/dy)^2}`, if false then :math:`L = dI/dx + dI/dy`.
+ :type L2gradient: bool
+
+ This function calculates the edges of an image using the Canny edge detection algorithm, which is built upon the Sobel
+ algorithm, which calculates derivatives of an image. REFERENCE TO OPENCV HERE.
+ """
+ self.image = cv2.Canny(self.image, threshold1, threshold2, apertureSize = apertureSize, L2gradient = L2gradient)
+ return
+
+ def colorFilter(self, logic, roi = None):
+ """
+ :param logic: The logic you want to run on the image.
+ :type logic: str
+ :param roi: The roi you want to apply the filter to
+ :type roi: list or roi file
+
+ This function applies a color filter defined by the input logic, to a
+ targeted region defined by the input roi. The roi is defined the same,
+ [ystart, yend, xstart, xend]. The logic string itself is fairly complicated.
+ The string supports the following operators: '+', '-', '*', '/', '>', '>=',
+ '==', '<', '<=', 'and', 'or', '(', ')', 'r', 'g', 'b', as well as any numeric
+ value. The logic string itself is confined to symbolic logic rules -- each
+ operation, arg1 operator arg2, must be surrounded by parenthesis. For example,
+ if you want to check the intensity of the pixel, your logic string would be:
+ '(((r + g) + b) < 100)'. This string in particular will only keep pixels whose
+ intensity is less than 100. Similar rules apply for 'and' and 'or' operators.
+ Let's say we only want to keep pixels whose intensity is less than 100, OR both
+ the red and blue channels are greater than 150, the logic string would be:
+ '((((r + g) + b) < 100) or ((r > 150) and (b > 150)))'.
+ """
+ filter = ColorFilter(logic)
+ roi = self._loadROI(roi)
+ self.image = filter.apply(self.image, roi)
+ return
+
+ def bitwise_not(self):
+ """
+ Inverts the image. If the given image has multiple channels (i.e. is a color image) each channel is processed independently.
+ """
+ self.image = cv2.bitwise_not(self.image)
+ return
+
+ def bitwise_and(self, comp):
+ """
+ :param comp: The comparison image.
+ :type comp: str or np.ndarray
+ :return: The resulting mask.
+ :rtype: numpy.ndarray
+
+ Performs logical and on the class image, and reference image.
+ Assumes the two images are the correct type.
+ """
+ self.image = cv2.bitwise_and(self.image, self._loadResource(comp)[1])
+ return
+
+ def bitwise_or(self, comp):
+ """
+ :param comp: The comparison image.
+ :type comp: str or np.ndarray
+ :return: The resulting mask.
+ :rtype: numpy.ndarray
+
+ Performs bitwise or logic on the class image, and reference image.
+ Assumes the two images are the correct type.
+ """
+ self.image = cv2.bitwise_or(self.image, self._loadResource(comp)[1])
+ return
+
+ def bitwise_xor(self, comp):
+ """
+ :param comp: The comparison image.
+ :type comp: str or np.ndarray
+ :return: The resulting mask.
+ :rtype: numpy.ndarray
+
+ Performs bitwise exclusive or logic on the class image, and reference image.
+ Assumes the two images are the correct type.
+ """
+ self.image = cv2.bitwise_xor(self.image, self._loadResource(comp)[1])
+ return
+
+ def extractFinalPath(self):
+ """
+ This function writes the absolute path of the output file to the database.
+ """
+ if self.conn:
+ finalpath = "/".join(os.path.abspath(self.input).split("/")[-6:])
+ self._addColumn("outputPath")
+ self.conn.execute("update images set outputPath=? where pegasusid=?", (finalpath, self.dbid))
+ self.conn.commit()
+ return
+
+ def extractMoments(self):
+ """
+ :return: A dictionary corresponding to the different moments of the image.
+ :rtype: dict
+
+ Calculates the moments of the image, and returns a dicitonary based on them.
+ Spatial moments are prefixed with 'm', central moments are prefixed with 'mu',
+ and central normalized moments are prefixed with 'nu'.
+ REFERENCE TO OPENCV DOCUMENTATION
+ REFERENCE TO GREEN'S THEOREM
+ """
+ moments = cv2.moments(cv2.inRange(self.image, np.array([1, 1, 1], np.uint8), np.array([255, 255, 255], np.uint8)))
+ if self.conn:
+ for id in moments:
+ self._addColumn(id)
+ self.conn.execute("update images set " + id + "=? where pegasusid=?", (moments[id], self.dbid))
+ self.conn.commit()
+ return
+ else:
+ return moments
+
+ def extractDimensions(self):
+ """
+ :return: A list corresponding to the height and width of the image.
+ :rtype: list
+
+ Returns a list with the following form: [height, width]
+ """
+ if self.conn:
+ self._addColumn("height")
+ self._addColumn("width")
+ self.conn.execute("update images set height=?,width=? where pegasusid=?", (self.y, self.x, self.dbid))
+ self.conn.commit()
+ return
+ else:
+ return [self.y, self.x]
+
+ def extractPixels(self):
+ """
+ :return: The number of non-black pixels in the image.
+ :rtype: int
+
+ Returns the number of non-black pixels in the image. Creates
+ a temporary binary image to do this. The point of this function
+ is not to threshold, so the binary image is created by all
+ pixels that fall into the range [1, 1, 1], [255, 255, 255].
+ """
+ pixelCount = cv2.countNonZero(cv2.inRange(self.image, np.array([1, 1, 1], np.uint8), np.array([255, 255, 255], np.uint8)))
+ if self.conn:
+ self._addColumn("pixels")
+ self.conn.execute("update images set pixels=? where pegasusid=?", (pixelCount, self.dbid))
+ self.conn.commit()
+ return
+ else:
+ return pixelCount
+
+ def extractColorData(self, nonzero = True, returnhist = False):
+ """
+ :param nonzero: Whether or not to look at only nonzero pixels. Default true.
+ :type nonzero: bool
+ :return: Mean & median for each channel.
+ :rtype: list
+
+ This function calculates a normalized histogram of each individual color channel of
+ the image, and returns the mean & median of the histograms for the channels
+ specified. Because images are imported with the channels ordered as B,G,R,
+ the output list is returned the same way. The returned list always looks like
+ this: [ [BlueMean, BlueMedian], [GreenMean, GreenMedian], [RedMean, RedMedian] ].
+ Mean values always come before median values. If nonzero is set to true (default)
+ the function will only calculate mediapytn and means based on the non-black pixels.
+ """
+ hist = self._colorHistogram()
+ if returnhist:
+ return hist
+ colors = [ [np.mean(np.nonzero(hist[0]) if nonzero else hist[0]), np.median(np.nonzero(hist[0]) if nonzero else hist[0])],
+ [np.mean(np.nonzero(hist[1]) if nonzero else hist[1]), np.median(np.nonzero(hist[1]) if nonzero else hist[1])],
+ [np.mean(np.nonzero(hist[2]) if nonzero else hist[2]), np.median(np.nonzero(hist[2]) if nonzero else hist[2])]
+ ]
+ if self.conn:
+ self._addColumn("rmean")
+ self._addColumn("rmed")
+ self._addColumn("gmean")
+ self._addColumn("gmed")
+ self._addColumn("bmean")
+ self._addColumn("bmed")
+ query = "update images set rmean=?,rmed=?,gmean=?,gmed=?,bmean=?,bmed=?"
+ values = [colors[2][0], colors[2][1], colors[1][0], colors[1][1], colors[0][0], colors[0][1]]
+ for x,c in enumerate(["bhist", "ghist", "rhist"]):
+ for i in range(0, 256):
+ self._addColumn(c + str(i))
+ query += "," + c + str(i) + "=?"
+ values.append(int(hist[x][i]))
+ query += " where pegasusid=?"
+ values.append(self.dbid)
+ self.conn.execute(query, tuple(values))
+ self.conn.commit()
+ return
+ else:
+ return colors
+
+ def extractColorChannels(self):
+ b, g, r = cv2.split(self.image)
+ bdata, gdata, rdata = [], [], []
+ for i in range(0, 256):
+ bdata.append(np.count_nonzero(np.where(b == i, True, False)))
+ gdata.append(np.count_nonzero(np.where(g == i, True, False)))
+ rdata.append(np.count_nonzero(np.where(r == i, True, False)))
+ data = [bdata, gdata, rdata]
+ if self.conn:
+ query = "update images set "
+ values = []
+ for x,c in enumerate(["b", "g", "r"]):
+ for i in range(0, 256):
+ self._addColumn(c + str(i))
+ if i == 0:
+ query += c + str(i) + "=?"
+ else:
+ query += "," + c + str(i) + "=?"
+ values.append(data[x][i])
+ query += " where pegasusid=?"
+ values.append(self.dbid)
+ self.conn.execute(query, tuple(values))
+ self.conn.commit()
+ return
+ else:
+ return (bdata, gdata, rdata)
+
+ def extractBins(self, binlist):
+ """
+ :param binlist: The specified bins (color ranges) to count.
+ :type binlist: list
+ :return: The number of pixels that fall in each bin.
+ :rtype: list
+
+ This function counts the number of pixels that fall into the range as
+ specified by each bin. This function expects the input to be a list of
+ dictionaries as follows:
+
+ .. code-block:: python
+
+ binlist = [
+ {"name": "bin1",
+ "min": [B, G, R],
+ "max": [B, G, R]
+ },
+ {"name": "bin2",
+ ...
+ ]
+
+ Each range is defined by 6 values. A minimum and maximum blue,
+ green, and red value. The returned list is very similar to the
+ input list, except a 'count' key is added to each dictionary:
+
+ .. code-block:: python
+
+ returnlist = [
+ {"name": "bin1",
+ "min": [B, G, R],
+ "max": [B, G, R],
+ "count": VALUE
+ },
+ ...
+ ]
+
+ Where 'VALUE' is the number of pixels that fall into the
+ corresponding range.
+ A list is used instead of a dictionary as the base structure
+ to maintain order for writing to the output database. When
+ using this function within a workflow, the order you specify
+ your bins is the order in which they will show up in the
+ database, and the name you specify for you bin will be
+ the column name in the database.
+ """
+ binlist = self._loadBins(binlist)
+ for i in range(0, len(binlist)):
+ binlist[i]["count"] = cv2.countNonZero(cv2.inRange(self.image, np.array(binlist[i]["min"], np.uint8), np.array(binlist[i]["max"], np.uint8)))
+ if self.conn:
+ for bin in binlist:
+ self._addColumn(bin["name"])
+ self.conn.execute("update images set " + bin["name"] + "=? where pegasusid=?", (bin["count"], self.dbid))
+ self.conn.commit()
+ return
+ else:
+ return binlist
+
+
diff --git a/build/lib/htpia/statistics.py b/build/lib/htpia/statistics.py
new file mode 100644
index 0000000000000000000000000000000000000000..1cd019b55452f0686245a836d5d4460bbb82c8ff
--- /dev/null
+++ b/build/lib/htpia/statistics.py
@@ -0,0 +1,652 @@
+import math
+import os
+import sqlite3
+import conf
+import datetime
+import numpy as np
+import pandas
+import htpia.imgproc
+import cv2
+import json
+import traceback
+from scipy import stats
+
+class Stats:
+
+ def __init__(self, db):
+ self.db = db
+ self.conn = self._openConnection()
+ return
+
+ def _openConnection(self, db = None):
+ db = self.db if not db else db
+ if os.path.isfile(db):
+ conn = sqlite3.connect(db, check_same_thread = False)
+ conn.row_factory = sqlite3.Row
+ result = conn.execute("select pegasusid from images limit 0,1")
+ if not result.fetchone():
+ raise Exception("Database '%s' has no entries!" % (db,))
+ # Have to enable foreign keys EVERY time.
+ conn.execute("PRAGMA foreign_keys = ON")
+ conn.commit()
+ else:
+ raise Exception("Database file '%s' does not exist." % (db,))
+ return conn
+
+ def _closeConnection(self, conn = None):
+ conn = self.conn if not conn else conn
+ conn.close()
+ return
+
+ def _tableExists(self, tablename, conn = None):
+ conn = self.conn if not conn else conn
+ result = conn.execute("select name from sqlite_master where type='table' and name=?", (tablename,))
+ if not result.fetchone():
+ return False
+ else:
+ return True
+
+ def _validate(self, funcname, intable, outtable, overwrite, conn = None):
+ conn = self.conn if not conn else conn
+ if funcname in conf.statsColumns:
+ if self._tableExists(intable):
+ cols = [x[1] for x in conn.execute("PRAGMA table_info('" + intable + "')")]
+ if set(conf.statsColumns[funcname]["required"]) <= set(cols):
+ if self._tableExists(outtable, conn) and not overwrite:
+ raise Exception("Output table '" + outtable + "' already exists.")
+ else:
+ raise Exception("Table '" + intable + "' doesn't have all the required columns: '" + str(conf.statsColumns[funcname]["required"]) + "'.")
+ else:
+ raise Exception("Table '" + intable + "' doesn't exist.")
+ else:
+ raise Exception("Function '" + funcname + "' doesn't exist.")
+ return
+
+ def _columnExists(self, column, tablename, conn = None):
+ conn = self.conn if not conn else conn
+ if column in [row["name"] for row in self.conn.execute("PRAGMA table_info('" + tablename + "')")]:
+ return True
+ else:
+ return False
+
+ def _addColumn(self, column, tablename = "images", conn = None):
+ conn = self.conn if not conn else conn
+ if not self._columnExists(column, tablename, conn):
+ conn.execute("alter table '" + tablename + "' add column " + column + ";")
+ conn.commit()
+ return
+
+ def _addKeyColumn(self, parent, parentCol, child, childCol, conn = None):
+ conn = self.conn if not conn else conn
+ if parentCol not in [row["name"] for row in conn.execute("PRAGMA table_info('" + parent + "');")] and childCol in [row["name"] for row in conn.execute("PRAGMA table_info('" + child + "');")]:
+ conn.execute("alter table '" + parent + "' add column '" + parentCol + "' REFERENCES '" + child + "'('" + childCol + "');")
+ conn.commit()
+ return
+
+ def _createTable(self, funcname, intable, outtable, overwrite, conn = None):
+ conn = self.conn if not conn else conn
+ tablestr = "(pegasusid INTEGER PRIMARY KEY"
+ cols = [x[1] for x in conn.execute("pragma table_info('" + intable + "')")]
+ if "all" not in conf.statsColumns[funcname]["exclude"]:
+ for col in cols:
+ if col not in conf.statsColumns[funcname]["exclude"] and col[:3] != "ref":
+ tablestr += "," + str(col)
+ for col in conf.statsColumns[funcname]["add"]:
+ tablestr += "," + str(col)
+ tablestr += ")"
+ if overwrite:
+ conn.execute("DROP TABLE IF EXISTS " + outtable)
+ conn.commit()
+ conn.execute("CREATE TABLE " + outtable + " " + tablestr)
+ conn.commit()
+ if conf.statsColumns[funcname]["ref"]:
+ self._addKeyColumn(intable, "ref_" + outtable, outtable, "pegasusid", conn)
+ return
+
+ def _getHeaders(self, table, conn = None):
+ conn = self.conn if not conn else conn
+ return [str(x[1]) for x in conn.execute("pragma table_info(" + table + ")") if x[1] != "pegasusid"]
+
+ def _getImageTypes(self, table, conn = None):
+ conn = self.conn if not conn else conn
+ return [str(x[0]) for x in conn.execute("select distinct imtype from " + table)]
+
+ def _getDates(self, table, conn = None):
+ conn = self.conn if not conn else conn
+ return [str(x[0]) for x in conn.execute("select distinct date from " + table)]
+
+ def _loadLemnaData(self, dataFile, dataHeaders):
+ """
+ :param dataFile: The input dataFile
+ :type dataFile: str
+ :param dataHeaders: The input data headers
+ :type dataHeaders: dict
+
+ dataHeaders should be:
+ {
+ "id": "Snapshot ID Tag",
+ "date": "Snapshot Time Stamp",
+ "dateFormat": "%m/%d/%y",
+ "metric": "Projected Shoot Area [pixels]"
+ }
+ """
+ if os.path.isfile(dataFile):
+ if all(key in dataHeaders for key in ["id", "date", "dateFormat", "metric"]):
+ with open(dataFile) as rh:
+ lines = rh.readlines()
+ firstline = lines[0].strip().split(",")
+ if dataHeaders["id"] in firstline:
+ if dataHeaders["date"] in firstline:
+ if dataHeaders["metric"] in firstline:
+ idIndex = firstline.index(dataHeaders["id"])
+ dateIndex = firstline.index(dataHeaders["date"])
+ metricIndex = firstline.index(dataHeaders["metric"])
+ lemnaData = {}
+ for line in lines[1:]:
+ info = line.strip().split(",")
+ if (info[metricIndex] != "NA"):
+ id = info[idIndex][-8:]
+ date = datetime.datetime.strptime(info[dateIndex].split()[0], dataHeaders["dateFormat"]).strftime("%Y-%m-%d")
+ try:
+ metric = float(info[metricIndex])
+ if id not in lemnaData:
+ lemnaData[id] = {}
+ if date not in lemnaData[id]:
+ lemnaData[id][date] = {}
+ lemnaData[id][date]["metric"] = metric
+ except:
+ pass
+ return lemnaData
+ else:
+ raise Exception("Metric Column: ",dataHeaders["metric"]," does not exist.")
+ else:
+ raise Exception("Date Column: ",dataHeaders["date"]," does not exist.")
+ else:
+ raise Exception("Id Column: ",dataHeaders["id"]," does not exist.")
+ else:
+ raise Exception("Data Dictionary does not have all required keys ['id', 'date', 'dateFormat', 'metric']")
+ else:
+ raise Exception("Data File: " + dataFile + " does not exist!")
+ return
+
+ def loadSql(self, dblist):
+ for i,f in enumerate(dblist):
+ if os.path.isfile(f):
+ conn = self._openConnection(f)
+ cols = self._getHeaders("images", conn)
+ for col in cols:
+ self._addColumn(col, "images")
+ result = conn.execute("select pegasusid," + ",".join(cols) + " from images")
+ query = "update images set " + ",".join([col + "=?" for col in cols]) + " where pegasusid=?"
+ values = [tuple([row[col] for col in cols] + [row["pegasusid"]]) for row in result]
+ self.conn.executemany(query, values)
+ self.conn.commit()
+ self._closeConnection(conn)
+ else:
+ print "DB File: '%s' does not exist." % (f,)
+ return
+
+
+
+ def logErrors(self, logfile, table = "images"):
+ """
+ :param logfile: The logfile to write errors to
+ :type logfile: str
+ :param table: The table to load errors from
+ :type table: str
+
+ This function writes all errors from a given table to a log file,
+ usually used at the end of image processing to write all images that
+ did not process correctly.
+ """
+ with open(logfile, "w") as wh:
+ wh.write("Image processing error log\n")
+ wh.write("==========================\n")
+ result = self.conn.execute("select pegasusid,path,error from '" + table + "' where error is not null")
+ firstrow = result.fetchone()
+ if firstrow:
+ wh.write("Error with image id '" + firstrow["pegasusid"] + "', located at path '" + firstrow["path"] + "', error: '" + firstrow["error"] + "'. \n")
+ for row in result:
+ wh.write("Error with image id '" + row["pegasusid"] + "', located at path '" + row["path"] + "', error: '" + row["error"] + "'. \n")
+ else:
+ wh.write("All images processed successfully! Nice job!\n")
+ return
+
+ def shootArea(self, intable, outtable, grouping, overwrite = False):
+ """
+ :param intable: The input table to load information from
+ :type intable: str
+ :param outtable: The output table to write information to.
+ :type outtable: str
+ :param grouping: Which imtypes to group
+ :type grouping: list
+
+ This function adds the numeric values of multiple image types together.
+ In general, it is used to combine side view + top view images of the same spectrum.
+ If you plan on correlating your data to lemnaTec's data, lemnaTec uses SV1 + SV2 + TV,
+ so you should aggregate your data likewise.
+ """
+ self._validate("shootArea", intable, outtable, overwrite)
+ self._createTable("shootArea", intable, outtable, overwrite)
+ headers = self._getHeaders(outtable)
+ result = self.conn.execute("select pegasusid," + ",".join(headers) + " from " + intable + " where " + " or ".join(["imtype=?" for x in grouping]), tuple([x for x in grouping]))
+ for row in result:
+ exists = self.conn.execute("select * from " + outtable + " where experiment=? and id=? and genotype=? and date=? and treatment=? and imtype=?", (row["experiment"], row["id"], row["genotype"], row["date"], row["treatment"], conf.typeMap[row["imtype"]]))
+ outrow = exists.fetchone()
+ if not outrow:
+ lastid = self.conn.execute("insert into " + outtable + " (" + ",".join(headers) + ") values (" + ",".join(["?"] * len(headers)) + ")", tuple([str(row[x]) if x != "imtype" else conf.typeMap[row[x]] for x in headers])).lastrowid
+ else:
+ lastid = outrow["pegasusid"]
+ vals = dict((header, float(row[header]) + float(outrow[header])) for header in headers if header not in conf.allHeaders)
+ self.conn.execute("update " + outtable + " set " + ",".join([str(x) + "=" + str(vals[x]) for x in vals]) + " where pegasusid=?", (outrow["pegasusid"],))
+ self.conn.execute("update " + intable + " set ref_" + outtable + "=? where pegasusid=?", (lastid, row["pegasusid"]))
+ self.conn.commit()
+ return
+
+ def normalize(self, intable, outtable, column = "pixels", overwrite = False):
+ """
+ :param intable: The input table to load information from
+ :type intable: str
+ :param outtable: The output table to write information to.
+ :type outtable: str
+ :param column: The column to normalize information to
+ :type column: str
+
+ Normalizes all numerical information to the specific column. This
+ function is usually used with 'pixels' as the specified column, which
+ expresses all numeric information as a percentage of the total pixels
+ in the image.
+ """
+ self._validate("normalize", intable, outtable, overwrite)
+ if self._columnExists(column, intable):
+ conf.statsColumns["normalize"]["exclude"] += [column]
+ self._createTable("normalize", intable, outtable, overwrite)
+ headers = self._getHeaders(outtable)
+ result = self.conn.execute("select pegasusid," + column + "," + ",".join(headers) + " from " + intable)
+ for row in result:
+ if all([row[x] is not None for x in headers if x not in conf.allHeaders]):
+ vals = tuple([row[x] if x in conf.allHeaders else float(row[x]) / float(row[column]) for x in headers])
+ lastid = self.conn.execute("insert into " + outtable + " (" + ",".join(headers) + ") values (" + ",".join(["?"] * len(headers)) + ")", vals).lastrowid
+ self.conn.execute("update " + intable + " set ref_" + outtable + "=? where pegasusid=?", (lastid, row["pegasusid"]))
+ self.conn.commit()
+ return
+
+ def extractAll(self, options):
+ basepath = os.path.dirname(os.path.dirname(os.path.abspath(self.db) + "/"))
+ if "workflows" in options:
+ for type in options["workflows"]:
+ self._openConnection()
+ tmp = self.conn.execute("select pegasusid,experiment,id,date,imtype,imgname from images where imtype=?", (type,))
+ result = tmp.fetchall()
+ for row in result:
+ finalpath = row["experiment"].replace(" ","") + "/" + row["id"].replace(" ","") + "/" + row["date"].replace(" ","") + "/" + row["imtype"].replace(" ","") + "/" + row["imgname"].replace(" ","") + "/" + row["pegasusid"] + "_" + options["workflows"][type]["inputs"][0] + ".png"
+ #finalpath = row["pegasusid"] + "_" + options["workflows"][type]["inputs"][0] + ".png"
+ self._closeConnection()
+ if os.path.isfile(finalpath):
+ try:
+ plant = htpia.imgproc.Image(finalpath, db = self.db, dbid = row["pegasusid"])
+ plant.extractFinalPath()
+ if "--dimensions" in options["workflows"][type]["arguments"]:
+ plant.extractDimensions()
+ if "--pixels" in options["workflows"][type]["arguments"]:
+ plant.extractPixels()
+ if "--moments" in options["workflows"][type]["arguments"]:
+ plant.extractMoments()
+ if "--colors" in options["workflows"][type]["arguments"]:
+ plant.extractColorData()
+ if "--channels" in options["workflows"][type]["arguments"]:
+ plant.extractColorChannels()
+ if "--bins" in options["workflows"][type]["arguments"]:
+ plant.extractBins(options["workflows"][type]["arguments"]["--bins"])
+ except Exception as e:
+ print traceback.format_exc()
+ else:
+ print "PATH DOES NOT EXIST: %s." % (finalpath,)
+ if "histogram-bin" in options:
+ self._openConnection()
+ self.histogramBinning("images", "histogramBins", dict((type,options["workflows"][type]["inputs"][0]) for type in options["workflows"]), options["histogram-bin"]["--group"], options["histogram-bin"]["--chunks"], options["histogram-bin"]["--channels"], True)
+ return
+
+ def histogramBinning(self, intable, outtable, grouping, chunks, channels, jsonwrite = False, overwrite = False):
+ color_vector = {}
+ for name in grouping:
+ self._validate("histogramBins", intable, name + "_" + outtable, overwrite)
+ for name in grouping:
+ self._createTable("histogramBins", intable, name + "_" + outtable, overwrite)
+ color_vector[name] = [0, 0, 0]
+ map = dict((type, name) for name in grouping for type in grouping[name])
+ basequery = "select "
+ for x,c in enumerate(["bhist", "ghist", "rhist"]):
+ for i in range(0, 256):
+ if i == 0 and x == 0:
+ basequery += "SUM(" + c + str(i) + ")"
+ else:
+ basequery += ",SUM(" + c + str(i) + ")"
+ basequery += " from images where "
+ for name in grouping:
+ query = basequery + " or ".join(["imtype=?" for x in grouping[name]])
+ result = self.conn.execute(query, tuple(grouping[name]))
+ data = list(result.fetchone())
+ for i in range(0, 3):
+ color_vector[name][i] = data[i*256:(i + 1)*256]
+ bins = {}
+ for name in grouping:
+ bins[name] = self._generateBins(self._splitHist(color_vector[name], chunks[name], channels[name]), name)
+ self.conn.executemany("insert into " + name + "_" + outtable + " (name, minr, ming, minb, maxr, maxg, maxb) values (?, ?, ?, ?, ?, ?, ?)", [(bin["name"], int(bin["min"][2]), int(bin["min"][1]), int(bin["min"][0]), int(bin["max"][2]), int(bin["max"][1]), int(bin["max"][0])) for bin in bins[name]])
+# for bin in bins[name]:
+# self.conn.execute("insert into " + name + "_" + outtable + " (name, minr, ming, minb, maxr, maxg, maxb) values (?, ?, ?, ?, ?, ?, ?)", (name + bin["name"], int(bin["min"][2]), int(bin["min"][1]), int(bin["min"][0]), int(bin["max"][2]), int(bin["max"][1]), int(bin["max"][0])))
+# self.conn.commit()
+ self.conn.commit()
+ if jsonwrite:
+ for name in grouping:
+ with open(name + "_hist_bins.json", "w") as wh:
+ json.dump(bins[name], wh)
+ return
+
+
+ def _splitHist(self, hist, chunks, channels):
+ returnlist = [ [1], [1], [1] ]
+ s = [sum(x) for x in hist]
+ #s = [int(x) for x in np.sum(hist, axis = 1)]
+ for i in channels:
+ tmp = 0
+ integral = s[i] / chunks
+ for j,item in enumerate(hist[i]):
+ tmp += item
+ if (tmp > integral):
+ returnlist[i].append(j)
+ tmp = 0
+ returnlist[0].append(255)
+ returnlist[1].append(255)
+ returnlist[2].append(255)
+ return returnlist
+
+ def _generateBins(self, vector, type):
+ bins = []
+ num = 1
+ for i in range (0, len(vector[0]) - 1):
+ for j in range(0, len(vector[1]) - 1):
+ for k in range(0, len(vector[2]) - 1):
+ bins.append({
+ "name": type + "_bin" + str(num),
+ "min": np.array([vector[0][i],vector[1][j],vector[2][k]], dtype=np.uint8).tolist(),
+ "max": np.array([vector[0][i+1],vector[1][j+1],vector[2][k+1]], dtype=np.uint8).tolist()
+ })
+ num += 1
+ return bins
+
+
+ def correlation(self, intable, outtable, dataFile, dataHeaders, overwrite = False):
+ """
+ :param intable: The input table to load information from
+ :type intable: str
+ :param outtable: The output table to write information to.
+ :type outtable: str
+ :param dataFile: The csv data file to load
+ :type dataFile: str
+ :param dataHeaders: Column names for relevant table headers.
+ :type dataHeaders: str
+
+ This function correlates all numeric values with values in the given file.
+ The input data file is assumed to be in csv format. In dataHeaders, you must
+ specify four keys, 'id', 'date', 'dateFormat', and 'metric'. Each of these should
+ be column names. Id corresponds to the lemnaTec style identifier ex: '023535-S'.
+ All dates are converted into Y-m-d form, you must provide a valid format in 'dateFormat',
+ that way the dates can be converted correctly. The 'metric' column is the actual value you
+ want to correlate to.
+ """
+ self._validate("correlation", intable, outtable, overwrite)
+ lemnaData = self._loadLemnaData(dataFile, dataHeaders)
+ self._createTable("correlation", intable, outtable, overwrite)
+ headers = self._getHeaders(outtable)
+ numeric = [h for h in headers if h not in conf.allHeaders]
+ for id in lemnaData:
+ for imtype in self._getImageTypes(intable):
+ x = {}
+ y = []
+ corr = {}
+ result = self.conn.execute("select pegasusid," + ",".join(headers + ["date"]) + " from " + intable + " where id=? and imtype=? order by date", (id,imtype))
+ if result.fetchone():
+ for row in result:
+ if row["date"] in lemnaData[id]:
+ y.append(lemnaData[id][row["date"]]["metric"])
+ for header in numeric:
+ if header not in x:
+ x[header] = []
+ try:
+ x[header].append(float(row[header]))
+ except:
+ pass
+ if any([x[header] for header in numeric]):
+ for header in numeric:
+ if len(x[header]) == len(y):
+ corr[header] = np.corrcoef(x[header], y)[0][1]
+ else:
+ corr[header] = "na"
+ lastid = self.conn.execute("insert into " + outtable + " (" + ",".join(headers) + ") values (" + ",".join(["?"] * len(headers)) + ")", tuple([row[header] if header in conf.allHeaders else corr[header] for header in headers])).lastrowid
+ self.conn.execute("update " + intable + " set ref_" + outtable + "=? where id=? and imtype=?", (lastid, id, imtype))
+ self.conn.commit()
+ return
+
+ def anova(self, intable, outtable, grouping, overwrite = False):
+ """
+ :param intable: The input table to load information from
+ :type intable: str
+ :param outtable: The output table to write information to.
+ :type outtable: str
+ :param grouping: The list of image types to group by.
+ :type grouping: list
+
+ Computes the analysis of variation of all numeric information based on 3 factors,
+ treatment, date, and the interaction between the two. Analysis of variation is
+ different than the rest of the stats functions, in that a lot of information is
+ lost after running it. The results themselves correspond to columns (pixels, rmed, binx...)
+ instead of actual images.
+ """
+ self._validate("anova", intable, outtable, overwrite)
+ headers = self._getHeaders(intable)
+ numeric = [h for h in headers if h not in conf.allHeaders]
+ self._createTable("anova", intable, outtable, overwrite)
+ outHeaders = self._getHeaders(outtable)
+ result = self.conn.execute("select * from images")
+ rowdata = []
+ for row in result:
+ rowdata.append(dict(row))
+ data = pandas.DataFrame(rowdata).dropna()
+ anova = {}
+ for col in numeric:
+ anova[col] = {}
+ dateT = []
+ treatmentT = []
+ date_treatmentT = []
+ for date in self._getDates(intable):
+ dateT.append(data[data["date"] == date][col])
+ for treatment in ["Control", "Stress"]:
+ treatmentT.append(data[data["treatment"] == treatment][col])
+ date_treatmentT.append(data[np.where(np.logical_and(data["treatment"] == treatment,data["date"] == date), True, False)][col])
+ f_val, d_pval = stats.f_oneway(*dateT)
+ f_val, t_pval = stats.f_oneway(*treatmentT)
+ f_val, dt_pval = stats.f_oneway(*date_treatmentT)
+ anova[col]["date"] = d_pval
+ anova[col]["treatment"] = t_pval
+ anova[col]["date_treatment"] = dt_pval
+ for type in ["date", "treatment", "date_treatment"]:
+ vals = [group] + [anova[x][type] for x in numeric] + [type]
+ self.conn.execute("insert into " + outtable + " (" + ",".join(outHeaders) + ") values (" + ",".join(["?"] * len(outHeaders)) + ")", tuple(vals))
+ self.conn.commit()
+ return
+
+ def tTest(self, intable, outtable, comp = "imtype", overwrite = False):
+ """
+ :param intable: The input table to perform the T test on.
+ :type intable: str
+ :param outtable: The output table to write the results to.
+ :type outtable: str
+ :param comp: Whether to compare image types or image names.
+ :type comp: str
+ :param overwrite: Whether or not to overwrite the output database
+ :type overwrite: bool
+
+ This function computes a ttest of the input table for all numeric headers.
+ The comparison is either done based on image types or image names. Default
+ functionality is a comparison between image types, specify comp = 'imgname'
+ to compare image names.
+ """
+
+ self._validate("ttest", intable, outtable, overwrite)
+ self._createTable("ttest", intable, outtable, overwrite)
+ comp = "imtype" if comp == "imtype" else "imgname"
+ headers = self._getHeaders(outtable)
+ numeric = [h for h in headers if h not in conf.allHeaders]
+ meta = [h for h in headers if h not in numeric]
+ data = {}
+ result = self.conn.execute("select pegasusid,treatment," + ",".join(headers) + " from " + intable)
+ for row in result:
+ if row[comp] not in data:
+ data[row[comp]] = {}
+ if row["date"] not in data[row[comp]]:
+ data[row[comp]][row["date"]] = {"meta": dict(row), "id": [], "values": {}}
+ data[row[comp]][row["date"]]["id"].append(row["pegasusid"])
+ if row["treatment"] not in data[row[comp]][row["date"]]["values"]:
+ data[row[comp]][row["date"]]["values"][row["treatment"]] = [[row[h]] for h in numeric]
+ else:
+ for i,h in enumerate(numeric):
+ data[row[comp]][row["date"]]["values"][row["treatment"]][i].append(row[h])
+ for comp in data:
+ for date in data[comp]:
+ vals = [data[comp][date]["meta"][x] for x in meta]
+ for a,b in zip(data[comp][date]["values"]["Control"], data[comp][date]["values"]["Stress"]):
+ try:
+ res = stats.ttest_ind(a, b)[1]
+ except:
+ res = "null"
+ vals += [res]
+ lastid = self.conn.execute("insert into " + outtable + " (" + ",".join(headers) + ") values (" + ",".join(["?"] * len(headers)) + ")", vals).lastrowid
+ updateVals = (lastid,) + tuple(data[comp][date]["id"])
+ self.conn.execute("update " + intable + " set ref_" + outtable + "=? where id in (" + ",".join(["?"] * len(data[comp][date]["id"])) + ")", updateVals)
+ self.conn.commit()
+ return
+
+ def treatmentComp(self, intable, outtable, type = "ratio", direction = "Control", comp = "imtype", overwrite = False):
+ """
+ :param intable: The input table to load information from
+ :type intable: str
+ :param outtable: The output table to write information to.
+ :type outtable: str
+ :param type: The type of calculation to do between treatments. Should be ratio or difference.
+ :type type: str
+ :param direction: Whether to compute C ~ S, or S ~ C, default is Control first.
+ :type direction: str
+ :param comp: Whether to compare by imtype or imgname
+ :type comp: str
+
+ This function compares information between treatments -- It finds plants that are identical
+ except for treatment, and computes either a ratio or difference between them. Direction
+ is specified as the column you want first, so direction = "Control" will compute C ~ S, and
+ direction = "Stress" will compute S ~ C. If you have already normalized your table, difference
+ will provide better information than ratio.
+ """
+ t1 = "Stress" if direction == "Stress" else "Control"
+ t2 = "Stress" if direction == "Control" else "Control"
+ if type == "ratio":
+ op = lambda left, right: (left / right)
+ else:
+ op = lambda left, right: (left - right)
+ comp = "imtype" if comp == "imtype" else "imgname"
+ self._validate("treatmentComp", intable, outtable, overwrite)
+ self._createTable("treatmentComp", intable, outtable, overwrite)
+ headers = self._getHeaders(outtable)
+ numeric = [h for h in headers if h not in conf.allHeaders]
+ meta = [h for h in headers if h not in numeric]
+ data = {}
+ result = self.conn.execute("select pegasusid," + ",".join(headers) + " from " + intable)
+ for row in result:
+ if row["genotype"] not in data:
+ data[row["genotype"]] = {"id": [], "values": {}, "meta": {}}
+ data[row["genotype"]]["meta"][row[comp]] = dict(row)
+ data[row["genotype"]]["id"].append(row["pegasusid"])
+ if row[comp] not in data[row["genotype"]]["values"]:
+ data[row["genotype"]]["values"][row[comp]] = {}
+ if row["date"] not in data[row["genotype"]]["values"][row[comp]]:
+ data[row["genotype"]]["values"][row[comp]][row["date"]] = {}
+ if row["treatment"] not in data[row["genotype"]]["values"][row[comp]][row["date"]]:
+ data[row["genotype"]]["values"][row[comp]][row["date"]][row["treatment"]] = [row[h] for h in numeric]
+ for genotype in data:
+ for comp in data[genotype]["values"]:
+ for date in data[genotype]["values"][comp]:
+ vals = [data[genotype]["meta"][comp][x] for x in meta]
+ for a,b in zip(data[genotype]["values"][comp][date][t1], data[genotype]["values"][comp][date][t2]):
+ try:
+ res = op(float(a), float(b))
+ except:
+ res = "null"
+ vals += [res]
+ lastid = self.conn.execute("insert into " + outtable + " (" + ",".join(headers) + ") values (" + ",".join(["?"] * len(headers)) + ")", vals).lastrowid
+ updateVals = (lastid,) + tuple(data[genotype]["id"])
+ self.conn.execute("update " + intable + " set ref_" + outtable + "=? where id in (" + ",".join(["?"] * len(data[genotype]["id"])) + ")", updateVals)
+ self.conn.commit()
+ return
+
+ def threshold(self, intable, outtable, thresh = 0.01, overwrite = False):
+ """
+ :param intable: The input table to load information from
+ :type intable: str
+ :param outtable: The output table to write information to.
+ :type outtable: str
+ :param thresh: The threshold value.
+ :type thresh: float
+
+ This function thresholds the table based on the given value. All values
+ that fall below the threhsold are 'updated' in place with 'null'. Normalize
+ is often called before thresholding.
+ """
+ self._validate("threshold", intable, outtable, overwrite)
+ self._createTable("threshold", intable, outtable, overwrite)
+ headers = self._getHeaders(outtable)
+ numeric = [h for h in headers if h not in conf.allHeaders]
+ result = self.conn.execute("select pegasusid," + ",".join(headers) + " from " + intable)
+ for row in result:
+ vals = tuple([row[h] if h in conf.allHeaders else row[h] if float(row[h]) > thresh else "null" for h in headers])
+ lastid = self.conn.execute("insert into " + outtable + " (" + ",".join(headers) + ") values (" + ",".join(["?"] * len(headers)) + ")", vals).lastrowid
+ self.conn.execute("update " + intable + " set ref_" + outtable + "=? where pegasusid=?", (lastid, row["pegasusid"]))
+ self.conn.commit()
+ return
+
+ def SOMANYGRAPHINGFUNCTIONS(self):
+
+ return
+
+ def export(self, table, processed = True, grouping = None, fname = None):
+ """
+ :param table: The table to write to csv
+ :type table: str
+ :param processed: Whether or not to extract processed data
+ :type processed: bool
+ :param grouping: Which image types to extract from the database.
+ :type grouping: list
+ :param fname: The file name to write to.
+ :type fname: str
+
+ This function simply extracts data from a database and writes it to csv format.
+ Default functionality is to extract only data that has been processed. This is
+ checked by finding if an outputPath has been set. Additionally,
+ you can specify a list of image types to extract, if not, the default list contains
+ all rgb and fluo images. Finally, if no file name is specified, the name
+ of the table is used as the filename.
+ """
+
+ grouping = grouping if isinstance(grouping, list) else self._getImageTypes(table)
+ fname = fname if fname else table + ".csv"
+ query = "select * from " + table
+ values = tuple()
+ if processed:
+ query += " where outputPath is not null"
+ if grouping:
+ query += " and (" + " or ".join(["imtype=?" for x in grouping])
+ values = tuple([x for x in grouping])
+ elif grouping:
+ query += " " + " or ".join(["imtype=?" for x in grouping])
+ values = tuple([x for x in grouping])
+ table = pandas.io.sql.read_frame(query, values)
+ table.to_csv(fname)
+ return
diff --git a/build/lib/htpia/validator.py b/build/lib/htpia/validator.py
new file mode 100644
index 0000000000000000000000000000000000000000..b4bc259a15528bf0bada5c7596b484c440768ad2
--- /dev/null
+++ b/build/lib/htpia/validator.py
@@ -0,0 +1,675 @@
+import os
+import conf
+import sys
+import json
+import re
+import csv
+import datetime
+import sqlite3
+import textwrap
+import shutil
+import errno
+import copy
+import traceback
+from Pegasus.DAX3 import *
+
+class Validator(object):
+ """
+ A very, very generic validator.
+ """
+ def __init__(self, f, type):
+ self.err = ""
+ if not os.path.isfile(f):
+ self.err += "Path Error: Input '%s' doesn't exist.\n" % (f,)
+ if not self.err:
+ if type == "file":
+ with open(f, "r") as rh:
+ try:
+ self.data = json.load(rh)
+ except Exception as e:
+ self.err += "Json Error: File '%s', %s\n" % (f, str(e))
+ elif type == "db":
+ self.conn = sqlite3.connect(f)
+ self.conn.row_factory = sqlite3.Row
+ try:
+ result = self.conn.execute("select * from images")
+ if not result.fetchone():
+ self.err += "Database Error: No information in images table\n"
+ except Exception as e:
+ self.err += "Database Error: %s\n" % (str(e), )
+ else:
+ self.err += "Validator Error: Invalid type, must be either 'file' or 'db'\n"
+ self.rawFiles = {}
+ self.type = type
+ self.validate()
+ return
+
+ def printErrors(self):
+ """
+ Prints out errors from validation and then exits.
+ """
+ if self.err:
+ print self.err.strip()
+ else:
+ print "No Validation Errors."
+ return
+
+ def isValid(self):
+ """
+ A convenience function. If validation ran successfully,
+ return True, else return False.
+ """
+ if not self.err:
+ return True
+ else:
+ return False
+
+ def validate(self):
+ """
+ This function should be overloaded
+ """
+ return
+
+class Workflow(object):
+
+ def __init__(self, template, config, database):
+ self.workflow = Validator(template, "file")
+ self.config = Validator(config, "file")
+ self.db = Validator(database, "db")
+ self.err = ""
+ if self.workflow.isValid() and self.db.isValid() and self.config.isValid():
+ self.validate()
+ else:
+ self.err += "Workflow components did not validate individually. \n"
+ self.err += self.workflow.err
+ self.err += self.config.err
+ self.err += self.db.err
+ return
+
+ def isValid(self):
+ """
+ A convenience function.
+ """
+ if not self.err:
+ return True
+ else:
+ return False
+
+ def printErrors(self):
+ if self.err:
+ print self.err.strip()
+ else:
+ print "No Validation Errors"
+ return
+
+ def _loadOverwriteArgument(self, job, arg):
+ job["arguments"][arg] = conf.valid[job["executable"]]["arguments"][arg]["value"]
+ return
+
+ def _loadDerivedArgument(self, job, arg, jtype):
+ key = conf.valid[job["executable"]]["arguments"][arg]["key"]
+ index = conf.valid[job["executable"]]["arguments"][arg]["index"]
+ if key in job:
+ if isinstance(job[key], list):
+ if index <= len(job[key]) - 1:
+ if "value" in conf.valid[job["executable"]]["arguments"][arg]:
+ job["arguments"][arg] = conf.valid[job["executable"]]["arguments"][arg]["value"]
+ else:
+ job["arguments"][arg] = job[key][index]
+ else:
+ if "required" in conf.valid[job["executable"]]["arguments"][arg]:
+ self.err += "Workflow, Argument Error: Type '%s' job '%s', derived argument '%s' requires index '%s' for definition '%s', no such index. \n" % (jtype, job["name"], arg, index, key)
+ else:
+ if "required" in conf.valid[job["executable"]]["arguments"][arg]:
+ self.err += "Workflow, Argument Error: Type '%s' job '%s', derived argument '%s' requires definition for '%s' to be of type list, definition is of type '%s'. \n" % (jtype, job["name"], arg, key, type(job[key]).__name__)
+ else:
+ if "required" in conf.valid[job["executable"]]["arguments"][arg]:
+ self.err += "Workflow, Argument Error: Type '%s' job '%s', derived argument '%s' requires job definition for '%s', no such definition. \n" % (jtype, job["name"], arg, key)
+ return
+
+ def _validateArgumentType(self, job, arg, type):
+ if arg in job["arguments"]:
+ if not isinstance(job["arguments"][arg], {
+ "list": list,
+ "string": (str, unicode),
+ "dict": dict,
+ "numeric": (int, long, float),
+ "exist": object,
+ "derived": object
+ }[conf.valid[job["executable"]]["arguments"][arg]["type"]]):
+ self.err += "Workflow, Argument Error: Type '%s' job '%s', argument '%s' given value '%s', should be of type '%s'. \n" % (type, job["name"], arg, job["arguments"][arg], conf.valid[job["executable"]]["arguments"][arg]["type"])
+ else:
+ if isinstance(job["arguments"][arg], list) and "join" in conf.valid[job["executable"]]["arguments"][arg]:
+ job["arguments"][arg] = conf.valid[job["executable"]]["arguments"][arg]["join"].join(job["arguments"][arg])
+ elif (isinstance(job["arguments"][arg], dict) or isinstance(job["arguments"][arg], list)):
+ job["arguments"][arg] = str(job["arguments"][arg])
+ elif (isinstance(job["arguments"][arg], (str, unicode)) and conf.valid[job["executable"]]["arguments"][arg]["type"] and "complex" in conf.valid[job["executable"]]["arguments"][arg]):
+ job["arguments"][arg] = '"' + job["arguments"][arg] + '"'
+ return
+
+ def _validateArgumentRequired(self, job, arg, type):
+ if "required" in conf.valid[job["executable"]]["arguments"][arg]:
+ if arg in job["arguments"]:
+ if not job["arguments"][arg]:
+ self.err += "Workflow, Argument Error: Type '%s' job '%s', has empty required argument '%s' \n" % (type, job["name"], arg)
+ else:
+ self.err += "Workflow, Argument Error: Type '%s' job '%s', requires argument '%s', no such argument found. \n" % (type, job["name"], arg)
+ return
+
+ def _validateArgumentDictionary(self, job, arg, type):
+ arglist = job["arguments"][arg] if isinstance(job["arguments"][arg], list) else [job["arguments"][arg]]
+ if conf.valid[job["executable"]]["arguments"][arg]["validation"] == "dictionary":
+ d = conf.valid[job["executable"]]["arguments"][arg]["value"] if "key" not in conf.valid[job["executable"]]["arguments"][arg] else conf.valid[job["executable"]]["arguments"][arg]["value"].get(job["arguments"][conf.valid[job["executable"]]["arguments"][arg]["key"]])
+ for val in arglist:
+ if val not in d:
+ self.err += "Workflow, Argument Error: Type '%s' job '%s', has invalid value '%s' for argument '%s'. \n" % (type, job["name"], val, arg)
+ return
+
+ def _validateArgumentList(self, job, arg, type):
+ arglist = job["arguments"][arg] if isinstance(job["arguments"][arg], list) else [job["arguments"][arg]]
+ l = conf.valid[job["executable"]]["arguments"][arg]["value"]
+ for val in arglist:
+ if val not in l:
+ self.err += "Workflow, Argument Error: Type '%s' job '%s', has invalid value '%s' for argument '%s'. \n" % (type, job["name"], val, arg)
+ return
+
+ def _validateArguments(self, job, type):
+ if not job["arguments"]:
+ job["arguments"] = {}
+ for arg in conf.valid[job["executable"]]["arguments"]:
+ if conf.valid[job["executable"]]["arguments"][arg]["type"] == "derived":
+ self._loadDerivedArgument(job, arg, type)
+ if "required" in conf.valid[job["executable"]]["arguments"][arg] or arg in job["arguments"]:
+ if conf.valid[job["executable"]]["arguments"][arg]["type"] == "overwrite":
+ self._loadOverwriteArgument(job, arg, type)
+ else:
+ self._validateArgumentRequired(job, arg, type)
+ self._validateArgumentType(job, arg, type)
+
+ if "validation" in conf.valid[job["executable"]]["arguments"][arg]:
+ if arg in job["arguments"]:
+ validate = {
+ "dictionary": self._validateArgumentDictionary,
+ "list": self._validateArgumentList
+ }[conf.valid[job["executable"]]["arguments"][arg]["validation"]](job, arg, type)
+
+ for arg in job["arguments"]:
+ if arg not in conf.valid[job["executable"]]["arguments"]:
+ self.err += "Workflow, Argument Error: Type '%s' job '%s', has invalid argument '%s'. \n" % (type, job["name"], arg)
+ return
+
+ def _validateDependencies(self, job, type):
+ try:
+ names = [x["name"] for x in self.workflow.data["workflows"][type]]
+ unres = copy.deepcopy(job["inputs"])
+ for input in job["inputs"]:
+ if os.path.isfile(input):
+ unres.remove(input)
+ self.workflow.rawFiles[type].append(input)
+ elif input in self.workflow.data["workflows"][type][0]["inputs"]:
+ unres.remove(input)
+ if "depends" in job:
+ for dependency in job["depends"]:
+ if dependency in names:
+ i = names.index(dependency)
+ for output in self.workflow.data["workflows"][type][i]["outputs"]:
+ if output in unres:
+ unres = [x for x in unres if x != output]
+ else:
+ self.err += "Workflow, Dependency Error: Type '%s' job '%s' depends on job '%s', no such job exists. \n" % (type, job["name"], dependency)
+ for val in set(unres):
+ self.err += "Workflow, Input Error: Type '%s' job '%s' depends on input '%s'. Cannot find matching output, or raw file. \n" % (type, job["name"], val)
+ for x,input in enumerate(job["inputs"]):
+ if "depends" in job:
+ for dependency in job["depends"]:
+ if dependency in names:
+ i = names.index(dependency)
+ if input in self.workflow.data["workflows"][type][i]["outputs"]:
+ j = self.workflow.data["workflows"][type][i]["outputs"].index(input)
+ if conf.valid[job["executable"]]["inputs"][x] != conf.valid[self.workflow.data["workflows"][type][i]["executable"]]["outputs"][j]:
+ self.err += "Workflow, Dependency Error: Type '%s' job '%s' input '%s' in position '%s' should be of type '%s', however, output '%s' in position '%s' of job '%s' is of type '%s'. \n" % (type, job["name"], input, x, conf.valid[job["executable"]]["inputs"][x], self.workflow.data["workflows"][type][i]["outputs"][j], j, self.workflow.data["workflows"][type][i]["name"], conf.valid[self.workflow.data["workflows"][type][i]["executable"]]["outputs"][j])
+ except:
+ self.printErrors()
+ print "Validation halted at type '%s' job '%s'. Fix errors before re-running. \n" % (type, job)
+ sys.exit()
+ return
+
+ def _validateDB(self):
+ """
+ Valides the input database file.
+ DIFFERENT FOR WORKFLOWS
+ OVERLOAD THIS
+ """
+
+ return
+
+ def _validateConfig(self):
+ """
+ Validates the input configuration template.
+ SAME FOR BOTH TYPES OF WORKFLOWS
+ """
+ if self.config.data:
+ if set(conf.templateKeys["config"]["required"]) < set(self.config.data.keys()):
+ if not os.path.isdir(self.config.data["installdir"]):
+ self.err += "Config, Path Error: Path '%s' specified for 'installdir' does not exist. \n" % (self.config.data["installdir"],)
+ for key in self.config.data:
+ if key not in conf.templateKeys["config"]["required"] and key not in conf.templateKeys["config"]["optional"]:
+ self.err += "Config, Key Error: Invalid key '%s' specified. Allowed keys are '%s'. \n" % (key, conf.templateKeys["config"]["required"] + conf.templateKeys["config"]["optional"])
+ for namespace in self.config.data["profile"]:
+ for key in self.config.data["profile"][namespace]:
+ if "path" in key.lower():
+ if not isinstance(self.config.data["profile"][namespace][key], list):
+ self.config.data["profile"][namespace][key] = [self.config.data["profile"][namespace][key]]
+ for path in self.config.data["profile"][namespace][key]:
+ if not os.path.isdir(path):
+ self.err += "Config, Path Error: Path '%s' specified for namespace '%s', key '%s' does not exist. \n" % (path, namespace, key)
+ else:
+ self.err += "Config, Template Error: Config file does not have all the required keys:" + str(conf.templateKeys["config"]["required"]) + " \n"
+ else:
+ self.err += "Config, Load Error: Could not load configuration info. \n"
+ return
+
+ def _getImageTypes(self):
+ return [x["imtype"] for x in self.db.conn.execute("select distinct imtype from images")]
+
+ def validate(self):
+ """
+ This should be overloaded again.
+ """
+ return
+
+
+class ImageProcessor(Workflow):
+
+ def __init__(self, template, config, database):
+ super(ImageProcessor, self).__init__(template, config, database)
+ return
+
+ def validate(self):
+ """
+ Validates all inputted files. Because the workflow is
+ dependenet on the config and metadata, workflow validation
+ is only done if config and metadata validate successfully.
+ """
+ if not self.err:
+ self._validateConfig()
+ self._validateDB()
+ if not self.err:
+ self._validateWorkflow()
+ return
+
+ def _validateWorkflowJobs(self):
+ types = self._getImageTypes()
+ for type in self.workflow.data["workflows"]:
+ if type not in types:
+ self.err += "Imgproc, Type Error: Workflow definition exists for type '%s', no images have been loaded for that type. \n" % (type,)
+ self.workflow.rawFiles[type] = []
+ names = [x["name"] for x in self.workflow.data["workflows"][type]]
+ if len(names) == len(set(names)):
+ for job in self.workflow.data["workflows"][type]:
+ if set(conf.templateKeys["imgproc"]["job"]["required"]) <= set(job.keys()):
+ for key in job.keys():
+ if key not in conf.templateKeys["imgproc"]["job"]["required"] and key not in conf.templateKeys["imgproc"]["job"]["optional"]:
+ self.err += "Imgproc, Key Error: Job '%s' has invalid key '%s' specified. Allowed keys are '%s'. \n" % (job["name"], key, conf.templateKeys["imgproc"]["job"]["required"] + conf.templateKeys["imgproc"]["job"]["optional"])
+ if job["executable"] in conf.valid:
+ if not os.path.isfile(self.config.data["installdir"] + "/" + job["executable"]):
+ self.err += "Imgproc, Path Error: Job '%s' executable '%s' does not exist. \n" % (job["name"], self.config.data["installdir"] + "/" + job["executable"])
+ if conf.valid[job["executable"]]["type"] == "imgproc":
+ self._validateArguments(job, type)
+ self._validateDependencies(job, type)
+ else:
+ self.err += "Imgproc, Executable Error: Job '%s' has invalid executable '%s' specified. Only image processing scripts are allowed. \n" % (job["name"], job["executable"])
+ else:
+ self.err += "Imgproc, Executable Error: Job '%s' has non-existant executable '%s' specified. \n" % (job["name"], job["executable"])
+ else:
+ self.err += "Imgproc, Key Error: Job '%s' doesn't have all required keys: '%s'. \n" % (job["name"], conf.templateKeys["imgproc"]["job"]["required"])
+ else:
+ self.err += "Imgproc, Name Error: Cannot parse ambiguous workflow. Workflow defined for type '%s' contains multiple jobs with the same name. \n" % (type,)
+ return
+
+ def _validateWorkflowOptions(self):
+ if set(conf.templateKeys["imgproc"]["options"]["required"]) <= set(self.workflow.data["options"].keys()):
+ for key in self.workflow.data["options"]:
+ if key not in conf.templateKeys["imgproc"]["options"]["required"] and key not in conf.templateKeys["imgproc"]["options"]["optional"]:
+ self.err += "Imgproc, Option Error: Invalid option '%s' specified. \n " % (key,)
+ else:
+ self.err += "Imgproc, Option Error: Option specification doesn't have all required keys: '%s'. \n " % (conf.templateKeys["imgproc"]["options"]["required"],)
+ return
+
+ def _validateWorkflowExtract(self):
+ if set(conf.templateKeys["imgproc"]["extract"]["required"]) <= set(self.workflow.data["extract"].keys()):
+ for key in self.workflow.data["extract"]:
+ if key not in conf.templateKeys["imgproc"]["extract"]["required"] and key not in conf.templateKeys["imgproc"]["extract"]["optional"]:
+ self.err += "Imgproc, Extract Error: Invalid option '%s' specified. \n " % (key,)
+
+ ## Manual hist-bin validation ##
+ if "histogram-bin" in self.workflow.data["extract"]:
+ hist = {}
+ hist["executable"] = "pcv-stats-histogram-bin"
+ hist["inputs"] = ["images"]
+ hist["outputs"] = ["none"]
+ hist["name"] = "histogramBin"
+ hist["arguments"] = self.workflow.data["extract"]["histogram-bin"].copy()
+ self._validateArguments(hist, "extract")
+ if not self.err:
+ if set(self.workflow.data["extract"]["histogram-bin"]["--group"].keys()) != set(self.workflow.data["extract"]["histogram-bin"]["--channels"].keys()):
+ self.err += "Imgproc, Extract Error: Histogram bin group names don't match between '--group' and '--channels'. \n"
+ else:
+ pass
+
+ if not self.err:
+ for type in self.workflow.data["extract"]["workflows"]:
+ if type in self.workflow.data["workflows"]:
+ job = self.workflow.data["extract"]["workflows"][type]
+ job["executable"] = "pcv-extract"
+ job["outputs"] = ["none"]
+ job["name"] = type + "_extract"
+ self._validateArguments(job, type)
+ self._validateDependencies(job, type)
+ else:
+ self.err += "Imgproc, Extract Error: Extraction specified for type '%s'. No processing workflow defined for that type." % (type,)
+ else:
+ pass
+ else:
+ self.err += "Imgproc, Extract Error: Extract specification doesn't have all required keys: '%s'. \n" % (conf.templateKeys["imgproc"]["extract"]["required"],)
+ return
+
+
+ def _validateWorkflow(self):
+ """
+ Validates the input workflow template, making sure all required
+ keys are inputted, and all names resolve
+ """
+ if set(conf.templateKeys["imgproc"]["required"]) <= set(self.workflow.data.keys()):
+ for key in self.workflow.data.keys():
+ if key not in conf.templateKeys["imgproc"]["required"] and key not in conf.templateKeys["imgproc"]["optional"]:
+ self.err += "Imgproc, Key error: Invalid key '%s' specified. Allowed keys are '%s'. \n" % (key, conf.templateKeys["imgproc"]["required"] + conf.templateKeys["imgproc"]["optional"])
+ try:
+ self._validateWorkflowJobs()
+ self._validateWorkflowOptions()
+ self._validateWorkflowExtract()
+ except Exception as e:
+ print traceback.format_exc()
+ self.err += "Validation halted. Fix current issues before re-running. \n"
+ self.printErrors()
+ else:
+ self.err += "Imgproc, Template Error: Workflow file does not have all the required keys: '%s'. \n" % (conf.templateKeys["imgproc"]["required"],)
+ return
+
+ def _validateDB(self):
+ """
+ Validates the inputted metadata db, ensuring the appropriate
+ column names are in the database.
+ """
+ if self.db:
+ cols = [row[1] for row in self.db.conn.execute("PRAGMA table_info(images)")]
+ if set(conf.outHeaders) <= set(cols):
+ testpath = self.db.conn.execute("select path from images limit 0,1").next()[0]
+ if not os.path.isfile(testpath):
+ self.err += "DB, Path Error: Test file: '%s' could not be found. \n" % (testpath,)
+ else:
+ self.err += "DB, Key Error: Meta-data file does not have all the required headers: %s \n" % (str(conf.outHeaders),)
+ else:
+ self.err += "DB, Load Error: Could not connect to meta-data db. \n"
+ return
+
+
+
+class Statistics(Workflow):
+
+ def __init__(self, template, config, database):
+ super(Statistics, self).__init__(template, config, database)
+
+ return
+
+ def validate(self):
+ """
+ Validates all inputted files. Because the workflow is
+ dependenet on the config and metadata, workflow validation
+ is only done if config and metadata validate successfully.
+ """
+ if not self.err:
+ self._validateConfig()
+ self._validateDB()
+ if not self.err:
+ self._validateWorkflow()
+ return
+
+ def _validateDB(self):
+ try:
+ result = self.db.conn.execute("select * from images")
+ cols = [row[1] for row in self.db.conn.execute("PRAGMA table_info(images)")]
+ if not set(cols) > set(conf.outHeaders):
+ self.err += "Stats, Database Error: Database specified does not contain any numeric columns, process images first. \n"
+ if not set(conf.outHeaders) <= set(cols):
+ self.err += "Stats, Database Error: Database specified does not contain all the required column names: '%s'. \n " % (conf.outHeaders,)
+ if not result.fetchone():
+ self.err += "Stats, Database Error: Database specified does not contain an image table with any entries. \n"
+ except sqlite3.DatabaseError:
+ self.err += "Stats, Database Error: File specified is not a valid database file. \n"
+ return
+
+ def _validateWorkflow(self):
+ if self.workflow.data:
+ for key in self.workflow.data.keys():
+ if key not in conf.templateKeys["stats"]["required"] and key not in conf.templateKeys["stats"]["optional"]:
+ self.err += "Stats, Key error: Invalid key '%s' specified. Allowed keys are '%s'. \n" % (key, conf.templateKeys["stats"]["required"] + conf.templateKeys["stats"]["optional"])
+ for type in self.workflow.data["workflows"]:
+ self.workflow.rawFiles[type] = []
+ names = [x["name"] for x in self.workflow.data["workflows"][type]]
+ if len(names) == len(set(names)):
+ for job in self.workflow.data["workflows"][type]:
+ if set(conf.templateKeys["stats"]["job"]["required"]) <= set(job.keys()):
+ for key in job.keys():
+ if key not in conf.templateKeys["stats"]["job"]["required"] and key not in conf.templateKeys["stats"]["job"]["optional"]:
+ self.err += "Stats, Key Error: Job '%s' has invalid key '%s' specified. Allowed keys are '%s'. \n" % (job["name"], key, conf.templateKeys["stats"]["job"]["required"] + conf.templateKeys["stats"]["job"]["optional"])
+ if job["executable"] in conf.valid:
+ if conf.valid[job["executable"]]["type"] == "statistics":
+ if os.path.isfile(self.config.data["installdir"] + "/" + job["executable"]):
+ self._validateArguments(job, type)
+ self._validateDependencies(job, type)
+ else:
+ self.err += "Stats, Path Error: Job '%s' executable '%s' does not exist. \n" % (job["name"], self.config["installdir"] + "/" + job["executable"])
+ else:
+ self.err += "Stats, Executable Error: Job '%s' has invalid executable '%s' specified. Only statistics scripts are allowed. \n" % (job["name"], job["executable"])
+ else:
+ self.err += "Stats, Executable Error: Job '%s' executable '%s' is not a valid executable. \n" % (job["name"], job["executable"])
+ else:
+ self.err += "Stats, Key Error: Job '%s' doesn't have all required keys: '%s'. \n" % (job["name"], conf.templateKeys["stats"]["job"]["required"])
+ else:
+ self.err += "Stats, Name Error: Cannot parse ambiguous workflow. Workflow defined for type '%s' contains multiple jobs with the same name. \n" % (type,)
+ else:
+ self.err += "Stats, Load Error: Could not load stats file. \n"
+ return
+
+class ImageLoader(Validator):
+
+ def __init__(self, f):
+ super(ImageLoader, self).__init__(f, "file")
+ return
+
+ def validate(self):
+ """
+ Validates the given template.
+ """
+ if self.isValid():
+ if set(conf.templateKeys["loading"]["required"]) <= set(self.data.keys()):
+ for key in self.data:
+ if key not in conf.templateKeys["loading"]["required"] and key not in conf.templateKeys["loading"]["optional"]:
+ self.err += "Loader, Key Error: Invalid key '%s' specified. \\n" % (key,)
+
+ if not self.err:
+ for key in self.data:
+ d = {
+ "path": self._validatePath,
+ "base": self._validateBase,
+ "data": self._validateData,
+ "translations": self._validateTranslations,
+ "order": self._validateOrder,
+ "filetype": self._validateFtype,
+ }[key]()
+ else:
+ self.err += "Loader, Key Error: Not all required keys specified: '%s' \n" % (conf.templateKeys["loading"]["required"])
+ return
+
+ def _validateFtype(self):
+ if self.data["filetype"]:
+ if self.data["filetype"] not in conf.imageExtensions:
+ self.err += "Loader, File Error: Value '%s' specified for 'filetype' is invalid. Must be on of '%s'. \n" % (self.data["filetype"], conf.imageExtensions)
+ else:
+ self.err += "Loader, File Error: No value specified for 'filetype'. \n"
+
+ def _validatePath(self):
+ """
+ Validates the path. Because the path contains potential references, path existence
+ cannot be checked at this stage.
+ """
+ if not self.data["path"]:
+ self.err += "Loader, Path Error: No value specified for 'path'.\n"
+ return
+
+ def _validateBase(self):
+ """
+ Validates the base walk path. Checks existence of a value, if the value
+ is a subset of path, and if the path exists.
+ """
+ if self.data["base"]:
+ if self.data["base"] in self.data["path"]:
+ if not os.path.exists(self.data["base"]):
+ self.err += "Loader, Base Error: Value for 'base' is not a valid path. \n"
+ else:
+ self.err += "Loader, Base Error: Value for 'base' is not a subset of 'path'. \n"
+ else:
+ self.err += "Loader, Base Error: No value specified for 'base'.\n"
+ pass
+
+ def _validateData(self):
+ """
+ Validates the data! Uses a seperate function for each data type.
+ """
+ if self.data["data"]:
+ for key in self.data["data"]:
+ if "type" in self.data["data"][key]:
+ if self.data["data"][key]["type"] in conf.templateKeys["loading"]["data"]["type"]:
+ if key in self.data["order"]:
+ d = {
+ "value": self._validateDataValue,
+ "file": self._validateDataFile,
+ "date": self._validateDataDate
+ }[self.data["data"][key]["type"]](key)
+ else:
+ self.err += "Loader, Data Error: Definition for data key '%s', no corresponding definition in 'order'. \n" % (key,)
+ else:
+ self.err += "Loader, Data Error: Invalid type '%s' specified for data key '%s', must be one of '%s'. \n" % (self.data["data"][key]["type"], key, conf.templateKeys["loading"]["data"]["type"])
+ else:
+ self.err += "Loader, Data Error: No value specified for 'type' of data key '%s'. \n" % (key,)
+ else:
+ self.err += "Loader, Value Error: No value specified for 'data'. \n"
+ pass
+
+ def _validateDataValue(self, key):
+ """
+ Validates type 'value'. Values can be combinations of hard-coded text
+ as well as references to path identifiers Checks existence of a value,
+ if all the references are valid, and if translation is specified, that
+ translations exist.
+ """
+ if self.data["data"][key]["value"]:
+ if set(conf.templateKeys["loading"]["data"]["value"]["required"]) <= set(self.data["data"][key].keys()):
+
+ for subkey in self.data["data"][key]:
+ if subkey not in conf.templateKeys["loading"]["data"]["value"]["required"] and subkey not in conf.templateKeys["loading"]["data"]["value"]["optional"]:
+ self.err += "Loader, Data Value Error: Invalid key '%s' specified for data key '%s'. \n" % (subkey,key)
+
+ m = re.findall(r"%(\w+)%", self.data["data"][key]["value"])
+ for val in m:
+ if "%" + val + "%" not in self.data["path"]:
+ self.err += "Loader, Data Value Reference Error: Could not reference identifier '%s' for data key '%s'. \n" % (val, key)
+ if "translate" in self.data["data"][key]:
+ if key not in self.data["translations"]:
+ self.err += "Loader, Data Value Translation Error: Can't translate data key '%s', no translation specified. \n" % (key,)
+ else:
+ print set(conf.templateKeys["loading"]["data"]["value"]["required"])
+ print set(self.data["data"][key].keys())
+ self.err += "Loader, Data Value Error: Data key '%s' does not have all required keys '%s'. \n" % (key, conf.templateKeys["loading"]["data"]["value"]["required"])
+ else:
+ self.err += "Loader, Data Value Error: No value specified for data key '%s'. \n " % (key,)
+ return
+
+ def _validateDataFile(self, key):
+ """
+ Validates type 'file'. Checks to ensure that a file is specified,
+ that file exists, and that a value is specified for key, keyColumn,
+ and valueColumn. Assumes the file is of csv format.
+ """
+ if set(conf.templateKeys["loading"]["data"]["file"]["required"]) <= set(self.data["data"][key].keys()):
+
+ for subkey in self.data["data"][key]:
+ if subkey not in conf.templateKeys["loading"]["data"]["file"]["required"] and subkey not in conf.templateKeys["loading"]["data"]["file"]["optional"]:
+ self.err += "Loader, Data File Error: Invalid key '%s' specified for data key '%s'. \n" % (subkey, key)
+
+ if os.path.exists(self.data["data"][key]["value"]):
+ with open(self.data["data"][key]["value"], "r") as rh:
+ firstline = rh.readline()
+ sep = self.data["data"][key]["separator"] if "separator" in self.data["data"][key] else ","
+ maxlength = len(firstline.split(sep))
+ if maxlength <= self.data["data"][key]["keyColumn"]:
+ self.err += "Loader, Data File Error: Key column for data key '%s' out of range. \n" % (key,)
+ if maxlength <= self.data["data"][key]["valueColumn"]:
+ self.err += "Loader, Data File Error: Value column for data key '%s' out of range. \n" % (key,)
+ else:
+ self.err += "Loader, Data Filer Error: File '%s' specified for data key '%s' does not exist. \n" % (self.data["data"][key]["value"], key)
+
+ m = re.findall(r"%(\w+)%", self.data["data"][key]["key"])
+ for val in m:
+ if "%" + val + "%" not in self.data["path"]:
+ self.err += "Loader, Data Value Reference Error: Could not reference identifier '%s' for data key '%s'. \n" % (val, key)
+ else:
+ self.err += "Loader, Data File Error: Data key '%s' does not have all required keys '%s'. \n" % (key, conf.templateKeys["loading"]["data"]["file"]["required"])
+ return
+
+ def _validateDataDate(self, key):
+ """
+ Validates type 'date'. Checks to ensure that a value exists, a format
+ exists, and that the format is semi-valid. True validity of format is
+ checked when values are given in the crawling step.
+ """
+ if set(conf.templateKeys["loading"]["data"]["date"]["required"]) <= set(self.data["data"][key].keys()):
+
+ for subkey in self.data["data"][key]:
+ if subkey not in conf.templateKeys["loading"]["data"]["date"]["required"] and subkey not in conf.templateKeys["loading"]["data"]["date"]["optional"]:
+ self.err += "Loader, Data Date Error: Invalid key '%s' specified for data key '%s'. \n" % (subkey, key)
+
+ if not set(self.data["data"][key]["format"]) <= set(conf.dateFormat + conf.dateSep):
+ self.err += "Loader, Data Date Error: Invalid values in data key '%s', format only supports '%s'. \n" % (key, conf.dateFormat + conf.dateSep)
+
+ m = re.findall(r"%(\w+)%", self.data["data"][key]["value"])
+ for val in m:
+ if "%" + val + "%" not in self.data["path"]:
+ self.err += "Loader, Data Value Reference Error: Could not reference identifier '%s' for data key '%s'. \n" % (val, key)
+ else:
+ self.err += "Loader, Data Date Error: Data key '%s' does not have all required keys '%s'. \n" % (key, conf.templateKeys["loading"]["data"]["date"]["required"])
+ return
+
+ def _validateTranslations(self):
+ """
+ Nothing to see here, move along.
+ """
+ for key in self.data["translations"]:
+ if key not in self.data["data"]:
+ self.err += "Loader, Translation Error: Translation defined for '%s', however, no such data value exists. \n" % (key,)
+ return
+
+ def _validateOrder(self):
+ """
+ Validates the order -- the order you want to write values to the csv.
+ Checks existence of a value, as well as ensuring all values specified
+ have corresponding data values.
+ """
+ if self.data["order"]:
+ if not set(self.data["order"]) == set(self.data["data"].keys() + ["path"]):
+ self.err += "Loader, Order Error: Order must contain ALL data keys AND 'path'. \n"
+ else:
+ self.err += "Loader, Order Error: No value specified for order. \n"
+ return
+
diff --git a/build/lib/htpia/workflow.py b/build/lib/htpia/workflow.py
new file mode 100644
index 0000000000000000000000000000000000000000..0cc4cb195b99eacb136522efc4997f87a84127e9
--- /dev/null
+++ b/build/lib/htpia/workflow.py
@@ -0,0 +1,985 @@
+"""
+
+.. module:: workflow
+ :platform: Mac, Linux
+ :synopsis: Custom workflow creation, and workflow submission.
+
+.. moduleauthor:: Avi Knecht <avi@kurtknecht.com>
+
+"""
+
+import os
+import conf
+import sys
+import json
+import re
+import csv
+import datetime
+import sqlite3
+import shutil
+import errno
+import textwrap
+import copy
+import htpia.validator
+import xml.dom.minidom
+from Pegasus.DAX3 import *
+
+
+class Workflow(object):
+
+ """
+ Generic workflow creation class.
+ """
+
+ def __init__(self, jobhome, basename = None):
+ """
+ :param jobhome: The base directory for job submission.
+ :type jobhome: str
+
+ Creates a Workflow class based on the input directory. Only loads and
+ validates the config file by default.
+ """
+ self.err = ""
+ self.jobhome = os.path.abspath(jobhome)
+ self.jobname = os.path.basename(os.path.dirname(self.jobhome + "/"))
+ self.basename = basename
+ self.dax = ADAG(self.jobname)
+ self.executables = {}
+ self.files = {self.dax: {}}
+ self.jobs = {self.dax: {}}
+ self.deps = {}
+ return
+
+ def _loadInputFiles(self):
+ """
+ Loads the input files into the appropriate variables
+ This should be overloaded.
+ """
+ return
+
+ def _isFile(self, name, dax, imtype, inout):
+ """
+ Convenience function to check if a given file exists.
+ """
+ if name in self.files[dax][imtype][inout]:
+ return True
+ return False
+
+ def _isJob(self, name, dax):
+ """
+ Convenience function to check if a given job exists.
+ """
+ if name in self.jobs[dax]:
+ return True
+ return False
+
+ def _isExecutable(self, name):
+ """
+ Convenience function to check if a given executable exists.
+ """
+ if name in self.executables:
+ return True
+ return False
+
+ def _createSetup(self):
+ """
+ Creates the base structure for job submission. Everything is contained
+ within a folder based on the current timestamp.
+ """
+ self.basepath = self.jobhome + "/" + self.basename if self.basename else self.jobhome + "/" + datetime.datetime.now().strftime("%Y-%m-%d_%H%M%S")
+ if not os.path.exists(self.basepath):
+ os.makedirs(self.basepath)
+ if not os.path.exists(self.basepath + "/input"):
+ os.makedirs(self.basepath + "/input")
+ if not os.path.exists(self.basepath + "/output"):
+ os.makedirs(self.basepath + "/output")
+ if not os.path.exists(self.basepath + "input/templates"):
+ os.makedirs(self.basepath + "/input/templates")
+ if not os.path.exists(self.basepath + "/input/rawfiles"):
+ os.makedirs(self.basepath + "/input/rawfiles")
+ return
+
+ def _addFile(self, name, imtype, inout, path = None, dax = None):
+ """
+ Adds the inputted file to the dax, as well as the internal variable self.files
+ """
+ dax = dax if dax else self.dax
+ if not self._isFile(name, dax, imtype, inout):
+ self.files[dax][imtype][inout][name] = {"file": File(name), "path": ""}
+ if inout == "input":
+ self.files[dax][imtype][inout][name]["path"] = path if path else name
+ self.files[dax][imtype][inout][name]["file"].addPFN(PFN("file://" + path.replace(" ","%20"), "local"))
+ dax.addFile(self.files[dax][imtype][inout][name]["file"])
+ return
+
+ def _addJob(self, jobname, executable, inputs, outputs, arguments, dependencies = None, dax = None, label = None):
+ dax = dax if dax else self.dax
+ if not self._isJob(jobname, dax):
+ self.jobs[dax][jobname] = Job(executable)
+ dax.addJob(self.jobs[dax][jobname])
+ for key in inputs:
+ self.jobs[dax][jobname].uses(inputs[key]["file"], link = Link.INPUT)
+ for key in outputs:
+ self.jobs[dax][jobname].uses(outputs[key]["file"], link = Link.OUTPUT, transfer = outputs[key]["transfer"])
+ arglist = []
+ for arg in arguments:
+ arglist.append(arg)
+ if str(arguments[arg]) in inputs:
+ arglist.append(inputs[str(arguments[arg])]["file"])
+ elif str(arguments[arg]) in outputs:
+ arglist.append(outputs[str(arguments[arg])]["file"])
+ else:
+ arglist.append(str(arguments[arg]))
+ self.jobs[dax][jobname].addArguments(*arglist)
+ if dependencies:
+ for depend in dependencies:
+ dax.depends(child = self.jobs[dax][jobname], parent = self.jobs[dax][depend])
+ if label:
+ self.jobs[dax][jobname].profile(Namespace.PEGASUS, "label", label)
+ return
+
+ def create(self):
+ """
+ Creates a new pegasus submission directory based on the current timestamp,
+ and populates it with all required information to submit a pegasus job.
+ This function should be overloaded.
+ """
+ return
+
+
+class Statistics(Workflow):
+
+ """
+ A class specifically for statistics workflow
+ validation and submission.
+ """
+
+ def __init__(self, jobhome, basename, validOnly = False):
+ super(Statistics, self).__init__(jobhome, basename)
+ self.configfile = jobhome + "/input/" + conf.configFile
+ self.statsfile = jobhome + "/input/" + conf.statsFile
+ self.dbfile = jobhome + "/" + basename + "/output/" + conf.outputdb
+ self.validOnly = validOnly
+ self.rawFiles = {}
+ self._loadInputFiles()
+ return
+
+ def _getImageTypes(self):
+ return [x[0] for x in self.db.execute("select distinct imtype from images")]
+
+
+ def _loadInputFiles(self):
+ self.validator = htpia.validator.Statistics(self.statsfile, self.configfile, self.dbfile)
+ if not self.validator.isValid() or self.validOnly:
+ self.validator.printErrors()
+ sys.exit()
+ else:
+ self.stats = self.validator.workflow.data
+ self.db = self.validator.db.conn
+ self.config = self.validator.config.data
+ self.rawFiles = self.validator.workflow.rawFiles
+ return
+
+ def _copyFiles(self):
+ """
+ Copies all input files to the correct location.
+ """
+ if not os.path.exists(self.basepath + "/input/stats"):
+ os.makedirs(self.basepath + "/input/stats")
+ shutil.copyfile(self.statsfile, self.basepath + "/input/templates/" + os.path.basename(self.statsfile))
+ return
+
+ def _loadFiles(self, loc):
+ """
+ Loads all files (input and output) into the dax and the self.files variable
+ """
+ self.files[self.dax] = {}
+ self.files[self.dax]["raw"] = {"input": {}, "output": {}}
+ self._addFile("output.db", "raw", "input", self.basepath + "/output/output.db")
+ for type in self.stats["workflows"]:
+ self.files[self.dax][type] = {"input": {}, "output": {}}
+ for f in self.rawFiles[type]:
+ shutil.copyfile(f, self.basepath + "/input/rawfiles/" + os.path.basename(f))
+ self._addFile(os.path.basename(f), type, "input", self.basepath + "/input/rawfiles/" + os.path.basename(f))
+ return
+
+ def _loadExecutables(self, os="linux", arch="x86_64"):
+ """
+ Loads all executables (as specified in the conf) into
+ the dax, as well as the internal self.executables variable
+ """
+ for ex in conf.valid:
+ self.executables[ex] = Executable(name=ex, os=os, arch=arch)
+ self.executables[ex].addPFN(PFN("file://" + self.config["installdir"] + "/" + ex, "local"))
+ #if "cluster" in self.config:
+ # self.executables[ex].addProfile(Profile(Namespace.PEGASUS, "clusters.size", self.config["cluster"]))
+ self.dax.addExecutable(self.executables[ex])
+ return
+
+ def _loadJobInputs(self, job, type):
+ inputs = {"output.db": "output.db"}
+ for i,input in enumerate(job["inputs"]):
+ ftype = conf.valid[job["executable"]]["inputs"][i]
+ if input in self.rawFiles[type]:
+ inputs[input] = input
+ return inputs
+
+ def _createDax(self, loc):
+ """
+ Loads all jobs into the dax, and then writes the dax
+ to input/loc/stats.dax
+ """
+ serial = []
+ for type in self.stats["workflows"]:
+ for job in self.stats["workflows"][type]:
+ jobname = type + "_" + job["name"]
+ job["arguments"]["--intable"] = type + "_" + job["arguments"]["--intable"] if job["arguments"]["--intable"] != "images" else job["arguments"]["--intable"]
+ job["arguments"]["--outtable"] = type + "_" + job["arguments"]["--outtable"]
+ job["arguments"]["--db"] = "output.db"
+ inputs = {"output.db": "output.db"}
+ inputs = self._loadJobInputs(job, type)
+ outputs = {}
+ depends = [type + "_" + depend for depend in job["depends"]] if "depends" in job else serial
+ if self.stats["workflows"][type].index(job) == len(self.stats["workflows"][type]) - 1:
+ serial = [jobname]
+ else:
+ serial = []
+ self._addJob(jobname, job["executable"], inputs, outputs, job["arguments"], depends)
+ with open(self.basepath + "/" + loc + "/stats.dax", "w") as wh:
+ self.dax.writeXML(wh)
+ return
+
+ def _createReplica(self, loc):
+ """
+ Creates the pegasus configuration replica catalog. input/conf.rc
+ """
+ with open(self.basepath + "/" + loc + "/conf.rc", "w") as wh:
+ pegasusrc = textwrap.dedent("""\
+ pegasus.catalog.site = XML
+ pegasus.catalog.site.file = %s/sites.xml
+
+ pegasus.condor.logs.symlink = false
+
+ pegasus.transfer.links = true
+
+ pegasus.data.configuration = sharedfs
+
+ """ % (self.basepath + "/" + loc))
+ wh.write(pegasusrc)
+ return
+
+ def _createSites(self, loc):
+ """
+ Creates the pegasus site catalog. input/sites.xml
+ """
+ with open(self.basepath + "/" + loc + "/sites.xml", "w") as wh:
+ sites = """\
+ <sitecatalog xmlns="http://pegasus.isi.edu/schema/sitecatalog" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://pegasus.isi.edu/schema/sitecatalog http://pegasus.isi.edu/schema/sc-4.0.xsd" version="4.0">
+
+ <site handle="local" arch="x86_64" os="LINUX">
+ <directory type="shared-scratch" path="%s">
+ <file-server operation="all" url="file://%s" />
+ </directory>
+ <directory type="local-storage" path="%s">
+ <file-server operation="all" url="file://%s" />
+ </directory>
+ """ % (self.basepath + "/work/stats/", self.basepath + "/work/stats/", self.basepath + "/output/", self.basepath + "/output/")
+ for namespace in self.config["profile"]:
+ for key in self.config["profile"][namespace]:
+ val = ":".join(self.config["profile"][namespace][key]) if "path" in key.lower() else self.config["profile"][namespace][key]
+ sites += """\n\t<profile namespace="%s" key="%s">%s</profile> """ % (namespace, key, val)
+ sites += "</site></sitecatalog>"
+ sites = sites.replace("\n","")
+ wh.write("\n".join([line for line in xml.dom.minidom.parseString(sites).toprettyxml().split('\n') if line.strip()]))
+ return
+
+ def _createSubmit(self, loc):
+ """
+ Creates the pegasus submit script. submit.sh
+ """
+ with open(self.basepath + "/" + loc + "/submit.sh", "w") as wh:
+ submit = textwrap.dedent("""\
+ #!/bin/bash
+
+ plan=`pegasus-plan \\
+ --conf "%s" \\
+ --sites local \\
+ --dir "%s" \\
+ --output-site local \\
+ --dax "%s" \\
+ --randomdir \\""" % (self.basepath + "/" + loc + "/conf.rc", self.basepath + "/work/stats", self.basepath + "/" + loc + "/stats.dax"))
+ if "cluster" in self.config:
+ submit += """--cluster horizontal \\\n"""
+ submit += textwrap.dedent("""\
+ --submit`
+
+ status=`echo "$plan" | grep pegasus-status | tr -s ' '| cut -d ' ' -f 6`
+ echo -e "#!/bin/bash
+ pegasus-status -l $status" > status.sh
+ chmod 744 status.sh
+
+ remove=`echo "$plan" | grep pegasus-remove | tr -s ' '| cut -d ' ' -f 5`
+ echo -e "#!/bin/bash
+ pegasus-remove $remove" > remove.sh
+ chmod 744 remove.sh
+
+ echo "$plan"
+ echo "Alternatively, you can use the status & remove scripts in the current directory!"
+
+ """)
+ wh.write(submit)
+ os.chmod(self.basepath + "/" + loc + "/submit.sh", 0755)
+ return
+
+ def create(self):
+ """
+ Creates a new pegasus submission directory based on the current timestamp,
+ and populates it with all required information to submit a pegasus job.
+ """
+ loc = "/input/stats/"
+ self._createSetup()
+ self._copyFiles()
+ self._loadFiles(loc)
+ self._loadExecutables()
+ self._createDax(loc)
+ self._createReplica(loc)
+ self._createSites(loc)
+ self._createSubmit(loc)
+ return
+
+
+
+
+
+class ImageProcessor(Workflow):
+
+ """
+ A class specifically for image processing workflow
+ validation and submission.
+ """
+
+ def __init__(self, jobhome, basename = None, validOnly = False):
+ """
+ :param jobhome: The base directory for job submission.
+ :type jobhome: str
+
+ Creates a Workflow class based on the input directory. Loads and validates all input files,
+ and quits out if something doesn't exist or is defined innapropriately.
+ """
+ super(ImageProcessor, self).__init__(jobhome, basename)
+ self.validOnly = validOnly
+ self.workfile = jobhome + "/input/" + conf.workflowFile
+ self.metafile = jobhome + "/input/" + conf.dbFile
+ self.configfile = jobhome + "/input/" + conf.configFile
+ self._loadInputFiles()
+ self.exdax = ADAG("extract-" + self.jobname)
+ self.jobs[self.exdax] = {}
+ self.files[self.exdax] = {}
+ return
+
+ def _loadInputFiles(self):
+ """
+ Loads the input files into the appropriate variables
+ """
+ self.validator = htpia.validator.ImageProcessor(self.workfile, self.configfile, self.metafile)
+ if not self.validator.isValid() or self.validOnly:
+ self.validator.printErrors()
+ sys.exit()
+ else:
+ self.workflow = self.validator.workflow.data
+ self.metadata = self.validator.db.conn
+ self.config = self.validator.config.data
+ self.rawFiles = self.validator.workflow.rawFiles
+ return
+
+ def _getImageTypes(self):
+ """
+ Convenience function to get all image types from the database.
+ """
+ return [x[0] for x in self.metadata.execute("select distinct imtype from images")]
+
+ def _copyFiles(self):
+ """
+ Copies all input files to the correct location.
+ """
+ if not os.path.exists(self.basepath + "/input/imgproc"):
+ os.makedirs(self.basepath + "/input/imgproc")
+ shutil.copyfile(self.workfile, self.basepath + "/input/templates/" + os.path.basename(self.workfile))
+ shutil.copyfile(self.configfile, self.basepath + "/input/templates/" + os.path.basename(self.configfile))
+ shutil.copyfile(self.metafile, self.basepath + "/output/output.db")
+ for type in self.rawFiles:
+ for input in self.rawFiles[type]:
+ shutil.copyfile(input, self.basepath + "/input/rawfiles/" + os.path.basename(input))
+ return
+
+ def _loadFiles(self, loc):
+ """
+ Loads all files (input and output) into the dax and the self.files variable
+ """
+ with open(self.basepath + "/input/rawfiles/extract.json", "w") as wh:
+ json.dump(self.workflow["extract"], wh)
+ with open(self.basepath + "/" + loc + "/map.rc", "w") as wh:
+ self.exInput = {"db": "img.db", "extract.json": "extract.json"}
+ self.files[self.dax] = {}
+ self.files[self.exdax] = {}
+ self.files[self.exdax]["all"] = {"input": {}, "output": {}}
+ self.files[self.dax]["raw"] = {"input": {}, "output": {}}
+ self._addFile("img.db", "raw", "input", self.basepath + "/output/output.db")
+ self._addFile("img.db", "all", "input", self.basepath + "/output/output.db", dax = self.exdax)
+ self._addFile("img.log", "raw", "output", self.basepath + "/output/imgproc.log")
+ self._addFile("extract.json", "raw", "input", self.basepath + "/input/rawfiles/extract.json")
+ self._addFile("extract.json", "all", "input", self.basepath + "/input/rawfiles/extract.json", dax = self.exdax)
+ for type in self.workflow["workflows"]:
+ self.files[self.dax][type] = {"input": {}, "output": {}}
+ for input in self.rawFiles[type]:
+ self._addFile(os.path.basename(input), type, "input", self.basepath + "/input/rawfiles/" + os.path.basename(input))
+ wh.write("img.log file://" + self.basepath + "/output/imgproc.log pool=\"local\"\n")
+ inputImages = [self.workflow["workflows"][type][0]["inputs"][i] for i,x in enumerate(conf.valid[self.workflow["workflows"][type][0]["executable"]]["inputs"]) if x == "image"]
+ outputImages = [self.workflow["workflows"][type][z]["outputs"][i] for z in range(0, len(self.workflow["workflows"][type])) for i,x in enumerate(conf.valid[self.workflow["workflows"][type][z]["executable"]]["outputs"]) if x == "image"]
+ outputFiles = dict((self.workflow["workflows"][type][z]["outputs"][i], conf.fileExtensions[conf.valid[self.workflow["workflows"][type][z]["executable"]]["outputs"][i]]) for z in range(0, len(self.workflow["workflows"][type])) for i,x in enumerate(conf.valid[self.workflow["workflows"][type][z]["executable"]]["outputs"]) if x != "image" and x != "none" and len(self.workflow["workflows"][type][z]["outputs"]) > i)
+ for row in self.metadata.execute("select pegasusid, experiment, id, date, imgname, path from images where imtype=?", (type,)):
+ realname = row["path"].split("/")[-1].split(".")[0]
+ #derivedPath = row["experiment"].replace(" ","%20") + "/" + row["id"].replace(" ","%20") + "/" + row["date"].replace(" ","%20") + "/" + type + "/" + row["imgname"].replace(" ","%20") + "/"
+ derivedPath = row["experiment"].replace(" ","") + "/" + row["id"].replace(" ","") + "/" + row["date"].replace(" ","") + "/" + type + "/" + row["imgname"].replace(" ","") + "/"
+ for input in inputImages:
+ self._addFile(derivedPath + row["pegasusid"] + "_" + input + "." + row["path"].split(".")[1], type, "input", row["path"])
+ for output in outputImages:
+ if output in self.workflow["extract"]["workflows"][type]["inputs"]:
+ self.exInput[derivedPath + row["pegasusid"] + "_" + output + ".png"] = derivedPath + row["pegasusid"] + "_" + output + ".png"
+ self._addFile(derivedPath + row["pegasusid"] + "_" + output + ".png", "all", "input", self.basepath + "/output/" + derivedPath + row["pegasusid"] + "_" + output + ".png", dax = self.exdax)
+ self._addFile(derivedPath + row["pegasusid"] + "_" + output + ".png", type, "output")
+ wh.write(derivedPath + row["pegasusid"] + "_" + output + ".png file://" + self.basepath + "/output/" + derivedPath + row["pegasusid"].replace(" ","%20") + "_" + output + ".png pool=\"local\"\n")
+ for output in outputFiles:
+ outname = output + outputFiles[output]
+ self._addFile(derivedPath + row["pegasusid"] + "_" + outname, type, "output")
+ wh.write(derivedPath + row["pegasusid"] + "_" + outname + " file://" + self.basepath + "/output/" + derivedPath.replace("_","%20") + outname + " pool=\"local\"\n")
+ return
+
+ def _loadNotify(self):
+ if "email" in self.config:
+ self.dax.invoke("at_end", self.basepath + "/input/imgproc/notify.sh")
+ self.exdax.invoke("at_end", self.basepath + "/input/imgproc/notify.sh")
+ with open(self.basepath + "/input/imgproc/notify.sh", "w") as wh:
+ notify = textwrap.dedent("""\
+ #!/bin/bash
+ $PEGASUS_HOME/notification/email -t %s
+ """ % (self.config["email"],))
+ wh.write(notify)
+ os.chmod(self.basepath + "/input/imgproc/notify.sh", 0755)
+ return
+
+ def _loadExecutables(self, os="linux", arch="x86_64"):
+ """
+ Loads all executables (as specified in the conf) into
+ the dax, as well as the internal self.executables variable
+ """
+ for ex in conf.valid:
+ self.executables[ex] = Executable(name=ex, os=os, arch=arch)
+ self.executables[ex].addPFN(PFN("file://" + self.config["installdir"] + "/" + ex, "local"))
+ #if "cluster" in self.config:
+ # val = int(self.config["cluster"] * conf.valid[ex]["weight"]) if "weight" in conf.valid[ex] else self.config["cluster"]
+ # self.executables[ex].addProfile(Profile(Namespace.PEGASUS, "clusters.size", val))
+ self.dax.addExecutable(self.executables[ex])
+ self.exdax.addExecutable(self.executables[ex])
+ return
+
+ def _loadJobInputs(self, job, type, basename, extension, save = False):
+ inputs = {}
+ for i,input in enumerate(job["inputs"]):
+ ftype = conf.valid[job["executable"]]["inputs"][i]
+ if input in self.rawFiles[type]:
+ inputs[input] = {"file": os.path.basename(input), "transfer": save}
+ else:
+ ex = extension if job["name"] == self.workflow["workflows"][type][0]["name"] else conf.fileExtensions[ftype]
+ inputs[input] = {"file": basename + "_" + input + ex, "transfer": save}
+ return inputs
+
+ def _loadJobOutputs(self, job, type, basename, save):
+ outputs = {}
+ for i,output in enumerate(job["outputs"]):
+ if output != "none":
+ outputs[output] = {"file": basename + "_" + output + conf.fileExtensions[conf.valid[job["executable"]]["outputs"][i]], "transfer": save}
+ return outputs
+
+ #def _loadJobOutputs(self, job, type, basename):
+ # return dict((output, basename + "_" + output + conf.fileExtensions[conf.valid[job["executable"]]["outputs"][i]]) for i,output in enumerate(job["outputs"]) if output != "none")
+
+ def _createDax(self, loc):
+ """
+ Loads all jobs into the dax, and then writes the dax
+ to input/workflow.dax
+ """
+ exDep = {}
+ exInput = {}
+ clusternum = {}
+ meancluster = {}
+
+ save = True if "save-steps" in self.workflow["options"] else False
+ for type in self.workflow["workflows"]:
+ exDep[type] = [[]]
+ exInput[type] = [{}]
+ jobnum = -1
+ clusternum[type] = 0
+ meancluster[type] = 0
+ exNames = self.workflow["extract"]["workflows"][type]["depends"]
+ for infile in [x for x in self.files[self.dax][type]["input"] if "." + x.split(".")[1] in conf.imageExtensions]:
+ if "cluster" in self.config:
+ jobnum += 1
+ if jobnum == self.config["cluster"]:
+ jobnum = 0
+ clusternum[type] += 1
+ exDep[type].append([])
+ exInput[type].append({})
+ elif ((clusternum[type] * 100 + jobnum) % int(self.config["cluster"] * 0.3)) == 0:
+ meancluster[type] += 1
+ extension = "." + infile.split(".")[1]
+ derivedPath = infile.split("_")[0]
+ realname = self.files[self.dax][type]["input"][infile]["path"].split("/")[-1].split(".")[0]
+ for stepnum,job in enumerate(self.workflow["workflows"][type]):
+ jobname = derivedPath + "_" + job["name"]
+ inputs = self._loadJobInputs(job, type, derivedPath, extension)
+ if job["name"] in exNames:
+ outputs = self._loadJobOutputs(job, type, derivedPath, True)
+ exDep[type][clusternum[type]].append(jobname)
+ reqFile = derivedPath + "_" + self.workflow["extract"]["workflows"][type]["inputs"][0] + ".png"
+ exInput[type][clusternum[type]][reqFile] = {"file": reqFile, "transfer": save}
+ else:
+ outputs = self._loadJobOutputs(job, type, derivedPath, save)
+ depends = [derivedPath + "_" + depend for depend in job["depends"]] if "depends" in job else []
+ if job["executable"] == "pcv-meanshift":
+ self._addJob(jobname, job["executable"], inputs, outputs, job["arguments"], depends, label = type + "_step" + str(stepnum) + "_cluster" + str(meancluster[type]) if "cluster" in self.config else None)
+ else:
+ self._addJob(jobname, job["executable"], inputs, outputs, job["arguments"], depends, label = type + "_step" + str(stepnum) + "_cluster" + str(clusternum[type]) if "cluster" in self.config else None)
+
+
+ maprc = open(self.basepath + "/" + loc + "/map.rc", "a")
+ binDep = []
+ aggIn = {}
+ for type in self.workflow["workflows"]:
+ for q in range(0, clusternum[type] + 1):
+ arguments = self.workflow["extract"]["workflows"][type]["arguments"]
+ if "--input" in arguments:
+ del arguments["--input"]
+ if "histogram-bin" in self.workflow["extract"]:
+ if type in [imtype for key in self.workflow["extract"]["histogram-bin"]["--group"] for imtype in self.workflow["extract"]["histogram-bin"]["--group"][key]]:
+ arguments["--colors"] = ""
+ arguments["--db"] = "db"
+ arguments["--createdb"] = ""
+ arguments["--inputs"] = " ".join(exInput[type][q].keys())
+ self._addFile(type + str(q) + ".db", type, "output")
+ self._addJob(type + "_extract" + str(q), "pcv-extract-multi", exInput[type][q], {"db": {"file": type + str(q) + ".db", "transfer": False}}, arguments, exDep[type][q])
+ self._addJob(type + "_extract" + str(q), "pcv-extract-multi", exInput[type][q], {"db": {"file": type + str(q) + ".db", "transfer": False}}, arguments, [], dax = self.exdax)
+ maprc.write(type + str(q) + ".db" + " file://" + self.basepath + "/output/" + type + str(q) + ".db" + " pool=\"local\"\n")
+ binDep.append(type + "_extract" + str(q))
+ aggIn[type + str(q) + ".db"] = {"file": type + str(q) + ".db", "transfer": False}
+ aggIn["db"] = {"file": "img.db", "transfer": False}
+ self._addJob("sql_aggregate1", "pcv-sql-aggregate", aggIn, {}, {"--db": "db", "--inputs": " ".join([aggIn[x]["file"] for x in aggIn if x != "db"])}, binDep)
+ self._addJob("sql_aggregate1", "pcv-sql-aggregate", aggIn, {}, {"--db": "db", "--inputs": " ".join([aggIn[x]["file"] for x in aggIn if x != "db"])}, binDep, dax = self.exdax)
+
+ if "histogram-bin" in self.workflow["extract"]:
+ outputs = {}
+ for name in self.workflow["extract"]["histogram-bin"]["--group"]:
+ self._addFile(name + "_hist_bins.json", "raw", "output")
+ maprc.write(name + "_hist_bins.json" + " file://" + self.basepath + "/output/" + name + "_hist_bins.json" + " pool=\"local\"\n")
+ outputs[name + "_hist_bins.json"] = {"file": name + "_hist_bins.json", "transfer": True}
+ self._addJob("bin_creation", "pcv-stats-histogram-bin", {"db": {"file": "img.db", "transfer": True}, "extract.json": {"file": "extract.json", "transfer": False}}, outputs, {"--db": "db", "--options": "extract.json", "--intable": "images", "--outtable": "histogramBins", "--jsonwrite": ""}, ["sql_aggregate1"])
+ self._addJob("bin_creation", "pcv-stats-histogram-bin", {"db": {"file": "img.db", "transfer": True}, "extract.json": {"file": "extract.json", "transfer": False}}, outputs, {"--db": "db", "--options": "extract.json", "--intable": "images", "--outtable": "histogramBins", "--jsonwrite": "", "--overwrite": ""}, ["sql_aggregate1"], dax = self.exdax)
+
+ binDep = []
+ map = {}
+
+ for group in self.workflow["extract"]["histogram-bin"]["--group"]:
+ for type in self.workflow["extract"]["histogram-bin"]["--group"][group]:
+ map[type] = group
+
+ for type in self.workflow["workflows"]:
+ for q in range(0, clusternum[type] + 1):
+ arguments = {}
+ arguments["--db"] = "db"
+ arguments["--inputs"] = " ".join(exInput[type][q].keys())
+ exInput[type][q]["db"] = {"file": type + str(q) + ".db", "transfer": False}
+ exInput[type][q]["binfile"] = {"file": map[type] + "_hist_bins.json", "transfer": False}
+ arguments["--bins"] = "binfile"
+ self._addJob(type + "_extractBins" + str(q), "pcv-extract-multi", exInput[type][q], {}, arguments, ["bin_creation"])
+ self._addJob(type + "_extractBins" + str(q), "pcv-extract-multi", exInput[type][q], {}, arguments, ["bin_creation"], dax = self.exdax)
+ binDep.append(type + "_extractBins" + str(q))
+ self._addJob("sql_aggregate2", "pcv-sql-aggregate", aggIn, {}, {"--db": "db", "--inputs": " ".join([aggIn[x]["file"] for x in aggIn if x != "db"])}, binDep)
+ self._addJob("sql_aggregate2", "pcv-sql-aggregate", aggIn, {}, {"--db": "db", "--inputs": " ".join([aggIn[x]["file"] for x in aggIn if x != "db"])}, binDep, dax = self.exdax)
+
+ z = 2 if "histogram-bin" in self.workflow["extract"] else 1
+ self._addJob("error-log", "pcv-error-log", {"db": {"file": "img.db", "transfer": False}}, {"output": {"file": "img.log", "transfer": True}}, {"--db": "db", "--output": "output"}, ["sql_aggregate" + str(z)])
+ with open(self.basepath + "/" + loc + "/workflow.dax", "w") as wh:
+ self.dax.writeXML(wh)
+ return
+
+ def _createExtract(self, loc):
+ """
+ Creates the extraction step only dax!
+ """
+ #self._addJob("extractOnly", "pcv-extract-all", self.exInput, {}, {"--db": "db", "--options": "extract.json"}, dax = self.exdax)
+ with open(self.basepath + "/" + loc + "/extract.dax", "w") as wh:
+ self.exdax.writeXML(wh)
+ return
+
+ def _createReplica(self, loc):
+ """
+ Creates the pegasus configuration replica catalog. input/conf.rc
+ """
+ with open(self.basepath + "/" + loc + "/conf.rc", "w") as wh:
+ pegasusrc = textwrap.dedent("""\
+ pegasus.catalog.site = XML
+ pegasus.catalog.site.file = %s/sites.xml
+
+ pegasus.condor.logs.symlink = false
+
+ pegasus.transfer.links = true
+
+ pegasus.data.configuration = sharedfs
+
+ pegasus.dir.storage.mapper = Replica
+ pegasus.dir.storage.mapper.replica = File
+ pegasus.dir.storage.mapper.replica.file = %s/map.rc
+ """ % (self.basepath + "/" + loc, self.basepath + "/" + loc))
+ wh.write(pegasusrc)
+ return
+
+ def _createSites(self, loc):
+ """
+ Creates the pegasus site catalog. input/sites.xml
+ """
+ with open(self.basepath + "/" + loc + "/sites.xml", "w") as wh:
+ sites = """\
+ <sitecatalog xmlns="http://pegasus.isi.edu/schema/sitecatalog" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://pegasus.isi.edu/schema/sitecatalog http://pegasus.isi.edu/schema/sc-4.0.xsd" version="4.0">
+
+ <site handle="local" arch="x86_64" os="LINUX">
+ <directory type="shared-scratch" path="%s">
+ <file-server operation="all" url="file://%s" />
+ </directory>
+ <directory type="local-storage" path="%s">
+ <file-server operation="all" url="file://%s" />
+ </directory>
+ """ % (self.basepath + "/work/imgproc/", self.basepath + "/work/imgproc/", self.basepath + "/output/", self.basepath + "/output/")
+ for namespace in self.config["profile"]:
+ for key in self.config["profile"][namespace]:
+ val = ":".join(self.config["profile"][namespace][key]) if "path" in key.lower() else self.config["profile"][namespace][key]
+ sites += """\n\t<profile namespace="%s" key="%s">%s</profile> """ % (namespace, key, val)
+ sites += "</site></sitecatalog>"
+ sites = sites.replace("\n","")
+ wh.write("\n".join([line for line in xml.dom.minidom.parseString(sites).toprettyxml().split('\n') if line.strip()]))
+ return
+
+ def _createSubmit(self, loc):
+ """
+ Creates the pegasus submit script. submit.sh
+ """
+ with open(self.basepath + "/" + loc + "/submit.sh", "w") as wh:
+ submit = textwrap.dedent("""\
+ #!/bin/bash
+ if [ "$1" = "--extract-only" ] || [ "$1" = "--extract" ] || [ "$1" = "-e" ]; then
+ DAX="%s"
+ else
+ DAX="%s"
+ fi
+ plan=`pegasus-plan \\
+ --conf "%s" \\
+ --sites local \\
+ --dir "%s" \\
+ --output-site local \\
+ --dax "$DAX" \\
+ --randomdir \\
+ """ % (self.basepath + "/" + loc + "/extract.dax", self.basepath + "/" + loc + "/workflow.dax", self.basepath + "/" + loc + "/conf.rc", self.basepath + "/work/imgproc"))
+ if "cluster" in self.config:
+ submit += """--cluster label \\\n"""
+ submit += textwrap.dedent("""\
+ --submit`
+
+ status=`echo "$plan" | grep pegasus-status | tr -s ' '| cut -d ' ' -f 6`
+ echo -e "#!/bin/bash
+ pegasus-status -l $status" > status.sh
+ chmod 744 status.sh
+
+ remove=`echo "$plan" | grep pegasus-remove | tr -s ' '| cut -d ' ' -f 5`
+ echo -e "#!/bin/bash
+ pegasus-remove $remove" > remove.sh
+ chmod 744 remove.sh
+
+ echo "$plan"
+ echo "Alternatively, you can use the status & remove scripts in the current directory!"
+
+ """)
+ wh.write(submit)
+ os.chmod(self.basepath + "/" + loc + "/submit.sh", 0755)
+ return
+
+ def create(self):
+ """
+ Creates a new pegasus submission directory based on the current timestamp,
+ and populates it with all required information to submit a pegasus job.
+ """
+ print "Generating workflow. Please wait."
+ loc = "/input/imgproc/"
+ self._createSetup()
+ self._copyFiles()
+ self._loadFiles(loc)
+ self._loadExecutables()
+ self._loadNotify()
+ self._createDax(loc)
+ self._createExtract(loc)
+ self._createReplica(loc)
+ self._createSites(loc)
+ self._createSubmit(loc)
+ return
+
+
+class ImageLoader:
+ """
+ This should handle all meta-data definitions
+ """
+
+ def __init__(self, template, output, validOnly = False, overwrite = False):
+ """
+ :param template: Path to input template file, should be valid json.
+ :type template: str
+ """
+ self.templatePath = os.path.abspath(template)
+ self.err = ""
+ self.output = output + "/input/"
+ try:
+ open(self.output + "/images.db")
+ except IOError:
+ self.err += "Path Error: Cannot open output db file. \n"
+ self.validator = htpia.validator.ImageLoader(self.templatePath)
+ if not self.validator.isValid() or validOnly:
+ self.validator.printErrors()
+ sys.exit()
+ self.overwrite = overwrite
+ self.template = self.validator.data
+ self.template["order"].insert(0, "pegasusid")
+ self.count = {}
+ self.depth = len(self.template["path"].split("/")) - 1
+ self.structure = self._dictTemplate()
+ self.data = []
+ return
+
+ def _success(self):
+ if self.overwrite:
+ print "Directory re-crawled!"
+ print "Use pcv-run to submit your jobs."
+ else:
+ print "Directory setup successful!"
+ print "Define the required templates in " + self.output + "."
+ print "Then use pcv-run to submit your jobs."
+ return
+
+ def _dictTemplate(self):
+ """
+ Creates the first of two intermediary dictionaries for crawling. This relates
+ identifiers in the path, to a specified depth, as well as operators to split
+ the value at that depth.
+ """
+ m = [x for x in re.findall(r"%(\w+)%", self.template["path"]) if x != "null"]
+ sp = self.template["path"].split("/")
+ d = {}
+ for key in m:
+ d[key] = {}
+ d[key]["depth"] = [n for n,x in enumerate(sp) if key in x][0]
+ d[key]["split"] = []
+ val = sp[d[key]["depth"]]
+ for operator in [" ", "_", "-"]:
+ if operator in val:
+ b = val.split(operator)
+ x = [n for n,x in enumerate(b) if key in x][0]
+ d[key]["split"].append({"operator": operator, "index": x})
+ val = b[x]
+ return d
+
+ def _loadStructure(self, splitPath):
+ """
+ Creates the second of two intermediary dictionaries for crawling.
+ This utilizes the template created in _dictTemplate, and creates
+ a dictionary with actual values instead of structure.
+ """
+ d ={}
+ for key in self.structure:
+ val = splitPath[self.structure[key]["depth"]]
+ for operator in self.structure[key]["split"]:
+ val = val.split(operator["operator"])[operator["index"]]
+ d[key] = val
+ return d
+
+ def _loadDataFile(self, dict, structure, key):
+ """
+ Loads data from a data file. If the specified key isn't in the file,
+ write 'UNKNOWN' instead.
+ """
+ keyVal = self._convertReferences(structure, self.template["data"][key]["key"])
+ if keyVal in self.filedata[self.template["data"][key]["value"]]:
+ dict[key] = self.filedata[self.template["data"][key]["value"]][keyVal]
+ else:
+ dict[key] = "UNKNOWN"
+ return
+
+ def _loadDataValue(self, dict, structure, key):
+ """
+ Loads a data value.
+ """
+ val = self._convertReferences(structure, self.template["data"][key]["value"])
+ if "translate" in self.template["data"][key]:
+ if val in self.template["translations"][key]:
+ val = self.template["translations"][key][val]
+ dict[key] = val
+ return
+
+ def _loadDataDate(self, dict, structure, key):
+ """
+ Loads a date.
+ """
+ val = self._convertReferences(structure, self.template["data"][key]["value"])
+ format = "".join([x.replace(x, "%" + x) if x in conf.dateFormat else x for x in self.template["data"][key]["format"]])
+ val = datetime.datetime.strptime(val, format).strftime("%Y-%m-%d")
+ dict[key] = val
+ return
+
+ def _convertReferences(self, structure, val):
+ """
+ Replaces all references ('%%') to actual values.
+ """
+ idList = [x for x in re.findall(r"%(\w+)%", val) if x != "null"]
+ for identifier in idList:
+ if identifier in structure:
+ val = val.replace("%" + identifier + "%", structure[identifier])
+ return val
+
+ def _loadData(self, path):
+ """
+ Loads all data for a particular path.
+ """
+ temp = {}
+ final = {}
+ splitPath = path.split("/")
+ structure = self._loadStructure(splitPath)
+ for key in self.template["data"]:
+ d = {
+ "value": self._loadDataValue,
+ "file": self._loadDataFile,
+ "date": self._loadDataDate
+ }[self.template["data"][key]["type"]](final, structure, key)
+ final["path"] = path
+ if final["imtype"] not in self.count:
+ self.count[final["imtype"]] = 1
+ else:
+ self.count[final["imtype"]] += 1
+ final["pegasusid"] = final["imtype"] + str(self.count[final["imtype"]])
+ return final
+
+ def _loadFiles(self):
+ """
+ Reads all data from all specified files.
+ """
+ self.filedata = {}
+ for key in self.template["data"]:
+ if self.template["data"][key]["type"] == "file":
+ if self.template["data"][key]["value"] not in self.filedata:
+ self.filedata[self.template["data"][key]["value"]] = {}
+ with open(self.template["data"][key]["value"], "r") as rh:
+ for line in rh.readlines():
+ info = line.strip().split(",")
+ self.filedata[self.template["data"][key]["value"]][info[self.template["data"][key]["keyColumn"]]] = info[self.template["data"][key]["valueColumn"]]
+ return
+
+ def crawl(self):
+ """
+ Recursively walks through directories in base, and loads
+ the appropriate data.
+ """
+ self._loadFiles()
+ for root, dirs, files in os.walk(self.template["base"]):
+ arr = root.split("/")
+ depth = len(arr)
+ if (depth == self.depth):
+ for file in files:
+ if file[-len(self.template["filetype"]):] == self.template["filetype"] and file[0] != ".":
+ d = self._loadData(root + "/" + file)
+ self.data.append(d)
+ return
+
+ def write(self):
+ """
+ Writes the data loaded from crawl into csv format based on 'order'
+ """
+ if self.data:
+ conn = sqlite3.connect(self.output + "/images.db")
+ tablestr = "(pegasusid PRIMARY KEY"
+ for x in self.template["order"]:
+ if x != "pegasusid":
+ tablestr += "," + str(x)
+ tablestr += ")"
+ if self.overwrite:
+ conn.execute("DROP TABLE IF EXISTS images")
+ conn.commit()
+ conn.execute("CREATE TABLE images " + tablestr)
+ writedata = []
+ for row in self.data:
+ writedata.append(tuple([str(row[x]) for x in self.template["order"]]))
+ query = "insert into images " + str(tuple([str(x) for x in self.template["order"]])) + " values (" + ("?," * len(self.template["order"]))[:-1] + ")"
+ conn.executemany(query, writedata)
+ conn.commit()
+ if not self.overwrite:
+ shutil.copyfile(self.templatePath, self.output + "/crawl.json")
+ else:
+ print "Call crawl first!"
+ return
+
+class DirectorySetup:
+
+ def __init__(self, jobhome):
+ """
+ :param jobhome: The base directory to setup a job.
+ :type jobhome: str
+ """
+ if not os.path.isdir(os.path.dirname(os.path.dirname(os.path.abspath(jobhome) + "/"))):
+ print "Can't create job folder, path doesn't exist!"
+ sys.exit()
+ self.jobhome = jobhome
+ return
+
+ def _makeDir(self, dirpath):
+ """
+ Makes a directory if it doesn't exist. Catches and
+ prints out common errors.
+ """
+ try:
+ os.makedirs(dirpath)
+ except OSError as e:
+ raise Exception({
+ errno.EEXIST: "Directory " + dirpath + " already exists!",
+ errno.EACCES: "You don't have permission to create directory " + dirpath + ".",
+ }.get(e.errno, "Error for directory " + dirpath + " error:" + str(e)))
+ return
+
+ def _makeFile(self, filepath):
+ """
+ Opens a file to create it, uses append mode
+ so it doesn't overwrite any existing files.
+ """
+ try:
+ open(filepath, "a")
+ except OSError as e:
+ raise Exception({
+
+ }.get(e, "Unsepcified error for file " + filepath))
+ return
+
+ def setup(self):
+ """
+ Creates the directory structure needed to submit jobs,
+ and creates empty template files needed for job submission.
+ """
+ self._makeDir(self.jobhome)
+ self._makeDir(self.jobhome + "/input/")
+ for fname in conf.jobFiles:
+ self._makeFile(self.jobhome + "/input/" + fname)
+ return
+
+
+
diff --git a/build/lib/ih/__init__.py b/build/lib/ih/__init__.py
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/build/lib/ih/conf.py b/build/lib/ih/conf.py
new file mode 100644
index 0000000000000000000000000000000000000000..e1f1b4ec036c8962a290b3a60b50998a3cf4f375
--- /dev/null
+++ b/build/lib/ih/conf.py
@@ -0,0 +1,1305 @@
+import cv2
+
+"""
+A dictionary used to map input-output types to a cv2 color code
+"""
+colors = {
+ "bgr": {
+ "gray": [cv2.COLOR_BGR2GRAY],
+ "hsv": [cv2.COLOR_BGR2HSV],
+ "lab": [cv2.COLOR_BGR2LAB],
+ "ycrcb": [cv2.COLOR_BGR2YCR_CB]
+ },
+ "gray": {
+ "bgr": [cv2.COLOR_GRAY2BGR],
+ "hsv": [cv2.COLOR_GRAY2BGR, cv2.COLOR_BGR2HSV],
+ "lab": [cv2.COLOR_GRAY2BGR, cv2.COLOR_BGR2LAB],
+ "ycrcb": [cv2.COLOR_GRAY2BGR, cv2.COLOR_BGR2YCR_CB]
+ },
+ "hsv": {
+ "bgr": [cv2.COLOR_HSV2BGR],
+ "gray": [cv2.COLOR_HSV2BGR, cv2.COLOR_BGR2GRAY],
+ "lab": [cv2.COLOR_YCR_CB2BGR, cv2.COLOR_BGR2LAB],
+ "ycrcb": [cv2.COLOR_YCR_CB2BGR, cv2.COLOR_BGR2YCR_CB]
+ },
+ "lab": {
+ "bgr": [cv2.COLOR_LAB2BGR],
+ "gray": [cv2.COLOR_LAB2BGR, cv2.COLOR_BGR2GRAY],
+ "hsv": [cv2.COLOR_LAB2BGR, cv2.COLOR_BGR2HSV],
+ "ycrcb": [cv2.COLOR_LAB2BGR, cv2.COLOR_BGR2YCR_CB]
+ },
+ "ycrcb": {
+ "bgr": [cv2.COLOR_YCR_CB2BGR],
+ "gray": [cv2.COLOR_YCR_CB2BGR, cv2.COLOR_BGR2GRAY],
+ "hsv": [cv2.COLOR_YCR_CB2BGR, cv2.COLOR_BGR2HSV],
+ "lab": [cv2.COLOR_YCR_CB2BGR, cv2.COLOR_BGR2LAB]
+ }
+}
+
+"""
+A dicitonary used to map threshold-types to cv2 threshold codes
+"""
+thresholds = {
+ "binary": cv2.THRESH_BINARY,
+ "inverse": cv2.THRESH_BINARY_INV,
+ "truncate": cv2.THRESH_TRUNC,
+ "tozero": cv2.THRESH_TOZERO,
+ "otsu": cv2.THRESH_BINARY + cv2.THRESH_OTSU
+}
+
+"""
+A dictionary used to map adaptive-types to cv2 adaptive codes
+"""
+adaptives = {
+ "mean": cv2.ADAPTIVE_THRESH_MEAN_C,
+ "gauss": cv2.ADAPTIVE_THRESH_GAUSSIAN_C,
+ "gaussian": cv2.ADAPTIVE_THRESH_GAUSSIAN_C
+}
+
+"""
+A dictionary used to map border-types to cv2 border codes
+"""
+borders = {
+ "default": cv2.BORDER_DEFAULT,
+ "constant": cv2.BORDER_CONSTANT,
+ "reflect": cv2.BORDER_REFLECT,
+ "replicate": cv2.BORDER_REPLICATE,
+ "transparent": cv2.BORDER_TRANSPARENT,
+ "wrap": cv2.BORDER_WRAP
+}
+
+"""
+A dictionary used to map morphology types to cv2 morphology codes
+"""
+morph = {
+ "dilate": cv2.MORPH_DILATE,
+ "erode": cv2.MORPH_ERODE,
+ "open": cv2.MORPH_OPEN,
+ "close": cv2.MORPH_CLOSE,
+ "gradient": cv2.MORPH_GRADIENT,
+ "tophat": cv2.MORPH_TOPHAT,
+ "blackhat": cv2.MORPH_BLACKHAT
+}
+
+"""
+A dictionary used to map kernel types to cv2 kernel codes
+"""
+kernels = {
+ "rect": cv2.MORPH_RECT,
+ "ellipse": cv2.MORPH_ELLIPSE,
+ "cross": cv2.MORPH_CROSS
+}
+
+"""
+A dictionary used to map center types to cv2 center codes
+"""
+centers = {
+ "random": cv2.KMEANS_RANDOM_CENTERS,
+ "pp": cv2.KMEANS_PP_CENTERS
+}
+
+"""
+A dictionary used to map termination types to cv2 termination codes
+"""
+ktermination = {
+ "accuracy": cv2.TERM_CRITERIA_EPS,
+ "iteration": cv2.TERM_CRITERIA_MAX_ITER,
+ "either": cv2.TERM_CRITERIA_EPS + cv2.TERM_CRITERIA_MAX_ITER
+}
+
+"""
+Defines the maximum size of a displayed image in total pixels.
+"""
+maxArea = 360000
+
+"""
+Defines imtype mapping
+"""
+typeMap = {
+ "rgbsv": "rgb",
+ "rgbtv": "rgb",
+ "fluosv": "fluo",
+ "fluotv": "fluo"
+}
+
+"""
+Defines all optional / required keys for all templates.
+"""
+
+templateKeys = {
+ "loading": {
+ "required": ["path", "base", "data", "order"],
+ "optional": ["translations", "filetype"],
+ "data": {
+ "required": ["type"],
+ "type": ["value", "file", "date"],
+ "value": {
+ "required": ["value", "type"],
+ "optional": ["translate"]
+ },
+ "file": {
+ "required": ["type", "value", "key", "keyColumn", "valueColumn"],
+ "optional": ["translate", "separator"]
+ },
+ "date": {
+ "required": ["type", "value", "format"],
+ "optional": []
+ }
+ },
+ "translations": {
+
+ }
+ },
+ "config": {
+ "required": ["installdir", "profile"],
+ "optional": ["cluster", "notify", "maxwalltime"],
+ "maxwalltime": {
+ "optional": ["images", "stats"]
+ },
+ "notify": {
+ "required": ["email", "pegasus_home"]
+ }
+ },
+ "imgproc": {
+ "required": ["workflows", "extract"],
+ "optional": ["options"],
+ "job": {
+ "required": ["executable", "inputs", "outputs", "arguments", "name"],
+ "optional": ["depends"]
+ },
+ "options": {
+ "required": [],
+ "optional": ["save-steps"]
+ },
+ "extract": {
+ "required": ["workflows"],
+ "optional": ["histogram-bin"],
+ "workflows": {
+ "required": [], # imtype are required, handled at run time.
+ "optional": []
+ },
+ "histogram-bin": {
+ "required": ["chunks", "group", "channels"],
+ "optional": []
+ }
+ }
+ },
+ "stats": {
+ "required": ["workflows"],
+ "optional": ["options"],
+ "job": {
+ "required": ["executable", "inputs", "outputs", "arguments", "name"],
+ "optional": ["depends"]
+ }
+ }
+}
+
+"""
+Defines valid date format character
+"""
+dateFormat = ["Y", "y", "M", "m", "d", "B", "b"]
+dateSep = ["/", "-", "_", " "]
+
+"""
+Defines required headers for output
+"""
+outHeaders = ["pegasusid", "experiment", "id", "genotype", "date", "treatment", "imgname", "imtype", "path"]
+
+"""
+Defines ALL possible output headers
+"""
+allHeaders = outHeaders + ["error", "rowNum", "colNum"]
+
+"""
+Defines required files for job checking
+"""
+jobFiles = ["crawl.json", "config.json", "imgproc.json", "stats.json", "images.db"]
+imgprocFiles = ["config.json", "imgproc.json", "images.db"]
+statisticsFiles = ["config.json", "stats.json"]
+
+workflowFile = "imgproc.json"
+configFile = "config.json"
+dbFile = "images.db"
+statsFile = "stats.json"
+outputdb = "output.db"
+
+
+"""
+Defines two things for stats functions.
+'Required' columns are the metadata columns a function needs to execute properly.
+'Exclude' columns are the metadata columns that become uninteresting after execution.
+"""
+statsColumns = {
+ "histogramBins": {
+ "ref": False,
+ "add": ["name", "minr", "ming", "minb", "maxr", "maxg", "maxb"],
+ "required": ["pegasusid", "experiment", "id", "date", "imtype", "imgname", "outputPath"],
+ "exclude": ["all"],
+ "overwrite": []
+ },
+ "ttest": {
+ "ref": True,
+ "add": [],
+ "required": ["pegasusid", "date", "imtype"],
+ "exclude": ["pegasusid", "path", "outputPath", "error", "id", "genotype", "treatment"],
+ "overwrite": []
+ },
+ "treatmentComp": {
+ "ref": True,
+ "add": [],
+ "required": ["pegasusid", "id", "genotype", "date", "treatment", "imtype"],
+ "exclude": ["pegasusid", "id", "path", "outputPath", "error"],
+ "overwrite": ["treatment"]
+ },
+ "shootArea": {
+ "ref": True,
+ "add": [],
+ "required": ["pegasusid", "id", "genotype", "date", "treatment", "imtype"],
+ "exclude": ["pegasusid", "imgname", "path", "outputPath", "error", "rowNum", "colNum"],
+ "overwrite": ["imtype"]
+ },
+ "normalize": {
+ "ref": True,
+ "add": [],
+ "required": ["pegasusid"],
+ "exclude": ["pegasusid", "path", "outputPath", "error"],
+ "overwrite": []
+ },
+ "correlation": {
+ "ref": True,
+ "add": [],
+ "required": ["pegasusid", "id", "date"],
+ "exclude": ["pegasusid", "path", "outputPath", "error", "rowNum", "colNum", "date", "imgname"],
+ "overwrite": []
+ },
+ "threshold": {
+ "ref": True,
+ "add": [],
+ "required": ["pegasusid"],
+ "exclude": ["pegasusid", "path", "outputPath", "error"],
+ "overwrite": []
+ },
+ "anova": {
+ "ref": False,
+ "add": ["factors"],
+ "required": ["pegasusid", "treatment", "date", "imtype"],
+ "exclude": ["pegasusid", "experiment", "id", "genotype", "date", "treatment", "imgname", "path", "outputPath", "error"],
+ "overwrite": ["imtype"]
+ }
+}
+
+"""
+Defines allowed image extensions, png is preferred.
+"""
+imageExtensions = [".png", ".jpg", ".jpeg", ".gif"]
+
+"""
+Defines allowed file extensions
+"""
+fileExtensions = {
+ "image": ".png",
+ "roi": ".json",
+ "binfile": ".json",
+ "csv": ".csv",
+}
+
+
+"""
+Defines valid arguments for stats and image processing
+functions.
+"""
+valid = {
+ "ih-resize": {
+ "type": "imgproc",
+ "inputs": ["image"],
+ "outputs": ["image"],
+ "arguments": {
+ "--input": {
+ "type": "derived",
+ "key": "inputs",
+ "index": 0,
+ "required": "true"
+ },
+ "--output": {
+ "type": "derived",
+ "key": "outputs",
+ "index": 0,
+ "required": "true"
+ },
+ "--outputdir": {
+ "type": "overwrite",
+ "value": "."
+ },
+ "--scale": {
+ "type": "numeric"
+ },
+ "--width": {
+ "type": "numeric",
+ "validation": "list",
+ "value": range(1, 5001)
+ },
+ "--height": {
+ "type": "numeric",
+ "validation": "list",
+ "value": range(1, 5001)
+ }
+ }
+ },
+ "ih-color-filter": {
+ "type": "imgproc",
+ "inputs": ["image", "roi"],
+ "outputs": ["image"],
+ "arguments": {
+ "--input": {
+ "type": "derived",
+ "key": "inputs",
+ "index": 0,
+ "required": "true"
+ },
+ "--output": {
+ "type": "derived",
+ "key": "outputs",
+ "index": 0,
+ "required": "true"
+ },
+ "--outputdir": {
+ "type": "overwrite",
+ "value": "."
+ },
+ "--roi": {
+ "type": "derived",
+ "key": "inputs",
+ "index": 1
+ },
+ "--logic": {
+ "type": "string",
+ "required": "true",
+ "complex": "true"
+ }
+ }
+ },
+ "ih-edges": {
+ "type": "imgproc",
+ "inputs": ["image"],
+ "outputs": ["image"],
+ "arguments": {
+ "--input": {
+ "type": "derived",
+ "key": "inputs",
+ "index": 0,
+ "required": "true"
+ },
+ "--output": {
+ "type": "derived",
+ "key": "outputs",
+ "index": 0,
+ "required": "true"
+ },
+ "--outputdir": {
+ "type": "overwrite",
+ "value": "."
+ },
+ "--threshold1": {
+ "type": "numeric",
+ "required": "true"
+ },
+ "--threshold2": {
+ "type": "numeric",
+ "required": "true"
+ },
+ "--apertureSize": {
+ "type": "numeric",
+ "validation": "list",
+ "value": range(1, 50)
+ },
+ "--L2gradient": {
+ "type": "exist"
+ }
+ }
+ },
+ "ih-contour-cut": {
+ "type": "imgproc",
+ "inputs": ["image", "image"],
+ "outputs": ["image", "roi"],
+ "arguments": {
+ "--input": {
+ "type": "derived",
+ "key": "inputs",
+ "index": 0,
+ "required": "true"
+ },
+ "--binary": {
+ "type": "derived",
+ "key": "inputs",
+ "index": 1,
+ "required": "true"
+ },
+ "--output": {
+ "type": "derived",
+ "key": "outputs",
+ "index": 0,
+ "required": "true"
+ },
+ "--outputdir": {
+ "type": "overwrite",
+ "value": "."
+ },
+ "--basemin": {
+ "type": "numeric"
+ },
+ "--padminx": {
+ "type": "numeric"
+ },
+ "--padmaxx": {
+ "type": "numeric"
+ },
+ "--padminy": {
+ "type": "numeric"
+ },
+ "--padmaxy": {
+ "type": "numeric"
+ },
+ "--resize": {
+ "type": "exist"
+ },
+ "--returnBound": {
+ "type": "derived",
+ "key": "outputs",
+ "index": 1,
+ "value": ""
+ },
+ "--roiwrite": {
+ "type": "derived",
+ "key": "outputs",
+ "index": 1
+ }
+ }
+ },
+ "ih-crop": {
+ "type": "imgproc",
+ "inputs": ["image", "roi"],
+ "outputs": ["image"],
+ "arguments": {
+ "--input": {
+ "type": "derived",
+ "key": "inputs",
+ "index": 0,
+ "required": "true"
+ },
+ "--output": {
+ "type": "derived",
+ "key": "outputs",
+ "index": 0,
+ "required": "true"
+ },
+ "--outputdir": {
+ "type": "overwrite",
+ "value": "."
+ },
+ "--roi": {
+ "type": "derived",
+ "key": "inputs",
+ "index": 1,
+ "required": "true"
+ },
+ "--resize": {
+ "type": "exist"
+ }
+ }
+ },
+ "ih-morphology": {
+ "type": "imgproc",
+ "inputs": ["image"],
+ "outputs": ["image"],
+ "arguments": {
+ "--input": {
+ "type": "derived",
+ "key": "inputs",
+ "index": 0,
+ "required": "true"
+ },
+ "--output": {
+ "type": "derived",
+ "key": "outputs",
+ "index": 0,
+ "required": "true"
+ },
+ "--outputdir": {
+ "type": "overwrite",
+ "value": "."
+ },
+ "--morphType": {
+ "type": "string",
+ "validation": "dictionary",
+ "value": morph,
+ "required": "true"
+ },
+ "--ktype": {
+ "type": "string",
+ "validation": "dictionary",
+ "value": kernels,
+ "required": "true"
+ },
+ "--kwidth": {
+ "type": "numeric",
+ "validation": "list",
+ "value": range(1, 256, 2),
+ "required": "true"
+ },
+ "--kheight": {
+ "type": "numeric",
+ "validation": "list",
+ "value": range(1, 256, 2),
+ "required": "true"
+ },
+ "--anchorx": {
+ "type": "numeric",
+ "validation": "list",
+ "value": range(-255, 256),
+ },
+ "--anchory": {
+ "type": "numeric",
+ "validation": "list",
+ "value": range(-255, 256),
+ },
+ "--iterations": {
+ "type": "numeric",
+ "validation": "list",
+ "value": range(1, 100)
+ },
+ "--border": {
+ "type": "string",
+ "validation": "dictionary",
+ "value": borders
+ }
+ }
+ },
+ "ih-normalize-intensity": {
+ "type": "imgproc",
+ "inputs": ["image"],
+ "outputs": ["image"],
+ "arguments": {
+ "--input": {
+ "type": "derived",
+ "key": "inputs",
+ "index": 0,
+ "required": "true"
+ },
+ "--output": {
+ "type": "derived",
+ "key": "outputs",
+ "index": 0,
+ "required": "true"
+ },
+ "--outputdir": {
+ "type": "overwrite",
+ "value": "."
+ }
+ }
+ },
+ "ih-gaussian-blur": {
+ "type": "imgproc",
+ "inputs": ["image"],
+ "outputs": ["image"],
+ "arguments": {
+ "--input": {
+ "type": "derived",
+ "key": "inputs",
+ "index": 0,
+ "required": "true"
+ },
+ "--output": {
+ "type": "derived",
+ "key": "outputs",
+ "index": 0,
+ "required": "true"
+ },
+ "--outputdir": {
+ "type": "overwrite",
+ "value": "."
+ },
+ "--kwidth": {
+ "type": "numeric",
+ "validation": "list",
+ "value": range(1, 256, 2),
+ "required": "true"
+ },
+ "--kheight": {
+ "type": "numeric",
+ "validation": "list",
+ "value": range(1, 256, 2),
+ "required": "true"
+ },
+ "--sigmax": {
+ "type": "numeric"
+ },
+ "--sigmay": {
+ "type": "numeric"
+ },
+ "--border": {
+ "type": "string",
+ "validation": "dictionary",
+ "value": borders
+ }
+ }
+ },
+ "ih-median-blur": {
+ "type": "imgproc",
+ "inputs": ["image"],
+ "outputs": ["image"],
+ "arguments": {
+ "--input": {
+ "type": "derived",
+ "key": "inputs",
+ "index": 0,
+ "required": "true"
+ },
+ "--output": {
+ "type": "derived",
+ "key": "outputs",
+ "index": 0,
+ "required": "true"
+ },
+ "--outputdir": {
+ "type": "overwrite",
+ "value": "."
+ },
+ "--ksize": {
+ "type": "numeric",
+ "validation": "list",
+ "value": range(1, 256, 2),
+ "required": "true"
+ }
+ }
+ },
+ "ih-blur": {
+ "type": "imgproc",
+ "inputs": ["image"],
+ "outputs": ["image"],
+ "arguments": {
+ "--input": {
+ "type": "derived",
+ "key": "inputs",
+ "index": 0,
+ "required": "true"
+ },
+ "--output": {
+ "type": "derived",
+ "key": "outputs",
+ "index": 0,
+ "required": "true"
+ },
+ "--outputdir": {
+ "type": "overwrite",
+ "value": "."
+ },
+ "--kwidth": {
+ "type": "numeric",
+ "validation": "list",
+ "value": range(1, 256, 2),
+ "required": "true"
+ },
+ "--kheight": {
+ "type": "numeric",
+ "validation": "list",
+ "value": range(1, 256, 2),
+ "required": "true"
+ },
+ "--anchorx": {
+ "type": "numeric",
+ "validation": "list",
+ "value": range(-255, 256),
+ },
+ "--anchory": {
+ "type": "numeric",
+ "validation": "list",
+ "value": range(-255, 256),
+ },
+ "--border": {
+ "type": "string",
+ "validation": "dictionary",
+ "value": borders
+ }
+ }
+ },
+ "ih-adaptive-threshold": {
+ "type": "imgproc",
+ "inputs": ["image"],
+ "outputs": ["image"],
+ "arguments": {
+ "--input": {
+ "type": "derived",
+ "key": "inputs",
+ "index": 0,
+ "required": "true"
+ },
+ "--output": {
+ "type": "derived",
+ "key": "outputs",
+ "index": 0,
+ "required": "true"
+ },
+ "--outputdir": {
+ "type": "overwrite",
+ "value": "."
+ },
+ "--value": {
+ "type": "numeric",
+ "validation": "list",
+ "value": range(0, 256),
+ "required": "true"
+ },
+ "--adaptiveType": {
+ "type": "string",
+ "validation": "dictionary",
+ "value": adaptives,
+ "required": "true"
+ },
+ "--thresholdType": {
+ "type": "string",
+ "validation": "dictionary",
+ "value": {"binary": "", "inverse": ""},
+ "required": "true"
+ },
+ "--blockSize": {
+ "type": "numeric",
+ "validation": "list",
+ "value": range(1, 256, 2),
+ "required": "true"
+ },
+ "--C": {
+ "type": "numeric",
+ "required": "true",
+ }
+ }
+ },
+ "ih-meanshift": {
+ "type": "imgproc",
+ "inputs": ["image"],
+ "outputs": ["image"],
+ "weight": .3,
+ "arguments": {
+ "--input": {
+ "type": "derived",
+ "key": "inputs",
+ "index": 0,
+ "required": "true"
+ },
+ "--output": {
+ "type": "derived",
+ "key": "outputs",
+ "index": 0,
+ "required": "true"
+ },
+ "--outputdir": {
+ "type": "overwrite",
+ "value": "."
+ },
+ "--spatial_radius": {
+ "type": "numeric",
+ "required": "true"
+ },
+ "--range_radius": {
+ "type": "numeric",
+ "required": "true"
+ },
+ "--min_density": {
+ "type": "numeric",
+ "required": "true"
+ }
+ }
+ },
+ "ih-convert-color": {
+ "type": "imgproc",
+ "inputs": ["image"],
+ "outputs": ["image"],
+ "arguments": {
+ "--input": {
+ "type": "derived",
+ "key": "inputs",
+ "index": 0,
+ "required": "true"
+ },
+ "--output": {
+ "type": "derived",
+ "key": "outputs",
+ "index": 0,
+ "required": "true"
+ },
+ "--outputdir": {
+ "type": "overwrite",
+ "value": "."
+ },
+ "--intype": {
+ "type": "string",
+ "validation": "dictionary",
+ "value": colors,
+ "required": "true"
+ },
+ "--outtype": {
+ "type": "string",
+ "validation": "dictionary",
+ "key": "--intype",
+ "value": colors,
+ "required": "true"
+ }
+ }
+ },
+ "ih-threshold": {
+ "type": "imgproc",
+ "inputs": ["image"],
+ "outputs": ["image"],
+ "arguments": {
+ "--input": {
+ "type": "derived",
+ "key": "inputs",
+ "index": 0,
+ "required": "true"
+ },
+ "--output": {
+ "type": "derived",
+ "key": "outputs",
+ "index": 0,
+ "required": "true"
+ },
+ "--outputdir": {
+ "type": "overwrite",
+ "value": "."
+ },
+ "--thresh": {
+ "type": "numeric"
+ },
+ "--max": {
+ "type": "numeric",
+ "validation": "list",
+ "value": range(0, 256)
+ },
+ "--type": {
+ "type": "string",
+ "validation": "list",
+ "value": ["binary", "trunc", "otsu", "tozero"]
+ }
+ }
+ },
+ "ih-bitwise-or": {
+ "type": "imgproc",
+ "inputs": ["image", "image"],
+ "outputs": ["image"],
+ "arguments": {
+ "--input1": {
+ "type": "derived",
+ "key": "inputs",
+ "index": 0,
+ "required": "true"
+ },
+ "--input2": {
+ "type": "derived",
+ "key": "inputs",
+ "index": 1,
+ "required": "true"
+ },
+ "--output": {
+ "type": "derived",
+ "key": "outputs",
+ "index": 0,
+ "required": "true"
+ },
+ "--outputdir": {
+ "type": "overwrite",
+ "value": "."
+ }
+ }
+ },
+ "ih-bitwise-xor": {
+ "type": "imgproc",
+ "inputs": ["image", "image"],
+ "outputs": ["image"],
+ "arguments": {
+ "--input1": {
+ "type": "derived",
+ "key": "inputs",
+ "index": 0,
+ "required": "true"
+ },
+ "--input2": {
+ "type": "derived",
+ "key": "inputs",
+ "index": 1,
+ "required": "true"
+ },
+ "--output": {
+ "type": "derived",
+ "key": "outputs",
+ "index": 0,
+ "required": "true"
+ },
+ "--outputdir": {
+ "type": "overwrite",
+ "value": "."
+ }
+ }
+ },
+ "ih-bitwise-not": {
+ "type": "imgproc",
+ "inputs": ["image"],
+ "outputs": ["image"],
+ "arguments": {
+ "--input": {
+ "type": "derived",
+ "key": "inputs",
+ "index": 0,
+ "required": "true"
+ },
+ "--output": {
+ "type": "derived",
+ "key": "outputs",
+ "index": 0,
+ "required": "true"
+ },
+ "--outputdir": {
+ "type": "overwrite",
+ "value": "."
+ }
+ }
+ },
+ "ih-bitwise-and": {
+ "type": "imgproc",
+ "inputs": ["image", "image"],
+ "outputs": ["image"],
+ "arguments": {
+ "--input1": {
+ "type": "derived",
+ "key": "inputs",
+ "index": 0,
+ "required": "true"
+ },
+ "--input2": {
+ "type": "derived",
+ "key": "inputs",
+ "index": 1,
+ "required": "true"
+ },
+ "--output": {
+ "type": "derived",
+ "key": "outputs",
+ "index": 0,
+ "required": "true"
+ },
+ "--outputdir": {
+ "type": "overwrite",
+ "value": "."
+ }
+ }
+ },
+ "ih-extract": {
+ "type": "system",
+ "inputs": ["image", "binfile"],
+ "outputs": ["none"],
+ "arguments": {
+ "--input": {
+ "type": "derived",
+ "key": "inputs",
+ "index": 0,
+ "required": "true"
+ },
+ "--dimensions": {
+ "type": "exist"
+ },
+ "--pixels": {
+ "type": "exist"
+ },
+ "--moments": {
+ "type": "exist"
+ },
+ "--bins": {
+ "type": "string"
+ },
+ "--channels": {
+ "type": "exist"
+ }
+ }
+ },
+ "ih-error-log": {
+ "type": "imgproc"
+ },
+ "ih-extract-all": {
+ "type": "system"
+ },
+ "ih-extract-multi": {
+ "type": "system"
+ },
+ "ih-sql-aggregate": {
+ "type": "system"
+ },
+ "ih-stats-export": {
+ "type": "statistics",
+ "inputs": ["table"],
+ "outputs": ["csv"],
+ "arguments": {
+ "--table": {
+ "type": "derived",
+ "key": "inputs",
+ "index": 0,
+ "required": "true"
+ },
+ "--fname": {
+ "type": "derived",
+ "key": "outputs",
+ "index": 0,
+ "required": "true"
+ }
+ }
+ },
+ "ih-stats-histogram-bin": {
+ "type": "system",
+ "inputs": ["table"],
+ "outputs": ["table"],
+ "arguments": {
+ "--intable": {
+ "type": "derived",
+ "key": "inputs",
+ "index": 0,
+ "required": "true"
+ },
+ "--outtable": {
+ "type": "derived",
+ "key": "outputs",
+ "index": 0,
+ "required": "true"
+ },
+ "--channels": {
+ "type": "dict",
+ "required": "true"
+ },
+ "--group": {
+ "type": "dict",
+ "required": "true"
+ },
+ "--chunks": {
+ "type": "dict",
+ "required": "true"
+ }
+ }
+ },
+ "ih-stats-ttest": {
+ "type": "statistics",
+ "inputs": ["table"],
+ "outputs": ["table"],
+ "arguments": {
+ "--intable": {
+ "type": "derived",
+ "key": "inputs",
+ "index": 0,
+ "required": "true"
+ },
+ "--outtable": {
+ "type": "derived",
+ "key": "outputs",
+ "index": 0,
+ "required": "true"
+ },
+ "--comp": {
+ "type": "string",
+ "validation": "list",
+ "value": ["imtype", "imgname"],
+ "required": "true"
+ },
+ "--overwrite": {
+ "type": "overwrite",
+ "value": "",
+ "required": "true"
+ }
+ }
+ },
+ "ih-stats-treatment-comp": {
+ "type": "statistics",
+ "inputs": ["table"],
+ "outputs": ["table"],
+ "arguments": {
+ "--intable": {
+ "type": "derived",
+ "key": "inputs",
+ "index": 0,
+ "required": "true"
+ },
+ "--outtable": {
+ "type": "derived",
+ "key": "outputs",
+ "index": 0,
+ "required": "true"
+ },
+ "--type": {
+ "type": "string",
+ "validation": "list",
+ "value": ["ratio", "difference"],
+ "required": "true"
+ },
+ "--direction": {
+ "type": "string",
+ "validation": "list",
+ "value": ["Control", "Stress"],
+ "required": "true"
+ },
+ "--comp": {
+ "type": "string",
+ "validation": "list",
+ "value": ["imtype", "imgname"],
+ "required": "true"
+ },
+ "--overwrite": {
+ "type": "overwrite",
+ "value": "",
+ "required": "true"
+ }
+ }
+ },
+ "ih-stats-anova": {
+ "type": "statistics",
+ "inputs": ["table"],
+ "outputs": ["table"],
+ "arguments": {
+ "--group": {
+ "type": "list",
+ "required": "true",
+ "join": " "
+ },
+ "--intable": {
+ "type": "derived",
+ "key": "inputs",
+ "index": 0,
+ "required": "true"
+ },
+ "--outtable": {
+ "type": "derived",
+ "key": "outputs",
+ "index": 0,
+ "required": "true"
+ },
+ "--overwrite": {
+ "type": "overwrite",
+ "value": "",
+ "required": "true"
+ }
+ }
+ },
+ "ih-stats-shoot-area": {
+ "type": "statistics",
+ "inputs": ["table"],
+ "outputs": ["table"],
+ "arguments": {
+ "--group": {
+ "type": "list",
+ "required": "true",
+ "join": " "
+ },
+ "--intable": {
+ "type": "derived",
+ "key": "inputs",
+ "index": 0,
+ "required": "true"
+ },
+ "--outtable": {
+ "type": "derived",
+ "key": "outputs",
+ "index": 0,
+ "required": "true"
+ },
+ "--overwrite": {
+ "type": "overwrite",
+ "value": "",
+ "required": "true"
+ }
+ }
+ },
+ "ih-stats-threshold": {
+ "type": "statistics",
+ "inputs": ["table"],
+ "outputs": ["table"],
+ "arguments": {
+ "--thresh": {
+ "type": "numeric",
+ "required": "true"
+ },
+ "--intable": {
+ "type": "derived",
+ "key": "inputs",
+ "index": 0,
+ "required": "true"
+ },
+ "--outtable": {
+ "type": "derived",
+ "key": "outputs",
+ "index": 0,
+ "required": "true"
+ },
+ "--overwrite": {
+ "type": "overwrite",
+ "value": "",
+ "required": "true"
+ }
+ }
+ },
+ "ih-stats-normalize": {
+ "type": "statistics",
+ "inputs": ["table"],
+ "outputs": ["table"],
+ "arguments": {
+ "--column": {
+ "type": "string"
+ },
+ "--intable": {
+ "type": "derived",
+ "key": "inputs",
+ "index": 0,
+ "required": "true"
+ },
+ "--outtable": {
+ "type": "derived",
+ "key": "outputs",
+ "index": 0,
+ "required": "true"
+ },
+ "--overwrite": {
+ "type": "overwrite",
+ "value": "",
+ "required": "true"
+ }
+ }
+ },
+ "ih-stats-correlate": {
+ "type": "statistics",
+ "inputs": ["table", "csv", "csv"],
+ "outputs": ["table"],
+ "arguments": {
+ "--intable": {
+ "type": "derived",
+ "key": "inputs",
+ "index": 0,
+ "required": "true"
+ },
+ "--outtable": {
+ "type": "derived",
+ "key": "outputs",
+ "index": 0,
+ "required": "true"
+ },
+ "--datafile": {
+ "type": "derived",
+ "key": "inputs",
+ "index": 1,
+ "required": "true"
+ },
+ "--dataheaders": {
+ "type": "derived",
+ "key": "inputs",
+ "index": 2,
+ "required": "true"
+ },
+ "--overwrite": {
+ "type": "overwrite",
+ "value": "",
+ "required": "true"
+ }
+ }
+ }
+}
diff --git a/build/lib/ih/imgproc.py b/build/lib/ih/imgproc.py
new file mode 100644
index 0000000000000000000000000000000000000000..54b3845a321d1267a01328c134abef5e1a0e1776
--- /dev/null
+++ b/build/lib/ih/imgproc.py
@@ -0,0 +1,1077 @@
+"""
+This file is part of Image Harvest.
+
+Image Harvest is free software: you can redistribute it and/or modify
+it under the terms of the GNU General Public License as published by
+the Free Software Foundation, either version 3 of the License, or
+(at your option) any later version.
+
+Image Harvest is distributed in the hope that it will be useful,
+but WITHOUT ANY WARRANTY; without even the implied warranty of
+MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+GNU General Public License for more details.
+
+You should have received a copy of the GNU General Public License
+along with Image Harvest. If not, see <http://www.gnu.org/licenses/>.
+
+.. module:: imgproc
+ :platform: Mac, Linux
+ :synopsis: Image processing function wrappers to opencv.
+
+.. moduleauthor:: Avi Knecht <avi@kurtknecht.com>
+
+"""
+
+import os
+import cv2
+import numpy as np
+import math
+import conf
+import sqlite3
+import pymeanshift as pms
+import traceback
+import json
+
+class ColorFilter(object):
+
+ """
+ Color Filtration logic container.
+ """
+ def __init__(self, filter):
+ self.tokens = {
+ "True": True,
+ "False": False,
+ "and": lambda left, right: np.logical_and(left, right),
+ "or": lambda left, right: np.logical_or(left, right),
+ ">": lambda left, right: left > right,
+ "<": lambda left, right: left < right,
+ ">=": lambda left, right: left >= right,
+ "<=": lambda left, right: left <= right,
+ "=": lambda left, right: left == right,
+ "+": lambda left, right: left + right,
+ "-": lambda left, right: left - right,
+ "*": lambda left, right: left * right,
+ "/": lambda left, right: left / right,
+ "max": lambda left, right: np.maximum(left, right),
+ "min": lambda left, right: np.minimum(left, right),
+ "not": lambda left, right: np.invert(left),
+ "(": "(",
+ ")": ")",
+ }
+ self.filterString = filter
+ self.emptyRes = True
+ return
+
+ def _createArgList(self):
+ s = self.filterString.replace("(", " ( ")
+ s = s.replace(")", " ) ")
+ self.filter = []
+ for item in s.split():
+ if item in self.tokens:
+ self.filter.append(self.tokens[item])
+ else:
+ try:
+ val = int(item)
+ self.filter.append(val)
+ except:
+ raise Exception("Invalid logic string.")
+ #self.filter = [self.tokens[x] if x in self.tokens else int(x) for x in s.split()]
+ return
+
+ def _find(self, what, start = 0):
+ return [i for i,x in enumerate(self.filter) if x == what and i >= start]
+
+ def _parens(self):
+ left_1st = self._find("(")
+ if not left_1st:
+ return False, -1, -1
+ left = left_1st[-1]
+ right = self._find(")", left + 2)[0]
+ return True, left, right
+
+ def _eval(self, filter):
+ return filter[1](filter[0], filter[2])
+
+ def _formattedEval(self, filter):
+ if not filter:
+ return self.emptyRes
+ if len(filter) == 1:
+ return filter[0]
+
+ has_parens, l_paren, r_paren = self._parens()
+
+ if not has_parens:
+ return self._eval(filter)
+
+ filter[l_paren:r_paren + 1] = [self._eval(filter[l_paren+1:r_paren])]
+ self.emptyRes = self._eval
+ return self._formattedEval(filter)
+
+ def apply(self, image, roi):
+ self.tokens["r"] = image[:,:,2].astype(float)
+ self.tokens["g"] = image[:,:,1].astype(float)
+ self.tokens["b"] = image[:,:,0].astype(float)
+ self._createArgList()
+ result = cv2.cvtColor(np.where(self._formattedEval(self.filter), 255, 0).astype(np.uint8), cv2.COLOR_GRAY2BGR)
+ image[roi[0]:roi[1], roi[2]:roi[3]] = cv2.bitwise_and(image[roi[0]:roi[1], roi[2]:roi[3]], result[roi[0]:roi[1], roi[2]:roi[3]])
+ return image
+
+
+
+class Image(object):
+
+ """
+ An individual image. Each image is loaded in as its own instance of the Image class for processing.
+ """
+ def __init__(self, input, outputdir = ".", writename = None, dev = False, db = None, dbid = None):
+ """
+ :param input: The input resource, either a path to an image or a raw numpy array.
+ :type resource: numpy.ndarray or str
+ :param outputdir: The directory to write output files
+ :type outputdir: str
+ :param writename: The name to write the output file as, should include extension.
+ :type writename: str
+ :param dev: Dev mode will do something...
+ :type dev: bool
+ """
+ if os.path.isdir(outputdir):
+ self.states = {}
+ self._loadDb(db, dbid)
+ self.input = input
+ self.fname, self.image = self._loadResource(input)
+ self.y = self.image.shape[0]
+ self.x = self.image.shape[1]
+ self.outputdir = os.path.abspath(outputdir)
+ if writename:
+ self.writename = writename
+ elif isinstance(input, np.ndarray):
+ self.writename = "out.png"
+ else:
+ self.writename = os.path.basename(input)
+ self.dev = dev
+ self.window = 1
+ else:
+ raise Exception("Invalid output!")
+ return
+
+ def _closeDb(self):
+ if self.conn:
+ self.conn.close()
+ return
+
+ def _loadDb(self, db, dbid):
+ if db:
+ if os.path.isfile(db):
+ if dbid:
+ self.dbid = dbid
+ self.conn = sqlite3.connect(db, check_same_thread = False)
+ self.conn.row_factory = sqlite3.Row
+ result = self.conn.execute("select pegasusid from images where pegasusid=?", (self.dbid,))
+ if not result.fetchone():
+ raise Exception("Invalid pegasusid given!")
+ self._addColumn("error")
+ else:
+ raise Exception("A database id must be provided if you give a database.")
+ else:
+ raise Exception("Invalid database given!")
+ else:
+ self.conn = False
+ return
+
+ def _addColumn(self, column, tablename = "images"):
+ if self.conn:
+ if column not in [row["name"] for row in self.conn.execute("PRAGMA table_info(" + tablename + ");")]:
+ self.conn.execute("alter table " + tablename + " add column " + column + ";")
+ self.conn.commit()
+ return
+
+ def _loadROIArg(self, arg, i):
+ vals = {
+ 0: 0,
+ 1: self.y,
+ 2: 0,
+ 3: self.x
+ }
+ arg = str(arg)
+ if arg == "-1":
+ return vals[i]
+ arg = arg.replace("x", str(self.x)).replace("y", str(self.y)).replace(" ","")
+ if "-" in arg:
+ try:
+ left, right = arg.split("-")
+ return int(left) - int(right)
+ except:
+ raise Exception("Could not load roi arg '%s'" % (arg,))
+ elif "+" in arg:
+ try:
+ left, right = arg.split("+")
+ return int(left) + int(right)
+ except:
+ raise Exception("Could not load roi arg '%s'" % (arg,))
+ else:
+ return int(arg)
+
+ def _loadROI(self, roi):
+ """
+ :param roi: The region of interest to load.
+ :type roi: list or file
+ :return: The region of interest of form [ystart, yend, xstart, xend]
+ :rtype: list
+ :raises OSError: if the input path does not exist.
+
+ Loads a region of interest, either a path to an roi or a raw list.
+ """
+ if not roi:
+ roi = [-1, -1, -1, -1]
+ if isinstance(roi, list):
+ return [self._loadROIArg(z, i) for i,z in enumerate(roi)]
+ else:
+ if os.path.isfile(roi):
+ try:
+ with open(roi, "r") as rh:
+ r = json.load(rh)
+ if all(x in r for x in ["xstart", "xend", "ystart", "yend"]):
+ return [self._loadROIArg(r["ystart"], 0), self._loadROIArg(r["yend"], 1), self._loadROIArg(r["xstart"], 2), self._loadROIArg(r["xend"], 3)]
+ else:
+ raise Exception("Input roi file '%s' needs xstart, xend, ystart, and yend definitions!" % (roi,))
+ except Exception as e:
+ print traceback.format_exc()
+ raise Exception("Input roi file '%s' is not valid json!" % (roi,))
+ else:
+ raise Exception("Input path to roi file '%s' does not exist!" % (roi,))
+ return
+
+ def _writeROI(self, roi, output):
+ """
+ :param roi: The region of interest to write.
+ :type roi: list
+ """
+ try:
+ with open(self.outputdir + "/" + output, "w") as wh:
+ wh.write(json.dumps({"ystart": roi[0], "yend": roi[1], "xstart": roi[2], "xend": roi[3]}, indent = 4))
+ except:
+ raise Exception("Could not write roi.")
+ return
+
+ def _loadBins(self, binlist):
+ """
+ :param bin: The bin to load
+ :type bin: list or file
+ """
+
+ if isinstance(binlist, list):
+ return binlist
+ else:
+ if os.path.isfile(binlist):
+ try:
+ with open(binlist, "r") as rh:
+ return json.load(rh)
+ except:
+ raise Exception("Bin list not valid json!")
+ else:
+ raise Exception("Bin file does not exist.")
+ return
+
+ def _loadResource(self, resource):
+ """
+ :param resource: The resource to load.
+ :type resource: numpy.ndarray or file
+ :return: The image
+ :rtype: numpy.ndarray
+ :raises OSError: if the input path does not exist.
+
+ Loads a resource, either a path to an image or a raw numpy array.
+ """
+ if isinstance(resource, np.ndarray):
+ return ("unknown", resource.copy())
+ else:
+ if resource in self.states:
+ return (resource, self.states[resource].copy())
+ elif os.path.isfile(resource):
+ image = cv2.imread(resource)
+ if image is not None:
+ return (os.path.basename(resource), image)
+ else:
+ if self.conn:
+ self.conn.execute("update images set error =? where pegasusid = ?", ("Load Error, input is not an image.", self.dbid))
+ self.conn.commit()
+ raise Exception("Input is not an image.")
+ else:
+ if self.conn:
+ self.conn.execute("update images set error = ? where pegasusid = ?", ("Load Error, input path doesn't exist or specified resource is not a saved state.", self.dbid))
+ self.conn.commit()
+ raise Exception("Input path to resource does not exist.")
+ return
+
+ def _colorHistogram(self):
+ """
+ :return: A list of histograms, corresponding to R, G, B.
+ :rtype: List of numpy arrays.
+
+ Calculates a normalized colorHistogram of the current image.
+ The intensity is normalized between 0 and 255.
+ """
+ returnhist = []
+
+ for ch in range(0, 3):
+ hist_item = cv2.calcHist([self.image], [ch], None, [256], [1,255])
+ cv2.normalize(hist_item, hist_item, 0, 255, cv2.NORM_MINMAX)
+ hist = np.int32(np.around(hist_item))
+ returnhist.append(hist)
+ return returnhist
+
+ def _isColor(self, image = None):
+ image = self.image if image is None else image
+ return len(image.shape) == 3
+
+ def save(self, name):
+ """
+ :param name: The name to save the image under.
+ :type name: str OR any hashable type.
+
+ This function saves the current image in the 'states' variable under
+ the specified name. It can then be reloaded using the :py:meth:`~ih.imgproc.Image.restore`
+ method.
+ """
+ self.states[name] = self.image.copy()
+ return
+
+ def restore(self, name):
+ """
+ :param name: The name the image is saved under.
+ :type name: str OR any hashable type.
+
+ Reloads a previously saved image from the 'states' variable.
+ """
+ if name in self.states:
+ self.image = self.states[name].copy()
+ self.y = self.image.shape[0]
+ self.x = self.image.shape[1]
+ else:
+ print "Invalid state specified."
+ return
+
+ def list(self):
+ """
+ Lists all saved states.
+ """
+ for state in self.states:
+ print state
+ return
+
+ def destroy(self):
+ """
+ Destroys all currently open windows.
+ """
+ cv2.destroyAllWindows()
+ return
+
+ def wait(self):
+ """
+ Waits until a key is pressed, then destroys all windows and
+ continues program execution.
+ """
+ cv2.waitKey(0)
+ self.destroy()
+ return
+
+ def show(self, title = None):
+ """
+ :param title: The title to give the display window, if left blank one will be created.
+ :type title: str
+ :return: None
+
+ Displays the image in a window. Utilizes the :py:meth:`~ih.imgproc.Image.resize` function.
+ If a title is not specified, the window will be named 'windowX' where X is the number of times
+ show has been called.
+
+ """
+ cv2.imshow(title if title else "window " + str(self.window), self.resize())
+ self.window += 1
+ return
+
+ def resizeSelf(self, scale = None, width = None, height = None):
+ """
+ :param scale: Value to scale image by.
+ :type scale: float
+ :param width: Target width of image.
+ :type width: int
+ :param height: Target height of image.
+ :type height: int
+
+ Resizes the current image. If scale is set, it simply resizes the
+ width and height of the image based on the scale. If only one of width
+ or height is set, it scales the other accordingly. If both width
+ and height are set, it scales the image to the exact size specified.
+ """
+ if scale or width or height:
+ if scale:
+ self.image = cv2.resize(self.image, (int(self.x * scale), int(self.y * scale)))
+ elif width and height:
+ self.image = cv2.resize(self.image, height, width)
+ elif width:
+ scale = float(width) / float(self.x)
+ self.image = cv2.resize(self.image, (int(self.x * scale), int(self.y * scale)))
+ elif height:
+ scale = float(height) / float(self.y)
+ self.image = cv2.resize(self.image, (int(self.x * scale), int(self.y * scale)))
+ self.y = self.image.shape[0]
+ self.x = self.image.shape[1]
+ return
+
+ def resize(self):
+ """
+ If the image is large than conf.maxArea, resize its total area down to conf.maxArea.
+ This function is primarily used for viewing purposes, and as such, it does not resize
+ the base image, but creates a copy to resize instead.
+ """
+ if (self.image.shape[0] * self.image.shape[1] > conf.maxArea):
+ scale = 1 / math.sqrt((self.image.shape[1] * self.image.shape[0]) / conf.maxArea)
+ return cv2.resize(self.image.copy(), (int(self.x*scale), int(self.y*scale)))
+ else:
+ return self.image
+
+ def write(self, name = None):
+ """
+ Writes the current image to the given output directory, with the given name.
+ """
+ writename = self.writename if not name else name
+ cv2.imwrite(self.outputdir + "/" + writename, self.image)
+ return
+
+ def convertColor(self, intype, outtype):
+ """
+ :param intype: The input image type
+ :type intype: str
+ :param outtype: The output image type
+ :type outtype: str
+ :return: The converted image.
+ :rtype: numpy.ndarray
+ :raises: KeyError
+
+ Converts the given image between color spaces, based on the given types.
+ Supported types are: bgr, gray, hsv, lab, and ycrcb. Note, you cannot
+ restore color to a gray image with this function, for that you must use
+ bitwise_and with an appropriate mask + image.
+ """
+ if intype in conf.colors:
+ if outtype in conf.colors[intype]:
+ for code in conf.colors[intype][outtype]:
+ self.image = cv2.cvtColor(self.image, code)
+ else:
+ raise KeyError(outtype + " is not a valid output type for the input type: " + intype)
+ else:
+ raise KeyError(intype + " is not a valid image type.")
+ return
+
+ def threshold(self, thresh, max = 255, type = "binary"):
+ """
+ :param thresh: Threshold value.
+ :type thresh: int
+ :param max: Write value for binary threshold.
+ :type max: int
+ :param type: Threhsold type.
+ :type type: str
+ :return: The thresholded image.
+ :rtype: numpy.ndarray
+ :raises KeyError: if the specified threshold type doesn't exist.
+
+ Thresholds the image based on the given type. The image must be
+ grayscale to be thresholded. If the image is of type 'bgr' it is
+ automatically converted to grayscale before thresholding.
+ Supported types are: binary, truncate, tozero, and otsu.
+ """
+ if self._isColor():
+ self.convertColor("bgr", "gray")
+ if type in conf.thresholds:
+ self.image = cv2.threshold(self.image, thresh, max, conf.thresholds[type])[1]
+ else:
+ raise KeyError(type + " is not a valid threshold type.")
+ return
+
+ def kmeans(self, k, criteria, maxiter = 10, accuracy = 1.0, attempts = 10, flags = "random"):
+ """
+ :param k: Number of colors in final image.
+ :type k: int
+ :param criteria: Determination of how the algorithm stops execution. Should be one of 'accuracy', 'iteration', or 'either'.
+ :type criteria: str
+ :param maxiter: Maximum number of iterations of the algorithm.
+ :type maxiter: int
+ :param accuracy: Minimum accuracy before algorithm finishes executing.
+ :type accuracy: float
+ :param attempts: Number of times the algorithm is executed using different initial guesses.
+ :type attempts: int
+ :param flags: How to determine initial centers should be either 'random' or 'pp'.
+ :type flags: str
+
+ This function is a wrapper to the OpenCV function `kmeans <http://docs.opencv.org/modules/core/doc/clustering.html>`_
+ Adjusts the colors in the image to find the most compact 'central' colors. The amount of colors
+ in the resulting image is the specified value 'k'. The colors are chosen based upon the minimum
+ amount of adjustment in the image necessary. The criteria parameter determines when the algorithm
+ stops. If 'accuracy' is specified, the algorithm runs until the specified accuracy is reached. If 'iteration'
+ is specified, the algorithm runs the specified number of iterations. If 'either' is specified, the algorithm
+ runs until one of the conditions is satisfied. The flags parameter determines the initial central colors,
+ and should be either 'random' -- to generate a random initial guess -- or 'pp' to use center initialization by Arthur and Vassilvitskii.
+ """
+ if flags in conf.centers:
+ if criteria in conf.ktermination:
+ reshaped = self.image.reshape((-1,3))
+ reshaped = np.float32(reshaped)
+ ret, label, center = cv2.kmeans(reshaped, k, (conf.ktermination[criteria], maxiter, accuracy), attempts, conf.centers[flags])
+ center = np.uint8(center)
+ res = center[label.flatten()]
+ self.image = res.reshape((self.image.shape))
+ else:
+ raise KeyError(criteria + " is not a valid termination type. Should be one of 'accuracy', 'iteration', or 'either'")
+ else:
+ raise KeyError(flags + " is not a valid center type. Should be either 'random' or 'pp'.")
+ return
+
+
+ def meanshift(self, spatial_radius, range_radius, min_density):
+ """
+ :param spatial_radius: Spatial Radius
+ :type spatial_radius: float
+ :param range_radius: Range Radius.
+ :type range_radius: float
+ :param min_density: Minimum Density.
+ :type min_density: int
+ :return: The mean-shifted image.
+ :rtype: numpy.ndarray
+
+ Segments the image into clusters based on nearest neighbors. This function
+ is a wrapper to the `pymeanshift <https://code.google.com/p/pymeanshift/>`_
+ module. For details on the algorithm itself: `Mean shift: A robust approach toward feature space analysis <http://dx.doi.org/10.1109/34.1000236>`_.
+ """
+ (self.image, labels_image, number_regions) = pms.segment(self.image, spatial_radius = spatial_radius, range_radius = range_radius, min_density = min_density)
+ return
+
+ def adaptiveThreshold(self, value, adaptiveType, thresholdType, blockSize, C):
+ """
+ :param value: Intensity value for the pixels based on the thresholding conditions.
+ :type param: int
+ :param adaptiveType: Adaptive algorithm to use, should be either 'mean' or 'gaussian'.
+ :type adaptiveType: str
+ :param thresholdType: Threshold type, should be either 'binary' or 'inverse'.
+ :type thresholdType: str
+ :param blockSize: The window size to consider while thresholding, should only be an odd number.
+ :type blockSize: int
+ :param C: A constant subtracted from the calculated mean in each window.
+ :type C: int
+
+ Thresholds an image by considering the image in several different windows instead of the image
+ as a whole. This function is a wrapper to the OpenCV function `adaptiveThreshold <http://docs.opencv.org/modules/imgproc/doc/miscellaneous_transformations.html#adaptivethreshold>`_.
+ Specifying 'mean' for adaptiveType calculates a simple mean of the area, wheras specifying 'gaussian' calculates a weighted sum
+ based upon a `Gaussian Kernel <http://docs.opencv.org/modules/imgproc/doc/filtering.html#Mat getGaussianKernel(int ksize, double sigma, int ktype)>`_.
+ Specifying 'binary' for thresholdType means that a particular intensity value must beat the threshold to be kept, whereas
+ specifying 'inverse' means that a particular intensity value must lose to the threshold to be kept.
+ Similar to a normal thresholding function, the image must be converted to grayscale first. This can be done using the
+ :meth:`~ih.imgproc.Image.convertColor` function, however, if your image is of type 'bgr', this is handled automatically.
+ """
+ if self._isColor():
+ self.convertColor("bgr", "gray")
+ if adaptiveType in conf.adaptives:
+ if thresholdType == "binary" or thresholdType == "inverse":
+ self.image = cv2.adaptiveThreshold(self.image, value, conf.adaptives[adaptiveType], conf.thresholds[thresholdType], blockSize, C)
+ else:
+ raise Exception("Threshold type: " + thresholdType + " must be either binary or inverse.")
+ else:
+ raise Exception("Adaptive type: " + adaptiveType + " is not a valid adaptive threshold type, should be either 'mean' or 'gaussian'")
+ return
+
+ def blur(self, ksize, anchor = (-1, -1), borderType = "default"):
+ """
+ :param ksize: The size of the kernel represented by a tuple (width, height). Both numbers should be odd and positive.
+ :type ksize: tuple
+ :param anchor: The anchor point for filtering. Default is (-1, -1) which is the center of the kernel.
+ :type anchor: tuple
+ :param borderType: The type of border mode used to extrapolate pixels outside the image.
+ :type borderType: str
+
+ Smoothes an image using the normalized box filter. This function is a wrapper to the OpenCV function
+ `blur <http://docs.opencv.org/modules/imgproc/doc/filtering.html#blur>`_. Increasing the kernel size increase
+ the window considered when applying a blur. The anchor by default is the center of the kernel,
+ however you can alter the anchor to consider different areas of the kernel. When blurring on the edge
+ of the image, values for pixels that would be outside of the image are extrapolated. The method
+ of extrapolation depends on the specified 'borderType', and can be one of 'default', 'constant',
+ 'reflect', or 'replicate'.
+ """
+ if borderType in conf.borders:
+ self.image = cv2.blur(self.image, ksize, anchor = anchor, borderType = conf.borders[borderType])
+ else:
+ raise Exception("Invalid border type, should be one of: " + ",".join(conf.borders.keys()) + ".")
+ return
+
+ def medianBlur(self, ksize):
+ """
+ :param ksize: The size of the kernel (ksize x ksize). Should be odd and positive.
+ :type ksize: int
+
+ This function smoothes an image using the median filter. The kernel is set to size (ksize, ksize).
+ The anchor position is assumed to be the center.
+ REFERENCE OPENCV MEDIAN BLUR
+ """
+ self.image = cv2.medianBlur(self.image, ksize)
+ return
+
+ def gaussianBlur(self, ksize, sigmaX = 0, sigmaY = 0, borderType = "default"):
+ """
+ :param ksize: The size of the kernel represented by a tuple (width, height). Both numers should be odd and positive.
+ :type ksize: tuple
+ :param sigmaX: The standard deviation in the x direction. If 0, the value is calculated based on the kernel size.
+ :type sigmaX: float
+ :param sigmaY: The standard deviation in the y direction. If 0, the value is equal to sigmaX.
+ :type sigmaY: float
+ :param borderType: The type of border mode used to extrapolate pixels outside the image.
+ :type borderType: str
+
+ This function blurs an image based on a Gaussian kernel. When blurring on the edge
+ of the image, values for pixels that would be outside of the image are extrapolated. The method
+ of extrapolation depends on the specified 'borderType', and can be one of 'default', 'constant',
+ 'reflect', or 'replicate'. This function is a wrapper to the OpenCV function `GaussianBlur <http://docs.opencv.org/modules/imgproc/doc/filtering.html#gaussianblur>`_.
+ """
+ if borderType in conf.borders:
+ sigmaY = sigmaX if sigmaY == 0 else sigmaY
+ self.image = cv2.GaussianBlur(self.image, ksize, sigmaX, sigmaY, borderType = conf.borders[borderType])
+ else:
+ raise Exception("Invalid border type, should be one of: " + ",".join(conf.borders.keys()) + ".")
+ return
+
+ def normalizeByIntensity(self):
+ """
+ Normalizes each channel of the pixel by its intensity. For each pixel, the intensity is defined as
+ :math:`I = R + G + B`, where :math:`R,G,B` are the color values for that pixel. We calculate new color values by
+ multiplying the original number by 255, and dividing by the intensity, that is, :math:`r = \\frac{255 \\cdot R}{I}
+ , g = \\frac{255 \\cdot G}{I}, b = \\frac{255 \\cdot B}{I}`.
+ """
+ f = self.image.astype(float)
+ combined = np.add(np.add(f[:,:,0], f[:,:,1]), f[:,:,2])
+ scaled = np.multiply(f, [255])
+ self.image = np.divide(scaled, combined[:,:,None]).astype(np.uint8)
+ return
+
+ def morphology(self, morphType, ktype, ksize, anchor = (-1, -1), iterations = 1, borderType = "default"):
+ """
+ :param morphType: The type of morphology to perform. Should be dilate, erode, open, close, gradient, tophat, or blackhat.
+ :type morphType: str
+ :param ktype: the type of the kernel, should be rect, ellipse, or cross.
+ :type ktype: str
+ :param ksize: The size of the kernel represented by a tuple (width, height). Both numbers should be odd and positive.
+ :type ksize: tuple
+ :param anchor: The anchor point for filtering. Default is (-1, -1) which is the center of the kernel.
+ :type anchor: tuple
+ :param iterations: The number of times to perform the specified morphology.
+ :type iterations: int
+ :param borderType: The type of border mode used to extrapolate pixels outside the image.
+ :type borderType: str
+
+ This function performs morphological operations based on the inputted values. This function is
+ a wrapper to the OpenCv function `morphologyEx <http://docs.opencv.org/modules/imgproc/doc/filtering.html#morphologyex>`_. When performing the morphology on the edges
+ of the image, values for pixels that would be outside of the image are extrapolated. The method
+ of extrapolation depends on the specified 'borderType', and can be one of 'default', 'constant',
+ 'reflect', or 'replicate'.
+ """
+ if morphType in conf.morph:
+ if ktype in conf.kernels:
+ if borderType in conf.borders:
+ kernel = cv2.getStructuringElement(conf.kernels[ktype], ksize, anchor)
+ self.image = cv2.morphologyEx(self.image, conf.morph[morphType], kernel, anchor = anchor, iterations = iterations, borderType = conf.borders[borderType])
+ else:
+ raise Exception("Invalid border type, should be one of: " + ",".join(conf.borders.keys()) + ".")
+ else:
+ raise Exception("Invalid kernel type, should be one of: " + ",".join(conf.kernels.keys()) + ".")
+ else:
+ raise Exception("Invalid morphology type, should be one of: " + ",".join(conf.morph.keys()) + ".")
+
+ def crop(self, roi, resize = False):
+ """
+ :param roi: A list corresponding to the area of the image you want. List should be of the form [ystart, yend, xstart, xend]
+ :type roi: list or roi file
+ :param resize: If True, actually adjusts the size of the image, otherwise just draws over the part of the image not in the roi.
+ :type resize: bool
+
+ This function crops the image based on the given roi [ystart, yend, xstart, xend]. There are two crop options,
+ by default, the function doesn't actually resize the image. Instead, it sets each pixel not in the roi to black.
+ If resize is set to True, the function will actually crop the image down to the roi.
+ """
+ roi = self._loadROI(roi)
+ ystart, yend, xstart, xend = roi
+ if (resize):
+ self.image = self.image[ystart: yend, xstart: xend]
+ self.x = self.image.shape[1]
+ self.y = self.image.shape[0]
+ else:
+ maxx = self.x
+ maxy = self.y
+ off = [0, 0, 0] if self._isColor() else [0]
+ self.image[0:ystart, 0:maxx] = off
+ self.image[yend:maxy, 0:maxx] = off
+ self.image[0:maxy, 0:xstart] = off
+ self.image[0:maxy, xend:maxx] = off
+ return
+
+ def contourCut(self, binary, basemin = 100, padding = [0, 0, 0, 0], resize = False, returnBound = False, roiwrite = "roi.json"):
+ """
+ :param binary: The binary image to find contours of.
+ :type binary: str or np.ndarray
+ :param basemin: The minimum area a contour must have to be consider part of the foreground.
+ :type basemin: int
+ :param padding: Padding add to all sides of the final roi.
+ :type padding: int
+ :param returnBound: If set, instead of cropping the image, simply write the detected roi.
+ :type returnBound: bool
+ :param resize: Whether or not to resize the image.
+ :type resize: bool
+
+ This function crops an image based on the size of detected contours in the image --
+ clusters of pixels in the image. The image is cropped such that all contours
+ that are greater than the specified area are included in the final output image.
+ image is cropped such that all contours that are greater than the specified area are
+ included in the final output image. If returnBound is set, instead of actually
+ cropping the image, the detected roi is written to a file instead. Otherwise,
+ the detected roi is passed into the :py:meth:`~ih.imgproc.Image.crop` function,
+ with the given resize value. This function is useful for getting accurate
+ height and width of a specific plant, as well as removing outlying clusters
+ of non-important pixels.
+ """
+ bname, binary = self._loadResource(binary)
+ if self._isColor(binary):
+ binary = cv2.cvtColor(binary, cv2.COLOR_BGR2GRAY)
+ contours = cv2.findContours(binary, cv2.RETR_TREE, cv2.CHAIN_APPROX_SIMPLE)[0]
+ minx = binary.shape[1]
+ miny = binary.shape[0]
+ maxx = 0
+ maxy = 0
+ for cnt in contours:
+ x,y,w,h = cv2.boundingRect(cnt)
+ if (basemin < cv2.contourArea(cnt)):
+ if (x < minx):
+ minx = x
+ if (y < miny):
+ miny = y
+ if (x + w > maxx):
+ maxx = x + w
+ if (y + h > maxy):
+ maxy = y + h
+ roi = [0 if miny - padding[0] < 0 else miny - padding[0], binary.shape[0] if maxy + padding[1] > binary.shape[0] else maxy + padding[1], 0 if minx - padding[2] < 0 else minx - padding[2], binary.shape[1] if maxx + padding[3] > binary.shape[1] else maxx + padding[3]]
+ if returnBound:
+ self._writeROI(roi, roiwrite)
+ self.crop(roi, resize)
+ return
+
+ def edges(self, threshold1, threshold2, apertureSize = 3, L2gradient = False):
+ """
+ :param threshold1: First threshold for the hysteresis procedure.
+ :type threshold1: int
+ :param threshold2: Second threshold for the hysteresis procedure.
+ :type threshold2: int
+ :param apertureSize: aperture size used for the Sobel algorithm. Must be odd, postive, and less than 8.
+ :type apertureSize: int
+ :L2gradient: Used to calculate Image gradient magnitude, if true then :math:`L = \sqrt{(dI/dx)^2 + (dI/dy)^2}`, if false then :math:`L = dI/dx + dI/dy`.
+ :type L2gradient: bool
+
+ This function calculates the edges of an image using the Canny edge detection algorithm, which is built upon the Sobel
+ algorithm. This function is a wrapper to the OpenCV function `Canny <http://docs.opencv.org/modules/imgproc/doc/feature_detection.html#canny>`_.
+ """
+ self.image = cv2.Canny(self.image, threshold1, threshold2, apertureSize = apertureSize, L2gradient = L2gradient)
+ return
+
+ def colorFilter(self, logic, roi = None):
+ """
+ :param logic: The logic you want to run on the image.
+ :type logic: str
+ :param roi: The roi you want to apply the filter to
+ :type roi: list or roi file
+
+ This function applies a color filter defined by the input logic, to a
+ targeted region defined by the input roi. The roi is defined the same,
+ [ystart, yend, xstart, xend]. The logic string itself is fairly complicated.
+ The string supports the following characters: '+', '-', '*', '/', '>', '>=',
+ '==', '<', '<=', 'and', 'or', '(', ')', 'r', 'g', 'b', 'max', and 'min' as well as any numeric
+ value. The logic string itself must be well formed -- each
+ operation, arg1 operator arg2, must be surrounded by parenthesis, and the entire statement
+ must be surrounded by parenthesis. For example,
+ if you want to check the intensity of the pixel, your logic string would be:
+ '(((r + g) + b) < 100)'. This string in particular will only keep pixels whose
+ intensity is less than 100. Similar rules apply for 'and' and 'or' operators.
+ Let's say we only want to keep pixels whose intensity is less than 100, OR both
+ the red and blue channels are greater than 150, the logic string would be:
+ '((((r + g) + b) < 100) or ((r > 150) and (b > 150)))'. The more complex
+ your logic is the harder it is to read, so you may want to consider breaking
+ up complex filtering into multiple steps for readability. Finally, despite
+ the fact this function solves arbitrary logic, it is very fast.
+ """
+ filter = ColorFilter(logic)
+ roi = self._loadROI(roi)
+ self.image = filter.apply(self.image, roi)
+ return
+
+ def bitwise_not(self):
+ """
+ Inverts the image. If the given image has multiple channels (i.e. is a color image) each channel is processed independently.
+ """
+ self.image = cv2.bitwise_not(self.image)
+ return
+
+ def bitwise_and(self, comp):
+ """
+ :param comp: The comparison image.
+ :type comp: str or np.ndarray
+ :return: The resulting mask.
+ :rtype: numpy.ndarray
+
+ Performs logical AND between the input image and the comp image.
+ The comp input is very versatile, and can be one of three input types,
+ an image, a path, or a saved state. An image input is a raw numpy array,
+ and this input type will be passed through to the function without modification.
+ If a path is specified, ih attempts to load the file as an image, and pass it
+ to the function. Finally, the input is checked against the currently saved
+ image states. If it matches, the corresponding state is passed to the function.
+ The function assumes that the two input images are of matching type --
+ if they are not an error will be thrown. By default, images loaded from a
+ path are loaded as 'bgr' type images.
+ For more information on states, see :py:meth:`~ih.imgproc.Image.save`.
+ """
+ self.image = cv2.bitwise_and(self.image, self._loadResource(comp)[1])
+ return
+
+ def bitwise_or(self, comp):
+ """
+ :param comp: The comparison image.
+ :type comp: str or np.ndarray
+ :return: The resulting mask.
+ :rtype: numpy.ndarray
+
+ Performs logical OR between the input image and the comp image.
+ The comp input is very versatile, and can be one of three input types,
+ an image, a path, or a saved state. An image input is a raw numpy array,
+ and this input type will be passed through to the function without modification.
+ If a path is specified, ih attempts to load the file as an image, and pass it
+ to the function. Finally, the input is checked against the currently saved
+ image states. If it matches, the corresponding state is passed to the function.
+ The function assumes that the two input images are of matching type --
+ if they are not an error will be thrown. By default, images loaded from a
+ path are loaded as 'bgr' type images.
+ For more information on states, see :py:meth:`~ih.imgproc.Image.save`.
+ """
+ self.image = cv2.bitwise_or(self.image, self._loadResource(comp)[1])
+ return
+
+ def bitwise_xor(self, comp):
+ """
+ :param comp: The comparison image.
+ :type comp: str or np.ndarray
+ :return: The resulting mask.
+ :rtype: numpy.ndarray
+
+ Performs exclusive logical OR between the input image and the comp image.
+ The comp input is very versatile, and can be one of three input types,
+ an image, a path, or a saved state. An image input is a raw numpy array,
+ and this input type will be passed through to the function without modification.
+ If a path is specified, ih attempts to load the file as an image, and pass it
+ to the function. Finally, the input is checked against the currently saved
+ image states. If it matches, the corresponding state is passed to the function.
+ The function assumes that the two input images are of matching type --
+ if they are not an error will be thrown. By default, images loaded from a
+ path are loaded as 'bgr' type images.
+ For more information on states, see :py:meth:`~ih.imgproc.Image.save`.
+ """
+ self.image = cv2.bitwise_xor(self.image, self._loadResource(comp)[1])
+ return
+
+ def extractFinalPath(self):
+ """
+ This function writes the absolute path of the output file to the database.
+ """
+ if self.conn:
+ finalpath = "/".join(os.path.abspath(self.input).split("/")[-6:])
+ self._addColumn("outputPath")
+ self.conn.execute("update images set outputPath=? where pegasusid=?", (finalpath, self.dbid))
+ self.conn.commit()
+ return
+
+ def extractMoments(self):
+ """
+ :return: A dictionary corresponding to the different moments of the image.
+ :rtype: dict
+
+ Calculates the moments of the image, and returns a dicitonary based on them.
+ Spatial moments are prefixed with 'm', central moments are prefixed with 'mu',
+ and central normalized moments are prefixed with 'nu'. This function
+ is a wrapper to the OpenCV function `moments <http://docs.opencv.org/modules/imgproc/doc/structural_analysis_and_shape_descriptors.html#moments>`_.
+ """
+ moments = cv2.moments(cv2.inRange(self.image, np.array([1, 1, 1], np.uint8), np.array([255, 255, 255], np.uint8)))
+ if self.conn:
+ for id in moments:
+ self._addColumn(id)
+ self.conn.execute("update images set " + id + "=? where pegasusid=?", (moments[id], self.dbid))
+ self.conn.commit()
+ return
+ else:
+ return moments
+
+ def extractDimensions(self):
+ """
+ :return: A list corresponding to the height and width of the image.
+ :rtype: list
+
+ Returns a list with the following form: [height, width]
+ """
+ if self.conn:
+ self._addColumn("height")
+ self._addColumn("width")
+ self.conn.execute("update images set height=?,width=? where pegasusid=?", (self.y, self.x, self.dbid))
+ self.conn.commit()
+ return
+ else:
+ return [self.y, self.x]
+
+ def extractPixels(self):
+ """
+ :return: The number of non-black pixels in the image.
+ :rtype: int
+
+ Returns the number of non-black pixels in the image. Creates
+ a temporary binary image to do this. The point of this function
+ is not to threshold, so the binary image is created by all
+ pixels that fall into the range [1, 1, 1], [255, 255, 255].
+ """
+ pixelCount = cv2.countNonZero(cv2.inRange(self.image, np.array([1, 1, 1], np.uint8), np.array([255, 255, 255], np.uint8)))
+ if self.conn:
+ self._addColumn("pixels")
+ self.conn.execute("update images set pixels=? where pegasusid=?", (pixelCount, self.dbid))
+ self.conn.commit()
+ return
+ else:
+ return pixelCount
+
+ def extractColorData(self, nonzero = True, returnhist = False):
+ """
+ :param nonzero: Whether or not to look at only nonzero pixels. Default true.
+ :type nonzero: bool
+ :return: Mean & median for each channel.
+ :rtype: list
+
+ This function calculates a normalized histogram of each individual color channel of
+ the image, and returns the mean & median of the histograms for the channels
+ specified. Because images are imported with the channels ordered as B,G,R,
+ the output list is returned the same way. The returned list always looks like
+ this: [ [BlueMean, BlueMedian], [GreenMean, GreenMedian], [RedMean, RedMedian] ].
+ Mean values always come before median values. If nonzero is set to true (default)
+ the function will only calculate mediapytn and means based on the non-black pixels.
+ """
+ hist = self._colorHistogram()
+ if returnhist:
+ return hist
+ colors = [ [np.mean(np.nonzero(hist[0]) if nonzero else hist[0]), np.median(np.nonzero(hist[0]) if nonzero else hist[0])],
+ [np.mean(np.nonzero(hist[1]) if nonzero else hist[1]), np.median(np.nonzero(hist[1]) if nonzero else hist[1])],
+ [np.mean(np.nonzero(hist[2]) if nonzero else hist[2]), np.median(np.nonzero(hist[2]) if nonzero else hist[2])]
+ ]
+ if self.conn:
+ self._addColumn("rmean")
+ self._addColumn("rmed")
+ self._addColumn("gmean")
+ self._addColumn("gmed")
+ self._addColumn("bmean")
+ self._addColumn("bmed")
+ query = "update images set rmean=?,rmed=?,gmean=?,gmed=?,bmean=?,bmed=?"
+ values = [colors[2][0], colors[2][1], colors[1][0], colors[1][1], colors[0][0], colors[0][1]]
+ for x,c in enumerate(["bhist", "ghist", "rhist"]):
+ for i in range(0, 256):
+ self._addColumn(c + str(i))
+ query += "," + c + str(i) + "=?"
+ values.append(int(hist[x][i]))
+ query += " where pegasusid=?"
+ values.append(self.dbid)
+ self.conn.execute(query, tuple(values))
+ self.conn.commit()
+ return
+ else:
+ return colors
+
+ def extractColorChannels(self):
+ b, g, r = cv2.split(self.image)
+ bdata, gdata, rdata = [], [], []
+ for i in range(0, 256):
+ bdata.append(np.count_nonzero(np.where(b == i, True, False)))
+ gdata.append(np.count_nonzero(np.where(g == i, True, False)))
+ rdata.append(np.count_nonzero(np.where(r == i, True, False)))
+ data = [bdata, gdata, rdata]
+ if self.conn:
+ query = "update images set "
+ values = []
+ for x,c in enumerate(["b", "g", "r"]):
+ for i in range(0, 256):
+ self._addColumn(c + str(i))
+ if i == 0:
+ query += c + str(i) + "=?"
+ else:
+ query += "," + c + str(i) + "=?"
+ values.append(data[x][i])
+ query += " where pegasusid=?"
+ values.append(self.dbid)
+ self.conn.execute(query, tuple(values))
+ self.conn.commit()
+ return
+ else:
+ return (bdata, gdata, rdata)
+
+ def extractBins(self, binlist):
+ """
+ :param binlist: The specified bins (color ranges) to count.
+ :type binlist: list
+ :return: The number of pixels that fall in each bin.
+ :rtype: list
+
+ This function counts the number of pixels that fall into the range as
+ specified by each bin. This function expects the input to be a list of
+ dictionaries as follows:
+
+ .. code-block:: python
+
+ binlist = [
+ {"name": "bin1",
+ "min": [B, G, R],
+ "max": [B, G, R]
+ },
+ {"name": "bin2",
+ ...
+ ]
+
+ Each range is defined by 6 values. A minimum and maximum blue,
+ green, and red value. The returned list is very similar to the
+ input list, except a 'count' key is added to each dictionary:
+
+ .. code-block:: python
+
+ returnlist = [
+ {"name": "bin1",
+ "min": [B, G, R],
+ "max": [B, G, R],
+ "count": VALUE
+ },
+ ...
+ ]
+
+ Where 'VALUE' is the number of pixels that fall into the
+ corresponding range.
+ A list is used instead of a dictionary as the base structure
+ to maintain order for writing to the output database. When
+ using this function within a workflow, the order you specify
+ your bins is the order in which they will show up in the
+ database, and the name you specify for you bin will be
+ the column name in the database.
+ """
+ binlist = self._loadBins(binlist)
+ for i in range(0, len(binlist)):
+ binlist[i]["count"] = cv2.countNonZero(cv2.inRange(self.image, np.array(binlist[i]["min"], np.uint8), np.array(binlist[i]["max"], np.uint8)))
+ if self.conn:
+ for bin in binlist:
+ self._addColumn(bin["name"])
+ self.conn.execute("update images set " + bin["name"] + "=? where pegasusid=?", (bin["count"], self.dbid))
+ self.conn.commit()
+ return
+ else:
+ return binlist
+
+
diff --git a/build/lib/ih/statistics.py b/build/lib/ih/statistics.py
new file mode 100644
index 0000000000000000000000000000000000000000..c865be9f86b179d16fe6093894c029e6ce17819a
--- /dev/null
+++ b/build/lib/ih/statistics.py
@@ -0,0 +1,724 @@
+import math
+import os
+import sqlite3
+import conf
+import datetime
+import numpy as np
+import pandas
+import ih.imgproc
+import cv2
+import json
+import traceback
+from scipy import stats
+
+class Stats:
+
+ def __init__(self, db):
+ self.db = db
+ self.conn = self._openConnection()
+ return
+
+ def _openConnection(self, db = None):
+ db = self.db if not db else db
+ if os.path.isfile(db):
+ conn = sqlite3.connect(db, check_same_thread = False)
+ conn.row_factory = sqlite3.Row
+ result = conn.execute("select pegasusid from images limit 0,1")
+ if not result.fetchone():
+ raise Exception("Database '%s' has no entries!" % (db,))
+ # Have to enable foreign keys EVERY time.
+ conn.execute("PRAGMA foreign_keys = ON")
+ conn.commit()
+ else:
+ raise Exception("Database file '%s' does not exist." % (db,))
+ return conn
+
+ def _closeConnection(self, conn = None):
+ conn = self.conn if not conn else conn
+ conn.close()
+ return
+
+ def _tableExists(self, tablename, conn = None):
+ conn = self.conn if not conn else conn
+ result = conn.execute("select name from sqlite_master where type='table' and name=?", (tablename,))
+ if not result.fetchone():
+ return False
+ else:
+ return True
+
+ def _validate(self, funcname, intable, outtable, overwrite, conn = None):
+ conn = self.conn if not conn else conn
+ if funcname in conf.statsColumns:
+ if self._tableExists(intable):
+ cols = [x[1] for x in conn.execute("PRAGMA table_info('" + intable + "')")]
+ if set(conf.statsColumns[funcname]["required"]) <= set(cols):
+ if self._tableExists(outtable, conn) and not overwrite:
+ raise Exception("Output table '" + outtable + "' already exists.")
+ else:
+ raise Exception("Table '" + intable + "' doesn't have all the required columns: '" + str(conf.statsColumns[funcname]["required"]) + "'.")
+ else:
+ raise Exception("Table '" + intable + "' doesn't exist.")
+ else:
+ raise Exception("Function '" + funcname + "' doesn't exist.")
+ return
+
+ def _massage(self, table, headers, imtypes = None, conn = None):
+ conn = self.conn if not conn else conn
+ if not imtypes:
+ imtypes = self._getImageTypes(table, conn)
+ elif not isinstance(imtypes, list):
+ imtypes = [imtypes]
+
+ for header in headers:
+ self.conn.execute("update " + table + " set " + header + "=? where " + header + " is null and (" + "or".join(["imtype=?" for x in imtypes]) + ")", (0,) + tuple(imtypes))
+ self.conn.commit()
+ return
+
+ def _columnExists(self, column, tablename, conn = None):
+ conn = self.conn if not conn else conn
+ if column in [row["name"] for row in self.conn.execute("PRAGMA table_info('" + tablename + "')")]:
+ return True
+ else:
+ return False
+
+ def _addColumn(self, column, tablename = "images", conn = None):
+ conn = self.conn if not conn else conn
+ if not self._columnExists(column, tablename, conn):
+ conn.execute("alter table '" + tablename + "' add column " + column + ";")
+ conn.commit()
+ return
+
+ def _addKeyColumn(self, parent, parentCol, child, childCol, conn = None):
+ conn = self.conn if not conn else conn
+ if parentCol not in [row["name"] for row in conn.execute("PRAGMA table_info('" + parent + "');")] and childCol in [row["name"] for row in conn.execute("PRAGMA table_info('" + child + "');")]:
+ conn.execute("alter table '" + parent + "' add column '" + parentCol + "' REFERENCES '" + child + "'('" + childCol + "');")
+ conn.commit()
+ return
+
+ def _createTable(self, funcname, intable, outtable, overwrite, conn = None):
+ conn = self.conn if not conn else conn
+ tablestr = "(pegasusid INTEGER PRIMARY KEY"
+ cols = [x[1] for x in conn.execute("pragma table_info('" + intable + "')")]
+ if "all" not in conf.statsColumns[funcname]["exclude"]:
+ for col in cols:
+ if col not in conf.statsColumns[funcname]["exclude"] and col[:3] != "ref":
+ tablestr += "," + str(col)
+ for col in conf.statsColumns[funcname]["add"]:
+ tablestr += "," + str(col)
+ tablestr += ")"
+ if overwrite:
+ if conf.statsColumns[funcname]["ref"]:
+ if self._columnExists("ref_" + outtable, intable, conn):
+ conn.execute("update " + intable + " set ref_" + outtable + "=? where ref_" + outtable + " is not null", (None,))
+ conn.commit()
+ conn.execute("DROP TABLE IF EXISTS " + outtable)
+ conn.commit()
+ conn.execute("CREATE TABLE " + outtable + " " + tablestr)
+ conn.commit()
+ if conf.statsColumns[funcname]["ref"]:
+ self._addKeyColumn(intable, "ref_" + outtable, outtable, "pegasusid", conn)
+ return
+
+ def _getHeaders(self, table, conn = None):
+ conn = self.conn if not conn else conn
+ return [str(x[1]) for x in conn.execute("pragma table_info(" + table + ")") if x[1] != "pegasusid"]
+
+ def _getImageTypes(self, table, conn = None):
+ conn = self.conn if not conn else conn
+ return [str(x[0]) for x in conn.execute("select distinct imtype from " + table)]
+
+ def _getDates(self, table, conn = None):
+ conn = self.conn if not conn else conn
+ return [str(x[0]) for x in conn.execute("select distinct date from " + table)]
+
+ def _checkNull(self, value):
+ return True if value is None or str(value).lower() == "none" else False
+
+ def _loadLemnaData(self, dataFile, dataHeaders):
+ """
+ :param dataFile: The input dataFile
+ :type dataFile: str
+ :param dataHeaders: The input data headers
+ :type dataHeaders: dict
+
+ dataHeaders should be:
+ {
+ "id": "Snapshot ID Tag",
+ "date": "Snapshot Time Stamp",
+ "dateFormat": "%m/%d/%y",
+ "metric": "Projected Shoot Area [pixels]"
+ }
+ """
+ if os.path.isfile(dataFile):
+ if all(key in dataHeaders for key in ["id", "date", "dateFormat", "metric"]):
+ with open(dataFile) as rh:
+ lines = rh.readlines()
+ firstline = lines[0].strip().split(",")
+ if dataHeaders["id"] in firstline:
+ if dataHeaders["date"] in firstline:
+ if dataHeaders["metric"] in firstline:
+ idIndex = firstline.index(dataHeaders["id"])
+ dateIndex = firstline.index(dataHeaders["date"])
+ metricIndex = firstline.index(dataHeaders["metric"])
+ lemnaData = {}
+ for line in lines[1:]:
+ info = line.strip().split(",")
+ if (info[metricIndex] != "NA"):
+ id = info[idIndex][-8:]
+ date = datetime.datetime.strptime(info[dateIndex].split()[0], dataHeaders["dateFormat"]).strftime("%Y-%m-%d")
+ try:
+ metric = float(info[metricIndex])
+ if id not in lemnaData:
+ lemnaData[id] = {}
+ if date not in lemnaData[id]:
+ lemnaData[id][date] = {}
+ lemnaData[id][date]["metric"] = metric
+ except:
+ pass
+ return lemnaData
+ else:
+ raise Exception("Metric Column: ",dataHeaders["metric"]," does not exist.")
+ else:
+ raise Exception("Date Column: ",dataHeaders["date"]," does not exist.")
+ else:
+ raise Exception("Id Column: ",dataHeaders["id"]," does not exist.")
+ else:
+ raise Exception("Data Dictionary does not have all required keys ['id', 'date', 'dateFormat', 'metric']")
+ else:
+ raise Exception("Data File: " + dataFile + " does not exist!")
+ return
+
+ def loadSql(self, dblist):
+ for i,f in enumerate(dblist):
+ if os.path.isfile(f):
+ conn = self._openConnection(f)
+ cols = self._getHeaders("images", conn)
+ for col in cols:
+ self._addColumn(col, "images")
+ result = conn.execute("select pegasusid," + ",".join(cols) + " from images")
+ query = "update images set " + ",".join([col + "=?" for col in cols]) + " where pegasusid=?"
+ values = [tuple([row[col] for col in cols] + [row["pegasusid"]]) for row in result]
+ self.conn.executemany(query, values)
+ self.conn.commit()
+ self._closeConnection(conn)
+ else:
+ print "DB File: '%s' does not exist." % (f,)
+ return
+
+
+
+ def logErrors(self, logfile, table = "images"):
+ """
+ :param logfile: The logfile to write errors to
+ :type logfile: str
+ :param table: The table to load errors from
+ :type table: str
+
+ This function writes all errors from a given table to a log file,
+ usually used at the end of image processing to write all images that
+ did not process correctly.
+ """
+ with open(logfile, "w") as wh:
+ wh.write("Image processing error log\n")
+ wh.write("==========================\n")
+ result = self.conn.execute("select pegasusid,path,error from '" + table + "' where error is not null")
+ firstrow = result.fetchone()
+ if firstrow:
+ wh.write("Image with id '%s' loaded from input path '%s' was not processed successfully.\n" % (firstrow["pegasusid"], firstrow["path"]))
+ for row in result:
+ wh.write("Image with id '%s' loaded from input path '%s' was not processed successfully.\n" % (row["pegasusid"], row["path"]))
+ else:
+ wh.write("All images processed successfully! Nice job!\n")
+ return
+
+ def shootArea(self, intable, outtable, grouping, overwrite = False):
+ """
+ :param intable: The input table to load information from
+ :type intable: str
+ :param outtable: The output table to write information to.
+ :type outtable: str
+ :param grouping: Which imtypes to group
+ :type grouping: list
+
+ This function adds the numeric values of multiple image types together.
+ In general, it is used to combine side view + top view images of the same spectrum.
+ If you plan on correlating your data to lemnaTec's data, lemnaTec uses SV1 + SV2 + TV,
+ so you should aggregate your data likewise.
+ """
+ self._validate("shootArea", intable, outtable, overwrite)
+ self._createTable("shootArea", intable, outtable, overwrite)
+ headers = self._getHeaders(outtable)
+ dataHeaders = [header for header in headers if header not in conf.allHeaders and "ref" not in header]
+ start = len(headers) - len(dataHeaders)
+ """
+ map = {
+ "genotype": {
+ "date": {
+ "treatment": {
+ "writeback": [],
+ "values": ()
+ }
+ }
+ }
+ }
+ """
+ dataMap = {}
+ result = self.conn.execute("select pegasusid," + ",".join(headers) + " from " + intable + " where " + " or ".join(["imtype=?" for x in grouping]), tuple([x for x in grouping]))
+ for row in result:
+ if row["genotype"] not in dataMap:
+ dataMap[row["genotype"]] = {}
+ if row["date"] not in dataMap[row["genotype"]]:
+ dataMap[row["genotype"]][row["date"]] = {}
+ if row["treatment"] not in dataMap[row["genotype"]][row["date"]]:
+ dataMap[row["genotype"]][row["date"]][row["treatment"]] = {"writeback": [row["pegasusid"]], "values": tuple([row[x] for x in headers])}
+ else:
+ dataMap[row["genotype"]][row["date"]][row["treatment"]]["writeback"].append(row["pegasusid"])
+ values = []
+ for i,(x,y) in enumerate(zip(dataMap[row["genotype"]][row["date"]][row["treatment"]]["values"], tuple([row[x] for x in headers]))):
+ if i < start:
+ values.append(x)
+ else:
+ try:
+ values.append(x + y)
+ except:
+ values.append(None)
+ dataMap[row["genotype"]][row["date"]][row["treatment"]]["values"] = tuple(values)
+
+ #Loop through dataMap, insert values and writeback accordingly
+ for genotype in dataMap:
+ for date in dataMap[genotype]:
+ for treatment in dataMap[genotype][date]:
+ lastid = self.conn.execute("insert into " + outtable + " (" + ",".join(headers) + ") values (" + ",".join(["?"] * len(headers)) + ")", dataMap[genotype][date][treatment]["values"]).lastrowid
+ self.conn.executemany("update " + intable + " set ref_" + outtable + "=? where pegasusid=?", tuple([(lastid, x) for x in dataMap[row["genotype"]][row["date"]][row["treatment"]]["writeback"]]))
+ self.conn.commit()
+ return
+
+ def normalize(self, intable, outtable, column = "pixels", overwrite = False):
+ """
+ :param intable: The input table to load information from
+ :type intable: str
+ :param outtable: The output table to write information to.
+ :type outtable: str
+ :param column: The column to normalize information to
+ :type column: str
+
+ Normalizes all numerical information to the specific column. This
+ function is usually used with 'pixels' as the specified column, which
+ expresses all numeric information as a percentage of the total pixels
+ in the image.
+ """
+ self._validate("normalize", intable, outtable, overwrite)
+ if self._columnExists(column, intable):
+ conf.statsColumns["normalize"]["exclude"] += [column]
+ self._createTable("normalize", intable, outtable, overwrite)
+ headers = self._getHeaders(outtable)
+ dataHeaders = [header for header in headers if header not in conf.allHeaders and "ref" not in header]
+ result = self.conn.execute("select pegasusid," + column + "," + ",".join(headers) + " from " + intable)
+ vals = ()
+ for row in result:
+ vals = []
+ for x in headers:
+ if x in conf.allHeaders:
+ vals.append(row[x])
+ else:
+ if not self._checkNull(row[x]):
+ if not self._checkNull(row[column]) and row[column]:
+ vals.append(float(row[x]) / float(row[column]))
+ else:
+ vals.append(None)
+ else:
+ vals.append(None)
+ lastid = self.conn.execute("insert into " + outtable + " (" + ",".join(headers) + ") values (" + ",".join(["?"] * len(headers)) + ")", tuple(vals)).lastrowid
+ self.conn.execute("update " + intable + " set ref_" + outtable + "=? where pegasusid=?", (lastid, row["pegasusid"]))
+ self.conn.commit()
+ return
+
+ def extractAll(self, options):
+ basepath = os.path.dirname(os.path.dirname(os.path.abspath(self.db) + "/"))
+ if "workflows" in options:
+ for type in options["workflows"]:
+ self._openConnection()
+ tmp = self.conn.execute("select pegasusid,experiment,id,date,imtype,imgname from images where imtype=?", (type,))
+ result = tmp.fetchall()
+ for row in result:
+ finalpath = row["experiment"].replace(" ","") + "/" + row["id"].replace(" ","") + "/" + row["date"].replace(" ","") + "/" + row["imtype"].replace(" ","") + "/" + row["imgname"].replace(" ","") + "/" + row["pegasusid"] + "_" + options["workflows"][type]["inputs"][0] + ".png"
+ #finalpath = row["pegasusid"] + "_" + options["workflows"][type]["inputs"][0] + ".png"
+ self._closeConnection()
+ if os.path.isfile(finalpath):
+ try:
+ plant = ih.imgproc.Image(finalpath, db = self.db, dbid = row["pegasusid"])
+ plant.extractFinalPath()
+ if "--dimensions" in options["workflows"][type]["arguments"]:
+ plant.extractDimensions()
+ if "--pixels" in options["workflows"][type]["arguments"]:
+ plant.extractPixels()
+ if "--moments" in options["workflows"][type]["arguments"]:
+ plant.extractMoments()
+ if "--colors" in options["workflows"][type]["arguments"]:
+ plant.extractColorData()
+ if "--channels" in options["workflows"][type]["arguments"]:
+ plant.extractColorChannels()
+ if "--bins" in options["workflows"][type]["arguments"]:
+ plant.extractBins(options["workflows"][type]["arguments"]["--bins"])
+ except Exception as e:
+ print traceback.format_exc()
+ else:
+ print "PATH DOES NOT EXIST: %s." % (finalpath,)
+ if "histogram-bin" in options:
+ self._openConnection()
+ self.histogramBinning("images", "histogramBins", dict((type,options["workflows"][type]["inputs"][0]) for type in options["workflows"]), options["histogram-bin"]["--group"], options["histogram-bin"]["--chunks"], options["histogram-bin"]["--channels"], True)
+ return
+
+ def histogramBinning(self, intable, outtable, grouping, chunks, channels, jsonwrite = False, overwrite = False):
+ color_vector = {}
+ for name in grouping:
+ self._validate("histogramBins", intable, name + "_" + outtable, overwrite)
+ for name in grouping:
+ self._createTable("histogramBins", intable, name + "_" + outtable, overwrite)
+ color_vector[name] = [0, 0, 0]
+ map = dict((type, name) for name in grouping for type in grouping[name])
+ basequery = "select "
+ for x,c in enumerate(["bhist", "ghist", "rhist"]):
+ for i in range(0, 256):
+ if i == 0 and x == 0:
+ basequery += "SUM(" + c + str(i) + ")"
+ else:
+ basequery += ",SUM(" + c + str(i) + ")"
+ basequery += " from images where "
+ for name in grouping:
+ query = basequery + " or ".join(["imtype=?" for x in grouping[name]])
+ result = self.conn.execute(query, tuple(grouping[name]))
+ data = list(result.fetchone())
+ for i in range(0, 3):
+ color_vector[name][i] = data[i*256:(i + 1)*256]
+ bins = {}
+ for name in grouping:
+ bins[name] = self._generateBins(self._splitHist(color_vector[name], chunks[name], channels[name]), name)
+ self.conn.executemany("insert into " + name + "_" + outtable + " (name, minr, ming, minb, maxr, maxg, maxb) values (?, ?, ?, ?, ?, ?, ?)", [(bin["name"], int(bin["min"][2]), int(bin["min"][1]), int(bin["min"][0]), int(bin["max"][2]), int(bin["max"][1]), int(bin["max"][0])) for bin in bins[name]])
+# for bin in bins[name]:
+# self.conn.execute("insert into " + name + "_" + outtable + " (name, minr, ming, minb, maxr, maxg, maxb) values (?, ?, ?, ?, ?, ?, ?)", (name + bin["name"], int(bin["min"][2]), int(bin["min"][1]), int(bin["min"][0]), int(bin["max"][2]), int(bin["max"][1]), int(bin["max"][0])))
+# self.conn.commit()
+ self.conn.commit()
+ if jsonwrite:
+ for name in grouping:
+ with open(name + "_hist_bins.json", "w") as wh:
+ json.dump(bins[name], wh)
+ return
+
+
+ def _splitHist(self, hist, chunks, channels):
+ returnlist = [ [1], [1], [1] ]
+ s = [sum(x) for x in hist]
+ #s = [int(x) for x in np.sum(hist, axis = 1)]
+ for i in channels:
+ tmp = 0
+ integral = s[i] / chunks
+ for j,item in enumerate(hist[i]):
+ tmp += item
+ if (tmp > integral):
+ returnlist[i].append(j)
+ tmp = 0
+ returnlist[0].append(255)
+ returnlist[1].append(255)
+ returnlist[2].append(255)
+ return returnlist
+
+ def _generateBins(self, vector, type):
+ bins = []
+ num = 1
+ for i in range (0, len(vector[0]) - 1):
+ for j in range(0, len(vector[1]) - 1):
+ for k in range(0, len(vector[2]) - 1):
+ bins.append({
+ "name": type + "_bin" + str(num),
+ "min": np.array([vector[0][i],vector[1][j],vector[2][k]], dtype=np.uint8).tolist(),
+ "max": np.array([vector[0][i+1],vector[1][j+1],vector[2][k+1]], dtype=np.uint8).tolist()
+ })
+ num += 1
+ return bins
+
+
+ def correlation(self, intable, outtable, dataFile, dataHeaders, overwrite = False):
+ """
+ :param intable: The input table to load information from
+ :type intable: str
+ :param outtable: The output table to write information to.
+ :type outtable: str
+ :param dataFile: The csv data file to load
+ :type dataFile: str
+ :param dataHeaders: Column names for relevant table headers.
+ :type dataHeaders: str
+
+ This function correlates all numeric values with values in the given file.
+ The input data file is assumed to be in csv format. In dataHeaders, you must
+ specify four keys, 'id', 'date', 'dateFormat', and 'metric'. Each of these should
+ be column names. Id corresponds to the lemnaTec style identifier ex: '023535-S'.
+ All dates are converted into Y-m-d form, you must provide a valid format in 'dateFormat',
+ that way the dates can be converted correctly. The 'metric' column is the actual value you
+ want to correlate to.
+ """
+ self._validate("correlation", intable, outtable, overwrite)
+ lemnaData = self._loadLemnaData(dataFile, dataHeaders)
+ self._createTable("correlation", intable, outtable, overwrite)
+ headers = self._getHeaders(outtable)
+ numeric = [h for h in headers if h not in conf.allHeaders]
+ for id in lemnaData:
+ for imtype in self._getImageTypes(intable):
+ x = {}
+ y = []
+ corr = {}
+ result = self.conn.execute("select pegasusid," + ",".join(headers + ["date"]) + " from " + intable + " where id=? and imtype=? order by date", (id,imtype))
+ if result.fetchone():
+ for row in result:
+ if row["date"] in lemnaData[id]:
+ y.append(lemnaData[id][row["date"]]["metric"])
+ for header in numeric:
+ if header not in x:
+ x[header] = []
+ try:
+ x[header].append(float(row[header]))
+ except:
+ pass
+ if any([x[header] for header in numeric]):
+ for header in numeric:
+ if len(x[header]) == len(y):
+ corr[header] = np.corrcoef(x[header], y)[0][1]
+ else:
+ corr[header] = None
+ lastid = self.conn.execute("insert into " + outtable + " (" + ",".join(headers) + ") values (" + ",".join(["?"] * len(headers)) + ")", tuple([row[header] if header in conf.allHeaders else corr[header] for header in headers])).lastrowid
+ self.conn.execute("update " + intable + " set ref_" + outtable + "=? where id=? and imtype=?", (lastid, id, imtype))
+ self.conn.commit()
+ return
+
+ def anova(self, intable, outtable, grouping, overwrite = False):
+ """
+ :param intable: The input table to load information from
+ :type intable: str
+ :param outtable: The output table to write information to.
+ :type outtable: str
+ :param grouping: The list of image types to group by.
+ :type grouping: list
+
+ Computes the analysis of variation of all numeric information based on 3 factors,
+ treatment, date, and the interaction between the two. Analysis of variation is
+ different than the rest of the stats functions, in that a lot of information is
+ lost after running it. The results themselves correspond to columns (pixels, rmed, binx...)
+ instead of actual images.
+ """
+ self._validate("anova", intable, outtable, overwrite)
+ headers = self._getHeaders(intable)
+ numeric = [h for h in headers if h not in conf.allHeaders]
+ self._createTable("anova", intable, outtable, overwrite)
+ outHeaders = self._getHeaders(outtable)
+ result = self.conn.execute("select * from images")
+ rowdata = []
+ for row in result:
+ rowdata.append(dict(row))
+ data = pandas.DataFrame(rowdata).dropna()
+ anova = {}
+ for col in numeric:
+ anova[col] = {}
+ dateT = []
+ treatmentT = []
+ date_treatmentT = []
+ for date in self._getDates(intable):
+ dateT.append(data[data["date"] == date][col])
+ for treatment in ["Control", "Stress"]:
+ treatmentT.append(data[data["treatment"] == treatment][col])
+ date_treatmentT.append(data[np.where(np.logical_and(data["treatment"] == treatment,data["date"] == date), True, False)][col])
+ f_val, d_pval = stats.f_oneway(*dateT)
+ f_val, t_pval = stats.f_oneway(*treatmentT)
+ f_val, dt_pval = stats.f_oneway(*date_treatmentT)
+ anova[col]["date"] = d_pval
+ anova[col]["treatment"] = t_pval
+ anova[col]["date_treatment"] = dt_pval
+ for type in ["date", "treatment", "date_treatment"]:
+ vals = [group] + [anova[x][type] for x in numeric] + [type]
+ self.conn.execute("insert into " + outtable + " (" + ",".join(outHeaders) + ") values (" + ",".join(["?"] * len(outHeaders)) + ")", tuple(vals))
+ self.conn.commit()
+ return
+
+ def tTest(self, intable, outtable, comp = "imtype", overwrite = False):
+ """
+ :param intable: The input table to perform the T test on.
+ :type intable: str
+ :param outtable: The output table to write the results to.
+ :type outtable: str
+ :param comp: Whether to compare image types or image names.
+ :type comp: str
+ :param overwrite: Whether or not to overwrite the output database
+ :type overwrite: bool
+
+ This function computes a ttest of the input table for all numeric headers.
+ The comparison is either done based on image types or image names. Default
+ functionality is a comparison between image types, specify comp = 'imgname'
+ to compare image names.
+ """
+
+ self._validate("ttest", intable, outtable, overwrite)
+ self._createTable("ttest", intable, outtable, overwrite)
+ comp = "imtype" if comp == "imtype" else "imgname"
+ headers = self._getHeaders(outtable)
+ numeric = [h for h in headers if h not in conf.allHeaders]
+ meta = [h for h in headers if h not in numeric]
+ data = {}
+ result = self.conn.execute("select pegasusid,treatment," + ",".join(headers) + " from " + intable)
+ for row in result:
+ if row[comp] not in data:
+ data[row[comp]] = {}
+ if row["date"] not in data[row[comp]]:
+ data[row[comp]][row["date"]] = {"meta": dict(row), "id": [], "values": {}}
+ data[row[comp]][row["date"]]["id"].append(row["pegasusid"])
+ if row["treatment"] not in data[row[comp]][row["date"]]["values"]:
+ data[row[comp]][row["date"]]["values"][row["treatment"]] = [[row[h]] for h in numeric]
+ else:
+ for i,h in enumerate(numeric):
+ data[row[comp]][row["date"]]["values"][row["treatment"]][i].append(row[h])
+ for comp in data:
+ for date in data[comp]:
+ vals = [data[comp][date]["meta"][x] for x in meta]
+ for a,b in zip(data[comp][date]["values"]["Control"], data[comp][date]["values"]["Stress"]):
+ try:
+ res = stats.ttest_ind(a, b)[1]
+ except:
+ res = None
+ vals += [res]
+ lastid = self.conn.execute("insert into " + outtable + " (" + ",".join(headers) + ") values (" + ",".join(["?"] * len(headers)) + ")", vals).lastrowid
+ updateVals = (lastid,) + tuple(data[comp][date]["id"])
+ self.conn.execute("update " + intable + " set ref_" + outtable + "=? where id in (" + ",".join(["?"] * len(data[comp][date]["id"])) + ")", updateVals)
+ self.conn.commit()
+ return
+
+ def treatmentComp(self, intable, outtable, type = "ratio", direction = "Control", comp = "imtype", overwrite = False):
+ """
+ :param intable: The input table to load information from
+ :type intable: str
+ :param outtable: The output table to write information to.
+ :type outtable: str
+ :param type: The type of calculation to do between treatments. Should be ratio or difference.
+ :type type: str
+ :param direction: Whether to compute C ~ S, or S ~ C, default is Control first.
+ :type direction: str
+ :param comp: Whether to compare by imtype or imgname
+ :type comp: str
+
+ This function compares information between treatments -- It finds plants that are identical
+ except for treatment, and computes either a ratio or difference between them. Direction
+ is specified as the column you want first, so direction = "Control" will compute C ~ S, and
+ direction = "Stress" will compute S ~ C. If you have already normalized your table, difference
+ will provide better information than ratio.
+ """
+ t1 = "Stress" if direction == "Stress" else "Control"
+ t2 = "Stress" if direction == "Control" else "Control"
+ if type == "ratio":
+ op = lambda left, right: (left / right)
+ else:
+ op = lambda left, right: (left - right)
+ comp = "imtype" if comp == "imtype" else "imgname"
+ self._validate("treatmentComp", intable, outtable, overwrite)
+ self._createTable("treatmentComp", intable, outtable, overwrite)
+ headers = self._getHeaders(outtable)
+ numeric = [h for h in headers if h not in conf.allHeaders]
+ meta = [h for h in headers if h not in numeric]
+ data = {}
+ result = self.conn.execute("select pegasusid," + ",".join(headers) + " from " + intable)
+ for row in result:
+ if row["genotype"] not in data:
+ data[row["genotype"]] = {"id": [], "values": {}, "meta": {}}
+ data[row["genotype"]]["meta"][row[comp]] = dict(row)
+ data[row["genotype"]]["id"].append(row["pegasusid"])
+ if row[comp] not in data[row["genotype"]]["values"]:
+ data[row["genotype"]]["values"][row[comp]] = {}
+ if row["date"] not in data[row["genotype"]]["values"][row[comp]]:
+ data[row["genotype"]]["values"][row[comp]][row["date"]] = {}
+ if row["treatment"] not in data[row["genotype"]]["values"][row[comp]][row["date"]]:
+ data[row["genotype"]]["values"][row[comp]][row["date"]][row["treatment"]] = [row[h] for h in numeric]
+ for genotype in data:
+ for comp in data[genotype]["values"]:
+ for date in data[genotype]["values"][comp]:
+ vals = [data[genotype]["meta"][comp][x] for x in meta]
+ for a,b in zip(data[genotype]["values"][comp][date][t1], data[genotype]["values"][comp][date][t2]):
+ try:
+ res = op(float(a), float(b))
+ except:
+ res = None
+ vals.append(res)
+ lastid = self.conn.execute("insert into " + outtable + " (" + ",".join(headers) + ") values (" + ",".join(["?"] * len(headers)) + ")", vals).lastrowid
+ updateVals = (lastid,) + tuple(data[genotype]["id"])
+ self.conn.execute("update " + intable + " set ref_" + outtable + "=? where id in (" + ",".join(["?"] * len(data[genotype]["id"])) + ")", updateVals)
+ self.conn.commit()
+ return
+
+ def threshold(self, intable, outtable, thresh = 0.01, overwrite = False):
+ """
+ :param intable: The input table to load information from
+ :type intable: str
+ :param outtable: The output table to write information to.
+ :type outtable: str
+ :param thresh: The threshold value.
+ :type thresh: float
+
+ This function thresholds the table based on the given value. All values
+ that fall below the threhsold are 'updated' in place with 'null'. Normalize
+ is often called before thresholding.
+ """
+ self._validate("threshold", intable, outtable, overwrite)
+ self._createTable("threshold", intable, outtable, overwrite)
+ headers = self._getHeaders(outtable)
+ numeric = [h for h in headers if h not in conf.allHeaders]
+ result = self.conn.execute("select pegasusid," + ",".join(headers) + " from " + intable)
+ for row in result:
+ vals = []
+ for x in headers:
+ if x in conf.allHeaders:
+ vals.append(row[x])
+ else:
+ if not self._checkNull(row[x]):
+ if float(row[x]) > thresh:
+ vals.append(row[x])
+ else:
+ vals.append(None)
+ else:
+ vals.append(None)
+ lastid = self.conn.execute("insert into " + outtable + " (" + ",".join(headers) + ") values (" + ",".join(["?"] * len(headers)) + ")", tuple(vals)).lastrowid
+ self.conn.execute("update " + intable + " set ref_" + outtable + "=? where pegasusid=?", (lastid, row["pegasusid"]))
+ self.conn.commit()
+ return
+
+ def SOMANYGRAPHINGFUNCTIONS(self):
+
+ return
+
+ def export(self, table, processed = True, group = None, fname = None):
+ """
+ :param table: The table to write to csv
+ :type table: str
+ :param processed: Whether or not to extract processed data
+ :type processed: bool
+ :param group: Which image types to extract from the database.
+ :type group: list
+ :param fname: The file name to write to.
+ :type fname: str
+
+ This function simply extracts data from a database and writes it to csv format.
+ Default functionality is to extract only data that has been processed. This is
+ checked by finding if an outputPath has been set. Additionally,
+ you can specify a list of image types to extract, if not, the default list contains
+ all rgb and fluo images. Finally, if no file name is specified, the name
+ of the table is used as the filename.
+ """
+ group = group if isinstance(group, list) else self._getImageTypes(table)
+ fname = fname if fname else table + ".csv"
+ query = "select * from " + table
+ values = tuple()
+ if processed:
+ query += " where outputPath is not null"
+ if group:
+ query += " and (" + " or ".join(["imtype=?" for x in group])
+ values = tuple([x for x in group])
+ elif group:
+ query += " where " + " or ".join(["imtype=?" for x in group])
+ values = tuple([x for x in group])
+ table = pandas.io.sql.read_sql(sql = query, params = values, con = self.conn)
+ table.to_csv(fname)
+ return
diff --git a/build/lib/ih/validator.py b/build/lib/ih/validator.py
new file mode 100644
index 0000000000000000000000000000000000000000..88afe6dfb592f193f519263636a773dd8a4eec70
--- /dev/null
+++ b/build/lib/ih/validator.py
@@ -0,0 +1,702 @@
+"""
+This file is part of Image Harvest.
+
+Image Harvest is free software: you can redistribute it and/or modify
+it under the terms of the GNU General Public License as published by
+the Free Software Foundation, either version 3 of the License, or
+(at your option) any later version.
+
+Image Harvest is distributed in the hope that it will be useful,
+but WITHOUT ANY WARRANTY; without even the implied warranty of
+MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+GNU General Public License for more details.
+
+You should have received a copy of the GNU General Public License
+along with Image Harvest. If not, see <http://www.gnu.org/licenses/>.
+"""
+import os
+import conf
+import sys
+import json
+import re
+import csv
+import datetime
+import sqlite3
+import textwrap
+import shutil
+import errno
+import copy
+import traceback
+from Pegasus.DAX3 import *
+
+class Validator(object):
+ """
+ A very, very generic validator.
+ """
+ def __init__(self, f, type):
+ self.err = ""
+ if not os.path.isfile(f):
+ self.err += "Path Error: Input '%s' doesn't exist.\n" % (f,)
+ if not self.err:
+ if type == "file":
+ with open(f, "r") as rh:
+ try:
+ self.data = json.load(rh)
+ except Exception as e:
+ self.err += "Json Error: File '%s', %s\n" % (f, str(e))
+ elif type == "db":
+ self.conn = sqlite3.connect(f)
+ self.conn.row_factory = sqlite3.Row
+ try:
+ result = self.conn.execute("select * from images")
+ if not result.fetchone():
+ self.err += "Database Error: No information in images table\n"
+ except Exception as e:
+ self.err += "Database Error: %s\n" % (str(e), )
+ else:
+ self.err += "Validator Error: Invalid type, must be either 'file' or 'db'\n"
+ self.rawFiles = {}
+ self.type = type
+ self.validate()
+ return
+
+ def printErrors(self):
+ """
+ Prints out errors from validation and then exits.
+ """
+ if self.err:
+ print self.err.strip()
+ else:
+ print "No Validation Errors."
+ return
+
+ def isValid(self):
+ """
+ A convenience function. If validation ran successfully,
+ return True, else return False.
+ """
+ if not self.err:
+ return True
+ else:
+ return False
+
+ def validate(self):
+ """
+ This function should be overloaded
+ """
+ return
+
+class Workflow(object):
+
+ def __init__(self, template, config, database):
+ self.workflow = Validator(template, "file")
+ self.config = Validator(config, "file")
+ self.db = Validator(database, "db")
+ self.err = ""
+ if self.workflow.isValid() and self.db.isValid() and self.config.isValid():
+ self.validate()
+ else:
+ self.err += "Workflow components did not validate individually. \n"
+ self.err += self.workflow.err
+ self.err += self.config.err
+ self.err += self.db.err
+ return
+
+ def isValid(self):
+ """
+ A convenience function.
+ """
+ if not self.err:
+ return True
+ else:
+ return False
+
+ def printErrors(self):
+ if self.err:
+ print self.err.strip()
+ else:
+ print "No Validation Errors"
+ return
+
+ def _loadOverwriteArgument(self, job, arg):
+ job["arguments"][arg] = conf.valid[job["executable"]]["arguments"][arg]["value"]
+ return
+
+ def _loadDerivedArgument(self, job, arg, jtype):
+ key = conf.valid[job["executable"]]["arguments"][arg]["key"]
+ index = conf.valid[job["executable"]]["arguments"][arg]["index"]
+ if key in job:
+ if isinstance(job[key], list):
+ if index <= len(job[key]) - 1:
+ if "value" in conf.valid[job["executable"]]["arguments"][arg]:
+ job["arguments"][arg] = conf.valid[job["executable"]]["arguments"][arg]["value"]
+ else:
+ job["arguments"][arg] = job[key][index]
+ else:
+ if "required" in conf.valid[job["executable"]]["arguments"][arg]:
+ self.err += "Workflow, Argument Error: Type '%s' job '%s', derived argument '%s' requires index '%s' for definition '%s', no such index. \n" % (jtype, job["name"], arg, index, key)
+ else:
+ if "required" in conf.valid[job["executable"]]["arguments"][arg]:
+ self.err += "Workflow, Argument Error: Type '%s' job '%s', derived argument '%s' requires definition for '%s' to be of type list, definition is of type '%s'. \n" % (jtype, job["name"], arg, key, type(job[key]).__name__)
+ else:
+ if "required" in conf.valid[job["executable"]]["arguments"][arg]:
+ self.err += "Workflow, Argument Error: Type '%s' job '%s', derived argument '%s' requires job definition for '%s', no such definition. \n" % (jtype, job["name"], arg, key)
+ return
+
+ def _validateArgumentType(self, job, arg, type):
+ if arg in job["arguments"]:
+ if not isinstance(job["arguments"][arg], {
+ "list": list,
+ "string": (str, unicode),
+ "dict": dict,
+ "numeric": (int, long, float),
+ "exist": object,
+ "derived": object
+ }[conf.valid[job["executable"]]["arguments"][arg]["type"]]):
+ self.err += "Workflow, Argument Error: Type '%s' job '%s', argument '%s' given value '%s', should be of type '%s'. \n" % (type, job["name"], arg, job["arguments"][arg], conf.valid[job["executable"]]["arguments"][arg]["type"])
+ else:
+ if isinstance(job["arguments"][arg], list) and "join" in conf.valid[job["executable"]]["arguments"][arg]:
+ job["arguments"][arg] = conf.valid[job["executable"]]["arguments"][arg]["join"].join(job["arguments"][arg])
+ elif (isinstance(job["arguments"][arg], dict) or isinstance(job["arguments"][arg], list)):
+ job["arguments"][arg] = str(job["arguments"][arg])
+ elif (isinstance(job["arguments"][arg], (str, unicode)) and conf.valid[job["executable"]]["arguments"][arg]["type"] and "complex" in conf.valid[job["executable"]]["arguments"][arg]):
+ job["arguments"][arg] = '"' + job["arguments"][arg] + '"'
+ return
+
+ def _validateArgumentRequired(self, job, arg, type):
+ if "required" in conf.valid[job["executable"]]["arguments"][arg]:
+ if arg in job["arguments"]:
+ if not job["arguments"][arg]:
+ self.err += "Workflow, Argument Error: Type '%s' job '%s', has empty required argument '%s' \n" % (type, job["name"], arg)
+ else:
+ self.err += "Workflow, Argument Error: Type '%s' job '%s', requires argument '%s', no such argument found. \n" % (type, job["name"], arg)
+ return
+
+ def _validateArgumentDictionary(self, job, arg, type):
+ arglist = job["arguments"][arg] if isinstance(job["arguments"][arg], list) else [job["arguments"][arg]]
+ if conf.valid[job["executable"]]["arguments"][arg]["validation"] == "dictionary":
+ d = conf.valid[job["executable"]]["arguments"][arg]["value"] if "key" not in conf.valid[job["executable"]]["arguments"][arg] else conf.valid[job["executable"]]["arguments"][arg]["value"].get(job["arguments"][conf.valid[job["executable"]]["arguments"][arg]["key"]])
+ for val in arglist:
+ if val not in d:
+ self.err += "Workflow, Argument Error: Type '%s' job '%s', has invalid value '%s' for argument '%s'. \n" % (type, job["name"], val, arg)
+ return
+
+ def _validateArgumentList(self, job, arg, type):
+ arglist = job["arguments"][arg] if isinstance(job["arguments"][arg], list) else [job["arguments"][arg]]
+ l = conf.valid[job["executable"]]["arguments"][arg]["value"]
+ for val in arglist:
+ if val not in l:
+ self.err += "Workflow, Argument Error: Type '%s' job '%s', has invalid value '%s' for argument '%s'. \n" % (type, job["name"], val, arg)
+ return
+
+ def _validateArguments(self, job, type):
+ if not job["arguments"]:
+ job["arguments"] = {}
+ for arg in conf.valid[job["executable"]]["arguments"]:
+ if conf.valid[job["executable"]]["arguments"][arg]["type"] == "derived":
+ self._loadDerivedArgument(job, arg, type)
+ if "required" in conf.valid[job["executable"]]["arguments"][arg] or arg in job["arguments"]:
+ if conf.valid[job["executable"]]["arguments"][arg]["type"] == "overwrite":
+ self._loadOverwriteArgument(job, arg)
+ else:
+ self._validateArgumentRequired(job, arg, type)
+ self._validateArgumentType(job, arg, type)
+
+ if "validation" in conf.valid[job["executable"]]["arguments"][arg]:
+ if arg in job["arguments"]:
+ validate = {
+ "dictionary": self._validateArgumentDictionary,
+ "list": self._validateArgumentList
+ }[conf.valid[job["executable"]]["arguments"][arg]["validation"]](job, arg, type)
+
+ for arg in job["arguments"]:
+ if arg not in conf.valid[job["executable"]]["arguments"]:
+ self.err += "Workflow, Argument Error: Type '%s' job '%s', has invalid argument '%s'. \n" % (type, job["name"], arg)
+ return
+
+ def _validateDependencies(self, job, type):
+ try:
+ names = [x["name"] for x in self.workflow.data["workflows"][type]]
+ unres = copy.deepcopy(job["inputs"])
+ for input in job["inputs"]:
+ if os.path.isfile(input):
+ unres.remove(input)
+ self.workflow.rawFiles[type].append(input)
+ elif input in self.workflow.data["workflows"][type][0]["inputs"]:
+ unres.remove(input)
+ if "depends" in job:
+ for dependency in job["depends"]:
+ if dependency in names:
+ i = names.index(dependency)
+ for output in self.workflow.data["workflows"][type][i]["outputs"]:
+ if output in unres:
+ unres = [x for x in unres if x != output]
+ else:
+ self.err += "Workflow, Dependency Error: Type '%s' job '%s' depends on job '%s', no such job exists. \n" % (type, job["name"], dependency)
+ for val in set(unres):
+ self.err += "Workflow, Input Error: Type '%s' job '%s' depends on input '%s'. Cannot find matching output, or raw file. \n" % (type, job["name"], val)
+ for x,input in enumerate(job["inputs"]):
+ if "depends" in job:
+ for dependency in job["depends"]:
+ if dependency in names:
+ i = names.index(dependency)
+ if input in self.workflow.data["workflows"][type][i]["outputs"]:
+ j = self.workflow.data["workflows"][type][i]["outputs"].index(input)
+ if conf.valid[job["executable"]]["inputs"][x] != conf.valid[self.workflow.data["workflows"][type][i]["executable"]]["outputs"][j]:
+ self.err += "Workflow, Dependency Error: Type '%s' job '%s' input '%s' in position '%s' should be of type '%s', however, output '%s' in position '%s' of job '%s' is of type '%s'. \n" % (type, job["name"], input, x, conf.valid[job["executable"]]["inputs"][x], self.workflow.data["workflows"][type][i]["outputs"][j], j, self.workflow.data["workflows"][type][i]["name"], conf.valid[self.workflow.data["workflows"][type][i]["executable"]]["outputs"][j])
+ except:
+ self.printErrors()
+ print "Validation halted at type '%s' job '%s'. Fix errors before re-running. \n" % (type, job)
+ sys.exit()
+ return
+
+ def _validateDB(self):
+ """
+ Valides the input database file.
+ DIFFERENT FOR WORKFLOWS
+ OVERLOAD THIS
+ """
+
+ return
+
+ def _validateConfig(self):
+ """
+ Validates the input configuration template.
+ SAME FOR BOTH TYPES OF WORKFLOWS
+ """
+ if self.config.data:
+ if set(conf.templateKeys["config"]["required"]) < set(self.config.data.keys()):
+ if not os.path.isdir(self.config.data["installdir"]):
+ self.err += "Config, Path Error: Path '%s' specified for 'installdir' does not exist. \n" % (self.config.data["installdir"],)
+ for key in self.config.data:
+ if key not in conf.templateKeys["config"]["required"] and key not in conf.templateKeys["config"]["optional"]:
+ self.err += "Config, Key Error: Invalid key '%s' specified. Allowed keys are '%s'. \n" % (key, conf.templateKeys["config"]["required"] + conf.templateKeys["config"]["optional"])
+ if "maxwalltime" in self.config.data:
+ for key in self.config.data["maxwalltime"]:
+ if key not in conf.templateKeys["config"]["maxwalltime"]["optional"]:
+ self.err += "Config, Key Error: Invalid key '%s' specified for 'maxwalltime'. Allowed keys are '%s'. \n" % (key, conf.templateKeys["config"]["maxwalltime"]["optional"])
+ if "notify" in self.config.data:
+ for key in conf.templateKeys["config"]["notify"]["required"]:
+ if key not in self.config.data["notify"]:
+ self.err += "Config, Key Error: Required key '%s' not specified for 'notify'. \n" % (key,)
+ elif key == "pegasus_home":
+ if not os.path.isfile(self.config.data["notify"]["pegasus_home"] + "/email"):
+ self.err += "Config, Path Error: Required key '%s' has invalid value. Path '%s' does not exist." % (key, self.config.data["notify"]["pegasus_home"] + "/email")
+ for namespace in self.config.data["profile"]:
+ for key in self.config.data["profile"][namespace]:
+ if "path" in key.lower():
+ if not isinstance(self.config.data["profile"][namespace][key], list):
+ self.config.data["profile"][namespace][key] = [self.config.data["profile"][namespace][key]]
+ for path in self.config.data["profile"][namespace][key]:
+ if not os.path.isdir(path):
+ self.err += "Config, Path Error: Path '%s' specified for namespace '%s', key '%s' does not exist. \n" % (path, namespace, key)
+ else:
+ self.err += "Config, Template Error: Config file does not have all the required keys:" + str(conf.templateKeys["config"]["required"]) + " \n"
+ else:
+ self.err += "Config, Load Error: Could not load configuration info. \n"
+ return
+
+ def _getImageTypes(self):
+ return [x["imtype"] for x in self.db.conn.execute("select distinct imtype from images")]
+
+ def validate(self):
+ """
+ This should be overloaded again.
+ """
+ return
+
+
+class ImageProcessor(Workflow):
+
+ def __init__(self, template, config, database):
+ super(ImageProcessor, self).__init__(template, config, database)
+ return
+
+ def validate(self):
+ """
+ Validates all inputted files. Because the workflow is
+ dependenet on the config and metadata, workflow validation
+ is only done if config and metadata validate successfully.
+ """
+ if not self.err:
+ self._validateConfig()
+ self._validateDB()
+ if not self.err:
+ self._validateWorkflow()
+ return
+
+ def _validateWorkflowJobs(self):
+ types = self._getImageTypes()
+ for type in self.workflow.data["workflows"]:
+ if type not in types:
+ self.err += "Imgproc, Type Error: Workflow definition exists for type '%s', no images have been loaded for that type. \n" % (type,)
+ self.workflow.rawFiles[type] = []
+ names = [x["name"] for x in self.workflow.data["workflows"][type]]
+ if len(names) == len(set(names)):
+ for job in self.workflow.data["workflows"][type]:
+ if set(conf.templateKeys["imgproc"]["job"]["required"]) <= set(job.keys()):
+ for key in job.keys():
+ if key not in conf.templateKeys["imgproc"]["job"]["required"] and key not in conf.templateKeys["imgproc"]["job"]["optional"]:
+ self.err += "Imgproc, Key Error: Job '%s' has invalid key '%s' specified. Allowed keys are '%s'. \n" % (job["name"], key, conf.templateKeys["imgproc"]["job"]["required"] + conf.templateKeys["imgproc"]["job"]["optional"])
+ if job["executable"] in conf.valid:
+ if not os.path.isfile(self.config.data["installdir"] + "/" + job["executable"]):
+ self.err += "Imgproc, Path Error: Job '%s' executable '%s' does not exist. \n" % (job["name"], self.config.data["installdir"] + "/" + job["executable"])
+ if conf.valid[job["executable"]]["type"] == "imgproc":
+ self._validateArguments(job, type)
+ self._validateDependencies(job, type)
+ else:
+ self.err += "Imgproc, Executable Error: Job '%s' has invalid executable '%s' specified. Only image processing scripts are allowed. \n" % (job["name"], job["executable"])
+ else:
+ self.err += "Imgproc, Executable Error: Job '%s' has non-existant executable '%s' specified. \n" % (job["name"], job["executable"])
+ else:
+ self.err += "Imgproc, Key Error: Job '%s' doesn't have all required keys: '%s'. \n" % (job["name"], conf.templateKeys["imgproc"]["job"]["required"])
+ else:
+ self.err += "Imgproc, Name Error: Cannot parse ambiguous workflow. Workflow defined for type '%s' contains multiple jobs with the same name. \n" % (type,)
+ return
+
+ def _validateWorkflowOptions(self):
+ if set(conf.templateKeys["imgproc"]["options"]["required"]) <= set(self.workflow.data["options"].keys()):
+ for key in self.workflow.data["options"]:
+ if key not in conf.templateKeys["imgproc"]["options"]["required"] and key not in conf.templateKeys["imgproc"]["options"]["optional"]:
+ self.err += "Imgproc, Option Error: Invalid option '%s' specified. \n " % (key,)
+ else:
+ self.err += "Imgproc, Option Error: Option specification doesn't have all required keys: '%s'. \n " % (conf.templateKeys["imgproc"]["options"]["required"],)
+ return
+
+ def _validateWorkflowExtract(self):
+ if set(conf.templateKeys["imgproc"]["extract"]["required"]) <= set(self.workflow.data["extract"].keys()):
+ for key in self.workflow.data["extract"]:
+ if key not in conf.templateKeys["imgproc"]["extract"]["required"] and key not in conf.templateKeys["imgproc"]["extract"]["optional"]:
+ self.err += "Imgproc, Extract Error: Invalid option '%s' specified. \n " % (key,)
+
+ ## Manual hist-bin validation ##
+ if "histogram-bin" in self.workflow.data["extract"]:
+ hist = {}
+ hist["executable"] = "ih-stats-histogram-bin"
+ hist["inputs"] = ["images"]
+ hist["outputs"] = ["none"]
+ hist["name"] = "histogramBin"
+ hist["arguments"] = self.workflow.data["extract"]["histogram-bin"].copy()
+ self._validateArguments(hist, "extract")
+ if not self.err:
+ if set(self.workflow.data["extract"]["histogram-bin"]["--group"].keys()) != set(self.workflow.data["extract"]["histogram-bin"]["--channels"].keys()):
+ self.err += "Imgproc, Extract Error: Histogram bin group names don't match between '--group' and '--channels'. \n"
+ else:
+ pass
+
+ if not self.err:
+ for type in self.workflow.data["extract"]["workflows"]:
+ if type in self.workflow.data["workflows"]:
+ job = self.workflow.data["extract"]["workflows"][type]
+ job["executable"] = "ih-extract"
+ job["outputs"] = ["none"]
+ job["name"] = type + "_extract"
+ self._validateArguments(job, type)
+ self._validateDependencies(job, type)
+ else:
+ self.err += "Imgproc, Extract Error: Extraction specified for type '%s'. No processing workflow defined for that type." % (type,)
+ else:
+ pass
+ else:
+ self.err += "Imgproc, Extract Error: Extract specification doesn't have all required keys: '%s'. \n" % (conf.templateKeys["imgproc"]["extract"]["required"],)
+ return
+
+
+ def _validateWorkflow(self):
+ """
+ Validates the input workflow template, making sure all required
+ keys are inputted, and all names resolve
+ """
+ if set(conf.templateKeys["imgproc"]["required"]) <= set(self.workflow.data.keys()):
+ for key in self.workflow.data.keys():
+ if key not in conf.templateKeys["imgproc"]["required"] and key not in conf.templateKeys["imgproc"]["optional"]:
+ self.err += "Imgproc, Key error: Invalid key '%s' specified. Allowed keys are '%s'. \n" % (key, conf.templateKeys["imgproc"]["required"] + conf.templateKeys["imgproc"]["optional"])
+ try:
+ self._validateWorkflowJobs()
+ self._validateWorkflowOptions()
+ self._validateWorkflowExtract()
+ except Exception as e:
+ print traceback.format_exc()
+ self.err += "Validation halted. Fix current issues before re-running. \n"
+ self.printErrors()
+ else:
+ self.err += "Imgproc, Template Error: Workflow file does not have all the required keys: '%s'. \n" % (conf.templateKeys["imgproc"]["required"],)
+ return
+
+ def _validateDB(self):
+ """
+ Validates the inputted metadata db, ensuring the appropriate
+ column names are in the database.
+ """
+ if self.db:
+ cols = [row[1] for row in self.db.conn.execute("PRAGMA table_info(images)")]
+ if set(conf.outHeaders) <= set(cols):
+ testpath = self.db.conn.execute("select path from images limit 0,1").next()[0]
+ if not os.path.isfile(testpath):
+ self.err += "DB, Path Error: Test file: '%s' could not be found. \n" % (testpath,)
+ else:
+ self.err += "DB, Key Error: Meta-data file does not have all the required headers: %s \n" % (str(conf.outHeaders),)
+ else:
+ self.err += "DB, Load Error: Could not connect to meta-data db. \n"
+ return
+
+
+
+class Statistics(Workflow):
+
+ def __init__(self, template, config, database):
+ super(Statistics, self).__init__(template, config, database)
+
+ return
+
+ def validate(self):
+ """
+ Validates all inputted files. Because the workflow is
+ dependenet on the config and metadata, workflow validation
+ is only done if config and metadata validate successfully.
+ """
+ if not self.err:
+ self._validateConfig()
+ self._validateDB()
+ if not self.err:
+ self._validateWorkflow()
+ return
+
+ def _validateDB(self):
+ try:
+ result = self.db.conn.execute("select * from images")
+ cols = [row[1] for row in self.db.conn.execute("PRAGMA table_info(images)")]
+ if not set(cols) > set(conf.outHeaders):
+ self.err += "Stats, Database Error: Database specified does not contain any numeric columns, process images first. \n"
+ if not set(conf.outHeaders) <= set(cols):
+ self.err += "Stats, Database Error: Database specified does not contain all the required column names: '%s'. \n " % (conf.outHeaders,)
+ if not result.fetchone():
+ self.err += "Stats, Database Error: Database specified does not contain an image table with any entries. \n"
+ except sqlite3.DatabaseError:
+ self.err += "Stats, Database Error: File specified is not a valid database file. \n"
+ return
+
+ def _validateWorkflow(self):
+ if self.workflow.data:
+ for key in self.workflow.data.keys():
+ if key not in conf.templateKeys["stats"]["required"] and key not in conf.templateKeys["stats"]["optional"]:
+ self.err += "Stats, Key error: Invalid key '%s' specified. Allowed keys are '%s'. \n" % (key, conf.templateKeys["stats"]["required"] + conf.templateKeys["stats"]["optional"])
+ for type in self.workflow.data["workflows"]:
+ self.workflow.rawFiles[type] = []
+ names = [x["name"] for x in self.workflow.data["workflows"][type]]
+ if len(names) == len(set(names)):
+ for job in self.workflow.data["workflows"][type]:
+ if set(conf.templateKeys["stats"]["job"]["required"]) <= set(job.keys()):
+ for key in job.keys():
+ if key not in conf.templateKeys["stats"]["job"]["required"] and key not in conf.templateKeys["stats"]["job"]["optional"]:
+ self.err += "Stats, Key Error: Job '%s' has invalid key '%s' specified. Allowed keys are '%s'. \n" % (job["name"], key, conf.templateKeys["stats"]["job"]["required"] + conf.templateKeys["stats"]["job"]["optional"])
+ if job["executable"] in conf.valid:
+ if conf.valid[job["executable"]]["type"] == "statistics":
+ if os.path.isfile(self.config.data["installdir"] + "/" + job["executable"]):
+ self._validateArguments(job, type)
+ self._validateDependencies(job, type)
+ else:
+ self.err += "Stats, Path Error: Job '%s' executable '%s' does not exist. \n" % (job["name"], self.config["installdir"] + "/" + job["executable"])
+ else:
+ self.err += "Stats, Executable Error: Job '%s' has invalid executable '%s' specified. Only statistics scripts are allowed. \n" % (job["name"], job["executable"])
+ else:
+ self.err += "Stats, Executable Error: Job '%s' executable '%s' is not a valid executable. \n" % (job["name"], job["executable"])
+ else:
+ self.err += "Stats, Key Error: Job '%s' doesn't have all required keys: '%s'. \n" % (job["name"], conf.templateKeys["stats"]["job"]["required"])
+ else:
+ self.err += "Stats, Name Error: Cannot parse ambiguous workflow. Workflow defined for type '%s' contains multiple jobs with the same name. \n" % (type,)
+ else:
+ self.err += "Stats, Load Error: Could not load stats file. \n"
+ return
+
+class ImageLoader(Validator):
+
+ def __init__(self, f):
+ super(ImageLoader, self).__init__(f, "file")
+ return
+
+ def validate(self):
+ """
+ Validates the given template.
+ """
+ if self.isValid():
+ if set(conf.templateKeys["loading"]["required"]) <= set(self.data.keys()):
+ for key in self.data:
+ if key not in conf.templateKeys["loading"]["required"] and key not in conf.templateKeys["loading"]["optional"]:
+ self.err += "Loader, Key Error: Invalid key '%s' specified. \\n" % (key,)
+
+ if not self.err:
+ for key in self.data:
+ d = {
+ "path": self._validatePath,
+ "base": self._validateBase,
+ "data": self._validateData,
+ "translations": self._validateTranslations,
+ "order": self._validateOrder,
+ "filetype": self._validateFtype,
+ }[key]()
+ else:
+ self.err += "Loader, Key Error: Not all required keys specified: '%s' \n" % (conf.templateKeys["loading"]["required"])
+ return
+
+ def _validateFtype(self):
+ if self.data["filetype"]:
+ if self.data["filetype"] not in conf.imageExtensions:
+ self.err += "Loader, File Error: Value '%s' specified for 'filetype' is invalid. Must be on of '%s'. \n" % (self.data["filetype"], conf.imageExtensions)
+ else:
+ self.err += "Loader, File Error: No value specified for 'filetype'. \n"
+
+ def _validatePath(self):
+ """
+ Validates the path. Because the path contains potential references, path existence
+ cannot be checked at this stage.
+ """
+ if not self.data["path"]:
+ self.err += "Loader, Path Error: No value specified for 'path'.\n"
+ return
+
+ def _validateBase(self):
+ """
+ Validates the base walk path. Checks existence of a value, if the value
+ is a subset of path, and if the path exists.
+ """
+ if self.data["base"]:
+ if self.data["base"] in self.data["path"]:
+ if not os.path.exists(self.data["base"]):
+ self.err += "Loader, Base Error: Value for 'base' is not a valid path. \n"
+ else:
+ self.err += "Loader, Base Error: Value for 'base' is not a subset of 'path'. \n"
+ else:
+ self.err += "Loader, Base Error: No value specified for 'base'.\n"
+ pass
+
+ def _validateData(self):
+ """
+ Validates the data! Uses a seperate function for each data type.
+ """
+ if self.data["data"]:
+ for key in self.data["data"]:
+ if "type" in self.data["data"][key]:
+ if self.data["data"][key]["type"] in conf.templateKeys["loading"]["data"]["type"]:
+ if key in self.data["order"]:
+ d = {
+ "value": self._validateDataValue,
+ "file": self._validateDataFile,
+ "date": self._validateDataDate
+ }[self.data["data"][key]["type"]](key)
+ else:
+ self.err += "Loader, Data Error: Definition for data key '%s', no corresponding definition in 'order'. \n" % (key,)
+ else:
+ self.err += "Loader, Data Error: Invalid type '%s' specified for data key '%s', must be one of '%s'. \n" % (self.data["data"][key]["type"], key, conf.templateKeys["loading"]["data"]["type"])
+ else:
+ self.err += "Loader, Data Error: No value specified for 'type' of data key '%s'. \n" % (key,)
+ else:
+ self.err += "Loader, Value Error: No value specified for 'data'. \n"
+ pass
+
+ def _validateDataValue(self, key):
+ """
+ Validates type 'value'. Values can be combinations of hard-coded text
+ as well as references to path identifiers Checks existence of a value,
+ if all the references are valid, and if translation is specified, that
+ translations exist.
+ """
+ if self.data["data"][key]["value"]:
+ if set(conf.templateKeys["loading"]["data"]["value"]["required"]) <= set(self.data["data"][key].keys()):
+
+ for subkey in self.data["data"][key]:
+ if subkey not in conf.templateKeys["loading"]["data"]["value"]["required"] and subkey not in conf.templateKeys["loading"]["data"]["value"]["optional"]:
+ self.err += "Loader, Data Value Error: Invalid key '%s' specified for data key '%s'. \n" % (subkey,key)
+
+ m = re.findall(r"%(\w+)%", self.data["data"][key]["value"])
+ for val in m:
+ if "%" + val + "%" not in self.data["path"]:
+ self.err += "Loader, Data Value Reference Error: Could not reference identifier '%s' for data key '%s'. \n" % (val, key)
+ if "translate" in self.data["data"][key]:
+ if key not in self.data["translations"]:
+ self.err += "Loader, Data Value Translation Error: Can't translate data key '%s', no translation specified. \n" % (key,)
+ else:
+ print set(conf.templateKeys["loading"]["data"]["value"]["required"])
+ print set(self.data["data"][key].keys())
+ self.err += "Loader, Data Value Error: Data key '%s' does not have all required keys '%s'. \n" % (key, conf.templateKeys["loading"]["data"]["value"]["required"])
+ else:
+ self.err += "Loader, Data Value Error: No value specified for data key '%s'. \n " % (key,)
+ return
+
+ def _validateDataFile(self, key):
+ """
+ Validates type 'file'. Checks to ensure that a file is specified,
+ that file exists, and that a value is specified for key, keyColumn,
+ and valueColumn. Assumes the file is of csv format.
+ """
+ if set(conf.templateKeys["loading"]["data"]["file"]["required"]) <= set(self.data["data"][key].keys()):
+
+ for subkey in self.data["data"][key]:
+ if subkey not in conf.templateKeys["loading"]["data"]["file"]["required"] and subkey not in conf.templateKeys["loading"]["data"]["file"]["optional"]:
+ self.err += "Loader, Data File Error: Invalid key '%s' specified for data key '%s'. \n" % (subkey, key)
+
+ if os.path.exists(self.data["data"][key]["value"]):
+ with open(self.data["data"][key]["value"], "r") as rh:
+ firstline = rh.readline()
+ sep = self.data["data"][key]["separator"] if "separator" in self.data["data"][key] else ","
+ maxlength = len(firstline.split(sep))
+ if maxlength <= self.data["data"][key]["keyColumn"]:
+ self.err += "Loader, Data File Error: Key column for data key '%s' out of range. \n" % (key,)
+ if maxlength <= self.data["data"][key]["valueColumn"]:
+ self.err += "Loader, Data File Error: Value column for data key '%s' out of range. \n" % (key,)
+ else:
+ self.err += "Loader, Data Filer Error: File '%s' specified for data key '%s' does not exist. \n" % (self.data["data"][key]["value"], key)
+
+ m = re.findall(r"%(\w+)%", self.data["data"][key]["key"])
+ for val in m:
+ if "%" + val + "%" not in self.data["path"]:
+ self.err += "Loader, Data Value Reference Error: Could not reference identifier '%s' for data key '%s'. \n" % (val, key)
+ else:
+ self.err += "Loader, Data File Error: Data key '%s' does not have all required keys '%s'. \n" % (key, conf.templateKeys["loading"]["data"]["file"]["required"])
+ return
+
+ def _validateDataDate(self, key):
+ """
+ Validates type 'date'. Checks to ensure that a value exists, a format
+ exists, and that the format is semi-valid. True validity of format is
+ checked when values are given in the crawling step.
+ """
+ if set(conf.templateKeys["loading"]["data"]["date"]["required"]) <= set(self.data["data"][key].keys()):
+
+ for subkey in self.data["data"][key]:
+ if subkey not in conf.templateKeys["loading"]["data"]["date"]["required"] and subkey not in conf.templateKeys["loading"]["data"]["date"]["optional"]:
+ self.err += "Loader, Data Date Error: Invalid key '%s' specified for data key '%s'. \n" % (subkey, key)
+
+ if not set(self.data["data"][key]["format"]) <= set(conf.dateFormat + conf.dateSep):
+ self.err += "Loader, Data Date Error: Invalid values in data key '%s', format only supports '%s'. \n" % (key, conf.dateFormat + conf.dateSep)
+
+ m = re.findall(r"%(\w+)%", self.data["data"][key]["value"])
+ for val in m:
+ if "%" + val + "%" not in self.data["path"]:
+ self.err += "Loader, Data Value Reference Error: Could not reference identifier '%s' for data key '%s'. \n" % (val, key)
+ else:
+ self.err += "Loader, Data Date Error: Data key '%s' does not have all required keys '%s'. \n" % (key, conf.templateKeys["loading"]["data"]["date"]["required"])
+ return
+
+ def _validateTranslations(self):
+ """
+ Nothing to see here, move along.
+ """
+ for key in self.data["translations"]:
+ if key not in self.data["data"]:
+ self.err += "Loader, Translation Error: Translation defined for '%s', however, no such data value exists. \n" % (key,)
+ return
+
+ def _validateOrder(self):
+ """
+ Validates the order -- the order you want to write values to the csv.
+ Checks existence of a value, as well as ensuring all values specified
+ have corresponding data values.
+ """
+ if self.data["order"]:
+ if not set(self.data["order"]) == set(self.data["data"].keys() + ["path"]):
+ self.err += "Loader, Order Error: Order must contain ALL data keys AND 'path'. \n"
+ else:
+ self.err += "Loader, Order Error: No value specified for order. \n"
+ return
+
diff --git a/build/lib/ih/workflow.py b/build/lib/ih/workflow.py
new file mode 100644
index 0000000000000000000000000000000000000000..f1515feab9a590974b784183d2937c6574641e26
--- /dev/null
+++ b/build/lib/ih/workflow.py
@@ -0,0 +1,1032 @@
+"""
+This file is part of Image Harvest.
+
+Image Harvest is free software: you can redistribute it and/or modify
+it under the terms of the GNU General Public License as published by
+the Free Software Foundation, either version 3 of the License, or
+(at your option) any later version.
+
+Image Harvest is distributed in the hope that it will be useful,
+but WITHOUT ANY WARRANTY; without even the implied warranty of
+MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+GNU General Public License for more details.
+
+You should have received a copy of the GNU General Public License
+along with Image Harvest. If not, see <http://www.gnu.org/licenses/>.
+"""
+
+import os
+import conf
+import sys
+import json
+import re
+import csv
+import datetime
+import sqlite3
+import shutil
+import errno
+import textwrap
+import copy
+import ih.validator
+import xml.dom.minidom
+from Pegasus.DAX3 import *
+
+
+class Workflow(object):
+
+ """
+ Generic workflow creation class.
+ """
+
+ def __init__(self, jobhome, basename = None):
+ """
+ :param jobhome: The base directory for job submission.
+ :type jobhome: str
+
+ Creates a Workflow class based on the input directory. Only loads and
+ validates the config file by default.
+ """
+ self.err = ""
+ self.jobhome = os.path.abspath(jobhome)
+ self.jobname = os.path.basename(os.path.dirname(self.jobhome + "/"))
+ self.basename = basename
+ self.dax = ADAG(self.jobname)
+ self.executables = {}
+ self.files = {self.dax: {}}
+ self.jobs = {self.dax: {}}
+ self.deps = {}
+ return
+
+ def _loadInputFiles(self):
+ """
+ Loads the input files into the appropriate variables
+ This should be overloaded.
+ """
+ return
+
+ def _isFile(self, name, dax, imtype, inout):
+ """
+ Convenience function to check if a given file exists.
+ """
+ if name in self.files[dax][imtype][inout]:
+ return True
+ return False
+
+ def _isJob(self, name, dax):
+ """
+ Convenience function to check if a given job exists.
+ """
+ if name in self.jobs[dax]:
+ return True
+ return False
+
+ def _isExecutable(self, name):
+ """
+ Convenience function to check if a given executable exists.
+ """
+ if name in self.executables:
+ return True
+ return False
+
+ def _createSetup(self):
+ """
+ Creates the base structure for job submission. Everything is contained
+ within a folder based on the current timestamp.
+ """
+ self.basepath = self.jobhome + "/" + self.basename if self.basename else self.jobhome + "/" + datetime.datetime.now().strftime("%Y-%m-%d_%H%M%S")
+ if not os.path.exists(self.basepath):
+ os.makedirs(self.basepath)
+ if not os.path.exists(self.basepath + "/input"):
+ os.makedirs(self.basepath + "/input")
+ if not os.path.exists(self.basepath + "/output"):
+ os.makedirs(self.basepath + "/output")
+ if not os.path.exists(self.basepath + "input/templates"):
+ os.makedirs(self.basepath + "/input/templates")
+ if not os.path.exists(self.basepath + "/input/rawfiles"):
+ os.makedirs(self.basepath + "/input/rawfiles")
+ return
+
+ def _addFile(self, name, imtype, inout, path = None, dax = None):
+ """
+ Adds the inputted file to the dax, as well as the internal variable self.files
+ """
+ dax = dax if dax else self.dax
+ if not self._isFile(name, dax, imtype, inout):
+ self.files[dax][imtype][inout][name] = {"file": File(name), "path": ""}
+ if inout == "input":
+ self.files[dax][imtype][inout][name]["path"] = path if path else name
+ self.files[dax][imtype][inout][name]["file"].addPFN(PFN("file://" + path.replace(" ","%20"), "local"))
+ dax.addFile(self.files[dax][imtype][inout][name]["file"])
+ return
+
+ def _addJob(self, jobname, executable, inputs, outputs, arguments, dependencies = None, dax = None, label = None, walltime = None):
+ dax = dax if dax else self.dax
+ if not self._isJob(jobname, dax):
+ self.jobs[dax][jobname] = Job(executable)
+ dax.addJob(self.jobs[dax][jobname])
+ for key in inputs:
+ self.jobs[dax][jobname].uses(inputs[key]["file"], link = Link.INPUT)
+ for key in outputs:
+ self.jobs[dax][jobname].uses(outputs[key]["file"], link = Link.OUTPUT, transfer = outputs[key]["transfer"])
+ arglist = []
+ for arg in arguments:
+ arglist.append(arg)
+ if str(arguments[arg]) in inputs:
+ arglist.append(inputs[str(arguments[arg])]["file"])
+ elif str(arguments[arg]) in outputs:
+ arglist.append(outputs[str(arguments[arg])]["file"])
+ else:
+ arglist.append(str(arguments[arg]))
+ self.jobs[dax][jobname].addArguments(*arglist)
+ if dependencies:
+ for depend in dependencies:
+ dax.depends(child = self.jobs[dax][jobname], parent = self.jobs[dax][depend])
+ if label:
+ self.jobs[dax][jobname].profile(Namespace.PEGASUS, "label", label)
+ if walltime:
+ self.jobs[dax][jobname].profile(Namespace.GLOBUS, "maxwalltime", walltime)
+ return
+
+ def create(self):
+ """
+ Creates a new pegasus submission directory based on the current timestamp,
+ and populates it with all required information to submit a pegasus job.
+ This function should be overloaded.
+ """
+ return
+
+
+class Statistics(Workflow):
+
+ """
+ A class specifically for statistics workflow
+ validation and submission.
+ """
+
+ def __init__(self, jobhome, basename, validOnly = False):
+ super(Statistics, self).__init__(jobhome, basename)
+ self.configfile = jobhome + "/input/" + conf.configFile
+ self.statsfile = jobhome + "/input/" + conf.statsFile
+ self.dbfile = jobhome + "/" + basename + "/output/" + conf.outputdb
+ self.validOnly = validOnly
+ self.rawFiles = {}
+ self._loadInputFiles()
+ return
+
+ def _getImageTypes(self):
+ return [x[0] for x in self.db.execute("select distinct imtype from images")]
+
+
+ def _loadInputFiles(self):
+ self.validator = ih.validator.Statistics(self.statsfile, self.configfile, self.dbfile)
+ if not self.validator.isValid() or self.validOnly:
+ self.validator.printErrors()
+ sys.exit()
+ else:
+ self.stats = self.validator.workflow.data
+ self.db = self.validator.db.conn
+ self.config = self.validator.config.data
+ self.rawFiles = self.validator.workflow.rawFiles
+ return
+
+ def _copyFiles(self):
+ """
+ Copies all input files to the correct location.
+ """
+ if not os.path.exists(self.basepath + "/input/stats"):
+ os.makedirs(self.basepath + "/input/stats")
+ shutil.copyfile(self.statsfile, self.basepath + "/input/templates/" + os.path.basename(self.statsfile))
+ return
+
+ def _loadFiles(self, loc):
+ """
+ Loads all files (input and output) into the dax and the self.files variable
+ """
+ self.files[self.dax] = {}
+ self.files[self.dax]["raw"] = {"input": {}, "output": {}}
+ self._addFile("output.db", "raw", "input", self.basepath + "/output/output.db")
+ for type in self.stats["workflows"]:
+ self.files[self.dax][type] = {"input": {}, "output": {}}
+ for f in self.rawFiles[type]:
+ shutil.copyfile(f, self.basepath + "/input/rawfiles/" + os.path.basename(f))
+ self._addFile(os.path.basename(f), type, "input", self.basepath + "/input/rawfiles/" + os.path.basename(f))
+ return
+
+ def _loadExecutables(self, os="linux", arch="x86_64"):
+ """
+ Loads all executables (as specified in the conf) into
+ the dax, as well as the internal self.executables variable
+ """
+ for ex in conf.valid:
+ self.executables[ex] = Executable(name=ex, os=os, arch=arch)
+ self.executables[ex].addPFN(PFN("file://" + self.config["installdir"] + "/" + ex, "local"))
+ #if "cluster" in self.config:
+ # self.executables[ex].addProfile(Profile(Namespace.PEGASUS, "clusters.size", self.config["cluster"]))
+ self.dax.addExecutable(self.executables[ex])
+ return
+
+ def _loadNotify(self):
+ if "notify" in self.config:
+ self.dax.invoke(When.AT_END, self.basepath + "/input/stats/notify.sh")
+ with open(self.basepath + "/input/stats/notify.sh", "w") as wh:
+ notify = textwrap.dedent("""\
+ #!/bin/bash
+ %s/email -t %s --report=pegasus-analyzer
+ """ % (self.config["notify"]["pegasus_home"], self.config["notify"]["email"]))
+ wh.write(notify)
+ os.chmod(self.basepath + "/input/stats/notify.sh", 0755)
+ return
+
+ def _loadJobInputs(self, job, type, basename, extension, save = False):
+ inputs = {}
+ for i,input in enumerate(job["inputs"]):
+ ftype = conf.valid[job["executable"]]["inputs"][i]
+ if input in self.rawFiles[type]:
+ inputs[input] = {"file": os.path.basename(input), "transfer": save}
+ else:
+ ex = extension if job["name"] == self.workflow["workflows"][type][0]["name"] else conf.fileExtensions[ftype]
+ inputs[input] = {"file": basename + "_" + input + ex, "transfer": save}
+ return inputs
+
+ def _loadJobInputs(self, job, type, save = False):
+ inputs = {"output.db": {"file": "output.db", "transfer": True}}
+ for i,input in enumerate(job["inputs"]):
+ ftype = conf.valid[job["executable"]]["inputs"][i]
+ if input in self.rawFiles[type]:
+ inputs[input] = {"file": os.path.basename(input), "transfer": save}
+ return inputs
+
+ def _createDax(self, loc):
+ """
+ Loads all jobs into the dax, and then writes the dax
+ to input/loc/stats.dax
+ """
+ serial = []
+ if "maxwalltime" in self.config:
+ if "stats" in self.config["maxwalltime"]:
+ maxwalltime = self.config["maxwalltime"]["stats"]
+ else:
+ maxwalltime = None
+ else:
+ maxwalltime = None
+ for type in self.stats["workflows"]:
+ for job in self.stats["workflows"][type]:
+ jobname = type + "_" + job["name"]
+ job["arguments"]["--intable"] = type + "_" + job["arguments"]["--intable"] if job["arguments"]["--intable"] != "images" else job["arguments"]["--intable"]
+ job["arguments"]["--outtable"] = type + "_" + job["arguments"]["--outtable"]
+ job["arguments"]["--db"] = "output.db"
+ inputs = self._loadJobInputs(job, type)
+ outputs = {}
+ depends = [type + "_" + depend for depend in job["depends"]] if "depends" in job else serial
+ if self.stats["workflows"][type].index(job) == len(self.stats["workflows"][type]) - 1:
+ serial = [jobname]
+ else:
+ serial = []
+ self._addJob(jobname, job["executable"], inputs, outputs, job["arguments"], depends, walltime = maxwalltime)
+ with open(self.basepath + "/" + loc + "/stats.dax", "w") as wh:
+ self.dax.writeXML(wh)
+ return
+
+ def _createReplica(self, loc):
+ """
+ Creates the pegasus configuration replica catalog. input/conf.rc
+ """
+ with open(self.basepath + "/" + loc + "/conf.rc", "w") as wh:
+ pegasusrc = textwrap.dedent("""\
+ pegasus.catalog.site = XML
+ pegasus.catalog.site.file = %s/sites.xml
+
+ pegasus.condor.logs.symlink = false
+
+ pegasus.transfer.links = true
+
+ pegasus.data.configuration = sharedfs
+
+ """ % (self.basepath + "/" + loc))
+ wh.write(pegasusrc)
+ return
+
+ def _createSites(self, loc):
+ """
+ Creates the pegasus site catalog. input/sites.xml
+ """
+ with open(self.basepath + "/" + loc + "/sites.xml", "w") as wh:
+ sites = """\
+ <sitecatalog xmlns="http://pegasus.isi.edu/schema/sitecatalog" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://pegasus.isi.edu/schema/sitecatalog http://pegasus.isi.edu/schema/sc-4.0.xsd" version="4.0">
+
+ <site handle="local" arch="x86_64" os="LINUX">
+ <directory type="shared-scratch" path="%s">
+ <file-server operation="all" url="file://%s" />
+ </directory>
+ <directory type="local-storage" path="%s">
+ <file-server operation="all" url="file://%s" />
+ </directory>
+ """ % (self.basepath + "/work/stats/", self.basepath + "/work/stats/", self.basepath + "/output/", self.basepath + "/output/")
+ for namespace in self.config["profile"]:
+ for key in self.config["profile"][namespace]:
+ val = ":".join(self.config["profile"][namespace][key]) if "path" in key.lower() else self.config["profile"][namespace][key]
+ sites += """\n\t<profile namespace="%s" key="%s">%s</profile> """ % (namespace, key, val)
+ sites += "</site></sitecatalog>"
+ sites = sites.replace("\n","")
+ wh.write("\n".join([line for line in xml.dom.minidom.parseString(sites).toprettyxml().split('\n') if line.strip()]))
+ return
+
+ def _createSubmit(self, loc):
+ """
+ Creates the pegasus submit script. submit.sh
+ """
+ with open(self.basepath + "/" + loc + "/submit.sh", "w") as wh:
+ submit = textwrap.dedent("""\
+ #!/bin/bash
+
+ plan=`pegasus-plan \\
+ --conf "%s" \\
+ --sites local \\
+ --dir "%s" \\
+ --output-site local \\
+ --dax "%s" \\
+ --randomdir \\""" % (self.basepath + "/" + loc + "/conf.rc", self.basepath + "/work/stats", self.basepath + "/" + loc + "/stats.dax"))
+ if "cluster" in self.config:
+ submit += """--cluster horizontal \\\n"""
+ submit += textwrap.dedent("""\
+ --submit`
+
+ status=`echo "$plan" | grep pegasus-status | tr -s ' '| cut -d ' ' -f 6`
+ echo -e "#!/bin/bash
+ pegasus-status -l $status" > status.sh
+ chmod 744 status.sh
+
+ remove=`echo "$plan" | grep pegasus-remove | tr -s ' '| cut -d ' ' -f 5`
+ echo -e "#!/bin/bash
+ pegasus-remove $remove" > remove.sh
+ chmod 744 remove.sh
+
+ echo "$plan"
+ echo "Alternatively, you can use the status & remove scripts in the current directory!"
+
+ """)
+ wh.write(submit)
+ os.chmod(self.basepath + "/" + loc + "/submit.sh", 0755)
+ return
+
+ def create(self):
+ """
+ Creates a new pegasus submission directory based on the current timestamp,
+ and populates it with all required information to submit a pegasus job.
+ """
+ loc = "/input/stats/"
+ self._createSetup()
+ self._copyFiles()
+ self._loadFiles(loc)
+ self._loadExecutables()
+ self._loadNotify()
+ self._createDax(loc)
+ self._createReplica(loc)
+ self._createSites(loc)
+ self._createSubmit(loc)
+ return
+
+
+
+
+
+class ImageProcessor(Workflow):
+
+ """
+ A class specifically for image processing workflow
+ validation and submission.
+ """
+
+ def __init__(self, jobhome, basename = None, validOnly = False):
+ """
+ :param jobhome: The base directory for job submission.
+ :type jobhome: str
+
+ Creates a Workflow class based on the input directory. Loads and validates all input files,
+ and quits out if something doesn't exist or is defined innapropriately.
+ """
+ super(ImageProcessor, self).__init__(jobhome, basename)
+ self.validOnly = validOnly
+ self.workfile = jobhome + "/input/" + conf.workflowFile
+ self.metafile = jobhome + "/input/" + conf.dbFile
+ self.configfile = jobhome + "/input/" + conf.configFile
+ self._loadInputFiles()
+ self.exdax = ADAG("extract-" + self.jobname)
+ self.jobs[self.exdax] = {}
+ self.files[self.exdax] = {}
+ return
+
+ def _loadInputFiles(self):
+ """
+ Loads the input files into the appropriate variables
+ """
+ self.validator = ih.validator.ImageProcessor(self.workfile, self.configfile, self.metafile)
+ if not self.validator.isValid() or self.validOnly:
+ self.validator.printErrors()
+ sys.exit()
+ else:
+ self.workflow = self.validator.workflow.data
+ self.metadata = self.validator.db.conn
+ self.config = self.validator.config.data
+ self.rawFiles = self.validator.workflow.rawFiles
+ return
+
+ def _getImageTypes(self):
+ """
+ Convenience function to get all image types from the database.
+ """
+ return [x[0] for x in self.metadata.execute("select distinct imtype from images")]
+
+ def _copyFiles(self):
+ """
+ Copies all input files to the correct location.
+ """
+ if not os.path.exists(self.basepath + "/input/imgproc"):
+ os.makedirs(self.basepath + "/input/imgproc")
+ shutil.copyfile(self.workfile, self.basepath + "/input/templates/" + os.path.basename(self.workfile))
+ shutil.copyfile(self.configfile, self.basepath + "/input/templates/" + os.path.basename(self.configfile))
+ shutil.copyfile(self.metafile, self.basepath + "/output/output.db")
+ for type in self.rawFiles:
+ for input in self.rawFiles[type]:
+ shutil.copyfile(input, self.basepath + "/input/rawfiles/" + os.path.basename(input))
+ return
+
+ def _loadFiles(self, loc):
+ """
+ Loads all files (input and output) into the dax and the self.files variable
+ """
+ with open(self.basepath + "/input/rawfiles/extract.json", "w") as wh:
+ json.dump(self.workflow["extract"], wh)
+ with open(self.basepath + "/" + loc + "/map.rc", "w") as wh:
+ self.exInput = {"db": "img.db", "extract.json": "extract.json"}
+ self.files[self.dax] = {}
+ self.files[self.exdax] = {}
+ self.files[self.exdax]["all"] = {"input": {}, "output": {}}
+ self.files[self.dax]["raw"] = {"input": {}, "output": {}}
+ self._addFile("img.db", "raw", "input", self.basepath + "/output/output.db")
+ self._addFile("img.db", "all", "input", self.basepath + "/output/output.db", dax = self.exdax)
+ self._addFile("img.log", "raw", "output", self.basepath + "/output/imgproc.log")
+ self._addFile("extract.json", "raw", "input", self.basepath + "/input/rawfiles/extract.json")
+ self._addFile("extract.json", "all", "input", self.basepath + "/input/rawfiles/extract.json", dax = self.exdax)
+ for type in self.workflow["workflows"]:
+ self.files[self.dax][type] = {"input": {}, "output": {}}
+ for input in self.rawFiles[type]:
+ self._addFile(os.path.basename(input), type, "input", self.basepath + "/input/rawfiles/" + os.path.basename(input))
+ wh.write("img.log file://" + self.basepath + "/output/imgproc.log pool=\"local\"\n")
+ inputImages = [self.workflow["workflows"][type][0]["inputs"][i] for i,x in enumerate(conf.valid[self.workflow["workflows"][type][0]["executable"]]["inputs"]) if x == "image"]
+ outputImages = [self.workflow["workflows"][type][z]["outputs"][i] for z in range(0, len(self.workflow["workflows"][type])) for i,x in enumerate(conf.valid[self.workflow["workflows"][type][z]["executable"]]["outputs"]) if x == "image"]
+ outputFiles = dict((self.workflow["workflows"][type][z]["outputs"][i], conf.fileExtensions[conf.valid[self.workflow["workflows"][type][z]["executable"]]["outputs"][i]]) for z in range(0, len(self.workflow["workflows"][type])) for i,x in enumerate(conf.valid[self.workflow["workflows"][type][z]["executable"]]["outputs"]) if x != "image" and x != "none" and len(self.workflow["workflows"][type][z]["outputs"]) > i)
+ for row in self.metadata.execute("select pegasusid, experiment, id, date, imgname, path from images where imtype=?", (type,)):
+ realname = row["path"].split("/")[-1].split(".")[0]
+ #derivedPath = row["experiment"].replace(" ","%20") + "/" + row["id"].replace(" ","%20") + "/" + row["date"].replace(" ","%20") + "/" + type + "/" + row["imgname"].replace(" ","%20") + "/"
+ derivedPath = row["experiment"].replace(" ","") + "/" + row["id"].replace(" ","") + "/" + row["date"].replace(" ","") + "/" + type + "/" + row["imgname"].replace(" ","") + "/"
+ for input in inputImages:
+ self._addFile(derivedPath + row["pegasusid"] + "_" + input + "." + row["path"].split(".")[1], type, "input", row["path"])
+ for output in outputImages:
+ if output in self.workflow["extract"]["workflows"][type]["inputs"]:
+ self.exInput[derivedPath + row["pegasusid"] + "_" + output + ".png"] = derivedPath + row["pegasusid"] + "_" + output + ".png"
+ self._addFile(derivedPath + row["pegasusid"] + "_" + output + ".png", "all", "input", self.basepath + "/output/" + derivedPath + row["pegasusid"] + "_" + output + ".png", dax = self.exdax)
+ self._addFile(derivedPath + row["pegasusid"] + "_" + output + ".png", type, "output")
+ wh.write(derivedPath + row["pegasusid"] + "_" + output + ".png file://" + self.basepath + "/output/" + derivedPath + row["pegasusid"].replace(" ","%20") + "_" + output + ".png pool=\"local\"\n")
+ for output in outputFiles:
+ outname = output + outputFiles[output]
+ self._addFile(derivedPath + row["pegasusid"] + "_" + outname, type, "output")
+ wh.write(derivedPath + row["pegasusid"] + "_" + outname + " file://" + self.basepath + "/output/" + derivedPath.replace("_","%20") + outname + " pool=\"local\"\n")
+ return
+
+ def _loadNotify(self):
+ if "notify" in self.config:
+ self.dax.invoke(When.AT_END, self.basepath + "/input/imgproc/notify.sh")
+ self.exdax.invoke(When.AT_END, self.basepath + "/input/imgproc/notify.sh")
+ with open(self.basepath + "/input/imgproc/notify.sh", "w") as wh:
+ notify = textwrap.dedent("""\
+ #!/bin/bash
+ %s/email -t %s --report=pegasus-analyzer
+ """ % (self.config["notify"]["pegasus_home"], self.config["notify"]["email"]))
+ wh.write(notify)
+ os.chmod(self.basepath + "/input/imgproc/notify.sh", 0755)
+ return
+
+ def _loadExecutables(self, os="linux", arch="x86_64"):
+ """
+ Loads all executables (as specified in the conf) into
+ the dax, as well as the internal self.executables variable
+ """
+ for ex in conf.valid:
+ self.executables[ex] = Executable(name=ex, os=os, arch=arch)
+ self.executables[ex].addPFN(PFN("file://" + self.config["installdir"] + "/" + ex, "local"))
+ #if "cluster" in self.config:
+ # val = int(self.config["cluster"] * conf.valid[ex]["weight"]) if "weight" in conf.valid[ex] else self.config["cluster"]
+ # self.executables[ex].addProfile(Profile(Namespace.PEGASUS, "clusters.size", val))
+ self.dax.addExecutable(self.executables[ex])
+ self.exdax.addExecutable(self.executables[ex])
+ return
+
+ def _loadJobInputs(self, job, type, basename, extension, save = False):
+ inputs = {}
+ for i,input in enumerate(job["inputs"]):
+ ftype = conf.valid[job["executable"]]["inputs"][i]
+ if input in self.rawFiles[type]:
+ inputs[input] = {"file": os.path.basename(input), "transfer": save}
+ else:
+ ex = extension if job["name"] == self.workflow["workflows"][type][0]["name"] else conf.fileExtensions[ftype]
+ inputs[input] = {"file": basename + "_" + input + ex, "transfer": save}
+ return inputs
+
+ def _loadJobOutputs(self, job, type, basename, save):
+ outputs = {}
+ for i,output in enumerate(job["outputs"]):
+ if output != "none":
+ outputs[output] = {"file": basename + "_" + output + conf.fileExtensions[conf.valid[job["executable"]]["outputs"][i]], "transfer": save}
+ return outputs
+
+ #def _loadJobOutputs(self, job, type, basename):
+ # return dict((output, basename + "_" + output + conf.fileExtensions[conf.valid[job["executable"]]["outputs"][i]]) for i,output in enumerate(job["outputs"]) if output != "none")
+
+ def _createDax(self, loc):
+ """
+ Loads all jobs into the dax, and then writes the dax
+ to input/workflow.dax
+ """
+ exDep = {}
+ exInput = {}
+ clusternum = {}
+ meancluster = {}
+
+ if "maxwalltime" in self.config:
+ if "images" in self.config["maxwalltime"]:
+ maxwalltime = self.config["maxwalltime"]["images"]
+ else:
+ maxwalltime = None
+ else:
+ maxwalltime = None
+
+ save = True if "save-steps" in self.workflow["options"] else False
+ for type in self.workflow["workflows"]:
+ exDep[type] = [[]]
+ exInput[type] = [{}]
+ jobnum = -1
+ clusternum[type] = 0
+ meancluster[type] = 0
+ exNames = self.workflow["extract"]["workflows"][type]["depends"]
+ for infile in [x for x in self.files[self.dax][type]["input"] if "." + x.split(".")[1] in conf.imageExtensions]:
+ if "cluster" in self.config:
+ jobnum += 1
+ if jobnum == self.config["cluster"]:
+ jobnum = 0
+ clusternum[type] += 1
+ exDep[type].append([])
+ exInput[type].append({})
+ elif ((clusternum[type] * 100 + jobnum) % int(self.config["cluster"] * 0.3)) == 0:
+ meancluster[type] += 1
+ extension = "." + infile.split(".")[1]
+ derivedPath = infile.split("_")[0]
+ realname = self.files[self.dax][type]["input"][infile]["path"].split("/")[-1].split(".")[0]
+ for stepnum,job in enumerate(self.workflow["workflows"][type]):
+ jobname = derivedPath + "_" + job["name"]
+ inputs = self._loadJobInputs(job, type, derivedPath, extension)
+ if job["name"] in exNames:
+ outputs = self._loadJobOutputs(job, type, derivedPath, True)
+ exDep[type][clusternum[type]].append(jobname)
+ reqFile = derivedPath + "_" + self.workflow["extract"]["workflows"][type]["inputs"][0] + ".png"
+ exInput[type][clusternum[type]][reqFile] = {"file": reqFile, "transfer": save}
+ else:
+ outputs = self._loadJobOutputs(job, type, derivedPath, save)
+ depends = [derivedPath + "_" + depend for depend in job["depends"]] if "depends" in job else []
+ if job["executable"] == "ih-meanshift":
+ self._addJob(jobname, job["executable"], inputs, outputs, job["arguments"], depends, label = type + "_step" + str(stepnum) + "_cluster" + str(meancluster[type]) if "cluster" in self.config else None, walltime = maxwalltime)
+ else:
+ self._addJob(jobname, job["executable"], inputs, outputs, job["arguments"], depends, label = type + "_step" + str(stepnum) + "_cluster" + str(clusternum[type]) if "cluster" in self.config else None, walltime = maxwalltime)
+
+
+ maprc = open(self.basepath + "/" + loc + "/map.rc", "a")
+ binDep = []
+ aggIn = {}
+ for type in self.workflow["workflows"]:
+ for q in range(0, clusternum[type] + 1):
+ arguments = self.workflow["extract"]["workflows"][type]["arguments"]
+ if "--input" in arguments:
+ del arguments["--input"]
+ if "histogram-bin" in self.workflow["extract"]:
+ if type in [imtype for key in self.workflow["extract"]["histogram-bin"]["--group"] for imtype in self.workflow["extract"]["histogram-bin"]["--group"][key]]:
+ arguments["--colors"] = ""
+ arguments["--db"] = "db"
+ arguments["--createdb"] = ""
+ arguments["--inputs"] = " ".join(exInput[type][q].keys())
+ self._addFile(type + str(q) + ".db", type, "output")
+ self._addJob(type + "_extract" + str(q), "ih-extract-multi", exInput[type][q], {"db": {"file": type + str(q) + ".db", "transfer": False}}, arguments, exDep[type][q])
+ self._addJob(type + "_extract" + str(q), "ih-extract-multi", exInput[type][q], {"db": {"file": type + str(q) + ".db", "transfer": False}}, arguments, [], dax = self.exdax)
+ maprc.write(type + str(q) + ".db" + " file://" + self.basepath + "/output/" + type + str(q) + ".db" + " pool=\"local\"\n")
+ binDep.append(type + "_extract" + str(q))
+ aggIn[type + str(q) + ".db"] = {"file": type + str(q) + ".db", "transfer": False}
+ aggIn["db"] = {"file": "img.db", "transfer": False}
+ self._addJob("sql_aggregate1", "ih-sql-aggregate", aggIn, {}, {"--db": "db", "--inputs": " ".join([aggIn[x]["file"] for x in aggIn if x != "db"])}, binDep)
+ self._addJob("sql_aggregate1", "ih-sql-aggregate", aggIn, {}, {"--db": "db", "--inputs": " ".join([aggIn[x]["file"] for x in aggIn if x != "db"])}, binDep, dax = self.exdax)
+
+ if "histogram-bin" in self.workflow["extract"]:
+ outputs = {}
+ for name in self.workflow["extract"]["histogram-bin"]["--group"]:
+ self._addFile(name + "_hist_bins.json", "raw", "output")
+ maprc.write(name + "_hist_bins.json" + " file://" + self.basepath + "/output/" + name + "_hist_bins.json" + " pool=\"local\"\n")
+ outputs[name + "_hist_bins.json"] = {"file": name + "_hist_bins.json", "transfer": True}
+ self._addJob("bin_creation", "ih-stats-histogram-bin", {"db": {"file": "img.db", "transfer": True}, "extract.json": {"file": "extract.json", "transfer": False}}, outputs, {"--db": "db", "--options": "extract.json", "--intable": "images", "--outtable": "histogramBins", "--jsonwrite": "", "--overwrite": ""}, ["sql_aggregate1"])
+ self._addJob("bin_creation", "ih-stats-histogram-bin", {"db": {"file": "img.db", "transfer": True}, "extract.json": {"file": "extract.json", "transfer": False}}, outputs, {"--db": "db", "--options": "extract.json", "--intable": "images", "--outtable": "histogramBins", "--jsonwrite": "", "--overwrite": ""}, ["sql_aggregate1"], dax = self.exdax)
+
+ binDep = []
+ map = {}
+
+ for group in self.workflow["extract"]["histogram-bin"]["--group"]:
+ for type in self.workflow["extract"]["histogram-bin"]["--group"][group]:
+ map[type] = group
+
+ for type in self.workflow["workflows"]:
+ for q in range(0, clusternum[type] + 1):
+ arguments = {}
+ arguments["--db"] = "db"
+ arguments["--inputs"] = " ".join(exInput[type][q].keys())
+ exInput[type][q]["db"] = {"file": type + str(q) + ".db", "transfer": False}
+ exInput[type][q]["binfile"] = {"file": map[type] + "_hist_bins.json", "transfer": False}
+ arguments["--bins"] = "binfile"
+ self._addJob(type + "_extractBins" + str(q), "ih-extract-multi", exInput[type][q], {}, arguments, ["bin_creation"])
+ self._addJob(type + "_extractBins" + str(q), "ih-extract-multi", exInput[type][q], {}, arguments, ["bin_creation"], dax = self.exdax)
+ binDep.append(type + "_extractBins" + str(q))
+ self._addJob("sql_aggregate2", "ih-sql-aggregate", aggIn, {}, {"--db": "db", "--inputs": " ".join([aggIn[x]["file"] for x in aggIn if x != "db"])}, binDep)
+ self._addJob("sql_aggregate2", "ih-sql-aggregate", aggIn, {}, {"--db": "db", "--inputs": " ".join([aggIn[x]["file"] for x in aggIn if x != "db"])}, binDep, dax = self.exdax)
+
+ z = 2 if "histogram-bin" in self.workflow["extract"] else 1
+ self._addJob("error-log", "ih-error-log", {"db": {"file": "img.db", "transfer": False}}, {"output": {"file": "img.log", "transfer": True}}, {"--db": "db", "--output": "output"}, ["sql_aggregate" + str(z)])
+ with open(self.basepath + "/" + loc + "/workflow.dax", "w") as wh:
+ self.dax.writeXML(wh)
+ return
+
+ def _createExtract(self, loc):
+ """
+ Creates the extraction step only dax!
+ """
+ #self._addJob("extractOnly", "ih-extract-all", self.exInput, {}, {"--db": "db", "--options": "extract.json"}, dax = self.exdax)
+ with open(self.basepath + "/" + loc + "/extract.dax", "w") as wh:
+ self.exdax.writeXML(wh)
+ return
+
+ def _createReplica(self, loc):
+ """
+ Creates the pegasus configuration replica catalog. input/conf.rc
+ """
+ with open(self.basepath + "/" + loc + "/conf.rc", "w") as wh:
+ pegasusrc = textwrap.dedent("""\
+ pegasus.catalog.site = XML
+ pegasus.catalog.site.file = %s/sites.xml
+
+ pegasus.condor.logs.symlink = false
+
+ pegasus.transfer.links = true
+
+ pegasus.data.configuration = sharedfs
+
+ pegasus.dir.storage.mapper = Replica
+ pegasus.dir.storage.mapper.replica = File
+ pegasus.dir.storage.mapper.replica.file = %s/map.rc
+ """ % (self.basepath + "/" + loc, self.basepath + "/" + loc))
+ wh.write(pegasusrc)
+ return
+
+ def _createSites(self, loc):
+ """
+ Creates the pegasus site catalog. input/sites.xml
+ """
+ with open(self.basepath + "/" + loc + "/sites.xml", "w") as wh:
+ sites = """\
+ <sitecatalog xmlns="http://pegasus.isi.edu/schema/sitecatalog" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://pegasus.isi.edu/schema/sitecatalog http://pegasus.isi.edu/schema/sc-4.0.xsd" version="4.0">
+
+ <site handle="local" arch="x86_64" os="LINUX">
+ <directory type="shared-scratch" path="%s">
+ <file-server operation="all" url="file://%s" />
+ </directory>
+ <directory type="local-storage" path="%s">
+ <file-server operation="all" url="file://%s" />
+ </directory>
+ """ % (self.basepath + "/work/imgproc/", self.basepath + "/work/imgproc/", self.basepath + "/output/", self.basepath + "/output/")
+ for namespace in self.config["profile"]:
+ for key in self.config["profile"][namespace]:
+ val = ":".join(self.config["profile"][namespace][key]) if "path" in key.lower() else self.config["profile"][namespace][key]
+ sites += """\n\t<profile namespace="%s" key="%s">%s</profile> """ % (namespace, key, val)
+ sites += "</site></sitecatalog>"
+ sites = sites.replace("\n","")
+ wh.write("\n".join([line for line in xml.dom.minidom.parseString(sites).toprettyxml().split('\n') if line.strip()]))
+ return
+
+ def _createSubmit(self, loc):
+ """
+ Creates the pegasus submit script. submit.sh
+ """
+ with open(self.basepath + "/" + loc + "/submit.sh", "w") as wh:
+ submit = textwrap.dedent("""\
+ #!/bin/bash
+ if [ "$1" = "--extract-only" ] || [ "$1" = "--extract" ] || [ "$1" = "-e" ]; then
+ DAX="%s"
+ else
+ DAX="%s"
+ fi
+ plan=`pegasus-plan \\
+ --conf "%s" \\
+ --sites local \\
+ --dir "%s" \\
+ --output-site local \\
+ --dax "$DAX" \\
+ --randomdir \\
+ """ % (self.basepath + "/" + loc + "/extract.dax", self.basepath + "/" + loc + "/workflow.dax", self.basepath + "/" + loc + "/conf.rc", self.basepath + "/work/imgproc"))
+ if "cluster" in self.config:
+ submit += """--cluster label \\\n"""
+ submit += textwrap.dedent("""\
+ --submit`
+
+ status=`echo "$plan" | grep pegasus-status | tr -s ' '| cut -d ' ' -f 6`
+ echo -e "#!/bin/bash
+ pegasus-status -l $status" > status.sh
+ chmod 744 status.sh
+
+ remove=`echo "$plan" | grep pegasus-remove | tr -s ' '| cut -d ' ' -f 5`
+ echo -e "#!/bin/bash
+ pegasus-remove $remove" > remove.sh
+ chmod 744 remove.sh
+
+ echo "$plan"
+ echo "Alternatively, you can use the status & remove scripts in the current directory!"
+
+ """)
+ wh.write(submit)
+ os.chmod(self.basepath + "/" + loc + "/submit.sh", 0755)
+ return
+
+ def create(self):
+ """
+ Creates a new pegasus submission directory based on the current timestamp,
+ and populates it with all required information to submit a pegasus job.
+ """
+ print "Generating workflow. Please wait."
+ loc = "/input/imgproc/"
+ self._createSetup()
+ self._copyFiles()
+ self._loadFiles(loc)
+ self._loadExecutables()
+ self._loadNotify()
+ self._createDax(loc)
+ self._createExtract(loc)
+ self._createReplica(loc)
+ self._createSites(loc)
+ self._createSubmit(loc)
+ return
+
+
+class ImageLoader:
+ """
+ This should handle all meta-data definitions
+ """
+
+ def __init__(self, template, output, validOnly = False, overwrite = False):
+ """
+ :param template: Path to input template file, should be valid json.
+ :type template: str
+ """
+ self.templatePath = os.path.abspath(template)
+ self.err = ""
+ self.output = output + "/input/"
+ try:
+ open(self.output + "/images.db")
+ except IOError:
+ self.err += "Path Error: Cannot open output db file. \n"
+ self.validator = ih.validator.ImageLoader(self.templatePath)
+ if not self.validator.isValid() or validOnly:
+ self.validator.printErrors()
+ sys.exit()
+ self.overwrite = overwrite
+ self.template = self.validator.data
+ self.template["order"].insert(0, "pegasusid")
+ self.count = {}
+ self.depth = len(self.template["path"].split("/")) - 1
+ self.structure = self._dictTemplate()
+ self.data = []
+ return
+
+ def _success(self):
+ if self.overwrite:
+ print "Directory re-crawled!"
+ print "Use ih-run to submit your jobs."
+ else:
+ print "Directory setup successful!"
+ print "Define the required templates in " + self.output + "."
+ print "Then use ih-run to submit your jobs."
+ return
+
+ def _dictTemplate(self):
+ """
+ Creates the first of two intermediary dictionaries for crawling. This relates
+ identifiers in the path, to a specified depth, as well as operators to split
+ the value at that depth.
+ """
+ m = [x for x in re.findall(r"%(\w+)%", self.template["path"]) if x != "null"]
+ sp = self.template["path"].split("/")
+ d = {}
+ for key in m:
+ d[key] = {}
+ d[key]["depth"] = [n for n,x in enumerate(sp) if key in x][0]
+ d[key]["split"] = []
+ val = sp[d[key]["depth"]]
+ for operator in [" ", "_", "-"]:
+ if operator in val:
+ b = val.split(operator)
+ x = [n for n,x in enumerate(b) if key in x][0]
+ d[key]["split"].append({"operator": operator, "index": x})
+ val = b[x]
+ return d
+
+ def _loadStructure(self, splitPath):
+ """
+ Creates the second of two intermediary dictionaries for crawling.
+ This utilizes the template created in _dictTemplate, and creates
+ a dictionary with actual values instead of structure.
+ """
+ d ={}
+ for key in self.structure:
+ val = splitPath[self.structure[key]["depth"]]
+ for operator in self.structure[key]["split"]:
+ val = val.split(operator["operator"])[operator["index"]]
+ d[key] = val
+ return d
+
+ def _loadDataFile(self, dict, structure, key):
+ """
+ Loads data from a data file. If the specified key isn't in the file,
+ write 'UNKNOWN' instead.
+ """
+ keyVal = self._convertReferences(structure, self.template["data"][key]["key"])
+ if keyVal in self.filedata[self.template["data"][key]["value"]]:
+ dict[key] = self.filedata[self.template["data"][key]["value"]][keyVal]
+ else:
+ dict[key] = "UNKNOWN"
+ return
+
+ def _loadDataValue(self, dict, structure, key):
+ """
+ Loads a data value.
+ """
+ val = self._convertReferences(structure, self.template["data"][key]["value"])
+ if "translate" in self.template["data"][key]:
+ if val in self.template["translations"][key]:
+ val = self.template["translations"][key][val]
+ dict[key] = val
+ return
+
+ def _loadDataDate(self, dict, structure, key):
+ """
+ Loads a date.
+ """
+ val = self._convertReferences(structure, self.template["data"][key]["value"])
+ format = "".join([x.replace(x, "%" + x) if x in conf.dateFormat else x for x in self.template["data"][key]["format"]])
+ val = datetime.datetime.strptime(val, format).strftime("%Y-%m-%d")
+ dict[key] = val
+ return
+
+ def _convertReferences(self, structure, val):
+ """
+ Replaces all references ('%%') to actual values.
+ """
+ idList = [x for x in re.findall(r"%(\w+)%", val) if x != "null"]
+ for identifier in idList:
+ if identifier in structure:
+ val = val.replace("%" + identifier + "%", structure[identifier])
+ return val
+
+ def _loadData(self, path):
+ """
+ Loads all data for a particular path.
+ """
+ temp = {}
+ final = {}
+ splitPath = path.split("/")
+ structure = self._loadStructure(splitPath)
+ for key in self.template["data"]:
+ d = {
+ "value": self._loadDataValue,
+ "file": self._loadDataFile,
+ "date": self._loadDataDate
+ }[self.template["data"][key]["type"]](final, structure, key)
+ final["path"] = path
+ if final["imtype"] not in self.count:
+ self.count[final["imtype"]] = 1
+ else:
+ self.count[final["imtype"]] += 1
+ final["pegasusid"] = final["imtype"] + str(self.count[final["imtype"]])
+ return final
+
+ def _loadFiles(self):
+ """
+ Reads all data from all specified files.
+ """
+ self.filedata = {}
+ for key in self.template["data"]:
+ if self.template["data"][key]["type"] == "file":
+ if self.template["data"][key]["value"] not in self.filedata:
+ self.filedata[self.template["data"][key]["value"]] = {}
+ with open(self.template["data"][key]["value"], "r") as rh:
+ for line in rh.readlines():
+ info = line.strip().split(",")
+ self.filedata[self.template["data"][key]["value"]][info[self.template["data"][key]["keyColumn"]]] = info[self.template["data"][key]["valueColumn"]]
+ return
+
+ def crawl(self):
+ """
+ Recursively walks through directories in base, and loads
+ the appropriate data.
+ """
+ self._loadFiles()
+ for root, dirs, files in os.walk(self.template["base"]):
+ arr = root.split("/")
+ depth = len(arr)
+ if (depth == self.depth):
+ for file in files:
+ if file[-len(self.template["filetype"]):] == self.template["filetype"] and file[0] != ".":
+ d = self._loadData(root + "/" + file)
+ self.data.append(d)
+ return
+
+ def write(self):
+ """
+ Writes the data loaded from crawl into csv format based on 'order'
+ """
+ if self.data:
+ conn = sqlite3.connect(self.output + "/images.db")
+ tablestr = "(pegasusid PRIMARY KEY"
+ for x in self.template["order"]:
+ if x != "pegasusid":
+ tablestr += "," + str(x)
+ tablestr += ")"
+ if self.overwrite:
+ conn.execute("DROP TABLE IF EXISTS images")
+ conn.commit()
+ conn.execute("CREATE TABLE images " + tablestr)
+ writedata = []
+ for row in self.data:
+ writedata.append(tuple([str(row[x]) for x in self.template["order"]]))
+ query = "insert into images " + str(tuple([str(x) for x in self.template["order"]])) + " values (" + ("?," * len(self.template["order"]))[:-1] + ")"
+ conn.executemany(query, writedata)
+ conn.commit()
+ if not self.overwrite:
+ shutil.copyfile(self.templatePath, self.output + "/crawl.json")
+ else:
+ print "Call crawl first!"
+ return
+
+class DirectorySetup:
+
+ def __init__(self, jobhome):
+ """
+ :param jobhome: The base directory to setup a job.
+ :type jobhome: str
+ """
+ if not os.path.isdir(os.path.dirname(os.path.dirname(os.path.abspath(jobhome) + "/"))):
+ print "Can't create job folder, path doesn't exist!"
+ sys.exit()
+ self.jobhome = jobhome
+ return
+
+ def _makeDir(self, dirpath):
+ """
+ Makes a directory if it doesn't exist. Catches and
+ prints out common errors.
+ """
+ try:
+ os.makedirs(dirpath)
+ except OSError as e:
+ raise Exception({
+ errno.EEXIST: "Directory " + dirpath + " already exists!",
+ errno.EACCES: "You don't have permission to create directory " + dirpath + ".",
+ }.get(e.errno, "Error for directory " + dirpath + " error:" + str(e)))
+ return
+
+ def _makeFile(self, filepath):
+ """
+ Opens a file to create it, uses append mode
+ so it doesn't overwrite any existing files.
+ """
+ try:
+ open(filepath, "a")
+ except OSError as e:
+ raise Exception({
+
+ }.get(e, "Unsepcified error for file " + filepath))
+ return
+
+ def setup(self):
+ """
+ Creates the directory structure needed to submit jobs,
+ and creates empty template files needed for job submission.
+ """
+ self._makeDir(self.jobhome)
+ self._makeDir(self.jobhome + "/input/")
+ for fname in conf.jobFiles:
+ self._makeFile(self.jobhome + "/input/" + fname)
+ return
+
+
+
diff --git a/build/scripts-2.7/htpia-adaptive-threshold b/build/scripts-2.7/htpia-adaptive-threshold
new file mode 100755
index 0000000000000000000000000000000000000000..dda57117670897bbd752f4c352c956c9aa135321
--- /dev/null
+++ b/build/scripts-2.7/htpia-adaptive-threshold
@@ -0,0 +1,22 @@
+#!/usr/bin/python
+import argparse
+import traceback
+import plantcv.imgproc
+
+parser = argparse.ArgumentParser(description = "Thresholds an image based on windows.")
+parser.add_argument("--input", dest="input", help="Path to input image.", required = True)
+parser.add_argument("--value", dest="value", type=int, help="Value to write to pixels. Usually 255 or 0.", required = True)
+parser.add_argument("--adaptiveType", dest="adaptiveType", help="Adaptive type to use. Either 'mean' or 'gaussian'.", required = True)
+parser.add_argument("--thresholdType", dest="thresholdType", help="Threshold type to use. Either 'binary' or 'inverse'.", required = True)
+parser.add_argument("--blockSize", dest="blockSize", type=int, help="Window size to consider. Should be an odd number.", required = True)
+parser.add_argument("--C", dest="C", type=int, help="Constant to subtract from window mean.", required = True)
+parser.add_argument("--outputdir", dest="outputdir", default=".", help="Path to write output files, if not specified use current directory.")
+parser.add_argument("--output", default=None, dest="output", help="Name of output image to write, if not specified, use input image name.")
+args = parser.parse_args()
+
+try:
+ plant = plantcv.imgproc.Image(args.input, args.outputdir, args.output, False)
+ plant.adaptiveThreshold(args.value, args.adaptiveType, args.thresholdType, args.blockSize, args.C)
+ plant.write()
+except Exception as e:
+ print traceback.format_exc()
\ No newline at end of file
diff --git a/build/scripts-2.7/htpia-bitwise-and b/build/scripts-2.7/htpia-bitwise-and
new file mode 100755
index 0000000000000000000000000000000000000000..f54e604f931ccfc9efe06b2ac22f9f39d85c10fc
--- /dev/null
+++ b/build/scripts-2.7/htpia-bitwise-and
@@ -0,0 +1,18 @@
+#!/usr/bin/python
+import argparse
+import traceback
+import plantcv.imgproc
+
+parser = argparse.ArgumentParser(description = "Converts an image between color spectrums.")
+parser.add_argument("--input1", dest="input1", help="Path to first input image.", required = True)
+parser.add_argument("--input2", dest="input2", help="Path to second input image.", required = True)
+parser.add_argument("--outputdir", dest="outputdir", default=".", help="Path to write output files, if not specified use current directory.")
+parser.add_argument("--output", default=None, dest="output", help="Name of output image to write, if not specified, use input image name.")
+args = parser.parse_args()
+
+try:
+ plant = plantcv.imgproc.Image(args.input1, args.outputdir, args.output, False)
+ plant.bitwise_and(args.input2)
+ plant.write()
+except Exception as e:
+ print traceback.format_exc()
\ No newline at end of file
diff --git a/build/scripts-2.7/htpia-bitwise-not b/build/scripts-2.7/htpia-bitwise-not
new file mode 100755
index 0000000000000000000000000000000000000000..c024a8d15338ae7d8deb25da43700ba1e5ccb829
--- /dev/null
+++ b/build/scripts-2.7/htpia-bitwise-not
@@ -0,0 +1,17 @@
+#!/usr/bin/python
+import argparse
+import traceback
+import plantcv.imgproc
+
+parser = argparse.ArgumentParser(description = "Converts an image between color spectrums.")
+parser.add_argument("--input", dest="input", help="Path to first input image.", required = True)
+parser.add_argument("--outputdir", dest="outputdir", default=".", help="Path to write output files, if not specified use current directory.")
+parser.add_argument("--output", default=None, dest="output", help="Name of output image to write, if not specified, use input image name.")
+args = parser.parse_args()
+
+try:
+ plant = plantcv.imgproc.Image(args.input, args.outputdir, args.output, False)
+ plant.bitwise_not()
+ plant.write()
+except Exception as e:
+ print traceback.format_exc()
\ No newline at end of file
diff --git a/build/scripts-2.7/htpia-bitwise-or b/build/scripts-2.7/htpia-bitwise-or
new file mode 100755
index 0000000000000000000000000000000000000000..786bbade7e37af69906c21dff2162390cb2a1414
--- /dev/null
+++ b/build/scripts-2.7/htpia-bitwise-or
@@ -0,0 +1,18 @@
+#!/usr/bin/python
+import argparse
+import traceback
+import plantcv.imgproc
+
+parser = argparse.ArgumentParser(description = "Converts an image between color spectrums.")
+parser.add_argument("--input1", dest="input1", help="Path to first input image.", required = True)
+parser.add_argument("--input2", dest="input2", help="Path to second input image.", required = True)
+parser.add_argument("--outputdir", dest="outputdir", default=".", help="Path to write output files, if not specified use current directory.")
+parser.add_argument("--output", default=None, dest="output", help="Name of output image to write, if not specified, use input image name.")
+args = parser.parse_args()
+
+try:
+ plant = plantcv.imgproc.Image(args.input1, args.outputdir, args.output, False)
+ plant.bitwise_or(args.input2)
+ plant.write()
+except Exception as e:
+ print traceback.format_exc()
\ No newline at end of file
diff --git a/build/scripts-2.7/htpia-bitwise-xor b/build/scripts-2.7/htpia-bitwise-xor
new file mode 100755
index 0000000000000000000000000000000000000000..e2d5523ed08e588e912a4f9f224cdac2b1fdd683
--- /dev/null
+++ b/build/scripts-2.7/htpia-bitwise-xor
@@ -0,0 +1,18 @@
+#!/usr/bin/python
+import argparse
+import traceback
+import plantcv.imgproc
+
+parser = argparse.ArgumentParser(description = "Converts an image between color spectrums.")
+parser.add_argument("--input1", dest="input1", help="Path to first input image.", required = True)
+parser.add_argument("--input2", dest="input2", help="Path to second input image.", required = True)
+parser.add_argument("--outputdir", dest="outputdir", default=".", help="Path to write output files, if not specified use current directory.")
+parser.add_argument("--output", default=None, dest="output", help="Name of output image to write, if not specified, use input image name.")
+args = parser.parse_args()
+
+try:
+ plant = plantcv.imgproc.Image(args.input1, args.outputdir, args.output, False)
+ plant.bitwise_xor(args.input2)
+ plant.write()
+except Exception as e:
+ print traceback.format_exc()
\ No newline at end of file
diff --git a/build/scripts-2.7/htpia-blur b/build/scripts-2.7/htpia-blur
new file mode 100755
index 0000000000000000000000000000000000000000..38666da83cfdf9599e9451d288ba92794f9e18c6
--- /dev/null
+++ b/build/scripts-2.7/htpia-blur
@@ -0,0 +1,22 @@
+#!/usr/bin/python
+import argparse
+import traceback
+import plantcv.imgproc
+
+parser = argparse.ArgumentParser(description = "Smoothes an image based on a evenly distributed kernel.")
+parser.add_argument("--input", dest="input", help="Path to input image.", required = True)
+parser.add_argument("--kwidth", dest="kwidth", type=int, help="Width of the kernel", required = True)
+parser.add_argument("--kheight", dest="kheight", type=int, help="Height of the kernel", required = True)
+parser.add_argument("--anchorx", default=-1, dest="anchorx", type=int, help="X position of the anchor")
+parser.add_argument("--anchory", default=-1, dest="anchory", type=int, help="Y position of the anchor")
+parser.add_argument("--border", default="default", dest="border", help="Border type for extrapolation.")
+parser.add_argument("--outputdir", dest="outputdir", default=".", help="Path to write output files, if not specified use current directory.")
+parser.add_argument("--output", default=None, dest="output", help="Name of output image to write, if not specified, use input image name.")
+args = parser.parse_args()
+
+try:
+ plant = plantcv.imgproc.Image(args.input, args.outputdir, args.output, False)
+ plant.blur((args.kwidth, args.kheight), (args.anchorx, args.anchory), args.border)
+ plant.write()
+except Exception as e:
+ print traceback.format_exc()
\ No newline at end of file
diff --git a/build/scripts-2.7/htpia-color-filter b/build/scripts-2.7/htpia-color-filter
new file mode 100755
index 0000000000000000000000000000000000000000..e2697db6eb968bce1f207401f0dedfbee589583a
--- /dev/null
+++ b/build/scripts-2.7/htpia-color-filter
@@ -0,0 +1,27 @@
+#!/usr/bin/python
+import argparse
+import traceback
+import plantcv.imgproc
+
+parser = argparse.ArgumentParser(description = "Smoothes an image based on a evenly distributed kernel.")
+parser.add_argument("--input", dest="input", help="Path to input image.", required = True)
+parser.add_argument("--logic", dest="logic", help="Logic string to compute.", required = True)
+parser.add_argument("--roi", dest="roi", help="roi file")
+parser.add_argument("--ystart", dest="ystart", default=-1, help="Minimum Y of the roi.")
+parser.add_argument("--yend", dest="yend", default=-1, help="Maximum Y of the roi.")
+parser.add_argument("--xstart", dest="xstart", default=-1, help="Minimum X of the roi.")
+parser.add_argument("--xend", dest="xend", default=-1, help="Maximum X of the roi.")
+parser.add_argument("--outputdir", dest="outputdir", default=".", help="Path to write output files, if not specified use current directory.")
+parser.add_argument("--output", default=None, dest="output", help="Name of output image to write, if not specified, use input image name.")
+
+args = parser.parse_args()
+
+try:
+ plant = plantcv.imgproc.Image(args.input, args.outputdir, args.output, False)
+ if args.roi:
+ plant.colorFilter(args.logic, args.roi)
+ else:
+ plant.colorFilter(args.logic, [args.ystart, args.yend, args.xstart, args.xend])
+ plant.write()
+except Exception as e:
+ print traceback.format_exc()
\ No newline at end of file
diff --git a/build/scripts-2.7/htpia-contour-cut b/build/scripts-2.7/htpia-contour-cut
new file mode 100755
index 0000000000000000000000000000000000000000..cb788ed3ac3365b4c977155437c2a22ceff27e41
--- /dev/null
+++ b/build/scripts-2.7/htpia-contour-cut
@@ -0,0 +1,26 @@
+#!/usr/bin/python
+import argparse
+import traceback
+import plantcv.imgproc
+
+parser = argparse.ArgumentParser(description = "Smoothes an image based on a evenly distributed kernel.")
+parser.add_argument("--input", dest="input", help="Path to input image.", required = True)
+parser.add_argument("--binary", dest="binary", help="Binary image to calculate contours from", required = True)
+parser.add_argument("--basemin", default=100, dest="basemin", type=int, help="Minimum area of contour required to keep in final image.")
+parser.add_argument("--padminx", default=0, dest="padminx", type=int, help="Padding added to left.")
+parser.add_argument("--padmaxx", default=0, dest="padmaxx", type=int, help="Padding added to right.")
+parser.add_argument("--padminy", default=0, dest="padminy", type=int, help="Padding added to top.")
+parser.add_argument("--padmaxy", default=0, dest="padmaxy", type=int, help="Padding added to bottom.")
+parser.add_argument("--resize", default=False, dest="resize", action="store_true", help="Whether or not to resize the actual image.")
+parser.add_argument("--returnBound", default=False, dest="returnBound", action="store_true", help="Whether or not to write the bound.")
+parser.add_argument("--roiwrite", default="roi.json", dest="roiwrite", help="The name of the roi file to write.")
+parser.add_argument("--outputdir", dest="outputdir", default=".", help="Path to write output files, if not specified use current directory.")
+parser.add_argument("--output", default=None, dest="output", help="Name of output image to write, if not specified, use input image name.")
+args = parser.parse_args()
+
+try:
+ plant = plantcv.imgproc.Image(args.input, args.outputdir, args.output, False)
+ plant.contourCut(args.binary, args.basemin, [args.padminy, args.padmaxy, args.padminx, args.padmaxx], args.resize, args.returnBound, args.roiwrite)
+ plant.write()
+except Exception as e:
+ print traceback.format_exc()
\ No newline at end of file
diff --git a/build/scripts-2.7/htpia-convert-color b/build/scripts-2.7/htpia-convert-color
new file mode 100755
index 0000000000000000000000000000000000000000..ed96f60005266fb240c83def21af0f258dec2833
--- /dev/null
+++ b/build/scripts-2.7/htpia-convert-color
@@ -0,0 +1,19 @@
+#!/usr/bin/python
+import argparse
+import traceback
+import plantcv.imgproc
+
+parser = argparse.ArgumentParser(description = "Converts an image between color spectrums.")
+parser.add_argument("--input", dest="input", help="Path to input image.", required = True)
+parser.add_argument("--intype", dest="intype", help="Type of input image, one of [bgr, gray, hsv, lab, ycrcb]", required = True)
+parser.add_argument("--outtype", dest="outtype", help="Type of output image, one of [bgr, gray, hsv, lab, ycrcb]", required = True)
+parser.add_argument("--outputdir", dest="outputdir", default=".", help="Path to write output files, if not specified use current directory.")
+parser.add_argument("--output", default=None, dest="output", help="Name of output image to write, if not specified, use input image name.")
+args = parser.parse_args()
+
+try:
+ plant = plantcv.imgproc.Image(args.input, args.outputdir, args.output, False)
+ plant.convertColor(args.intype, args.outtype)
+ plant.write()
+except Exception as e:
+ print traceback.format_exc()
\ No newline at end of file
diff --git a/build/scripts-2.7/htpia-crop b/build/scripts-2.7/htpia-crop
new file mode 100755
index 0000000000000000000000000000000000000000..4482f23eb35eddee51cbff2bd00faa642e4a0b88
--- /dev/null
+++ b/build/scripts-2.7/htpia-crop
@@ -0,0 +1,26 @@
+#!/usr/bin/python
+import argparse
+import traceback
+import plantcv.imgproc
+
+parser = argparse.ArgumentParser(description = "Smoothes an image based on a evenly distributed kernel.")
+parser.add_argument("--input", dest="input", help="Path to input image.", required = True)
+parser.add_argument("--roi", dest="roi", help="roi file")
+parser.add_argument("--ystart", dest="ystart", help="Minimum Y of the roi.")
+parser.add_argument("--yend", dest="yend", help="Maximum Y of the roi.")
+parser.add_argument("--xstart", dest="xstart", help="Minimum X of the roi.")
+parser.add_argument("--xend", dest="xend", help="Maximum X of the roi.")
+parser.add_argument("--resize", default=False, dest="resize", action="store_true", help="Whether or not to actually resize the image.")
+parser.add_argument("--outputdir", dest="outputdir", default=".", help="Path to write output files, if not specified use current directory.")
+parser.add_argument("--output", default=None, dest="output", help="Name of output image to write, if not specified, use input image name.")
+args = parser.parse_args()
+
+try:
+ plant = plantcv.imgproc.Image(args.input, args.outputdir, args.output, False)
+ if args.roi:
+ plant.crop(args.roi, args.resize)
+ else:
+ plant.crop([args.ystart, args.yend, args.xtart, args.xend], args.resize)
+ plant.write()
+except Exception as e:
+ print traceback.format_exc()
\ No newline at end of file
diff --git a/build/scripts-2.7/htpia-edges b/build/scripts-2.7/htpia-edges
new file mode 100755
index 0000000000000000000000000000000000000000..358ba76191fa89a7daab602eec03119e5436353d
--- /dev/null
+++ b/build/scripts-2.7/htpia-edges
@@ -0,0 +1,21 @@
+#!/usr/bin/python
+import argparse
+import traceback
+import plantcv.imgproc
+
+parser = argparse.ArgumentParser(description = "Smoothes an image based on a evenly distributed kernel.")
+parser.add_argument("--input", dest="input", help="Path to input image.", required = True)
+parser.add_argument("--threshold1", dest="threshold1", type=int, help="Minimum threshold value.", required = True)
+parser.add_argument("--threshold2", dest="threshold2", type=int, help="Maximum threshold value.", required = True)
+parser.add_argument("--apertureSize", default = 3, dest="apertureSize", type=int, help="Aperture size for Sobel algorithm.")
+parser.add_argument("--L2gradient", default = False, dest="L2gradient", action="store_true", help="Determines method to calculate gradient magnitutde.")
+parser.add_argument("--outputdir", dest="outputdir", default=".", help="Path to write output files, if not specified use current directory.")
+parser.add_argument("--output", default=None, dest="output", help="Name of output image to write, if not specified, use input image name.")
+args = parser.parse_args()
+
+try:
+ plant = plantcv.imgproc.Image(args.input, args.outputdir, args.output, False)
+ plant.edges(args.threshold1, args.threshold2, args.apertureSize, args.L2gradient)
+ plant.write()
+except Exception as e:
+ print traceback.format_exc()
\ No newline at end of file
diff --git a/build/scripts-2.7/htpia-error-log b/build/scripts-2.7/htpia-error-log
new file mode 100755
index 0000000000000000000000000000000000000000..d1bbc2c9eb65a2cbe23951e4dc781b039bc1c7c5
--- /dev/null
+++ b/build/scripts-2.7/htpia-error-log
@@ -0,0 +1,15 @@
+#!/usr/bin/python
+import argparse
+import traceback
+import plantcv.statistics
+
+parser = argparse.ArgumentParser(description = "Extracts numerical information from an image.")
+parser.add_argument("--db", dest="db", help="Path to database to write", required = True)
+parser.add_argument("--output", dest="output", help="Path to output log file.", required = True)
+args = parser.parse_args()
+
+try:
+ stats = plantcv.statistics.Stats(args.db)
+ stats.logErrors(args.output)
+except Exception as e:
+ print traceback.format_exc()
\ No newline at end of file
diff --git a/build/scripts-2.7/htpia-extract b/build/scripts-2.7/htpia-extract
new file mode 100755
index 0000000000000000000000000000000000000000..0dff2bd1fed5e9216f450e979c060a5efa8de211
--- /dev/null
+++ b/build/scripts-2.7/htpia-extract
@@ -0,0 +1,44 @@
+#!/usr/bin/python
+import argparse
+import traceback
+import plantcv.imgproc
+import os
+import sqlite3
+
+parser = argparse.ArgumentParser(description = "Extracts numerical information from an image.")
+parser.add_argument("--input", dest="input", help="Path to processed image.", required = True)
+parser.add_argument("--dbid", dest="dbid", help="Image Id, used for database writing", required = True)
+parser.add_argument("--db", dest="db", help="Path to database to write", required = True)
+parser.add_argument("--dimensions", dest="dimensions", default=False, action="store_true", help="Extract dimensions.")
+parser.add_argument("--pixels", dest="pixels", default=False, action="store_true", help="Extract pixels.")
+parser.add_argument("--colors", dest="colors", default=False, action="store_true", help="Extract color data.")
+parser.add_argument("--channels", dest="channels", default=False, action="store_true", help="Extract channel data.")
+parser.add_argument("--bins", dest="bins", default=None, help="Path to bin file.")
+parser.add_argument("--moments", dest="moments", default=False, action="store_true", help="Extract moment data.")
+args = parser.parse_args()
+
+try:
+ plant = plantcv.imgproc.Image(args.input, ".", db = args.db, dbid = args.dbid)
+
+ plant.extractFinalPath()
+
+ if args.dimensions:
+ plant.extractDimensions()
+
+ if args.pixels:
+ plant.extractPixels()
+
+ if args.moments:
+ plant.extractMoments()
+
+ if args.colors:
+ plant.extractColorData()
+
+ if args.channels:
+ plant.extractColorChannels()
+
+ if args.bins:
+ plant.extractBins(args.bins)
+
+except Exception as e:
+ print traceback.format_exc()
\ No newline at end of file
diff --git a/build/scripts-2.7/htpia-extract-all b/build/scripts-2.7/htpia-extract-all
new file mode 100755
index 0000000000000000000000000000000000000000..cd49d26cc753099c889c17c562efbbaae29c1ff3
--- /dev/null
+++ b/build/scripts-2.7/htpia-extract-all
@@ -0,0 +1,21 @@
+#!/usr/bin/python
+import argparse
+import traceback
+import plantcv.imgproc
+import plantcv.statistics
+import os
+import sqlite3
+import json
+
+parser = argparse.ArgumentParser(description = "Extracts numerical information from all images in a database.")
+parser.add_argument("--db", dest="db", help="Database to load processed images from.", required = True)
+parser.add_argument("--options", dest="options", help="Path to options json file.", required = True)
+args = parser.parse_args()
+
+try:
+ with open (args.options, "r") as rh:
+ options = json.load(rh)
+ stats = plantcv.statistics.Stats(args.db)
+ stats.extractAll(options)
+except Exception as e:
+ print traceback.format_exc()
\ No newline at end of file
diff --git a/build/scripts-2.7/htpia-extract-multi b/build/scripts-2.7/htpia-extract-multi
new file mode 100755
index 0000000000000000000000000000000000000000..b8e2e7cc61624c7057b2b4d29504a2b5bf402214
--- /dev/null
+++ b/build/scripts-2.7/htpia-extract-multi
@@ -0,0 +1,55 @@
+#!/usr/bin/python
+import argparse
+import traceback
+import plantcv.imgproc
+import os
+import sqlite3
+
+parser = argparse.ArgumentParser(description = "Extracts numerical information from multiple images.")
+parser.add_argument("--inputs", dest="inputs", nargs="+", help="Path to processed image.", required = True)
+parser.add_argument("--db", dest="db", help="Path to database to write", required = True)
+parser.add_argument("--createdb", dest="createdb", default=False, action="store_true", help = "Create database file specified by db")
+parser.add_argument("--dimensions", dest="dimensions", default=False, action="store_true", help="Extract dimensions.")
+parser.add_argument("--pixels", dest="pixels", default=False, action="store_true", help="Extract pixels.")
+parser.add_argument("--colors", dest="colors", default=False, action="store_true", help="Extract color data.")
+parser.add_argument("--channels", dest="channels", default=False, action="store_true", help="Extract channel data.")
+parser.add_argument("--bins", dest="bins", default=None, help="Path to bin file.")
+parser.add_argument("--moments", dest="moments", default=False, action="store_true", help="Extract moment data.")
+args = parser.parse_args()
+
+try:
+ if args.createdb:
+ conn = sqlite3.connect(args.db)
+ conn.execute("drop table if exists images")
+ conn.commit()
+ conn.execute("create table images (pegasusid PRIMARY KEY)")
+ conn.commit()
+ conn.executemany("insert into images (pegasusid) values (?)", [(os.path.basename(x).split("_")[0],) for x in args.inputs])
+ conn.commit()
+ conn.close()
+ for input in args.inputs:
+ dbid = "_".join(os.path.basename(input).split("_")[:-1])
+ plant = plantcv.imgproc.Image(input, ".", db = args.db, dbid = dbid)
+
+ plant.extractFinalPath()
+
+ if args.dimensions:
+ plant.extractDimensions()
+
+ if args.pixels:
+ plant.extractPixels()
+
+ if args.moments:
+ plant.extractMoments()
+
+ if args.colors:
+ plant.extractColorData()
+
+ if args.channels:
+ plant.extractColorChannels()
+
+ if args.bins:
+ plant.extractBins(args.bins)
+
+except Exception as e:
+ print traceback.format_exc()
\ No newline at end of file
diff --git a/build/scripts-2.7/htpia-gaussian-blur b/build/scripts-2.7/htpia-gaussian-blur
new file mode 100755
index 0000000000000000000000000000000000000000..911c53d6785d61dc19124fe1af581784f3c00e8e
--- /dev/null
+++ b/build/scripts-2.7/htpia-gaussian-blur
@@ -0,0 +1,22 @@
+#!/usr/bin/python
+import argparse
+import traceback
+import plantcv.imgproc
+
+parser = argparse.ArgumentParser(description = "Smooths an image based on a Gaussian kernel.")
+parser.add_argument("--input", dest="input", help="Path to input image.", required = True)
+parser.add_argument("--kwidth", dest="kwidth", type=int, help="Width of the kernel", required = True)
+parser.add_argument("--kheight", dest="kheight", type=int, help="Height of the kernel", required = True)
+parser.add_argument("--sigmax", default=0, dest="sigmax", type=int, help="Standard deviation in the x direction.")
+parser.add_argument("--sigmay", default=0, dest="sigmay", type=int, help="Standard deviation in the y direction.")
+parser.add_argument("--border", default="default", dest="border", help="Border type for extrapolation.")
+parser.add_argument("--outputdir", dest="outputdir", default=".", help="Path to write output files, if not specified use current directory.")
+parser.add_argument("--output", default=None, dest="output", help="Name of output image to write, if not specified, use input image name.")
+args = parser.parse_args()
+
+try:
+ plant = plantcv.imgproc.Image(args.input, args.outputdir, args.output, False)
+ plant.gaussianBlur((args.kwidth, args.kheight), args.sigmax, args.sigmay, args.border)
+ plant.write()
+except Exception as e:
+ print traceback.format_exc()
\ No newline at end of file
diff --git a/build/scripts-2.7/htpia-meanshift b/build/scripts-2.7/htpia-meanshift
new file mode 100755
index 0000000000000000000000000000000000000000..95a2a544aa157898c970f026658a7496499cd955
--- /dev/null
+++ b/build/scripts-2.7/htpia-meanshift
@@ -0,0 +1,20 @@
+#!/usr/bin/python
+import argparse
+import traceback
+import plantcv.imgproc
+
+parser = argparse.ArgumentParser(description = "Shifts colors in an image based on nearest neighbors.")
+parser.add_argument("--input", dest="input", help="Path to input image.", required = True)
+parser.add_argument("--spatial_radius", dest="spatial_radius", type=float, help="Spatial Radius.", required = True)
+parser.add_argument("--range_radius", dest="range_radius", type=float, help="Range Radius.", required = True)
+parser.add_argument("--min_density", dest="min_density", type=float, help="Minimum Density.", required = True)
+parser.add_argument("--outputdir", dest="outputdir", default=".", help="Path to write output files, if not specified use current directory.")
+parser.add_argument("--output", default=None, dest="output", help="Name of output image to write, if not specified, use input image name.")
+args = parser.parse_args()
+
+try:
+ plant = plantcv.imgproc.Image(args.input, args.outputdir, args.output, False)
+ plant.meanshift(args.spatial_radius, args.range_radius, args.min_density)
+ plant.write()
+except Exception as e:
+ print traceback.format_exc()
\ No newline at end of file
diff --git a/build/scripts-2.7/htpia-median-blur b/build/scripts-2.7/htpia-median-blur
new file mode 100755
index 0000000000000000000000000000000000000000..36de5aaad12c376d5c2388c51d99f0e4da0673ad
--- /dev/null
+++ b/build/scripts-2.7/htpia-median-blur
@@ -0,0 +1,18 @@
+#!/usr/bin/python
+import argparse
+import traceback
+import plantcv.imgproc
+
+parser = argparse.ArgumentParser(description = "Thresholds an image based on windows.")
+parser.add_argument("--input", dest="input", help="Path to input image.")
+parser.add_argument("--ksize", dest="ksize", type=int, help="Size of the kernel. Should be odd and positive.", required = True)
+parser.add_argument("--outputdir", dest="outputdir", default=".", help="Path to write output files, if not specified use current directory.")
+parser.add_argument("--output", default=None, dest="output", help="Name of output image to write, if not specified, use input image name.")
+args = parser.parse_args()
+
+try:
+ plant = plantcv.imgproc.Image(args.input, args.outputdir, args.output, False)
+ plant.medianBlur(args.ksize)
+ plant.write()
+except Exception as e:
+ print traceback.format_exc()
\ No newline at end of file
diff --git a/build/scripts-2.7/htpia-morphology b/build/scripts-2.7/htpia-morphology
new file mode 100755
index 0000000000000000000000000000000000000000..7a51033406a2fe7b286358c862ed5aa7c2f8a3d5
--- /dev/null
+++ b/build/scripts-2.7/htpia-morphology
@@ -0,0 +1,25 @@
+#!/usr/bin/python
+import argparse
+import traceback
+import plantcv.imgproc
+
+parser = argparse.ArgumentParser(description = "Converts an image between color spectrums.")
+parser.add_argument("--input", dest="input", help="Path to input image.", required = True)
+parser.add_argument("--morphType", dest="morphType", help="Type of morphology to perform.", required = True)
+parser.add_argument("--ktype", dest="ktype", help="Type of kernel to generate.", required = True)
+parser.add_argument("--kwidth", dest="kwidth", type=int, help="Width of the kernel.", required = True)
+parser.add_argument("--kheight", dest="kheight", type=int, help="Height of the kernel.", required = True)
+parser.add_argument("--anchorx", default=-1, dest="anchorx", type=int, help="X position of the anchor")
+parser.add_argument("--anchory", default=-1, dest="anchory", type=int, help="Y position of the anchor")
+parser.add_argument("--iterations", default=1, dest="iterations", type=int, help="Number of times to perform the morphology.")
+parser.add_argument("--border", default="default", dest="border", help="Border type for extrapolation.")
+parser.add_argument("--outputdir", dest="outputdir", default=".", help="Path to write output files, if not specified use current directory.")
+parser.add_argument("--output", default=None, dest="output", help="Name of output image to write, if not specified, use input image name.")
+args = parser.parse_args()
+
+try:
+ plant = plantcv.imgproc.Image(args.input, args.outputdir, args.output, False)
+ plant.morphology(args.morphType, args.ktype, (args.kwidth, args.kheight), (args.anchorx, args.anchory), args.iterations, args.border)
+ plant.write()
+except Exception as e:
+ print traceback.format_exc()
\ No newline at end of file
diff --git a/build/scripts-2.7/htpia-normalize-intensity b/build/scripts-2.7/htpia-normalize-intensity
new file mode 100755
index 0000000000000000000000000000000000000000..aadd95b9e618ebea6199f1cef6fb69a3e4729c8d
--- /dev/null
+++ b/build/scripts-2.7/htpia-normalize-intensity
@@ -0,0 +1,17 @@
+#!/usr/bin/python
+import argparse
+import traceback
+import plantcv.imgproc
+
+parser = argparse.ArgumentParser(description = "Normalizes an image by per-pixel intensity.")
+parser.add_argument("--input", dest="input", help="Path to first input image.", required = True)
+parser.add_argument("--outputdir", dest="outputdir", default=".", help="Path to write output files, if not specified use current directory.")
+parser.add_argument("--output", default=None, dest="output", help="Name of output image to write, if not specified, use input image name.")
+args = parser.parse_args()
+
+try:
+ plant = plantcv.imgproc.Image(args.input, args.outputdir, args.output, False)
+ plant.normalizeByIntensity()
+ plant.write()
+except Exception as e:
+ print traceback.format_exc()
\ No newline at end of file
diff --git a/build/scripts-2.7/htpia-run b/build/scripts-2.7/htpia-run
new file mode 100755
index 0000000000000000000000000000000000000000..9ed9d52d4f1edceba7a9a96dbd44aaa14c6e6b2e
--- /dev/null
+++ b/build/scripts-2.7/htpia-run
@@ -0,0 +1,26 @@
+#!/usr/bin/python
+import argparse
+import traceback
+import plantcv.workflow
+import datetime
+
+parser = argparse.ArgumentParser(description = "Initial setup for job submission")
+parser.add_argument("--jobhome", dest="jobhome", default=".", help="Job root. Should be the output directory from pcv-setup. If left blank, will use current directory.")
+parser.add_argument("--basename", dest="basename", default=None, help="Base submission directory name. If left blank, this will generate a timestamped directory.")
+parser.add_argument("--stats", dest="stats", action="store_true", default=False, help="Write the statistics workflow instead of imgproc workflow. Requires --basename.")
+parser.add_argument("--validate", dest="validate", action="store_true", default=False, help="If specified only validates the workflow. Does not generate submission.")
+args = parser.parse_args()
+
+try:
+ basename = datetime.datetime.now().strftime("%Y-%m-%d_%H%M%S") if not args.basename else args.basename
+ if args.stats:
+ if args.basename:
+ stats = plantcv.workflow.Statistics(args.jobhome, basename, args.validate)
+ stats.create()
+ else:
+ print "Stats requires an already processed folder. Specify --basename."
+ else:
+ workflow = plantcv.workflow.ImageProcessor(args.jobhome, basename, args.validate)
+ workflow.create()
+except Exception as e:
+ print traceback.format_exc()
\ No newline at end of file
diff --git a/build/scripts-2.7/htpia-setup b/build/scripts-2.7/htpia-setup
new file mode 100755
index 0000000000000000000000000000000000000000..49d38556eace978974bb6fc00b7ecda53ae3b27a
--- /dev/null
+++ b/build/scripts-2.7/htpia-setup
@@ -0,0 +1,23 @@
+#!/usr/bin/python
+import argparse
+import traceback
+import plantcv.workflow
+
+parser = argparse.ArgumentParser(description = "Initial setup for job submission")
+parser.add_argument("--dir", dest="dir", help="Base directory name.")
+parser.add_argument("--overwrite", dest="overwrite", action="store_true", help="Overwrite existing database. Stops initial directory setup as well.")
+parser.add_argument("--template", dest="template", help="Name of template file to use for directory crawling.")
+parser.add_argument("--validate", dest="validate", action="store_true", help="If specified only validates the workflow. Does not generate submission.")
+args = parser.parse_args()
+
+try:
+ if not args.validate and not args.overwrite:
+ setup = plantcv.workflow.DirectorySetup(args.dir)
+ setup.setup()
+
+ loader = plantcv.workflow.ImageLoader(args.template, args.dir, args.validate, args.overwrite)
+ loader.crawl()
+ loader.write()
+ loader._success()
+except Exception as e:
+ print traceback.format_exc()
\ No newline at end of file
diff --git a/build/scripts-2.7/htpia-sql-aggregate b/build/scripts-2.7/htpia-sql-aggregate
new file mode 100755
index 0000000000000000000000000000000000000000..e08672ca6b07fffdc3c421723c50766a0b79653d
--- /dev/null
+++ b/build/scripts-2.7/htpia-sql-aggregate
@@ -0,0 +1,15 @@
+#!/usr/bin/python
+import argparse
+import traceback
+import plantcv.statistics
+
+parser = argparse.ArgumentParser(description = "Writes data from many small sql files to main db.")
+parser.add_argument("--db", dest="db", help="Main database to load data into.", required = True)
+parser.add_argument("--inputs", dest="inputs", nargs="+", help="Small db's to load into main one.", required = True)
+args = parser.parse_args()
+
+try:
+ stats = plantcv.statistics.Stats(args.db)
+ stats.loadSql(args.inputs)
+except Exception as e:
+ print traceback.format_exc()
\ No newline at end of file
diff --git a/build/scripts-2.7/htpia-stats-anova b/build/scripts-2.7/htpia-stats-anova
new file mode 100755
index 0000000000000000000000000000000000000000..0487ff6c0cdb5e5bb45cf169a6607e7108577c57
--- /dev/null
+++ b/build/scripts-2.7/htpia-stats-anova
@@ -0,0 +1,20 @@
+#!/usr/bin/python
+import argparse
+import traceback
+import plantcv.statistics
+import json
+
+parser = argparse.ArgumentParser(description = "Gathers shoot area information based on specified groupings.")
+parser.add_argument("--db", dest="db", help="Database to run statistics on.", required = True)
+parser.add_argument("--intable", dest="intable", help="Input table to gather data from.", required = True)
+parser.add_argument("--outtable", dest="outtable", help="Output table to write data to.", required = True)
+parser.add_argument("--group", dest="group", help="Image types to group by. Should be in json format.", required = True)
+parser.add_argument("--overwrite", dest="overwrite", action="store_true", help="If specified, will overwrite the output table.")
+args = parser.parse_args()
+
+try:
+ group = json.loads(args.group) if args.group else None
+ stats = plantcv.statistics.Stats(args.db)
+ stats.anova(args.intable, args.outtable, group, args.overwrite)
+except Exception as e:
+ print traceback.format_exc()
\ No newline at end of file
diff --git a/build/scripts-2.7/htpia-stats-correlate b/build/scripts-2.7/htpia-stats-correlate
new file mode 100755
index 0000000000000000000000000000000000000000..a25ab51ef0e70bfa3581d7b5f344df06f9023cfa
--- /dev/null
+++ b/build/scripts-2.7/htpia-stats-correlate
@@ -0,0 +1,22 @@
+#!/usr/bin/python
+import argparse
+import traceback
+import plantcv.statistics
+import json
+
+parser = argparse.ArgumentParser(description = "Gathers shoot area information based on specified groupings.")
+parser.add_argument("--db", dest="db", help="Database to run statistics on.", required = True)
+parser.add_argument("--intable", dest="intable", help="Input table to gather data from.", required = True)
+parser.add_argument("--outtable", dest="outtable", help="Output table to write data to.", required = True)
+parser.add_argument("--datafile", dest="datafile", help="LemanTec data file to correlate to.", required = True)
+parser.add_argument("--dataheaders", dest="dataheaders", help="Json header file.", required = True)
+parser.add_argument("--overwrite", dest="overwrite", action="store_true", help="If specified, will overwrite the output table.")
+args = parser.parse_args()
+
+try:
+ with open(args.dataheaders, "r") as rh:
+ dataHeaders = json.load(rh)
+ stats = plantcv.statistics.Stats(args.db)
+ stats.correlation(args.intable, args.outtable, args.datafile, dataHeaders, args.overwrite)
+except Exception as e:
+ print traceback.format_exc()
\ No newline at end of file
diff --git a/build/scripts-2.7/htpia-stats-export b/build/scripts-2.7/htpia-stats-export
new file mode 100755
index 0000000000000000000000000000000000000000..2c5f2e2b4181d629e8121d849e1abff18764a2cd
--- /dev/null
+++ b/build/scripts-2.7/htpia-stats-export
@@ -0,0 +1,17 @@
+#!/usr/bin/python
+import argparse
+import traceback
+import plantcv.statistics
+import json
+
+parser = argparse.ArgumentParser(description = "Gathers shoot area information based on specified groupings.", required = True)
+parser.add_argument("--db", dest="db", help="Database to run statistics on.", required = True)
+parser.add_argument("--table", dest="table", help="Input table to write to a file.", required = True)
+parser.add_argument("--fname", dest="fname", help="File to write to, if unspecified, file will be written in the current directory with the specified table name.")
+args = parser.parse_args()
+
+try:
+ stats = plantcv.statistics.Stats(args.db)
+ stats.export(args.table, args.fname)
+except Exception as e:
+ print traceback.format_exc()
\ No newline at end of file
diff --git a/build/scripts-2.7/htpia-stats-histogram-bin b/build/scripts-2.7/htpia-stats-histogram-bin
new file mode 100755
index 0000000000000000000000000000000000000000..4fee37332b81256e74ce27b037b706042ebdf0a2
--- /dev/null
+++ b/build/scripts-2.7/htpia-stats-histogram-bin
@@ -0,0 +1,25 @@
+#!/usr/bin/python
+import argparse
+import traceback
+import plantcv.statistics
+import json
+
+parser = argparse.ArgumentParser(description = "Gathers shoot area information based on specified groupings.")
+parser.add_argument("--db", dest="db", help="Database to run statistics on.", required = True)
+parser.add_argument("--options", dest="options", help="Path to options json file.", required = True)
+parser.add_argument("--intable", dest="intable", help="Input table to gather data from.", required = True)
+parser.add_argument("--outtable", dest="outtable", help="Output table to write data to.", required = True)
+parser.add_argument("--jsonwrite", dest="jsonwrite", default = False, action="store_true", help="If specified, writes json output.")
+parser.add_argument("--overwrite", dest="overwrite", default = False, action="store_true", help="If specified, will overwrite the output table.")
+args = parser.parse_args()
+
+try:
+ with open(args.options, "r") as rh:
+ options = json.load(rh)
+ if "histogram-bin" in options:
+ stats = plantcv.statistics.Stats(args.db)
+ stats.histogramBinning(args.intable, args.outtable, options["histogram-bin"]["--group"], options["histogram-bin"]["--chunks"], options["histogram-bin"]["--channels"], args.jsonwrite, args.overwrite)
+ else:
+ print "Key Error: key 'histogram-bin' must be in options file!"
+except Exception as e:
+ print traceback.format_exc()
\ No newline at end of file
diff --git a/build/scripts-2.7/htpia-stats-normalize b/build/scripts-2.7/htpia-stats-normalize
new file mode 100755
index 0000000000000000000000000000000000000000..11b625d76cf73106fada304ca8a628099affc74b
--- /dev/null
+++ b/build/scripts-2.7/htpia-stats-normalize
@@ -0,0 +1,19 @@
+#!/usr/bin/python
+import argparse
+import traceback
+import plantcv.statistics
+import json
+
+parser = argparse.ArgumentParser(description = "Gathers shoot area information based on specified groupings.")
+parser.add_argument("--db", dest="db", help="Database to run statistics on.", required = True)
+parser.add_argument("--intable", dest="intable", help="Input table to gather data from.", required = True)
+parser.add_argument("--outtable", dest="outtable", help="Output table to write data to.", required = True)
+parser.add_argument("--column", dest="column", help="Column to normalize numeric values to.", required = True)
+parser.add_argument("--overwrite", dest="overwrite", action="store_true", help="If specified, will overwrite the output table.")
+args = parser.parse_args()
+
+try:
+ stats = plantcv.statistics.Stats(args.db)
+ stats.normalize(args.intable, args.outtable, args.column, args.overwrite)
+except Exception as e:
+ print traceback.format_exc()
\ No newline at end of file
diff --git a/build/scripts-2.7/htpia-stats-shoot-area b/build/scripts-2.7/htpia-stats-shoot-area
new file mode 100755
index 0000000000000000000000000000000000000000..c2057227f2289628258ad3142347d1b798e19242
--- /dev/null
+++ b/build/scripts-2.7/htpia-stats-shoot-area
@@ -0,0 +1,19 @@
+#!/usr/bin/python
+import argparse
+import traceback
+import plantcv.statistics
+import json
+
+parser = argparse.ArgumentParser(description = "Gathers shoot area information based on specified groupings.")
+parser.add_argument("--db", dest="db", help="Database to run statistics on.", required = True)
+parser.add_argument("--intable", dest="intable", help="Input table to gather data from.", required = True)
+parser.add_argument("--outtable", dest="outtable", help="Output table to write data to.", required = True)
+parser.add_argument("--group", dest="group", nargs="+", help="Image types to group by. Should be in json format.", required = True)
+parser.add_argument("--overwrite", dest="overwrite", action="store_true", help="If specified, will overwrite the output table.")
+args = parser.parse_args()
+
+try:
+ stats = plantcv.statistics.Stats(args.db)
+ stats.shootArea(args.intable, args.outtable, args.group, args.overwrite)
+except Exception as e:
+ print traceback.format_exc()
\ No newline at end of file
diff --git a/build/scripts-2.7/htpia-stats-threshold b/build/scripts-2.7/htpia-stats-threshold
new file mode 100755
index 0000000000000000000000000000000000000000..78affc060b3d18fece3dfddb6bcd7c35841632b1
--- /dev/null
+++ b/build/scripts-2.7/htpia-stats-threshold
@@ -0,0 +1,19 @@
+#!/usr/bin/python
+import argparse
+import traceback
+import plantcv.statistics
+import json
+
+parser = argparse.ArgumentParser(description = "Gathers shoot area information based on specified groupings.")
+parser.add_argument("--db", dest="db", help="Database to run statistics on.", required = True)
+parser.add_argument("--intable", dest="intable", help="Input table to gather data from.", required = True)
+parser.add_argument("--outtable", dest="outtable", help="Output table to write data to.", required = True)
+parser.add_argument("--thresh", dest="thresh", type=float, help="Threhsold value.", required = True)
+parser.add_argument("--overwrite", dest="overwrite", action="store_true", help="If specified, will overwrite the output table.")
+args = parser.parse_args()
+
+try:
+ stats = plantcv.statistics.Stats(args.db)
+ stats.threshold(args.intable, args.outtable, args.thresh, args.overwrite)
+except Exception as e:
+ print traceback.format_exc()
\ No newline at end of file
diff --git a/build/scripts-2.7/htpia-stats-treatment-comp b/build/scripts-2.7/htpia-stats-treatment-comp
new file mode 100755
index 0000000000000000000000000000000000000000..2d05ebce2d3146edfa36957f101adea220c82979
--- /dev/null
+++ b/build/scripts-2.7/htpia-stats-treatment-comp
@@ -0,0 +1,23 @@
+#!/usr/bin/python
+import argparse
+import traceback
+import plantcv.statistics
+import json
+
+parser = argparse.ArgumentParser(description = "Gathers shoot area information based on specified groupings.")
+parser.add_argument("--db", dest="db", help="Database to run statistics on.", required = True)
+parser.add_argument("--intable", dest="intable", help="Input table to gather data from.", required = True)
+parser.add_argument("--outtable", dest="outtable", help="Output table to write data to.", required = True)
+parser.add_argument("--type", dest="type", default="ratio", help="Whether to perform division or subtraction between treatments.")
+paresr.add_argument("--direction", dest="direction", default="Control", help="Whether to perform C ~ S, or S ~ C.")
+parser.add_argument("--comp", dest="comp", default="imtype", help="Whether or not to use imtype or imgname as the primary comparison.")
+parser.add_argument("--overwrite", dest="overwrite", action="store_true", help="If specified, will overwrite the output table.")
+
+args = parser.parse_args()
+
+try:
+ group = json.loads(args.group) if args.group else None
+ stats = plantcv.statistics.Stats(args.db)
+ stats.treatmentComp(args.intable, args.outtable, args.type, args.direction, args.comp, args.overwrite)
+except Exception as e:
+ print traceback.format_exc()
\ No newline at end of file
diff --git a/build/scripts-2.7/htpia-stats-ttest b/build/scripts-2.7/htpia-stats-ttest
new file mode 100755
index 0000000000000000000000000000000000000000..d84bd603f45b25ff342c65f161b840e4d16264ac
--- /dev/null
+++ b/build/scripts-2.7/htpia-stats-ttest
@@ -0,0 +1,22 @@
+#!/usr/bin/python
+import argparse
+import traceback
+import plantcv.statistics
+import json
+
+parser = argparse.ArgumentParser(description = "Gathers shoot area information based on specified groupings.")
+parser.add_argument("--db", dest="db", help="Database to run statistics on.", required = True)
+parser.add_argument("--intable", dest="intable", help="Input table to gather data from.", required = True)
+parser.add_argument("--outtable", dest="outtable", help="Output table to write data to.", required = True)
+parser.add_argument("--comp", dest="comp", default="imtype", help="Whether or not to use imtype or imgname as the primary comparison.")
+parser.add_argument("--overwrite", dest="overwrite", action="store_true", help="If specified, will overwrite the output table.")
+
+args = parser.parse_args()
+
+try:
+ group = json.loads(args.group) if args.group else None
+ stats = plantcv.statistics.Stats(args.db)
+ stats.ttest(args.intable, args.outtable, args.comp)
+ stats.treatmentComp(args.intable, args.outtable, args.type, args.direction, args.comp, args.overwrite)
+except Exception as e:
+ print traceback.format_exc()
\ No newline at end of file
diff --git a/build/scripts-2.7/htpia-threshold b/build/scripts-2.7/htpia-threshold
new file mode 100755
index 0000000000000000000000000000000000000000..dc286efebf85a4a1c8dd6b4ade7f5d92d2e267d4
--- /dev/null
+++ b/build/scripts-2.7/htpia-threshold
@@ -0,0 +1,21 @@
+#!/usr/bin/python
+import argparse
+import traceback
+import plantcv.imgproc
+
+parser = argparse.ArgumentParser(description = "Converts an image between color spectrums.")
+parser.add_argument("--input", dest="input", help="Path to input image.", required = True)
+parser.add_argument("--thresh", dest="thresh", default=127, type=int, help="Threshold cutoff value.")
+parser.add_argument("--max", dest="max", default=255, type=int, help="Write value for binary threhsold")
+parser.add_argument("--type", dest="type", default="binary", help="Threshold type, one of: binary, trunc, tozero, otsu.")
+parser.add_argument("--outputdir", dest="outputdir", default=".", help="Path to write output files, if not specified use current directory.")
+parser.add_argument("--output", dest="output", default=None, help="Name of output image to write, if not specified, use input image name.")
+
+args = parser.parse_args()
+
+try:
+ plant = plantcv.imgproc.Image(args.input, args.outputdir, args.output, False)
+ plant.threshold(args.thresh, args.max, args.type)
+ plant.write()
+except Exception as e:
+ print traceback.format_exc()
\ No newline at end of file
diff --git a/build/scripts-2.7/ih-adaptive-threshold b/build/scripts-2.7/ih-adaptive-threshold
new file mode 100755
index 0000000000000000000000000000000000000000..cd9078d5a97707b7f3096a89c6f01ecd1b32d025
--- /dev/null
+++ b/build/scripts-2.7/ih-adaptive-threshold
@@ -0,0 +1,22 @@
+#!/usr/bin/python
+import argparse
+import traceback
+import ih.imgproc
+
+parser = argparse.ArgumentParser(description = "Thresholds an image based on windows.")
+parser.add_argument("--input", dest="input", help="Path to input image.", required = True)
+parser.add_argument("--value", dest="value", type=int, help="Value to write to pixels. Usually 255 or 0.", required = True)
+parser.add_argument("--adaptiveType", dest="adaptiveType", help="Adaptive type to use. Either 'mean' or 'gaussian'.", required = True)
+parser.add_argument("--thresholdType", dest="thresholdType", help="Threshold type to use. Either 'binary' or 'inverse'.", required = True)
+parser.add_argument("--blockSize", dest="blockSize", type=int, help="Window size to consider. Should be an odd number.", required = True)
+parser.add_argument("--C", dest="C", type=int, help="Constant to subtract from window mean.", required = True)
+parser.add_argument("--outputdir", dest="outputdir", default=".", help="Path to write output files, if not specified use current directory.")
+parser.add_argument("--output", default=None, dest="output", help="Name of output image to write, if not specified, use input image name.")
+args = parser.parse_args()
+
+try:
+ plant = ih.imgproc.Image(args.input, args.outputdir, args.output, False)
+ plant.adaptiveThreshold(args.value, args.adaptiveType, args.thresholdType, args.blockSize, args.C)
+ plant.write()
+except Exception as e:
+ print traceback.format_exc()
diff --git a/build/scripts-2.7/ih-bitwise-and b/build/scripts-2.7/ih-bitwise-and
new file mode 100755
index 0000000000000000000000000000000000000000..db3ab249fc1e679acf4bdccb525657e7f43724ef
--- /dev/null
+++ b/build/scripts-2.7/ih-bitwise-and
@@ -0,0 +1,18 @@
+#!/usr/bin/python
+import argparse
+import traceback
+import ih.imgproc
+
+parser = argparse.ArgumentParser(description = "Converts an image between color spectrums.")
+parser.add_argument("--input1", dest="input1", help="Path to first input image.", required = True)
+parser.add_argument("--input2", dest="input2", help="Path to second input image.", required = True)
+parser.add_argument("--outputdir", dest="outputdir", default=".", help="Path to write output files, if not specified use current directory.")
+parser.add_argument("--output", default=None, dest="output", help="Name of output image to write, if not specified, use input image name.")
+args = parser.parse_args()
+
+try:
+ plant = ih.imgproc.Image(args.input1, args.outputdir, args.output, False)
+ plant.bitwise_and(args.input2)
+ plant.write()
+except Exception as e:
+ print traceback.format_exc()
diff --git a/build/scripts-2.7/ih-bitwise-not b/build/scripts-2.7/ih-bitwise-not
new file mode 100755
index 0000000000000000000000000000000000000000..43b38cbaf76caf3c12faa4ff09646854fc02bfdb
--- /dev/null
+++ b/build/scripts-2.7/ih-bitwise-not
@@ -0,0 +1,17 @@
+#!/usr/bin/python
+import argparse
+import traceback
+import ih.imgproc
+
+parser = argparse.ArgumentParser(description = "Converts an image between color spectrums.")
+parser.add_argument("--input", dest="input", help="Path to first input image.", required = True)
+parser.add_argument("--outputdir", dest="outputdir", default=".", help="Path to write output files, if not specified use current directory.")
+parser.add_argument("--output", default=None, dest="output", help="Name of output image to write, if not specified, use input image name.")
+args = parser.parse_args()
+
+try:
+ plant = ih.imgproc.Image(args.input, args.outputdir, args.output, False)
+ plant.bitwise_not()
+ plant.write()
+except Exception as e:
+ print traceback.format_exc()
diff --git a/build/scripts-2.7/ih-bitwise-or b/build/scripts-2.7/ih-bitwise-or
new file mode 100755
index 0000000000000000000000000000000000000000..087db32be33abc12658c2f4f1e3bb5853f28a390
--- /dev/null
+++ b/build/scripts-2.7/ih-bitwise-or
@@ -0,0 +1,18 @@
+#!/usr/bin/python
+import argparse
+import traceback
+import ih.imgproc
+
+parser = argparse.ArgumentParser(description = "Converts an image between color spectrums.")
+parser.add_argument("--input1", dest="input1", help="Path to first input image.", required = True)
+parser.add_argument("--input2", dest="input2", help="Path to second input image.", required = True)
+parser.add_argument("--outputdir", dest="outputdir", default=".", help="Path to write output files, if not specified use current directory.")
+parser.add_argument("--output", default=None, dest="output", help="Name of output image to write, if not specified, use input image name.")
+args = parser.parse_args()
+
+try:
+ plant = ih.imgproc.Image(args.input1, args.outputdir, args.output, False)
+ plant.bitwise_or(args.input2)
+ plant.write()
+except Exception as e:
+ print traceback.format_exc()
diff --git a/build/scripts-2.7/ih-bitwise-xor b/build/scripts-2.7/ih-bitwise-xor
new file mode 100755
index 0000000000000000000000000000000000000000..f2141f6b4e35288f1b07174d72ec7784816c9fab
--- /dev/null
+++ b/build/scripts-2.7/ih-bitwise-xor
@@ -0,0 +1,18 @@
+#!/usr/bin/python
+import argparse
+import traceback
+import ih.imgproc
+
+parser = argparse.ArgumentParser(description = "Converts an image between color spectrums.")
+parser.add_argument("--input1", dest="input1", help="Path to first input image.", required = True)
+parser.add_argument("--input2", dest="input2", help="Path to second input image.", required = True)
+parser.add_argument("--outputdir", dest="outputdir", default=".", help="Path to write output files, if not specified use current directory.")
+parser.add_argument("--output", default=None, dest="output", help="Name of output image to write, if not specified, use input image name.")
+args = parser.parse_args()
+
+try:
+ plant = ih.imgproc.Image(args.input1, args.outputdir, args.output, False)
+ plant.bitwise_xor(args.input2)
+ plant.write()
+except Exception as e:
+ print traceback.format_exc()
diff --git a/build/scripts-2.7/ih-blur b/build/scripts-2.7/ih-blur
new file mode 100755
index 0000000000000000000000000000000000000000..344ff9b73561ceea899e47061e73d5079d45c774
--- /dev/null
+++ b/build/scripts-2.7/ih-blur
@@ -0,0 +1,22 @@
+#!/usr/bin/python
+import argparse
+import traceback
+import ih.imgproc
+
+parser = argparse.ArgumentParser(description = "Smoothes an image based on a evenly distributed kernel.")
+parser.add_argument("--input", dest="input", help="Path to input image.", required = True)
+parser.add_argument("--kwidth", dest="kwidth", type=int, help="Width of the kernel", required = True)
+parser.add_argument("--kheight", dest="kheight", type=int, help="Height of the kernel", required = True)
+parser.add_argument("--anchorx", default=-1, dest="anchorx", type=int, help="X position of the anchor")
+parser.add_argument("--anchory", default=-1, dest="anchory", type=int, help="Y position of the anchor")
+parser.add_argument("--border", default="default", dest="border", help="Border type for extrapolation.")
+parser.add_argument("--outputdir", dest="outputdir", default=".", help="Path to write output files, if not specified use current directory.")
+parser.add_argument("--output", default=None, dest="output", help="Name of output image to write, if not specified, use input image name.")
+args = parser.parse_args()
+
+try:
+ plant = ih.imgproc.Image(args.input, args.outputdir, args.output, False)
+ plant.blur((args.kwidth, args.kheight), (args.anchorx, args.anchory), args.border)
+ plant.write()
+except Exception as e:
+ print traceback.format_exc()
diff --git a/build/scripts-2.7/ih-color-filter b/build/scripts-2.7/ih-color-filter
new file mode 100755
index 0000000000000000000000000000000000000000..85cde83ac6824ec63fce7276398350700e241807
--- /dev/null
+++ b/build/scripts-2.7/ih-color-filter
@@ -0,0 +1,27 @@
+#!/usr/bin/python
+import argparse
+import traceback
+import ih.imgproc
+
+parser = argparse.ArgumentParser(description = "Smoothes an image based on a evenly distributed kernel.")
+parser.add_argument("--input", dest="input", help="Path to input image.", required = True)
+parser.add_argument("--logic", dest="logic", help="Logic string to compute.", required = True)
+parser.add_argument("--roi", dest="roi", help="roi file")
+parser.add_argument("--ystart", dest="ystart", default=-1, help="Minimum Y of the roi.")
+parser.add_argument("--yend", dest="yend", default=-1, help="Maximum Y of the roi.")
+parser.add_argument("--xstart", dest="xstart", default=-1, help="Minimum X of the roi.")
+parser.add_argument("--xend", dest="xend", default=-1, help="Maximum X of the roi.")
+parser.add_argument("--outputdir", dest="outputdir", default=".", help="Path to write output files, if not specified use current directory.")
+parser.add_argument("--output", default=None, dest="output", help="Name of output image to write, if not specified, use input image name.")
+
+args = parser.parse_args()
+
+try:
+ plant = ih.imgproc.Image(args.input, args.outputdir, args.output, False)
+ if args.roi:
+ plant.colorFilter(args.logic, args.roi)
+ else:
+ plant.colorFilter(args.logic, [args.ystart, args.yend, args.xstart, args.xend])
+ plant.write()
+except Exception as e:
+ print traceback.format_exc()
diff --git a/build/scripts-2.7/ih-contour-cut b/build/scripts-2.7/ih-contour-cut
new file mode 100755
index 0000000000000000000000000000000000000000..e315eb70243800668d33a96476077d47770bc8a0
--- /dev/null
+++ b/build/scripts-2.7/ih-contour-cut
@@ -0,0 +1,26 @@
+#!/usr/bin/python
+import argparse
+import traceback
+import ih.imgproc
+
+parser = argparse.ArgumentParser(description = "Smoothes an image based on a evenly distributed kernel.")
+parser.add_argument("--input", dest="input", help="Path to input image.", required = True)
+parser.add_argument("--binary", dest="binary", help="Binary image to calculate contours from", required = True)
+parser.add_argument("--basemin", default=100, dest="basemin", type=int, help="Minimum area of contour required to keep in final image.")
+parser.add_argument("--padminx", default=0, dest="padminx", type=int, help="Padding added to left.")
+parser.add_argument("--padmaxx", default=0, dest="padmaxx", type=int, help="Padding added to right.")
+parser.add_argument("--padminy", default=0, dest="padminy", type=int, help="Padding added to top.")
+parser.add_argument("--padmaxy", default=0, dest="padmaxy", type=int, help="Padding added to bottom.")
+parser.add_argument("--resize", default=False, dest="resize", action="store_true", help="Whether or not to resize the actual image.")
+parser.add_argument("--returnBound", default=False, dest="returnBound", action="store_true", help="Whether or not to write the bound.")
+parser.add_argument("--roiwrite", default="roi.json", dest="roiwrite", help="The name of the roi file to write.")
+parser.add_argument("--outputdir", dest="outputdir", default=".", help="Path to write output files, if not specified use current directory.")
+parser.add_argument("--output", default=None, dest="output", help="Name of output image to write, if not specified, use input image name.")
+args = parser.parse_args()
+
+try:
+ plant = ih.imgproc.Image(args.input, args.outputdir, args.output, False)
+ plant.contourCut(args.binary, args.basemin, [args.padminy, args.padmaxy, args.padminx, args.padmaxx], args.resize, args.returnBound, args.roiwrite)
+ plant.write()
+except Exception as e:
+ print traceback.format_exc()
diff --git a/build/scripts-2.7/ih-convert-color b/build/scripts-2.7/ih-convert-color
new file mode 100755
index 0000000000000000000000000000000000000000..f61261b461920774ae611fdcfbab33222289c056
--- /dev/null
+++ b/build/scripts-2.7/ih-convert-color
@@ -0,0 +1,19 @@
+#!/usr/bin/python
+import argparse
+import traceback
+import ih.imgproc
+
+parser = argparse.ArgumentParser(description = "Converts an image between color spectrums.")
+parser.add_argument("--input", dest="input", help="Path to input image.", required = True)
+parser.add_argument("--intype", dest="intype", help="Type of input image, one of [bgr, gray, hsv, lab, ycrcb]", required = True)
+parser.add_argument("--outtype", dest="outtype", help="Type of output image, one of [bgr, gray, hsv, lab, ycrcb]", required = True)
+parser.add_argument("--outputdir", dest="outputdir", default=".", help="Path to write output files, if not specified use current directory.")
+parser.add_argument("--output", default=None, dest="output", help="Name of output image to write, if not specified, use input image name.")
+args = parser.parse_args()
+
+try:
+ plant = ih.imgproc.Image(args.input, args.outputdir, args.output, False)
+ plant.convertColor(args.intype, args.outtype)
+ plant.write()
+except Exception as e:
+ print traceback.format_exc()
diff --git a/build/scripts-2.7/ih-crawl b/build/scripts-2.7/ih-crawl
new file mode 100755
index 0000000000000000000000000000000000000000..2ec8a80c7e796bfd0ffea705c0ff4d28a85b146e
--- /dev/null
+++ b/build/scripts-2.7/ih-crawl
@@ -0,0 +1,18 @@
+#!/usr/bin/python
+import argparse
+import traceback
+import ih.workflow
+
+parser = argparse.ArgumentParser(description = "Initial setup for job submission")
+parser.add_argument("--dir", dest="dir", default=".", help="Base directory name.")
+parser.add_argument("--template", default="input/crawl.json", dest="template", help="Name of template file to use for directory crawling.")
+parser.add_argument("--validate", dest="validate", action="store_true", help="If specified only validates the workflow. Does not generate submission.")
+args = parser.parse_args()
+
+try:
+ loader = ih.workflow.ImageLoader(args.template, args.dir, args.validate, True)
+ loader.crawl()
+ loader.write()
+ loader._success()
+except Exception as e:
+ print traceback.format_exc()
diff --git a/build/scripts-2.7/ih-crop b/build/scripts-2.7/ih-crop
new file mode 100755
index 0000000000000000000000000000000000000000..47fca988253cd64fb28c1d4c4d62e0146f6bcf83
--- /dev/null
+++ b/build/scripts-2.7/ih-crop
@@ -0,0 +1,26 @@
+#!/usr/bin/python
+import argparse
+import traceback
+import ih.imgproc
+
+parser = argparse.ArgumentParser(description = "Smoothes an image based on a evenly distributed kernel.")
+parser.add_argument("--input", dest="input", help="Path to input image.", required = True)
+parser.add_argument("--roi", dest="roi", help="roi file")
+parser.add_argument("--ystart", dest="ystart", help="Minimum Y of the roi.")
+parser.add_argument("--yend", dest="yend", help="Maximum Y of the roi.")
+parser.add_argument("--xstart", dest="xstart", help="Minimum X of the roi.")
+parser.add_argument("--xend", dest="xend", help="Maximum X of the roi.")
+parser.add_argument("--resize", default=False, dest="resize", action="store_true", help="Whether or not to actually resize the image.")
+parser.add_argument("--outputdir", dest="outputdir", default=".", help="Path to write output files, if not specified use current directory.")
+parser.add_argument("--output", default=None, dest="output", help="Name of output image to write, if not specified, use input image name.")
+args = parser.parse_args()
+
+try:
+ plant = ih.imgproc.Image(args.input, args.outputdir, args.output, False)
+ if args.roi:
+ plant.crop(args.roi, args.resize)
+ else:
+ plant.crop([args.ystart, args.yend, args.xtart, args.xend], args.resize)
+ plant.write()
+except Exception as e:
+ print traceback.format_exc()
diff --git a/build/scripts-2.7/ih-edges b/build/scripts-2.7/ih-edges
new file mode 100755
index 0000000000000000000000000000000000000000..3dbe0c9a0bb0beb012e2aecb7117fa138a05113e
--- /dev/null
+++ b/build/scripts-2.7/ih-edges
@@ -0,0 +1,21 @@
+#!/usr/bin/python
+import argparse
+import traceback
+import ih.imgproc
+
+parser = argparse.ArgumentParser(description = "Smoothes an image based on a evenly distributed kernel.")
+parser.add_argument("--input", dest="input", help="Path to input image.", required = True)
+parser.add_argument("--threshold1", dest="threshold1", type=int, help="Minimum threshold value.", required = True)
+parser.add_argument("--threshold2", dest="threshold2", type=int, help="Maximum threshold value.", required = True)
+parser.add_argument("--apertureSize", default = 3, dest="apertureSize", type=int, help="Aperture size for Sobel algorithm.")
+parser.add_argument("--L2gradient", default = False, dest="L2gradient", action="store_true", help="Determines method to calculate gradient magnitutde.")
+parser.add_argument("--outputdir", dest="outputdir", default=".", help="Path to write output files, if not specified use current directory.")
+parser.add_argument("--output", default=None, dest="output", help="Name of output image to write, if not specified, use input image name.")
+args = parser.parse_args()
+
+try:
+ plant = ih.imgproc.Image(args.input, args.outputdir, args.output, False)
+ plant.edges(args.threshold1, args.threshold2, args.apertureSize, args.L2gradient)
+ plant.write()
+except Exception as e:
+ print traceback.format_exc()
diff --git a/build/scripts-2.7/ih-error-log b/build/scripts-2.7/ih-error-log
new file mode 100755
index 0000000000000000000000000000000000000000..13ab4f56b2d3d42577729421dba793e098191fcb
--- /dev/null
+++ b/build/scripts-2.7/ih-error-log
@@ -0,0 +1,15 @@
+#!/usr/bin/python
+import argparse
+import traceback
+import ih.statistics
+
+parser = argparse.ArgumentParser(description = "Extracts numerical information from an image.")
+parser.add_argument("--db", dest="db", help="Path to database to write", required = True)
+parser.add_argument("--output", dest="output", help="Path to output log file.", required = True)
+args = parser.parse_args()
+
+try:
+ stats = ih.statistics.Stats(args.db)
+ stats.logErrors(args.output)
+except Exception as e:
+ print traceback.format_exc()
diff --git a/build/scripts-2.7/ih-extract b/build/scripts-2.7/ih-extract
new file mode 100755
index 0000000000000000000000000000000000000000..a4d3ff108a904506d382f64d3046871c4a552c47
--- /dev/null
+++ b/build/scripts-2.7/ih-extract
@@ -0,0 +1,44 @@
+#!/usr/bin/python
+import argparse
+import traceback
+import ih.imgproc
+import os
+import sqlite3
+
+parser = argparse.ArgumentParser(description = "Extracts numerical information from an image.")
+parser.add_argument("--input", dest="input", help="Path to processed image.", required = True)
+parser.add_argument("--dbid", dest="dbid", help="Image Id, used for database writing", required = True)
+parser.add_argument("--db", dest="db", help="Path to database to write", required = True)
+parser.add_argument("--dimensions", dest="dimensions", default=False, action="store_true", help="Extract dimensions.")
+parser.add_argument("--pixels", dest="pixels", default=False, action="store_true", help="Extract pixels.")
+parser.add_argument("--colors", dest="colors", default=False, action="store_true", help="Extract color data.")
+parser.add_argument("--channels", dest="channels", default=False, action="store_true", help="Extract channel data.")
+parser.add_argument("--bins", dest="bins", default=None, help="Path to bin file.")
+parser.add_argument("--moments", dest="moments", default=False, action="store_true", help="Extract moment data.")
+args = parser.parse_args()
+
+try:
+ plant = ih.imgproc.Image(args.input, ".", db = args.db, dbid = args.dbid)
+
+ plant.extractFinalPath()
+
+ if args.dimensions:
+ plant.extractDimensions()
+
+ if args.pixels:
+ plant.extractPixels()
+
+ if args.moments:
+ plant.extractMoments()
+
+ if args.colors:
+ plant.extractColorData()
+
+ if args.channels:
+ plant.extractColorChannels()
+
+ if args.bins:
+ plant.extractBins(args.bins)
+
+except Exception as e:
+ print traceback.format_exc()
diff --git a/build/scripts-2.7/ih-extract-all b/build/scripts-2.7/ih-extract-all
new file mode 100755
index 0000000000000000000000000000000000000000..20f12464514e44ae53f6150e3fea371558cac5e5
--- /dev/null
+++ b/build/scripts-2.7/ih-extract-all
@@ -0,0 +1,21 @@
+#!/usr/bin/python
+import argparse
+import traceback
+import ih.imgproc
+import ih.statistics
+import os
+import sqlite3
+import json
+
+parser = argparse.ArgumentParser(description = "Extracts numerical information from all images in a database.")
+parser.add_argument("--db", dest="db", help="Database to load processed images from.", required = True)
+parser.add_argument("--options", dest="options", help="Path to options json file.", required = True)
+args = parser.parse_args()
+
+try:
+ with open (args.options, "r") as rh:
+ options = json.load(rh)
+ stats = ih.statistics.Stats(args.db)
+ stats.extractAll(options)
+except Exception as e:
+ print traceback.format_exc()
diff --git a/build/scripts-2.7/ih-extract-multi b/build/scripts-2.7/ih-extract-multi
new file mode 100755
index 0000000000000000000000000000000000000000..862b1d33e0ce230732edaaf230bad5acb0aeafc7
--- /dev/null
+++ b/build/scripts-2.7/ih-extract-multi
@@ -0,0 +1,61 @@
+#!/usr/bin/python
+import argparse
+import traceback
+import ih.imgproc
+import os
+import sqlite3
+
+parser = argparse.ArgumentParser(description = "Extracts numerical information from multiple images.")
+parser.add_argument("--inputs", dest="inputs", nargs="+", help="Path to processed image.", required = True)
+parser.add_argument("--db", dest="db", help="Path to database to write", required = True)
+parser.add_argument("--createdb", dest="createdb", default=False, action="store_true", help = "Create database file specified by db")
+parser.add_argument("--dimensions", dest="dimensions", default=False, action="store_true", help="Extract dimensions.")
+parser.add_argument("--pixels", dest="pixels", default=False, action="store_true", help="Extract pixels.")
+parser.add_argument("--colors", dest="colors", default=False, action="store_true", help="Extract color data.")
+parser.add_argument("--channels", dest="channels", default=False, action="store_true", help="Extract channel data.")
+parser.add_argument("--bins", dest="bins", default=None, help="Path to bin file.")
+parser.add_argument("--moments", dest="moments", default=False, action="store_true", help="Extract moment data.")
+args = parser.parse_args()
+
+try:
+ if args.createdb:
+ conn = sqlite3.connect(args.db)
+ conn.execute("drop table if exists images")
+ conn.commit()
+ conn.execute("create table images (pegasusid PRIMARY KEY)")
+ conn.commit()
+ conn.executemany("insert into images (pegasusid) values (?)", [(os.path.basename(x).split("_")[0],) for x in args.inputs])
+ conn.commit()
+ conn.close()
+ for input in args.inputs:
+ try:
+ dbid = "_".join(os.path.basename(input).split("_")[:-1])
+ plant = ih.imgproc.Image(input, ".", db = args.db, dbid = dbid)
+
+ plant.extractFinalPath()
+
+ if args.dimensions:
+ plant.extractDimensions()
+
+ if args.pixels:
+ plant.extractPixels()
+
+ if args.moments:
+ plant.extractMoments()
+
+ if args.colors:
+ plant.extractColorData()
+
+ if args.channels:
+ plant.extractColorChannels()
+
+ if args.bins:
+ plant.extractBins(args.bins)
+
+ plant._closeDb()
+
+ except:
+ print traceback.format_exc()
+
+except Exception as e:
+ print traceback.format_exc()
diff --git a/build/scripts-2.7/ih-gaussian-blur b/build/scripts-2.7/ih-gaussian-blur
new file mode 100755
index 0000000000000000000000000000000000000000..00eb1930c553ac2d4c0c3724baa970c8d18c11d8
--- /dev/null
+++ b/build/scripts-2.7/ih-gaussian-blur
@@ -0,0 +1,22 @@
+#!/usr/bin/python
+import argparse
+import traceback
+import ih.imgproc
+
+parser = argparse.ArgumentParser(description = "Smooths an image based on a Gaussian kernel.")
+parser.add_argument("--input", dest="input", help="Path to input image.", required = True)
+parser.add_argument("--kwidth", dest="kwidth", type=int, help="Width of the kernel", required = True)
+parser.add_argument("--kheight", dest="kheight", type=int, help="Height of the kernel", required = True)
+parser.add_argument("--sigmax", default=0, dest="sigmax", type=int, help="Standard deviation in the x direction.")
+parser.add_argument("--sigmay", default=0, dest="sigmay", type=int, help="Standard deviation in the y direction.")
+parser.add_argument("--border", default="default", dest="border", help="Border type for extrapolation.")
+parser.add_argument("--outputdir", dest="outputdir", default=".", help="Path to write output files, if not specified use current directory.")
+parser.add_argument("--output", default=None, dest="output", help="Name of output image to write, if not specified, use input image name.")
+args = parser.parse_args()
+
+try:
+ plant = ih.imgproc.Image(args.input, args.outputdir, args.output, False)
+ plant.gaussianBlur((args.kwidth, args.kheight), args.sigmax, args.sigmay, args.border)
+ plant.write()
+except Exception as e:
+ print traceback.format_exc()
diff --git a/build/scripts-2.7/ih-meanshift b/build/scripts-2.7/ih-meanshift
new file mode 100755
index 0000000000000000000000000000000000000000..b1a93f56108ba951569a2e4e47f086ffbf508e06
--- /dev/null
+++ b/build/scripts-2.7/ih-meanshift
@@ -0,0 +1,20 @@
+#!/usr/bin/python
+import argparse
+import traceback
+import ih.imgproc
+
+parser = argparse.ArgumentParser(description = "Shifts colors in an image based on nearest neighbors.")
+parser.add_argument("--input", dest="input", help="Path to input image.", required = True)
+parser.add_argument("--spatial_radius", dest="spatial_radius", type=float, help="Spatial Radius.", required = True)
+parser.add_argument("--range_radius", dest="range_radius", type=float, help="Range Radius.", required = True)
+parser.add_argument("--min_density", dest="min_density", type=float, help="Minimum Density.", required = True)
+parser.add_argument("--outputdir", dest="outputdir", default=".", help="Path to write output files, if not specified use current directory.")
+parser.add_argument("--output", default=None, dest="output", help="Name of output image to write, if not specified, use input image name.")
+args = parser.parse_args()
+
+try:
+ plant = ih.imgproc.Image(args.input, args.outputdir, args.output, False)
+ plant.meanshift(args.spatial_radius, args.range_radius, args.min_density)
+ plant.write()
+except Exception as e:
+ print traceback.format_exc()
diff --git a/build/scripts-2.7/ih-median-blur b/build/scripts-2.7/ih-median-blur
new file mode 100755
index 0000000000000000000000000000000000000000..aa4e9ab4439a9b8596e648b66dc375cc688ca55a
--- /dev/null
+++ b/build/scripts-2.7/ih-median-blur
@@ -0,0 +1,18 @@
+#!/usr/bin/python
+import argparse
+import traceback
+import ih.imgproc
+
+parser = argparse.ArgumentParser(description = "Thresholds an image based on windows.")
+parser.add_argument("--input", dest="input", help="Path to input image.")
+parser.add_argument("--ksize", dest="ksize", type=int, help="Size of the kernel. Should be odd and positive.", required = True)
+parser.add_argument("--outputdir", dest="outputdir", default=".", help="Path to write output files, if not specified use current directory.")
+parser.add_argument("--output", default=None, dest="output", help="Name of output image to write, if not specified, use input image name.")
+args = parser.parse_args()
+
+try:
+ plant = ih.imgproc.Image(args.input, args.outputdir, args.output, False)
+ plant.medianBlur(args.ksize)
+ plant.write()
+except Exception as e:
+ print traceback.format_exc()
diff --git a/build/scripts-2.7/ih-morphology b/build/scripts-2.7/ih-morphology
new file mode 100755
index 0000000000000000000000000000000000000000..6936cafbbe39e8fb7c816279055d6c51bd801153
--- /dev/null
+++ b/build/scripts-2.7/ih-morphology
@@ -0,0 +1,25 @@
+#!/usr/bin/python
+import argparse
+import traceback
+import ih.imgproc
+
+parser = argparse.ArgumentParser(description = "Converts an image between color spectrums.")
+parser.add_argument("--input", dest="input", help="Path to input image.", required = True)
+parser.add_argument("--morphType", dest="morphType", help="Type of morphology to perform.", required = True)
+parser.add_argument("--ktype", dest="ktype", help="Type of kernel to generate.", required = True)
+parser.add_argument("--kwidth", dest="kwidth", type=int, help="Width of the kernel.", required = True)
+parser.add_argument("--kheight", dest="kheight", type=int, help="Height of the kernel.", required = True)
+parser.add_argument("--anchorx", default=-1, dest="anchorx", type=int, help="X position of the anchor")
+parser.add_argument("--anchory", default=-1, dest="anchory", type=int, help="Y position of the anchor")
+parser.add_argument("--iterations", default=1, dest="iterations", type=int, help="Number of times to perform the morphology.")
+parser.add_argument("--border", default="default", dest="border", help="Border type for extrapolation.")
+parser.add_argument("--outputdir", dest="outputdir", default=".", help="Path to write output files, if not specified use current directory.")
+parser.add_argument("--output", default=None, dest="output", help="Name of output image to write, if not specified, use input image name.")
+args = parser.parse_args()
+
+try:
+ plant = ih.imgproc.Image(args.input, args.outputdir, args.output, False)
+ plant.morphology(args.morphType, args.ktype, (args.kwidth, args.kheight), (args.anchorx, args.anchory), args.iterations, args.border)
+ plant.write()
+except Exception as e:
+ print traceback.format_exc()
diff --git a/build/scripts-2.7/ih-normalize-intensity b/build/scripts-2.7/ih-normalize-intensity
new file mode 100755
index 0000000000000000000000000000000000000000..1df0ef02e4c7deb062e9be6fdaa180f0093f28fb
--- /dev/null
+++ b/build/scripts-2.7/ih-normalize-intensity
@@ -0,0 +1,17 @@
+#!/usr/bin/python
+import argparse
+import traceback
+import ih.imgproc
+
+parser = argparse.ArgumentParser(description = "Normalizes an image by per-pixel intensity.")
+parser.add_argument("--input", dest="input", help="Path to first input image.", required = True)
+parser.add_argument("--outputdir", dest="outputdir", default=".", help="Path to write output files, if not specified use current directory.")
+parser.add_argument("--output", default=None, dest="output", help="Name of output image to write, if not specified, use input image name.")
+args = parser.parse_args()
+
+try:
+ plant = ih.imgproc.Image(args.input, args.outputdir, args.output, False)
+ plant.normalizeByIntensity()
+ plant.write()
+except Exception as e:
+ print traceback.format_exc()
diff --git a/build/scripts-2.7/ih-resize b/build/scripts-2.7/ih-resize
new file mode 100755
index 0000000000000000000000000000000000000000..2704315015bcbbf9ab14dfb2625b7848dd24ef64
--- /dev/null
+++ b/build/scripts-2.7/ih-resize
@@ -0,0 +1,20 @@
+#!/usr/bin/python
+import argparse
+import traceback
+import ih.imgproc
+
+parser = argparse.ArgumentParser(description = "Smoothes an image based on a evenly distributed kernel.")
+parser.add_argument("--input", dest="input", help="Path to input image.", required = True)
+parser.add_argument("--scale", dest="scale", default=None, type=float, help="Scaling factor.")
+parser.add_argument("--width", dest="width", default=None, type=int, help="Target width.")
+parser.add_argument("--height", dest="height", default=None, type=int, help="Target height.")
+parser.add_argument("--outputdir", dest="outputdir", default=".", help="Path to write output files, if not specified use current directory.")
+parser.add_argument("--output", default=None, dest="output", help="Name of output image to write, if not specified, use input image name.")
+args = parser.parse_args()
+
+try:
+ plant = ih.imgproc.Image(args.input, args.outputdir, args.output, False)
+ plant.resizeSelf(args.scale, args.width, args.height)
+ plant.write()
+except Exception as e:
+ print traceback.format_exc()
diff --git a/build/scripts-2.7/ih-run b/build/scripts-2.7/ih-run
new file mode 100755
index 0000000000000000000000000000000000000000..8b8ecce8435c12395efd3650cd34c3880bf83261
--- /dev/null
+++ b/build/scripts-2.7/ih-run
@@ -0,0 +1,26 @@
+#!/usr/bin/python
+import argparse
+import traceback
+import ih.workflow
+import datetime
+
+parser = argparse.ArgumentParser(description = "Initial setup for job submission")
+parser.add_argument("--jobhome", dest="jobhome", default=".", help="Job root. Should be the output directory from ih-setup. If left blank, will use current directory.")
+parser.add_argument("--basename", dest="basename", default=None, help="Base submission directory name. If left blank, this will generate a timestamped directory.")
+parser.add_argument("--stats", dest="stats", action="store_true", default=False, help="Write the statistics workflow instead of imgproc workflow. Requires --basename.")
+parser.add_argument("--validate", dest="validate", action="store_true", default=False, help="If specified only validates the workflow. Does not generate submission.")
+args = parser.parse_args()
+
+try:
+ basename = datetime.datetime.now().strftime("%Y-%m-%d_%H%M%S") if not args.basename else args.basename
+ if args.stats:
+ if args.basename:
+ stats = ih.workflow.Statistics(args.jobhome, basename, args.validate)
+ stats.create()
+ else:
+ print "Stats requires an already processed folder. Specify --basename."
+ else:
+ workflow = ih.workflow.ImageProcessor(args.jobhome, basename, args.validate)
+ workflow.create()
+except Exception as e:
+ print traceback.format_exc()
diff --git a/build/scripts-2.7/ih-setup b/build/scripts-2.7/ih-setup
new file mode 100755
index 0000000000000000000000000000000000000000..121ff7b70218651b76b73da8321b4309a9a26bca
--- /dev/null
+++ b/build/scripts-2.7/ih-setup
@@ -0,0 +1,14 @@
+#!/usr/bin/python
+import argparse
+import traceback
+import ih.workflow
+
+parser = argparse.ArgumentParser(description = "Initial setup for job submission")
+parser.add_argument("--dir", dest="dir", help="Base directory name.")
+args = parser.parse_args()
+
+try:
+ setup = ih.workflow.DirectorySetup(args.dir)
+ setup.setup()
+except Exception as e:
+ print traceback.format_exc()
diff --git a/build/scripts-2.7/ih-sql-aggregate b/build/scripts-2.7/ih-sql-aggregate
new file mode 100755
index 0000000000000000000000000000000000000000..5df654130a5249aaa060c1c31b08a5997cf3fd90
--- /dev/null
+++ b/build/scripts-2.7/ih-sql-aggregate
@@ -0,0 +1,15 @@
+#!/usr/bin/python
+import argparse
+import traceback
+import ih.statistics
+
+parser = argparse.ArgumentParser(description = "Writes data from many small sql files to main db.")
+parser.add_argument("--db", dest="db", help="Main database to load data into.", required = True)
+parser.add_argument("--inputs", dest="inputs", nargs="+", help="Small db's to load into main one.", required = True)
+args = parser.parse_args()
+
+try:
+ stats = ih.statistics.Stats(args.db)
+ stats.loadSql(args.inputs)
+except Exception as e:
+ print traceback.format_exc()
diff --git a/build/scripts-2.7/ih-stats-anova b/build/scripts-2.7/ih-stats-anova
new file mode 100755
index 0000000000000000000000000000000000000000..786d8c60bf6614d49d5672e2b11d7ed1423612cd
--- /dev/null
+++ b/build/scripts-2.7/ih-stats-anova
@@ -0,0 +1,17 @@
+#!/usr/bin/python
+import argparse
+import traceback
+import ih.statistics
+import json
+
+parser = argparse.ArgumentParser(description = "Gathers shoot area information based on specified groupings.")
+parser.add_argument("--db", dest="db", help="Database to run statistics on.", required = True)
+parser.add_argument("--intable", dest="intable", help="Input table to gather data from.", required = True)
+parser.add_argument("--outtable", dest="outtable", help="Output table to write data to.", required = True)
+parser.add_argument("--group", dest="group", nargs="+", help="Image types to group by. Should be in json format.", required = True)
+parser.add_argument("--overwrite", dest="overwrite", action="store_true", help="If specified, will overwrite the output table.")
+args = parser.parse_args()
+
+stats = ih.statistics.Stats(args.db)
+stats.anova(args.intable, args.outtable, args.group, args.overwrite)
+stats._closeConnection()
diff --git a/build/scripts-2.7/ih-stats-correlate b/build/scripts-2.7/ih-stats-correlate
new file mode 100755
index 0000000000000000000000000000000000000000..6f7e5c9eba687e93e3b3d4744a7bac9b50a80b23
--- /dev/null
+++ b/build/scripts-2.7/ih-stats-correlate
@@ -0,0 +1,20 @@
+#!/usr/bin/python
+import argparse
+import traceback
+import ih.statistics
+import json
+
+parser = argparse.ArgumentParser(description = "Gathers shoot area information based on specified groupings.")
+parser.add_argument("--db", dest="db", help="Database to run statistics on.", required = True)
+parser.add_argument("--intable", dest="intable", help="Input table to gather data from.", required = True)
+parser.add_argument("--outtable", dest="outtable", help="Output table to write data to.", required = True)
+parser.add_argument("--datafile", dest="datafile", help="LemanTec data file to correlate to.", required = True)
+parser.add_argument("--dataheaders", dest="dataheaders", help="Json header file.", required = True)
+parser.add_argument("--overwrite", dest="overwrite", action="store_true", help="If specified, will overwrite the output table.")
+args = parser.parse_args()
+
+with open(args.dataheaders, "r") as rh:
+ dataHeaders = json.load(rh)
+stats = ih.statistics.Stats(args.db)
+stats.correlation(args.intable, args.outtable, args.datafile, dataHeaders, args.overwrite)
+stats._closeConnection()
diff --git a/build/scripts-2.7/ih-stats-export b/build/scripts-2.7/ih-stats-export
new file mode 100755
index 0000000000000000000000000000000000000000..942bfc7448264311451f1325f6c563a325fe67b5
--- /dev/null
+++ b/build/scripts-2.7/ih-stats-export
@@ -0,0 +1,19 @@
+#!/usr/bin/python
+import argparse
+import traceback
+import ih.statistics
+import json
+
+parser = argparse.ArgumentParser(description = "Export sqlite tables to csv.")
+parser.add_argument("--db", dest="db", help="Database to run statistics on.", required = True)
+parser.add_argument("--table", dest="table", help="Input table to write to a file.", required = True)
+parser.add_argument("--group", dest="group", nargs="+", help="Image types to extract.")
+parser.add_argument("--fname", dest="fname", help="File to write to, if unspecified, file will be written in the current directory with the specified table name.")
+args = parser.parse_args()
+
+try:
+ stats = ih.statistics.Stats(args.db)
+ stats.export(args.table, args.fname, group = args.group)
+ stats._closeConnection()
+except Exception as e:
+ print traceback.format_exc()
diff --git a/build/scripts-2.7/ih-stats-histogram-bin b/build/scripts-2.7/ih-stats-histogram-bin
new file mode 100755
index 0000000000000000000000000000000000000000..b6c38e344d6a0f9508ff664eb5f24723d77b48e3
--- /dev/null
+++ b/build/scripts-2.7/ih-stats-histogram-bin
@@ -0,0 +1,23 @@
+#!/usr/bin/python
+import argparse
+import traceback
+import ih.statistics
+import json
+
+parser = argparse.ArgumentParser(description = "Gathers shoot area information based on specified groupings.")
+parser.add_argument("--db", dest="db", help="Database to run statistics on.", required = True)
+parser.add_argument("--options", dest="options", help="Path to options json file.", required = True)
+parser.add_argument("--intable", dest="intable", help="Input table to gather data from.", required = True)
+parser.add_argument("--outtable", dest="outtable", help="Output table to write data to.", required = True)
+parser.add_argument("--jsonwrite", dest="jsonwrite", default = False, action="store_true", help="If specified, writes json output.")
+parser.add_argument("--overwrite", dest="overwrite", default = False, action="store_true", help="If specified, will overwrite the output table.")
+args = parser.parse_args()
+
+with open(args.options, "r") as rh:
+ options = json.load(rh)
+if "histogram-bin" in options:
+ stats = ih.statistics.Stats(args.db)
+ stats.histogramBinning(args.intable, args.outtable, options["histogram-bin"]["--group"], options["histogram-bin"]["--chunks"], options["histogram-bin"]["--channels"], args.jsonwrite, args.overwrite)
+ stats._closeConnection()
+else:
+ print "Key Error: key 'histogram-bin' must be in options file!"
diff --git a/build/scripts-2.7/ih-stats-normalize b/build/scripts-2.7/ih-stats-normalize
new file mode 100755
index 0000000000000000000000000000000000000000..d33ebe5ae0312f0ed06df9b05b7e1125b12cc0db
--- /dev/null
+++ b/build/scripts-2.7/ih-stats-normalize
@@ -0,0 +1,17 @@
+#!/usr/bin/python
+import argparse
+import traceback
+import ih.statistics
+import json
+
+parser = argparse.ArgumentParser(description = "Gathers shoot area information based on specified groupings.")
+parser.add_argument("--db", dest="db", help="Database to run statistics on.", required = True)
+parser.add_argument("--intable", dest="intable", help="Input table to gather data from.", required = True)
+parser.add_argument("--outtable", dest="outtable", help="Output table to write data to.", required = True)
+parser.add_argument("--column", dest="column", help="Column to normalize numeric values to.", required = True)
+parser.add_argument("--overwrite", dest="overwrite", action="store_true", help="If specified, will overwrite the output table.")
+args = parser.parse_args()
+
+stats = ih.statistics.Stats(args.db)
+stats.normalize(args.intable, args.outtable, args.column, args.overwrite)
+stats._closeConnection()
\ No newline at end of file
diff --git a/build/scripts-2.7/ih-stats-shoot-area b/build/scripts-2.7/ih-stats-shoot-area
new file mode 100755
index 0000000000000000000000000000000000000000..8dacec95d7b2952375b82844576bf6d920037eef
--- /dev/null
+++ b/build/scripts-2.7/ih-stats-shoot-area
@@ -0,0 +1,17 @@
+#!/usr/bin/python
+import argparse
+import traceback
+import ih.statistics
+import json
+
+parser = argparse.ArgumentParser(description = "Gathers shoot area information based on specified groupings.")
+parser.add_argument("--db", dest="db", help="Database to run statistics on.", required = True)
+parser.add_argument("--intable", dest="intable", help="Input table to gather data from.", required = True)
+parser.add_argument("--outtable", dest="outtable", help="Output table to write data to.", required = True)
+parser.add_argument("--group", dest="group", nargs="+", help="Image types to group by. Should be in json format.", required = True)
+parser.add_argument("--overwrite", dest="overwrite", action="store_true", help="If specified, will overwrite the output table.")
+args = parser.parse_args()
+
+stats = ih.statistics.Stats(args.db)
+stats.shootArea(args.intable, args.outtable, args.group, args.overwrite)
+stats._closeConnection()
diff --git a/build/scripts-2.7/ih-stats-threshold b/build/scripts-2.7/ih-stats-threshold
new file mode 100755
index 0000000000000000000000000000000000000000..4399cfb45370998cf192509297085e8f6307d77e
--- /dev/null
+++ b/build/scripts-2.7/ih-stats-threshold
@@ -0,0 +1,17 @@
+#!/usr/bin/python
+import argparse
+import traceback
+import ih.statistics
+import json
+
+parser = argparse.ArgumentParser(description = "Gathers shoot area information based on specified groupings.")
+parser.add_argument("--db", dest="db", help="Database to run statistics on.", required = True)
+parser.add_argument("--intable", dest="intable", help="Input table to gather data from.", required = True)
+parser.add_argument("--outtable", dest="outtable", help="Output table to write data to.", required = True)
+parser.add_argument("--thresh", dest="thresh", type=float, help="Threhsold value.", required = True)
+parser.add_argument("--overwrite", dest="overwrite", action="store_true", help="If specified, will overwrite the output table.")
+args = parser.parse_args()
+
+stats = ih.statistics.Stats(args.db)
+stats.threshold(args.intable, args.outtable, args.thresh, args.overwrite)
+stats._closeConnection()
diff --git a/build/scripts-2.7/ih-stats-treatment-comp b/build/scripts-2.7/ih-stats-treatment-comp
new file mode 100755
index 0000000000000000000000000000000000000000..207d7e89496a0d2e660e4f32099860f40e1d33a0
--- /dev/null
+++ b/build/scripts-2.7/ih-stats-treatment-comp
@@ -0,0 +1,20 @@
+#!/usr/bin/python
+import argparse
+import traceback
+import ih.statistics
+import json
+
+parser = argparse.ArgumentParser(description = "Gathers shoot area information based on specified groupings.")
+parser.add_argument("--db", dest="db", help="Database to run statistics on.", required = True)
+parser.add_argument("--intable", dest="intable", help="Input table to gather data from.", required = True)
+parser.add_argument("--outtable", dest="outtable", help="Output table to write data to.", required = True)
+parser.add_argument("--type", dest="type", default="ratio", help="Whether to perform division or subtraction between treatments.")
+paresr.add_argument("--direction", dest="direction", default="Control", help="Whether to perform C ~ S, or S ~ C.")
+parser.add_argument("--comp", dest="comp", default="imtype", help="Whether or not to use imtype or imgname as the primary comparison.")
+parser.add_argument("--overwrite", dest="overwrite", action="store_true", help="If specified, will overwrite the output table.")
+
+args = parser.parse_args()
+
+stats = ih.statistics.Stats(args.db)
+stats.treatmentComp(args.intable, args.outtable, args.type, args.direction, args.comp, args.overwrite)
+stats._closeConnection()
diff --git a/build/scripts-2.7/ih-stats-ttest b/build/scripts-2.7/ih-stats-ttest
new file mode 100755
index 0000000000000000000000000000000000000000..8120d5e583d02aaa184105b5175c1d8d11217cde
--- /dev/null
+++ b/build/scripts-2.7/ih-stats-ttest
@@ -0,0 +1,19 @@
+#!/usr/bin/python
+import argparse
+import traceback
+import ih.statistics
+import json
+
+parser = argparse.ArgumentParser(description = "Gathers shoot area information based on specified groupings.")
+parser.add_argument("--db", dest="db", help="Database to run statistics on.", required = True)
+parser.add_argument("--intable", dest="intable", help="Input table to gather data from.", required = True)
+parser.add_argument("--outtable", dest="outtable", help="Output table to write data to.", required = True)
+parser.add_argument("--comp", dest="comp", default="imtype", help="Whether or not to use imtype or imgname as the primary comparison.")
+parser.add_argument("--overwrite", dest="overwrite", action="store_true", help="If specified, will overwrite the output table.")
+
+args = parser.parse_args()
+
+stats = ih.statistics.Stats(args.db)
+stats.ttest(args.intable, args.outtable, args.comp)
+stats.treatmentComp(args.intable, args.outtable, args.type, args.direction, args.comp, args.overwrite)
+stats._closeConnection()
\ No newline at end of file
diff --git a/build/scripts-2.7/ih-threshold b/build/scripts-2.7/ih-threshold
new file mode 100755
index 0000000000000000000000000000000000000000..64efb49e6223f71bb5c604fb6ea9211bc23e91c7
--- /dev/null
+++ b/build/scripts-2.7/ih-threshold
@@ -0,0 +1,21 @@
+#!/usr/bin/python
+import argparse
+import traceback
+import ih.imgproc
+
+parser = argparse.ArgumentParser(description = "Converts an image between color spectrums.")
+parser.add_argument("--input", dest="input", help="Path to input image.", required = True)
+parser.add_argument("--thresh", dest="thresh", default=127, type=int, help="Threshold cutoff value.")
+parser.add_argument("--max", dest="max", default=255, type=int, help="Write value for binary threhsold")
+parser.add_argument("--type", dest="type", default="binary", help="Threshold type, one of: binary, trunc, tozero, otsu.")
+parser.add_argument("--outputdir", dest="outputdir", default=".", help="Path to write output files, if not specified use current directory.")
+parser.add_argument("--output", dest="output", default=None, help="Name of output image to write, if not specified, use input image name.")
+
+args = parser.parse_args()
+
+try:
+ plant = ih.imgproc.Image(args.input, args.outputdir, args.output, False)
+ plant.threshold(args.thresh, args.max, args.type)
+ plant.write()
+except Exception as e:
+ print traceback.format_exc()
diff --git a/docs/.DS_Store b/docs/.DS_Store
new file mode 100644
index 0000000000000000000000000000000000000000..09ba03b6ae0f41397edbc146363c79ac9a82677a
Binary files /dev/null and b/docs/.DS_Store differ
diff --git a/docs/build/doctrees/environment.pickle b/docs/build/doctrees/environment.pickle
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index 0000000000000000000000000000000000000000..6ba25b342d1e5e3ae96dd725d8e14a303af26d3e
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diff --git a/docs/build/doctrees/ex_script_color1.doctree b/docs/build/doctrees/ex_script_color1.doctree
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index 0000000000000000000000000000000000000000..b7e15369e2cb67d009ff4c298bafcfd24d216c87
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diff --git a/docs/build/doctrees/ex_script_core1.doctree b/docs/build/doctrees/ex_script_core1.doctree
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index 0000000000000000000000000000000000000000..de683c36eaa0fb02caf8a436a20f077b3d9e7947
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diff --git a/docs/build/doctrees/ex_script_core2.doctree b/docs/build/doctrees/ex_script_core2.doctree
new file mode 100644
index 0000000000000000000000000000000000000000..11c459b02db49a80eefc8cd7a6629846a66adfde
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diff --git a/docs/build/doctrees/ex_workflow_1.doctree b/docs/build/doctrees/ex_workflow_1.doctree
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index 0000000000000000000000000000000000000000..79190f7bb13557f51d3e5fe609270d9e7718d6ed
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diff --git a/docs/build/doctrees/examples.doctree b/docs/build/doctrees/examples.doctree
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diff --git a/docs/build/doctrees/indexing.doctree b/docs/build/doctrees/indexing.doctree
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diff --git a/docs/build/doctrees/installation.doctree b/docs/build/doctrees/installation.doctree
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diff --git a/docs/build/doctrees/processing.doctree b/docs/build/doctrees/processing.doctree
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diff --git a/docs/build/doctrees/start.doctree b/docs/build/doctrees/start.doctree
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diff --git a/docs/build/doctrees/statistics.doctree b/docs/build/doctrees/statistics.doctree
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diff --git a/docs/build/doctrees/viewer.doctree b/docs/build/doctrees/viewer.doctree
new file mode 100644
index 0000000000000000000000000000000000000000..a1e5dfd18750299b39743c43216159d08199c48b
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diff --git a/docs/build/doctrees/workflowimage.doctree b/docs/build/doctrees/workflowimage.doctree
new file mode 100644
index 0000000000000000000000000000000000000000..fac8967146a09b772fa4c66ce2ebe700df4b0119
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diff --git a/docs/build/doctrees/workflowstats.doctree b/docs/build/doctrees/workflowstats.doctree
new file mode 100644
index 0000000000000000000000000000000000000000..ae94cfbc570230e87eece93dbdb575eb4c62fb4f
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diff --git a/docs/build/html/.buildinfo b/docs/build/html/.buildinfo
new file mode 100644
index 0000000000000000000000000000000000000000..0885fbe1fb7815bef3702a23c8ad1510832e4d1c
--- /dev/null
+++ b/docs/build/html/.buildinfo
@@ -0,0 +1,4 @@
+# Sphinx build info version 1
+# This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
+config:
+tags:
diff --git a/docs/build/html/_downloads/GenKey.csv b/docs/build/html/_downloads/GenKey.csv
new file mode 100644
index 0000000000000000000000000000000000000000..39451661df36aace83fa6d5e56ac3e951063fb6e
--- /dev/null
+++ b/docs/build/html/_downloads/GenKey.csv
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diff --git a/docs/build/html/_downloads/base.png b/docs/build/html/_downloads/base.png
new file mode 100644
index 0000000000000000000000000000000000000000..ca0078b83aecc9c39c58eb028c46b7e6cf9695b1
Binary files /dev/null and b/docs/build/html/_downloads/base.png differ
diff --git a/docs/build/html/_downloads/base1.png b/docs/build/html/_downloads/base1.png
new file mode 100644
index 0000000000000000000000000000000000000000..1782a2e03241d84cb8aaf1bf6b5bc111e8fe39dc
Binary files /dev/null and b/docs/build/html/_downloads/base1.png differ
diff --git a/docs/build/html/_downloads/color1.py b/docs/build/html/_downloads/color1.py
new file mode 100644
index 0000000000000000000000000000000000000000..5c4d1811b9229e8d6e8c3ca12926d373b8d2e647
--- /dev/null
+++ b/docs/build/html/_downloads/color1.py
@@ -0,0 +1,22 @@
+import ih.imgproc
+
+plant = ih.imgproc.Image("/path/to/your/image")
+plant.save("base")
+
+logicList = [
+"(((r + g) + b) > 350)",
+"(r >= 250)",
+"((b > 150) and (b < 220))",
+"((((b max g) max r) - ((b min g) min r)) > 20)",
+"((((r + g) + b) > 700) or (((r + g) + b) < 100))",
+"((r - g) > 50)",
+"(((g - r) > 15) and (b < g))"
+]
+
+for logic in logicList:
+ plant.restore("base")
+ plant.show("base")
+ plant.colorFilter(logic)
+ plant.show(logic)
+ plant.wait()
+
diff --git a/docs/build/html/_downloads/color1.sh b/docs/build/html/_downloads/color1.sh
new file mode 100644
index 0000000000000000000000000000000000000000..f1f6f147492a113133ea8393ec16cb8e5d9467f0
--- /dev/null
+++ b/docs/build/html/_downloads/color1.sh
@@ -0,0 +1,9 @@
+#!/bin/bash
+
+ih-color-filter --input "/path/to/your/image" --output "logic0.png" --logic "(((r + g) + b) > 350)"
+ih-color-filter --input "/path/to/your/image" --output "logic1.png" --logic "(r >= 250)"
+ih-color-filter --input "/path/to/your/image" --output "logic2.png" --logic "((b > 150) and (b < 220))"
+ih-color-filter --input "/path/to/your/image" --output "logic3.png" --logic "((((b max g) max r) - ((b min g) min r)) > 20)"
+ih-color-filter --input "/path/to/your/image" --output "logic4.png" --logic "((((r + g) + b) > 700) or (((r + g) + b) < 100))"
+ih-color-filter --input "/path/to/your/image" --output "logic5.png" --logic "((r - g) > 50)"
+ih-color-filter --input "/path/to/your/image" --output "logic6.png" --logic "(((g - r) > 15) and (b < g))"
\ No newline at end of file
diff --git a/docs/build/html/_downloads/config.json b/docs/build/html/_downloads/config.json
new file mode 100644
index 0000000000000000000000000000000000000000..2dcae475e689e8863562757904203f1057eef1ff
--- /dev/null
+++ b/docs/build/html/_downloads/config.json
@@ -0,0 +1,25 @@
+{
+ "installdir": "/work/walia/common/ih/pymodules/bin/",
+ "profile": {
+ "pegasus": {
+ "style": "glite"
+ },
+ "condor": {
+ "grid_resource": "pbs",
+ "universe": "vanilla"
+ },
+ "env": {
+ "PATH": "/work/walia/common/ih/pymodules/bin/",
+ "LD_LIBRARY_PATH": "/work/walia/common/ih/pymodules/opencv_lib/"
+ }
+ },
+ "cluster": 100,
+ "maxwalltime": {
+ "images": 2,
+ "stats": 300
+ },
+ "notify": {
+ "email": "avi@kurtknecht.com",
+ "pegasus_home": "/usr/share/pegasus/"
+ }
+}
diff --git a/docs/build/html/_downloads/core1.py b/docs/build/html/_downloads/core1.py
new file mode 100644
index 0000000000000000000000000000000000000000..53943339f7392307a51ba380b41db565e2c7a341
--- /dev/null
+++ b/docs/build/html/_downloads/core1.py
@@ -0,0 +1,31 @@
+import ih.imgproc
+
+plant = ih.imgproc.Image("/Volumes/BLOO/Work/hcc/ih/paper/fluosv/step0.png")
+
+plant.save("base")
+plant.show("base")
+plant.write("base.png")
+
+plant.convertColor("bgr", "gray")
+plant.save("gray")
+plant.show("gray")
+plant.write("gray.png")
+
+plant.threshold(50)
+plant.save("thresh50")
+plant.show("thresh50")
+plant.restore("gray")
+
+plant.threshold(75)
+plant.save("thresh75")
+plant.show("thresh75")
+plant.restore("gray")
+
+plant.threshold(100)
+plant.save("thresh100")
+plant.show("thresh100")
+plant.restore("gray")
+
+plant.wait()
+plant.restore("thresh50")
+plant.write("thresh50.png")
diff --git a/docs/build/html/_downloads/core1.sh b/docs/build/html/_downloads/core1.sh
new file mode 100644
index 0000000000000000000000000000000000000000..eb3dc58d456779afb86bd22d4545e25d2309b16e
--- /dev/null
+++ b/docs/build/html/_downloads/core1.sh
@@ -0,0 +1,6 @@
+#!/bin/bash
+
+ih-convert-color --input "/path/to/your/image" --output "gray.png" --intype "bgr" --outtype "gray"
+ih-threshold --input "gray.png" --output "thresh50.png" --thresh 50
+ih-threshold --input "gray.png" --output "thresh75.png" --thresh 75
+ih-threshold --input "gray.png" --output "thresh100.png" --thresh 100
diff --git a/docs/build/html/_downloads/core2.py b/docs/build/html/_downloads/core2.py
new file mode 100644
index 0000000000000000000000000000000000000000..7b71f5078cf75bb325cba371127602c0a36890e5
--- /dev/null
+++ b/docs/build/html/_downloads/core2.py
@@ -0,0 +1,52 @@
+import ih.imgproc
+
+plant = ih.imgproc.Image("/path/to/your/image")
+
+plant.save("base")
+plant.show("base")
+plant.write("base.png")
+
+plant.convertColor("bgr", "gray")
+plant.show("grayscale")
+plant.write("gray.png")
+
+plant.gaussianBlur((5, 5))
+plant.show("blur")
+plant.write("blur.png")
+
+plant.adaptiveThreshold(255, "mean", "binary", 15, 3)
+plant.show("adaptive threshold")
+plant.write("thresh.png")
+
+plant.bitwise_not()
+plant.show("invert")
+plant.write("invert.png")
+
+plant.convertColor("gray", "bgr")
+plant.bitwise_and("base")
+plant.show("recolor")
+plant.write("recolor.png")
+
+plant.morphology("open", "rect", (3, 3))
+plant.show("morph")
+plant.write("morph.png")
+
+plant.colorFilter("(((max - min) > 40) and ((b - g) < 30))", [plant.y - 350, plant.y, -1, -1])
+plant.show("filter")
+plant.write("filter.png")
+plant.save("filter")
+
+plant.convertColor("bgr", "gray")
+plant.threshold(0)
+plant.save("binary")
+plant.restore("filter")
+
+plant.contourCut("binary", basemin = 500, resize = True)
+plant.show("final")
+plant.write("final.png")
+
+print "total plant pixels = ",plant.extractPixels()
+print "[plant height, plant width] = ",plant.extractDimensions()
+print "Nonzero color data -- [ [bmean, bmed], [gmean, gmed], [rmean, rmed] ] = ",plant.extractColorData()
+print "With zero color data -- [ [bmean, bmed], [gmean, gmed], [rmean, rmed] ] = ",plant.extractColorData(nonzero = False)
+plant.wait()
diff --git a/docs/build/html/_downloads/core2.sh b/docs/build/html/_downloads/core2.sh
new file mode 100644
index 0000000000000000000000000000000000000000..92bb47605d5c74ee6371b628f65f5a5aa3b94c29
--- /dev/null
+++ b/docs/build/html/_downloads/core2.sh
@@ -0,0 +1,12 @@
+#!/bin/bash
+
+ih-convert-color --input "base.png" --output "gray.png" --intype "bgr" --outtype "gray"
+ih-gaussian-blur --input "gray.png" --output "blur.png" --kwidth 5 --kheight 5
+ih-adaptive-threshold --input "blur.png" --output "thresh.png" --value 255 --adaptiveType "mean" --thresholdType "binary" --blockSize 15 --C 3
+ih-bitwise-not --input "thresh.png" --output "invert.png"
+ih-bitwise-and --input1 "base.png" --input2 "invert.png" --output "recolor.png"
+ih-morphology --input "recolor.png" --output "morph.png" --morphType "open" --ktype "rect" --kwidth 3 --kheight 3
+ih-color-filter --input "morph.png" --output "filter.png" --logic "(((max - min) > 40) and ((b - g) < 30))" --ystart "y - 350"
+ih-threshold --input "filter.png" --output "binary.png" --thresh 0
+ih-contour-cut --input "filter.png" --binary "binary.png" --output "final.png" --basemin 500 --resize
+
diff --git a/docs/build/html/_downloads/crawl.json b/docs/build/html/_downloads/crawl.json
new file mode 100644
index 0000000000000000000000000000000000000000..43030bc747bc93c16d1d641de27600fb029b5541
--- /dev/null
+++ b/docs/build/html/_downloads/crawl.json
@@ -0,0 +1,65 @@
+{
+ "path": "/work/walia/common/ih/rawdata/0184 Uni Nebraska Rice 1/%null%/%null%_%idnum%-%idchar%_%date%/%imgname%/0_0.png",
+ "base": "/work/walia/common/ih/rawdata/0184 Uni Nebraska Rice 1/",
+ "filetype": ".png",
+ "order": ["experiment", "id", "genotype", "date", "treatment", "imgname", "imtype", "path"],
+ "data": {
+ "experiment": {
+ "type": "value",
+ "value": "0184"
+ },
+ "id": {
+ "type": "value",
+ "value": "%idnum%-%idchar%"
+ },
+ "genotype": {
+ "type": "file",
+ "value": "/Users/aknecht/git/ih/old_scripts/2014-09-03/GenKey.csv",
+ "key": "%idnum%-%idchar%",
+ "keyColumn": 0,
+ "valueColumn": 1
+
+ },
+ "date": {
+ "type": "value",
+ "value": "%date%",
+ "format": "Y-m-d"
+ },
+ "treatment": {
+ "type": "value",
+ "translate": "true",
+ "value": "%idchar%"
+ },
+ "imgname": {
+ "type": "value",
+ "value": "%imgname%"
+ },
+ "imtype": {
+ "type": "value",
+ "translate": "true",
+ "value": "%imgname%"
+ }
+ },
+ "translations": {
+ "treatment": {
+ "S": "Stress",
+ "s": "Stress",
+ "C": "Control",
+ "c": "Control"
+ },
+ "imtype": {
+ "RGB SV1": "rgbsv",
+ "RGB SV2": "rgbsv",
+ "RGB TV": "rgbtv",
+ "FLUO SV1": "fluosv",
+ "FLUO SV2": "fluosv",
+ "FLUO TV": "fluotv",
+ "NIR SV1": "nirsv",
+ "NIR SV2": "nirsv",
+ "NIR TV": "nirtv",
+ "IR SV1": "irsv",
+ "IR SV2": "irsv",
+ "IR TV": "irtv"
+ }
+ }
+}
diff --git a/docs/build/html/_downloads/imgproc.json b/docs/build/html/_downloads/imgproc.json
new file mode 100644
index 0000000000000000000000000000000000000000..0cc7253dab5b2cef4b872b5c22f09f1f062d9baf
--- /dev/null
+++ b/docs/build/html/_downloads/imgproc.json
@@ -0,0 +1,327 @@
+{
+ "workflows": {
+ "fluosv": [
+ {
+ "name": "pot_filter_1",
+ "executable": "ih-color-filter",
+ "inputs": ["base", "/Volumes/BLOO/Work/hcc/plantcv/new/workflow1/input/fluosv_pot1.json"],
+ "outputs": ["pot1"],
+ "arguments": {
+ "--logic": "(((((((r - g) < 30) and (((r + g) + b) < 110)) or ((((r + g) + b) > 110) and ((r - g) < 50))) or (((r - g) < 25) and ((g - r) < 25))) or (g > 60)) not 1)"
+ }
+ },
+ {
+ "name": "pot_filter_2",
+ "executable": "ih-color-filter",
+ "inputs": ["pot1", "/Volumes/BLOO/Work/hcc/plantcv/new/workflow1/input/fluosv_pot2.json"],
+ "outputs": ["pot2"],
+ "arguments": {
+ "--logic": "(((r + g) + b) > 120)"
+ },
+ "depends": ["pot_filter_1"]
+ },
+ {
+ "name": "main_filter",
+ "executable": "ih-color-filter",
+ "inputs": ["pot2"],
+ "outputs": ["filter"],
+ "arguments": {
+ "--logic": "((r - g) > 10)"
+ },
+ "depends": ["pot_filter_2"]
+ },
+ {
+ "name": "crop",
+ "executable": "ih-crop",
+ "inputs": ["filter", "/Volumes/BLOO/Work/hcc/plantcv/new/workflow1/input/fluosv_edge.json"],
+ "outputs": ["edged"],
+ "arguments": {},
+ "depends": ["main_filter"]
+ },
+ {
+ "name": "cut",
+ "executable": "ih-contour-cut",
+ "inputs": ["edged", "edged"],
+ "outputs": ["final"],
+ "arguments": {
+ "--resize": "",
+ "--basemin": 75
+ },
+ "depends": ["crop"]
+ }
+ ],
+ "rgbtv": [
+ {
+ "name": "normalize",
+ "executable": "ih-normalize-intensity",
+ "inputs": ["base"],
+ "outputs": ["normal"],
+ "arguments": {}
+ },
+ {
+ "name": "meanshift",
+ "executable": "ih-meanshift",
+ "inputs": ["normal"],
+ "outputs": ["shift"],
+ "arguments": {
+ "--spatial_radius": 4,
+ "--range_radius": 4,
+ "--min_density": 40
+ },
+ "depends": ["normalize"]
+ },
+ {
+ "name": "main_filter",
+ "executable": "ih-color-filter",
+ "inputs": ["shift"],
+ "outputs": ["filter"],
+ "arguments": {
+ "--logic": "(((g > r) and (g > b)) and ((((b max g) max r) - ((b min g) min r)) > 20))"
+ },
+ "depends": ["meanshift"]
+ },
+ {
+ "name": "closing",
+ "executable": "ih-morphology",
+ "inputs": ["filter"],
+ "outputs": ["morphed"],
+ "arguments": {
+ "--ktype": "ellipse",
+ "--kwidth": 5,
+ "--kheight": 5,
+ "--morphType": "close"
+ },
+ "depends": ["main_filter"]
+ },
+ {
+ "name": "crop",
+ "executable": "ih-crop",
+ "inputs": ["morphed", "/Volumes/BLOO/Work/hcc/plantcv/new/workflow1/input/rgbtv_edge.json"],
+ "outputs": ["edged"],
+ "arguments": {},
+ "depends": ["closing"]
+ },
+ {
+ "name": "reconstitute",
+ "executable": "ih-bitwise-and",
+ "inputs": ["edged", "base"],
+ "outputs": ["recolor"],
+ "arguments": {},
+ "depends": ["crop"]
+ },
+ {
+ "name": "cut",
+ "executable": "ih-contour-cut",
+ "inputs": ["recolor", "recolor"],
+ "outputs": ["final"],
+ "arguments": {
+ "--basemin": 200,
+ "--resize": ""
+ },
+ "depends": ["reconstitute"]
+ }
+ ],
+ "rgbsv": [
+ {
+ "name": "pot-detect",
+ "executable": "ih-color-filter",
+ "inputs": ["base"],
+ "outputs": ["pot"],
+ "arguments": {
+ "--logic": "((((r + g) + b) < 100) or (((b - r) > 40) and ((b - g) > 30)))"
+ }
+ },
+ {
+ "name": "pot-crop",
+ "executable": "ih-contour-cut",
+ "inputs": ["pot", "pot"],
+ "outputs": ["unused_1", "pot_roi"],
+ "arguments": {
+ "--basemin": 100,
+ "--padminy": 100,
+ "--padmaxy": 2000,
+ "--padminx": -25,
+ "--padmaxx": -25,
+ "--returnBound": ""
+ },
+ "depends": ["pot-detect"]
+ },
+ {
+ "name": "box-crop",
+ "executable": "ih-contour-cut",
+ "inputs": ["pot", "pot"],
+ "outputs": ["unused_2", "box_roi"],
+ "arguments": {
+ "--basemin": 100,
+ "--padminy": 35,
+ "--padmaxy": 2000,
+ "--padminx": 50,
+ "--padmaxx": 50,
+ "--returnBound": ""
+ },
+ "depends": ["pot-detect"]
+ },
+ {
+ "name": "gray",
+ "executable": "ih-convert-color",
+ "inputs": ["base"],
+ "outputs": ["grayscale"],
+ "arguments": {
+ "--intype": "bgr",
+ "--outtype": "gray"
+ }
+ },
+ {
+ "name": "blur",
+ "executable": "ih-gaussian-blur",
+ "inputs": ["grayscale"],
+ "outputs": ["blurred"],
+ "arguments": {
+ "--kwidth": 5,
+ "--kheight": 5
+ },
+ "depends": ["gray"]
+ },
+ {
+ "name": "thresh",
+ "executable": "ih-adaptive-threshold",
+ "inputs": ["blurred"],
+ "outputs": ["thresh"],
+ "arguments": {
+ "--value": 255,
+ "--thresholdType": "inverse",
+ "--adaptiveType": "mean",
+ "--blockSize": 15,
+ "--C": 3
+ },
+ "depends": ["blur"]
+ },
+ {
+ "name": "reconstitute1",
+ "executable": "ih-bitwise-and",
+ "inputs": ["thresh", "base"],
+ "outputs": ["recolor1"],
+ "arguments": {},
+ "depends": ["thresh"]
+ },
+ {
+ "name": "meanshift",
+ "executable": "ih-meanshift",
+ "inputs": ["recolor1"],
+ "outputs": ["shift"],
+ "arguments": {
+ "--spatial_radius": 2,
+ "--range_radius": 2,
+ "--min_density": 50
+ },
+ "depends": ["reconstitute1"]
+ },
+ {
+ "name": "pot-filter",
+ "executable": "ih-color-filter",
+ "inputs": ["shift", "pot_roi"],
+ "outputs": ["pot_filtered"],
+ "arguments": {
+ "--logic": "((((((((((r > g) and (r > b)) and (((b max g) - (b min g)) < (((r + g) + b) / 20))) or ((((b max g) max r) - ((b min g) min r)) < 10)) or ((b > r) and ((b > g) or (g > r)))) or (((r + g) + b) < 220)) or ((((r + g) + b) < 350) and ((((b max g) max r) - ((b min g) min r)) < 25))) or ((b > g) and (r > g))) or (((((r - g) > 5) and ((g - b) > 5)) and ((r - g) < 25)) and ((g - b) < 25))) not 1)"
+ },
+ "depends": ["meanshift", "pot-crop"]
+ },
+ {
+ "name": "box-filter",
+ "executable": "ih-color-filter",
+ "inputs": ["pot_filtered", "box_roi"],
+ "outputs": ["box_filtered"],
+ "arguments": {
+ "--logic": "(((g - b) > 30) or ((r - b) > 30))"
+ },
+ "depends": ["pot-filter", "box-crop"]
+ },
+ {
+ "name": "gfilter1",
+ "executable": "ih-color-filter",
+ "inputs": ["box_filtered", "/Volumes/BLOO/Work/hcc/plantcv/new/workflow1/input/rgbsv_gray1.json"],
+ "outputs": ["gray_filtered1"],
+ "arguments": {
+ "--logic": "((((b max g) max r) - ((b min g) min r)) > 50)"
+ },
+ "depends": ["box-filter", "box-crop"]
+ },
+ {
+ "name": "gfilter2",
+ "executable": "ih-color-filter",
+ "inputs": ["gray_filtered1", "/Volumes/BLOO/Work/hcc/plantcv/new/workflow1/input/rgbsv_gray2.json"],
+ "outputs": ["gray_filtered2"],
+ "arguments": {
+ "--logic": "((((b max g) max r) - ((b min g) min r)) > 100)"
+ },
+ "depends": ["gfilter1"]
+ },
+ {
+ "name": "crop",
+ "executable": "ih-crop",
+ "inputs": ["gray_filtered2", "/Volumes/BLOO/Work/hcc/plantcv/new/workflow1/input/rgbsv_edge.json"],
+ "outputs": ["edged"],
+ "arguments": {},
+ "depends": ["gfilter2"]
+ },
+ {
+ "name": "reconstitute2",
+ "executable": "ih-bitwise-and",
+ "inputs": ["edged", "base"],
+ "outputs": ["recolor2"],
+ "arguments": {},
+ "depends": ["crop"]
+ },
+ {
+ "name": "cut",
+ "executable": "ih-contour-cut",
+ "inputs": ["recolor2", "recolor2"],
+ "outputs": ["final"],
+ "arguments": {
+ "--basemin": 50,
+ "--resize": ""
+ },
+ "depends": ["reconstitute2"]
+ }
+ ]
+ },
+ "options": {
+
+ },
+ "extract": {
+ "histogram-bin": {
+ "--group": {"rgb": ["rgbsv", "rgbtv"], "fluo": ["fluosv"]},
+ "--chunks": {"rgb": 5, "fluo": 6},
+ "--channels": {"rgb": [0, 1, 2], "fluo": [1, 2]}
+ },
+ "workflows": {
+ "rgbsv": {
+ "inputs": ["final"],
+ "arguments": {
+ "--dimensions": "",
+ "--pixels": "",
+ "--moments": ""
+ },
+ "depends": ["cut"]
+ },
+ "rgbtv": {
+ "inputs": ["final"],
+ "arguments": {
+ "--dimensions": "",
+ "--pixels": "",
+ "--moments": ""
+ },
+ "depends": ["cut"]
+ },
+ "fluosv": {
+ "inputs": ["final"],
+ "arguments": {
+ "--dimensions": "",
+ "--pixels": "",
+ "--moments": ""
+ },
+ "depends": ["cut"]
+ }
+ }
+ }
+}
diff --git a/docs/build/html/_downloads/rgbtv1.png b/docs/build/html/_downloads/rgbtv1.png
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diff --git a/docs/build/html/_modules/htpia/imgproc.html b/docs/build/html/_modules/htpia/imgproc.html
new file mode 100644
index 0000000000000000000000000000000000000000..d5444314aa73af074e12918a0abdfb2c549e4a1b
--- /dev/null
+++ b/docs/build/html/_modules/htpia/imgproc.html
@@ -0,0 +1,1090 @@
+<!DOCTYPE html>
+
+
+<html xmlns="http://www.w3.org/1999/xhtml">
+ <head>
+ <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
+
+ <title>htpia.imgproc — Image Harvest 1.0.1 documentation</title>
+
+ <link rel="stylesheet" href="../../_static/basic.css" type="text/css" />
+ <link rel="stylesheet" href="../../_static/pygments.css" type="text/css" />
+ <link rel="stylesheet" href="../../_static/bootstrap-3.2.0/css/bootstrap.min.css" type="text/css" />
+ <link rel="stylesheet" href="../../_static/bootstrap-3.2.0/css/bootstrap-theme.min.css" type="text/css" />
+ <link rel="stylesheet" href="../../_static/bootstrap-sphinx.css" type="text/css" />
+
+ <script type="text/javascript">
+ var DOCUMENTATION_OPTIONS = {
+ URL_ROOT: '../../',
+ VERSION: '1.0.1',
+ COLLAPSE_INDEX: false,
+ FILE_SUFFIX: '.html',
+ HAS_SOURCE: true
+ };
+ </script>
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+
+ <h1>Source code for htpia.imgproc</h1><div class="highlight"><pre>
+<span class="sd">"""</span>
+
+<span class="sd">.. module:: imgproc</span>
+<span class="sd"> :platform: Mac, Linux</span>
+<span class="sd"> :synopsis: Image processing function wrappers to opencv.</span>
+
+<span class="sd">.. moduleauthor:: Avi Knecht <avi@kurtknecht.com></span>
+
+<span class="sd">"""</span>
+
+<span class="kn">import</span> <span class="nn">os</span>
+<span class="kn">import</span> <span class="nn">cv2</span>
+<span class="kn">import</span> <span class="nn">numpy</span> <span class="kn">as</span> <span class="nn">np</span>
+<span class="kn">import</span> <span class="nn">math</span>
+<span class="kn">import</span> <span class="nn">conf</span>
+<span class="kn">import</span> <span class="nn">sqlite3</span>
+<span class="kn">import</span> <span class="nn">pymeanshift</span> <span class="kn">as</span> <span class="nn">pms</span>
+<span class="kn">import</span> <span class="nn">traceback</span>
+<span class="kn">import</span> <span class="nn">json</span>
+
+<span class="k">class</span> <span class="nc">ColorFilter</span><span class="p">(</span><span class="nb">object</span><span class="p">):</span>
+
+ <span class="sd">"""</span>
+<span class="sd"> Color Filtration logic container.</span>
+<span class="sd"> """</span>
+ <span class="k">def</span> <span class="nf">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="nb">filter</span><span class="p">):</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">tokens</span> <span class="o">=</span> <span class="p">{</span>
+ <span class="s">"True"</span><span class="p">:</span> <span class="bp">True</span><span class="p">,</span>
+ <span class="s">"False"</span><span class="p">:</span> <span class="bp">False</span><span class="p">,</span>
+ <span class="s">"and"</span><span class="p">:</span> <span class="k">lambda</span> <span class="n">left</span><span class="p">,</span> <span class="n">right</span><span class="p">:</span> <span class="n">np</span><span class="o">.</span><span class="n">logical_and</span><span class="p">(</span><span class="n">left</span><span class="p">,</span> <span class="n">right</span><span class="p">),</span>
+ <span class="s">"or"</span><span class="p">:</span> <span class="k">lambda</span> <span class="n">left</span><span class="p">,</span> <span class="n">right</span><span class="p">:</span> <span class="n">np</span><span class="o">.</span><span class="n">logical_or</span><span class="p">(</span><span class="n">left</span><span class="p">,</span> <span class="n">right</span><span class="p">),</span>
+ <span class="s">">"</span><span class="p">:</span> <span class="k">lambda</span> <span class="n">left</span><span class="p">,</span> <span class="n">right</span><span class="p">:</span> <span class="n">left</span> <span class="o">></span> <span class="n">right</span><span class="p">,</span>
+ <span class="s">"<"</span><span class="p">:</span> <span class="k">lambda</span> <span class="n">left</span><span class="p">,</span> <span class="n">right</span><span class="p">:</span> <span class="n">left</span> <span class="o"><</span> <span class="n">right</span><span class="p">,</span>
+ <span class="s">">="</span><span class="p">:</span> <span class="k">lambda</span> <span class="n">left</span><span class="p">,</span> <span class="n">right</span><span class="p">:</span> <span class="n">left</span> <span class="o">>=</span> <span class="n">right</span><span class="p">,</span>
+ <span class="s">"<="</span><span class="p">:</span> <span class="k">lambda</span> <span class="n">left</span><span class="p">,</span> <span class="n">right</span><span class="p">:</span> <span class="n">left</span> <span class="o"><=</span> <span class="n">right</span><span class="p">,</span>
+ <span class="s">"="</span><span class="p">:</span> <span class="k">lambda</span> <span class="n">left</span><span class="p">,</span> <span class="n">right</span><span class="p">:</span> <span class="n">left</span> <span class="o">==</span> <span class="n">right</span><span class="p">,</span>
+ <span class="s">"+"</span><span class="p">:</span> <span class="k">lambda</span> <span class="n">left</span><span class="p">,</span> <span class="n">right</span><span class="p">:</span> <span class="n">left</span> <span class="o">+</span> <span class="n">right</span><span class="p">,</span>
+ <span class="s">"-"</span><span class="p">:</span> <span class="k">lambda</span> <span class="n">left</span><span class="p">,</span> <span class="n">right</span><span class="p">:</span> <span class="n">left</span> <span class="o">-</span> <span class="n">right</span><span class="p">,</span>
+ <span class="s">"*"</span><span class="p">:</span> <span class="k">lambda</span> <span class="n">left</span><span class="p">,</span> <span class="n">right</span><span class="p">:</span> <span class="n">left</span> <span class="o">*</span> <span class="n">right</span><span class="p">,</span>
+ <span class="s">"/"</span><span class="p">:</span> <span class="k">lambda</span> <span class="n">left</span><span class="p">,</span> <span class="n">right</span><span class="p">:</span> <span class="n">left</span> <span class="o">/</span> <span class="n">right</span><span class="p">,</span>
+ <span class="s">"max"</span><span class="p">:</span> <span class="k">lambda</span> <span class="n">left</span><span class="p">,</span> <span class="n">right</span><span class="p">:</span> <span class="n">np</span><span class="o">.</span><span class="n">maximum</span><span class="p">(</span><span class="n">left</span><span class="p">,</span> <span class="n">right</span><span class="p">),</span>
+ <span class="s">"min"</span><span class="p">:</span> <span class="k">lambda</span> <span class="n">left</span><span class="p">,</span> <span class="n">right</span><span class="p">:</span> <span class="n">np</span><span class="o">.</span><span class="n">minimum</span><span class="p">(</span><span class="n">left</span><span class="p">,</span> <span class="n">right</span><span class="p">),</span>
+ <span class="s">"not"</span><span class="p">:</span> <span class="k">lambda</span> <span class="n">left</span><span class="p">,</span> <span class="n">right</span><span class="p">:</span> <span class="n">np</span><span class="o">.</span><span class="n">invert</span><span class="p">(</span><span class="n">left</span><span class="p">),</span>
+ <span class="s">"("</span><span class="p">:</span> <span class="s">"("</span><span class="p">,</span>
+ <span class="s">")"</span><span class="p">:</span> <span class="s">")"</span><span class="p">,</span>
+ <span class="p">}</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">filterString</span> <span class="o">=</span> <span class="nb">filter</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">emptyRes</span> <span class="o">=</span> <span class="bp">True</span>
+ <span class="k">return</span>
+
+ <span class="k">def</span> <span class="nf">_createArgList</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+ <span class="n">s</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">filterString</span><span class="o">.</span><span class="n">replace</span><span class="p">(</span><span class="s">"("</span><span class="p">,</span> <span class="s">" ( "</span><span class="p">)</span>
+ <span class="n">s</span> <span class="o">=</span> <span class="n">s</span><span class="o">.</span><span class="n">replace</span><span class="p">(</span><span class="s">")"</span><span class="p">,</span> <span class="s">" ) "</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">filter</span> <span class="o">=</span> <span class="p">[]</span>
+ <span class="k">for</span> <span class="n">item</span> <span class="ow">in</span> <span class="n">s</span><span class="o">.</span><span class="n">split</span><span class="p">():</span>
+ <span class="k">if</span> <span class="n">item</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">tokens</span><span class="p">:</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">filter</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">tokens</span><span class="p">[</span><span class="n">item</span><span class="p">])</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="k">try</span><span class="p">:</span>
+ <span class="n">val</span> <span class="o">=</span> <span class="nb">int</span><span class="p">(</span><span class="n">item</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">filter</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">val</span><span class="p">)</span>
+ <span class="k">except</span><span class="p">:</span>
+ <span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="s">"Invalid logic string."</span><span class="p">)</span>
+ <span class="c">#self.filter = [self.tokens[x] if x in self.tokens else int(x) for x in s.split()]</span>
+ <span class="k">return</span>
+
+ <span class="k">def</span> <span class="nf">_find</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">what</span><span class="p">,</span> <span class="n">start</span> <span class="o">=</span> <span class="mi">0</span><span class="p">):</span>
+ <span class="k">return</span> <span class="p">[</span><span class="n">i</span> <span class="k">for</span> <span class="n">i</span><span class="p">,</span><span class="n">x</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">filter</span><span class="p">)</span> <span class="k">if</span> <span class="n">x</span> <span class="o">==</span> <span class="n">what</span> <span class="ow">and</span> <span class="n">i</span> <span class="o">>=</span> <span class="n">start</span><span class="p">]</span>
+
+ <span class="k">def</span> <span class="nf">_parens</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+ <span class="n">left_1st</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_find</span><span class="p">(</span><span class="s">"("</span><span class="p">)</span>
+ <span class="k">if</span> <span class="ow">not</span> <span class="n">left_1st</span><span class="p">:</span>
+ <span class="k">return</span> <span class="bp">False</span><span class="p">,</span> <span class="o">-</span><span class="mi">1</span><span class="p">,</span> <span class="o">-</span><span class="mi">1</span>
+ <span class="n">left</span> <span class="o">=</span> <span class="n">left_1st</span><span class="p">[</span><span class="o">-</span><span class="mi">1</span><span class="p">]</span>
+ <span class="n">right</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_find</span><span class="p">(</span><span class="s">")"</span><span class="p">,</span> <span class="n">left</span> <span class="o">+</span> <span class="mi">2</span><span class="p">)[</span><span class="mi">0</span><span class="p">]</span>
+ <span class="k">return</span> <span class="bp">True</span><span class="p">,</span> <span class="n">left</span><span class="p">,</span> <span class="n">right</span>
+
+ <span class="k">def</span> <span class="nf">_eval</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="nb">filter</span><span class="p">):</span>
+ <span class="k">return</span> <span class="nb">filter</span><span class="p">[</span><span class="mi">1</span><span class="p">](</span><span class="nb">filter</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span> <span class="nb">filter</span><span class="p">[</span><span class="mi">2</span><span class="p">])</span>
+
+ <span class="k">def</span> <span class="nf">_formattedEval</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="nb">filter</span><span class="p">):</span>
+ <span class="k">if</span> <span class="ow">not</span> <span class="nb">filter</span><span class="p">:</span>
+ <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">emptyRes</span>
+ <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="nb">filter</span><span class="p">)</span> <span class="o">==</span> <span class="mi">1</span><span class="p">:</span>
+ <span class="k">return</span> <span class="nb">filter</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span>
+
+ <span class="n">has_parens</span><span class="p">,</span> <span class="n">l_paren</span><span class="p">,</span> <span class="n">r_paren</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_parens</span><span class="p">()</span>
+
+ <span class="k">if</span> <span class="ow">not</span> <span class="n">has_parens</span><span class="p">:</span>
+ <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">_eval</span><span class="p">(</span><span class="nb">filter</span><span class="p">)</span>
+
+ <span class="nb">filter</span><span class="p">[</span><span class="n">l_paren</span><span class="p">:</span><span class="n">r_paren</span> <span class="o">+</span> <span class="mi">1</span><span class="p">]</span> <span class="o">=</span> <span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">_eval</span><span class="p">(</span><span class="nb">filter</span><span class="p">[</span><span class="n">l_paren</span><span class="o">+</span><span class="mi">1</span><span class="p">:</span><span class="n">r_paren</span><span class="p">])]</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">emptyRes</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_eval</span>
+ <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">_formattedEval</span><span class="p">(</span><span class="nb">filter</span><span class="p">)</span>
+
+ <span class="k">def</span> <span class="nf">apply</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">image</span><span class="p">,</span> <span class="n">roi</span><span class="p">):</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">tokens</span><span class="p">[</span><span class="s">"r"</span><span class="p">]</span> <span class="o">=</span> <span class="n">image</span><span class="p">[:,:,</span><span class="mi">2</span><span class="p">]</span><span class="o">.</span><span class="n">astype</span><span class="p">(</span><span class="nb">float</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">tokens</span><span class="p">[</span><span class="s">"g"</span><span class="p">]</span> <span class="o">=</span> <span class="n">image</span><span class="p">[:,:,</span><span class="mi">1</span><span class="p">]</span><span class="o">.</span><span class="n">astype</span><span class="p">(</span><span class="nb">float</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">tokens</span><span class="p">[</span><span class="s">"b"</span><span class="p">]</span> <span class="o">=</span> <span class="n">image</span><span class="p">[:,:,</span><span class="mi">0</span><span class="p">]</span><span class="o">.</span><span class="n">astype</span><span class="p">(</span><span class="nb">float</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_createArgList</span><span class="p">()</span>
+ <span class="n">result</span> <span class="o">=</span> <span class="n">cv2</span><span class="o">.</span><span class="n">cvtColor</span><span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">where</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">_formattedEval</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">filter</span><span class="p">),</span> <span class="mi">255</span><span class="p">,</span> <span class="mi">0</span><span class="p">)</span><span class="o">.</span><span class="n">astype</span><span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">uint8</span><span class="p">),</span> <span class="n">cv2</span><span class="o">.</span><span class="n">COLOR_GRAY2BGR</span><span class="p">)</span>
+ <span class="n">image</span><span class="p">[</span><span class="n">roi</span><span class="p">[</span><span class="mi">0</span><span class="p">]:</span><span class="n">roi</span><span class="p">[</span><span class="mi">1</span><span class="p">],</span> <span class="n">roi</span><span class="p">[</span><span class="mi">2</span><span class="p">]:</span><span class="n">roi</span><span class="p">[</span><span class="mi">3</span><span class="p">]]</span> <span class="o">=</span> <span class="n">cv2</span><span class="o">.</span><span class="n">bitwise_and</span><span class="p">(</span><span class="n">image</span><span class="p">[</span><span class="n">roi</span><span class="p">[</span><span class="mi">0</span><span class="p">]:</span><span class="n">roi</span><span class="p">[</span><span class="mi">1</span><span class="p">],</span> <span class="n">roi</span><span class="p">[</span><span class="mi">2</span><span class="p">]:</span><span class="n">roi</span><span class="p">[</span><span class="mi">3</span><span class="p">]],</span> <span class="n">result</span><span class="p">[</span><span class="n">roi</span><span class="p">[</span><span class="mi">0</span><span class="p">]:</span><span class="n">roi</span><span class="p">[</span><span class="mi">1</span><span class="p">],</span> <span class="n">roi</span><span class="p">[</span><span class="mi">2</span><span class="p">]:</span><span class="n">roi</span><span class="p">[</span><span class="mi">3</span><span class="p">]])</span>
+ <span class="k">return</span> <span class="n">image</span>
+
+
+
+<div class="viewcode-block" id="Image"><a class="viewcode-back" href="../../processing.html#htpia.imgproc.Image">[docs]</a><span class="k">class</span> <span class="nc">Image</span><span class="p">(</span><span class="nb">object</span><span class="p">):</span>
+
+ <span class="sd">"""</span>
+<span class="sd"> Each image is instantiated as a class</span>
+<span class="sd"> """</span>
+ <span class="k">def</span> <span class="nf">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="nb">input</span><span class="p">,</span> <span class="n">outputdir</span> <span class="o">=</span> <span class="s">"."</span><span class="p">,</span> <span class="n">writename</span> <span class="o">=</span> <span class="bp">None</span><span class="p">,</span> <span class="n">dev</span> <span class="o">=</span> <span class="bp">False</span><span class="p">,</span> <span class="n">db</span> <span class="o">=</span> <span class="bp">None</span><span class="p">,</span> <span class="n">dbid</span> <span class="o">=</span> <span class="bp">None</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> :param input: The input resource, either a path to an image or a raw numpy array.</span>
+<span class="sd"> :type resource: numpy.ndarray or str</span>
+<span class="sd"> :param outputdir: The directory to write output files</span>
+<span class="sd"> :type outputdir: str</span>
+<span class="sd"> :param writename: The name to write the output file as, should include extension.</span>
+<span class="sd"> :type writename: str</span>
+<span class="sd"> :param dev: Dev mode will do something...</span>
+<span class="sd"> :type dev: bool</span>
+<span class="sd"> """</span>
+ <span class="k">if</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">isdir</span><span class="p">(</span><span class="n">outputdir</span><span class="p">):</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">states</span> <span class="o">=</span> <span class="p">{}</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_loadDb</span><span class="p">(</span><span class="n">db</span><span class="p">,</span> <span class="n">dbid</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">input</span> <span class="o">=</span> <span class="nb">input</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">fname</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">image</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_loadResource</span><span class="p">(</span><span class="nb">input</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">y</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">image</span><span class="o">.</span><span class="n">shape</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">x</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">image</span><span class="o">.</span><span class="n">shape</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">outputdir</span> <span class="o">=</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">abspath</span><span class="p">(</span><span class="n">outputdir</span><span class="p">)</span>
+ <span class="k">if</span> <span class="n">writename</span><span class="p">:</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">writename</span> <span class="o">=</span> <span class="n">writename</span>
+ <span class="k">elif</span> <span class="nb">isinstance</span><span class="p">(</span><span class="nb">input</span><span class="p">,</span> <span class="n">np</span><span class="o">.</span><span class="n">ndarray</span><span class="p">):</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">writename</span> <span class="o">=</span> <span class="s">"out.png"</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">writename</span> <span class="o">=</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">basename</span><span class="p">(</span><span class="nb">input</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">dev</span> <span class="o">=</span> <span class="n">dev</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">window</span> <span class="o">=</span> <span class="mi">1</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="s">"Invalid output!"</span><span class="p">)</span>
+ <span class="k">return</span>
+
+ <span class="k">def</span> <span class="nf">_loadDb</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">db</span><span class="p">,</span> <span class="n">dbid</span><span class="p">):</span>
+ <span class="k">if</span> <span class="n">db</span><span class="p">:</span>
+ <span class="k">if</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">isfile</span><span class="p">(</span><span class="n">db</span><span class="p">):</span>
+ <span class="k">if</span> <span class="n">dbid</span><span class="p">:</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">dbid</span> <span class="o">=</span> <span class="n">dbid</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">conn</span> <span class="o">=</span> <span class="n">sqlite3</span><span class="o">.</span><span class="n">connect</span><span class="p">(</span><span class="n">db</span><span class="p">,</span> <span class="n">check_same_thread</span> <span class="o">=</span> <span class="bp">False</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">conn</span><span class="o">.</span><span class="n">row_factory</span> <span class="o">=</span> <span class="n">sqlite3</span><span class="o">.</span><span class="n">Row</span>
+ <span class="n">result</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">conn</span><span class="o">.</span><span class="n">execute</span><span class="p">(</span><span class="s">"select pegasusid from images where pegasusid=?"</span><span class="p">,</span> <span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">dbid</span><span class="p">,))</span>
+ <span class="k">if</span> <span class="ow">not</span> <span class="n">result</span><span class="o">.</span><span class="n">fetchone</span><span class="p">():</span>
+ <span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="s">"Invalid pegasusid given!"</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_addColumn</span><span class="p">(</span><span class="s">"error"</span><span class="p">)</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="s">"A database id must be provided if you give a database."</span><span class="p">)</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="s">"Invalid database given!"</span><span class="p">)</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">conn</span> <span class="o">=</span> <span class="bp">False</span>
+ <span class="k">return</span>
+
+ <span class="k">def</span> <span class="nf">_addColumn</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">column</span><span class="p">,</span> <span class="n">tablename</span> <span class="o">=</span> <span class="s">"images"</span><span class="p">):</span>
+ <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">conn</span><span class="p">:</span>
+ <span class="k">if</span> <span class="n">column</span> <span class="ow">not</span> <span class="ow">in</span> <span class="p">[</span><span class="n">row</span><span class="p">[</span><span class="s">"name"</span><span class="p">]</span> <span class="k">for</span> <span class="n">row</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">conn</span><span class="o">.</span><span class="n">execute</span><span class="p">(</span><span class="s">"PRAGMA table_info("</span> <span class="o">+</span> <span class="n">tablename</span> <span class="o">+</span> <span class="s">");"</span><span class="p">)]:</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">conn</span><span class="o">.</span><span class="n">execute</span><span class="p">(</span><span class="s">"alter table "</span> <span class="o">+</span> <span class="n">tablename</span> <span class="o">+</span> <span class="s">" add column "</span> <span class="o">+</span> <span class="n">column</span> <span class="o">+</span> <span class="s">";"</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">conn</span><span class="o">.</span><span class="n">commit</span><span class="p">()</span>
+ <span class="k">return</span>
+
+ <span class="k">def</span> <span class="nf">_loadROIArg</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">arg</span><span class="p">,</span> <span class="n">i</span><span class="p">):</span>
+ <span class="n">vals</span> <span class="o">=</span> <span class="p">{</span>
+ <span class="mi">0</span><span class="p">:</span> <span class="s">"0"</span><span class="p">,</span>
+ <span class="mi">1</span><span class="p">:</span> <span class="nb">str</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">y</span><span class="p">),</span>
+ <span class="mi">2</span><span class="p">:</span> <span class="s">"0"</span><span class="p">,</span>
+ <span class="mi">3</span><span class="p">:</span> <span class="nb">str</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">x</span><span class="p">)</span>
+ <span class="p">}</span>
+ <span class="n">arg</span> <span class="o">=</span> <span class="nb">str</span><span class="p">(</span><span class="n">arg</span><span class="p">)</span>
+ <span class="n">arg</span> <span class="o">=</span> <span class="n">arg</span><span class="o">.</span><span class="n">replace</span><span class="p">(</span><span class="s">"x"</span><span class="p">,</span> <span class="nb">str</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">x</span><span class="p">))</span><span class="o">.</span><span class="n">replace</span><span class="p">(</span><span class="s">"y"</span><span class="p">,</span> <span class="nb">str</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">y</span><span class="p">))</span><span class="o">.</span><span class="n">replace</span><span class="p">(</span><span class="s">" "</span><span class="p">,</span><span class="s">""</span><span class="p">)</span><span class="o">.</span><span class="n">replace</span><span class="p">(</span><span class="s">"-1"</span><span class="p">,</span><span class="n">vals</span><span class="p">[</span><span class="n">i</span><span class="p">])</span>
+ <span class="k">if</span> <span class="s">"-"</span> <span class="ow">in</span> <span class="n">arg</span><span class="p">:</span>
+ <span class="k">try</span><span class="p">:</span>
+ <span class="n">left</span><span class="p">,</span> <span class="n">right</span> <span class="o">=</span> <span class="n">arg</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s">"-"</span><span class="p">)</span>
+ <span class="k">return</span> <span class="nb">int</span><span class="p">(</span><span class="n">left</span><span class="p">)</span> <span class="o">-</span> <span class="nb">int</span><span class="p">(</span><span class="n">right</span><span class="p">)</span>
+ <span class="k">except</span><span class="p">:</span>
+ <span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="s">"Could not load roi arg '</span><span class="si">%s</span><span class="s">'"</span> <span class="o">%</span> <span class="p">(</span><span class="n">arg</span><span class="p">,))</span>
+ <span class="k">elif</span> <span class="s">"+"</span> <span class="ow">in</span> <span class="n">arg</span><span class="p">:</span>
+ <span class="k">try</span><span class="p">:</span>
+ <span class="n">left</span><span class="p">,</span> <span class="n">right</span> <span class="o">=</span> <span class="n">arg</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s">"+"</span><span class="p">)</span>
+ <span class="k">return</span> <span class="nb">int</span><span class="p">(</span><span class="n">left</span><span class="p">)</span> <span class="o">+</span> <span class="nb">int</span><span class="p">(</span><span class="n">right</span><span class="p">)</span>
+ <span class="k">except</span><span class="p">:</span>
+ <span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="s">"Could not load roi arg '</span><span class="si">%s</span><span class="s">'"</span> <span class="o">%</span> <span class="p">(</span><span class="n">arg</span><span class="p">,))</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="k">return</span> <span class="nb">int</span><span class="p">(</span><span class="n">arg</span><span class="p">)</span>
+
+ <span class="k">def</span> <span class="nf">_loadROI</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">roi</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> :param roi: The region of interest to load.</span>
+<span class="sd"> :type roi: list or file</span>
+<span class="sd"> :return: The region of interest of form [ystart, yend, xstart, xend]</span>
+<span class="sd"> :rtype: list</span>
+<span class="sd"> :raises OSError: if the input path does not exist.</span>
+<span class="sd"> </span>
+<span class="sd"> Loads a region of interest, either a path to an roi or a raw list.</span>
+<span class="sd"> """</span>
+ <span class="k">if</span> <span class="ow">not</span> <span class="n">roi</span><span class="p">:</span>
+ <span class="n">roi</span> <span class="o">=</span> <span class="p">[</span><span class="o">-</span><span class="mi">1</span><span class="p">,</span> <span class="o">-</span><span class="mi">1</span><span class="p">,</span> <span class="o">-</span><span class="mi">1</span><span class="p">,</span> <span class="o">-</span><span class="mi">1</span><span class="p">]</span>
+ <span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">roi</span><span class="p">,</span> <span class="nb">list</span><span class="p">):</span>
+ <span class="k">return</span> <span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">_loadROIArg</span><span class="p">(</span><span class="n">z</span><span class="p">,</span> <span class="n">i</span><span class="p">)</span> <span class="k">for</span> <span class="n">i</span><span class="p">,</span><span class="n">z</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="n">roi</span><span class="p">)]</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="k">if</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">isfile</span><span class="p">(</span><span class="n">roi</span><span class="p">):</span>
+ <span class="k">try</span><span class="p">:</span>
+ <span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="n">roi</span><span class="p">,</span> <span class="s">"r"</span><span class="p">)</span> <span class="k">as</span> <span class="n">rh</span><span class="p">:</span>
+ <span class="n">r</span> <span class="o">=</span> <span class="n">json</span><span class="o">.</span><span class="n">load</span><span class="p">(</span><span class="n">rh</span><span class="p">)</span>
+ <span class="k">if</span> <span class="nb">all</span><span class="p">(</span><span class="n">x</span> <span class="ow">in</span> <span class="n">r</span> <span class="k">for</span> <span class="n">x</span> <span class="ow">in</span> <span class="p">[</span><span class="s">"xstart"</span><span class="p">,</span> <span class="s">"xend"</span><span class="p">,</span> <span class="s">"ystart"</span><span class="p">,</span> <span class="s">"yend"</span><span class="p">]):</span>
+ <span class="k">return</span> <span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">_loadROIArg</span><span class="p">(</span><span class="n">r</span><span class="p">[</span><span class="s">"ystart"</span><span class="p">],</span> <span class="mi">0</span><span class="p">),</span> <span class="bp">self</span><span class="o">.</span><span class="n">_loadROIArg</span><span class="p">(</span><span class="n">r</span><span class="p">[</span><span class="s">"yend"</span><span class="p">],</span> <span class="mi">1</span><span class="p">),</span> <span class="bp">self</span><span class="o">.</span><span class="n">_loadROIArg</span><span class="p">(</span><span class="n">r</span><span class="p">[</span><span class="s">"xstart"</span><span class="p">],</span> <span class="mi">2</span><span class="p">),</span> <span class="bp">self</span><span class="o">.</span><span class="n">_loadROIArg</span><span class="p">(</span><span class="n">r</span><span class="p">[</span><span class="s">"xend"</span><span class="p">],</span> <span class="mi">3</span><span class="p">)]</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="s">"Input roi file '</span><span class="si">%s</span><span class="s">' needs xstart, xend, ystart, and yend definitions!"</span> <span class="o">%</span> <span class="p">(</span><span class="n">roi</span><span class="p">,))</span>
+ <span class="k">except</span> <span class="ne">Exception</span> <span class="k">as</span> <span class="n">e</span><span class="p">:</span>
+ <span class="k">print</span> <span class="n">traceback</span><span class="o">.</span><span class="n">format_exc</span><span class="p">()</span>
+ <span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="s">"Input roi file '</span><span class="si">%s</span><span class="s">' is not valid json!"</span> <span class="o">%</span> <span class="p">(</span><span class="n">roi</span><span class="p">,))</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="s">"Input path to roi file '</span><span class="si">%s</span><span class="s">' does not exist!"</span> <span class="o">%</span> <span class="p">(</span><span class="n">roi</span><span class="p">,))</span>
+ <span class="k">return</span>
+
+ <span class="k">def</span> <span class="nf">_writeROI</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">roi</span><span class="p">,</span> <span class="n">output</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> :param roi: The region of interest to write.</span>
+<span class="sd"> :type roi: list</span>
+<span class="sd"> """</span>
+ <span class="k">try</span><span class="p">:</span>
+ <span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">outputdir</span> <span class="o">+</span> <span class="s">"/"</span> <span class="o">+</span> <span class="n">output</span><span class="p">,</span> <span class="s">"w"</span><span class="p">)</span> <span class="k">as</span> <span class="n">wh</span><span class="p">:</span>
+ <span class="n">wh</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="n">json</span><span class="o">.</span><span class="n">dumps</span><span class="p">({</span><span class="s">"ystart"</span><span class="p">:</span> <span class="n">roi</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span> <span class="s">"yend"</span><span class="p">:</span> <span class="n">roi</span><span class="p">[</span><span class="mi">1</span><span class="p">],</span> <span class="s">"xstart"</span><span class="p">:</span> <span class="n">roi</span><span class="p">[</span><span class="mi">2</span><span class="p">],</span> <span class="s">"xend"</span><span class="p">:</span> <span class="n">roi</span><span class="p">[</span><span class="mi">3</span><span class="p">]},</span> <span class="n">indent</span> <span class="o">=</span> <span class="mi">4</span><span class="p">))</span>
+ <span class="k">except</span><span class="p">:</span>
+ <span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="s">"Could not write roi."</span><span class="p">)</span>
+ <span class="k">return</span>
+
+ <span class="k">def</span> <span class="nf">_loadBins</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">binlist</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> :param bin: The bin to load</span>
+<span class="sd"> :type bin: list or file</span>
+<span class="sd"> """</span>
+
+ <span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">binlist</span><span class="p">,</span> <span class="nb">list</span><span class="p">):</span>
+ <span class="k">return</span> <span class="n">binlist</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="k">if</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">isfile</span><span class="p">(</span><span class="n">binlist</span><span class="p">):</span>
+ <span class="k">try</span><span class="p">:</span>
+ <span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="n">binlist</span><span class="p">,</span> <span class="s">"r"</span><span class="p">)</span> <span class="k">as</span> <span class="n">rh</span><span class="p">:</span>
+ <span class="k">return</span> <span class="n">json</span><span class="o">.</span><span class="n">load</span><span class="p">(</span><span class="n">rh</span><span class="p">)</span>
+ <span class="k">except</span><span class="p">:</span>
+ <span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="s">"Bin list not valid json!"</span><span class="p">)</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="s">"Bin file does not exist."</span><span class="p">)</span>
+ <span class="k">return</span>
+
+ <span class="k">def</span> <span class="nf">_loadResource</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">resource</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> :param resource: The resource to load.</span>
+<span class="sd"> :type resource: numpy.ndarray or file</span>
+<span class="sd"> :return: The image</span>
+<span class="sd"> :rtype: numpy.ndarray</span>
+<span class="sd"> :raises OSError: if the input path does not exist.</span>
+<span class="sd"> </span>
+<span class="sd"> Loads a resource, either a path to an image or a raw numpy array.</span>
+<span class="sd"> """</span>
+ <span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">resource</span><span class="p">,</span> <span class="n">np</span><span class="o">.</span><span class="n">ndarray</span><span class="p">):</span>
+ <span class="k">return</span> <span class="p">(</span><span class="s">"unknown"</span><span class="p">,</span> <span class="n">resource</span><span class="o">.</span><span class="n">copy</span><span class="p">())</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="k">if</span> <span class="n">resource</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">states</span><span class="p">:</span>
+ <span class="k">return</span> <span class="p">(</span><span class="n">resource</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">states</span><span class="p">[</span><span class="n">resource</span><span class="p">]</span><span class="o">.</span><span class="n">copy</span><span class="p">())</span>
+ <span class="k">elif</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">isfile</span><span class="p">(</span><span class="n">resource</span><span class="p">):</span>
+ <span class="n">image</span> <span class="o">=</span> <span class="n">cv2</span><span class="o">.</span><span class="n">imread</span><span class="p">(</span><span class="n">resource</span><span class="p">)</span>
+ <span class="k">if</span> <span class="n">image</span> <span class="ow">is</span> <span class="ow">not</span> <span class="bp">None</span><span class="p">:</span>
+ <span class="k">return</span> <span class="p">(</span><span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">basename</span><span class="p">(</span><span class="n">resource</span><span class="p">),</span> <span class="n">image</span><span class="p">)</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">conn</span><span class="p">:</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">conn</span><span class="o">.</span><span class="n">execute</span><span class="p">(</span><span class="s">"update images set error =? where pegasusid = ?"</span><span class="p">,</span> <span class="p">(</span><span class="s">"Load Error, input is not an image."</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">dbid</span><span class="p">))</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">conn</span><span class="o">.</span><span class="n">commit</span><span class="p">()</span>
+ <span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="s">"Input is not an image."</span><span class="p">)</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">conn</span><span class="p">:</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">conn</span><span class="o">.</span><span class="n">execute</span><span class="p">(</span><span class="s">"update images set error = ? where pegasusid = ?"</span><span class="p">,</span> <span class="p">(</span><span class="s">"Load Error, input path doesn't exist or specified resource is not a saved state."</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">dbid</span><span class="p">))</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">conn</span><span class="o">.</span><span class="n">commit</span><span class="p">()</span>
+ <span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="s">"Input path to resource does not exist."</span><span class="p">)</span>
+ <span class="k">return</span>
+
+ <span class="k">def</span> <span class="nf">_colorHistogram</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> :return: A list of histograms, corresponding to R, G, B.</span>
+<span class="sd"> :rtype: List of numpy arrays.</span>
+<span class="sd"> </span>
+<span class="sd"> Calculates a normalized colorHistogram of the current image. </span>
+<span class="sd"> The intensity is normalized between 0 and 255.</span>
+<span class="sd"> """</span>
+ <span class="n">returnhist</span> <span class="o">=</span> <span class="p">[]</span>
+
+ <span class="k">for</span> <span class="n">ch</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="mi">0</span><span class="p">,</span> <span class="mi">3</span><span class="p">):</span>
+ <span class="n">hist_item</span> <span class="o">=</span> <span class="n">cv2</span><span class="o">.</span><span class="n">calcHist</span><span class="p">([</span><span class="bp">self</span><span class="o">.</span><span class="n">image</span><span class="p">],</span> <span class="p">[</span><span class="n">ch</span><span class="p">],</span> <span class="bp">None</span><span class="p">,</span> <span class="p">[</span><span class="mi">256</span><span class="p">],</span> <span class="p">[</span><span class="mi">1</span><span class="p">,</span><span class="mi">255</span><span class="p">])</span>
+ <span class="n">cv2</span><span class="o">.</span><span class="n">normalize</span><span class="p">(</span><span class="n">hist_item</span><span class="p">,</span> <span class="n">hist_item</span><span class="p">,</span> <span class="mi">0</span><span class="p">,</span> <span class="mi">255</span><span class="p">,</span> <span class="n">cv2</span><span class="o">.</span><span class="n">NORM_MINMAX</span><span class="p">)</span>
+ <span class="n">hist</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">int32</span><span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">around</span><span class="p">(</span><span class="n">hist_item</span><span class="p">))</span>
+ <span class="n">returnhist</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">hist</span><span class="p">)</span>
+ <span class="k">return</span> <span class="n">returnhist</span>
+
+ <span class="k">def</span> <span class="nf">_isColor</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">image</span> <span class="o">=</span> <span class="bp">None</span><span class="p">):</span>
+ <span class="n">image</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">image</span> <span class="k">if</span> <span class="n">image</span> <span class="ow">is</span> <span class="bp">None</span> <span class="k">else</span> <span class="n">image</span>
+ <span class="k">return</span> <span class="nb">len</span><span class="p">(</span><span class="n">image</span><span class="o">.</span><span class="n">shape</span><span class="p">)</span> <span class="o">==</span> <span class="mi">3</span>
+
+<div class="viewcode-block" id="Image.save"><a class="viewcode-back" href="../../processing.html#htpia.imgproc.Image.save">[docs]</a> <span class="k">def</span> <span class="nf">save</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">name</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> :param name: The name to save the image under.</span>
+<span class="sd"> :type name: str OR any hashable type.</span>
+<span class="sd"> </span>
+<span class="sd"> This function saves the current image in the 'states' variable under</span>
+<span class="sd"> the specified name. It can then be reloaded using the :py:meth:`~htpia.imgproc.Image.restore`</span>
+<span class="sd"> method.</span>
+<span class="sd"> """</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">states</span><span class="p">[</span><span class="n">name</span><span class="p">]</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">image</span><span class="o">.</span><span class="n">copy</span><span class="p">()</span>
+ <span class="k">return</span>
+ </div>
+<div class="viewcode-block" id="Image.restore"><a class="viewcode-back" href="../../processing.html#htpia.imgproc.Image.restore">[docs]</a> <span class="k">def</span> <span class="nf">restore</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">name</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> :param name: The name the image is saved under.</span>
+<span class="sd"> :type name: str OR any hashable type.</span>
+<span class="sd"> </span>
+<span class="sd"> Reloads a previously saved image from the 'states' variable.</span>
+<span class="sd"> """</span>
+ <span class="k">if</span> <span class="n">name</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">states</span><span class="p">:</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">image</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">states</span><span class="p">[</span><span class="n">name</span><span class="p">]</span><span class="o">.</span><span class="n">copy</span><span class="p">()</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="k">print</span> <span class="s">"Invalid state specified."</span>
+ <span class="k">return</span>
+ </div>
+<div class="viewcode-block" id="Image.list"><a class="viewcode-back" href="../../processing.html#htpia.imgproc.Image.list">[docs]</a> <span class="k">def</span> <span class="nf">list</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> Lists all saved states.</span>
+<span class="sd"> """</span>
+ <span class="k">for</span> <span class="n">state</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">states</span><span class="p">:</span>
+ <span class="k">print</span> <span class="n">state</span>
+ <span class="k">return</span>
+ </div>
+<div class="viewcode-block" id="Image.destroy"><a class="viewcode-back" href="../../processing.html#htpia.imgproc.Image.destroy">[docs]</a> <span class="k">def</span> <span class="nf">destroy</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> Destroys all currently open windows.</span>
+<span class="sd"> """</span>
+ <span class="n">cv2</span><span class="o">.</span><span class="n">destroyAllWindows</span><span class="p">()</span>
+ <span class="k">return</span>
+ </div>
+<div class="viewcode-block" id="Image.wait"><a class="viewcode-back" href="../../processing.html#htpia.imgproc.Image.wait">[docs]</a> <span class="k">def</span> <span class="nf">wait</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> Waits until a key is pressed, then destroys all windows and</span>
+<span class="sd"> continues program execution.</span>
+<span class="sd"> """</span>
+ <span class="n">cv2</span><span class="o">.</span><span class="n">waitKey</span><span class="p">(</span><span class="mi">0</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">destroy</span><span class="p">()</span>
+ <span class="k">return</span>
+ </div>
+<div class="viewcode-block" id="Image.show"><a class="viewcode-back" href="../../processing.html#htpia.imgproc.Image.show">[docs]</a> <span class="k">def</span> <span class="nf">show</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">title</span> <span class="o">=</span> <span class="bp">None</span><span class="p">):</span>
+ <span class="sd">""" </span>
+<span class="sd"> :param title: The title to give the display window, if left blank one will be created.</span>
+<span class="sd"> :type title: str</span>
+<span class="sd"> :return: None</span>
+<span class="sd"> </span>
+<span class="sd"> Displays the image in a window. Utilizes the :py:meth:`~htpia.ImageProcessor.Image.resize` function.</span>
+<span class="sd"> If a title is not specified, the window will be named 'windowX' where X is the number of times</span>
+<span class="sd"> show has been called.</span>
+<span class="sd"> </span>
+<span class="sd"> """</span>
+ <span class="n">cv2</span><span class="o">.</span><span class="n">imshow</span><span class="p">(</span><span class="n">title</span> <span class="k">if</span> <span class="n">title</span> <span class="k">else</span> <span class="s">"window "</span> <span class="o">+</span> <span class="nb">str</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">window</span><span class="p">),</span> <span class="bp">self</span><span class="o">.</span><span class="n">resize</span><span class="p">())</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">window</span> <span class="o">+=</span> <span class="mi">1</span>
+ <span class="k">return</span>
+ </div>
+<div class="viewcode-block" id="Image.resize"><a class="viewcode-back" href="../../processing.html#htpia.imgproc.Image.resize">[docs]</a> <span class="k">def</span> <span class="nf">resize</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> If the image is large than conf.maxArea, resize its total area down to conf.maxArea.</span>
+<span class="sd"> This function is primarily used for viewing purposes, and as such, it does not resize</span>
+<span class="sd"> the base image, but creates a copy to resize instead.</span>
+<span class="sd"> """</span>
+ <span class="k">if</span> <span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">image</span><span class="o">.</span><span class="n">shape</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="o">*</span> <span class="bp">self</span><span class="o">.</span><span class="n">image</span><span class="o">.</span><span class="n">shape</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span> <span class="o">></span> <span class="n">conf</span><span class="o">.</span><span class="n">maxArea</span><span class="p">):</span>
+ <span class="n">scale</span> <span class="o">=</span> <span class="mi">1</span> <span class="o">/</span> <span class="n">math</span><span class="o">.</span><span class="n">sqrt</span><span class="p">((</span><span class="bp">self</span><span class="o">.</span><span class="n">image</span><span class="o">.</span><span class="n">shape</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span> <span class="o">*</span> <span class="bp">self</span><span class="o">.</span><span class="n">image</span><span class="o">.</span><span class="n">shape</span><span class="p">[</span><span class="mi">0</span><span class="p">])</span> <span class="o">/</span> <span class="n">conf</span><span class="o">.</span><span class="n">maxArea</span><span class="p">)</span>
+ <span class="k">return</span> <span class="n">cv2</span><span class="o">.</span><span class="n">resize</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">image</span><span class="o">.</span><span class="n">copy</span><span class="p">(),</span> <span class="p">(</span><span class="nb">int</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">image</span><span class="o">.</span><span class="n">shape</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span><span class="o">*</span><span class="n">scale</span><span class="p">),</span> <span class="nb">int</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">image</span><span class="o">.</span><span class="n">shape</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">*</span><span class="n">scale</span><span class="p">)))</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">image</span>
+ </div>
+<div class="viewcode-block" id="Image.write"><a class="viewcode-back" href="../../processing.html#htpia.imgproc.Image.write">[docs]</a> <span class="k">def</span> <span class="nf">write</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">name</span> <span class="o">=</span> <span class="bp">None</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> Writes the current image to the given output directory, with the given name.</span>
+<span class="sd"> """</span>
+ <span class="n">writename</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">writename</span> <span class="k">if</span> <span class="ow">not</span> <span class="n">name</span> <span class="k">else</span> <span class="n">name</span>
+ <span class="n">cv2</span><span class="o">.</span><span class="n">imwrite</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">outputdir</span> <span class="o">+</span> <span class="s">"/"</span> <span class="o">+</span> <span class="n">writename</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">image</span><span class="p">)</span>
+ <span class="k">return</span>
+ </div>
+<div class="viewcode-block" id="Image.convertColor"><a class="viewcode-back" href="../../processing.html#htpia.imgproc.Image.convertColor">[docs]</a> <span class="k">def</span> <span class="nf">convertColor</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">intype</span><span class="p">,</span> <span class="n">outtype</span><span class="p">):</span>
+ <span class="sd">""" </span>
+<span class="sd"> :param intype: The input image type</span>
+<span class="sd"> :type intype: str</span>
+<span class="sd"> :param outtype: The output image type</span>
+<span class="sd"> :type outtype: str</span>
+<span class="sd"> :return: The converted image.</span>
+<span class="sd"> :rtype: numpy.ndarray</span>
+<span class="sd"> :raises: KeyError</span>
+<span class="sd"> </span>
+<span class="sd"> Converts the given image between color spaces, based on the given types.</span>
+<span class="sd"> Supported types are: rgb, bgr, gray, hsv, lab, and ycrcb</span>
+<span class="sd"> """</span>
+ <span class="k">if</span> <span class="n">intype</span> <span class="ow">in</span> <span class="n">conf</span><span class="o">.</span><span class="n">colors</span><span class="p">:</span>
+ <span class="k">if</span> <span class="n">outtype</span> <span class="ow">in</span> <span class="n">conf</span><span class="o">.</span><span class="n">colors</span><span class="p">[</span><span class="n">intype</span><span class="p">]:</span>
+ <span class="k">for</span> <span class="n">code</span> <span class="ow">in</span> <span class="n">conf</span><span class="o">.</span><span class="n">colors</span><span class="p">[</span><span class="n">intype</span><span class="p">][</span><span class="n">outtype</span><span class="p">]:</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">image</span> <span class="o">=</span> <span class="n">cv2</span><span class="o">.</span><span class="n">cvtColor</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">image</span><span class="p">,</span> <span class="n">code</span><span class="p">)</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="k">raise</span> <span class="ne">KeyError</span><span class="p">(</span><span class="n">outtype</span> <span class="o">+</span> <span class="s">" is not a valid image type."</span><span class="p">)</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="k">raise</span> <span class="ne">KeyError</span><span class="p">(</span><span class="n">intype</span> <span class="o">+</span> <span class="s">" is not a valid image type."</span><span class="p">)</span>
+ <span class="k">return</span>
+ </div>
+<div class="viewcode-block" id="Image.threshold"><a class="viewcode-back" href="../../processing.html#htpia.imgproc.Image.threshold">[docs]</a> <span class="k">def</span> <span class="nf">threshold</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">thresh</span><span class="p">,</span> <span class="nb">max</span> <span class="o">=</span> <span class="mi">255</span><span class="p">,</span> <span class="nb">type</span> <span class="o">=</span> <span class="s">"binary"</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> :param thresh: Threshold value.</span>
+<span class="sd"> :type thresh: int</span>
+<span class="sd"> :param max: Write value for binary threshold.</span>
+<span class="sd"> :type max: int</span>
+<span class="sd"> :param type: Threhsold type.</span>
+<span class="sd"> :type type: str</span>
+<span class="sd"> :return: The thresholded image.</span>
+<span class="sd"> :rtype: numpy.ndarray</span>
+<span class="sd"> :raises KeyError: if the specified threshold type doesn't exist.</span>
+<span class="sd"> </span>
+<span class="sd"> Thresholds the image based on the given type.</span>
+<span class="sd"> Supported types are: binary, truncate, tozero, and otsu.</span>
+<span class="sd"> """</span>
+ <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">_isColor</span><span class="p">():</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">convertColor</span><span class="p">(</span><span class="s">"bgr"</span><span class="p">,</span> <span class="s">"gray"</span><span class="p">)</span>
+ <span class="k">if</span> <span class="nb">type</span> <span class="ow">in</span> <span class="n">conf</span><span class="o">.</span><span class="n">thresholds</span><span class="p">:</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">image</span> <span class="o">=</span> <span class="n">cv2</span><span class="o">.</span><span class="n">threshold</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">image</span><span class="p">,</span> <span class="n">thresh</span><span class="p">,</span> <span class="nb">max</span><span class="p">,</span> <span class="n">conf</span><span class="o">.</span><span class="n">thresholds</span><span class="p">[</span><span class="nb">type</span><span class="p">])[</span><span class="mi">1</span><span class="p">]</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="k">raise</span> <span class="ne">KeyError</span><span class="p">(</span><span class="nb">type</span> <span class="o">+</span> <span class="s">" is not a valid threshold type."</span><span class="p">)</span>
+ <span class="k">return</span>
+ </div>
+<div class="viewcode-block" id="Image.meanshift"><a class="viewcode-back" href="../../processing.html#htpia.imgproc.Image.meanshift">[docs]</a> <span class="k">def</span> <span class="nf">meanshift</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">spatial_radius</span><span class="p">,</span> <span class="n">range_radius</span><span class="p">,</span> <span class="n">min_density</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> :param spatial_radius: Spatial Radius</span>
+<span class="sd"> :type spatial_radius: float</span>
+<span class="sd"> :param range_radius: Range Radius.</span>
+<span class="sd"> :type range_radius: float</span>
+<span class="sd"> :param min_density: Minimum Density.</span>
+<span class="sd"> :type min_density: int</span>
+<span class="sd"> :return: The mean-shifted image.</span>
+<span class="sd"> :rtype: numpy.ndarray</span>
+<span class="sd"> </span>
+<span class="sd"> Reference to paper HERE: http://dx.doi.org/10.1109/34.1000236</span>
+<span class="sd"> Reference to pymeanshift HERE: https://code.google.com/p/pymeanshift/</span>
+<span class="sd"> Segments the image into clusters based on nearest neighbors.</span>
+<span class="sd"> """</span>
+ <span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">image</span><span class="p">,</span> <span class="n">labels_image</span><span class="p">,</span> <span class="n">number_regions</span><span class="p">)</span> <span class="o">=</span> <span class="n">pms</span><span class="o">.</span><span class="n">segment</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">image</span><span class="p">,</span> <span class="n">spatial_radius</span> <span class="o">=</span> <span class="n">spatial_radius</span><span class="p">,</span> <span class="n">range_radius</span> <span class="o">=</span> <span class="n">range_radius</span><span class="p">,</span> <span class="n">min_density</span> <span class="o">=</span> <span class="n">min_density</span><span class="p">)</span>
+ <span class="k">return</span>
+ </div>
+<div class="viewcode-block" id="Image.adaptiveThreshold"><a class="viewcode-back" href="../../processing.html#htpia.imgproc.Image.adaptiveThreshold">[docs]</a> <span class="k">def</span> <span class="nf">adaptiveThreshold</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">value</span><span class="p">,</span> <span class="n">adaptiveType</span><span class="p">,</span> <span class="n">thresholdType</span><span class="p">,</span> <span class="n">blockSize</span><span class="p">,</span> <span class="n">C</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> :param value: Write value for the pixels based on the conditions.</span>
+<span class="sd"> :type param: int</span>
+<span class="sd"> :param adaptiveType: Adaptive algorithm to use, should be either 'mean' or 'gaussian'.</span>
+<span class="sd"> :type adaptiveType: str</span>
+<span class="sd"> :param thresholdType: Threshold type, should be either 'binary' or 'inverse'.</span>
+<span class="sd"> :type thresholdType: str</span>
+<span class="sd"> :param blockSize: The window size to consider while thresholding, should only be an odd number.</span>
+<span class="sd"> :type blockSize: int</span>
+<span class="sd"> :param C: A constant subtracted from the calculated mean in each window.</span>
+<span class="sd"> :type C: int</span>
+<span class="sd"> </span>
+<span class="sd"> Thresholds an image by considering the image in several different windows instead of the image</span>
+<span class="sd"> as a whole. MATH HERE, REFERENCE OPENCV DOCS.</span>
+<span class="sd"> """</span>
+ <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">_isColor</span><span class="p">():</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">convertColor</span><span class="p">(</span><span class="s">"bgr"</span><span class="p">,</span> <span class="s">"gray"</span><span class="p">)</span>
+ <span class="k">if</span> <span class="n">adaptiveType</span> <span class="ow">in</span> <span class="n">conf</span><span class="o">.</span><span class="n">adaptives</span><span class="p">:</span>
+ <span class="k">if</span> <span class="n">thresholdType</span> <span class="o">==</span> <span class="s">"binary"</span> <span class="ow">or</span> <span class="n">thresholdType</span> <span class="o">==</span> <span class="s">"inverse"</span><span class="p">:</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">image</span> <span class="o">=</span> <span class="n">cv2</span><span class="o">.</span><span class="n">adaptiveThreshold</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">image</span><span class="p">,</span> <span class="n">value</span><span class="p">,</span> <span class="n">conf</span><span class="o">.</span><span class="n">adaptives</span><span class="p">[</span><span class="n">adaptiveType</span><span class="p">],</span> <span class="n">conf</span><span class="o">.</span><span class="n">thresholds</span><span class="p">[</span><span class="n">thresholdType</span><span class="p">],</span> <span class="n">blockSize</span><span class="p">,</span> <span class="n">C</span><span class="p">)</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="s">"Threshold type: "</span> <span class="o">+</span> <span class="n">thresholdType</span> <span class="o">+</span> <span class="s">" must be either binary or inverse."</span><span class="p">)</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="s">"Adaptive type: "</span> <span class="o">+</span> <span class="n">adaptiveType</span> <span class="o">+</span> <span class="s">" is not a valid adaptive threshold type, should be either 'mean' or 'gaussian'"</span><span class="p">)</span>
+ <span class="k">return</span>
+ </div>
+<div class="viewcode-block" id="Image.blur"><a class="viewcode-back" href="../../processing.html#htpia.imgproc.Image.blur">[docs]</a> <span class="k">def</span> <span class="nf">blur</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">ksize</span><span class="p">,</span> <span class="n">anchor</span> <span class="o">=</span> <span class="p">(</span><span class="o">-</span><span class="mi">1</span><span class="p">,</span> <span class="o">-</span><span class="mi">1</span><span class="p">),</span> <span class="n">borderType</span> <span class="o">=</span> <span class="s">"default"</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> :param ksize: The size of the kernel represented by a tuple (width, height). Both numbers should be odd and positive.</span>
+<span class="sd"> :type ksize: tuple</span>
+<span class="sd"> :param anchor: The anchor point for filtering. Default is (-1, -1) which is the center of the kernel.</span>
+<span class="sd"> :type anchor: tuple</span>
+<span class="sd"> :param borderType: The type of border mode used to extrapolate pixels outside the image. Literally no information on this.</span>
+<span class="sd"> :type borderType: str</span>
+<span class="sd"> </span>
+<span class="sd"> This function smoothes an image using the following kernel: MATH HERE.</span>
+<span class="sd"> </span>
+<span class="sd"> Changing the anchor point changes the location considered by the kernel. If you have</span>
+<span class="sd"> the kernel: MATH, when the anchor point is in the center, you consider 1 pixel in each</span>
+<span class="sd"> direciton around your target pixel. If you move the anchor point to the top, you consider</span>
+<span class="sd"> no pixels above, and more below. MORE MATH.</span>
+<span class="sd"> REFERENCE OPENCV DOCS.</span>
+<span class="sd"> """</span>
+ <span class="k">if</span> <span class="n">borderType</span> <span class="ow">in</span> <span class="n">conf</span><span class="o">.</span><span class="n">borders</span><span class="p">:</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">image</span> <span class="o">=</span> <span class="n">cv2</span><span class="o">.</span><span class="n">blur</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">image</span><span class="p">,</span> <span class="n">anchor</span> <span class="o">=</span> <span class="n">anchor</span><span class="p">,</span> <span class="n">borderType</span> <span class="o">=</span> <span class="n">conf</span><span class="o">.</span><span class="n">borders</span><span class="p">[</span><span class="n">borderType</span><span class="p">])</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="s">"Invalid border type, should be one of: "</span> <span class="o">+</span> <span class="s">","</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">conf</span><span class="o">.</span><span class="n">borders</span><span class="o">.</span><span class="n">keys</span><span class="p">())</span> <span class="o">+</span> <span class="s">"."</span><span class="p">)</span>
+ <span class="k">return</span>
+ </div>
+<div class="viewcode-block" id="Image.medianBlur"><a class="viewcode-back" href="../../processing.html#htpia.imgproc.Image.medianBlur">[docs]</a> <span class="k">def</span> <span class="nf">medianBlur</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">ksize</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> :param ksize: The size of the kernel (ksize x ksize). Should be odd and positive.</span>
+<span class="sd"> :type ksize: int</span>
+<span class="sd"> </span>
+<span class="sd"> This function smoothes an image using the median filter. The kernel is set to size (ksize, ksize).</span>
+<span class="sd"> The anchor position is assumed to be the center.</span>
+<span class="sd"> REFERENCE OPENCV MEDIAN BLUR</span>
+<span class="sd"> """</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">image</span> <span class="o">=</span> <span class="n">cv2</span><span class="o">.</span><span class="n">medianBlur</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">image</span><span class="p">,</span> <span class="n">ksize</span><span class="p">)</span>
+ <span class="k">return</span>
+ </div>
+<div class="viewcode-block" id="Image.gaussianBlur"><a class="viewcode-back" href="../../processing.html#htpia.imgproc.Image.gaussianBlur">[docs]</a> <span class="k">def</span> <span class="nf">gaussianBlur</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">ksize</span><span class="p">,</span> <span class="n">sigmaX</span> <span class="o">=</span> <span class="mi">0</span><span class="p">,</span> <span class="n">sigmaY</span> <span class="o">=</span> <span class="mi">0</span><span class="p">,</span> <span class="n">borderType</span> <span class="o">=</span> <span class="s">"default"</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> :param ksize: The size of the kernel represented by a tuple (width, height). Both numers should be odd and positive.</span>
+<span class="sd"> :type ksize: tuple</span>
+<span class="sd"> :param sigmaX: The standard deviation in the x direction. If 0, the value is calculated based on the kernel size.</span>
+<span class="sd"> :type sigmaX: float</span>
+<span class="sd"> :param sigmaY: The standard deviation in the y direction. If 0, the value is equal to sigmaX.</span>
+<span class="sd"> :type sigmaY: float</span>
+<span class="sd"> :param borderType: The type of border mode used to extrapolate pixels outside the image. Literally no information on this.</span>
+<span class="sd"> :type borderType: str</span>
+<span class="sd"> </span>
+<span class="sd"> This function blurs an image based on a Gaussian kernel -- which is defined as: MATH.</span>
+<span class="sd"> REFERENCE to OPENCV GAUSSIAN BLUR</span>
+<span class="sd"> REFERENCE OPENCV GAUSSIAN KERNEL</span>
+<span class="sd"> """</span>
+ <span class="k">if</span> <span class="n">borderType</span> <span class="ow">in</span> <span class="n">conf</span><span class="o">.</span><span class="n">borders</span><span class="p">:</span>
+ <span class="n">sigmaY</span> <span class="o">=</span> <span class="n">sigmaX</span> <span class="k">if</span> <span class="n">sigmaY</span> <span class="o">==</span> <span class="mi">0</span> <span class="k">else</span> <span class="n">sigmaY</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">image</span> <span class="o">=</span> <span class="n">cv2</span><span class="o">.</span><span class="n">GaussianBlur</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">image</span><span class="p">,</span> <span class="n">ksize</span><span class="p">,</span> <span class="n">sigmaX</span><span class="p">,</span> <span class="n">sigmaY</span><span class="p">,</span> <span class="n">borderType</span> <span class="o">=</span> <span class="n">conf</span><span class="o">.</span><span class="n">borders</span><span class="p">[</span><span class="n">borderType</span><span class="p">])</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="s">"Invalid border type, should be one of: "</span> <span class="o">+</span> <span class="s">","</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">conf</span><span class="o">.</span><span class="n">borders</span><span class="o">.</span><span class="n">keys</span><span class="p">())</span> <span class="o">+</span> <span class="s">"."</span><span class="p">)</span>
+ <span class="k">return</span>
+ </div>
+<div class="viewcode-block" id="Image.normalizeByIntensity"><a class="viewcode-back" href="../../processing.html#htpia.imgproc.Image.normalizeByIntensity">[docs]</a> <span class="k">def</span> <span class="nf">normalizeByIntensity</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> Normalizes each channel of by pixel intensity. That is, for each pixel:</span>
+<span class="sd"> I = R + G + B</span>
+<span class="sd"> newr = R * 255 / I</span>
+<span class="sd"> newg = G * 255 / I</span>
+<span class="sd"> newb = B * 255 / I</span>
+<span class="sd"> """</span>
+ <span class="n">f</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">image</span><span class="o">.</span><span class="n">astype</span><span class="p">(</span><span class="nb">float</span><span class="p">)</span>
+ <span class="n">combined</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">add</span><span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">add</span><span class="p">(</span><span class="n">f</span><span class="p">[:,:,</span><span class="mi">0</span><span class="p">],</span> <span class="n">f</span><span class="p">[:,:,</span><span class="mi">1</span><span class="p">]),</span> <span class="n">f</span><span class="p">[:,:,</span><span class="mi">2</span><span class="p">])</span>
+ <span class="n">scaled</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">multiply</span><span class="p">(</span><span class="n">f</span><span class="p">,</span> <span class="p">[</span><span class="mi">255</span><span class="p">])</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">image</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">divide</span><span class="p">(</span><span class="n">scaled</span><span class="p">,</span> <span class="n">combined</span><span class="p">[:,:,</span><span class="bp">None</span><span class="p">])</span><span class="o">.</span><span class="n">astype</span><span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">uint8</span><span class="p">)</span>
+ <span class="k">return</span>
+ </div>
+<div class="viewcode-block" id="Image.morphology"><a class="viewcode-back" href="../../processing.html#htpia.imgproc.Image.morphology">[docs]</a> <span class="k">def</span> <span class="nf">morphology</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">morphType</span><span class="p">,</span> <span class="n">ktype</span><span class="p">,</span> <span class="n">ksize</span><span class="p">,</span> <span class="n">anchor</span> <span class="o">=</span> <span class="p">(</span><span class="o">-</span><span class="mi">1</span><span class="p">,</span> <span class="o">-</span><span class="mi">1</span><span class="p">),</span> <span class="n">iterations</span> <span class="o">=</span> <span class="mi">1</span><span class="p">,</span> <span class="n">borderType</span> <span class="o">=</span> <span class="s">"default"</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> :param morphType: The type of morphology to perform. Should be dilate, erode, open, close, gradient, tophat, or blackhat.</span>
+<span class="sd"> :type morphType: str</span>
+<span class="sd"> :param ktype: the type of the kernel, should be rect, ellipse, or cross.</span>
+<span class="sd"> :type ktype: str</span>
+<span class="sd"> :param ksize: The size of the kernel represented by a tuple (width, height). Both numbers should be odd and positive.</span>
+<span class="sd"> :type ksize: tuple</span>
+<span class="sd"> :param anchor: The anchor point for filtering. Default is (-1, -1) which is the center of the kernel.</span>
+<span class="sd"> :type anchor: tuple</span>
+<span class="sd"> :param iterations: The number of times to perform the specified morphology.</span>
+<span class="sd"> :type iterations: int</span>
+<span class="sd"> :param borderType: The type of border mode used to extrapolate pixels outside the image. Literally no information on this.</span>
+<span class="sd"> :type borderType: str</span>
+<span class="sd"> </span>
+<span class="sd"> This function performs morphological operations based on the inputted values.</span>
+<span class="sd"> REFERENCE to OPENCV MORPHOLOGY</span>
+<span class="sd"> SHOW MORPHOLOGY EXAMPLES</span>
+<span class="sd"> """</span>
+ <span class="k">if</span> <span class="n">morphType</span> <span class="ow">in</span> <span class="n">conf</span><span class="o">.</span><span class="n">morph</span><span class="p">:</span>
+ <span class="k">if</span> <span class="n">ktype</span> <span class="ow">in</span> <span class="n">conf</span><span class="o">.</span><span class="n">kernels</span><span class="p">:</span>
+ <span class="k">if</span> <span class="n">borderType</span> <span class="ow">in</span> <span class="n">conf</span><span class="o">.</span><span class="n">borders</span><span class="p">:</span>
+ <span class="n">kernel</span> <span class="o">=</span> <span class="n">cv2</span><span class="o">.</span><span class="n">getStructuringElement</span><span class="p">(</span><span class="n">conf</span><span class="o">.</span><span class="n">kernels</span><span class="p">[</span><span class="n">ktype</span><span class="p">],</span> <span class="n">ksize</span><span class="p">,</span> <span class="n">anchor</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">image</span> <span class="o">=</span> <span class="n">cv2</span><span class="o">.</span><span class="n">morphologyEx</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">image</span><span class="p">,</span> <span class="n">conf</span><span class="o">.</span><span class="n">morph</span><span class="p">[</span><span class="n">morphType</span><span class="p">],</span> <span class="n">kernel</span><span class="p">,</span> <span class="n">anchor</span> <span class="o">=</span> <span class="n">anchor</span><span class="p">,</span> <span class="n">iterations</span> <span class="o">=</span> <span class="n">iterations</span><span class="p">,</span> <span class="n">borderType</span> <span class="o">=</span> <span class="n">conf</span><span class="o">.</span><span class="n">borders</span><span class="p">[</span><span class="n">borderType</span><span class="p">])</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="s">"Invalid border type, should be one of: "</span> <span class="o">+</span> <span class="s">","</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">conf</span><span class="o">.</span><span class="n">borders</span><span class="o">.</span><span class="n">keys</span><span class="p">())</span> <span class="o">+</span> <span class="s">"."</span><span class="p">)</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="s">"Invalid kernel type, should be one of: "</span> <span class="o">+</span> <span class="s">","</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">conf</span><span class="o">.</span><span class="n">kernels</span><span class="o">.</span><span class="n">keys</span><span class="p">())</span> <span class="o">+</span> <span class="s">"."</span><span class="p">)</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="s">"Invalid morphology type, should be one of: "</span> <span class="o">+</span> <span class="s">","</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">conf</span><span class="o">.</span><span class="n">morph</span><span class="o">.</span><span class="n">keys</span><span class="p">())</span> <span class="o">+</span> <span class="s">"."</span><span class="p">)</span>
+ </div>
+<div class="viewcode-block" id="Image.crop"><a class="viewcode-back" href="../../processing.html#htpia.imgproc.Image.crop">[docs]</a> <span class="k">def</span> <span class="nf">crop</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">roi</span><span class="p">,</span> <span class="n">resize</span> <span class="o">=</span> <span class="bp">False</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> :param roi: A list corresponding to the area of the image you want. List should be of the form [ystart, yend, xstart, xend]</span>
+<span class="sd"> :type roi: list or roi file</span>
+<span class="sd"> :param resize: If True, actually adjusts the size of the image, otherwise just draws over the part of the image not in the roi.</span>
+<span class="sd"> :type resize: bool</span>
+<span class="sd"> </span>
+<span class="sd"> This function crops the image based on the given roi [ystart, yend, xstart, xend]. There are two crop options,</span>
+<span class="sd"> by default, the function doesn't actually resize the image. Instead, it sets each pixel not in the roi to black.</span>
+<span class="sd"> If resize is set to True, the function will actually crop the image down to the roi.</span>
+<span class="sd"> """</span>
+ <span class="n">roi</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_loadROI</span><span class="p">(</span><span class="n">roi</span><span class="p">)</span>
+ <span class="n">ystart</span><span class="p">,</span> <span class="n">yend</span><span class="p">,</span> <span class="n">xstart</span><span class="p">,</span> <span class="n">xend</span> <span class="o">=</span> <span class="n">roi</span>
+ <span class="k">if</span> <span class="p">(</span><span class="n">resize</span><span class="p">):</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">image</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">image</span><span class="p">[</span><span class="n">ystart</span><span class="p">:</span> <span class="n">yend</span><span class="p">,</span> <span class="n">xstart</span><span class="p">:</span> <span class="n">xend</span><span class="p">]</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">x</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">image</span><span class="o">.</span><span class="n">shape</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">y</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">image</span><span class="o">.</span><span class="n">shape</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="n">maxx</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">x</span>
+ <span class="n">maxy</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">y</span>
+ <span class="n">off</span> <span class="o">=</span> <span class="p">[</span><span class="mi">0</span><span class="p">,</span> <span class="mi">0</span><span class="p">,</span> <span class="mi">0</span><span class="p">]</span> <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">_isColor</span><span class="p">()</span> <span class="k">else</span> <span class="p">[</span><span class="mi">0</span><span class="p">]</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">image</span><span class="p">[</span><span class="mi">0</span><span class="p">:</span><span class="n">ystart</span><span class="p">,</span> <span class="mi">0</span><span class="p">:</span><span class="n">maxx</span><span class="p">]</span> <span class="o">=</span> <span class="n">off</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">image</span><span class="p">[</span><span class="n">yend</span><span class="p">:</span><span class="n">maxy</span><span class="p">,</span> <span class="mi">0</span><span class="p">:</span><span class="n">maxx</span><span class="p">]</span> <span class="o">=</span> <span class="n">off</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">image</span><span class="p">[</span><span class="mi">0</span><span class="p">:</span><span class="n">maxy</span><span class="p">,</span> <span class="mi">0</span><span class="p">:</span><span class="n">xstart</span><span class="p">]</span> <span class="o">=</span> <span class="n">off</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">image</span><span class="p">[</span><span class="mi">0</span><span class="p">:</span><span class="n">maxy</span><span class="p">,</span> <span class="n">xend</span><span class="p">:</span><span class="n">maxx</span><span class="p">]</span> <span class="o">=</span> <span class="n">off</span>
+ <span class="k">return</span>
+ </div>
+<div class="viewcode-block" id="Image.contourCut"><a class="viewcode-back" href="../../processing.html#htpia.imgproc.Image.contourCut">[docs]</a> <span class="k">def</span> <span class="nf">contourCut</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">binary</span><span class="p">,</span> <span class="n">basemin</span> <span class="o">=</span> <span class="mi">100</span><span class="p">,</span> <span class="n">padding</span> <span class="o">=</span> <span class="p">[</span><span class="mi">0</span><span class="p">,</span> <span class="mi">0</span><span class="p">,</span> <span class="mi">0</span><span class="p">,</span> <span class="mi">0</span><span class="p">],</span> <span class="n">resize</span> <span class="o">=</span> <span class="bp">False</span><span class="p">,</span> <span class="n">returnBound</span> <span class="o">=</span> <span class="bp">False</span><span class="p">,</span> <span class="n">roiwrite</span> <span class="o">=</span> <span class="s">"roi.json"</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> :param binary: The binary image to find contours of.</span>
+<span class="sd"> :type binary: str or np.ndarray</span>
+<span class="sd"> :param basemin: The minimum area a contour must have to be consider part of the foreground.</span>
+<span class="sd"> :type basemin: int</span>
+<span class="sd"> :param padding: Padding add to all sides of the final roi.</span>
+<span class="sd"> :type padding: int</span>
+<span class="sd"> :param returnBound: If set, instead of cropping the image, simply write the detected roi.</span>
+<span class="sd"> :type returnBound: bool</span>
+<span class="sd"> :param resize: Whether or not to resize the image.</span>
+<span class="sd"> :type resize: bool</span>
+<span class="sd"> </span>
+<span class="sd"> This function crops an image based on the size of detected contours in the image. The</span>
+<span class="sd"> image is cropped such that all contours that are greater than the specified area are</span>
+<span class="sd"> included in the final output image. If returnBound is set, instead of actually</span>
+<span class="sd"> cropping the image, the detected roi is written to a file instead. Otherwise,</span>
+<span class="sd"> the detected roi is passed into the :py:meth:`~htpia.imgproc.crop` function,</span>
+<span class="sd"> with the given resize value.</span>
+<span class="sd"> """</span>
+ <span class="n">bname</span><span class="p">,</span> <span class="n">binary</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_loadResource</span><span class="p">(</span><span class="n">binary</span><span class="p">)</span>
+ <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">_isColor</span><span class="p">(</span><span class="n">binary</span><span class="p">):</span>
+ <span class="n">binary</span> <span class="o">=</span> <span class="n">cv2</span><span class="o">.</span><span class="n">cvtColor</span><span class="p">(</span><span class="n">binary</span><span class="p">,</span> <span class="n">cv2</span><span class="o">.</span><span class="n">COLOR_BGR2GRAY</span><span class="p">)</span>
+ <span class="n">contours</span> <span class="o">=</span> <span class="n">cv2</span><span class="o">.</span><span class="n">findContours</span><span class="p">(</span><span class="n">binary</span><span class="p">,</span> <span class="n">cv2</span><span class="o">.</span><span class="n">RETR_TREE</span><span class="p">,</span> <span class="n">cv2</span><span class="o">.</span><span class="n">CHAIN_APPROX_SIMPLE</span><span class="p">)[</span><span class="mi">0</span><span class="p">]</span>
+ <span class="n">minx</span> <span class="o">=</span> <span class="n">binary</span><span class="o">.</span><span class="n">shape</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span>
+ <span class="n">miny</span> <span class="o">=</span> <span class="n">binary</span><span class="o">.</span><span class="n">shape</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span>
+ <span class="n">maxx</span> <span class="o">=</span> <span class="mi">0</span>
+ <span class="n">maxy</span> <span class="o">=</span> <span class="mi">0</span>
+ <span class="k">for</span> <span class="n">cnt</span> <span class="ow">in</span> <span class="n">contours</span><span class="p">:</span>
+ <span class="n">x</span><span class="p">,</span><span class="n">y</span><span class="p">,</span><span class="n">w</span><span class="p">,</span><span class="n">h</span> <span class="o">=</span> <span class="n">cv2</span><span class="o">.</span><span class="n">boundingRect</span><span class="p">(</span><span class="n">cnt</span><span class="p">)</span>
+ <span class="k">if</span> <span class="p">(</span><span class="n">basemin</span> <span class="o"><</span> <span class="n">cv2</span><span class="o">.</span><span class="n">contourArea</span><span class="p">(</span><span class="n">cnt</span><span class="p">)):</span>
+ <span class="k">if</span> <span class="p">(</span><span class="n">x</span> <span class="o"><</span> <span class="n">minx</span><span class="p">):</span>
+ <span class="n">minx</span> <span class="o">=</span> <span class="n">x</span>
+ <span class="k">if</span> <span class="p">(</span><span class="n">y</span> <span class="o"><</span> <span class="n">miny</span><span class="p">):</span>
+ <span class="n">miny</span> <span class="o">=</span> <span class="n">y</span>
+ <span class="k">if</span> <span class="p">(</span><span class="n">x</span> <span class="o">+</span> <span class="n">w</span> <span class="o">></span> <span class="n">maxx</span><span class="p">):</span>
+ <span class="n">maxx</span> <span class="o">=</span> <span class="n">x</span> <span class="o">+</span> <span class="n">w</span>
+ <span class="k">if</span> <span class="p">(</span><span class="n">y</span> <span class="o">+</span> <span class="n">h</span> <span class="o">></span> <span class="n">maxy</span><span class="p">):</span>
+ <span class="n">maxy</span> <span class="o">=</span> <span class="n">y</span> <span class="o">+</span> <span class="n">h</span>
+ <span class="n">roi</span> <span class="o">=</span> <span class="p">[</span><span class="mi">0</span> <span class="k">if</span> <span class="n">miny</span> <span class="o">-</span> <span class="n">padding</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="o"><</span> <span class="mi">0</span> <span class="k">else</span> <span class="n">miny</span> <span class="o">-</span> <span class="n">padding</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span> <span class="n">binary</span><span class="o">.</span><span class="n">shape</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="k">if</span> <span class="n">maxy</span> <span class="o">+</span> <span class="n">padding</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span> <span class="o">></span> <span class="n">binary</span><span class="o">.</span><span class="n">shape</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="k">else</span> <span class="n">maxy</span> <span class="o">+</span> <span class="n">padding</span><span class="p">[</span><span class="mi">1</span><span class="p">],</span> <span class="mi">0</span> <span class="k">if</span> <span class="n">minx</span> <span class="o">-</span> <span class="n">padding</span><span class="p">[</span><span class="mi">2</span><span class="p">]</span> <span class="o"><</span> <span class="mi">0</span> <span class="k">else</span> <span class="n">minx</span> <span class="o">-</span> <span class="n">padding</span><span class="p">[</span><span class="mi">2</span><span class="p">],</span> <span class="n">binary</span><span class="o">.</span><span class="n">shape</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span> <span class="k">if</span> <span class="n">maxx</span> <span class="o">+</span> <span class="n">padding</span><span class="p">[</span><span class="mi">3</span><span class="p">]</span> <span class="o">></span> <span class="n">binary</span><span class="o">.</span><span class="n">shape</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span> <span class="k">else</span> <span class="n">maxx</span> <span class="o">+</span> <span class="n">padding</span><span class="p">[</span><span class="mi">3</span><span class="p">]]</span>
+ <span class="k">if</span> <span class="n">returnBound</span><span class="p">:</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_writeROI</span><span class="p">(</span><span class="n">roi</span><span class="p">,</span> <span class="n">roiwrite</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">crop</span><span class="p">(</span><span class="n">roi</span><span class="p">,</span> <span class="n">resize</span><span class="p">)</span>
+ <span class="k">return</span>
+ </div>
+<div class="viewcode-block" id="Image.edges"><a class="viewcode-back" href="../../processing.html#htpia.imgproc.Image.edges">[docs]</a> <span class="k">def</span> <span class="nf">edges</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">threshold1</span><span class="p">,</span> <span class="n">threshold2</span><span class="p">,</span> <span class="n">apertureSize</span> <span class="o">=</span> <span class="mi">3</span><span class="p">,</span> <span class="n">L2gradient</span> <span class="o">=</span> <span class="bp">False</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> :param threshold1: First threshold for the hysteresis procedure.</span>
+<span class="sd"> :type threshold1: int</span>
+<span class="sd"> :param threshold2: Second threshold for the hysteresis procedure.</span>
+<span class="sd"> :type threshold2: int</span>
+<span class="sd"> :param apertureSize: aperture size used for the Sobel algorithm.</span>
+<span class="sd"> :type apertureSize: int</span>
+<span class="sd"> :L2gradient: Used to calculate Image gradient magnitude, if true then :math:`L = \sqrt{(dI/dx)^2 + (dI/dy)^2}`, if false then :math:`L = dI/dx + dI/dy`.</span>
+<span class="sd"> :type L2gradient: bool</span>
+<span class="sd"> </span>
+<span class="sd"> This function calculates the edges of an image using the Canny edge detection algorithm, which is built upon the Sobel</span>
+<span class="sd"> algorithm, which calculates derivatives of an image. REFERENCE TO OPENCV HERE.</span>
+<span class="sd"> """</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">image</span> <span class="o">=</span> <span class="n">cv2</span><span class="o">.</span><span class="n">Canny</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">image</span><span class="p">,</span> <span class="n">threshold1</span><span class="p">,</span> <span class="n">threshold2</span><span class="p">,</span> <span class="n">apertureSize</span> <span class="o">=</span> <span class="n">apertureSize</span><span class="p">,</span> <span class="n">L2gradient</span> <span class="o">=</span> <span class="n">L2gradient</span><span class="p">)</span>
+ <span class="k">return</span>
+ </div>
+<div class="viewcode-block" id="Image.colorFilter"><a class="viewcode-back" href="../../processing.html#htpia.imgproc.Image.colorFilter">[docs]</a> <span class="k">def</span> <span class="nf">colorFilter</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">logic</span><span class="p">,</span> <span class="n">roi</span> <span class="o">=</span> <span class="bp">None</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> :param logic: The logic you want to run on the image.</span>
+<span class="sd"> :type logic: str</span>
+<span class="sd"> :param roi: The roi you want to apply the filter to</span>
+<span class="sd"> :type roi: list or roi file</span>
+<span class="sd"> </span>
+<span class="sd"> This function applies a color filter defined by the input logic, to a</span>
+<span class="sd"> targeted region defined by the input roi. The roi is defined the same,</span>
+<span class="sd"> [ystart, yend, xstart, xend]. The logic string itself is fairly complicated.</span>
+<span class="sd"> The string supports the following operators: '+', '-', '*', '/', '>', '>=',</span>
+<span class="sd"> '==', '<', '<=', 'and', 'or', '(', ')', 'r', 'g', 'b', as well as any numeric</span>
+<span class="sd"> value. The logic string itself is confined to symbolic logic rules -- each </span>
+<span class="sd"> operation, arg1 operator arg2, must be surrounded by parenthesis. For example,</span>
+<span class="sd"> if you want to check the intensity of the pixel, your logic string would be:</span>
+<span class="sd"> '(((r + g) + b) < 100)'. This string in particular will only keep pixels whose</span>
+<span class="sd"> intensity is less than 100. Similar rules apply for 'and' and 'or' operators.</span>
+<span class="sd"> Let's say we only want to keep pixels whose intensity is less than 100, OR both</span>
+<span class="sd"> the red and blue channels are greater than 150, the logic string would be: </span>
+<span class="sd"> '((((r + g) + b) < 100) or ((r > 150) and (b > 150)))'.</span>
+<span class="sd"> """</span>
+ <span class="nb">filter</span> <span class="o">=</span> <span class="n">ColorFilter</span><span class="p">(</span><span class="n">logic</span><span class="p">)</span>
+ <span class="n">roi</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_loadROI</span><span class="p">(</span><span class="n">roi</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">image</span> <span class="o">=</span> <span class="nb">filter</span><span class="o">.</span><span class="n">apply</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">image</span><span class="p">,</span> <span class="n">roi</span><span class="p">)</span>
+ <span class="k">return</span>
+ </div>
+<div class="viewcode-block" id="Image.bitwise_not"><a class="viewcode-back" href="../../processing.html#htpia.imgproc.Image.bitwise_not">[docs]</a> <span class="k">def</span> <span class="nf">bitwise_not</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> Inverts the image. If the given image has multiple channels (i.e. is a color image) each channel is processed independently.</span>
+<span class="sd"> """</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">image</span> <span class="o">=</span> <span class="n">cv2</span><span class="o">.</span><span class="n">bitwise_not</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">image</span><span class="p">)</span>
+ <span class="k">return</span>
+ </div>
+<div class="viewcode-block" id="Image.bitwise_and"><a class="viewcode-back" href="../../processing.html#htpia.imgproc.Image.bitwise_and">[docs]</a> <span class="k">def</span> <span class="nf">bitwise_and</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">comp</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> :param comp: The comparison image.</span>
+<span class="sd"> :type comp: str or np.ndarray</span>
+<span class="sd"> :return: The resulting mask.</span>
+<span class="sd"> :rtype: numpy.ndarray</span>
+<span class="sd"> </span>
+<span class="sd"> Performs logical and on the class image, and reference image.</span>
+<span class="sd"> Assumes the two images are the correct type.</span>
+<span class="sd"> """</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">image</span> <span class="o">=</span> <span class="n">cv2</span><span class="o">.</span><span class="n">bitwise_and</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">image</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">_loadResource</span><span class="p">(</span><span class="n">comp</span><span class="p">)[</span><span class="mi">1</span><span class="p">])</span>
+ <span class="k">return</span>
+ </div>
+<div class="viewcode-block" id="Image.bitwise_or"><a class="viewcode-back" href="../../processing.html#htpia.imgproc.Image.bitwise_or">[docs]</a> <span class="k">def</span> <span class="nf">bitwise_or</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">comp</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> :param comp: The comparison image.</span>
+<span class="sd"> :type comp: str or np.ndarray</span>
+<span class="sd"> :return: The resulting mask.</span>
+<span class="sd"> :rtype: numpy.ndarray</span>
+<span class="sd"> </span>
+<span class="sd"> Performs bitwise or logic on the class image, and reference image.</span>
+<span class="sd"> Assumes the two images are the correct type.</span>
+<span class="sd"> """</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">image</span> <span class="o">=</span> <span class="n">cv2</span><span class="o">.</span><span class="n">bitwise_or</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">image</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">_loadResource</span><span class="p">(</span><span class="n">comp</span><span class="p">)[</span><span class="mi">1</span><span class="p">])</span>
+ <span class="k">return</span>
+ </div>
+<div class="viewcode-block" id="Image.bitwise_xor"><a class="viewcode-back" href="../../processing.html#htpia.imgproc.Image.bitwise_xor">[docs]</a> <span class="k">def</span> <span class="nf">bitwise_xor</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">comp</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> :param comp: The comparison image.</span>
+<span class="sd"> :type comp: str or np.ndarray</span>
+<span class="sd"> :return: The resulting mask.</span>
+<span class="sd"> :rtype: numpy.ndarray</span>
+<span class="sd"> </span>
+<span class="sd"> Performs bitwise exclusive or logic on the class image, and reference image.</span>
+<span class="sd"> Assumes the two images are the correct type.</span>
+<span class="sd"> """</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">image</span> <span class="o">=</span> <span class="n">cv2</span><span class="o">.</span><span class="n">bitwise_xor</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">image</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">_loadResource</span><span class="p">(</span><span class="n">comp</span><span class="p">)[</span><span class="mi">1</span><span class="p">])</span>
+ <span class="k">return</span>
+ </div>
+<div class="viewcode-block" id="Image.extractFinalPath"><a class="viewcode-back" href="../../processing.html#htpia.imgproc.Image.extractFinalPath">[docs]</a> <span class="k">def</span> <span class="nf">extractFinalPath</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> This function writes the absolute path of the output file to the database.</span>
+<span class="sd"> """</span>
+ <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">conn</span><span class="p">:</span>
+ <span class="n">finalpath</span> <span class="o">=</span> <span class="s">"/"</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">abspath</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">input</span><span class="p">)</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s">"/"</span><span class="p">)[</span><span class="o">-</span><span class="mi">6</span><span class="p">:])</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_addColumn</span><span class="p">(</span><span class="s">"outputPath"</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">conn</span><span class="o">.</span><span class="n">execute</span><span class="p">(</span><span class="s">"update images set outputPath=? where pegasusid=?"</span><span class="p">,</span> <span class="p">(</span><span class="n">finalpath</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">dbid</span><span class="p">))</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">conn</span><span class="o">.</span><span class="n">commit</span><span class="p">()</span>
+ <span class="k">return</span>
+ </div>
+<div class="viewcode-block" id="Image.extractMoments"><a class="viewcode-back" href="../../processing.html#htpia.imgproc.Image.extractMoments">[docs]</a> <span class="k">def</span> <span class="nf">extractMoments</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> :return: A dictionary corresponding to the different moments of the image.</span>
+<span class="sd"> :rtype: dict</span>
+<span class="sd"> </span>
+<span class="sd"> Calculates the moments of the image, and returns a dicitonary based on them.</span>
+<span class="sd"> Spatial moments are prefixed with 'm', central moments are prefixed with 'mu',</span>
+<span class="sd"> and central normalized moments are prefixed with 'nu'.</span>
+<span class="sd"> REFERENCE TO OPENCV DOCUMENTATION</span>
+<span class="sd"> REFERENCE TO GREEN'S THEOREM</span>
+<span class="sd"> """</span>
+ <span class="n">moments</span> <span class="o">=</span> <span class="n">cv2</span><span class="o">.</span><span class="n">moments</span><span class="p">(</span><span class="n">cv2</span><span class="o">.</span><span class="n">inRange</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">image</span><span class="p">,</span> <span class="n">np</span><span class="o">.</span><span class="n">array</span><span class="p">([</span><span class="mi">1</span><span class="p">,</span> <span class="mi">1</span><span class="p">,</span> <span class="mi">1</span><span class="p">],</span> <span class="n">np</span><span class="o">.</span><span class="n">uint8</span><span class="p">),</span> <span class="n">np</span><span class="o">.</span><span class="n">array</span><span class="p">([</span><span class="mi">255</span><span class="p">,</span> <span class="mi">255</span><span class="p">,</span> <span class="mi">255</span><span class="p">],</span> <span class="n">np</span><span class="o">.</span><span class="n">uint8</span><span class="p">)))</span>
+ <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">conn</span><span class="p">:</span>
+ <span class="k">for</span> <span class="nb">id</span> <span class="ow">in</span> <span class="n">moments</span><span class="p">:</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_addColumn</span><span class="p">(</span><span class="nb">id</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">conn</span><span class="o">.</span><span class="n">execute</span><span class="p">(</span><span class="s">"update images set "</span> <span class="o">+</span> <span class="nb">id</span> <span class="o">+</span> <span class="s">"=? where pegasusid=?"</span><span class="p">,</span> <span class="p">(</span><span class="n">moments</span><span class="p">[</span><span class="nb">id</span><span class="p">],</span> <span class="bp">self</span><span class="o">.</span><span class="n">dbid</span><span class="p">))</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">conn</span><span class="o">.</span><span class="n">commit</span><span class="p">()</span>
+ <span class="k">return</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="k">return</span> <span class="n">moments</span>
+ </div>
+<div class="viewcode-block" id="Image.extractDimensions"><a class="viewcode-back" href="../../processing.html#htpia.imgproc.Image.extractDimensions">[docs]</a> <span class="k">def</span> <span class="nf">extractDimensions</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> :return: A list corresponding to the height and width of the image.</span>
+<span class="sd"> :rtype: list</span>
+<span class="sd"> </span>
+<span class="sd"> Returns a list with the following form: [height, width]</span>
+<span class="sd"> """</span>
+ <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">conn</span><span class="p">:</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_addColumn</span><span class="p">(</span><span class="s">"height"</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_addColumn</span><span class="p">(</span><span class="s">"width"</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">conn</span><span class="o">.</span><span class="n">execute</span><span class="p">(</span><span class="s">"update images set height=?,width=? where pegasusid=?"</span><span class="p">,</span> <span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">y</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">x</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">dbid</span><span class="p">))</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">conn</span><span class="o">.</span><span class="n">commit</span><span class="p">()</span>
+ <span class="k">return</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="k">return</span> <span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">y</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">x</span><span class="p">]</span>
+ </div>
+<div class="viewcode-block" id="Image.extractPixels"><a class="viewcode-back" href="../../processing.html#htpia.imgproc.Image.extractPixels">[docs]</a> <span class="k">def</span> <span class="nf">extractPixels</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> :return: The number of non-black pixels in the image.</span>
+<span class="sd"> :rtype: int</span>
+<span class="sd"> </span>
+<span class="sd"> Returns the number of non-black pixels in the image. Creates</span>
+<span class="sd"> a temporary binary image to do this. The point of this function</span>
+<span class="sd"> is not to threshold, so the binary image is created by all</span>
+<span class="sd"> pixels that fall into the range [1, 1, 1], [255, 255, 255].</span>
+<span class="sd"> """</span>
+ <span class="n">pixelCount</span> <span class="o">=</span> <span class="n">cv2</span><span class="o">.</span><span class="n">countNonZero</span><span class="p">(</span><span class="n">cv2</span><span class="o">.</span><span class="n">inRange</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">image</span><span class="p">,</span> <span class="n">np</span><span class="o">.</span><span class="n">array</span><span class="p">([</span><span class="mi">1</span><span class="p">,</span> <span class="mi">1</span><span class="p">,</span> <span class="mi">1</span><span class="p">],</span> <span class="n">np</span><span class="o">.</span><span class="n">uint8</span><span class="p">),</span> <span class="n">np</span><span class="o">.</span><span class="n">array</span><span class="p">([</span><span class="mi">255</span><span class="p">,</span> <span class="mi">255</span><span class="p">,</span> <span class="mi">255</span><span class="p">],</span> <span class="n">np</span><span class="o">.</span><span class="n">uint8</span><span class="p">)))</span>
+ <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">conn</span><span class="p">:</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_addColumn</span><span class="p">(</span><span class="s">"pixels"</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">conn</span><span class="o">.</span><span class="n">execute</span><span class="p">(</span><span class="s">"update images set pixels=? where pegasusid=?"</span><span class="p">,</span> <span class="p">(</span><span class="n">pixelCount</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">dbid</span><span class="p">))</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">conn</span><span class="o">.</span><span class="n">commit</span><span class="p">()</span>
+ <span class="k">return</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="k">return</span> <span class="n">pixelCount</span>
+ </div>
+<div class="viewcode-block" id="Image.extractColorData"><a class="viewcode-back" href="../../processing.html#htpia.imgproc.Image.extractColorData">[docs]</a> <span class="k">def</span> <span class="nf">extractColorData</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">nonzero</span> <span class="o">=</span> <span class="bp">True</span><span class="p">,</span> <span class="n">returnhist</span> <span class="o">=</span> <span class="bp">False</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> :param nonzero: Whether or not to look at only nonzero pixels. Default true.</span>
+<span class="sd"> :type nonzero: bool</span>
+<span class="sd"> :return: Mean & median for each channel.</span>
+<span class="sd"> :rtype: list</span>
+<span class="sd"> </span>
+<span class="sd"> This function calculates a normalized histogram of each individual color channel of </span>
+<span class="sd"> the image, and returns the mean & median of the histograms for the channels</span>
+<span class="sd"> specified. Because images are imported with the channels ordered as B,G,R,</span>
+<span class="sd"> the output list is returned the same way. The returned list always looks like</span>
+<span class="sd"> this: [ [BlueMean, BlueMedian], [GreenMean, GreenMedian], [RedMean, RedMedian] ].</span>
+<span class="sd"> Mean values always come before median values. If nonzero is set to true (default)</span>
+<span class="sd"> the function will only calculate mediapytn and means based on the non-black pixels.</span>
+<span class="sd"> """</span>
+ <span class="n">hist</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_colorHistogram</span><span class="p">()</span>
+ <span class="k">if</span> <span class="n">returnhist</span><span class="p">:</span>
+ <span class="k">return</span> <span class="n">hist</span>
+ <span class="n">colors</span> <span class="o">=</span> <span class="p">[</span> <span class="p">[</span><span class="n">np</span><span class="o">.</span><span class="n">mean</span><span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">nonzero</span><span class="p">(</span><span class="n">hist</span><span class="p">[</span><span class="mi">0</span><span class="p">])</span> <span class="k">if</span> <span class="n">nonzero</span> <span class="k">else</span> <span class="n">hist</span><span class="p">[</span><span class="mi">0</span><span class="p">]),</span> <span class="n">np</span><span class="o">.</span><span class="n">median</span><span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">nonzero</span><span class="p">(</span><span class="n">hist</span><span class="p">[</span><span class="mi">0</span><span class="p">])</span> <span class="k">if</span> <span class="n">nonzero</span> <span class="k">else</span> <span class="n">hist</span><span class="p">[</span><span class="mi">0</span><span class="p">])],</span>
+ <span class="p">[</span><span class="n">np</span><span class="o">.</span><span class="n">mean</span><span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">nonzero</span><span class="p">(</span><span class="n">hist</span><span class="p">[</span><span class="mi">1</span><span class="p">])</span> <span class="k">if</span> <span class="n">nonzero</span> <span class="k">else</span> <span class="n">hist</span><span class="p">[</span><span class="mi">1</span><span class="p">]),</span> <span class="n">np</span><span class="o">.</span><span class="n">median</span><span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">nonzero</span><span class="p">(</span><span class="n">hist</span><span class="p">[</span><span class="mi">1</span><span class="p">])</span> <span class="k">if</span> <span class="n">nonzero</span> <span class="k">else</span> <span class="n">hist</span><span class="p">[</span><span class="mi">1</span><span class="p">])],</span>
+ <span class="p">[</span><span class="n">np</span><span class="o">.</span><span class="n">mean</span><span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">nonzero</span><span class="p">(</span><span class="n">hist</span><span class="p">[</span><span class="mi">2</span><span class="p">])</span> <span class="k">if</span> <span class="n">nonzero</span> <span class="k">else</span> <span class="n">hist</span><span class="p">[</span><span class="mi">2</span><span class="p">]),</span> <span class="n">np</span><span class="o">.</span><span class="n">median</span><span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">nonzero</span><span class="p">(</span><span class="n">hist</span><span class="p">[</span><span class="mi">2</span><span class="p">])</span> <span class="k">if</span> <span class="n">nonzero</span> <span class="k">else</span> <span class="n">hist</span><span class="p">[</span><span class="mi">2</span><span class="p">])]</span>
+ <span class="p">]</span>
+ <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">conn</span><span class="p">:</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_addColumn</span><span class="p">(</span><span class="s">"rmean"</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_addColumn</span><span class="p">(</span><span class="s">"rmed"</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_addColumn</span><span class="p">(</span><span class="s">"gmean"</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_addColumn</span><span class="p">(</span><span class="s">"gmed"</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_addColumn</span><span class="p">(</span><span class="s">"bmean"</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_addColumn</span><span class="p">(</span><span class="s">"bmed"</span><span class="p">)</span>
+ <span class="n">query</span> <span class="o">=</span> <span class="s">"update images set rmean=?,rmed=?,gmean=?,gmed=?,bmean=?,bmed=?"</span>
+ <span class="n">values</span> <span class="o">=</span> <span class="p">[</span><span class="n">colors</span><span class="p">[</span><span class="mi">2</span><span class="p">][</span><span class="mi">0</span><span class="p">],</span> <span class="n">colors</span><span class="p">[</span><span class="mi">2</span><span class="p">][</span><span class="mi">1</span><span class="p">],</span> <span class="n">colors</span><span class="p">[</span><span class="mi">1</span><span class="p">][</span><span class="mi">0</span><span class="p">],</span> <span class="n">colors</span><span class="p">[</span><span class="mi">1</span><span class="p">][</span><span class="mi">1</span><span class="p">],</span> <span class="n">colors</span><span class="p">[</span><span class="mi">0</span><span class="p">][</span><span class="mi">0</span><span class="p">],</span> <span class="n">colors</span><span class="p">[</span><span class="mi">0</span><span class="p">][</span><span class="mi">1</span><span class="p">]]</span>
+ <span class="k">for</span> <span class="n">x</span><span class="p">,</span><span class="n">c</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">([</span><span class="s">"bhist"</span><span class="p">,</span> <span class="s">"ghist"</span><span class="p">,</span> <span class="s">"rhist"</span><span class="p">]):</span>
+ <span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="mi">0</span><span class="p">,</span> <span class="mi">256</span><span class="p">):</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_addColumn</span><span class="p">(</span><span class="n">c</span> <span class="o">+</span> <span class="nb">str</span><span class="p">(</span><span class="n">i</span><span class="p">))</span>
+ <span class="n">query</span> <span class="o">+=</span> <span class="s">","</span> <span class="o">+</span> <span class="n">c</span> <span class="o">+</span> <span class="nb">str</span><span class="p">(</span><span class="n">i</span><span class="p">)</span> <span class="o">+</span> <span class="s">"=?"</span>
+ <span class="n">values</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="nb">int</span><span class="p">(</span><span class="n">hist</span><span class="p">[</span><span class="n">x</span><span class="p">][</span><span class="n">i</span><span class="p">]))</span>
+ <span class="n">query</span> <span class="o">+=</span> <span class="s">" where pegasusid=?"</span>
+ <span class="n">values</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">dbid</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">conn</span><span class="o">.</span><span class="n">execute</span><span class="p">(</span><span class="n">query</span><span class="p">,</span> <span class="nb">tuple</span><span class="p">(</span><span class="n">values</span><span class="p">))</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">conn</span><span class="o">.</span><span class="n">commit</span><span class="p">()</span>
+ <span class="k">return</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="k">return</span> <span class="n">colors</span>
+ </div>
+ <span class="k">def</span> <span class="nf">extractColorChannels</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+ <span class="n">b</span><span class="p">,</span> <span class="n">g</span><span class="p">,</span> <span class="n">r</span> <span class="o">=</span> <span class="n">cv2</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">image</span><span class="p">)</span>
+ <span class="n">bdata</span><span class="p">,</span> <span class="n">gdata</span><span class="p">,</span> <span class="n">rdata</span> <span class="o">=</span> <span class="p">[],</span> <span class="p">[],</span> <span class="p">[]</span>
+ <span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="mi">0</span><span class="p">,</span> <span class="mi">256</span><span class="p">):</span>
+ <span class="n">bdata</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">count_nonzero</span><span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">where</span><span class="p">(</span><span class="n">b</span> <span class="o">==</span> <span class="n">i</span><span class="p">,</span> <span class="bp">True</span><span class="p">,</span> <span class="bp">False</span><span class="p">)))</span>
+ <span class="n">gdata</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">count_nonzero</span><span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">where</span><span class="p">(</span><span class="n">g</span> <span class="o">==</span> <span class="n">i</span><span class="p">,</span> <span class="bp">True</span><span class="p">,</span> <span class="bp">False</span><span class="p">)))</span>
+ <span class="n">rdata</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">count_nonzero</span><span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">where</span><span class="p">(</span><span class="n">r</span> <span class="o">==</span> <span class="n">i</span><span class="p">,</span> <span class="bp">True</span><span class="p">,</span> <span class="bp">False</span><span class="p">)))</span>
+ <span class="n">data</span> <span class="o">=</span> <span class="p">[</span><span class="n">bdata</span><span class="p">,</span> <span class="n">gdata</span><span class="p">,</span> <span class="n">rdata</span><span class="p">]</span>
+ <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">conn</span><span class="p">:</span>
+ <span class="n">query</span> <span class="o">=</span> <span class="s">"update images set "</span>
+ <span class="n">values</span> <span class="o">=</span> <span class="p">[]</span>
+ <span class="k">for</span> <span class="n">x</span><span class="p">,</span><span class="n">c</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">([</span><span class="s">"b"</span><span class="p">,</span> <span class="s">"g"</span><span class="p">,</span> <span class="s">"r"</span><span class="p">]):</span>
+ <span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="mi">0</span><span class="p">,</span> <span class="mi">256</span><span class="p">):</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_addColumn</span><span class="p">(</span><span class="n">c</span> <span class="o">+</span> <span class="nb">str</span><span class="p">(</span><span class="n">i</span><span class="p">))</span>
+ <span class="k">if</span> <span class="n">i</span> <span class="o">==</span> <span class="mi">0</span><span class="p">:</span>
+ <span class="n">query</span> <span class="o">+=</span> <span class="n">c</span> <span class="o">+</span> <span class="nb">str</span><span class="p">(</span><span class="n">i</span><span class="p">)</span> <span class="o">+</span> <span class="s">"=?"</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="n">query</span> <span class="o">+=</span> <span class="s">","</span> <span class="o">+</span> <span class="n">c</span> <span class="o">+</span> <span class="nb">str</span><span class="p">(</span><span class="n">i</span><span class="p">)</span> <span class="o">+</span> <span class="s">"=?"</span>
+ <span class="n">values</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">data</span><span class="p">[</span><span class="n">x</span><span class="p">][</span><span class="n">i</span><span class="p">])</span>
+ <span class="n">query</span> <span class="o">+=</span> <span class="s">" where pegasusid=?"</span>
+ <span class="n">values</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">dbid</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">conn</span><span class="o">.</span><span class="n">execute</span><span class="p">(</span><span class="n">query</span><span class="p">,</span> <span class="nb">tuple</span><span class="p">(</span><span class="n">values</span><span class="p">))</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">conn</span><span class="o">.</span><span class="n">commit</span><span class="p">()</span>
+ <span class="k">return</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="k">return</span> <span class="p">(</span><span class="n">bdata</span><span class="p">,</span> <span class="n">gdata</span><span class="p">,</span> <span class="n">rdata</span><span class="p">)</span>
+
+<div class="viewcode-block" id="Image.extractBins"><a class="viewcode-back" href="../../processing.html#htpia.imgproc.Image.extractBins">[docs]</a> <span class="k">def</span> <span class="nf">extractBins</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">binlist</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> :param binlist: The specified bins (color ranges) to count.</span>
+<span class="sd"> :type binlist: list</span>
+<span class="sd"> :return: The number of pixels that fall in each bin.</span>
+<span class="sd"> :rtype: list</span>
+<span class="sd"> </span>
+<span class="sd"> This function counts the number of pixels that fall into the range as</span>
+<span class="sd"> specified by each bin. This function expects the input to be a list of </span>
+<span class="sd"> dictionaries as follows:</span>
+<span class="sd"> </span>
+<span class="sd"> .. code-block:: python</span>
+<span class="sd"> </span>
+<span class="sd"> binlist = [</span>
+<span class="sd"> {"name": "bin1",</span>
+<span class="sd"> "min": [B, G, R],</span>
+<span class="sd"> "max": [B, G, R]</span>
+<span class="sd"> },</span>
+<span class="sd"> {"name": "bin2",</span>
+<span class="sd"> ...</span>
+<span class="sd"> ]</span>
+<span class="sd"> </span>
+<span class="sd"> Each range is defined by 6 values. A minimum and maximum blue,</span>
+<span class="sd"> green, and red value. The returned list is very similar to the </span>
+<span class="sd"> input list, except a 'count' key is added to each dictionary:</span>
+<span class="sd"> </span>
+<span class="sd"> .. code-block:: python</span>
+<span class="sd"> </span>
+<span class="sd"> returnlist = [</span>
+<span class="sd"> {"name": "bin1",</span>
+<span class="sd"> "min": [B, G, R],</span>
+<span class="sd"> "max": [B, G, R],</span>
+<span class="sd"> "count": VALUE</span>
+<span class="sd"> },</span>
+<span class="sd"> ...</span>
+<span class="sd"> ]</span>
+<span class="sd"> </span>
+<span class="sd"> Where 'VALUE' is the number of pixels that fall into the</span>
+<span class="sd"> corresponding range.</span>
+<span class="sd"> A list is used instead of a dictionary as the base structure</span>
+<span class="sd"> to maintain order for writing to the output database. When</span>
+<span class="sd"> using this function within a workflow, the order you specify</span>
+<span class="sd"> your bins is the order in which they will show up in the</span>
+<span class="sd"> database, and the name you specify for you bin will be</span>
+<span class="sd"> the column name in the database.</span>
+<span class="sd"> """</span>
+ <span class="n">binlist</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_loadBins</span><span class="p">(</span><span class="n">binlist</span><span class="p">)</span>
+ <span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="mi">0</span><span class="p">,</span> <span class="nb">len</span><span class="p">(</span><span class="n">binlist</span><span class="p">)):</span>
+ <span class="n">binlist</span><span class="p">[</span><span class="n">i</span><span class="p">][</span><span class="s">"count"</span><span class="p">]</span> <span class="o">=</span> <span class="n">cv2</span><span class="o">.</span><span class="n">countNonZero</span><span class="p">(</span><span class="n">cv2</span><span class="o">.</span><span class="n">inRange</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">image</span><span class="p">,</span> <span class="n">np</span><span class="o">.</span><span class="n">array</span><span class="p">(</span><span class="n">binlist</span><span class="p">[</span><span class="n">i</span><span class="p">][</span><span class="s">"min"</span><span class="p">],</span> <span class="n">np</span><span class="o">.</span><span class="n">uint8</span><span class="p">),</span> <span class="n">np</span><span class="o">.</span><span class="n">array</span><span class="p">(</span><span class="n">binlist</span><span class="p">[</span><span class="n">i</span><span class="p">][</span><span class="s">"max"</span><span class="p">],</span> <span class="n">np</span><span class="o">.</span><span class="n">uint8</span><span class="p">)))</span>
+ <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">conn</span><span class="p">:</span>
+ <span class="k">for</span> <span class="nb">bin</span> <span class="ow">in</span> <span class="n">binlist</span><span class="p">:</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_addColumn</span><span class="p">(</span><span class="nb">bin</span><span class="p">[</span><span class="s">"name"</span><span class="p">])</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">conn</span><span class="o">.</span><span class="n">execute</span><span class="p">(</span><span class="s">"update images set "</span> <span class="o">+</span> <span class="nb">bin</span><span class="p">[</span><span class="s">"name"</span><span class="p">]</span> <span class="o">+</span> <span class="s">"=? where pegasusid=?"</span><span class="p">,</span> <span class="p">(</span><span class="nb">bin</span><span class="p">[</span><span class="s">"count"</span><span class="p">],</span> <span class="bp">self</span><span class="o">.</span><span class="n">dbid</span><span class="p">))</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">conn</span><span class="o">.</span><span class="n">commit</span><span class="p">()</span>
+ <span class="k">return</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="k">return</span> <span class="n">binlist</span>
+
+ </div></div>
+</pre></div>
+
+ </div>
+
+ </div>
+</div>
+<footer class="footer">
+ <div class="container">
+ <p class="pull-right">
+ <a href="#">Back to top</a>
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+ </p>
+ <p>
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+ </body>
+</html>
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new file mode 100644
index 0000000000000000000000000000000000000000..86db4c82a4feb725b2c190874e3a52c63a912192
--- /dev/null
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@@ -0,0 +1,802 @@
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+<html xmlns="http://www.w3.org/1999/xhtml">
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+
+ <h1>Source code for htpia.statistics</h1><div class="highlight"><pre>
+<span class="kn">import</span> <span class="nn">math</span>
+<span class="kn">import</span> <span class="nn">os</span>
+<span class="kn">import</span> <span class="nn">sqlite3</span>
+<span class="kn">import</span> <span class="nn">conf</span>
+<span class="kn">import</span> <span class="nn">datetime</span>
+<span class="kn">import</span> <span class="nn">numpy</span> <span class="kn">as</span> <span class="nn">np</span>
+<span class="kn">import</span> <span class="nn">pandas</span>
+<span class="kn">import</span> <span class="nn">htpia.imgproc</span>
+<span class="kn">import</span> <span class="nn">cv2</span>
+<span class="kn">import</span> <span class="nn">json</span>
+<span class="kn">import</span> <span class="nn">traceback</span>
+<span class="kn">from</span> <span class="nn">scipy</span> <span class="kn">import</span> <span class="n">stats</span>
+
+<div class="viewcode-block" id="Stats"><a class="viewcode-back" href="../../statistics.html#htpia.statistics.Stats">[docs]</a><span class="k">class</span> <span class="nc">Stats</span><span class="p">:</span>
+
+ <span class="k">def</span> <span class="nf">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">db</span><span class="p">):</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">db</span> <span class="o">=</span> <span class="n">db</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">conn</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_openConnection</span><span class="p">()</span>
+ <span class="k">return</span>
+
+ <span class="k">def</span> <span class="nf">_openConnection</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">db</span> <span class="o">=</span> <span class="bp">None</span><span class="p">):</span>
+ <span class="n">db</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">db</span> <span class="k">if</span> <span class="ow">not</span> <span class="n">db</span> <span class="k">else</span> <span class="n">db</span>
+ <span class="k">if</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">isfile</span><span class="p">(</span><span class="n">db</span><span class="p">):</span>
+ <span class="n">conn</span> <span class="o">=</span> <span class="n">sqlite3</span><span class="o">.</span><span class="n">connect</span><span class="p">(</span><span class="n">db</span><span class="p">,</span> <span class="n">check_same_thread</span> <span class="o">=</span> <span class="bp">False</span><span class="p">)</span>
+ <span class="n">conn</span><span class="o">.</span><span class="n">row_factory</span> <span class="o">=</span> <span class="n">sqlite3</span><span class="o">.</span><span class="n">Row</span>
+ <span class="n">result</span> <span class="o">=</span> <span class="n">conn</span><span class="o">.</span><span class="n">execute</span><span class="p">(</span><span class="s">"select pegasusid from images limit 0,1"</span><span class="p">)</span>
+ <span class="k">if</span> <span class="ow">not</span> <span class="n">result</span><span class="o">.</span><span class="n">fetchone</span><span class="p">():</span>
+ <span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="s">"Database '</span><span class="si">%s</span><span class="s">' has no entries!"</span> <span class="o">%</span> <span class="p">(</span><span class="n">db</span><span class="p">,))</span>
+ <span class="c"># Have to enable foreign keys EVERY time.</span>
+ <span class="n">conn</span><span class="o">.</span><span class="n">execute</span><span class="p">(</span><span class="s">"PRAGMA foreign_keys = ON"</span><span class="p">)</span>
+ <span class="n">conn</span><span class="o">.</span><span class="n">commit</span><span class="p">()</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="s">"Database file '</span><span class="si">%s</span><span class="s">' does not exist."</span> <span class="o">%</span> <span class="p">(</span><span class="n">db</span><span class="p">,))</span>
+ <span class="k">return</span> <span class="n">conn</span>
+
+ <span class="k">def</span> <span class="nf">_closeConnection</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">conn</span> <span class="o">=</span> <span class="bp">None</span><span class="p">):</span>
+ <span class="n">conn</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">conn</span> <span class="k">if</span> <span class="ow">not</span> <span class="n">conn</span> <span class="k">else</span> <span class="n">conn</span>
+ <span class="n">conn</span><span class="o">.</span><span class="n">close</span><span class="p">()</span>
+ <span class="k">return</span>
+
+ <span class="k">def</span> <span class="nf">_tableExists</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">tablename</span><span class="p">,</span> <span class="n">conn</span> <span class="o">=</span> <span class="bp">None</span><span class="p">):</span>
+ <span class="n">conn</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">conn</span> <span class="k">if</span> <span class="ow">not</span> <span class="n">conn</span> <span class="k">else</span> <span class="n">conn</span>
+ <span class="n">result</span> <span class="o">=</span> <span class="n">conn</span><span class="o">.</span><span class="n">execute</span><span class="p">(</span><span class="s">"select name from sqlite_master where type='table' and name=?"</span><span class="p">,</span> <span class="p">(</span><span class="n">tablename</span><span class="p">,))</span>
+ <span class="k">if</span> <span class="ow">not</span> <span class="n">result</span><span class="o">.</span><span class="n">fetchone</span><span class="p">():</span>
+ <span class="k">return</span> <span class="bp">False</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="k">return</span> <span class="bp">True</span>
+
+ <span class="k">def</span> <span class="nf">_validate</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">funcname</span><span class="p">,</span> <span class="n">intable</span><span class="p">,</span> <span class="n">outtable</span><span class="p">,</span> <span class="n">overwrite</span><span class="p">,</span> <span class="n">conn</span> <span class="o">=</span> <span class="bp">None</span><span class="p">):</span>
+ <span class="n">conn</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">conn</span> <span class="k">if</span> <span class="ow">not</span> <span class="n">conn</span> <span class="k">else</span> <span class="n">conn</span>
+ <span class="k">if</span> <span class="n">funcname</span> <span class="ow">in</span> <span class="n">conf</span><span class="o">.</span><span class="n">statsColumns</span><span class="p">:</span>
+ <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">_tableExists</span><span class="p">(</span><span class="n">intable</span><span class="p">):</span>
+ <span class="n">cols</span> <span class="o">=</span> <span class="p">[</span><span class="n">x</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span> <span class="k">for</span> <span class="n">x</span> <span class="ow">in</span> <span class="n">conn</span><span class="o">.</span><span class="n">execute</span><span class="p">(</span><span class="s">"PRAGMA table_info('"</span> <span class="o">+</span> <span class="n">intable</span> <span class="o">+</span> <span class="s">"')"</span><span class="p">)]</span>
+ <span class="k">if</span> <span class="nb">set</span><span class="p">(</span><span class="n">conf</span><span class="o">.</span><span class="n">statsColumns</span><span class="p">[</span><span class="n">funcname</span><span class="p">][</span><span class="s">"required"</span><span class="p">])</span> <span class="o"><=</span> <span class="nb">set</span><span class="p">(</span><span class="n">cols</span><span class="p">):</span>
+ <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">_tableExists</span><span class="p">(</span><span class="n">outtable</span><span class="p">,</span> <span class="n">conn</span><span class="p">)</span> <span class="ow">and</span> <span class="ow">not</span> <span class="n">overwrite</span><span class="p">:</span>
+ <span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="s">"Output table '"</span> <span class="o">+</span> <span class="n">outtable</span> <span class="o">+</span> <span class="s">"' already exists."</span><span class="p">)</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="s">"Table '"</span> <span class="o">+</span> <span class="n">intable</span> <span class="o">+</span> <span class="s">"' doesn't have all the required columns: '"</span> <span class="o">+</span> <span class="nb">str</span><span class="p">(</span><span class="n">conf</span><span class="o">.</span><span class="n">statsColumns</span><span class="p">[</span><span class="n">funcname</span><span class="p">][</span><span class="s">"required"</span><span class="p">])</span> <span class="o">+</span> <span class="s">"'."</span><span class="p">)</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="s">"Table '"</span> <span class="o">+</span> <span class="n">intable</span> <span class="o">+</span> <span class="s">"' doesn't exist."</span><span class="p">)</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="s">"Function '"</span> <span class="o">+</span> <span class="n">funcname</span> <span class="o">+</span> <span class="s">"' doesn't exist."</span><span class="p">)</span>
+ <span class="k">return</span>
+
+ <span class="k">def</span> <span class="nf">_columnExists</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">column</span><span class="p">,</span> <span class="n">tablename</span><span class="p">,</span> <span class="n">conn</span> <span class="o">=</span> <span class="bp">None</span><span class="p">):</span>
+ <span class="n">conn</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">conn</span> <span class="k">if</span> <span class="ow">not</span> <span class="n">conn</span> <span class="k">else</span> <span class="n">conn</span>
+ <span class="k">if</span> <span class="n">column</span> <span class="ow">in</span> <span class="p">[</span><span class="n">row</span><span class="p">[</span><span class="s">"name"</span><span class="p">]</span> <span class="k">for</span> <span class="n">row</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">conn</span><span class="o">.</span><span class="n">execute</span><span class="p">(</span><span class="s">"PRAGMA table_info('"</span> <span class="o">+</span> <span class="n">tablename</span> <span class="o">+</span> <span class="s">"')"</span><span class="p">)]:</span>
+ <span class="k">return</span> <span class="bp">True</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="k">return</span> <span class="bp">False</span>
+
+ <span class="k">def</span> <span class="nf">_addColumn</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">column</span><span class="p">,</span> <span class="n">tablename</span> <span class="o">=</span> <span class="s">"images"</span><span class="p">,</span> <span class="n">conn</span> <span class="o">=</span> <span class="bp">None</span><span class="p">):</span>
+ <span class="n">conn</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">conn</span> <span class="k">if</span> <span class="ow">not</span> <span class="n">conn</span> <span class="k">else</span> <span class="n">conn</span>
+ <span class="k">if</span> <span class="ow">not</span> <span class="bp">self</span><span class="o">.</span><span class="n">_columnExists</span><span class="p">(</span><span class="n">column</span><span class="p">,</span> <span class="n">tablename</span><span class="p">,</span> <span class="n">conn</span><span class="p">):</span>
+ <span class="n">conn</span><span class="o">.</span><span class="n">execute</span><span class="p">(</span><span class="s">"alter table '"</span> <span class="o">+</span> <span class="n">tablename</span> <span class="o">+</span> <span class="s">"' add column "</span> <span class="o">+</span> <span class="n">column</span> <span class="o">+</span> <span class="s">";"</span><span class="p">)</span>
+ <span class="n">conn</span><span class="o">.</span><span class="n">commit</span><span class="p">()</span>
+ <span class="k">return</span>
+
+ <span class="k">def</span> <span class="nf">_addKeyColumn</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">parent</span><span class="p">,</span> <span class="n">parentCol</span><span class="p">,</span> <span class="n">child</span><span class="p">,</span> <span class="n">childCol</span><span class="p">,</span> <span class="n">conn</span> <span class="o">=</span> <span class="bp">None</span><span class="p">):</span>
+ <span class="n">conn</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">conn</span> <span class="k">if</span> <span class="ow">not</span> <span class="n">conn</span> <span class="k">else</span> <span class="n">conn</span>
+ <span class="k">if</span> <span class="n">parentCol</span> <span class="ow">not</span> <span class="ow">in</span> <span class="p">[</span><span class="n">row</span><span class="p">[</span><span class="s">"name"</span><span class="p">]</span> <span class="k">for</span> <span class="n">row</span> <span class="ow">in</span> <span class="n">conn</span><span class="o">.</span><span class="n">execute</span><span class="p">(</span><span class="s">"PRAGMA table_info('"</span> <span class="o">+</span> <span class="n">parent</span> <span class="o">+</span> <span class="s">"');"</span><span class="p">)]</span> <span class="ow">and</span> <span class="n">childCol</span> <span class="ow">in</span> <span class="p">[</span><span class="n">row</span><span class="p">[</span><span class="s">"name"</span><span class="p">]</span> <span class="k">for</span> <span class="n">row</span> <span class="ow">in</span> <span class="n">conn</span><span class="o">.</span><span class="n">execute</span><span class="p">(</span><span class="s">"PRAGMA table_info('"</span> <span class="o">+</span> <span class="n">child</span> <span class="o">+</span> <span class="s">"');"</span><span class="p">)]:</span>
+ <span class="n">conn</span><span class="o">.</span><span class="n">execute</span><span class="p">(</span><span class="s">"alter table '"</span> <span class="o">+</span> <span class="n">parent</span> <span class="o">+</span> <span class="s">"' add column '"</span> <span class="o">+</span> <span class="n">parentCol</span> <span class="o">+</span> <span class="s">"' REFERENCES '"</span> <span class="o">+</span> <span class="n">child</span> <span class="o">+</span> <span class="s">"'('"</span> <span class="o">+</span> <span class="n">childCol</span> <span class="o">+</span> <span class="s">"');"</span><span class="p">)</span>
+ <span class="n">conn</span><span class="o">.</span><span class="n">commit</span><span class="p">()</span>
+ <span class="k">return</span>
+
+ <span class="k">def</span> <span class="nf">_createTable</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">funcname</span><span class="p">,</span> <span class="n">intable</span><span class="p">,</span> <span class="n">outtable</span><span class="p">,</span> <span class="n">overwrite</span><span class="p">,</span> <span class="n">conn</span> <span class="o">=</span> <span class="bp">None</span><span class="p">):</span>
+ <span class="n">conn</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">conn</span> <span class="k">if</span> <span class="ow">not</span> <span class="n">conn</span> <span class="k">else</span> <span class="n">conn</span>
+ <span class="n">tablestr</span> <span class="o">=</span> <span class="s">"(pegasusid INTEGER PRIMARY KEY"</span>
+ <span class="n">cols</span> <span class="o">=</span> <span class="p">[</span><span class="n">x</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span> <span class="k">for</span> <span class="n">x</span> <span class="ow">in</span> <span class="n">conn</span><span class="o">.</span><span class="n">execute</span><span class="p">(</span><span class="s">"pragma table_info('"</span> <span class="o">+</span> <span class="n">intable</span> <span class="o">+</span> <span class="s">"')"</span><span class="p">)]</span>
+ <span class="k">if</span> <span class="s">"all"</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">conf</span><span class="o">.</span><span class="n">statsColumns</span><span class="p">[</span><span class="n">funcname</span><span class="p">][</span><span class="s">"exclude"</span><span class="p">]:</span>
+ <span class="k">for</span> <span class="n">col</span> <span class="ow">in</span> <span class="n">cols</span><span class="p">:</span>
+ <span class="k">if</span> <span class="n">col</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">conf</span><span class="o">.</span><span class="n">statsColumns</span><span class="p">[</span><span class="n">funcname</span><span class="p">][</span><span class="s">"exclude"</span><span class="p">]</span> <span class="ow">and</span> <span class="n">col</span><span class="p">[:</span><span class="mi">3</span><span class="p">]</span> <span class="o">!=</span> <span class="s">"ref"</span><span class="p">:</span>
+ <span class="n">tablestr</span> <span class="o">+=</span> <span class="s">","</span> <span class="o">+</span> <span class="nb">str</span><span class="p">(</span><span class="n">col</span><span class="p">)</span>
+ <span class="k">for</span> <span class="n">col</span> <span class="ow">in</span> <span class="n">conf</span><span class="o">.</span><span class="n">statsColumns</span><span class="p">[</span><span class="n">funcname</span><span class="p">][</span><span class="s">"add"</span><span class="p">]:</span>
+ <span class="n">tablestr</span> <span class="o">+=</span> <span class="s">","</span> <span class="o">+</span> <span class="nb">str</span><span class="p">(</span><span class="n">col</span><span class="p">)</span>
+ <span class="n">tablestr</span> <span class="o">+=</span> <span class="s">")"</span>
+ <span class="k">if</span> <span class="n">overwrite</span><span class="p">:</span>
+ <span class="n">conn</span><span class="o">.</span><span class="n">execute</span><span class="p">(</span><span class="s">"DROP TABLE IF EXISTS "</span> <span class="o">+</span> <span class="n">outtable</span><span class="p">)</span>
+ <span class="n">conn</span><span class="o">.</span><span class="n">commit</span><span class="p">()</span>
+ <span class="n">conn</span><span class="o">.</span><span class="n">execute</span><span class="p">(</span><span class="s">"CREATE TABLE "</span> <span class="o">+</span> <span class="n">outtable</span> <span class="o">+</span> <span class="s">" "</span> <span class="o">+</span> <span class="n">tablestr</span><span class="p">)</span>
+ <span class="n">conn</span><span class="o">.</span><span class="n">commit</span><span class="p">()</span>
+ <span class="k">if</span> <span class="n">conf</span><span class="o">.</span><span class="n">statsColumns</span><span class="p">[</span><span class="n">funcname</span><span class="p">][</span><span class="s">"ref"</span><span class="p">]:</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_addKeyColumn</span><span class="p">(</span><span class="n">intable</span><span class="p">,</span> <span class="s">"ref_"</span> <span class="o">+</span> <span class="n">outtable</span><span class="p">,</span> <span class="n">outtable</span><span class="p">,</span> <span class="s">"pegasusid"</span><span class="p">,</span> <span class="n">conn</span><span class="p">)</span>
+ <span class="k">return</span>
+
+ <span class="k">def</span> <span class="nf">_getHeaders</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">table</span><span class="p">,</span> <span class="n">conn</span> <span class="o">=</span> <span class="bp">None</span><span class="p">):</span>
+ <span class="n">conn</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">conn</span> <span class="k">if</span> <span class="ow">not</span> <span class="n">conn</span> <span class="k">else</span> <span class="n">conn</span>
+ <span class="k">return</span> <span class="p">[</span><span class="nb">str</span><span class="p">(</span><span class="n">x</span><span class="p">[</span><span class="mi">1</span><span class="p">])</span> <span class="k">for</span> <span class="n">x</span> <span class="ow">in</span> <span class="n">conn</span><span class="o">.</span><span class="n">execute</span><span class="p">(</span><span class="s">"pragma table_info("</span> <span class="o">+</span> <span class="n">table</span> <span class="o">+</span> <span class="s">")"</span><span class="p">)</span> <span class="k">if</span> <span class="n">x</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span> <span class="o">!=</span> <span class="s">"pegasusid"</span><span class="p">]</span>
+
+ <span class="k">def</span> <span class="nf">_getImageTypes</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">table</span><span class="p">,</span> <span class="n">conn</span> <span class="o">=</span> <span class="bp">None</span><span class="p">):</span>
+ <span class="n">conn</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">conn</span> <span class="k">if</span> <span class="ow">not</span> <span class="n">conn</span> <span class="k">else</span> <span class="n">conn</span>
+ <span class="k">return</span> <span class="p">[</span><span class="nb">str</span><span class="p">(</span><span class="n">x</span><span class="p">[</span><span class="mi">0</span><span class="p">])</span> <span class="k">for</span> <span class="n">x</span> <span class="ow">in</span> <span class="n">conn</span><span class="o">.</span><span class="n">execute</span><span class="p">(</span><span class="s">"select distinct imtype from "</span> <span class="o">+</span> <span class="n">table</span><span class="p">)]</span>
+
+ <span class="k">def</span> <span class="nf">_getDates</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">table</span><span class="p">,</span> <span class="n">conn</span> <span class="o">=</span> <span class="bp">None</span><span class="p">):</span>
+ <span class="n">conn</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">conn</span> <span class="k">if</span> <span class="ow">not</span> <span class="n">conn</span> <span class="k">else</span> <span class="n">conn</span>
+ <span class="k">return</span> <span class="p">[</span><span class="nb">str</span><span class="p">(</span><span class="n">x</span><span class="p">[</span><span class="mi">0</span><span class="p">])</span> <span class="k">for</span> <span class="n">x</span> <span class="ow">in</span> <span class="n">conn</span><span class="o">.</span><span class="n">execute</span><span class="p">(</span><span class="s">"select distinct date from "</span> <span class="o">+</span> <span class="n">table</span><span class="p">)]</span>
+
+ <span class="k">def</span> <span class="nf">_loadLemnaData</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">dataFile</span><span class="p">,</span> <span class="n">dataHeaders</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> :param dataFile: The input dataFile</span>
+<span class="sd"> :type dataFile: str</span>
+<span class="sd"> :param dataHeaders: The input data headers</span>
+<span class="sd"> :type dataHeaders: dict</span>
+<span class="sd"> </span>
+<span class="sd"> dataHeaders should be:</span>
+<span class="sd"> { </span>
+<span class="sd"> "id": "Snapshot ID Tag",</span>
+<span class="sd"> "date": "Snapshot Time Stamp",</span>
+<span class="sd"> "dateFormat": "%m/%d/%y",</span>
+<span class="sd"> "metric": "Projected Shoot Area [pixels]"</span>
+<span class="sd"> }</span>
+<span class="sd"> """</span>
+ <span class="k">if</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">isfile</span><span class="p">(</span><span class="n">dataFile</span><span class="p">):</span>
+ <span class="k">if</span> <span class="nb">all</span><span class="p">(</span><span class="n">key</span> <span class="ow">in</span> <span class="n">dataHeaders</span> <span class="k">for</span> <span class="n">key</span> <span class="ow">in</span> <span class="p">[</span><span class="s">"id"</span><span class="p">,</span> <span class="s">"date"</span><span class="p">,</span> <span class="s">"dateFormat"</span><span class="p">,</span> <span class="s">"metric"</span><span class="p">]):</span>
+ <span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="n">dataFile</span><span class="p">)</span> <span class="k">as</span> <span class="n">rh</span><span class="p">:</span>
+ <span class="n">lines</span> <span class="o">=</span> <span class="n">rh</span><span class="o">.</span><span class="n">readlines</span><span class="p">()</span>
+ <span class="n">firstline</span> <span class="o">=</span> <span class="n">lines</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">.</span><span class="n">strip</span><span class="p">()</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s">","</span><span class="p">)</span>
+ <span class="k">if</span> <span class="n">dataHeaders</span><span class="p">[</span><span class="s">"id"</span><span class="p">]</span> <span class="ow">in</span> <span class="n">firstline</span><span class="p">:</span>
+ <span class="k">if</span> <span class="n">dataHeaders</span><span class="p">[</span><span class="s">"date"</span><span class="p">]</span> <span class="ow">in</span> <span class="n">firstline</span><span class="p">:</span>
+ <span class="k">if</span> <span class="n">dataHeaders</span><span class="p">[</span><span class="s">"metric"</span><span class="p">]</span> <span class="ow">in</span> <span class="n">firstline</span><span class="p">:</span>
+ <span class="n">idIndex</span> <span class="o">=</span> <span class="n">firstline</span><span class="o">.</span><span class="n">index</span><span class="p">(</span><span class="n">dataHeaders</span><span class="p">[</span><span class="s">"id"</span><span class="p">])</span>
+ <span class="n">dateIndex</span> <span class="o">=</span> <span class="n">firstline</span><span class="o">.</span><span class="n">index</span><span class="p">(</span><span class="n">dataHeaders</span><span class="p">[</span><span class="s">"date"</span><span class="p">])</span>
+ <span class="n">metricIndex</span> <span class="o">=</span> <span class="n">firstline</span><span class="o">.</span><span class="n">index</span><span class="p">(</span><span class="n">dataHeaders</span><span class="p">[</span><span class="s">"metric"</span><span class="p">])</span>
+ <span class="n">lemnaData</span> <span class="o">=</span> <span class="p">{}</span>
+ <span class="k">for</span> <span class="n">line</span> <span class="ow">in</span> <span class="n">lines</span><span class="p">[</span><span class="mi">1</span><span class="p">:]:</span>
+ <span class="n">info</span> <span class="o">=</span> <span class="n">line</span><span class="o">.</span><span class="n">strip</span><span class="p">()</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s">","</span><span class="p">)</span>
+ <span class="k">if</span> <span class="p">(</span><span class="n">info</span><span class="p">[</span><span class="n">metricIndex</span><span class="p">]</span> <span class="o">!=</span> <span class="s">"NA"</span><span class="p">):</span>
+ <span class="nb">id</span> <span class="o">=</span> <span class="n">info</span><span class="p">[</span><span class="n">idIndex</span><span class="p">][</span><span class="o">-</span><span class="mi">8</span><span class="p">:]</span>
+ <span class="n">date</span> <span class="o">=</span> <span class="n">datetime</span><span class="o">.</span><span class="n">datetime</span><span class="o">.</span><span class="n">strptime</span><span class="p">(</span><span class="n">info</span><span class="p">[</span><span class="n">dateIndex</span><span class="p">]</span><span class="o">.</span><span class="n">split</span><span class="p">()[</span><span class="mi">0</span><span class="p">],</span> <span class="n">dataHeaders</span><span class="p">[</span><span class="s">"dateFormat"</span><span class="p">])</span><span class="o">.</span><span class="n">strftime</span><span class="p">(</span><span class="s">"%Y-%m-</span><span class="si">%d</span><span class="s">"</span><span class="p">)</span>
+ <span class="k">try</span><span class="p">:</span>
+ <span class="n">metric</span> <span class="o">=</span> <span class="nb">float</span><span class="p">(</span><span class="n">info</span><span class="p">[</span><span class="n">metricIndex</span><span class="p">])</span>
+ <span class="k">if</span> <span class="nb">id</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">lemnaData</span><span class="p">:</span>
+ <span class="n">lemnaData</span><span class="p">[</span><span class="nb">id</span><span class="p">]</span> <span class="o">=</span> <span class="p">{}</span>
+ <span class="k">if</span> <span class="n">date</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">lemnaData</span><span class="p">[</span><span class="nb">id</span><span class="p">]:</span>
+ <span class="n">lemnaData</span><span class="p">[</span><span class="nb">id</span><span class="p">][</span><span class="n">date</span><span class="p">]</span> <span class="o">=</span> <span class="p">{}</span>
+ <span class="n">lemnaData</span><span class="p">[</span><span class="nb">id</span><span class="p">][</span><span class="n">date</span><span class="p">][</span><span class="s">"metric"</span><span class="p">]</span> <span class="o">=</span> <span class="n">metric</span>
+ <span class="k">except</span><span class="p">:</span>
+ <span class="k">pass</span>
+ <span class="k">return</span> <span class="n">lemnaData</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="s">"Metric Column: "</span><span class="p">,</span><span class="n">dataHeaders</span><span class="p">[</span><span class="s">"metric"</span><span class="p">],</span><span class="s">" does not exist."</span><span class="p">)</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="s">"Date Column: "</span><span class="p">,</span><span class="n">dataHeaders</span><span class="p">[</span><span class="s">"date"</span><span class="p">],</span><span class="s">" does not exist."</span><span class="p">)</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="s">"Id Column: "</span><span class="p">,</span><span class="n">dataHeaders</span><span class="p">[</span><span class="s">"id"</span><span class="p">],</span><span class="s">" does not exist."</span><span class="p">)</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="s">"Data Dictionary does not have all required keys ['id', 'date', 'dateFormat', 'metric']"</span><span class="p">)</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="s">"Data File: "</span> <span class="o">+</span> <span class="n">dataFile</span> <span class="o">+</span> <span class="s">" does not exist!"</span><span class="p">)</span>
+ <span class="k">return</span>
+
+ <span class="k">def</span> <span class="nf">loadSql</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">dblist</span><span class="p">):</span>
+ <span class="k">for</span> <span class="n">i</span><span class="p">,</span><span class="n">f</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="n">dblist</span><span class="p">):</span>
+ <span class="k">if</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">isfile</span><span class="p">(</span><span class="n">f</span><span class="p">):</span>
+ <span class="n">conn</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_openConnection</span><span class="p">(</span><span class="n">f</span><span class="p">)</span>
+ <span class="n">cols</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_getHeaders</span><span class="p">(</span><span class="s">"images"</span><span class="p">,</span> <span class="n">conn</span><span class="p">)</span>
+ <span class="k">for</span> <span class="n">col</span> <span class="ow">in</span> <span class="n">cols</span><span class="p">:</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_addColumn</span><span class="p">(</span><span class="n">col</span><span class="p">,</span> <span class="s">"images"</span><span class="p">)</span>
+ <span class="n">result</span> <span class="o">=</span> <span class="n">conn</span><span class="o">.</span><span class="n">execute</span><span class="p">(</span><span class="s">"select pegasusid,"</span> <span class="o">+</span> <span class="s">","</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">cols</span><span class="p">)</span> <span class="o">+</span> <span class="s">" from images"</span><span class="p">)</span>
+ <span class="n">query</span> <span class="o">=</span> <span class="s">"update images set "</span> <span class="o">+</span> <span class="s">","</span><span class="o">.</span><span class="n">join</span><span class="p">([</span><span class="n">col</span> <span class="o">+</span> <span class="s">"=?"</span> <span class="k">for</span> <span class="n">col</span> <span class="ow">in</span> <span class="n">cols</span><span class="p">])</span> <span class="o">+</span> <span class="s">" where pegasusid=?"</span>
+ <span class="n">values</span> <span class="o">=</span> <span class="p">[</span><span class="nb">tuple</span><span class="p">([</span><span class="n">row</span><span class="p">[</span><span class="n">col</span><span class="p">]</span> <span class="k">for</span> <span class="n">col</span> <span class="ow">in</span> <span class="n">cols</span><span class="p">]</span> <span class="o">+</span> <span class="p">[</span><span class="n">row</span><span class="p">[</span><span class="s">"pegasusid"</span><span class="p">]])</span> <span class="k">for</span> <span class="n">row</span> <span class="ow">in</span> <span class="n">result</span><span class="p">]</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">conn</span><span class="o">.</span><span class="n">executemany</span><span class="p">(</span><span class="n">query</span><span class="p">,</span> <span class="n">values</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">conn</span><span class="o">.</span><span class="n">commit</span><span class="p">()</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_closeConnection</span><span class="p">(</span><span class="n">conn</span><span class="p">)</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="k">print</span> <span class="s">"DB File: '</span><span class="si">%s</span><span class="s">' does not exist."</span> <span class="o">%</span> <span class="p">(</span><span class="n">f</span><span class="p">,)</span>
+ <span class="k">return</span>
+
+
+
+<div class="viewcode-block" id="Stats.logErrors"><a class="viewcode-back" href="../../statistics.html#htpia.statistics.Stats.logErrors">[docs]</a> <span class="k">def</span> <span class="nf">logErrors</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">logfile</span><span class="p">,</span> <span class="n">table</span> <span class="o">=</span> <span class="s">"images"</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> :param logfile: The logfile to write errors to</span>
+<span class="sd"> :type logfile: str</span>
+<span class="sd"> :param table: The table to load errors from</span>
+<span class="sd"> :type table: str</span>
+<span class="sd"> </span>
+<span class="sd"> This function writes all errors from a given table to a log file,</span>
+<span class="sd"> usually used at the end of image processing to write all images that</span>
+<span class="sd"> did not process correctly.</span>
+<span class="sd"> """</span>
+ <span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="n">logfile</span><span class="p">,</span> <span class="s">"w"</span><span class="p">)</span> <span class="k">as</span> <span class="n">wh</span><span class="p">:</span>
+ <span class="n">wh</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s">"Image processing error log</span><span class="se">\n</span><span class="s">"</span><span class="p">)</span>
+ <span class="n">wh</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s">"==========================</span><span class="se">\n</span><span class="s">"</span><span class="p">)</span>
+ <span class="n">result</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">conn</span><span class="o">.</span><span class="n">execute</span><span class="p">(</span><span class="s">"select pegasusid,path,error from '"</span> <span class="o">+</span> <span class="n">table</span> <span class="o">+</span> <span class="s">"' where error is not null"</span><span class="p">)</span>
+ <span class="n">firstrow</span> <span class="o">=</span> <span class="n">result</span><span class="o">.</span><span class="n">fetchone</span><span class="p">()</span>
+ <span class="k">if</span> <span class="n">firstrow</span><span class="p">:</span>
+ <span class="n">wh</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s">"Error with image id '"</span> <span class="o">+</span> <span class="n">firstrow</span><span class="p">[</span><span class="s">"pegasusid"</span><span class="p">]</span> <span class="o">+</span> <span class="s">"', located at path '"</span> <span class="o">+</span> <span class="n">firstrow</span><span class="p">[</span><span class="s">"path"</span><span class="p">]</span> <span class="o">+</span> <span class="s">"', error: '"</span> <span class="o">+</span> <span class="n">firstrow</span><span class="p">[</span><span class="s">"error"</span><span class="p">]</span> <span class="o">+</span> <span class="s">"'. </span><span class="se">\n</span><span class="s">"</span><span class="p">)</span>
+ <span class="k">for</span> <span class="n">row</span> <span class="ow">in</span> <span class="n">result</span><span class="p">:</span>
+ <span class="n">wh</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s">"Error with image id '"</span> <span class="o">+</span> <span class="n">row</span><span class="p">[</span><span class="s">"pegasusid"</span><span class="p">]</span> <span class="o">+</span> <span class="s">"', located at path '"</span> <span class="o">+</span> <span class="n">row</span><span class="p">[</span><span class="s">"path"</span><span class="p">]</span> <span class="o">+</span> <span class="s">"', error: '"</span> <span class="o">+</span> <span class="n">row</span><span class="p">[</span><span class="s">"error"</span><span class="p">]</span> <span class="o">+</span> <span class="s">"'. </span><span class="se">\n</span><span class="s">"</span><span class="p">)</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="n">wh</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s">"All images processed successfully! Nice job!</span><span class="se">\n</span><span class="s">"</span><span class="p">)</span>
+ <span class="k">return</span>
+ </div>
+<div class="viewcode-block" id="Stats.shootArea"><a class="viewcode-back" href="../../statistics.html#htpia.statistics.Stats.shootArea">[docs]</a> <span class="k">def</span> <span class="nf">shootArea</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">intable</span><span class="p">,</span> <span class="n">outtable</span><span class="p">,</span> <span class="n">grouping</span><span class="p">,</span> <span class="n">overwrite</span> <span class="o">=</span> <span class="bp">False</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> :param intable: The input table to load information from</span>
+<span class="sd"> :type intable: str</span>
+<span class="sd"> :param outtable: The output table to write information to.</span>
+<span class="sd"> :type outtable: str</span>
+<span class="sd"> :param grouping: Which imtypes to group</span>
+<span class="sd"> :type grouping: list</span>
+<span class="sd"> </span>
+<span class="sd"> This function adds the numeric values of multiple image types together.</span>
+<span class="sd"> In general, it is used to combine side view + top view images of the same spectrum.</span>
+<span class="sd"> If you plan on correlating your data to lemnaTec's data, lemnaTec uses SV1 + SV2 + TV,</span>
+<span class="sd"> so you should aggregate your data likewise.</span>
+<span class="sd"> """</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_validate</span><span class="p">(</span><span class="s">"shootArea"</span><span class="p">,</span> <span class="n">intable</span><span class="p">,</span> <span class="n">outtable</span><span class="p">,</span> <span class="n">overwrite</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_createTable</span><span class="p">(</span><span class="s">"shootArea"</span><span class="p">,</span> <span class="n">intable</span><span class="p">,</span> <span class="n">outtable</span><span class="p">,</span> <span class="n">overwrite</span><span class="p">)</span>
+ <span class="n">headers</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_getHeaders</span><span class="p">(</span><span class="n">outtable</span><span class="p">)</span>
+ <span class="n">result</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">conn</span><span class="o">.</span><span class="n">execute</span><span class="p">(</span><span class="s">"select pegasusid,"</span> <span class="o">+</span> <span class="s">","</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">headers</span><span class="p">)</span> <span class="o">+</span> <span class="s">" from "</span> <span class="o">+</span> <span class="n">intable</span> <span class="o">+</span> <span class="s">" where "</span> <span class="o">+</span> <span class="s">" or "</span><span class="o">.</span><span class="n">join</span><span class="p">([</span><span class="s">"imtype=?"</span> <span class="k">for</span> <span class="n">x</span> <span class="ow">in</span> <span class="n">grouping</span><span class="p">]),</span> <span class="nb">tuple</span><span class="p">([</span><span class="n">x</span> <span class="k">for</span> <span class="n">x</span> <span class="ow">in</span> <span class="n">grouping</span><span class="p">]))</span>
+ <span class="k">for</span> <span class="n">row</span> <span class="ow">in</span> <span class="n">result</span><span class="p">:</span>
+ <span class="n">exists</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">conn</span><span class="o">.</span><span class="n">execute</span><span class="p">(</span><span class="s">"select * from "</span> <span class="o">+</span> <span class="n">outtable</span> <span class="o">+</span> <span class="s">" where experiment=? and id=? and genotype=? and date=? and treatment=? and imtype=?"</span><span class="p">,</span> <span class="p">(</span><span class="n">row</span><span class="p">[</span><span class="s">"experiment"</span><span class="p">],</span> <span class="n">row</span><span class="p">[</span><span class="s">"id"</span><span class="p">],</span> <span class="n">row</span><span class="p">[</span><span class="s">"genotype"</span><span class="p">],</span> <span class="n">row</span><span class="p">[</span><span class="s">"date"</span><span class="p">],</span> <span class="n">row</span><span class="p">[</span><span class="s">"treatment"</span><span class="p">],</span> <span class="n">conf</span><span class="o">.</span><span class="n">typeMap</span><span class="p">[</span><span class="n">row</span><span class="p">[</span><span class="s">"imtype"</span><span class="p">]]))</span>
+ <span class="n">outrow</span> <span class="o">=</span> <span class="n">exists</span><span class="o">.</span><span class="n">fetchone</span><span class="p">()</span>
+ <span class="k">if</span> <span class="ow">not</span> <span class="n">outrow</span><span class="p">:</span>
+ <span class="n">lastid</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">conn</span><span class="o">.</span><span class="n">execute</span><span class="p">(</span><span class="s">"insert into "</span> <span class="o">+</span> <span class="n">outtable</span> <span class="o">+</span> <span class="s">" ("</span> <span class="o">+</span> <span class="s">","</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">headers</span><span class="p">)</span> <span class="o">+</span> <span class="s">") values ("</span> <span class="o">+</span> <span class="s">","</span><span class="o">.</span><span class="n">join</span><span class="p">([</span><span class="s">"?"</span><span class="p">]</span> <span class="o">*</span> <span class="nb">len</span><span class="p">(</span><span class="n">headers</span><span class="p">))</span> <span class="o">+</span> <span class="s">")"</span><span class="p">,</span> <span class="nb">tuple</span><span class="p">([</span><span class="nb">str</span><span class="p">(</span><span class="n">row</span><span class="p">[</span><span class="n">x</span><span class="p">])</span> <span class="k">if</span> <span class="n">x</span> <span class="o">!=</span> <span class="s">"imtype"</span> <span class="k">else</span> <span class="n">conf</span><span class="o">.</span><span class="n">typeMap</span><span class="p">[</span><span class="n">row</span><span class="p">[</span><span class="n">x</span><span class="p">]]</span> <span class="k">for</span> <span class="n">x</span> <span class="ow">in</span> <span class="n">headers</span><span class="p">]))</span><span class="o">.</span><span class="n">lastrowid</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="n">lastid</span> <span class="o">=</span> <span class="n">outrow</span><span class="p">[</span><span class="s">"pegasusid"</span><span class="p">]</span>
+ <span class="n">vals</span> <span class="o">=</span> <span class="nb">dict</span><span class="p">((</span><span class="n">header</span><span class="p">,</span> <span class="nb">float</span><span class="p">(</span><span class="n">row</span><span class="p">[</span><span class="n">header</span><span class="p">])</span> <span class="o">+</span> <span class="nb">float</span><span class="p">(</span><span class="n">outrow</span><span class="p">[</span><span class="n">header</span><span class="p">]))</span> <span class="k">for</span> <span class="n">header</span> <span class="ow">in</span> <span class="n">headers</span> <span class="k">if</span> <span class="n">header</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">conf</span><span class="o">.</span><span class="n">allHeaders</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">conn</span><span class="o">.</span><span class="n">execute</span><span class="p">(</span><span class="s">"update "</span> <span class="o">+</span> <span class="n">outtable</span> <span class="o">+</span> <span class="s">" set "</span> <span class="o">+</span> <span class="s">","</span><span class="o">.</span><span class="n">join</span><span class="p">([</span><span class="nb">str</span><span class="p">(</span><span class="n">x</span><span class="p">)</span> <span class="o">+</span> <span class="s">"="</span> <span class="o">+</span> <span class="nb">str</span><span class="p">(</span><span class="n">vals</span><span class="p">[</span><span class="n">x</span><span class="p">])</span> <span class="k">for</span> <span class="n">x</span> <span class="ow">in</span> <span class="n">vals</span><span class="p">])</span> <span class="o">+</span> <span class="s">" where pegasusid=?"</span><span class="p">,</span> <span class="p">(</span><span class="n">outrow</span><span class="p">[</span><span class="s">"pegasusid"</span><span class="p">],))</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">conn</span><span class="o">.</span><span class="n">execute</span><span class="p">(</span><span class="s">"update "</span> <span class="o">+</span> <span class="n">intable</span> <span class="o">+</span> <span class="s">" set ref_"</span> <span class="o">+</span> <span class="n">outtable</span> <span class="o">+</span> <span class="s">"=? where pegasusid=?"</span><span class="p">,</span> <span class="p">(</span><span class="n">lastid</span><span class="p">,</span> <span class="n">row</span><span class="p">[</span><span class="s">"pegasusid"</span><span class="p">]))</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">conn</span><span class="o">.</span><span class="n">commit</span><span class="p">()</span>
+ <span class="k">return</span>
+ </div>
+<div class="viewcode-block" id="Stats.normalize"><a class="viewcode-back" href="../../statistics.html#htpia.statistics.Stats.normalize">[docs]</a> <span class="k">def</span> <span class="nf">normalize</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">intable</span><span class="p">,</span> <span class="n">outtable</span><span class="p">,</span> <span class="n">column</span> <span class="o">=</span> <span class="s">"pixels"</span><span class="p">,</span> <span class="n">overwrite</span> <span class="o">=</span> <span class="bp">False</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> :param intable: The input table to load information from</span>
+<span class="sd"> :type intable: str</span>
+<span class="sd"> :param outtable: The output table to write information to.</span>
+<span class="sd"> :type outtable: str</span>
+<span class="sd"> :param column: The column to normalize information to</span>
+<span class="sd"> :type column: str</span>
+<span class="sd"> </span>
+<span class="sd"> Normalizes all numerical information to the specific column. This</span>
+<span class="sd"> function is usually used with 'pixels' as the specified column, which</span>
+<span class="sd"> expresses all numeric information as a percentage of the total pixels </span>
+<span class="sd"> in the image.</span>
+<span class="sd"> """</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_validate</span><span class="p">(</span><span class="s">"normalize"</span><span class="p">,</span> <span class="n">intable</span><span class="p">,</span> <span class="n">outtable</span><span class="p">,</span> <span class="n">overwrite</span><span class="p">)</span>
+ <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">_columnExists</span><span class="p">(</span><span class="n">column</span><span class="p">,</span> <span class="n">intable</span><span class="p">):</span>
+ <span class="n">conf</span><span class="o">.</span><span class="n">statsColumns</span><span class="p">[</span><span class="s">"normalize"</span><span class="p">][</span><span class="s">"exclude"</span><span class="p">]</span> <span class="o">+=</span> <span class="p">[</span><span class="n">column</span><span class="p">]</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_createTable</span><span class="p">(</span><span class="s">"normalize"</span><span class="p">,</span> <span class="n">intable</span><span class="p">,</span> <span class="n">outtable</span><span class="p">,</span> <span class="n">overwrite</span><span class="p">)</span>
+ <span class="n">headers</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_getHeaders</span><span class="p">(</span><span class="n">outtable</span><span class="p">)</span>
+ <span class="n">result</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">conn</span><span class="o">.</span><span class="n">execute</span><span class="p">(</span><span class="s">"select pegasusid,"</span> <span class="o">+</span> <span class="n">column</span> <span class="o">+</span> <span class="s">","</span> <span class="o">+</span> <span class="s">","</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">headers</span><span class="p">)</span> <span class="o">+</span> <span class="s">" from "</span> <span class="o">+</span> <span class="n">intable</span><span class="p">)</span>
+ <span class="k">for</span> <span class="n">row</span> <span class="ow">in</span> <span class="n">result</span><span class="p">:</span>
+ <span class="k">if</span> <span class="nb">all</span><span class="p">([</span><span class="n">row</span><span class="p">[</span><span class="n">x</span><span class="p">]</span> <span class="ow">is</span> <span class="ow">not</span> <span class="bp">None</span> <span class="k">for</span> <span class="n">x</span> <span class="ow">in</span> <span class="n">headers</span> <span class="k">if</span> <span class="n">x</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">conf</span><span class="o">.</span><span class="n">allHeaders</span><span class="p">]):</span>
+ <span class="n">vals</span> <span class="o">=</span> <span class="nb">tuple</span><span class="p">([</span><span class="n">row</span><span class="p">[</span><span class="n">x</span><span class="p">]</span> <span class="k">if</span> <span class="n">x</span> <span class="ow">in</span> <span class="n">conf</span><span class="o">.</span><span class="n">allHeaders</span> <span class="k">else</span> <span class="nb">float</span><span class="p">(</span><span class="n">row</span><span class="p">[</span><span class="n">x</span><span class="p">])</span> <span class="o">/</span> <span class="nb">float</span><span class="p">(</span><span class="n">row</span><span class="p">[</span><span class="n">column</span><span class="p">])</span> <span class="k">for</span> <span class="n">x</span> <span class="ow">in</span> <span class="n">headers</span><span class="p">])</span>
+ <span class="n">lastid</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">conn</span><span class="o">.</span><span class="n">execute</span><span class="p">(</span><span class="s">"insert into "</span> <span class="o">+</span> <span class="n">outtable</span> <span class="o">+</span> <span class="s">" ("</span> <span class="o">+</span> <span class="s">","</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">headers</span><span class="p">)</span> <span class="o">+</span> <span class="s">") values ("</span> <span class="o">+</span> <span class="s">","</span><span class="o">.</span><span class="n">join</span><span class="p">([</span><span class="s">"?"</span><span class="p">]</span> <span class="o">*</span> <span class="nb">len</span><span class="p">(</span><span class="n">headers</span><span class="p">))</span> <span class="o">+</span> <span class="s">")"</span><span class="p">,</span> <span class="n">vals</span><span class="p">)</span><span class="o">.</span><span class="n">lastrowid</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">conn</span><span class="o">.</span><span class="n">execute</span><span class="p">(</span><span class="s">"update "</span> <span class="o">+</span> <span class="n">intable</span> <span class="o">+</span> <span class="s">" set ref_"</span> <span class="o">+</span> <span class="n">outtable</span> <span class="o">+</span> <span class="s">"=? where pegasusid=?"</span><span class="p">,</span> <span class="p">(</span><span class="n">lastid</span><span class="p">,</span> <span class="n">row</span><span class="p">[</span><span class="s">"pegasusid"</span><span class="p">]))</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">conn</span><span class="o">.</span><span class="n">commit</span><span class="p">()</span>
+ <span class="k">return</span>
+ </div>
+ <span class="k">def</span> <span class="nf">extractAll</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">options</span><span class="p">):</span>
+ <span class="n">basepath</span> <span class="o">=</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">dirname</span><span class="p">(</span><span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">dirname</span><span class="p">(</span><span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">abspath</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">db</span><span class="p">)</span> <span class="o">+</span> <span class="s">"/"</span><span class="p">))</span>
+ <span class="k">if</span> <span class="s">"workflows"</span> <span class="ow">in</span> <span class="n">options</span><span class="p">:</span>
+ <span class="k">for</span> <span class="nb">type</span> <span class="ow">in</span> <span class="n">options</span><span class="p">[</span><span class="s">"workflows"</span><span class="p">]:</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_openConnection</span><span class="p">()</span>
+ <span class="n">tmp</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">conn</span><span class="o">.</span><span class="n">execute</span><span class="p">(</span><span class="s">"select pegasusid,experiment,id,date,imtype,imgname from images where imtype=?"</span><span class="p">,</span> <span class="p">(</span><span class="nb">type</span><span class="p">,))</span>
+ <span class="n">result</span> <span class="o">=</span> <span class="n">tmp</span><span class="o">.</span><span class="n">fetchall</span><span class="p">()</span>
+ <span class="k">for</span> <span class="n">row</span> <span class="ow">in</span> <span class="n">result</span><span class="p">:</span>
+ <span class="n">finalpath</span> <span class="o">=</span> <span class="n">row</span><span class="p">[</span><span class="s">"experiment"</span><span class="p">]</span><span class="o">.</span><span class="n">replace</span><span class="p">(</span><span class="s">" "</span><span class="p">,</span><span class="s">""</span><span class="p">)</span> <span class="o">+</span> <span class="s">"/"</span> <span class="o">+</span> <span class="n">row</span><span class="p">[</span><span class="s">"id"</span><span class="p">]</span><span class="o">.</span><span class="n">replace</span><span class="p">(</span><span class="s">" "</span><span class="p">,</span><span class="s">""</span><span class="p">)</span> <span class="o">+</span> <span class="s">"/"</span> <span class="o">+</span> <span class="n">row</span><span class="p">[</span><span class="s">"date"</span><span class="p">]</span><span class="o">.</span><span class="n">replace</span><span class="p">(</span><span class="s">" "</span><span class="p">,</span><span class="s">""</span><span class="p">)</span> <span class="o">+</span> <span class="s">"/"</span> <span class="o">+</span> <span class="n">row</span><span class="p">[</span><span class="s">"imtype"</span><span class="p">]</span><span class="o">.</span><span class="n">replace</span><span class="p">(</span><span class="s">" "</span><span class="p">,</span><span class="s">""</span><span class="p">)</span> <span class="o">+</span> <span class="s">"/"</span> <span class="o">+</span> <span class="n">row</span><span class="p">[</span><span class="s">"imgname"</span><span class="p">]</span><span class="o">.</span><span class="n">replace</span><span class="p">(</span><span class="s">" "</span><span class="p">,</span><span class="s">""</span><span class="p">)</span> <span class="o">+</span> <span class="s">"/"</span> <span class="o">+</span> <span class="n">row</span><span class="p">[</span><span class="s">"pegasusid"</span><span class="p">]</span> <span class="o">+</span> <span class="s">"_"</span> <span class="o">+</span> <span class="n">options</span><span class="p">[</span><span class="s">"workflows"</span><span class="p">][</span><span class="nb">type</span><span class="p">][</span><span class="s">"inputs"</span><span class="p">][</span><span class="mi">0</span><span class="p">]</span> <span class="o">+</span> <span class="s">".png"</span>
+ <span class="c">#finalpath = row["pegasusid"] + "_" + options["workflows"][type]["inputs"][0] + ".png"</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_closeConnection</span><span class="p">()</span>
+ <span class="k">if</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">isfile</span><span class="p">(</span><span class="n">finalpath</span><span class="p">):</span>
+ <span class="k">try</span><span class="p">:</span>
+ <span class="n">plant</span> <span class="o">=</span> <span class="n">htpia</span><span class="o">.</span><span class="n">imgproc</span><span class="o">.</span><span class="n">Image</span><span class="p">(</span><span class="n">finalpath</span><span class="p">,</span> <span class="n">db</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">db</span><span class="p">,</span> <span class="n">dbid</span> <span class="o">=</span> <span class="n">row</span><span class="p">[</span><span class="s">"pegasusid"</span><span class="p">])</span>
+ <span class="n">plant</span><span class="o">.</span><span class="n">extractFinalPath</span><span class="p">()</span>
+ <span class="k">if</span> <span class="s">"--dimensions"</span> <span class="ow">in</span> <span class="n">options</span><span class="p">[</span><span class="s">"workflows"</span><span class="p">][</span><span class="nb">type</span><span class="p">][</span><span class="s">"arguments"</span><span class="p">]:</span>
+ <span class="n">plant</span><span class="o">.</span><span class="n">extractDimensions</span><span class="p">()</span>
+ <span class="k">if</span> <span class="s">"--pixels"</span> <span class="ow">in</span> <span class="n">options</span><span class="p">[</span><span class="s">"workflows"</span><span class="p">][</span><span class="nb">type</span><span class="p">][</span><span class="s">"arguments"</span><span class="p">]:</span>
+ <span class="n">plant</span><span class="o">.</span><span class="n">extractPixels</span><span class="p">()</span>
+ <span class="k">if</span> <span class="s">"--moments"</span> <span class="ow">in</span> <span class="n">options</span><span class="p">[</span><span class="s">"workflows"</span><span class="p">][</span><span class="nb">type</span><span class="p">][</span><span class="s">"arguments"</span><span class="p">]:</span>
+ <span class="n">plant</span><span class="o">.</span><span class="n">extractMoments</span><span class="p">()</span>
+ <span class="k">if</span> <span class="s">"--colors"</span> <span class="ow">in</span> <span class="n">options</span><span class="p">[</span><span class="s">"workflows"</span><span class="p">][</span><span class="nb">type</span><span class="p">][</span><span class="s">"arguments"</span><span class="p">]:</span>
+ <span class="n">plant</span><span class="o">.</span><span class="n">extractColorData</span><span class="p">()</span>
+ <span class="k">if</span> <span class="s">"--channels"</span> <span class="ow">in</span> <span class="n">options</span><span class="p">[</span><span class="s">"workflows"</span><span class="p">][</span><span class="nb">type</span><span class="p">][</span><span class="s">"arguments"</span><span class="p">]:</span>
+ <span class="n">plant</span><span class="o">.</span><span class="n">extractColorChannels</span><span class="p">()</span>
+ <span class="k">if</span> <span class="s">"--bins"</span> <span class="ow">in</span> <span class="n">options</span><span class="p">[</span><span class="s">"workflows"</span><span class="p">][</span><span class="nb">type</span><span class="p">][</span><span class="s">"arguments"</span><span class="p">]:</span>
+ <span class="n">plant</span><span class="o">.</span><span class="n">extractBins</span><span class="p">(</span><span class="n">options</span><span class="p">[</span><span class="s">"workflows"</span><span class="p">][</span><span class="nb">type</span><span class="p">][</span><span class="s">"arguments"</span><span class="p">][</span><span class="s">"--bins"</span><span class="p">])</span>
+ <span class="k">except</span> <span class="ne">Exception</span> <span class="k">as</span> <span class="n">e</span><span class="p">:</span>
+ <span class="k">print</span> <span class="n">traceback</span><span class="o">.</span><span class="n">format_exc</span><span class="p">()</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="k">print</span> <span class="s">"PATH DOES NOT EXIST: </span><span class="si">%s</span><span class="s">."</span> <span class="o">%</span> <span class="p">(</span><span class="n">finalpath</span><span class="p">,)</span>
+ <span class="k">if</span> <span class="s">"histogram-bin"</span> <span class="ow">in</span> <span class="n">options</span><span class="p">:</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_openConnection</span><span class="p">()</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">histogramBinning</span><span class="p">(</span><span class="s">"images"</span><span class="p">,</span> <span class="s">"histogramBins"</span><span class="p">,</span> <span class="nb">dict</span><span class="p">((</span><span class="nb">type</span><span class="p">,</span><span class="n">options</span><span class="p">[</span><span class="s">"workflows"</span><span class="p">][</span><span class="nb">type</span><span class="p">][</span><span class="s">"inputs"</span><span class="p">][</span><span class="mi">0</span><span class="p">])</span> <span class="k">for</span> <span class="nb">type</span> <span class="ow">in</span> <span class="n">options</span><span class="p">[</span><span class="s">"workflows"</span><span class="p">]),</span> <span class="n">options</span><span class="p">[</span><span class="s">"histogram-bin"</span><span class="p">][</span><span class="s">"--group"</span><span class="p">],</span> <span class="n">options</span><span class="p">[</span><span class="s">"histogram-bin"</span><span class="p">][</span><span class="s">"--chunks"</span><span class="p">],</span> <span class="n">options</span><span class="p">[</span><span class="s">"histogram-bin"</span><span class="p">][</span><span class="s">"--channels"</span><span class="p">],</span> <span class="bp">True</span><span class="p">)</span>
+ <span class="k">return</span>
+
+ <span class="k">def</span> <span class="nf">histogramBinning</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">intable</span><span class="p">,</span> <span class="n">outtable</span><span class="p">,</span> <span class="n">grouping</span><span class="p">,</span> <span class="n">chunks</span><span class="p">,</span> <span class="n">channels</span><span class="p">,</span> <span class="n">jsonwrite</span> <span class="o">=</span> <span class="bp">False</span><span class="p">,</span> <span class="n">overwrite</span> <span class="o">=</span> <span class="bp">False</span><span class="p">):</span>
+ <span class="n">color_vector</span> <span class="o">=</span> <span class="p">{}</span>
+ <span class="k">for</span> <span class="n">name</span> <span class="ow">in</span> <span class="n">grouping</span><span class="p">:</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_validate</span><span class="p">(</span><span class="s">"histogramBins"</span><span class="p">,</span> <span class="n">intable</span><span class="p">,</span> <span class="n">name</span> <span class="o">+</span> <span class="s">"_"</span> <span class="o">+</span> <span class="n">outtable</span><span class="p">,</span> <span class="n">overwrite</span><span class="p">)</span>
+ <span class="k">for</span> <span class="n">name</span> <span class="ow">in</span> <span class="n">grouping</span><span class="p">:</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_createTable</span><span class="p">(</span><span class="s">"histogramBins"</span><span class="p">,</span> <span class="n">intable</span><span class="p">,</span> <span class="n">name</span> <span class="o">+</span> <span class="s">"_"</span> <span class="o">+</span> <span class="n">outtable</span><span class="p">,</span> <span class="n">overwrite</span><span class="p">)</span>
+ <span class="n">color_vector</span><span class="p">[</span><span class="n">name</span><span class="p">]</span> <span class="o">=</span> <span class="p">[</span><span class="mi">0</span><span class="p">,</span> <span class="mi">0</span><span class="p">,</span> <span class="mi">0</span><span class="p">]</span>
+ <span class="nb">map</span> <span class="o">=</span> <span class="nb">dict</span><span class="p">((</span><span class="nb">type</span><span class="p">,</span> <span class="n">name</span><span class="p">)</span> <span class="k">for</span> <span class="n">name</span> <span class="ow">in</span> <span class="n">grouping</span> <span class="k">for</span> <span class="nb">type</span> <span class="ow">in</span> <span class="n">grouping</span><span class="p">[</span><span class="n">name</span><span class="p">])</span>
+ <span class="n">basequery</span> <span class="o">=</span> <span class="s">"select "</span>
+ <span class="k">for</span> <span class="n">x</span><span class="p">,</span><span class="n">c</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">([</span><span class="s">"bhist"</span><span class="p">,</span> <span class="s">"ghist"</span><span class="p">,</span> <span class="s">"rhist"</span><span class="p">]):</span>
+ <span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="mi">0</span><span class="p">,</span> <span class="mi">256</span><span class="p">):</span>
+ <span class="k">if</span> <span class="n">i</span> <span class="o">==</span> <span class="mi">0</span> <span class="ow">and</span> <span class="n">x</span> <span class="o">==</span> <span class="mi">0</span><span class="p">:</span>
+ <span class="n">basequery</span> <span class="o">+=</span> <span class="s">"SUM("</span> <span class="o">+</span> <span class="n">c</span> <span class="o">+</span> <span class="nb">str</span><span class="p">(</span><span class="n">i</span><span class="p">)</span> <span class="o">+</span> <span class="s">")"</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="n">basequery</span> <span class="o">+=</span> <span class="s">",SUM("</span> <span class="o">+</span> <span class="n">c</span> <span class="o">+</span> <span class="nb">str</span><span class="p">(</span><span class="n">i</span><span class="p">)</span> <span class="o">+</span> <span class="s">")"</span>
+ <span class="n">basequery</span> <span class="o">+=</span> <span class="s">" from images where "</span>
+ <span class="k">for</span> <span class="n">name</span> <span class="ow">in</span> <span class="n">grouping</span><span class="p">:</span>
+ <span class="n">query</span> <span class="o">=</span> <span class="n">basequery</span> <span class="o">+</span> <span class="s">" or "</span><span class="o">.</span><span class="n">join</span><span class="p">([</span><span class="s">"imtype=?"</span> <span class="k">for</span> <span class="n">x</span> <span class="ow">in</span> <span class="n">grouping</span><span class="p">[</span><span class="n">name</span><span class="p">]])</span>
+ <span class="n">result</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">conn</span><span class="o">.</span><span class="n">execute</span><span class="p">(</span><span class="n">query</span><span class="p">,</span> <span class="nb">tuple</span><span class="p">(</span><span class="n">grouping</span><span class="p">[</span><span class="n">name</span><span class="p">]))</span>
+ <span class="n">data</span> <span class="o">=</span> <span class="nb">list</span><span class="p">(</span><span class="n">result</span><span class="o">.</span><span class="n">fetchone</span><span class="p">())</span>
+ <span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="mi">0</span><span class="p">,</span> <span class="mi">3</span><span class="p">):</span>
+ <span class="n">color_vector</span><span class="p">[</span><span class="n">name</span><span class="p">][</span><span class="n">i</span><span class="p">]</span> <span class="o">=</span> <span class="n">data</span><span class="p">[</span><span class="n">i</span><span class="o">*</span><span class="mi">256</span><span class="p">:(</span><span class="n">i</span> <span class="o">+</span> <span class="mi">1</span><span class="p">)</span><span class="o">*</span><span class="mi">256</span><span class="p">]</span>
+ <span class="n">bins</span> <span class="o">=</span> <span class="p">{}</span>
+ <span class="k">for</span> <span class="n">name</span> <span class="ow">in</span> <span class="n">grouping</span><span class="p">:</span>
+ <span class="n">bins</span><span class="p">[</span><span class="n">name</span><span class="p">]</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_generateBins</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">_splitHist</span><span class="p">(</span><span class="n">color_vector</span><span class="p">[</span><span class="n">name</span><span class="p">],</span> <span class="n">chunks</span><span class="p">[</span><span class="n">name</span><span class="p">],</span> <span class="n">channels</span><span class="p">[</span><span class="n">name</span><span class="p">]),</span> <span class="n">name</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">conn</span><span class="o">.</span><span class="n">executemany</span><span class="p">(</span><span class="s">"insert into "</span> <span class="o">+</span> <span class="n">name</span> <span class="o">+</span> <span class="s">"_"</span> <span class="o">+</span> <span class="n">outtable</span> <span class="o">+</span> <span class="s">" (name, minr, ming, minb, maxr, maxg, maxb) values (?, ?, ?, ?, ?, ?, ?)"</span><span class="p">,</span> <span class="p">[(</span><span class="nb">bin</span><span class="p">[</span><span class="s">"name"</span><span class="p">],</span> <span class="nb">int</span><span class="p">(</span><span class="nb">bin</span><span class="p">[</span><span class="s">"min"</span><span class="p">][</span><span class="mi">2</span><span class="p">]),</span> <span class="nb">int</span><span class="p">(</span><span class="nb">bin</span><span class="p">[</span><span class="s">"min"</span><span class="p">][</span><span class="mi">1</span><span class="p">]),</span> <span class="nb">int</span><span class="p">(</span><span class="nb">bin</span><span class="p">[</span><span class="s">"min"</span><span class="p">][</span><span class="mi">0</span><span class="p">]),</span> <span class="nb">int</span><span class="p">(</span><span class="nb">bin</span><span class="p">[</span><span class="s">"max"</span><span class="p">][</span><span class="mi">2</span><span class="p">]),</span> <span class="nb">int</span><span class="p">(</span><span class="nb">bin</span><span class="p">[</span><span class="s">"max"</span><span class="p">][</span><span class="mi">1</span><span class="p">]),</span> <span class="nb">int</span><span class="p">(</span><span class="nb">bin</span><span class="p">[</span><span class="s">"max"</span><span class="p">][</span><span class="mi">0</span><span class="p">]))</span> <span class="k">for</span> <span class="nb">bin</span> <span class="ow">in</span> <span class="n">bins</span><span class="p">[</span><span class="n">name</span><span class="p">]])</span>
+<span class="c"># for bin in bins[name]:</span>
+<span class="c"># self.conn.execute("insert into " + name + "_" + outtable + " (name, minr, ming, minb, maxr, maxg, maxb) values (?, ?, ?, ?, ?, ?, ?)", (name + bin["name"], int(bin["min"][2]), int(bin["min"][1]), int(bin["min"][0]), int(bin["max"][2]), int(bin["max"][1]), int(bin["max"][0])))</span>
+<span class="c"># self.conn.commit()</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">conn</span><span class="o">.</span><span class="n">commit</span><span class="p">()</span>
+ <span class="k">if</span> <span class="n">jsonwrite</span><span class="p">:</span>
+ <span class="k">for</span> <span class="n">name</span> <span class="ow">in</span> <span class="n">grouping</span><span class="p">:</span>
+ <span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="n">name</span> <span class="o">+</span> <span class="s">"_hist_bins.json"</span><span class="p">,</span> <span class="s">"w"</span><span class="p">)</span> <span class="k">as</span> <span class="n">wh</span><span class="p">:</span>
+ <span class="n">json</span><span class="o">.</span><span class="n">dump</span><span class="p">(</span><span class="n">bins</span><span class="p">[</span><span class="n">name</span><span class="p">],</span> <span class="n">wh</span><span class="p">)</span>
+ <span class="k">return</span>
+
+
+ <span class="k">def</span> <span class="nf">_splitHist</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">hist</span><span class="p">,</span> <span class="n">chunks</span><span class="p">,</span> <span class="n">channels</span><span class="p">):</span>
+ <span class="n">returnlist</span> <span class="o">=</span> <span class="p">[</span> <span class="p">[</span><span class="mi">1</span><span class="p">],</span> <span class="p">[</span><span class="mi">1</span><span class="p">],</span> <span class="p">[</span><span class="mi">1</span><span class="p">]</span> <span class="p">]</span>
+ <span class="n">s</span> <span class="o">=</span> <span class="p">[</span><span class="nb">sum</span><span class="p">(</span><span class="n">x</span><span class="p">)</span> <span class="k">for</span> <span class="n">x</span> <span class="ow">in</span> <span class="n">hist</span><span class="p">]</span>
+ <span class="c">#s = [int(x) for x in np.sum(hist, axis = 1)]</span>
+ <span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="n">channels</span><span class="p">:</span>
+ <span class="n">tmp</span> <span class="o">=</span> <span class="mi">0</span>
+ <span class="n">integral</span> <span class="o">=</span> <span class="n">s</span><span class="p">[</span><span class="n">i</span><span class="p">]</span> <span class="o">/</span> <span class="n">chunks</span>
+ <span class="k">for</span> <span class="n">j</span><span class="p">,</span><span class="n">item</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="n">hist</span><span class="p">[</span><span class="n">i</span><span class="p">]):</span>
+ <span class="n">tmp</span> <span class="o">+=</span> <span class="n">item</span>
+ <span class="k">if</span> <span class="p">(</span><span class="n">tmp</span> <span class="o">></span> <span class="n">integral</span><span class="p">):</span>
+ <span class="n">returnlist</span><span class="p">[</span><span class="n">i</span><span class="p">]</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">j</span><span class="p">)</span>
+ <span class="n">tmp</span> <span class="o">=</span> <span class="mi">0</span>
+ <span class="n">returnlist</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="mi">255</span><span class="p">)</span>
+ <span class="n">returnlist</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="mi">255</span><span class="p">)</span>
+ <span class="n">returnlist</span><span class="p">[</span><span class="mi">2</span><span class="p">]</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="mi">255</span><span class="p">)</span>
+ <span class="k">return</span> <span class="n">returnlist</span>
+
+ <span class="k">def</span> <span class="nf">_generateBins</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">vector</span><span class="p">,</span> <span class="nb">type</span><span class="p">):</span>
+ <span class="n">bins</span> <span class="o">=</span> <span class="p">[]</span>
+ <span class="n">num</span> <span class="o">=</span> <span class="mi">1</span>
+ <span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="nb">range</span> <span class="p">(</span><span class="mi">0</span><span class="p">,</span> <span class="nb">len</span><span class="p">(</span><span class="n">vector</span><span class="p">[</span><span class="mi">0</span><span class="p">])</span> <span class="o">-</span> <span class="mi">1</span><span class="p">):</span>
+ <span class="k">for</span> <span class="n">j</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="mi">0</span><span class="p">,</span> <span class="nb">len</span><span class="p">(</span><span class="n">vector</span><span class="p">[</span><span class="mi">1</span><span class="p">])</span> <span class="o">-</span> <span class="mi">1</span><span class="p">):</span>
+ <span class="k">for</span> <span class="n">k</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="mi">0</span><span class="p">,</span> <span class="nb">len</span><span class="p">(</span><span class="n">vector</span><span class="p">[</span><span class="mi">2</span><span class="p">])</span> <span class="o">-</span> <span class="mi">1</span><span class="p">):</span>
+ <span class="n">bins</span><span class="o">.</span><span class="n">append</span><span class="p">({</span>
+ <span class="s">"name"</span><span class="p">:</span> <span class="nb">type</span> <span class="o">+</span> <span class="s">"_bin"</span> <span class="o">+</span> <span class="nb">str</span><span class="p">(</span><span class="n">num</span><span class="p">),</span>
+ <span class="s">"min"</span><span class="p">:</span> <span class="n">np</span><span class="o">.</span><span class="n">array</span><span class="p">([</span><span class="n">vector</span><span class="p">[</span><span class="mi">0</span><span class="p">][</span><span class="n">i</span><span class="p">],</span><span class="n">vector</span><span class="p">[</span><span class="mi">1</span><span class="p">][</span><span class="n">j</span><span class="p">],</span><span class="n">vector</span><span class="p">[</span><span class="mi">2</span><span class="p">][</span><span class="n">k</span><span class="p">]],</span> <span class="n">dtype</span><span class="o">=</span><span class="n">np</span><span class="o">.</span><span class="n">uint8</span><span class="p">)</span><span class="o">.</span><span class="n">tolist</span><span class="p">(),</span>
+ <span class="s">"max"</span><span class="p">:</span> <span class="n">np</span><span class="o">.</span><span class="n">array</span><span class="p">([</span><span class="n">vector</span><span class="p">[</span><span class="mi">0</span><span class="p">][</span><span class="n">i</span><span class="o">+</span><span class="mi">1</span><span class="p">],</span><span class="n">vector</span><span class="p">[</span><span class="mi">1</span><span class="p">][</span><span class="n">j</span><span class="o">+</span><span class="mi">1</span><span class="p">],</span><span class="n">vector</span><span class="p">[</span><span class="mi">2</span><span class="p">][</span><span class="n">k</span><span class="o">+</span><span class="mi">1</span><span class="p">]],</span> <span class="n">dtype</span><span class="o">=</span><span class="n">np</span><span class="o">.</span><span class="n">uint8</span><span class="p">)</span><span class="o">.</span><span class="n">tolist</span><span class="p">()</span>
+ <span class="p">})</span>
+ <span class="n">num</span> <span class="o">+=</span> <span class="mi">1</span>
+ <span class="k">return</span> <span class="n">bins</span>
+
+
+<div class="viewcode-block" id="Stats.correlation"><a class="viewcode-back" href="../../statistics.html#htpia.statistics.Stats.correlation">[docs]</a> <span class="k">def</span> <span class="nf">correlation</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">intable</span><span class="p">,</span> <span class="n">outtable</span><span class="p">,</span> <span class="n">dataFile</span><span class="p">,</span> <span class="n">dataHeaders</span><span class="p">,</span> <span class="n">overwrite</span> <span class="o">=</span> <span class="bp">False</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> :param intable: The input table to load information from</span>
+<span class="sd"> :type intable: str</span>
+<span class="sd"> :param outtable: The output table to write information to.</span>
+<span class="sd"> :type outtable: str</span>
+<span class="sd"> :param dataFile: The csv data file to load</span>
+<span class="sd"> :type dataFile: str</span>
+<span class="sd"> :param dataHeaders: Column names for relevant table headers.</span>
+<span class="sd"> :type dataHeaders: str</span>
+<span class="sd"> </span>
+<span class="sd"> This function correlates all numeric values with values in the given file.</span>
+<span class="sd"> The input data file is assumed to be in csv format. In dataHeaders, you must</span>
+<span class="sd"> specify four keys, 'id', 'date', 'dateFormat', and 'metric'. Each of these should</span>
+<span class="sd"> be column names. Id corresponds to the lemnaTec style identifier ex: '023535-S'.</span>
+<span class="sd"> All dates are converted into Y-m-d form, you must provide a valid format in 'dateFormat',</span>
+<span class="sd"> that way the dates can be converted correctly. The 'metric' column is the actual value you</span>
+<span class="sd"> want to correlate to.</span>
+<span class="sd"> """</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_validate</span><span class="p">(</span><span class="s">"correlation"</span><span class="p">,</span> <span class="n">intable</span><span class="p">,</span> <span class="n">outtable</span><span class="p">,</span> <span class="n">overwrite</span><span class="p">)</span>
+ <span class="n">lemnaData</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_loadLemnaData</span><span class="p">(</span><span class="n">dataFile</span><span class="p">,</span> <span class="n">dataHeaders</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_createTable</span><span class="p">(</span><span class="s">"correlation"</span><span class="p">,</span> <span class="n">intable</span><span class="p">,</span> <span class="n">outtable</span><span class="p">,</span> <span class="n">overwrite</span><span class="p">)</span>
+ <span class="n">headers</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_getHeaders</span><span class="p">(</span><span class="n">outtable</span><span class="p">)</span>
+ <span class="n">numeric</span> <span class="o">=</span> <span class="p">[</span><span class="n">h</span> <span class="k">for</span> <span class="n">h</span> <span class="ow">in</span> <span class="n">headers</span> <span class="k">if</span> <span class="n">h</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">conf</span><span class="o">.</span><span class="n">allHeaders</span><span class="p">]</span>
+ <span class="k">for</span> <span class="nb">id</span> <span class="ow">in</span> <span class="n">lemnaData</span><span class="p">:</span>
+ <span class="k">for</span> <span class="n">imtype</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">_getImageTypes</span><span class="p">(</span><span class="n">intable</span><span class="p">):</span>
+ <span class="n">x</span> <span class="o">=</span> <span class="p">{}</span>
+ <span class="n">y</span> <span class="o">=</span> <span class="p">[]</span>
+ <span class="n">corr</span> <span class="o">=</span> <span class="p">{}</span>
+ <span class="n">result</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">conn</span><span class="o">.</span><span class="n">execute</span><span class="p">(</span><span class="s">"select pegasusid,"</span> <span class="o">+</span> <span class="s">","</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">headers</span> <span class="o">+</span> <span class="p">[</span><span class="s">"date"</span><span class="p">])</span> <span class="o">+</span> <span class="s">" from "</span> <span class="o">+</span> <span class="n">intable</span> <span class="o">+</span> <span class="s">" where id=? and imtype=? order by date"</span><span class="p">,</span> <span class="p">(</span><span class="nb">id</span><span class="p">,</span><span class="n">imtype</span><span class="p">))</span>
+ <span class="k">if</span> <span class="n">result</span><span class="o">.</span><span class="n">fetchone</span><span class="p">():</span>
+ <span class="k">for</span> <span class="n">row</span> <span class="ow">in</span> <span class="n">result</span><span class="p">:</span>
+ <span class="k">if</span> <span class="n">row</span><span class="p">[</span><span class="s">"date"</span><span class="p">]</span> <span class="ow">in</span> <span class="n">lemnaData</span><span class="p">[</span><span class="nb">id</span><span class="p">]:</span>
+ <span class="n">y</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">lemnaData</span><span class="p">[</span><span class="nb">id</span><span class="p">][</span><span class="n">row</span><span class="p">[</span><span class="s">"date"</span><span class="p">]][</span><span class="s">"metric"</span><span class="p">])</span>
+ <span class="k">for</span> <span class="n">header</span> <span class="ow">in</span> <span class="n">numeric</span><span class="p">:</span>
+ <span class="k">if</span> <span class="n">header</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">x</span><span class="p">:</span>
+ <span class="n">x</span><span class="p">[</span><span class="n">header</span><span class="p">]</span> <span class="o">=</span> <span class="p">[]</span>
+ <span class="k">try</span><span class="p">:</span>
+ <span class="n">x</span><span class="p">[</span><span class="n">header</span><span class="p">]</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="nb">float</span><span class="p">(</span><span class="n">row</span><span class="p">[</span><span class="n">header</span><span class="p">]))</span>
+ <span class="k">except</span><span class="p">:</span>
+ <span class="k">pass</span>
+ <span class="k">if</span> <span class="nb">any</span><span class="p">([</span><span class="n">x</span><span class="p">[</span><span class="n">header</span><span class="p">]</span> <span class="k">for</span> <span class="n">header</span> <span class="ow">in</span> <span class="n">numeric</span><span class="p">]):</span>
+ <span class="k">for</span> <span class="n">header</span> <span class="ow">in</span> <span class="n">numeric</span><span class="p">:</span>
+ <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">x</span><span class="p">[</span><span class="n">header</span><span class="p">])</span> <span class="o">==</span> <span class="nb">len</span><span class="p">(</span><span class="n">y</span><span class="p">):</span>
+ <span class="n">corr</span><span class="p">[</span><span class="n">header</span><span class="p">]</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">corrcoef</span><span class="p">(</span><span class="n">x</span><span class="p">[</span><span class="n">header</span><span class="p">],</span> <span class="n">y</span><span class="p">)[</span><span class="mi">0</span><span class="p">][</span><span class="mi">1</span><span class="p">]</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="n">corr</span><span class="p">[</span><span class="n">header</span><span class="p">]</span> <span class="o">=</span> <span class="s">"na"</span>
+ <span class="n">lastid</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">conn</span><span class="o">.</span><span class="n">execute</span><span class="p">(</span><span class="s">"insert into "</span> <span class="o">+</span> <span class="n">outtable</span> <span class="o">+</span> <span class="s">" ("</span> <span class="o">+</span> <span class="s">","</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">headers</span><span class="p">)</span> <span class="o">+</span> <span class="s">") values ("</span> <span class="o">+</span> <span class="s">","</span><span class="o">.</span><span class="n">join</span><span class="p">([</span><span class="s">"?"</span><span class="p">]</span> <span class="o">*</span> <span class="nb">len</span><span class="p">(</span><span class="n">headers</span><span class="p">))</span> <span class="o">+</span> <span class="s">")"</span><span class="p">,</span> <span class="nb">tuple</span><span class="p">([</span><span class="n">row</span><span class="p">[</span><span class="n">header</span><span class="p">]</span> <span class="k">if</span> <span class="n">header</span> <span class="ow">in</span> <span class="n">conf</span><span class="o">.</span><span class="n">allHeaders</span> <span class="k">else</span> <span class="n">corr</span><span class="p">[</span><span class="n">header</span><span class="p">]</span> <span class="k">for</span> <span class="n">header</span> <span class="ow">in</span> <span class="n">headers</span><span class="p">]))</span><span class="o">.</span><span class="n">lastrowid</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">conn</span><span class="o">.</span><span class="n">execute</span><span class="p">(</span><span class="s">"update "</span> <span class="o">+</span> <span class="n">intable</span> <span class="o">+</span> <span class="s">" set ref_"</span> <span class="o">+</span> <span class="n">outtable</span> <span class="o">+</span> <span class="s">"=? where id=? and imtype=?"</span><span class="p">,</span> <span class="p">(</span><span class="n">lastid</span><span class="p">,</span> <span class="nb">id</span><span class="p">,</span> <span class="n">imtype</span><span class="p">))</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">conn</span><span class="o">.</span><span class="n">commit</span><span class="p">()</span>
+ <span class="k">return</span>
+ </div>
+<div class="viewcode-block" id="Stats.anova"><a class="viewcode-back" href="../../statistics.html#htpia.statistics.Stats.anova">[docs]</a> <span class="k">def</span> <span class="nf">anova</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">intable</span><span class="p">,</span> <span class="n">outtable</span><span class="p">,</span> <span class="n">grouping</span><span class="p">,</span> <span class="n">overwrite</span> <span class="o">=</span> <span class="bp">False</span><span class="p">):</span>
+ <span class="sd">""" </span>
+<span class="sd"> :param intable: The input table to load information from</span>
+<span class="sd"> :type intable: str</span>
+<span class="sd"> :param outtable: The output table to write information to.</span>
+<span class="sd"> :type outtable: str</span>
+<span class="sd"> :param grouping: The list of image types to group by.</span>
+<span class="sd"> :type grouping: list</span>
+<span class="sd"> </span>
+<span class="sd"> Computes the analysis of variation of all numeric information based on 3 factors,</span>
+<span class="sd"> treatment, date, and the interaction between the two. Analysis of variation is</span>
+<span class="sd"> different than the rest of the stats functions, in that a lot of information is </span>
+<span class="sd"> lost after running it. The results themselves correspond to columns (pixels, rmed, binx...)</span>
+<span class="sd"> instead of actual images. </span>
+<span class="sd"> """</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_validate</span><span class="p">(</span><span class="s">"anova"</span><span class="p">,</span> <span class="n">intable</span><span class="p">,</span> <span class="n">outtable</span><span class="p">,</span> <span class="n">overwrite</span><span class="p">)</span>
+ <span class="n">headers</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_getHeaders</span><span class="p">(</span><span class="n">intable</span><span class="p">)</span>
+ <span class="n">numeric</span> <span class="o">=</span> <span class="p">[</span><span class="n">h</span> <span class="k">for</span> <span class="n">h</span> <span class="ow">in</span> <span class="n">headers</span> <span class="k">if</span> <span class="n">h</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">conf</span><span class="o">.</span><span class="n">allHeaders</span><span class="p">]</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_createTable</span><span class="p">(</span><span class="s">"anova"</span><span class="p">,</span> <span class="n">intable</span><span class="p">,</span> <span class="n">outtable</span><span class="p">,</span> <span class="n">overwrite</span><span class="p">)</span>
+ <span class="n">outHeaders</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_getHeaders</span><span class="p">(</span><span class="n">outtable</span><span class="p">)</span>
+ <span class="n">result</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">conn</span><span class="o">.</span><span class="n">execute</span><span class="p">(</span><span class="s">"select * from images"</span><span class="p">)</span>
+ <span class="n">rowdata</span> <span class="o">=</span> <span class="p">[]</span>
+ <span class="k">for</span> <span class="n">row</span> <span class="ow">in</span> <span class="n">result</span><span class="p">:</span>
+ <span class="n">rowdata</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="nb">dict</span><span class="p">(</span><span class="n">row</span><span class="p">))</span>
+ <span class="n">data</span> <span class="o">=</span> <span class="n">pandas</span><span class="o">.</span><span class="n">DataFrame</span><span class="p">(</span><span class="n">rowdata</span><span class="p">)</span><span class="o">.</span><span class="n">dropna</span><span class="p">()</span>
+ <span class="n">anova</span> <span class="o">=</span> <span class="p">{}</span>
+ <span class="k">for</span> <span class="n">col</span> <span class="ow">in</span> <span class="n">numeric</span><span class="p">:</span>
+ <span class="n">anova</span><span class="p">[</span><span class="n">col</span><span class="p">]</span> <span class="o">=</span> <span class="p">{}</span>
+ <span class="n">dateT</span> <span class="o">=</span> <span class="p">[]</span>
+ <span class="n">treatmentT</span> <span class="o">=</span> <span class="p">[]</span>
+ <span class="n">date_treatmentT</span> <span class="o">=</span> <span class="p">[]</span>
+ <span class="k">for</span> <span class="n">date</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">_getDates</span><span class="p">(</span><span class="n">intable</span><span class="p">):</span>
+ <span class="n">dateT</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">data</span><span class="p">[</span><span class="n">data</span><span class="p">[</span><span class="s">"date"</span><span class="p">]</span> <span class="o">==</span> <span class="n">date</span><span class="p">][</span><span class="n">col</span><span class="p">])</span>
+ <span class="k">for</span> <span class="n">treatment</span> <span class="ow">in</span> <span class="p">[</span><span class="s">"Control"</span><span class="p">,</span> <span class="s">"Stress"</span><span class="p">]:</span>
+ <span class="n">treatmentT</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">data</span><span class="p">[</span><span class="n">data</span><span class="p">[</span><span class="s">"treatment"</span><span class="p">]</span> <span class="o">==</span> <span class="n">treatment</span><span class="p">][</span><span class="n">col</span><span class="p">])</span>
+ <span class="n">date_treatmentT</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">data</span><span class="p">[</span><span class="n">np</span><span class="o">.</span><span class="n">where</span><span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">logical_and</span><span class="p">(</span><span class="n">data</span><span class="p">[</span><span class="s">"treatment"</span><span class="p">]</span> <span class="o">==</span> <span class="n">treatment</span><span class="p">,</span><span class="n">data</span><span class="p">[</span><span class="s">"date"</span><span class="p">]</span> <span class="o">==</span> <span class="n">date</span><span class="p">),</span> <span class="bp">True</span><span class="p">,</span> <span class="bp">False</span><span class="p">)][</span><span class="n">col</span><span class="p">])</span>
+ <span class="n">f_val</span><span class="p">,</span> <span class="n">d_pval</span> <span class="o">=</span> <span class="n">stats</span><span class="o">.</span><span class="n">f_oneway</span><span class="p">(</span><span class="o">*</span><span class="n">dateT</span><span class="p">)</span>
+ <span class="n">f_val</span><span class="p">,</span> <span class="n">t_pval</span> <span class="o">=</span> <span class="n">stats</span><span class="o">.</span><span class="n">f_oneway</span><span class="p">(</span><span class="o">*</span><span class="n">treatmentT</span><span class="p">)</span>
+ <span class="n">f_val</span><span class="p">,</span> <span class="n">dt_pval</span> <span class="o">=</span> <span class="n">stats</span><span class="o">.</span><span class="n">f_oneway</span><span class="p">(</span><span class="o">*</span><span class="n">date_treatmentT</span><span class="p">)</span>
+ <span class="n">anova</span><span class="p">[</span><span class="n">col</span><span class="p">][</span><span class="s">"date"</span><span class="p">]</span> <span class="o">=</span> <span class="n">d_pval</span>
+ <span class="n">anova</span><span class="p">[</span><span class="n">col</span><span class="p">][</span><span class="s">"treatment"</span><span class="p">]</span> <span class="o">=</span> <span class="n">t_pval</span>
+ <span class="n">anova</span><span class="p">[</span><span class="n">col</span><span class="p">][</span><span class="s">"date_treatment"</span><span class="p">]</span> <span class="o">=</span> <span class="n">dt_pval</span>
+ <span class="k">for</span> <span class="nb">type</span> <span class="ow">in</span> <span class="p">[</span><span class="s">"date"</span><span class="p">,</span> <span class="s">"treatment"</span><span class="p">,</span> <span class="s">"date_treatment"</span><span class="p">]:</span>
+ <span class="n">vals</span> <span class="o">=</span> <span class="p">[</span><span class="n">group</span><span class="p">]</span> <span class="o">+</span> <span class="p">[</span><span class="n">anova</span><span class="p">[</span><span class="n">x</span><span class="p">][</span><span class="nb">type</span><span class="p">]</span> <span class="k">for</span> <span class="n">x</span> <span class="ow">in</span> <span class="n">numeric</span><span class="p">]</span> <span class="o">+</span> <span class="p">[</span><span class="nb">type</span><span class="p">]</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">conn</span><span class="o">.</span><span class="n">execute</span><span class="p">(</span><span class="s">"insert into "</span> <span class="o">+</span> <span class="n">outtable</span> <span class="o">+</span> <span class="s">" ("</span> <span class="o">+</span> <span class="s">","</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">outHeaders</span><span class="p">)</span> <span class="o">+</span> <span class="s">") values ("</span> <span class="o">+</span> <span class="s">","</span><span class="o">.</span><span class="n">join</span><span class="p">([</span><span class="s">"?"</span><span class="p">]</span> <span class="o">*</span> <span class="nb">len</span><span class="p">(</span><span class="n">outHeaders</span><span class="p">))</span> <span class="o">+</span> <span class="s">")"</span><span class="p">,</span> <span class="nb">tuple</span><span class="p">(</span><span class="n">vals</span><span class="p">))</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">conn</span><span class="o">.</span><span class="n">commit</span><span class="p">()</span>
+ <span class="k">return</span>
+ </div>
+<div class="viewcode-block" id="Stats.tTest"><a class="viewcode-back" href="../../statistics.html#htpia.statistics.Stats.tTest">[docs]</a> <span class="k">def</span> <span class="nf">tTest</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">intable</span><span class="p">,</span> <span class="n">outtable</span><span class="p">,</span> <span class="n">comp</span> <span class="o">=</span> <span class="s">"imtype"</span><span class="p">,</span> <span class="n">overwrite</span> <span class="o">=</span> <span class="bp">False</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> :param intable: The input table to perform the T test on.</span>
+<span class="sd"> :type intable: str</span>
+<span class="sd"> :param outtable: The output table to write the results to.</span>
+<span class="sd"> :type outtable: str</span>
+<span class="sd"> :param comp: Whether to compare image types or image names.</span>
+<span class="sd"> :type comp: str</span>
+<span class="sd"> :param overwrite: Whether or not to overwrite the output database</span>
+<span class="sd"> :type overwrite: bool</span>
+<span class="sd"> </span>
+<span class="sd"> This function computes a ttest of the input table for all numeric headers.</span>
+<span class="sd"> The comparison is either done based on image types or image names. Default</span>
+<span class="sd"> functionality is a comparison between image types, specify comp = 'imgname'</span>
+<span class="sd"> to compare image names.</span>
+<span class="sd"> """</span>
+
+ <span class="bp">self</span><span class="o">.</span><span class="n">_validate</span><span class="p">(</span><span class="s">"ttest"</span><span class="p">,</span> <span class="n">intable</span><span class="p">,</span> <span class="n">outtable</span><span class="p">,</span> <span class="n">overwrite</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_createTable</span><span class="p">(</span><span class="s">"ttest"</span><span class="p">,</span> <span class="n">intable</span><span class="p">,</span> <span class="n">outtable</span><span class="p">,</span> <span class="n">overwrite</span><span class="p">)</span>
+ <span class="n">comp</span> <span class="o">=</span> <span class="s">"imtype"</span> <span class="k">if</span> <span class="n">comp</span> <span class="o">==</span> <span class="s">"imtype"</span> <span class="k">else</span> <span class="s">"imgname"</span>
+ <span class="n">headers</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_getHeaders</span><span class="p">(</span><span class="n">outtable</span><span class="p">)</span>
+ <span class="n">numeric</span> <span class="o">=</span> <span class="p">[</span><span class="n">h</span> <span class="k">for</span> <span class="n">h</span> <span class="ow">in</span> <span class="n">headers</span> <span class="k">if</span> <span class="n">h</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">conf</span><span class="o">.</span><span class="n">allHeaders</span><span class="p">]</span>
+ <span class="n">meta</span> <span class="o">=</span> <span class="p">[</span><span class="n">h</span> <span class="k">for</span> <span class="n">h</span> <span class="ow">in</span> <span class="n">headers</span> <span class="k">if</span> <span class="n">h</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">numeric</span><span class="p">]</span>
+ <span class="n">data</span> <span class="o">=</span> <span class="p">{}</span>
+ <span class="n">result</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">conn</span><span class="o">.</span><span class="n">execute</span><span class="p">(</span><span class="s">"select pegasusid,treatment,"</span> <span class="o">+</span> <span class="s">","</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">headers</span><span class="p">)</span> <span class="o">+</span> <span class="s">" from "</span> <span class="o">+</span> <span class="n">intable</span><span class="p">)</span>
+ <span class="k">for</span> <span class="n">row</span> <span class="ow">in</span> <span class="n">result</span><span class="p">:</span>
+ <span class="k">if</span> <span class="n">row</span><span class="p">[</span><span class="n">comp</span><span class="p">]</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">data</span><span class="p">:</span>
+ <span class="n">data</span><span class="p">[</span><span class="n">row</span><span class="p">[</span><span class="n">comp</span><span class="p">]]</span> <span class="o">=</span> <span class="p">{}</span>
+ <span class="k">if</span> <span class="n">row</span><span class="p">[</span><span class="s">"date"</span><span class="p">]</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">data</span><span class="p">[</span><span class="n">row</span><span class="p">[</span><span class="n">comp</span><span class="p">]]:</span>
+ <span class="n">data</span><span class="p">[</span><span class="n">row</span><span class="p">[</span><span class="n">comp</span><span class="p">]][</span><span class="n">row</span><span class="p">[</span><span class="s">"date"</span><span class="p">]]</span> <span class="o">=</span> <span class="p">{</span><span class="s">"meta"</span><span class="p">:</span> <span class="nb">dict</span><span class="p">(</span><span class="n">row</span><span class="p">),</span> <span class="s">"id"</span><span class="p">:</span> <span class="p">[],</span> <span class="s">"values"</span><span class="p">:</span> <span class="p">{}}</span>
+ <span class="n">data</span><span class="p">[</span><span class="n">row</span><span class="p">[</span><span class="n">comp</span><span class="p">]][</span><span class="n">row</span><span class="p">[</span><span class="s">"date"</span><span class="p">]][</span><span class="s">"id"</span><span class="p">]</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">row</span><span class="p">[</span><span class="s">"pegasusid"</span><span class="p">])</span>
+ <span class="k">if</span> <span class="n">row</span><span class="p">[</span><span class="s">"treatment"</span><span class="p">]</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">data</span><span class="p">[</span><span class="n">row</span><span class="p">[</span><span class="n">comp</span><span class="p">]][</span><span class="n">row</span><span class="p">[</span><span class="s">"date"</span><span class="p">]][</span><span class="s">"values"</span><span class="p">]:</span>
+ <span class="n">data</span><span class="p">[</span><span class="n">row</span><span class="p">[</span><span class="n">comp</span><span class="p">]][</span><span class="n">row</span><span class="p">[</span><span class="s">"date"</span><span class="p">]][</span><span class="s">"values"</span><span class="p">][</span><span class="n">row</span><span class="p">[</span><span class="s">"treatment"</span><span class="p">]]</span> <span class="o">=</span> <span class="p">[[</span><span class="n">row</span><span class="p">[</span><span class="n">h</span><span class="p">]]</span> <span class="k">for</span> <span class="n">h</span> <span class="ow">in</span> <span class="n">numeric</span><span class="p">]</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="k">for</span> <span class="n">i</span><span class="p">,</span><span class="n">h</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="n">numeric</span><span class="p">):</span>
+ <span class="n">data</span><span class="p">[</span><span class="n">row</span><span class="p">[</span><span class="n">comp</span><span class="p">]][</span><span class="n">row</span><span class="p">[</span><span class="s">"date"</span><span class="p">]][</span><span class="s">"values"</span><span class="p">][</span><span class="n">row</span><span class="p">[</span><span class="s">"treatment"</span><span class="p">]][</span><span class="n">i</span><span class="p">]</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">row</span><span class="p">[</span><span class="n">h</span><span class="p">])</span>
+ <span class="k">for</span> <span class="n">comp</span> <span class="ow">in</span> <span class="n">data</span><span class="p">:</span>
+ <span class="k">for</span> <span class="n">date</span> <span class="ow">in</span> <span class="n">data</span><span class="p">[</span><span class="n">comp</span><span class="p">]:</span>
+ <span class="n">vals</span> <span class="o">=</span> <span class="p">[</span><span class="n">data</span><span class="p">[</span><span class="n">comp</span><span class="p">][</span><span class="n">date</span><span class="p">][</span><span class="s">"meta"</span><span class="p">][</span><span class="n">x</span><span class="p">]</span> <span class="k">for</span> <span class="n">x</span> <span class="ow">in</span> <span class="n">meta</span><span class="p">]</span>
+ <span class="k">for</span> <span class="n">a</span><span class="p">,</span><span class="n">b</span> <span class="ow">in</span> <span class="nb">zip</span><span class="p">(</span><span class="n">data</span><span class="p">[</span><span class="n">comp</span><span class="p">][</span><span class="n">date</span><span class="p">][</span><span class="s">"values"</span><span class="p">][</span><span class="s">"Control"</span><span class="p">],</span> <span class="n">data</span><span class="p">[</span><span class="n">comp</span><span class="p">][</span><span class="n">date</span><span class="p">][</span><span class="s">"values"</span><span class="p">][</span><span class="s">"Stress"</span><span class="p">]):</span>
+ <span class="k">try</span><span class="p">:</span>
+ <span class="n">res</span> <span class="o">=</span> <span class="n">stats</span><span class="o">.</span><span class="n">ttest_ind</span><span class="p">(</span><span class="n">a</span><span class="p">,</span> <span class="n">b</span><span class="p">)[</span><span class="mi">1</span><span class="p">]</span>
+ <span class="k">except</span><span class="p">:</span>
+ <span class="n">res</span> <span class="o">=</span> <span class="s">"null"</span>
+ <span class="n">vals</span> <span class="o">+=</span> <span class="p">[</span><span class="n">res</span><span class="p">]</span>
+ <span class="n">lastid</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">conn</span><span class="o">.</span><span class="n">execute</span><span class="p">(</span><span class="s">"insert into "</span> <span class="o">+</span> <span class="n">outtable</span> <span class="o">+</span> <span class="s">" ("</span> <span class="o">+</span> <span class="s">","</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">headers</span><span class="p">)</span> <span class="o">+</span> <span class="s">") values ("</span> <span class="o">+</span> <span class="s">","</span><span class="o">.</span><span class="n">join</span><span class="p">([</span><span class="s">"?"</span><span class="p">]</span> <span class="o">*</span> <span class="nb">len</span><span class="p">(</span><span class="n">headers</span><span class="p">))</span> <span class="o">+</span> <span class="s">")"</span><span class="p">,</span> <span class="n">vals</span><span class="p">)</span><span class="o">.</span><span class="n">lastrowid</span>
+ <span class="n">updateVals</span> <span class="o">=</span> <span class="p">(</span><span class="n">lastid</span><span class="p">,)</span> <span class="o">+</span> <span class="nb">tuple</span><span class="p">(</span><span class="n">data</span><span class="p">[</span><span class="n">comp</span><span class="p">][</span><span class="n">date</span><span class="p">][</span><span class="s">"id"</span><span class="p">])</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">conn</span><span class="o">.</span><span class="n">execute</span><span class="p">(</span><span class="s">"update "</span> <span class="o">+</span> <span class="n">intable</span> <span class="o">+</span> <span class="s">" set ref_"</span> <span class="o">+</span> <span class="n">outtable</span> <span class="o">+</span> <span class="s">"=? where id in ("</span> <span class="o">+</span> <span class="s">","</span><span class="o">.</span><span class="n">join</span><span class="p">([</span><span class="s">"?"</span><span class="p">]</span> <span class="o">*</span> <span class="nb">len</span><span class="p">(</span><span class="n">data</span><span class="p">[</span><span class="n">comp</span><span class="p">][</span><span class="n">date</span><span class="p">][</span><span class="s">"id"</span><span class="p">]))</span> <span class="o">+</span> <span class="s">")"</span><span class="p">,</span> <span class="n">updateVals</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">conn</span><span class="o">.</span><span class="n">commit</span><span class="p">()</span>
+ <span class="k">return</span>
+ </div>
+<div class="viewcode-block" id="Stats.treatmentComp"><a class="viewcode-back" href="../../statistics.html#htpia.statistics.Stats.treatmentComp">[docs]</a> <span class="k">def</span> <span class="nf">treatmentComp</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">intable</span><span class="p">,</span> <span class="n">outtable</span><span class="p">,</span> <span class="nb">type</span> <span class="o">=</span> <span class="s">"ratio"</span><span class="p">,</span> <span class="n">direction</span> <span class="o">=</span> <span class="s">"Control"</span><span class="p">,</span> <span class="n">comp</span> <span class="o">=</span> <span class="s">"imtype"</span><span class="p">,</span> <span class="n">overwrite</span> <span class="o">=</span> <span class="bp">False</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> :param intable: The input table to load information from</span>
+<span class="sd"> :type intable: str</span>
+<span class="sd"> :param outtable: The output table to write information to.</span>
+<span class="sd"> :type outtable: str</span>
+<span class="sd"> :param type: The type of calculation to do between treatments. Should be ratio or difference.</span>
+<span class="sd"> :type type: str</span>
+<span class="sd"> :param direction: Whether to compute C ~ S, or S ~ C, default is Control first.</span>
+<span class="sd"> :type direction: str</span>
+<span class="sd"> :param comp: Whether to compare by imtype or imgname</span>
+<span class="sd"> :type comp: str</span>
+<span class="sd"> </span>
+<span class="sd"> This function compares information between treatments -- It finds plants that are identical</span>
+<span class="sd"> except for treatment, and computes either a ratio or difference between them. Direction</span>
+<span class="sd"> is specified as the column you want first, so direction = "Control" will compute C ~ S, and </span>
+<span class="sd"> direction = "Stress" will compute S ~ C. If you have already normalized your table, difference</span>
+<span class="sd"> will provide better information than ratio.</span>
+<span class="sd"> """</span>
+ <span class="n">t1</span> <span class="o">=</span> <span class="s">"Stress"</span> <span class="k">if</span> <span class="n">direction</span> <span class="o">==</span> <span class="s">"Stress"</span> <span class="k">else</span> <span class="s">"Control"</span>
+ <span class="n">t2</span> <span class="o">=</span> <span class="s">"Stress"</span> <span class="k">if</span> <span class="n">direction</span> <span class="o">==</span> <span class="s">"Control"</span> <span class="k">else</span> <span class="s">"Control"</span>
+ <span class="k">if</span> <span class="nb">type</span> <span class="o">==</span> <span class="s">"ratio"</span><span class="p">:</span>
+ <span class="n">op</span> <span class="o">=</span> <span class="k">lambda</span> <span class="n">left</span><span class="p">,</span> <span class="n">right</span><span class="p">:</span> <span class="p">(</span><span class="n">left</span> <span class="o">/</span> <span class="n">right</span><span class="p">)</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="n">op</span> <span class="o">=</span> <span class="k">lambda</span> <span class="n">left</span><span class="p">,</span> <span class="n">right</span><span class="p">:</span> <span class="p">(</span><span class="n">left</span> <span class="o">-</span> <span class="n">right</span><span class="p">)</span>
+ <span class="n">comp</span> <span class="o">=</span> <span class="s">"imtype"</span> <span class="k">if</span> <span class="n">comp</span> <span class="o">==</span> <span class="s">"imtype"</span> <span class="k">else</span> <span class="s">"imgname"</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_validate</span><span class="p">(</span><span class="s">"treatmentComp"</span><span class="p">,</span> <span class="n">intable</span><span class="p">,</span> <span class="n">outtable</span><span class="p">,</span> <span class="n">overwrite</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_createTable</span><span class="p">(</span><span class="s">"treatmentComp"</span><span class="p">,</span> <span class="n">intable</span><span class="p">,</span> <span class="n">outtable</span><span class="p">,</span> <span class="n">overwrite</span><span class="p">)</span>
+ <span class="n">headers</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_getHeaders</span><span class="p">(</span><span class="n">outtable</span><span class="p">)</span>
+ <span class="n">numeric</span> <span class="o">=</span> <span class="p">[</span><span class="n">h</span> <span class="k">for</span> <span class="n">h</span> <span class="ow">in</span> <span class="n">headers</span> <span class="k">if</span> <span class="n">h</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">conf</span><span class="o">.</span><span class="n">allHeaders</span><span class="p">]</span>
+ <span class="n">meta</span> <span class="o">=</span> <span class="p">[</span><span class="n">h</span> <span class="k">for</span> <span class="n">h</span> <span class="ow">in</span> <span class="n">headers</span> <span class="k">if</span> <span class="n">h</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">numeric</span><span class="p">]</span>
+ <span class="n">data</span> <span class="o">=</span> <span class="p">{}</span>
+ <span class="n">result</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">conn</span><span class="o">.</span><span class="n">execute</span><span class="p">(</span><span class="s">"select pegasusid,"</span> <span class="o">+</span> <span class="s">","</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">headers</span><span class="p">)</span> <span class="o">+</span> <span class="s">" from "</span> <span class="o">+</span> <span class="n">intable</span><span class="p">)</span>
+ <span class="k">for</span> <span class="n">row</span> <span class="ow">in</span> <span class="n">result</span><span class="p">:</span>
+ <span class="k">if</span> <span class="n">row</span><span class="p">[</span><span class="s">"genotype"</span><span class="p">]</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">data</span><span class="p">:</span>
+ <span class="n">data</span><span class="p">[</span><span class="n">row</span><span class="p">[</span><span class="s">"genotype"</span><span class="p">]]</span> <span class="o">=</span> <span class="p">{</span><span class="s">"id"</span><span class="p">:</span> <span class="p">[],</span> <span class="s">"values"</span><span class="p">:</span> <span class="p">{},</span> <span class="s">"meta"</span><span class="p">:</span> <span class="p">{}}</span>
+ <span class="n">data</span><span class="p">[</span><span class="n">row</span><span class="p">[</span><span class="s">"genotype"</span><span class="p">]][</span><span class="s">"meta"</span><span class="p">][</span><span class="n">row</span><span class="p">[</span><span class="n">comp</span><span class="p">]]</span> <span class="o">=</span> <span class="nb">dict</span><span class="p">(</span><span class="n">row</span><span class="p">)</span>
+ <span class="n">data</span><span class="p">[</span><span class="n">row</span><span class="p">[</span><span class="s">"genotype"</span><span class="p">]][</span><span class="s">"id"</span><span class="p">]</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">row</span><span class="p">[</span><span class="s">"pegasusid"</span><span class="p">])</span>
+ <span class="k">if</span> <span class="n">row</span><span class="p">[</span><span class="n">comp</span><span class="p">]</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">data</span><span class="p">[</span><span class="n">row</span><span class="p">[</span><span class="s">"genotype"</span><span class="p">]][</span><span class="s">"values"</span><span class="p">]:</span>
+ <span class="n">data</span><span class="p">[</span><span class="n">row</span><span class="p">[</span><span class="s">"genotype"</span><span class="p">]][</span><span class="s">"values"</span><span class="p">][</span><span class="n">row</span><span class="p">[</span><span class="n">comp</span><span class="p">]]</span> <span class="o">=</span> <span class="p">{}</span>
+ <span class="k">if</span> <span class="n">row</span><span class="p">[</span><span class="s">"date"</span><span class="p">]</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">data</span><span class="p">[</span><span class="n">row</span><span class="p">[</span><span class="s">"genotype"</span><span class="p">]][</span><span class="s">"values"</span><span class="p">][</span><span class="n">row</span><span class="p">[</span><span class="n">comp</span><span class="p">]]:</span>
+ <span class="n">data</span><span class="p">[</span><span class="n">row</span><span class="p">[</span><span class="s">"genotype"</span><span class="p">]][</span><span class="s">"values"</span><span class="p">][</span><span class="n">row</span><span class="p">[</span><span class="n">comp</span><span class="p">]][</span><span class="n">row</span><span class="p">[</span><span class="s">"date"</span><span class="p">]]</span> <span class="o">=</span> <span class="p">{}</span>
+ <span class="k">if</span> <span class="n">row</span><span class="p">[</span><span class="s">"treatment"</span><span class="p">]</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">data</span><span class="p">[</span><span class="n">row</span><span class="p">[</span><span class="s">"genotype"</span><span class="p">]][</span><span class="s">"values"</span><span class="p">][</span><span class="n">row</span><span class="p">[</span><span class="n">comp</span><span class="p">]][</span><span class="n">row</span><span class="p">[</span><span class="s">"date"</span><span class="p">]]:</span>
+ <span class="n">data</span><span class="p">[</span><span class="n">row</span><span class="p">[</span><span class="s">"genotype"</span><span class="p">]][</span><span class="s">"values"</span><span class="p">][</span><span class="n">row</span><span class="p">[</span><span class="n">comp</span><span class="p">]][</span><span class="n">row</span><span class="p">[</span><span class="s">"date"</span><span class="p">]][</span><span class="n">row</span><span class="p">[</span><span class="s">"treatment"</span><span class="p">]]</span> <span class="o">=</span> <span class="p">[</span><span class="n">row</span><span class="p">[</span><span class="n">h</span><span class="p">]</span> <span class="k">for</span> <span class="n">h</span> <span class="ow">in</span> <span class="n">numeric</span><span class="p">]</span>
+ <span class="k">for</span> <span class="n">genotype</span> <span class="ow">in</span> <span class="n">data</span><span class="p">:</span>
+ <span class="k">for</span> <span class="n">comp</span> <span class="ow">in</span> <span class="n">data</span><span class="p">[</span><span class="n">genotype</span><span class="p">][</span><span class="s">"values"</span><span class="p">]:</span>
+ <span class="k">for</span> <span class="n">date</span> <span class="ow">in</span> <span class="n">data</span><span class="p">[</span><span class="n">genotype</span><span class="p">][</span><span class="s">"values"</span><span class="p">][</span><span class="n">comp</span><span class="p">]:</span>
+ <span class="n">vals</span> <span class="o">=</span> <span class="p">[</span><span class="n">data</span><span class="p">[</span><span class="n">genotype</span><span class="p">][</span><span class="s">"meta"</span><span class="p">][</span><span class="n">comp</span><span class="p">][</span><span class="n">x</span><span class="p">]</span> <span class="k">for</span> <span class="n">x</span> <span class="ow">in</span> <span class="n">meta</span><span class="p">]</span>
+ <span class="k">for</span> <span class="n">a</span><span class="p">,</span><span class="n">b</span> <span class="ow">in</span> <span class="nb">zip</span><span class="p">(</span><span class="n">data</span><span class="p">[</span><span class="n">genotype</span><span class="p">][</span><span class="s">"values"</span><span class="p">][</span><span class="n">comp</span><span class="p">][</span><span class="n">date</span><span class="p">][</span><span class="n">t1</span><span class="p">],</span> <span class="n">data</span><span class="p">[</span><span class="n">genotype</span><span class="p">][</span><span class="s">"values"</span><span class="p">][</span><span class="n">comp</span><span class="p">][</span><span class="n">date</span><span class="p">][</span><span class="n">t2</span><span class="p">]):</span>
+ <span class="k">try</span><span class="p">:</span>
+ <span class="n">res</span> <span class="o">=</span> <span class="n">op</span><span class="p">(</span><span class="nb">float</span><span class="p">(</span><span class="n">a</span><span class="p">),</span> <span class="nb">float</span><span class="p">(</span><span class="n">b</span><span class="p">))</span>
+ <span class="k">except</span><span class="p">:</span>
+ <span class="n">res</span> <span class="o">=</span> <span class="s">"null"</span>
+ <span class="n">vals</span> <span class="o">+=</span> <span class="p">[</span><span class="n">res</span><span class="p">]</span>
+ <span class="n">lastid</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">conn</span><span class="o">.</span><span class="n">execute</span><span class="p">(</span><span class="s">"insert into "</span> <span class="o">+</span> <span class="n">outtable</span> <span class="o">+</span> <span class="s">" ("</span> <span class="o">+</span> <span class="s">","</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">headers</span><span class="p">)</span> <span class="o">+</span> <span class="s">") values ("</span> <span class="o">+</span> <span class="s">","</span><span class="o">.</span><span class="n">join</span><span class="p">([</span><span class="s">"?"</span><span class="p">]</span> <span class="o">*</span> <span class="nb">len</span><span class="p">(</span><span class="n">headers</span><span class="p">))</span> <span class="o">+</span> <span class="s">")"</span><span class="p">,</span> <span class="n">vals</span><span class="p">)</span><span class="o">.</span><span class="n">lastrowid</span>
+ <span class="n">updateVals</span> <span class="o">=</span> <span class="p">(</span><span class="n">lastid</span><span class="p">,)</span> <span class="o">+</span> <span class="nb">tuple</span><span class="p">(</span><span class="n">data</span><span class="p">[</span><span class="n">genotype</span><span class="p">][</span><span class="s">"id"</span><span class="p">])</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">conn</span><span class="o">.</span><span class="n">execute</span><span class="p">(</span><span class="s">"update "</span> <span class="o">+</span> <span class="n">intable</span> <span class="o">+</span> <span class="s">" set ref_"</span> <span class="o">+</span> <span class="n">outtable</span> <span class="o">+</span> <span class="s">"=? where id in ("</span> <span class="o">+</span> <span class="s">","</span><span class="o">.</span><span class="n">join</span><span class="p">([</span><span class="s">"?"</span><span class="p">]</span> <span class="o">*</span> <span class="nb">len</span><span class="p">(</span><span class="n">data</span><span class="p">[</span><span class="n">genotype</span><span class="p">][</span><span class="s">"id"</span><span class="p">]))</span> <span class="o">+</span> <span class="s">")"</span><span class="p">,</span> <span class="n">updateVals</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">conn</span><span class="o">.</span><span class="n">commit</span><span class="p">()</span>
+ <span class="k">return</span>
+ </div>
+<div class="viewcode-block" id="Stats.threshold"><a class="viewcode-back" href="../../statistics.html#htpia.statistics.Stats.threshold">[docs]</a> <span class="k">def</span> <span class="nf">threshold</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">intable</span><span class="p">,</span> <span class="n">outtable</span><span class="p">,</span> <span class="n">thresh</span> <span class="o">=</span> <span class="mf">0.01</span><span class="p">,</span> <span class="n">overwrite</span> <span class="o">=</span> <span class="bp">False</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> :param intable: The input table to load information from</span>
+<span class="sd"> :type intable: str</span>
+<span class="sd"> :param outtable: The output table to write information to.</span>
+<span class="sd"> :type outtable: str</span>
+<span class="sd"> :param thresh: The threshold value.</span>
+<span class="sd"> :type thresh: float</span>
+<span class="sd"> </span>
+<span class="sd"> This function thresholds the table based on the given value. All values</span>
+<span class="sd"> that fall below the threhsold are 'updated' in place with 'null'. Normalize</span>
+<span class="sd"> is often called before thresholding.</span>
+<span class="sd"> """</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_validate</span><span class="p">(</span><span class="s">"threshold"</span><span class="p">,</span> <span class="n">intable</span><span class="p">,</span> <span class="n">outtable</span><span class="p">,</span> <span class="n">overwrite</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_createTable</span><span class="p">(</span><span class="s">"threshold"</span><span class="p">,</span> <span class="n">intable</span><span class="p">,</span> <span class="n">outtable</span><span class="p">,</span> <span class="n">overwrite</span><span class="p">)</span>
+ <span class="n">headers</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_getHeaders</span><span class="p">(</span><span class="n">outtable</span><span class="p">)</span>
+ <span class="n">numeric</span> <span class="o">=</span> <span class="p">[</span><span class="n">h</span> <span class="k">for</span> <span class="n">h</span> <span class="ow">in</span> <span class="n">headers</span> <span class="k">if</span> <span class="n">h</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">conf</span><span class="o">.</span><span class="n">allHeaders</span><span class="p">]</span>
+ <span class="n">result</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">conn</span><span class="o">.</span><span class="n">execute</span><span class="p">(</span><span class="s">"select pegasusid,"</span> <span class="o">+</span> <span class="s">","</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">headers</span><span class="p">)</span> <span class="o">+</span> <span class="s">" from "</span> <span class="o">+</span> <span class="n">intable</span><span class="p">)</span>
+ <span class="k">for</span> <span class="n">row</span> <span class="ow">in</span> <span class="n">result</span><span class="p">:</span>
+ <span class="n">vals</span> <span class="o">=</span> <span class="nb">tuple</span><span class="p">([</span><span class="n">row</span><span class="p">[</span><span class="n">h</span><span class="p">]</span> <span class="k">if</span> <span class="n">h</span> <span class="ow">in</span> <span class="n">conf</span><span class="o">.</span><span class="n">allHeaders</span> <span class="k">else</span> <span class="n">row</span><span class="p">[</span><span class="n">h</span><span class="p">]</span> <span class="k">if</span> <span class="nb">float</span><span class="p">(</span><span class="n">row</span><span class="p">[</span><span class="n">h</span><span class="p">])</span> <span class="o">></span> <span class="n">thresh</span> <span class="k">else</span> <span class="s">"null"</span> <span class="k">for</span> <span class="n">h</span> <span class="ow">in</span> <span class="n">headers</span><span class="p">])</span>
+ <span class="n">lastid</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">conn</span><span class="o">.</span><span class="n">execute</span><span class="p">(</span><span class="s">"insert into "</span> <span class="o">+</span> <span class="n">outtable</span> <span class="o">+</span> <span class="s">" ("</span> <span class="o">+</span> <span class="s">","</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">headers</span><span class="p">)</span> <span class="o">+</span> <span class="s">") values ("</span> <span class="o">+</span> <span class="s">","</span><span class="o">.</span><span class="n">join</span><span class="p">([</span><span class="s">"?"</span><span class="p">]</span> <span class="o">*</span> <span class="nb">len</span><span class="p">(</span><span class="n">headers</span><span class="p">))</span> <span class="o">+</span> <span class="s">")"</span><span class="p">,</span> <span class="n">vals</span><span class="p">)</span><span class="o">.</span><span class="n">lastrowid</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">conn</span><span class="o">.</span><span class="n">execute</span><span class="p">(</span><span class="s">"update "</span> <span class="o">+</span> <span class="n">intable</span> <span class="o">+</span> <span class="s">" set ref_"</span> <span class="o">+</span> <span class="n">outtable</span> <span class="o">+</span> <span class="s">"=? where pegasusid=?"</span><span class="p">,</span> <span class="p">(</span><span class="n">lastid</span><span class="p">,</span> <span class="n">row</span><span class="p">[</span><span class="s">"pegasusid"</span><span class="p">]))</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">conn</span><span class="o">.</span><span class="n">commit</span><span class="p">()</span>
+ <span class="k">return</span>
+ </div>
+ <span class="k">def</span> <span class="nf">SOMANYGRAPHINGFUNCTIONS</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+ <span class="k">return</span>
+
+<div class="viewcode-block" id="Stats.export"><a class="viewcode-back" href="../../statistics.html#htpia.statistics.Stats.export">[docs]</a> <span class="k">def</span> <span class="nf">export</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">table</span><span class="p">,</span> <span class="n">processed</span> <span class="o">=</span> <span class="bp">True</span><span class="p">,</span> <span class="n">grouping</span> <span class="o">=</span> <span class="bp">None</span><span class="p">,</span> <span class="n">fname</span> <span class="o">=</span> <span class="bp">None</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> :param table: The table to write to csv</span>
+<span class="sd"> :type table: str</span>
+<span class="sd"> :param processed: Whether or not to extract processed data</span>
+<span class="sd"> :type processed: bool</span>
+<span class="sd"> :param grouping: Which image types to extract from the database.</span>
+<span class="sd"> :type grouping: list</span>
+<span class="sd"> :param fname: The file name to write to.</span>
+<span class="sd"> :type fname: str</span>
+<span class="sd"> </span>
+<span class="sd"> This function simply extracts data from a database and writes it to csv format.</span>
+<span class="sd"> Default functionality is to extract only data that has been processed. This is</span>
+<span class="sd"> checked by finding if an outputPath has been set. Additionally,</span>
+<span class="sd"> you can specify a list of image types to extract, if not, the default list contains</span>
+<span class="sd"> all rgb and fluo images. Finally, if no file name is specified, the name</span>
+<span class="sd"> of the table is used as the filename.</span>
+<span class="sd"> """</span>
+
+ <span class="n">grouping</span> <span class="o">=</span> <span class="n">grouping</span> <span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">grouping</span><span class="p">,</span> <span class="nb">list</span><span class="p">)</span> <span class="k">else</span> <span class="bp">self</span><span class="o">.</span><span class="n">_getImageTypes</span><span class="p">(</span><span class="n">table</span><span class="p">)</span>
+ <span class="n">fname</span> <span class="o">=</span> <span class="n">fname</span> <span class="k">if</span> <span class="n">fname</span> <span class="k">else</span> <span class="n">table</span> <span class="o">+</span> <span class="s">".csv"</span>
+ <span class="n">query</span> <span class="o">=</span> <span class="s">"select * from "</span> <span class="o">+</span> <span class="n">table</span>
+ <span class="n">values</span> <span class="o">=</span> <span class="nb">tuple</span><span class="p">()</span>
+ <span class="k">if</span> <span class="n">processed</span><span class="p">:</span>
+ <span class="n">query</span> <span class="o">+=</span> <span class="s">" where outputPath is not null"</span>
+ <span class="k">if</span> <span class="n">grouping</span><span class="p">:</span>
+ <span class="n">query</span> <span class="o">+=</span> <span class="s">" and ("</span> <span class="o">+</span> <span class="s">" or "</span><span class="o">.</span><span class="n">join</span><span class="p">([</span><span class="s">"imtype=?"</span> <span class="k">for</span> <span class="n">x</span> <span class="ow">in</span> <span class="n">grouping</span><span class="p">])</span>
+ <span class="n">values</span> <span class="o">=</span> <span class="nb">tuple</span><span class="p">([</span><span class="n">x</span> <span class="k">for</span> <span class="n">x</span> <span class="ow">in</span> <span class="n">grouping</span><span class="p">])</span>
+ <span class="k">elif</span> <span class="n">grouping</span><span class="p">:</span>
+ <span class="n">query</span> <span class="o">+=</span> <span class="s">" "</span> <span class="o">+</span> <span class="s">" or "</span><span class="o">.</span><span class="n">join</span><span class="p">([</span><span class="s">"imtype=?"</span> <span class="k">for</span> <span class="n">x</span> <span class="ow">in</span> <span class="n">grouping</span><span class="p">])</span>
+ <span class="n">values</span> <span class="o">=</span> <span class="nb">tuple</span><span class="p">([</span><span class="n">x</span> <span class="k">for</span> <span class="n">x</span> <span class="ow">in</span> <span class="n">grouping</span><span class="p">])</span>
+ <span class="n">table</span> <span class="o">=</span> <span class="n">pandas</span><span class="o">.</span><span class="n">io</span><span class="o">.</span><span class="n">sql</span><span class="o">.</span><span class="n">read_frame</span><span class="p">(</span><span class="n">query</span><span class="p">,</span> <span class="n">values</span><span class="p">)</span>
+ <span class="n">table</span><span class="o">.</span><span class="n">to_csv</span><span class="p">(</span><span class="n">fname</span><span class="p">)</span>
+ <span class="k">return</span></div></div>
+</pre></div>
+
+ </div>
+
+ </div>
+</div>
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+ <div class="container">
+ <p class="pull-right">
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new file mode 100644
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+<li class="toctree-l1"><a class="reference internal" href="../../start.html">Getting Started</a></li>
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+<li class="toctree-l1"><a class="reference internal" href="../../ex_workflow_1.html">Workflow Example #1</a></li>
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+<li class="toctree-l1"><a class="reference internal" href="../../indexing.html">Image Loading</a></li>
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+
+ <h1>Source code for htpia.workflow</h1><div class="highlight"><pre>
+<span class="sd">"""</span>
+
+<span class="sd">.. module:: workflow</span>
+<span class="sd"> :platform: Mac, Linux</span>
+<span class="sd"> :synopsis: Custom workflow creation, and workflow submission.</span>
+
+<span class="sd">.. moduleauthor:: Avi Knecht <avi@kurtknecht.com></span>
+
+<span class="sd">"""</span>
+
+<span class="kn">import</span> <span class="nn">os</span>
+<span class="kn">import</span> <span class="nn">conf</span>
+<span class="kn">import</span> <span class="nn">sys</span>
+<span class="kn">import</span> <span class="nn">json</span>
+<span class="kn">import</span> <span class="nn">re</span>
+<span class="kn">import</span> <span class="nn">csv</span>
+<span class="kn">import</span> <span class="nn">datetime</span>
+<span class="kn">import</span> <span class="nn">sqlite3</span>
+<span class="kn">import</span> <span class="nn">shutil</span>
+<span class="kn">import</span> <span class="nn">errno</span>
+<span class="kn">import</span> <span class="nn">textwrap</span>
+<span class="kn">import</span> <span class="nn">copy</span>
+<span class="kn">import</span> <span class="nn">htpia.validator</span>
+<span class="kn">import</span> <span class="nn">xml.dom.minidom</span>
+<span class="kn">from</span> <span class="nn">Pegasus.DAX3</span> <span class="kn">import</span> <span class="o">*</span>
+
+
+<span class="k">class</span> <span class="nc">Workflow</span><span class="p">(</span><span class="nb">object</span><span class="p">):</span>
+
+ <span class="sd">"""</span>
+<span class="sd"> Generic workflow creation class.</span>
+<span class="sd"> """</span>
+
+ <span class="k">def</span> <span class="nf">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">jobhome</span><span class="p">,</span> <span class="n">basename</span> <span class="o">=</span> <span class="bp">None</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> :param jobhome: The base directory for job submission.</span>
+<span class="sd"> :type jobhome: str</span>
+<span class="sd"> </span>
+<span class="sd"> Creates a Workflow class based on the input directory. Only loads and </span>
+<span class="sd"> validates the config file by default.</span>
+<span class="sd"> """</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">err</span> <span class="o">=</span> <span class="s">""</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">jobhome</span> <span class="o">=</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">abspath</span><span class="p">(</span><span class="n">jobhome</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">jobname</span> <span class="o">=</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">basename</span><span class="p">(</span><span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">dirname</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">jobhome</span> <span class="o">+</span> <span class="s">"/"</span><span class="p">))</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">basename</span> <span class="o">=</span> <span class="n">basename</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">dax</span> <span class="o">=</span> <span class="n">ADAG</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">jobname</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">executables</span> <span class="o">=</span> <span class="p">{}</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">files</span> <span class="o">=</span> <span class="p">{</span><span class="bp">self</span><span class="o">.</span><span class="n">dax</span><span class="p">:</span> <span class="p">{}}</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">jobs</span> <span class="o">=</span> <span class="p">{</span><span class="bp">self</span><span class="o">.</span><span class="n">dax</span><span class="p">:</span> <span class="p">{}}</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">deps</span> <span class="o">=</span> <span class="p">{}</span>
+ <span class="k">return</span>
+
+ <span class="k">def</span> <span class="nf">_loadInputFiles</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> Loads the input files into the appropriate variables</span>
+<span class="sd"> This should be overloaded.</span>
+<span class="sd"> """</span>
+ <span class="k">return</span>
+
+ <span class="k">def</span> <span class="nf">_isFile</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">name</span><span class="p">,</span> <span class="n">dax</span><span class="p">,</span> <span class="n">imtype</span><span class="p">,</span> <span class="n">inout</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> Convenience function to check if a given file exists.</span>
+<span class="sd"> """</span>
+ <span class="k">if</span> <span class="n">name</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">files</span><span class="p">[</span><span class="n">dax</span><span class="p">][</span><span class="n">imtype</span><span class="p">][</span><span class="n">inout</span><span class="p">]:</span>
+ <span class="k">return</span> <span class="bp">True</span>
+ <span class="k">return</span> <span class="bp">False</span>
+
+ <span class="k">def</span> <span class="nf">_isJob</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">name</span><span class="p">,</span> <span class="n">dax</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> Convenience function to check if a given job exists.</span>
+<span class="sd"> """</span>
+ <span class="k">if</span> <span class="n">name</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">jobs</span><span class="p">[</span><span class="n">dax</span><span class="p">]:</span>
+ <span class="k">return</span> <span class="bp">True</span>
+ <span class="k">return</span> <span class="bp">False</span>
+
+ <span class="k">def</span> <span class="nf">_isExecutable</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">name</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> Convenience function to check if a given executable exists.</span>
+<span class="sd"> """</span>
+ <span class="k">if</span> <span class="n">name</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">executables</span><span class="p">:</span>
+ <span class="k">return</span> <span class="bp">True</span>
+ <span class="k">return</span> <span class="bp">False</span>
+
+ <span class="k">def</span> <span class="nf">_createSetup</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> Creates the base structure for job submission. Everything is contained </span>
+<span class="sd"> within a folder based on the current timestamp.</span>
+<span class="sd"> """</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">basepath</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">jobhome</span> <span class="o">+</span> <span class="s">"/"</span> <span class="o">+</span> <span class="bp">self</span><span class="o">.</span><span class="n">basename</span> <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">basename</span> <span class="k">else</span> <span class="bp">self</span><span class="o">.</span><span class="n">jobhome</span> <span class="o">+</span> <span class="s">"/"</span> <span class="o">+</span> <span class="n">datetime</span><span class="o">.</span><span class="n">datetime</span><span class="o">.</span><span class="n">now</span><span class="p">()</span><span class="o">.</span><span class="n">strftime</span><span class="p">(</span><span class="s">"%Y-%m-</span><span class="si">%d</span><span class="s">_%H%M%S"</span><span class="p">)</span>
+ <span class="k">if</span> <span class="ow">not</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">exists</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">basepath</span><span class="p">):</span>
+ <span class="n">os</span><span class="o">.</span><span class="n">makedirs</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">basepath</span><span class="p">)</span>
+ <span class="k">if</span> <span class="ow">not</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">exists</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">basepath</span> <span class="o">+</span> <span class="s">"/input"</span><span class="p">):</span>
+ <span class="n">os</span><span class="o">.</span><span class="n">makedirs</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">basepath</span> <span class="o">+</span> <span class="s">"/input"</span><span class="p">)</span>
+ <span class="k">if</span> <span class="ow">not</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">exists</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">basepath</span> <span class="o">+</span> <span class="s">"/output"</span><span class="p">):</span>
+ <span class="n">os</span><span class="o">.</span><span class="n">makedirs</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">basepath</span> <span class="o">+</span> <span class="s">"/output"</span><span class="p">)</span>
+ <span class="k">if</span> <span class="ow">not</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">exists</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">basepath</span> <span class="o">+</span> <span class="s">"input/templates"</span><span class="p">):</span>
+ <span class="n">os</span><span class="o">.</span><span class="n">makedirs</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">basepath</span> <span class="o">+</span> <span class="s">"/input/templates"</span><span class="p">)</span>
+ <span class="k">if</span> <span class="ow">not</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">exists</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">basepath</span> <span class="o">+</span> <span class="s">"/input/rawfiles"</span><span class="p">):</span>
+ <span class="n">os</span><span class="o">.</span><span class="n">makedirs</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">basepath</span> <span class="o">+</span> <span class="s">"/input/rawfiles"</span><span class="p">)</span>
+ <span class="k">return</span>
+
+ <span class="k">def</span> <span class="nf">_addFile</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">name</span><span class="p">,</span> <span class="n">imtype</span><span class="p">,</span> <span class="n">inout</span><span class="p">,</span> <span class="n">path</span> <span class="o">=</span> <span class="bp">None</span><span class="p">,</span> <span class="n">dax</span> <span class="o">=</span> <span class="bp">None</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> Adds the inputted file to the dax, as well as the internal variable self.files</span>
+<span class="sd"> """</span>
+ <span class="n">dax</span> <span class="o">=</span> <span class="n">dax</span> <span class="k">if</span> <span class="n">dax</span> <span class="k">else</span> <span class="bp">self</span><span class="o">.</span><span class="n">dax</span>
+ <span class="k">if</span> <span class="ow">not</span> <span class="bp">self</span><span class="o">.</span><span class="n">_isFile</span><span class="p">(</span><span class="n">name</span><span class="p">,</span> <span class="n">dax</span><span class="p">,</span> <span class="n">imtype</span><span class="p">,</span> <span class="n">inout</span><span class="p">):</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">files</span><span class="p">[</span><span class="n">dax</span><span class="p">][</span><span class="n">imtype</span><span class="p">][</span><span class="n">inout</span><span class="p">][</span><span class="n">name</span><span class="p">]</span> <span class="o">=</span> <span class="p">{</span><span class="s">"file"</span><span class="p">:</span> <span class="n">File</span><span class="p">(</span><span class="n">name</span><span class="p">),</span> <span class="s">"path"</span><span class="p">:</span> <span class="s">""</span><span class="p">}</span>
+ <span class="k">if</span> <span class="n">inout</span> <span class="o">==</span> <span class="s">"input"</span><span class="p">:</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">files</span><span class="p">[</span><span class="n">dax</span><span class="p">][</span><span class="n">imtype</span><span class="p">][</span><span class="n">inout</span><span class="p">][</span><span class="n">name</span><span class="p">][</span><span class="s">"path"</span><span class="p">]</span> <span class="o">=</span> <span class="n">path</span> <span class="k">if</span> <span class="n">path</span> <span class="k">else</span> <span class="n">name</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">files</span><span class="p">[</span><span class="n">dax</span><span class="p">][</span><span class="n">imtype</span><span class="p">][</span><span class="n">inout</span><span class="p">][</span><span class="n">name</span><span class="p">][</span><span class="s">"file"</span><span class="p">]</span><span class="o">.</span><span class="n">addPFN</span><span class="p">(</span><span class="n">PFN</span><span class="p">(</span><span class="s">"file://"</span> <span class="o">+</span> <span class="n">path</span><span class="o">.</span><span class="n">replace</span><span class="p">(</span><span class="s">" "</span><span class="p">,</span><span class="s">"%20"</span><span class="p">),</span> <span class="s">"local"</span><span class="p">))</span>
+ <span class="n">dax</span><span class="o">.</span><span class="n">addFile</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">files</span><span class="p">[</span><span class="n">dax</span><span class="p">][</span><span class="n">imtype</span><span class="p">][</span><span class="n">inout</span><span class="p">][</span><span class="n">name</span><span class="p">][</span><span class="s">"file"</span><span class="p">])</span>
+ <span class="k">return</span>
+
+ <span class="k">def</span> <span class="nf">_addJob</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">jobname</span><span class="p">,</span> <span class="n">executable</span><span class="p">,</span> <span class="n">inputs</span><span class="p">,</span> <span class="n">outputs</span><span class="p">,</span> <span class="n">arguments</span><span class="p">,</span> <span class="n">dependencies</span> <span class="o">=</span> <span class="bp">None</span><span class="p">,</span> <span class="n">dax</span> <span class="o">=</span> <span class="bp">None</span><span class="p">,</span> <span class="n">label</span> <span class="o">=</span> <span class="bp">None</span><span class="p">):</span>
+ <span class="n">dax</span> <span class="o">=</span> <span class="n">dax</span> <span class="k">if</span> <span class="n">dax</span> <span class="k">else</span> <span class="bp">self</span><span class="o">.</span><span class="n">dax</span>
+ <span class="k">if</span> <span class="ow">not</span> <span class="bp">self</span><span class="o">.</span><span class="n">_isJob</span><span class="p">(</span><span class="n">jobname</span><span class="p">,</span> <span class="n">dax</span><span class="p">):</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">jobs</span><span class="p">[</span><span class="n">dax</span><span class="p">][</span><span class="n">jobname</span><span class="p">]</span> <span class="o">=</span> <span class="n">Job</span><span class="p">(</span><span class="n">executable</span><span class="p">)</span>
+ <span class="n">dax</span><span class="o">.</span><span class="n">addJob</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">jobs</span><span class="p">[</span><span class="n">dax</span><span class="p">][</span><span class="n">jobname</span><span class="p">])</span>
+ <span class="k">for</span> <span class="n">key</span> <span class="ow">in</span> <span class="n">inputs</span><span class="p">:</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">jobs</span><span class="p">[</span><span class="n">dax</span><span class="p">][</span><span class="n">jobname</span><span class="p">]</span><span class="o">.</span><span class="n">uses</span><span class="p">(</span><span class="n">inputs</span><span class="p">[</span><span class="n">key</span><span class="p">][</span><span class="s">"file"</span><span class="p">],</span> <span class="n">link</span> <span class="o">=</span> <span class="n">Link</span><span class="o">.</span><span class="n">INPUT</span><span class="p">)</span>
+ <span class="k">for</span> <span class="n">key</span> <span class="ow">in</span> <span class="n">outputs</span><span class="p">:</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">jobs</span><span class="p">[</span><span class="n">dax</span><span class="p">][</span><span class="n">jobname</span><span class="p">]</span><span class="o">.</span><span class="n">uses</span><span class="p">(</span><span class="n">outputs</span><span class="p">[</span><span class="n">key</span><span class="p">][</span><span class="s">"file"</span><span class="p">],</span> <span class="n">link</span> <span class="o">=</span> <span class="n">Link</span><span class="o">.</span><span class="n">OUTPUT</span><span class="p">,</span> <span class="n">transfer</span> <span class="o">=</span> <span class="n">outputs</span><span class="p">[</span><span class="n">key</span><span class="p">][</span><span class="s">"transfer"</span><span class="p">])</span>
+ <span class="n">arglist</span> <span class="o">=</span> <span class="p">[]</span>
+ <span class="k">for</span> <span class="n">arg</span> <span class="ow">in</span> <span class="n">arguments</span><span class="p">:</span>
+ <span class="n">arglist</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">arg</span><span class="p">)</span>
+ <span class="k">if</span> <span class="nb">str</span><span class="p">(</span><span class="n">arguments</span><span class="p">[</span><span class="n">arg</span><span class="p">])</span> <span class="ow">in</span> <span class="n">inputs</span><span class="p">:</span>
+ <span class="n">arglist</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">inputs</span><span class="p">[</span><span class="nb">str</span><span class="p">(</span><span class="n">arguments</span><span class="p">[</span><span class="n">arg</span><span class="p">])][</span><span class="s">"file"</span><span class="p">])</span>
+ <span class="k">elif</span> <span class="nb">str</span><span class="p">(</span><span class="n">arguments</span><span class="p">[</span><span class="n">arg</span><span class="p">])</span> <span class="ow">in</span> <span class="n">outputs</span><span class="p">:</span>
+ <span class="n">arglist</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">outputs</span><span class="p">[</span><span class="nb">str</span><span class="p">(</span><span class="n">arguments</span><span class="p">[</span><span class="n">arg</span><span class="p">])][</span><span class="s">"file"</span><span class="p">])</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="n">arglist</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="nb">str</span><span class="p">(</span><span class="n">arguments</span><span class="p">[</span><span class="n">arg</span><span class="p">]))</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">jobs</span><span class="p">[</span><span class="n">dax</span><span class="p">][</span><span class="n">jobname</span><span class="p">]</span><span class="o">.</span><span class="n">addArguments</span><span class="p">(</span><span class="o">*</span><span class="n">arglist</span><span class="p">)</span>
+ <span class="k">if</span> <span class="n">dependencies</span><span class="p">:</span>
+ <span class="k">for</span> <span class="n">depend</span> <span class="ow">in</span> <span class="n">dependencies</span><span class="p">:</span>
+ <span class="n">dax</span><span class="o">.</span><span class="n">depends</span><span class="p">(</span><span class="n">child</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">jobs</span><span class="p">[</span><span class="n">dax</span><span class="p">][</span><span class="n">jobname</span><span class="p">],</span> <span class="n">parent</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">jobs</span><span class="p">[</span><span class="n">dax</span><span class="p">][</span><span class="n">depend</span><span class="p">])</span>
+ <span class="k">if</span> <span class="n">label</span><span class="p">:</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">jobs</span><span class="p">[</span><span class="n">dax</span><span class="p">][</span><span class="n">jobname</span><span class="p">]</span><span class="o">.</span><span class="n">profile</span><span class="p">(</span><span class="n">Namespace</span><span class="o">.</span><span class="n">PEGASUS</span><span class="p">,</span> <span class="s">"label"</span><span class="p">,</span> <span class="n">label</span><span class="p">)</span>
+ <span class="k">return</span>
+
+ <span class="k">def</span> <span class="nf">create</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> Creates a new pegasus submission directory based on the current timestamp,</span>
+<span class="sd"> and populates it with all required information to submit a pegasus job.</span>
+<span class="sd"> This function should be overloaded.</span>
+<span class="sd"> """</span>
+ <span class="k">return</span>
+
+
+<div class="viewcode-block" id="Statistics"><a class="viewcode-back" href="../../workflowstats.html#htpia.workflow.Statistics">[docs]</a><span class="k">class</span> <span class="nc">Statistics</span><span class="p">(</span><span class="n">Workflow</span><span class="p">):</span>
+
+ <span class="sd">"""</span>
+<span class="sd"> A class specifically for statistics workflow</span>
+<span class="sd"> validation and submission.</span>
+<span class="sd"> """</span>
+
+ <span class="k">def</span> <span class="nf">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">jobhome</span><span class="p">,</span> <span class="n">basename</span><span class="p">,</span> <span class="n">validOnly</span> <span class="o">=</span> <span class="bp">False</span><span class="p">):</span>
+ <span class="nb">super</span><span class="p">(</span><span class="n">Statistics</span><span class="p">,</span> <span class="bp">self</span><span class="p">)</span><span class="o">.</span><span class="n">__init__</span><span class="p">(</span><span class="n">jobhome</span><span class="p">,</span> <span class="n">basename</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">configfile</span> <span class="o">=</span> <span class="n">jobhome</span> <span class="o">+</span> <span class="s">"/input/"</span> <span class="o">+</span> <span class="n">conf</span><span class="o">.</span><span class="n">configFile</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">statsfile</span> <span class="o">=</span> <span class="n">jobhome</span> <span class="o">+</span> <span class="s">"/input/"</span> <span class="o">+</span> <span class="n">conf</span><span class="o">.</span><span class="n">statsFile</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">dbfile</span> <span class="o">=</span> <span class="n">jobhome</span> <span class="o">+</span> <span class="s">"/"</span> <span class="o">+</span> <span class="n">basename</span> <span class="o">+</span> <span class="s">"/output/"</span> <span class="o">+</span> <span class="n">conf</span><span class="o">.</span><span class="n">outputdb</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">validOnly</span> <span class="o">=</span> <span class="n">validOnly</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">rawFiles</span> <span class="o">=</span> <span class="p">{}</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_loadInputFiles</span><span class="p">()</span>
+ <span class="k">return</span>
+
+ <span class="k">def</span> <span class="nf">_getImageTypes</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+ <span class="k">return</span> <span class="p">[</span><span class="n">x</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="k">for</span> <span class="n">x</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">db</span><span class="o">.</span><span class="n">execute</span><span class="p">(</span><span class="s">"select distinct imtype from images"</span><span class="p">)]</span>
+
+
+ <span class="k">def</span> <span class="nf">_loadInputFiles</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">validator</span> <span class="o">=</span> <span class="n">htpia</span><span class="o">.</span><span class="n">validator</span><span class="o">.</span><span class="n">Statistics</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">statsfile</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">configfile</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">dbfile</span><span class="p">)</span>
+ <span class="k">if</span> <span class="ow">not</span> <span class="bp">self</span><span class="o">.</span><span class="n">validator</span><span class="o">.</span><span class="n">isValid</span><span class="p">()</span> <span class="ow">or</span> <span class="bp">self</span><span class="o">.</span><span class="n">validOnly</span><span class="p">:</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">validator</span><span class="o">.</span><span class="n">printErrors</span><span class="p">()</span>
+ <span class="n">sys</span><span class="o">.</span><span class="n">exit</span><span class="p">()</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">stats</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">validator</span><span class="o">.</span><span class="n">workflow</span><span class="o">.</span><span class="n">data</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">db</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">validator</span><span class="o">.</span><span class="n">db</span><span class="o">.</span><span class="n">conn</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">config</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">validator</span><span class="o">.</span><span class="n">config</span><span class="o">.</span><span class="n">data</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">rawFiles</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">validator</span><span class="o">.</span><span class="n">workflow</span><span class="o">.</span><span class="n">rawFiles</span>
+ <span class="k">return</span>
+
+ <span class="k">def</span> <span class="nf">_copyFiles</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> Copies all input files to the correct location.</span>
+<span class="sd"> """</span>
+ <span class="k">if</span> <span class="ow">not</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">exists</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">basepath</span> <span class="o">+</span> <span class="s">"/input/stats"</span><span class="p">):</span>
+ <span class="n">os</span><span class="o">.</span><span class="n">makedirs</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">basepath</span> <span class="o">+</span> <span class="s">"/input/stats"</span><span class="p">)</span>
+ <span class="n">shutil</span><span class="o">.</span><span class="n">copyfile</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">statsfile</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">basepath</span> <span class="o">+</span> <span class="s">"/input/templates/"</span> <span class="o">+</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">basename</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">statsfile</span><span class="p">))</span>
+ <span class="k">return</span>
+
+ <span class="k">def</span> <span class="nf">_loadFiles</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">loc</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> Loads all files (input and output) into the dax and the self.files variable</span>
+<span class="sd"> """</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">files</span><span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">dax</span><span class="p">]</span> <span class="o">=</span> <span class="p">{}</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">files</span><span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">dax</span><span class="p">][</span><span class="s">"raw"</span><span class="p">]</span> <span class="o">=</span> <span class="p">{</span><span class="s">"input"</span><span class="p">:</span> <span class="p">{},</span> <span class="s">"output"</span><span class="p">:</span> <span class="p">{}}</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_addFile</span><span class="p">(</span><span class="s">"output.db"</span><span class="p">,</span> <span class="s">"raw"</span><span class="p">,</span> <span class="s">"input"</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">basepath</span> <span class="o">+</span> <span class="s">"/output/output.db"</span><span class="p">)</span>
+ <span class="k">for</span> <span class="nb">type</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">stats</span><span class="p">[</span><span class="s">"workflows"</span><span class="p">]:</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">files</span><span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">dax</span><span class="p">][</span><span class="nb">type</span><span class="p">]</span> <span class="o">=</span> <span class="p">{</span><span class="s">"input"</span><span class="p">:</span> <span class="p">{},</span> <span class="s">"output"</span><span class="p">:</span> <span class="p">{}}</span>
+ <span class="k">for</span> <span class="n">f</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">rawFiles</span><span class="p">[</span><span class="nb">type</span><span class="p">]:</span>
+ <span class="n">shutil</span><span class="o">.</span><span class="n">copyfile</span><span class="p">(</span><span class="n">f</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">basepath</span> <span class="o">+</span> <span class="s">"/input/rawfiles/"</span> <span class="o">+</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">basename</span><span class="p">(</span><span class="n">f</span><span class="p">))</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_addFile</span><span class="p">(</span><span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">basename</span><span class="p">(</span><span class="n">f</span><span class="p">),</span> <span class="nb">type</span><span class="p">,</span> <span class="s">"input"</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">basepath</span> <span class="o">+</span> <span class="s">"/input/rawfiles/"</span> <span class="o">+</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">basename</span><span class="p">(</span><span class="n">f</span><span class="p">))</span>
+ <span class="k">return</span>
+
+ <span class="k">def</span> <span class="nf">_loadExecutables</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">os</span><span class="o">=</span><span class="s">"linux"</span><span class="p">,</span> <span class="n">arch</span><span class="o">=</span><span class="s">"x86_64"</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> Loads all executables (as specified in the conf) into</span>
+<span class="sd"> the dax, as well as the internal self.executables variable</span>
+<span class="sd"> """</span>
+ <span class="k">for</span> <span class="n">ex</span> <span class="ow">in</span> <span class="n">conf</span><span class="o">.</span><span class="n">valid</span><span class="p">:</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">executables</span><span class="p">[</span><span class="n">ex</span><span class="p">]</span> <span class="o">=</span> <span class="n">Executable</span><span class="p">(</span><span class="n">name</span><span class="o">=</span><span class="n">ex</span><span class="p">,</span> <span class="n">os</span><span class="o">=</span><span class="n">os</span><span class="p">,</span> <span class="n">arch</span><span class="o">=</span><span class="n">arch</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">executables</span><span class="p">[</span><span class="n">ex</span><span class="p">]</span><span class="o">.</span><span class="n">addPFN</span><span class="p">(</span><span class="n">PFN</span><span class="p">(</span><span class="s">"file://"</span> <span class="o">+</span> <span class="bp">self</span><span class="o">.</span><span class="n">config</span><span class="p">[</span><span class="s">"installdir"</span><span class="p">]</span> <span class="o">+</span> <span class="s">"/"</span> <span class="o">+</span> <span class="n">ex</span><span class="p">,</span> <span class="s">"local"</span><span class="p">))</span>
+ <span class="c">#if "cluster" in self.config:</span>
+ <span class="c"># self.executables[ex].addProfile(Profile(Namespace.PEGASUS, "clusters.size", self.config["cluster"]))</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">dax</span><span class="o">.</span><span class="n">addExecutable</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">executables</span><span class="p">[</span><span class="n">ex</span><span class="p">])</span>
+ <span class="k">return</span>
+
+ <span class="k">def</span> <span class="nf">_loadJobInputs</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">job</span><span class="p">,</span> <span class="nb">type</span><span class="p">):</span>
+ <span class="n">inputs</span> <span class="o">=</span> <span class="p">{</span><span class="s">"output.db"</span><span class="p">:</span> <span class="s">"output.db"</span><span class="p">}</span>
+ <span class="k">for</span> <span class="n">i</span><span class="p">,</span><span class="nb">input</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="n">job</span><span class="p">[</span><span class="s">"inputs"</span><span class="p">]):</span>
+ <span class="n">ftype</span> <span class="o">=</span> <span class="n">conf</span><span class="o">.</span><span class="n">valid</span><span class="p">[</span><span class="n">job</span><span class="p">[</span><span class="s">"executable"</span><span class="p">]][</span><span class="s">"inputs"</span><span class="p">][</span><span class="n">i</span><span class="p">]</span>
+ <span class="k">if</span> <span class="nb">input</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">rawFiles</span><span class="p">[</span><span class="nb">type</span><span class="p">]:</span>
+ <span class="n">inputs</span><span class="p">[</span><span class="nb">input</span><span class="p">]</span> <span class="o">=</span> <span class="nb">input</span>
+ <span class="k">return</span> <span class="n">inputs</span>
+
+ <span class="k">def</span> <span class="nf">_createDax</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">loc</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> Loads all jobs into the dax, and then writes the dax</span>
+<span class="sd"> to input/loc/stats.dax</span>
+<span class="sd"> """</span>
+ <span class="n">serial</span> <span class="o">=</span> <span class="p">[]</span>
+ <span class="k">for</span> <span class="nb">type</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">stats</span><span class="p">[</span><span class="s">"workflows"</span><span class="p">]:</span>
+ <span class="k">for</span> <span class="n">job</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">stats</span><span class="p">[</span><span class="s">"workflows"</span><span class="p">][</span><span class="nb">type</span><span class="p">]:</span>
+ <span class="n">jobname</span> <span class="o">=</span> <span class="nb">type</span> <span class="o">+</span> <span class="s">"_"</span> <span class="o">+</span> <span class="n">job</span><span class="p">[</span><span class="s">"name"</span><span class="p">]</span>
+ <span class="n">job</span><span class="p">[</span><span class="s">"arguments"</span><span class="p">][</span><span class="s">"--intable"</span><span class="p">]</span> <span class="o">=</span> <span class="nb">type</span> <span class="o">+</span> <span class="s">"_"</span> <span class="o">+</span> <span class="n">job</span><span class="p">[</span><span class="s">"arguments"</span><span class="p">][</span><span class="s">"--intable"</span><span class="p">]</span> <span class="k">if</span> <span class="n">job</span><span class="p">[</span><span class="s">"arguments"</span><span class="p">][</span><span class="s">"--intable"</span><span class="p">]</span> <span class="o">!=</span> <span class="s">"images"</span> <span class="k">else</span> <span class="n">job</span><span class="p">[</span><span class="s">"arguments"</span><span class="p">][</span><span class="s">"--intable"</span><span class="p">]</span>
+ <span class="n">job</span><span class="p">[</span><span class="s">"arguments"</span><span class="p">][</span><span class="s">"--outtable"</span><span class="p">]</span> <span class="o">=</span> <span class="nb">type</span> <span class="o">+</span> <span class="s">"_"</span> <span class="o">+</span> <span class="n">job</span><span class="p">[</span><span class="s">"arguments"</span><span class="p">][</span><span class="s">"--outtable"</span><span class="p">]</span>
+ <span class="n">job</span><span class="p">[</span><span class="s">"arguments"</span><span class="p">][</span><span class="s">"--db"</span><span class="p">]</span> <span class="o">=</span> <span class="s">"output.db"</span>
+ <span class="n">inputs</span> <span class="o">=</span> <span class="p">{</span><span class="s">"output.db"</span><span class="p">:</span> <span class="s">"output.db"</span><span class="p">}</span>
+ <span class="n">inputs</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_loadJobInputs</span><span class="p">(</span><span class="n">job</span><span class="p">,</span> <span class="nb">type</span><span class="p">)</span>
+ <span class="n">outputs</span> <span class="o">=</span> <span class="p">{}</span>
+ <span class="n">depends</span> <span class="o">=</span> <span class="p">[</span><span class="nb">type</span> <span class="o">+</span> <span class="s">"_"</span> <span class="o">+</span> <span class="n">depend</span> <span class="k">for</span> <span class="n">depend</span> <span class="ow">in</span> <span class="n">job</span><span class="p">[</span><span class="s">"depends"</span><span class="p">]]</span> <span class="k">if</span> <span class="s">"depends"</span> <span class="ow">in</span> <span class="n">job</span> <span class="k">else</span> <span class="n">serial</span>
+ <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">stats</span><span class="p">[</span><span class="s">"workflows"</span><span class="p">][</span><span class="nb">type</span><span class="p">]</span><span class="o">.</span><span class="n">index</span><span class="p">(</span><span class="n">job</span><span class="p">)</span> <span class="o">==</span> <span class="nb">len</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">stats</span><span class="p">[</span><span class="s">"workflows"</span><span class="p">][</span><span class="nb">type</span><span class="p">])</span> <span class="o">-</span> <span class="mi">1</span><span class="p">:</span>
+ <span class="n">serial</span> <span class="o">=</span> <span class="p">[</span><span class="n">jobname</span><span class="p">]</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="n">serial</span> <span class="o">=</span> <span class="p">[]</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_addJob</span><span class="p">(</span><span class="n">jobname</span><span class="p">,</span> <span class="n">job</span><span class="p">[</span><span class="s">"executable"</span><span class="p">],</span> <span class="n">inputs</span><span class="p">,</span> <span class="n">outputs</span><span class="p">,</span> <span class="n">job</span><span class="p">[</span><span class="s">"arguments"</span><span class="p">],</span> <span class="n">depends</span><span class="p">)</span>
+ <span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">basepath</span> <span class="o">+</span> <span class="s">"/"</span> <span class="o">+</span> <span class="n">loc</span> <span class="o">+</span> <span class="s">"/stats.dax"</span><span class="p">,</span> <span class="s">"w"</span><span class="p">)</span> <span class="k">as</span> <span class="n">wh</span><span class="p">:</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">dax</span><span class="o">.</span><span class="n">writeXML</span><span class="p">(</span><span class="n">wh</span><span class="p">)</span>
+ <span class="k">return</span>
+
+ <span class="k">def</span> <span class="nf">_createReplica</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">loc</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> Creates the pegasus configuration replica catalog. input/conf.rc</span>
+<span class="sd"> """</span>
+ <span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">basepath</span> <span class="o">+</span> <span class="s">"/"</span> <span class="o">+</span> <span class="n">loc</span> <span class="o">+</span> <span class="s">"/conf.rc"</span><span class="p">,</span> <span class="s">"w"</span><span class="p">)</span> <span class="k">as</span> <span class="n">wh</span><span class="p">:</span>
+ <span class="n">pegasusrc</span> <span class="o">=</span> <span class="n">textwrap</span><span class="o">.</span><span class="n">dedent</span><span class="p">(</span><span class="s">"""</span><span class="se">\</span>
+<span class="s"> pegasus.catalog.site = XML</span>
+<span class="s"> pegasus.catalog.site.file = </span><span class="si">%s</span><span class="s">/sites.xml</span>
+<span class="s"> </span>
+<span class="s"> pegasus.condor.logs.symlink = false</span>
+<span class="s"> </span>
+<span class="s"> pegasus.transfer.links = true</span>
+<span class="s"> </span>
+<span class="s"> pegasus.data.configuration = sharedfs</span>
+<span class="s"> </span>
+<span class="s"> """</span> <span class="o">%</span> <span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">basepath</span> <span class="o">+</span> <span class="s">"/"</span> <span class="o">+</span> <span class="n">loc</span><span class="p">))</span>
+ <span class="n">wh</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="n">pegasusrc</span><span class="p">)</span>
+ <span class="k">return</span>
+
+ <span class="k">def</span> <span class="nf">_createSites</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">loc</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> Creates the pegasus site catalog. input/sites.xml</span>
+<span class="sd"> """</span>
+ <span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">basepath</span> <span class="o">+</span> <span class="s">"/"</span> <span class="o">+</span> <span class="n">loc</span> <span class="o">+</span> <span class="s">"/sites.xml"</span><span class="p">,</span> <span class="s">"w"</span><span class="p">)</span> <span class="k">as</span> <span class="n">wh</span><span class="p">:</span>
+ <span class="n">sites</span> <span class="o">=</span> <span class="s">"""</span><span class="se">\</span>
+<span class="s"> <sitecatalog xmlns="http://pegasus.isi.edu/schema/sitecatalog" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://pegasus.isi.edu/schema/sitecatalog http://pegasus.isi.edu/schema/sc-4.0.xsd" version="4.0"></span>
+<span class="s"> </span>
+<span class="s"> <site handle="local" arch="x86_64" os="LINUX"></span>
+<span class="s"> <directory type="shared-scratch" path="</span><span class="si">%s</span><span class="s">"></span>
+<span class="s"> <file-server operation="all" url="file://</span><span class="si">%s</span><span class="s">" /></span>
+<span class="s"> </directory></span>
+<span class="s"> <directory type="local-storage" path="</span><span class="si">%s</span><span class="s">"></span>
+<span class="s"> <file-server operation="all" url="file://</span><span class="si">%s</span><span class="s">" /></span>
+<span class="s"> </directory></span>
+<span class="s"> """</span> <span class="o">%</span> <span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">basepath</span> <span class="o">+</span> <span class="s">"/work/stats/"</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">basepath</span> <span class="o">+</span> <span class="s">"/work/stats/"</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">basepath</span> <span class="o">+</span> <span class="s">"/output/"</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">basepath</span> <span class="o">+</span> <span class="s">"/output/"</span><span class="p">)</span>
+ <span class="k">for</span> <span class="n">namespace</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">config</span><span class="p">[</span><span class="s">"profile"</span><span class="p">]:</span>
+ <span class="k">for</span> <span class="n">key</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">config</span><span class="p">[</span><span class="s">"profile"</span><span class="p">][</span><span class="n">namespace</span><span class="p">]:</span>
+ <span class="n">val</span> <span class="o">=</span> <span class="s">":"</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">config</span><span class="p">[</span><span class="s">"profile"</span><span class="p">][</span><span class="n">namespace</span><span class="p">][</span><span class="n">key</span><span class="p">])</span> <span class="k">if</span> <span class="s">"path"</span> <span class="ow">in</span> <span class="n">key</span><span class="o">.</span><span class="n">lower</span><span class="p">()</span> <span class="k">else</span> <span class="bp">self</span><span class="o">.</span><span class="n">config</span><span class="p">[</span><span class="s">"profile"</span><span class="p">][</span><span class="n">namespace</span><span class="p">][</span><span class="n">key</span><span class="p">]</span>
+ <span class="n">sites</span> <span class="o">+=</span> <span class="s">"""</span><span class="se">\n\t</span><span class="s"><profile namespace="</span><span class="si">%s</span><span class="s">" key="</span><span class="si">%s</span><span class="s">"></span><span class="si">%s</span><span class="s"></profile> """</span> <span class="o">%</span> <span class="p">(</span><span class="n">namespace</span><span class="p">,</span> <span class="n">key</span><span class="p">,</span> <span class="n">val</span><span class="p">)</span>
+ <span class="n">sites</span> <span class="o">+=</span> <span class="s">"</site></sitecatalog>"</span>
+ <span class="n">sites</span> <span class="o">=</span> <span class="n">sites</span><span class="o">.</span><span class="n">replace</span><span class="p">(</span><span class="s">"</span><span class="se">\n</span><span class="s">"</span><span class="p">,</span><span class="s">""</span><span class="p">)</span>
+ <span class="n">wh</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s">"</span><span class="se">\n</span><span class="s">"</span><span class="o">.</span><span class="n">join</span><span class="p">([</span><span class="n">line</span> <span class="k">for</span> <span class="n">line</span> <span class="ow">in</span> <span class="n">xml</span><span class="o">.</span><span class="n">dom</span><span class="o">.</span><span class="n">minidom</span><span class="o">.</span><span class="n">parseString</span><span class="p">(</span><span class="n">sites</span><span class="p">)</span><span class="o">.</span><span class="n">toprettyxml</span><span class="p">()</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s">'</span><span class="se">\n</span><span class="s">'</span><span class="p">)</span> <span class="k">if</span> <span class="n">line</span><span class="o">.</span><span class="n">strip</span><span class="p">()]))</span>
+ <span class="k">return</span>
+
+ <span class="k">def</span> <span class="nf">_createSubmit</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">loc</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> Creates the pegasus submit script. submit.sh</span>
+<span class="sd"> """</span>
+ <span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">basepath</span> <span class="o">+</span> <span class="s">"/"</span> <span class="o">+</span> <span class="n">loc</span> <span class="o">+</span> <span class="s">"/submit.sh"</span><span class="p">,</span> <span class="s">"w"</span><span class="p">)</span> <span class="k">as</span> <span class="n">wh</span><span class="p">:</span>
+ <span class="n">submit</span> <span class="o">=</span> <span class="n">textwrap</span><span class="o">.</span><span class="n">dedent</span><span class="p">(</span><span class="s">"""</span><span class="se">\</span>
+<span class="s"> #!/bin/bash</span>
+<span class="s"> </span>
+<span class="s"> plan=`pegasus-plan </span><span class="se">\\</span><span class="s"></span>
+<span class="s"> --conf "</span><span class="si">%s</span><span class="s">" </span><span class="se">\\</span><span class="s"></span>
+<span class="s"> --sites local </span><span class="se">\\</span><span class="s"></span>
+<span class="s"> --dir "</span><span class="si">%s</span><span class="s">" </span><span class="se">\\</span><span class="s"></span>
+<span class="s"> --output-site local </span><span class="se">\\</span><span class="s"></span>
+<span class="s"> --dax "</span><span class="si">%s</span><span class="s">" </span><span class="se">\\</span><span class="s"></span>
+<span class="s"> --randomdir </span><span class="se">\\</span><span class="s">"""</span> <span class="o">%</span> <span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">basepath</span> <span class="o">+</span> <span class="s">"/"</span> <span class="o">+</span> <span class="n">loc</span> <span class="o">+</span> <span class="s">"/conf.rc"</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">basepath</span> <span class="o">+</span> <span class="s">"/work/stats"</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">basepath</span> <span class="o">+</span> <span class="s">"/"</span> <span class="o">+</span> <span class="n">loc</span> <span class="o">+</span> <span class="s">"/stats.dax"</span><span class="p">))</span>
+ <span class="k">if</span> <span class="s">"cluster"</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">config</span><span class="p">:</span>
+ <span class="n">submit</span> <span class="o">+=</span> <span class="s">"""--cluster horizontal </span><span class="se">\\\n</span><span class="s">"""</span>
+ <span class="n">submit</span> <span class="o">+=</span> <span class="n">textwrap</span><span class="o">.</span><span class="n">dedent</span><span class="p">(</span><span class="s">"""</span><span class="se">\</span>
+<span class="s"> --submit`</span>
+<span class="s"> </span>
+<span class="s"> status=`echo "$plan" | grep pegasus-status | tr -s ' '| cut -d ' ' -f 6`</span>
+<span class="s"> echo -e "#!/bin/bash</span>
+<span class="s"> pegasus-status -l $status" > status.sh</span>
+<span class="s"> chmod 744 status.sh</span>
+<span class="s"> </span>
+<span class="s"> remove=`echo "$plan" | grep pegasus-remove | tr -s ' '| cut -d ' ' -f 5`</span>
+<span class="s"> echo -e "#!/bin/bash</span>
+<span class="s"> pegasus-remove $remove" > remove.sh </span>
+<span class="s"> chmod 744 remove.sh</span>
+<span class="s"> </span>
+<span class="s"> echo "$plan"</span>
+<span class="s"> echo "Alternatively, you can use the status & remove scripts in the current directory!"</span>
+<span class="s"> </span>
+<span class="s"> """</span><span class="p">)</span>
+ <span class="n">wh</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="n">submit</span><span class="p">)</span>
+ <span class="n">os</span><span class="o">.</span><span class="n">chmod</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">basepath</span> <span class="o">+</span> <span class="s">"/"</span> <span class="o">+</span> <span class="n">loc</span> <span class="o">+</span> <span class="s">"/submit.sh"</span><span class="p">,</span> <span class="mo">0755</span><span class="p">)</span>
+ <span class="k">return</span>
+
+<div class="viewcode-block" id="Statistics.create"><a class="viewcode-back" href="../../workflowstats.html#htpia.workflow.Statistics.create">[docs]</a> <span class="k">def</span> <span class="nf">create</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> Creates a new pegasus submission directory based on the current timestamp,</span>
+<span class="sd"> and populates it with all required information to submit a pegasus job.</span>
+<span class="sd"> """</span>
+ <span class="n">loc</span> <span class="o">=</span> <span class="s">"/input/stats/"</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_createSetup</span><span class="p">()</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_copyFiles</span><span class="p">()</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_loadFiles</span><span class="p">(</span><span class="n">loc</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_loadExecutables</span><span class="p">()</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_createDax</span><span class="p">(</span><span class="n">loc</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_createReplica</span><span class="p">(</span><span class="n">loc</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_createSites</span><span class="p">(</span><span class="n">loc</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_createSubmit</span><span class="p">(</span><span class="n">loc</span><span class="p">)</span>
+ <span class="k">return</span>
+
+
+
+
+ </div></div>
+<div class="viewcode-block" id="ImageProcessor"><a class="viewcode-back" href="../../workflowimage.html#htpia.workflow.ImageProcessor">[docs]</a><span class="k">class</span> <span class="nc">ImageProcessor</span><span class="p">(</span><span class="n">Workflow</span><span class="p">):</span>
+
+ <span class="sd">"""</span>
+<span class="sd"> A class specifically for image processing workflow</span>
+<span class="sd"> validation and submission.</span>
+<span class="sd"> """</span>
+
+ <span class="k">def</span> <span class="nf">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">jobhome</span><span class="p">,</span> <span class="n">basename</span> <span class="o">=</span> <span class="bp">None</span><span class="p">,</span> <span class="n">validOnly</span> <span class="o">=</span> <span class="bp">False</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> :param jobhome: The base directory for job submission.</span>
+<span class="sd"> :type jobhome: str</span>
+<span class="sd"> </span>
+<span class="sd"> Creates a Workflow class based on the input directory. Loads and validates all input files,</span>
+<span class="sd"> and quits out if something doesn't exist or is defined innapropriately.</span>
+<span class="sd"> """</span>
+ <span class="nb">super</span><span class="p">(</span><span class="n">ImageProcessor</span><span class="p">,</span> <span class="bp">self</span><span class="p">)</span><span class="o">.</span><span class="n">__init__</span><span class="p">(</span><span class="n">jobhome</span><span class="p">,</span> <span class="n">basename</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">validOnly</span> <span class="o">=</span> <span class="n">validOnly</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">workfile</span> <span class="o">=</span> <span class="n">jobhome</span> <span class="o">+</span> <span class="s">"/input/"</span> <span class="o">+</span> <span class="n">conf</span><span class="o">.</span><span class="n">workflowFile</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">metafile</span> <span class="o">=</span> <span class="n">jobhome</span> <span class="o">+</span> <span class="s">"/input/"</span> <span class="o">+</span> <span class="n">conf</span><span class="o">.</span><span class="n">dbFile</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">configfile</span> <span class="o">=</span> <span class="n">jobhome</span> <span class="o">+</span> <span class="s">"/input/"</span> <span class="o">+</span> <span class="n">conf</span><span class="o">.</span><span class="n">configFile</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_loadInputFiles</span><span class="p">()</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">exdax</span> <span class="o">=</span> <span class="n">ADAG</span><span class="p">(</span><span class="s">"extract-"</span> <span class="o">+</span> <span class="bp">self</span><span class="o">.</span><span class="n">jobname</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">jobs</span><span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">exdax</span><span class="p">]</span> <span class="o">=</span> <span class="p">{}</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">files</span><span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">exdax</span><span class="p">]</span> <span class="o">=</span> <span class="p">{}</span>
+ <span class="k">return</span>
+
+ <span class="k">def</span> <span class="nf">_loadInputFiles</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> Loads the input files into the appropriate variables</span>
+<span class="sd"> """</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">validator</span> <span class="o">=</span> <span class="n">htpia</span><span class="o">.</span><span class="n">validator</span><span class="o">.</span><span class="n">ImageProcessor</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">workfile</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">configfile</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">metafile</span><span class="p">)</span>
+ <span class="k">if</span> <span class="ow">not</span> <span class="bp">self</span><span class="o">.</span><span class="n">validator</span><span class="o">.</span><span class="n">isValid</span><span class="p">()</span> <span class="ow">or</span> <span class="bp">self</span><span class="o">.</span><span class="n">validOnly</span><span class="p">:</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">validator</span><span class="o">.</span><span class="n">printErrors</span><span class="p">()</span>
+ <span class="n">sys</span><span class="o">.</span><span class="n">exit</span><span class="p">()</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">workflow</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">validator</span><span class="o">.</span><span class="n">workflow</span><span class="o">.</span><span class="n">data</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">metadata</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">validator</span><span class="o">.</span><span class="n">db</span><span class="o">.</span><span class="n">conn</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">config</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">validator</span><span class="o">.</span><span class="n">config</span><span class="o">.</span><span class="n">data</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">rawFiles</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">validator</span><span class="o">.</span><span class="n">workflow</span><span class="o">.</span><span class="n">rawFiles</span>
+ <span class="k">return</span>
+
+ <span class="k">def</span> <span class="nf">_getImageTypes</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> Convenience function to get all image types from the database.</span>
+<span class="sd"> """</span>
+ <span class="k">return</span> <span class="p">[</span><span class="n">x</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="k">for</span> <span class="n">x</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">metadata</span><span class="o">.</span><span class="n">execute</span><span class="p">(</span><span class="s">"select distinct imtype from images"</span><span class="p">)]</span>
+
+ <span class="k">def</span> <span class="nf">_copyFiles</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> Copies all input files to the correct location.</span>
+<span class="sd"> """</span>
+ <span class="k">if</span> <span class="ow">not</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">exists</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">basepath</span> <span class="o">+</span> <span class="s">"/input/imgproc"</span><span class="p">):</span>
+ <span class="n">os</span><span class="o">.</span><span class="n">makedirs</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">basepath</span> <span class="o">+</span> <span class="s">"/input/imgproc"</span><span class="p">)</span>
+ <span class="n">shutil</span><span class="o">.</span><span class="n">copyfile</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">workfile</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">basepath</span> <span class="o">+</span> <span class="s">"/input/templates/"</span> <span class="o">+</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">basename</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">workfile</span><span class="p">))</span>
+ <span class="n">shutil</span><span class="o">.</span><span class="n">copyfile</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">configfile</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">basepath</span> <span class="o">+</span> <span class="s">"/input/templates/"</span> <span class="o">+</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">basename</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">configfile</span><span class="p">))</span>
+ <span class="n">shutil</span><span class="o">.</span><span class="n">copyfile</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">metafile</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">basepath</span> <span class="o">+</span> <span class="s">"/output/output.db"</span><span class="p">)</span>
+ <span class="k">for</span> <span class="nb">type</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">rawFiles</span><span class="p">:</span>
+ <span class="k">for</span> <span class="nb">input</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">rawFiles</span><span class="p">[</span><span class="nb">type</span><span class="p">]:</span>
+ <span class="n">shutil</span><span class="o">.</span><span class="n">copyfile</span><span class="p">(</span><span class="nb">input</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">basepath</span> <span class="o">+</span> <span class="s">"/input/rawfiles/"</span> <span class="o">+</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">basename</span><span class="p">(</span><span class="nb">input</span><span class="p">))</span>
+ <span class="k">return</span>
+
+ <span class="k">def</span> <span class="nf">_loadFiles</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">loc</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> Loads all files (input and output) into the dax and the self.files variable</span>
+<span class="sd"> """</span>
+ <span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">basepath</span> <span class="o">+</span> <span class="s">"/input/rawfiles/extract.json"</span><span class="p">,</span> <span class="s">"w"</span><span class="p">)</span> <span class="k">as</span> <span class="n">wh</span><span class="p">:</span>
+ <span class="n">json</span><span class="o">.</span><span class="n">dump</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">workflow</span><span class="p">[</span><span class="s">"extract"</span><span class="p">],</span> <span class="n">wh</span><span class="p">)</span>
+ <span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">basepath</span> <span class="o">+</span> <span class="s">"/"</span> <span class="o">+</span> <span class="n">loc</span> <span class="o">+</span> <span class="s">"/map.rc"</span><span class="p">,</span> <span class="s">"w"</span><span class="p">)</span> <span class="k">as</span> <span class="n">wh</span><span class="p">:</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">exInput</span> <span class="o">=</span> <span class="p">{</span><span class="s">"db"</span><span class="p">:</span> <span class="s">"img.db"</span><span class="p">,</span> <span class="s">"extract.json"</span><span class="p">:</span> <span class="s">"extract.json"</span><span class="p">}</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">files</span><span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">dax</span><span class="p">]</span> <span class="o">=</span> <span class="p">{}</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">files</span><span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">exdax</span><span class="p">]</span> <span class="o">=</span> <span class="p">{}</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">files</span><span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">exdax</span><span class="p">][</span><span class="s">"all"</span><span class="p">]</span> <span class="o">=</span> <span class="p">{</span><span class="s">"input"</span><span class="p">:</span> <span class="p">{},</span> <span class="s">"output"</span><span class="p">:</span> <span class="p">{}}</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">files</span><span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">dax</span><span class="p">][</span><span class="s">"raw"</span><span class="p">]</span> <span class="o">=</span> <span class="p">{</span><span class="s">"input"</span><span class="p">:</span> <span class="p">{},</span> <span class="s">"output"</span><span class="p">:</span> <span class="p">{}}</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_addFile</span><span class="p">(</span><span class="s">"img.db"</span><span class="p">,</span> <span class="s">"raw"</span><span class="p">,</span> <span class="s">"input"</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">basepath</span> <span class="o">+</span> <span class="s">"/output/output.db"</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_addFile</span><span class="p">(</span><span class="s">"img.db"</span><span class="p">,</span> <span class="s">"all"</span><span class="p">,</span> <span class="s">"input"</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">basepath</span> <span class="o">+</span> <span class="s">"/output/output.db"</span><span class="p">,</span> <span class="n">dax</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">exdax</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_addFile</span><span class="p">(</span><span class="s">"img.log"</span><span class="p">,</span> <span class="s">"raw"</span><span class="p">,</span> <span class="s">"output"</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">basepath</span> <span class="o">+</span> <span class="s">"/output/imgproc.log"</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_addFile</span><span class="p">(</span><span class="s">"extract.json"</span><span class="p">,</span> <span class="s">"raw"</span><span class="p">,</span> <span class="s">"input"</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">basepath</span> <span class="o">+</span> <span class="s">"/input/rawfiles/extract.json"</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_addFile</span><span class="p">(</span><span class="s">"extract.json"</span><span class="p">,</span> <span class="s">"all"</span><span class="p">,</span> <span class="s">"input"</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">basepath</span> <span class="o">+</span> <span class="s">"/input/rawfiles/extract.json"</span><span class="p">,</span> <span class="n">dax</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">exdax</span><span class="p">)</span>
+ <span class="k">for</span> <span class="nb">type</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">workflow</span><span class="p">[</span><span class="s">"workflows"</span><span class="p">]:</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">files</span><span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">dax</span><span class="p">][</span><span class="nb">type</span><span class="p">]</span> <span class="o">=</span> <span class="p">{</span><span class="s">"input"</span><span class="p">:</span> <span class="p">{},</span> <span class="s">"output"</span><span class="p">:</span> <span class="p">{}}</span>
+ <span class="k">for</span> <span class="nb">input</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">rawFiles</span><span class="p">[</span><span class="nb">type</span><span class="p">]:</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_addFile</span><span class="p">(</span><span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">basename</span><span class="p">(</span><span class="nb">input</span><span class="p">),</span> <span class="nb">type</span><span class="p">,</span> <span class="s">"input"</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">basepath</span> <span class="o">+</span> <span class="s">"/input/rawfiles/"</span> <span class="o">+</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">basename</span><span class="p">(</span><span class="nb">input</span><span class="p">))</span>
+ <span class="n">wh</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s">"img.log file://"</span> <span class="o">+</span> <span class="bp">self</span><span class="o">.</span><span class="n">basepath</span> <span class="o">+</span> <span class="s">"/output/imgproc.log pool=</span><span class="se">\"</span><span class="s">local</span><span class="se">\"\n</span><span class="s">"</span><span class="p">)</span>
+ <span class="n">inputImages</span> <span class="o">=</span> <span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">workflow</span><span class="p">[</span><span class="s">"workflows"</span><span class="p">][</span><span class="nb">type</span><span class="p">][</span><span class="mi">0</span><span class="p">][</span><span class="s">"inputs"</span><span class="p">][</span><span class="n">i</span><span class="p">]</span> <span class="k">for</span> <span class="n">i</span><span class="p">,</span><span class="n">x</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="n">conf</span><span class="o">.</span><span class="n">valid</span><span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">workflow</span><span class="p">[</span><span class="s">"workflows"</span><span class="p">][</span><span class="nb">type</span><span class="p">][</span><span class="mi">0</span><span class="p">][</span><span class="s">"executable"</span><span class="p">]][</span><span class="s">"inputs"</span><span class="p">])</span> <span class="k">if</span> <span class="n">x</span> <span class="o">==</span> <span class="s">"image"</span><span class="p">]</span>
+ <span class="n">outputImages</span> <span class="o">=</span> <span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">workflow</span><span class="p">[</span><span class="s">"workflows"</span><span class="p">][</span><span class="nb">type</span><span class="p">][</span><span class="n">z</span><span class="p">][</span><span class="s">"outputs"</span><span class="p">][</span><span class="n">i</span><span class="p">]</span> <span class="k">for</span> <span class="n">z</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="mi">0</span><span class="p">,</span> <span class="nb">len</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">workflow</span><span class="p">[</span><span class="s">"workflows"</span><span class="p">][</span><span class="nb">type</span><span class="p">]))</span> <span class="k">for</span> <span class="n">i</span><span class="p">,</span><span class="n">x</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="n">conf</span><span class="o">.</span><span class="n">valid</span><span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">workflow</span><span class="p">[</span><span class="s">"workflows"</span><span class="p">][</span><span class="nb">type</span><span class="p">][</span><span class="n">z</span><span class="p">][</span><span class="s">"executable"</span><span class="p">]][</span><span class="s">"outputs"</span><span class="p">])</span> <span class="k">if</span> <span class="n">x</span> <span class="o">==</span> <span class="s">"image"</span><span class="p">]</span>
+ <span class="n">outputFiles</span> <span class="o">=</span> <span class="nb">dict</span><span class="p">((</span><span class="bp">self</span><span class="o">.</span><span class="n">workflow</span><span class="p">[</span><span class="s">"workflows"</span><span class="p">][</span><span class="nb">type</span><span class="p">][</span><span class="n">z</span><span class="p">][</span><span class="s">"outputs"</span><span class="p">][</span><span class="n">i</span><span class="p">],</span> <span class="n">conf</span><span class="o">.</span><span class="n">fileExtensions</span><span class="p">[</span><span class="n">conf</span><span class="o">.</span><span class="n">valid</span><span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">workflow</span><span class="p">[</span><span class="s">"workflows"</span><span class="p">][</span><span class="nb">type</span><span class="p">][</span><span class="n">z</span><span class="p">][</span><span class="s">"executable"</span><span class="p">]][</span><span class="s">"outputs"</span><span class="p">][</span><span class="n">i</span><span class="p">]])</span> <span class="k">for</span> <span class="n">z</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="mi">0</span><span class="p">,</span> <span class="nb">len</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">workflow</span><span class="p">[</span><span class="s">"workflows"</span><span class="p">][</span><span class="nb">type</span><span class="p">]))</span> <span class="k">for</span> <span class="n">i</span><span class="p">,</span><span class="n">x</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="n">conf</span><span class="o">.</span><span class="n">valid</span><span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">workflow</span><span class="p">[</span><span class="s">"workflows"</span><span class="p">][</span><span class="nb">type</span><span class="p">][</span><span class="n">z</span><span class="p">][</span><span class="s">"executable"</span><span class="p">]][</span><span class="s">"outputs"</span><span class="p">])</span> <span class="k">if</span> <span class="n">x</span> <span class="o">!=</span> <span class="s">"image"</span> <span class="ow">and</span> <span class="n">x</span> <span class="o">!=</span> <span class="s">"none"</span> <span class="ow">and</span> <span class="nb">len</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">workflow</span><span class="p">[</span><span class="s">"workflows"</span><span class="p">][</span><span class="nb">type</span><span class="p">][</span><span class="n">z</span><span class="p">][</span><span class="s">"outputs"</span><span class="p">])</span> <span class="o">></span> <span class="n">i</span><span class="p">)</span>
+ <span class="k">for</span> <span class="n">row</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">metadata</span><span class="o">.</span><span class="n">execute</span><span class="p">(</span><span class="s">"select pegasusid, experiment, id, date, imgname, path from images where imtype=?"</span><span class="p">,</span> <span class="p">(</span><span class="nb">type</span><span class="p">,)):</span>
+ <span class="n">realname</span> <span class="o">=</span> <span class="n">row</span><span class="p">[</span><span class="s">"path"</span><span class="p">]</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s">"/"</span><span class="p">)[</span><span class="o">-</span><span class="mi">1</span><span class="p">]</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s">"."</span><span class="p">)[</span><span class="mi">0</span><span class="p">]</span>
+ <span class="c">#derivedPath = row["experiment"].replace(" ","%20") + "/" + row["id"].replace(" ","%20") + "/" + row["date"].replace(" ","%20") + "/" + type + "/" + row["imgname"].replace(" ","%20") + "/"</span>
+ <span class="n">derivedPath</span> <span class="o">=</span> <span class="n">row</span><span class="p">[</span><span class="s">"experiment"</span><span class="p">]</span><span class="o">.</span><span class="n">replace</span><span class="p">(</span><span class="s">" "</span><span class="p">,</span><span class="s">""</span><span class="p">)</span> <span class="o">+</span> <span class="s">"/"</span> <span class="o">+</span> <span class="n">row</span><span class="p">[</span><span class="s">"id"</span><span class="p">]</span><span class="o">.</span><span class="n">replace</span><span class="p">(</span><span class="s">" "</span><span class="p">,</span><span class="s">""</span><span class="p">)</span> <span class="o">+</span> <span class="s">"/"</span> <span class="o">+</span> <span class="n">row</span><span class="p">[</span><span class="s">"date"</span><span class="p">]</span><span class="o">.</span><span class="n">replace</span><span class="p">(</span><span class="s">" "</span><span class="p">,</span><span class="s">""</span><span class="p">)</span> <span class="o">+</span> <span class="s">"/"</span> <span class="o">+</span> <span class="nb">type</span> <span class="o">+</span> <span class="s">"/"</span> <span class="o">+</span> <span class="n">row</span><span class="p">[</span><span class="s">"imgname"</span><span class="p">]</span><span class="o">.</span><span class="n">replace</span><span class="p">(</span><span class="s">" "</span><span class="p">,</span><span class="s">""</span><span class="p">)</span> <span class="o">+</span> <span class="s">"/"</span>
+ <span class="k">for</span> <span class="nb">input</span> <span class="ow">in</span> <span class="n">inputImages</span><span class="p">:</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_addFile</span><span class="p">(</span><span class="n">derivedPath</span> <span class="o">+</span> <span class="n">row</span><span class="p">[</span><span class="s">"pegasusid"</span><span class="p">]</span> <span class="o">+</span> <span class="s">"_"</span> <span class="o">+</span> <span class="nb">input</span> <span class="o">+</span> <span class="s">"."</span> <span class="o">+</span> <span class="n">row</span><span class="p">[</span><span class="s">"path"</span><span class="p">]</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s">"."</span><span class="p">)[</span><span class="mi">1</span><span class="p">],</span> <span class="nb">type</span><span class="p">,</span> <span class="s">"input"</span><span class="p">,</span> <span class="n">row</span><span class="p">[</span><span class="s">"path"</span><span class="p">])</span>
+ <span class="k">for</span> <span class="n">output</span> <span class="ow">in</span> <span class="n">outputImages</span><span class="p">:</span>
+ <span class="k">if</span> <span class="n">output</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">workflow</span><span class="p">[</span><span class="s">"extract"</span><span class="p">][</span><span class="s">"workflows"</span><span class="p">][</span><span class="nb">type</span><span class="p">][</span><span class="s">"inputs"</span><span class="p">]:</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">exInput</span><span class="p">[</span><span class="n">derivedPath</span> <span class="o">+</span> <span class="n">row</span><span class="p">[</span><span class="s">"pegasusid"</span><span class="p">]</span> <span class="o">+</span> <span class="s">"_"</span> <span class="o">+</span> <span class="n">output</span> <span class="o">+</span> <span class="s">".png"</span><span class="p">]</span> <span class="o">=</span> <span class="n">derivedPath</span> <span class="o">+</span> <span class="n">row</span><span class="p">[</span><span class="s">"pegasusid"</span><span class="p">]</span> <span class="o">+</span> <span class="s">"_"</span> <span class="o">+</span> <span class="n">output</span> <span class="o">+</span> <span class="s">".png"</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_addFile</span><span class="p">(</span><span class="n">derivedPath</span> <span class="o">+</span> <span class="n">row</span><span class="p">[</span><span class="s">"pegasusid"</span><span class="p">]</span> <span class="o">+</span> <span class="s">"_"</span> <span class="o">+</span> <span class="n">output</span> <span class="o">+</span> <span class="s">".png"</span><span class="p">,</span> <span class="s">"all"</span><span class="p">,</span> <span class="s">"input"</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">basepath</span> <span class="o">+</span> <span class="s">"/output/"</span> <span class="o">+</span> <span class="n">derivedPath</span> <span class="o">+</span> <span class="n">row</span><span class="p">[</span><span class="s">"pegasusid"</span><span class="p">]</span> <span class="o">+</span> <span class="s">"_"</span> <span class="o">+</span> <span class="n">output</span> <span class="o">+</span> <span class="s">".png"</span><span class="p">,</span> <span class="n">dax</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">exdax</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_addFile</span><span class="p">(</span><span class="n">derivedPath</span> <span class="o">+</span> <span class="n">row</span><span class="p">[</span><span class="s">"pegasusid"</span><span class="p">]</span> <span class="o">+</span> <span class="s">"_"</span> <span class="o">+</span> <span class="n">output</span> <span class="o">+</span> <span class="s">".png"</span><span class="p">,</span> <span class="nb">type</span><span class="p">,</span> <span class="s">"output"</span><span class="p">)</span>
+ <span class="n">wh</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="n">derivedPath</span> <span class="o">+</span> <span class="n">row</span><span class="p">[</span><span class="s">"pegasusid"</span><span class="p">]</span> <span class="o">+</span> <span class="s">"_"</span> <span class="o">+</span> <span class="n">output</span> <span class="o">+</span> <span class="s">".png file://"</span> <span class="o">+</span> <span class="bp">self</span><span class="o">.</span><span class="n">basepath</span> <span class="o">+</span> <span class="s">"/output/"</span> <span class="o">+</span> <span class="n">derivedPath</span> <span class="o">+</span> <span class="n">row</span><span class="p">[</span><span class="s">"pegasusid"</span><span class="p">]</span><span class="o">.</span><span class="n">replace</span><span class="p">(</span><span class="s">" "</span><span class="p">,</span><span class="s">"%20"</span><span class="p">)</span> <span class="o">+</span> <span class="s">"_"</span> <span class="o">+</span> <span class="n">output</span> <span class="o">+</span> <span class="s">".png pool=</span><span class="se">\"</span><span class="s">local</span><span class="se">\"\n</span><span class="s">"</span><span class="p">)</span>
+ <span class="k">for</span> <span class="n">output</span> <span class="ow">in</span> <span class="n">outputFiles</span><span class="p">:</span>
+ <span class="n">outname</span> <span class="o">=</span> <span class="n">output</span> <span class="o">+</span> <span class="n">outputFiles</span><span class="p">[</span><span class="n">output</span><span class="p">]</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_addFile</span><span class="p">(</span><span class="n">derivedPath</span> <span class="o">+</span> <span class="n">row</span><span class="p">[</span><span class="s">"pegasusid"</span><span class="p">]</span> <span class="o">+</span> <span class="s">"_"</span> <span class="o">+</span> <span class="n">outname</span><span class="p">,</span> <span class="nb">type</span><span class="p">,</span> <span class="s">"output"</span><span class="p">)</span>
+ <span class="n">wh</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="n">derivedPath</span> <span class="o">+</span> <span class="n">row</span><span class="p">[</span><span class="s">"pegasusid"</span><span class="p">]</span> <span class="o">+</span> <span class="s">"_"</span> <span class="o">+</span> <span class="n">outname</span> <span class="o">+</span> <span class="s">" file://"</span> <span class="o">+</span> <span class="bp">self</span><span class="o">.</span><span class="n">basepath</span> <span class="o">+</span> <span class="s">"/output/"</span> <span class="o">+</span> <span class="n">derivedPath</span><span class="o">.</span><span class="n">replace</span><span class="p">(</span><span class="s">"_"</span><span class="p">,</span><span class="s">"%20"</span><span class="p">)</span> <span class="o">+</span> <span class="n">outname</span> <span class="o">+</span> <span class="s">" pool=</span><span class="se">\"</span><span class="s">local</span><span class="se">\"\n</span><span class="s">"</span><span class="p">)</span>
+ <span class="k">return</span>
+
+ <span class="k">def</span> <span class="nf">_loadNotify</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+ <span class="k">if</span> <span class="s">"email"</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">config</span><span class="p">:</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">dax</span><span class="o">.</span><span class="n">invoke</span><span class="p">(</span><span class="s">"at_end"</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">basepath</span> <span class="o">+</span> <span class="s">"/input/imgproc/notify.sh"</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">exdax</span><span class="o">.</span><span class="n">invoke</span><span class="p">(</span><span class="s">"at_end"</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">basepath</span> <span class="o">+</span> <span class="s">"/input/imgproc/notify.sh"</span><span class="p">)</span>
+ <span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">basepath</span> <span class="o">+</span> <span class="s">"/input/imgproc/notify.sh"</span><span class="p">,</span> <span class="s">"w"</span><span class="p">)</span> <span class="k">as</span> <span class="n">wh</span><span class="p">:</span>
+ <span class="n">notify</span> <span class="o">=</span> <span class="n">textwrap</span><span class="o">.</span><span class="n">dedent</span><span class="p">(</span><span class="s">"""</span><span class="se">\</span>
+<span class="s"> #!/bin/bash</span>
+<span class="s"> $PEGASUS_HOME/notification/email -t </span><span class="si">%s</span><span class="s"></span>
+<span class="s"> """</span> <span class="o">%</span> <span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">config</span><span class="p">[</span><span class="s">"email"</span><span class="p">],))</span>
+ <span class="n">wh</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="n">notify</span><span class="p">)</span>
+ <span class="n">os</span><span class="o">.</span><span class="n">chmod</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">basepath</span> <span class="o">+</span> <span class="s">"/input/imgproc/notify.sh"</span><span class="p">,</span> <span class="mo">0755</span><span class="p">)</span>
+ <span class="k">return</span>
+
+ <span class="k">def</span> <span class="nf">_loadExecutables</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">os</span><span class="o">=</span><span class="s">"linux"</span><span class="p">,</span> <span class="n">arch</span><span class="o">=</span><span class="s">"x86_64"</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> Loads all executables (as specified in the conf) into</span>
+<span class="sd"> the dax, as well as the internal self.executables variable</span>
+<span class="sd"> """</span>
+ <span class="k">for</span> <span class="n">ex</span> <span class="ow">in</span> <span class="n">conf</span><span class="o">.</span><span class="n">valid</span><span class="p">:</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">executables</span><span class="p">[</span><span class="n">ex</span><span class="p">]</span> <span class="o">=</span> <span class="n">Executable</span><span class="p">(</span><span class="n">name</span><span class="o">=</span><span class="n">ex</span><span class="p">,</span> <span class="n">os</span><span class="o">=</span><span class="n">os</span><span class="p">,</span> <span class="n">arch</span><span class="o">=</span><span class="n">arch</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">executables</span><span class="p">[</span><span class="n">ex</span><span class="p">]</span><span class="o">.</span><span class="n">addPFN</span><span class="p">(</span><span class="n">PFN</span><span class="p">(</span><span class="s">"file://"</span> <span class="o">+</span> <span class="bp">self</span><span class="o">.</span><span class="n">config</span><span class="p">[</span><span class="s">"installdir"</span><span class="p">]</span> <span class="o">+</span> <span class="s">"/"</span> <span class="o">+</span> <span class="n">ex</span><span class="p">,</span> <span class="s">"local"</span><span class="p">))</span>
+ <span class="c">#if "cluster" in self.config:</span>
+ <span class="c"># val = int(self.config["cluster"] * conf.valid[ex]["weight"]) if "weight" in conf.valid[ex] else self.config["cluster"]</span>
+ <span class="c"># self.executables[ex].addProfile(Profile(Namespace.PEGASUS, "clusters.size", val))</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">dax</span><span class="o">.</span><span class="n">addExecutable</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">executables</span><span class="p">[</span><span class="n">ex</span><span class="p">])</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">exdax</span><span class="o">.</span><span class="n">addExecutable</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">executables</span><span class="p">[</span><span class="n">ex</span><span class="p">])</span>
+ <span class="k">return</span>
+
+ <span class="k">def</span> <span class="nf">_loadJobInputs</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">job</span><span class="p">,</span> <span class="nb">type</span><span class="p">,</span> <span class="n">basename</span><span class="p">,</span> <span class="n">extension</span><span class="p">,</span> <span class="n">save</span> <span class="o">=</span> <span class="bp">False</span><span class="p">):</span>
+ <span class="n">inputs</span> <span class="o">=</span> <span class="p">{}</span>
+ <span class="k">for</span> <span class="n">i</span><span class="p">,</span><span class="nb">input</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="n">job</span><span class="p">[</span><span class="s">"inputs"</span><span class="p">]):</span>
+ <span class="n">ftype</span> <span class="o">=</span> <span class="n">conf</span><span class="o">.</span><span class="n">valid</span><span class="p">[</span><span class="n">job</span><span class="p">[</span><span class="s">"executable"</span><span class="p">]][</span><span class="s">"inputs"</span><span class="p">][</span><span class="n">i</span><span class="p">]</span>
+ <span class="k">if</span> <span class="nb">input</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">rawFiles</span><span class="p">[</span><span class="nb">type</span><span class="p">]:</span>
+ <span class="n">inputs</span><span class="p">[</span><span class="nb">input</span><span class="p">]</span> <span class="o">=</span> <span class="p">{</span><span class="s">"file"</span><span class="p">:</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">basename</span><span class="p">(</span><span class="nb">input</span><span class="p">),</span> <span class="s">"transfer"</span><span class="p">:</span> <span class="n">save</span><span class="p">}</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="n">ex</span> <span class="o">=</span> <span class="n">extension</span> <span class="k">if</span> <span class="n">job</span><span class="p">[</span><span class="s">"name"</span><span class="p">]</span> <span class="o">==</span> <span class="bp">self</span><span class="o">.</span><span class="n">workflow</span><span class="p">[</span><span class="s">"workflows"</span><span class="p">][</span><span class="nb">type</span><span class="p">][</span><span class="mi">0</span><span class="p">][</span><span class="s">"name"</span><span class="p">]</span> <span class="k">else</span> <span class="n">conf</span><span class="o">.</span><span class="n">fileExtensions</span><span class="p">[</span><span class="n">ftype</span><span class="p">]</span>
+ <span class="n">inputs</span><span class="p">[</span><span class="nb">input</span><span class="p">]</span> <span class="o">=</span> <span class="p">{</span><span class="s">"file"</span><span class="p">:</span> <span class="n">basename</span> <span class="o">+</span> <span class="s">"_"</span> <span class="o">+</span> <span class="nb">input</span> <span class="o">+</span> <span class="n">ex</span><span class="p">,</span> <span class="s">"transfer"</span><span class="p">:</span> <span class="n">save</span><span class="p">}</span>
+ <span class="k">return</span> <span class="n">inputs</span>
+
+ <span class="k">def</span> <span class="nf">_loadJobOutputs</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">job</span><span class="p">,</span> <span class="nb">type</span><span class="p">,</span> <span class="n">basename</span><span class="p">,</span> <span class="n">save</span><span class="p">):</span>
+ <span class="n">outputs</span> <span class="o">=</span> <span class="p">{}</span>
+ <span class="k">for</span> <span class="n">i</span><span class="p">,</span><span class="n">output</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="n">job</span><span class="p">[</span><span class="s">"outputs"</span><span class="p">]):</span>
+ <span class="k">if</span> <span class="n">output</span> <span class="o">!=</span> <span class="s">"none"</span><span class="p">:</span>
+ <span class="n">outputs</span><span class="p">[</span><span class="n">output</span><span class="p">]</span> <span class="o">=</span> <span class="p">{</span><span class="s">"file"</span><span class="p">:</span> <span class="n">basename</span> <span class="o">+</span> <span class="s">"_"</span> <span class="o">+</span> <span class="n">output</span> <span class="o">+</span> <span class="n">conf</span><span class="o">.</span><span class="n">fileExtensions</span><span class="p">[</span><span class="n">conf</span><span class="o">.</span><span class="n">valid</span><span class="p">[</span><span class="n">job</span><span class="p">[</span><span class="s">"executable"</span><span class="p">]][</span><span class="s">"outputs"</span><span class="p">][</span><span class="n">i</span><span class="p">]],</span> <span class="s">"transfer"</span><span class="p">:</span> <span class="n">save</span><span class="p">}</span>
+ <span class="k">return</span> <span class="n">outputs</span>
+
+ <span class="c">#def _loadJobOutputs(self, job, type, basename):</span>
+ <span class="c"># return dict((output, basename + "_" + output + conf.fileExtensions[conf.valid[job["executable"]]["outputs"][i]]) for i,output in enumerate(job["outputs"]) if output != "none")</span>
+
+ <span class="k">def</span> <span class="nf">_createDax</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">loc</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> Loads all jobs into the dax, and then writes the dax</span>
+<span class="sd"> to input/workflow.dax</span>
+<span class="sd"> """</span>
+ <span class="n">exDep</span> <span class="o">=</span> <span class="p">{}</span>
+ <span class="n">exInput</span> <span class="o">=</span> <span class="p">{}</span>
+ <span class="n">clusternum</span> <span class="o">=</span> <span class="p">{}</span>
+ <span class="n">meancluster</span> <span class="o">=</span> <span class="p">{}</span>
+
+ <span class="n">save</span> <span class="o">=</span> <span class="bp">True</span> <span class="k">if</span> <span class="s">"save-steps"</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">workflow</span><span class="p">[</span><span class="s">"options"</span><span class="p">]</span> <span class="k">else</span> <span class="bp">False</span>
+ <span class="k">for</span> <span class="nb">type</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">workflow</span><span class="p">[</span><span class="s">"workflows"</span><span class="p">]:</span>
+ <span class="n">exDep</span><span class="p">[</span><span class="nb">type</span><span class="p">]</span> <span class="o">=</span> <span class="p">[[]]</span>
+ <span class="n">exInput</span><span class="p">[</span><span class="nb">type</span><span class="p">]</span> <span class="o">=</span> <span class="p">[{}]</span>
+ <span class="n">jobnum</span> <span class="o">=</span> <span class="o">-</span><span class="mi">1</span>
+ <span class="n">clusternum</span><span class="p">[</span><span class="nb">type</span><span class="p">]</span> <span class="o">=</span> <span class="mi">0</span>
+ <span class="n">meancluster</span><span class="p">[</span><span class="nb">type</span><span class="p">]</span> <span class="o">=</span> <span class="mi">0</span>
+ <span class="n">exNames</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">workflow</span><span class="p">[</span><span class="s">"extract"</span><span class="p">][</span><span class="s">"workflows"</span><span class="p">][</span><span class="nb">type</span><span class="p">][</span><span class="s">"depends"</span><span class="p">]</span>
+ <span class="k">for</span> <span class="n">infile</span> <span class="ow">in</span> <span class="p">[</span><span class="n">x</span> <span class="k">for</span> <span class="n">x</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">files</span><span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">dax</span><span class="p">][</span><span class="nb">type</span><span class="p">][</span><span class="s">"input"</span><span class="p">]</span> <span class="k">if</span> <span class="s">"."</span> <span class="o">+</span> <span class="n">x</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s">"."</span><span class="p">)[</span><span class="mi">1</span><span class="p">]</span> <span class="ow">in</span> <span class="n">conf</span><span class="o">.</span><span class="n">imageExtensions</span><span class="p">]:</span>
+ <span class="k">if</span> <span class="s">"cluster"</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">config</span><span class="p">:</span>
+ <span class="n">jobnum</span> <span class="o">+=</span> <span class="mi">1</span>
+ <span class="k">if</span> <span class="n">jobnum</span> <span class="o">==</span> <span class="bp">self</span><span class="o">.</span><span class="n">config</span><span class="p">[</span><span class="s">"cluster"</span><span class="p">]:</span>
+ <span class="n">jobnum</span> <span class="o">=</span> <span class="mi">0</span>
+ <span class="n">clusternum</span><span class="p">[</span><span class="nb">type</span><span class="p">]</span> <span class="o">+=</span> <span class="mi">1</span>
+ <span class="n">exDep</span><span class="p">[</span><span class="nb">type</span><span class="p">]</span><span class="o">.</span><span class="n">append</span><span class="p">([])</span>
+ <span class="n">exInput</span><span class="p">[</span><span class="nb">type</span><span class="p">]</span><span class="o">.</span><span class="n">append</span><span class="p">({})</span>
+ <span class="k">elif</span> <span class="p">((</span><span class="n">clusternum</span><span class="p">[</span><span class="nb">type</span><span class="p">]</span> <span class="o">*</span> <span class="mi">100</span> <span class="o">+</span> <span class="n">jobnum</span><span class="p">)</span> <span class="o">%</span> <span class="nb">int</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">config</span><span class="p">[</span><span class="s">"cluster"</span><span class="p">]</span> <span class="o">*</span> <span class="mf">0.3</span><span class="p">))</span> <span class="o">==</span> <span class="mi">0</span><span class="p">:</span>
+ <span class="n">meancluster</span><span class="p">[</span><span class="nb">type</span><span class="p">]</span> <span class="o">+=</span> <span class="mi">1</span>
+ <span class="n">extension</span> <span class="o">=</span> <span class="s">"."</span> <span class="o">+</span> <span class="n">infile</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s">"."</span><span class="p">)[</span><span class="mi">1</span><span class="p">]</span>
+ <span class="n">derivedPath</span> <span class="o">=</span> <span class="n">infile</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s">"_"</span><span class="p">)[</span><span class="mi">0</span><span class="p">]</span>
+ <span class="n">realname</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">files</span><span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">dax</span><span class="p">][</span><span class="nb">type</span><span class="p">][</span><span class="s">"input"</span><span class="p">][</span><span class="n">infile</span><span class="p">][</span><span class="s">"path"</span><span class="p">]</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s">"/"</span><span class="p">)[</span><span class="o">-</span><span class="mi">1</span><span class="p">]</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s">"."</span><span class="p">)[</span><span class="mi">0</span><span class="p">]</span>
+ <span class="k">for</span> <span class="n">stepnum</span><span class="p">,</span><span class="n">job</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">workflow</span><span class="p">[</span><span class="s">"workflows"</span><span class="p">][</span><span class="nb">type</span><span class="p">]):</span>
+ <span class="n">jobname</span> <span class="o">=</span> <span class="n">derivedPath</span> <span class="o">+</span> <span class="s">"_"</span> <span class="o">+</span> <span class="n">job</span><span class="p">[</span><span class="s">"name"</span><span class="p">]</span>
+ <span class="n">inputs</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_loadJobInputs</span><span class="p">(</span><span class="n">job</span><span class="p">,</span> <span class="nb">type</span><span class="p">,</span> <span class="n">derivedPath</span><span class="p">,</span> <span class="n">extension</span><span class="p">)</span>
+ <span class="k">if</span> <span class="n">job</span><span class="p">[</span><span class="s">"name"</span><span class="p">]</span> <span class="ow">in</span> <span class="n">exNames</span><span class="p">:</span>
+ <span class="n">outputs</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_loadJobOutputs</span><span class="p">(</span><span class="n">job</span><span class="p">,</span> <span class="nb">type</span><span class="p">,</span> <span class="n">derivedPath</span><span class="p">,</span> <span class="bp">True</span><span class="p">)</span>
+ <span class="n">exDep</span><span class="p">[</span><span class="nb">type</span><span class="p">][</span><span class="n">clusternum</span><span class="p">[</span><span class="nb">type</span><span class="p">]]</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">jobname</span><span class="p">)</span>
+ <span class="n">reqFile</span> <span class="o">=</span> <span class="n">derivedPath</span> <span class="o">+</span> <span class="s">"_"</span> <span class="o">+</span> <span class="bp">self</span><span class="o">.</span><span class="n">workflow</span><span class="p">[</span><span class="s">"extract"</span><span class="p">][</span><span class="s">"workflows"</span><span class="p">][</span><span class="nb">type</span><span class="p">][</span><span class="s">"inputs"</span><span class="p">][</span><span class="mi">0</span><span class="p">]</span> <span class="o">+</span> <span class="s">".png"</span>
+ <span class="n">exInput</span><span class="p">[</span><span class="nb">type</span><span class="p">][</span><span class="n">clusternum</span><span class="p">[</span><span class="nb">type</span><span class="p">]][</span><span class="n">reqFile</span><span class="p">]</span> <span class="o">=</span> <span class="p">{</span><span class="s">"file"</span><span class="p">:</span> <span class="n">reqFile</span><span class="p">,</span> <span class="s">"transfer"</span><span class="p">:</span> <span class="n">save</span><span class="p">}</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="n">outputs</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_loadJobOutputs</span><span class="p">(</span><span class="n">job</span><span class="p">,</span> <span class="nb">type</span><span class="p">,</span> <span class="n">derivedPath</span><span class="p">,</span> <span class="n">save</span><span class="p">)</span>
+ <span class="n">depends</span> <span class="o">=</span> <span class="p">[</span><span class="n">derivedPath</span> <span class="o">+</span> <span class="s">"_"</span> <span class="o">+</span> <span class="n">depend</span> <span class="k">for</span> <span class="n">depend</span> <span class="ow">in</span> <span class="n">job</span><span class="p">[</span><span class="s">"depends"</span><span class="p">]]</span> <span class="k">if</span> <span class="s">"depends"</span> <span class="ow">in</span> <span class="n">job</span> <span class="k">else</span> <span class="p">[]</span>
+ <span class="k">if</span> <span class="n">job</span><span class="p">[</span><span class="s">"executable"</span><span class="p">]</span> <span class="o">==</span> <span class="s">"pcv-meanshift"</span><span class="p">:</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_addJob</span><span class="p">(</span><span class="n">jobname</span><span class="p">,</span> <span class="n">job</span><span class="p">[</span><span class="s">"executable"</span><span class="p">],</span> <span class="n">inputs</span><span class="p">,</span> <span class="n">outputs</span><span class="p">,</span> <span class="n">job</span><span class="p">[</span><span class="s">"arguments"</span><span class="p">],</span> <span class="n">depends</span><span class="p">,</span> <span class="n">label</span> <span class="o">=</span> <span class="nb">type</span> <span class="o">+</span> <span class="s">"_step"</span> <span class="o">+</span> <span class="nb">str</span><span class="p">(</span><span class="n">stepnum</span><span class="p">)</span> <span class="o">+</span> <span class="s">"_cluster"</span> <span class="o">+</span> <span class="nb">str</span><span class="p">(</span><span class="n">meancluster</span><span class="p">[</span><span class="nb">type</span><span class="p">])</span> <span class="k">if</span> <span class="s">"cluster"</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">config</span> <span class="k">else</span> <span class="bp">None</span><span class="p">)</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_addJob</span><span class="p">(</span><span class="n">jobname</span><span class="p">,</span> <span class="n">job</span><span class="p">[</span><span class="s">"executable"</span><span class="p">],</span> <span class="n">inputs</span><span class="p">,</span> <span class="n">outputs</span><span class="p">,</span> <span class="n">job</span><span class="p">[</span><span class="s">"arguments"</span><span class="p">],</span> <span class="n">depends</span><span class="p">,</span> <span class="n">label</span> <span class="o">=</span> <span class="nb">type</span> <span class="o">+</span> <span class="s">"_step"</span> <span class="o">+</span> <span class="nb">str</span><span class="p">(</span><span class="n">stepnum</span><span class="p">)</span> <span class="o">+</span> <span class="s">"_cluster"</span> <span class="o">+</span> <span class="nb">str</span><span class="p">(</span><span class="n">clusternum</span><span class="p">[</span><span class="nb">type</span><span class="p">])</span> <span class="k">if</span> <span class="s">"cluster"</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">config</span> <span class="k">else</span> <span class="bp">None</span><span class="p">)</span>
+
+
+ <span class="n">maprc</span> <span class="o">=</span> <span class="nb">open</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">basepath</span> <span class="o">+</span> <span class="s">"/"</span> <span class="o">+</span> <span class="n">loc</span> <span class="o">+</span> <span class="s">"/map.rc"</span><span class="p">,</span> <span class="s">"a"</span><span class="p">)</span>
+ <span class="n">binDep</span> <span class="o">=</span> <span class="p">[]</span>
+ <span class="n">aggIn</span> <span class="o">=</span> <span class="p">{}</span>
+ <span class="k">for</span> <span class="nb">type</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">workflow</span><span class="p">[</span><span class="s">"workflows"</span><span class="p">]:</span>
+ <span class="k">for</span> <span class="n">q</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="mi">0</span><span class="p">,</span> <span class="n">clusternum</span><span class="p">[</span><span class="nb">type</span><span class="p">]</span> <span class="o">+</span> <span class="mi">1</span><span class="p">):</span>
+ <span class="n">arguments</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">workflow</span><span class="p">[</span><span class="s">"extract"</span><span class="p">][</span><span class="s">"workflows"</span><span class="p">][</span><span class="nb">type</span><span class="p">][</span><span class="s">"arguments"</span><span class="p">]</span>
+ <span class="k">if</span> <span class="s">"--input"</span> <span class="ow">in</span> <span class="n">arguments</span><span class="p">:</span>
+ <span class="k">del</span> <span class="n">arguments</span><span class="p">[</span><span class="s">"--input"</span><span class="p">]</span>
+ <span class="k">if</span> <span class="s">"histogram-bin"</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">workflow</span><span class="p">[</span><span class="s">"extract"</span><span class="p">]:</span>
+ <span class="k">if</span> <span class="nb">type</span> <span class="ow">in</span> <span class="p">[</span><span class="n">imtype</span> <span class="k">for</span> <span class="n">key</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">workflow</span><span class="p">[</span><span class="s">"extract"</span><span class="p">][</span><span class="s">"histogram-bin"</span><span class="p">][</span><span class="s">"--group"</span><span class="p">]</span> <span class="k">for</span> <span class="n">imtype</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">workflow</span><span class="p">[</span><span class="s">"extract"</span><span class="p">][</span><span class="s">"histogram-bin"</span><span class="p">][</span><span class="s">"--group"</span><span class="p">][</span><span class="n">key</span><span class="p">]]:</span>
+ <span class="n">arguments</span><span class="p">[</span><span class="s">"--colors"</span><span class="p">]</span> <span class="o">=</span> <span class="s">""</span>
+ <span class="n">arguments</span><span class="p">[</span><span class="s">"--db"</span><span class="p">]</span> <span class="o">=</span> <span class="s">"db"</span>
+ <span class="n">arguments</span><span class="p">[</span><span class="s">"--createdb"</span><span class="p">]</span> <span class="o">=</span> <span class="s">""</span>
+ <span class="n">arguments</span><span class="p">[</span><span class="s">"--inputs"</span><span class="p">]</span> <span class="o">=</span> <span class="s">" "</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">exInput</span><span class="p">[</span><span class="nb">type</span><span class="p">][</span><span class="n">q</span><span class="p">]</span><span class="o">.</span><span class="n">keys</span><span class="p">())</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_addFile</span><span class="p">(</span><span class="nb">type</span> <span class="o">+</span> <span class="nb">str</span><span class="p">(</span><span class="n">q</span><span class="p">)</span> <span class="o">+</span> <span class="s">".db"</span><span class="p">,</span> <span class="nb">type</span><span class="p">,</span> <span class="s">"output"</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_addJob</span><span class="p">(</span><span class="nb">type</span> <span class="o">+</span> <span class="s">"_extract"</span> <span class="o">+</span> <span class="nb">str</span><span class="p">(</span><span class="n">q</span><span class="p">),</span> <span class="s">"pcv-extract-multi"</span><span class="p">,</span> <span class="n">exInput</span><span class="p">[</span><span class="nb">type</span><span class="p">][</span><span class="n">q</span><span class="p">],</span> <span class="p">{</span><span class="s">"db"</span><span class="p">:</span> <span class="p">{</span><span class="s">"file"</span><span class="p">:</span> <span class="nb">type</span> <span class="o">+</span> <span class="nb">str</span><span class="p">(</span><span class="n">q</span><span class="p">)</span> <span class="o">+</span> <span class="s">".db"</span><span class="p">,</span> <span class="s">"transfer"</span><span class="p">:</span> <span class="bp">False</span><span class="p">}},</span> <span class="n">arguments</span><span class="p">,</span> <span class="n">exDep</span><span class="p">[</span><span class="nb">type</span><span class="p">][</span><span class="n">q</span><span class="p">])</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_addJob</span><span class="p">(</span><span class="nb">type</span> <span class="o">+</span> <span class="s">"_extract"</span> <span class="o">+</span> <span class="nb">str</span><span class="p">(</span><span class="n">q</span><span class="p">),</span> <span class="s">"pcv-extract-multi"</span><span class="p">,</span> <span class="n">exInput</span><span class="p">[</span><span class="nb">type</span><span class="p">][</span><span class="n">q</span><span class="p">],</span> <span class="p">{</span><span class="s">"db"</span><span class="p">:</span> <span class="p">{</span><span class="s">"file"</span><span class="p">:</span> <span class="nb">type</span> <span class="o">+</span> <span class="nb">str</span><span class="p">(</span><span class="n">q</span><span class="p">)</span> <span class="o">+</span> <span class="s">".db"</span><span class="p">,</span> <span class="s">"transfer"</span><span class="p">:</span> <span class="bp">False</span><span class="p">}},</span> <span class="n">arguments</span><span class="p">,</span> <span class="p">[],</span> <span class="n">dax</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">exdax</span><span class="p">)</span>
+ <span class="n">maprc</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="nb">type</span> <span class="o">+</span> <span class="nb">str</span><span class="p">(</span><span class="n">q</span><span class="p">)</span> <span class="o">+</span> <span class="s">".db"</span> <span class="o">+</span> <span class="s">" file://"</span> <span class="o">+</span> <span class="bp">self</span><span class="o">.</span><span class="n">basepath</span> <span class="o">+</span> <span class="s">"/output/"</span> <span class="o">+</span> <span class="nb">type</span> <span class="o">+</span> <span class="nb">str</span><span class="p">(</span><span class="n">q</span><span class="p">)</span> <span class="o">+</span> <span class="s">".db"</span> <span class="o">+</span> <span class="s">" pool=</span><span class="se">\"</span><span class="s">local</span><span class="se">\"\n</span><span class="s">"</span><span class="p">)</span>
+ <span class="n">binDep</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="nb">type</span> <span class="o">+</span> <span class="s">"_extract"</span> <span class="o">+</span> <span class="nb">str</span><span class="p">(</span><span class="n">q</span><span class="p">))</span>
+ <span class="n">aggIn</span><span class="p">[</span><span class="nb">type</span> <span class="o">+</span> <span class="nb">str</span><span class="p">(</span><span class="n">q</span><span class="p">)</span> <span class="o">+</span> <span class="s">".db"</span><span class="p">]</span> <span class="o">=</span> <span class="p">{</span><span class="s">"file"</span><span class="p">:</span> <span class="nb">type</span> <span class="o">+</span> <span class="nb">str</span><span class="p">(</span><span class="n">q</span><span class="p">)</span> <span class="o">+</span> <span class="s">".db"</span><span class="p">,</span> <span class="s">"transfer"</span><span class="p">:</span> <span class="bp">False</span><span class="p">}</span>
+ <span class="n">aggIn</span><span class="p">[</span><span class="s">"db"</span><span class="p">]</span> <span class="o">=</span> <span class="p">{</span><span class="s">"file"</span><span class="p">:</span> <span class="s">"img.db"</span><span class="p">,</span> <span class="s">"transfer"</span><span class="p">:</span> <span class="bp">False</span><span class="p">}</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_addJob</span><span class="p">(</span><span class="s">"sql_aggregate1"</span><span class="p">,</span> <span class="s">"pcv-sql-aggregate"</span><span class="p">,</span> <span class="n">aggIn</span><span class="p">,</span> <span class="p">{},</span> <span class="p">{</span><span class="s">"--db"</span><span class="p">:</span> <span class="s">"db"</span><span class="p">,</span> <span class="s">"--inputs"</span><span class="p">:</span> <span class="s">" "</span><span class="o">.</span><span class="n">join</span><span class="p">([</span><span class="n">aggIn</span><span class="p">[</span><span class="n">x</span><span class="p">][</span><span class="s">"file"</span><span class="p">]</span> <span class="k">for</span> <span class="n">x</span> <span class="ow">in</span> <span class="n">aggIn</span> <span class="k">if</span> <span class="n">x</span> <span class="o">!=</span> <span class="s">"db"</span><span class="p">])},</span> <span class="n">binDep</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_addJob</span><span class="p">(</span><span class="s">"sql_aggregate1"</span><span class="p">,</span> <span class="s">"pcv-sql-aggregate"</span><span class="p">,</span> <span class="n">aggIn</span><span class="p">,</span> <span class="p">{},</span> <span class="p">{</span><span class="s">"--db"</span><span class="p">:</span> <span class="s">"db"</span><span class="p">,</span> <span class="s">"--inputs"</span><span class="p">:</span> <span class="s">" "</span><span class="o">.</span><span class="n">join</span><span class="p">([</span><span class="n">aggIn</span><span class="p">[</span><span class="n">x</span><span class="p">][</span><span class="s">"file"</span><span class="p">]</span> <span class="k">for</span> <span class="n">x</span> <span class="ow">in</span> <span class="n">aggIn</span> <span class="k">if</span> <span class="n">x</span> <span class="o">!=</span> <span class="s">"db"</span><span class="p">])},</span> <span class="n">binDep</span><span class="p">,</span> <span class="n">dax</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">exdax</span><span class="p">)</span>
+
+ <span class="k">if</span> <span class="s">"histogram-bin"</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">workflow</span><span class="p">[</span><span class="s">"extract"</span><span class="p">]:</span>
+ <span class="n">outputs</span> <span class="o">=</span> <span class="p">{}</span>
+ <span class="k">for</span> <span class="n">name</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">workflow</span><span class="p">[</span><span class="s">"extract"</span><span class="p">][</span><span class="s">"histogram-bin"</span><span class="p">][</span><span class="s">"--group"</span><span class="p">]:</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_addFile</span><span class="p">(</span><span class="n">name</span> <span class="o">+</span> <span class="s">"_hist_bins.json"</span><span class="p">,</span> <span class="s">"raw"</span><span class="p">,</span> <span class="s">"output"</span><span class="p">)</span>
+ <span class="n">maprc</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="n">name</span> <span class="o">+</span> <span class="s">"_hist_bins.json"</span> <span class="o">+</span> <span class="s">" file://"</span> <span class="o">+</span> <span class="bp">self</span><span class="o">.</span><span class="n">basepath</span> <span class="o">+</span> <span class="s">"/output/"</span> <span class="o">+</span> <span class="n">name</span> <span class="o">+</span> <span class="s">"_hist_bins.json"</span> <span class="o">+</span> <span class="s">" pool=</span><span class="se">\"</span><span class="s">local</span><span class="se">\"\n</span><span class="s">"</span><span class="p">)</span>
+ <span class="n">outputs</span><span class="p">[</span><span class="n">name</span> <span class="o">+</span> <span class="s">"_hist_bins.json"</span><span class="p">]</span> <span class="o">=</span> <span class="p">{</span><span class="s">"file"</span><span class="p">:</span> <span class="n">name</span> <span class="o">+</span> <span class="s">"_hist_bins.json"</span><span class="p">,</span> <span class="s">"transfer"</span><span class="p">:</span> <span class="bp">True</span><span class="p">}</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_addJob</span><span class="p">(</span><span class="s">"bin_creation"</span><span class="p">,</span> <span class="s">"pcv-stats-histogram-bin"</span><span class="p">,</span> <span class="p">{</span><span class="s">"db"</span><span class="p">:</span> <span class="p">{</span><span class="s">"file"</span><span class="p">:</span> <span class="s">"img.db"</span><span class="p">,</span> <span class="s">"transfer"</span><span class="p">:</span> <span class="bp">True</span><span class="p">},</span> <span class="s">"extract.json"</span><span class="p">:</span> <span class="p">{</span><span class="s">"file"</span><span class="p">:</span> <span class="s">"extract.json"</span><span class="p">,</span> <span class="s">"transfer"</span><span class="p">:</span> <span class="bp">False</span><span class="p">}},</span> <span class="n">outputs</span><span class="p">,</span> <span class="p">{</span><span class="s">"--db"</span><span class="p">:</span> <span class="s">"db"</span><span class="p">,</span> <span class="s">"--options"</span><span class="p">:</span> <span class="s">"extract.json"</span><span class="p">,</span> <span class="s">"--intable"</span><span class="p">:</span> <span class="s">"images"</span><span class="p">,</span> <span class="s">"--outtable"</span><span class="p">:</span> <span class="s">"histogramBins"</span><span class="p">,</span> <span class="s">"--jsonwrite"</span><span class="p">:</span> <span class="s">""</span><span class="p">},</span> <span class="p">[</span><span class="s">"sql_aggregate1"</span><span class="p">])</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_addJob</span><span class="p">(</span><span class="s">"bin_creation"</span><span class="p">,</span> <span class="s">"pcv-stats-histogram-bin"</span><span class="p">,</span> <span class="p">{</span><span class="s">"db"</span><span class="p">:</span> <span class="p">{</span><span class="s">"file"</span><span class="p">:</span> <span class="s">"img.db"</span><span class="p">,</span> <span class="s">"transfer"</span><span class="p">:</span> <span class="bp">True</span><span class="p">},</span> <span class="s">"extract.json"</span><span class="p">:</span> <span class="p">{</span><span class="s">"file"</span><span class="p">:</span> <span class="s">"extract.json"</span><span class="p">,</span> <span class="s">"transfer"</span><span class="p">:</span> <span class="bp">False</span><span class="p">}},</span> <span class="n">outputs</span><span class="p">,</span> <span class="p">{</span><span class="s">"--db"</span><span class="p">:</span> <span class="s">"db"</span><span class="p">,</span> <span class="s">"--options"</span><span class="p">:</span> <span class="s">"extract.json"</span><span class="p">,</span> <span class="s">"--intable"</span><span class="p">:</span> <span class="s">"images"</span><span class="p">,</span> <span class="s">"--outtable"</span><span class="p">:</span> <span class="s">"histogramBins"</span><span class="p">,</span> <span class="s">"--jsonwrite"</span><span class="p">:</span> <span class="s">""</span><span class="p">,</span> <span class="s">"--overwrite"</span><span class="p">:</span> <span class="s">""</span><span class="p">},</span> <span class="p">[</span><span class="s">"sql_aggregate1"</span><span class="p">],</span> <span class="n">dax</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">exdax</span><span class="p">)</span>
+
+ <span class="n">binDep</span> <span class="o">=</span> <span class="p">[]</span>
+ <span class="nb">map</span> <span class="o">=</span> <span class="p">{}</span>
+
+ <span class="k">for</span> <span class="n">group</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">workflow</span><span class="p">[</span><span class="s">"extract"</span><span class="p">][</span><span class="s">"histogram-bin"</span><span class="p">][</span><span class="s">"--group"</span><span class="p">]:</span>
+ <span class="k">for</span> <span class="nb">type</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">workflow</span><span class="p">[</span><span class="s">"extract"</span><span class="p">][</span><span class="s">"histogram-bin"</span><span class="p">][</span><span class="s">"--group"</span><span class="p">][</span><span class="n">group</span><span class="p">]:</span>
+ <span class="nb">map</span><span class="p">[</span><span class="nb">type</span><span class="p">]</span> <span class="o">=</span> <span class="n">group</span>
+
+ <span class="k">for</span> <span class="nb">type</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">workflow</span><span class="p">[</span><span class="s">"workflows"</span><span class="p">]:</span>
+ <span class="k">for</span> <span class="n">q</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="mi">0</span><span class="p">,</span> <span class="n">clusternum</span><span class="p">[</span><span class="nb">type</span><span class="p">]</span> <span class="o">+</span> <span class="mi">1</span><span class="p">):</span>
+ <span class="n">arguments</span> <span class="o">=</span> <span class="p">{}</span>
+ <span class="n">arguments</span><span class="p">[</span><span class="s">"--db"</span><span class="p">]</span> <span class="o">=</span> <span class="s">"db"</span>
+ <span class="n">arguments</span><span class="p">[</span><span class="s">"--inputs"</span><span class="p">]</span> <span class="o">=</span> <span class="s">" "</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">exInput</span><span class="p">[</span><span class="nb">type</span><span class="p">][</span><span class="n">q</span><span class="p">]</span><span class="o">.</span><span class="n">keys</span><span class="p">())</span>
+ <span class="n">exInput</span><span class="p">[</span><span class="nb">type</span><span class="p">][</span><span class="n">q</span><span class="p">][</span><span class="s">"db"</span><span class="p">]</span> <span class="o">=</span> <span class="p">{</span><span class="s">"file"</span><span class="p">:</span> <span class="nb">type</span> <span class="o">+</span> <span class="nb">str</span><span class="p">(</span><span class="n">q</span><span class="p">)</span> <span class="o">+</span> <span class="s">".db"</span><span class="p">,</span> <span class="s">"transfer"</span><span class="p">:</span> <span class="bp">False</span><span class="p">}</span>
+ <span class="n">exInput</span><span class="p">[</span><span class="nb">type</span><span class="p">][</span><span class="n">q</span><span class="p">][</span><span class="s">"binfile"</span><span class="p">]</span> <span class="o">=</span> <span class="p">{</span><span class="s">"file"</span><span class="p">:</span> <span class="nb">map</span><span class="p">[</span><span class="nb">type</span><span class="p">]</span> <span class="o">+</span> <span class="s">"_hist_bins.json"</span><span class="p">,</span> <span class="s">"transfer"</span><span class="p">:</span> <span class="bp">False</span><span class="p">}</span>
+ <span class="n">arguments</span><span class="p">[</span><span class="s">"--bins"</span><span class="p">]</span> <span class="o">=</span> <span class="s">"binfile"</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_addJob</span><span class="p">(</span><span class="nb">type</span> <span class="o">+</span> <span class="s">"_extractBins"</span> <span class="o">+</span> <span class="nb">str</span><span class="p">(</span><span class="n">q</span><span class="p">),</span> <span class="s">"pcv-extract-multi"</span><span class="p">,</span> <span class="n">exInput</span><span class="p">[</span><span class="nb">type</span><span class="p">][</span><span class="n">q</span><span class="p">],</span> <span class="p">{},</span> <span class="n">arguments</span><span class="p">,</span> <span class="p">[</span><span class="s">"bin_creation"</span><span class="p">])</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_addJob</span><span class="p">(</span><span class="nb">type</span> <span class="o">+</span> <span class="s">"_extractBins"</span> <span class="o">+</span> <span class="nb">str</span><span class="p">(</span><span class="n">q</span><span class="p">),</span> <span class="s">"pcv-extract-multi"</span><span class="p">,</span> <span class="n">exInput</span><span class="p">[</span><span class="nb">type</span><span class="p">][</span><span class="n">q</span><span class="p">],</span> <span class="p">{},</span> <span class="n">arguments</span><span class="p">,</span> <span class="p">[</span><span class="s">"bin_creation"</span><span class="p">],</span> <span class="n">dax</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">exdax</span><span class="p">)</span>
+ <span class="n">binDep</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="nb">type</span> <span class="o">+</span> <span class="s">"_extractBins"</span> <span class="o">+</span> <span class="nb">str</span><span class="p">(</span><span class="n">q</span><span class="p">))</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_addJob</span><span class="p">(</span><span class="s">"sql_aggregate2"</span><span class="p">,</span> <span class="s">"pcv-sql-aggregate"</span><span class="p">,</span> <span class="n">aggIn</span><span class="p">,</span> <span class="p">{},</span> <span class="p">{</span><span class="s">"--db"</span><span class="p">:</span> <span class="s">"db"</span><span class="p">,</span> <span class="s">"--inputs"</span><span class="p">:</span> <span class="s">" "</span><span class="o">.</span><span class="n">join</span><span class="p">([</span><span class="n">aggIn</span><span class="p">[</span><span class="n">x</span><span class="p">][</span><span class="s">"file"</span><span class="p">]</span> <span class="k">for</span> <span class="n">x</span> <span class="ow">in</span> <span class="n">aggIn</span> <span class="k">if</span> <span class="n">x</span> <span class="o">!=</span> <span class="s">"db"</span><span class="p">])},</span> <span class="n">binDep</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_addJob</span><span class="p">(</span><span class="s">"sql_aggregate2"</span><span class="p">,</span> <span class="s">"pcv-sql-aggregate"</span><span class="p">,</span> <span class="n">aggIn</span><span class="p">,</span> <span class="p">{},</span> <span class="p">{</span><span class="s">"--db"</span><span class="p">:</span> <span class="s">"db"</span><span class="p">,</span> <span class="s">"--inputs"</span><span class="p">:</span> <span class="s">" "</span><span class="o">.</span><span class="n">join</span><span class="p">([</span><span class="n">aggIn</span><span class="p">[</span><span class="n">x</span><span class="p">][</span><span class="s">"file"</span><span class="p">]</span> <span class="k">for</span> <span class="n">x</span> <span class="ow">in</span> <span class="n">aggIn</span> <span class="k">if</span> <span class="n">x</span> <span class="o">!=</span> <span class="s">"db"</span><span class="p">])},</span> <span class="n">binDep</span><span class="p">,</span> <span class="n">dax</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">exdax</span><span class="p">)</span>
+
+ <span class="n">z</span> <span class="o">=</span> <span class="mi">2</span> <span class="k">if</span> <span class="s">"histogram-bin"</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">workflow</span><span class="p">[</span><span class="s">"extract"</span><span class="p">]</span> <span class="k">else</span> <span class="mi">1</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_addJob</span><span class="p">(</span><span class="s">"error-log"</span><span class="p">,</span> <span class="s">"pcv-error-log"</span><span class="p">,</span> <span class="p">{</span><span class="s">"db"</span><span class="p">:</span> <span class="p">{</span><span class="s">"file"</span><span class="p">:</span> <span class="s">"img.db"</span><span class="p">,</span> <span class="s">"transfer"</span><span class="p">:</span> <span class="bp">False</span><span class="p">}},</span> <span class="p">{</span><span class="s">"output"</span><span class="p">:</span> <span class="p">{</span><span class="s">"file"</span><span class="p">:</span> <span class="s">"img.log"</span><span class="p">,</span> <span class="s">"transfer"</span><span class="p">:</span> <span class="bp">True</span><span class="p">}},</span> <span class="p">{</span><span class="s">"--db"</span><span class="p">:</span> <span class="s">"db"</span><span class="p">,</span> <span class="s">"--output"</span><span class="p">:</span> <span class="s">"output"</span><span class="p">},</span> <span class="p">[</span><span class="s">"sql_aggregate"</span> <span class="o">+</span> <span class="nb">str</span><span class="p">(</span><span class="n">z</span><span class="p">)])</span>
+ <span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">basepath</span> <span class="o">+</span> <span class="s">"/"</span> <span class="o">+</span> <span class="n">loc</span> <span class="o">+</span> <span class="s">"/workflow.dax"</span><span class="p">,</span> <span class="s">"w"</span><span class="p">)</span> <span class="k">as</span> <span class="n">wh</span><span class="p">:</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">dax</span><span class="o">.</span><span class="n">writeXML</span><span class="p">(</span><span class="n">wh</span><span class="p">)</span>
+ <span class="k">return</span>
+
+ <span class="k">def</span> <span class="nf">_createExtract</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">loc</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> Creates the extraction step only dax!</span>
+<span class="sd"> """</span>
+ <span class="c">#self._addJob("extractOnly", "pcv-extract-all", self.exInput, {}, {"--db": "db", "--options": "extract.json"}, dax = self.exdax)</span>
+ <span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">basepath</span> <span class="o">+</span> <span class="s">"/"</span> <span class="o">+</span> <span class="n">loc</span> <span class="o">+</span> <span class="s">"/extract.dax"</span><span class="p">,</span> <span class="s">"w"</span><span class="p">)</span> <span class="k">as</span> <span class="n">wh</span><span class="p">:</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">exdax</span><span class="o">.</span><span class="n">writeXML</span><span class="p">(</span><span class="n">wh</span><span class="p">)</span>
+ <span class="k">return</span>
+
+ <span class="k">def</span> <span class="nf">_createReplica</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">loc</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> Creates the pegasus configuration replica catalog. input/conf.rc</span>
+<span class="sd"> """</span>
+ <span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">basepath</span> <span class="o">+</span> <span class="s">"/"</span> <span class="o">+</span> <span class="n">loc</span> <span class="o">+</span> <span class="s">"/conf.rc"</span><span class="p">,</span> <span class="s">"w"</span><span class="p">)</span> <span class="k">as</span> <span class="n">wh</span><span class="p">:</span>
+ <span class="n">pegasusrc</span> <span class="o">=</span> <span class="n">textwrap</span><span class="o">.</span><span class="n">dedent</span><span class="p">(</span><span class="s">"""</span><span class="se">\</span>
+<span class="s"> pegasus.catalog.site = XML</span>
+<span class="s"> pegasus.catalog.site.file = </span><span class="si">%s</span><span class="s">/sites.xml</span>
+<span class="s"> </span>
+<span class="s"> pegasus.condor.logs.symlink = false</span>
+<span class="s"> </span>
+<span class="s"> pegasus.transfer.links = true</span>
+<span class="s"> </span>
+<span class="s"> pegasus.data.configuration = sharedfs</span>
+<span class="s"> </span>
+<span class="s"> pegasus.dir.storage.mapper = Replica</span>
+<span class="s"> pegasus.dir.storage.mapper.replica = File</span>
+<span class="s"> pegasus.dir.storage.mapper.replica.file = </span><span class="si">%s</span><span class="s">/map.rc</span>
+<span class="s"> """</span> <span class="o">%</span> <span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">basepath</span> <span class="o">+</span> <span class="s">"/"</span> <span class="o">+</span> <span class="n">loc</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">basepath</span> <span class="o">+</span> <span class="s">"/"</span> <span class="o">+</span> <span class="n">loc</span><span class="p">))</span>
+ <span class="n">wh</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="n">pegasusrc</span><span class="p">)</span>
+ <span class="k">return</span>
+
+ <span class="k">def</span> <span class="nf">_createSites</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">loc</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> Creates the pegasus site catalog. input/sites.xml</span>
+<span class="sd"> """</span>
+ <span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">basepath</span> <span class="o">+</span> <span class="s">"/"</span> <span class="o">+</span> <span class="n">loc</span> <span class="o">+</span> <span class="s">"/sites.xml"</span><span class="p">,</span> <span class="s">"w"</span><span class="p">)</span> <span class="k">as</span> <span class="n">wh</span><span class="p">:</span>
+ <span class="n">sites</span> <span class="o">=</span> <span class="s">"""</span><span class="se">\</span>
+<span class="s"> <sitecatalog xmlns="http://pegasus.isi.edu/schema/sitecatalog" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://pegasus.isi.edu/schema/sitecatalog http://pegasus.isi.edu/schema/sc-4.0.xsd" version="4.0"></span>
+<span class="s"> </span>
+<span class="s"> <site handle="local" arch="x86_64" os="LINUX"></span>
+<span class="s"> <directory type="shared-scratch" path="</span><span class="si">%s</span><span class="s">"></span>
+<span class="s"> <file-server operation="all" url="file://</span><span class="si">%s</span><span class="s">" /></span>
+<span class="s"> </directory></span>
+<span class="s"> <directory type="local-storage" path="</span><span class="si">%s</span><span class="s">"></span>
+<span class="s"> <file-server operation="all" url="file://</span><span class="si">%s</span><span class="s">" /></span>
+<span class="s"> </directory></span>
+<span class="s"> """</span> <span class="o">%</span> <span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">basepath</span> <span class="o">+</span> <span class="s">"/work/imgproc/"</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">basepath</span> <span class="o">+</span> <span class="s">"/work/imgproc/"</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">basepath</span> <span class="o">+</span> <span class="s">"/output/"</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">basepath</span> <span class="o">+</span> <span class="s">"/output/"</span><span class="p">)</span>
+ <span class="k">for</span> <span class="n">namespace</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">config</span><span class="p">[</span><span class="s">"profile"</span><span class="p">]:</span>
+ <span class="k">for</span> <span class="n">key</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">config</span><span class="p">[</span><span class="s">"profile"</span><span class="p">][</span><span class="n">namespace</span><span class="p">]:</span>
+ <span class="n">val</span> <span class="o">=</span> <span class="s">":"</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">config</span><span class="p">[</span><span class="s">"profile"</span><span class="p">][</span><span class="n">namespace</span><span class="p">][</span><span class="n">key</span><span class="p">])</span> <span class="k">if</span> <span class="s">"path"</span> <span class="ow">in</span> <span class="n">key</span><span class="o">.</span><span class="n">lower</span><span class="p">()</span> <span class="k">else</span> <span class="bp">self</span><span class="o">.</span><span class="n">config</span><span class="p">[</span><span class="s">"profile"</span><span class="p">][</span><span class="n">namespace</span><span class="p">][</span><span class="n">key</span><span class="p">]</span>
+ <span class="n">sites</span> <span class="o">+=</span> <span class="s">"""</span><span class="se">\n\t</span><span class="s"><profile namespace="</span><span class="si">%s</span><span class="s">" key="</span><span class="si">%s</span><span class="s">"></span><span class="si">%s</span><span class="s"></profile> """</span> <span class="o">%</span> <span class="p">(</span><span class="n">namespace</span><span class="p">,</span> <span class="n">key</span><span class="p">,</span> <span class="n">val</span><span class="p">)</span>
+ <span class="n">sites</span> <span class="o">+=</span> <span class="s">"</site></sitecatalog>"</span>
+ <span class="n">sites</span> <span class="o">=</span> <span class="n">sites</span><span class="o">.</span><span class="n">replace</span><span class="p">(</span><span class="s">"</span><span class="se">\n</span><span class="s">"</span><span class="p">,</span><span class="s">""</span><span class="p">)</span>
+ <span class="n">wh</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s">"</span><span class="se">\n</span><span class="s">"</span><span class="o">.</span><span class="n">join</span><span class="p">([</span><span class="n">line</span> <span class="k">for</span> <span class="n">line</span> <span class="ow">in</span> <span class="n">xml</span><span class="o">.</span><span class="n">dom</span><span class="o">.</span><span class="n">minidom</span><span class="o">.</span><span class="n">parseString</span><span class="p">(</span><span class="n">sites</span><span class="p">)</span><span class="o">.</span><span class="n">toprettyxml</span><span class="p">()</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s">'</span><span class="se">\n</span><span class="s">'</span><span class="p">)</span> <span class="k">if</span> <span class="n">line</span><span class="o">.</span><span class="n">strip</span><span class="p">()]))</span>
+ <span class="k">return</span>
+
+ <span class="k">def</span> <span class="nf">_createSubmit</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">loc</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> Creates the pegasus submit script. submit.sh</span>
+<span class="sd"> """</span>
+ <span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">basepath</span> <span class="o">+</span> <span class="s">"/"</span> <span class="o">+</span> <span class="n">loc</span> <span class="o">+</span> <span class="s">"/submit.sh"</span><span class="p">,</span> <span class="s">"w"</span><span class="p">)</span> <span class="k">as</span> <span class="n">wh</span><span class="p">:</span>
+ <span class="n">submit</span> <span class="o">=</span> <span class="n">textwrap</span><span class="o">.</span><span class="n">dedent</span><span class="p">(</span><span class="s">"""</span><span class="se">\</span>
+<span class="s"> #!/bin/bash</span>
+<span class="s"> if [ "$1" = "--extract-only" ] || [ "$1" = "--extract" ] || [ "$1" = "-e" ]; then</span>
+<span class="s"> DAX="</span><span class="si">%s</span><span class="s">"</span>
+<span class="s"> else</span>
+<span class="s"> DAX="</span><span class="si">%s</span><span class="s">"</span>
+<span class="s"> fi</span>
+<span class="s"> plan=`pegasus-plan </span><span class="se">\\</span><span class="s"></span>
+<span class="s"> --conf "</span><span class="si">%s</span><span class="s">" </span><span class="se">\\</span><span class="s"></span>
+<span class="s"> --sites local </span><span class="se">\\</span><span class="s"></span>
+<span class="s"> --dir "</span><span class="si">%s</span><span class="s">" </span><span class="se">\\</span><span class="s"></span>
+<span class="s"> --output-site local </span><span class="se">\\</span><span class="s"></span>
+<span class="s"> --dax "$DAX" </span><span class="se">\\</span><span class="s"></span>
+<span class="s"> --randomdir </span><span class="se">\\</span><span class="s"></span>
+<span class="s"> """</span> <span class="o">%</span> <span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">basepath</span> <span class="o">+</span> <span class="s">"/"</span> <span class="o">+</span> <span class="n">loc</span> <span class="o">+</span> <span class="s">"/extract.dax"</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">basepath</span> <span class="o">+</span> <span class="s">"/"</span> <span class="o">+</span> <span class="n">loc</span> <span class="o">+</span> <span class="s">"/workflow.dax"</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">basepath</span> <span class="o">+</span> <span class="s">"/"</span> <span class="o">+</span> <span class="n">loc</span> <span class="o">+</span> <span class="s">"/conf.rc"</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">basepath</span> <span class="o">+</span> <span class="s">"/work/imgproc"</span><span class="p">))</span>
+ <span class="k">if</span> <span class="s">"cluster"</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">config</span><span class="p">:</span>
+ <span class="n">submit</span> <span class="o">+=</span> <span class="s">"""--cluster label </span><span class="se">\\\n</span><span class="s">"""</span>
+ <span class="n">submit</span> <span class="o">+=</span> <span class="n">textwrap</span><span class="o">.</span><span class="n">dedent</span><span class="p">(</span><span class="s">"""</span><span class="se">\</span>
+<span class="s"> --submit`</span>
+<span class="s"> </span>
+<span class="s"> status=`echo "$plan" | grep pegasus-status | tr -s ' '| cut -d ' ' -f 6`</span>
+<span class="s"> echo -e "#!/bin/bash</span>
+<span class="s"> pegasus-status -l $status" > status.sh</span>
+<span class="s"> chmod 744 status.sh</span>
+<span class="s"> </span>
+<span class="s"> remove=`echo "$plan" | grep pegasus-remove | tr -s ' '| cut -d ' ' -f 5`</span>
+<span class="s"> echo -e "#!/bin/bash</span>
+<span class="s"> pegasus-remove $remove" > remove.sh </span>
+<span class="s"> chmod 744 remove.sh</span>
+<span class="s"> </span>
+<span class="s"> echo "$plan"</span>
+<span class="s"> echo "Alternatively, you can use the status & remove scripts in the current directory!"</span>
+<span class="s"> </span>
+<span class="s"> """</span><span class="p">)</span>
+ <span class="n">wh</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="n">submit</span><span class="p">)</span>
+ <span class="n">os</span><span class="o">.</span><span class="n">chmod</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">basepath</span> <span class="o">+</span> <span class="s">"/"</span> <span class="o">+</span> <span class="n">loc</span> <span class="o">+</span> <span class="s">"/submit.sh"</span><span class="p">,</span> <span class="mo">0755</span><span class="p">)</span>
+ <span class="k">return</span>
+
+<div class="viewcode-block" id="ImageProcessor.create"><a class="viewcode-back" href="../../workflowimage.html#htpia.workflow.ImageProcessor.create">[docs]</a> <span class="k">def</span> <span class="nf">create</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> Creates a new pegasus submission directory based on the current timestamp,</span>
+<span class="sd"> and populates it with all required information to submit a pegasus job.</span>
+<span class="sd"> """</span>
+ <span class="k">print</span> <span class="s">"Generating workflow. Please wait."</span>
+ <span class="n">loc</span> <span class="o">=</span> <span class="s">"/input/imgproc/"</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_createSetup</span><span class="p">()</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_copyFiles</span><span class="p">()</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_loadFiles</span><span class="p">(</span><span class="n">loc</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_loadExecutables</span><span class="p">()</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_loadNotify</span><span class="p">()</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_createDax</span><span class="p">(</span><span class="n">loc</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_createExtract</span><span class="p">(</span><span class="n">loc</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_createReplica</span><span class="p">(</span><span class="n">loc</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_createSites</span><span class="p">(</span><span class="n">loc</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_createSubmit</span><span class="p">(</span><span class="n">loc</span><span class="p">)</span>
+ <span class="k">return</span>
+
+</div></div>
+<div class="viewcode-block" id="ImageLoader"><a class="viewcode-back" href="../../indexing.html#htpia.workflow.ImageLoader">[docs]</a><span class="k">class</span> <span class="nc">ImageLoader</span><span class="p">:</span>
+ <span class="sd">"""</span>
+<span class="sd"> This should handle all meta-data definitions</span>
+<span class="sd"> """</span>
+
+ <span class="k">def</span> <span class="nf">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">template</span><span class="p">,</span> <span class="n">output</span><span class="p">,</span> <span class="n">validOnly</span> <span class="o">=</span> <span class="bp">False</span><span class="p">,</span> <span class="n">overwrite</span> <span class="o">=</span> <span class="bp">False</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> :param template: Path to input template file, should be valid json.</span>
+<span class="sd"> :type template: str</span>
+<span class="sd"> """</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">templatePath</span> <span class="o">=</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">abspath</span><span class="p">(</span><span class="n">template</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">err</span> <span class="o">=</span> <span class="s">""</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">output</span> <span class="o">=</span> <span class="n">output</span> <span class="o">+</span> <span class="s">"/input/"</span>
+ <span class="k">try</span><span class="p">:</span>
+ <span class="nb">open</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">output</span> <span class="o">+</span> <span class="s">"/images.db"</span><span class="p">)</span>
+ <span class="k">except</span> <span class="ne">IOError</span><span class="p">:</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">err</span> <span class="o">+=</span> <span class="s">"Path Error: Cannot open output db file. </span><span class="se">\n</span><span class="s">"</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">validator</span> <span class="o">=</span> <span class="n">htpia</span><span class="o">.</span><span class="n">validator</span><span class="o">.</span><span class="n">ImageLoader</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">templatePath</span><span class="p">)</span>
+ <span class="k">if</span> <span class="ow">not</span> <span class="bp">self</span><span class="o">.</span><span class="n">validator</span><span class="o">.</span><span class="n">isValid</span><span class="p">()</span> <span class="ow">or</span> <span class="n">validOnly</span><span class="p">:</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">validator</span><span class="o">.</span><span class="n">printErrors</span><span class="p">()</span>
+ <span class="n">sys</span><span class="o">.</span><span class="n">exit</span><span class="p">()</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">overwrite</span> <span class="o">=</span> <span class="n">overwrite</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">template</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">validator</span><span class="o">.</span><span class="n">data</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">template</span><span class="p">[</span><span class="s">"order"</span><span class="p">]</span><span class="o">.</span><span class="n">insert</span><span class="p">(</span><span class="mi">0</span><span class="p">,</span> <span class="s">"pegasusid"</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">count</span> <span class="o">=</span> <span class="p">{}</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">depth</span> <span class="o">=</span> <span class="nb">len</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">template</span><span class="p">[</span><span class="s">"path"</span><span class="p">]</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s">"/"</span><span class="p">))</span> <span class="o">-</span> <span class="mi">1</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">structure</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_dictTemplate</span><span class="p">()</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">data</span> <span class="o">=</span> <span class="p">[]</span>
+ <span class="k">return</span>
+
+ <span class="k">def</span> <span class="nf">_success</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+ <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">overwrite</span><span class="p">:</span>
+ <span class="k">print</span> <span class="s">"Directory re-crawled!"</span>
+ <span class="k">print</span> <span class="s">"Use pcv-run to submit your jobs."</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="k">print</span> <span class="s">"Directory setup successful!"</span>
+ <span class="k">print</span> <span class="s">"Define the required templates in "</span> <span class="o">+</span> <span class="bp">self</span><span class="o">.</span><span class="n">output</span> <span class="o">+</span> <span class="s">"."</span>
+ <span class="k">print</span> <span class="s">"Then use pcv-run to submit your jobs."</span>
+ <span class="k">return</span>
+
+ <span class="k">def</span> <span class="nf">_dictTemplate</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> Creates the first of two intermediary dictionaries for crawling. This relates</span>
+<span class="sd"> identifiers in the path, to a specified depth, as well as operators to split</span>
+<span class="sd"> the value at that depth.</span>
+<span class="sd"> """</span>
+ <span class="n">m</span> <span class="o">=</span> <span class="p">[</span><span class="n">x</span> <span class="k">for</span> <span class="n">x</span> <span class="ow">in</span> <span class="n">re</span><span class="o">.</span><span class="n">findall</span><span class="p">(</span><span class="s">r"%(\w+)%"</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">template</span><span class="p">[</span><span class="s">"path"</span><span class="p">])</span> <span class="k">if</span> <span class="n">x</span> <span class="o">!=</span> <span class="s">"null"</span><span class="p">]</span>
+ <span class="n">sp</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">template</span><span class="p">[</span><span class="s">"path"</span><span class="p">]</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s">"/"</span><span class="p">)</span>
+ <span class="n">d</span> <span class="o">=</span> <span class="p">{}</span>
+ <span class="k">for</span> <span class="n">key</span> <span class="ow">in</span> <span class="n">m</span><span class="p">:</span>
+ <span class="n">d</span><span class="p">[</span><span class="n">key</span><span class="p">]</span> <span class="o">=</span> <span class="p">{}</span>
+ <span class="n">d</span><span class="p">[</span><span class="n">key</span><span class="p">][</span><span class="s">"depth"</span><span class="p">]</span> <span class="o">=</span> <span class="p">[</span><span class="n">n</span> <span class="k">for</span> <span class="n">n</span><span class="p">,</span><span class="n">x</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="n">sp</span><span class="p">)</span> <span class="k">if</span> <span class="n">key</span> <span class="ow">in</span> <span class="n">x</span><span class="p">][</span><span class="mi">0</span><span class="p">]</span>
+ <span class="n">d</span><span class="p">[</span><span class="n">key</span><span class="p">][</span><span class="s">"split"</span><span class="p">]</span> <span class="o">=</span> <span class="p">[]</span>
+ <span class="n">val</span> <span class="o">=</span> <span class="n">sp</span><span class="p">[</span><span class="n">d</span><span class="p">[</span><span class="n">key</span><span class="p">][</span><span class="s">"depth"</span><span class="p">]]</span>
+ <span class="k">for</span> <span class="n">operator</span> <span class="ow">in</span> <span class="p">[</span><span class="s">" "</span><span class="p">,</span> <span class="s">"_"</span><span class="p">,</span> <span class="s">"-"</span><span class="p">]:</span>
+ <span class="k">if</span> <span class="n">operator</span> <span class="ow">in</span> <span class="n">val</span><span class="p">:</span>
+ <span class="n">b</span> <span class="o">=</span> <span class="n">val</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="n">operator</span><span class="p">)</span>
+ <span class="n">x</span> <span class="o">=</span> <span class="p">[</span><span class="n">n</span> <span class="k">for</span> <span class="n">n</span><span class="p">,</span><span class="n">x</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="n">b</span><span class="p">)</span> <span class="k">if</span> <span class="n">key</span> <span class="ow">in</span> <span class="n">x</span><span class="p">][</span><span class="mi">0</span><span class="p">]</span>
+ <span class="n">d</span><span class="p">[</span><span class="n">key</span><span class="p">][</span><span class="s">"split"</span><span class="p">]</span><span class="o">.</span><span class="n">append</span><span class="p">({</span><span class="s">"operator"</span><span class="p">:</span> <span class="n">operator</span><span class="p">,</span> <span class="s">"index"</span><span class="p">:</span> <span class="n">x</span><span class="p">})</span>
+ <span class="n">val</span> <span class="o">=</span> <span class="n">b</span><span class="p">[</span><span class="n">x</span><span class="p">]</span>
+ <span class="k">return</span> <span class="n">d</span>
+
+ <span class="k">def</span> <span class="nf">_loadStructure</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">splitPath</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> Creates the second of two intermediary dictionaries for crawling.</span>
+<span class="sd"> This utilizes the template created in _dictTemplate, and creates</span>
+<span class="sd"> a dictionary with actual values instead of structure.</span>
+<span class="sd"> """</span>
+ <span class="n">d</span> <span class="o">=</span><span class="p">{}</span>
+ <span class="k">for</span> <span class="n">key</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">structure</span><span class="p">:</span>
+ <span class="n">val</span> <span class="o">=</span> <span class="n">splitPath</span><span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">structure</span><span class="p">[</span><span class="n">key</span><span class="p">][</span><span class="s">"depth"</span><span class="p">]]</span>
+ <span class="k">for</span> <span class="n">operator</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">structure</span><span class="p">[</span><span class="n">key</span><span class="p">][</span><span class="s">"split"</span><span class="p">]:</span>
+ <span class="n">val</span> <span class="o">=</span> <span class="n">val</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="n">operator</span><span class="p">[</span><span class="s">"operator"</span><span class="p">])[</span><span class="n">operator</span><span class="p">[</span><span class="s">"index"</span><span class="p">]]</span>
+ <span class="n">d</span><span class="p">[</span><span class="n">key</span><span class="p">]</span> <span class="o">=</span> <span class="n">val</span>
+ <span class="k">return</span> <span class="n">d</span>
+
+ <span class="k">def</span> <span class="nf">_loadDataFile</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="nb">dict</span><span class="p">,</span> <span class="n">structure</span><span class="p">,</span> <span class="n">key</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> Loads data from a data file. If the specified key isn't in the file,</span>
+<span class="sd"> write 'UNKNOWN' instead.</span>
+<span class="sd"> """</span>
+ <span class="n">keyVal</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_convertReferences</span><span class="p">(</span><span class="n">structure</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">template</span><span class="p">[</span><span class="s">"data"</span><span class="p">][</span><span class="n">key</span><span class="p">][</span><span class="s">"key"</span><span class="p">])</span>
+ <span class="k">if</span> <span class="n">keyVal</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">filedata</span><span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">template</span><span class="p">[</span><span class="s">"data"</span><span class="p">][</span><span class="n">key</span><span class="p">][</span><span class="s">"value"</span><span class="p">]]:</span>
+ <span class="nb">dict</span><span class="p">[</span><span class="n">key</span><span class="p">]</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">filedata</span><span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">template</span><span class="p">[</span><span class="s">"data"</span><span class="p">][</span><span class="n">key</span><span class="p">][</span><span class="s">"value"</span><span class="p">]][</span><span class="n">keyVal</span><span class="p">]</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="nb">dict</span><span class="p">[</span><span class="n">key</span><span class="p">]</span> <span class="o">=</span> <span class="s">"UNKNOWN"</span>
+ <span class="k">return</span>
+
+ <span class="k">def</span> <span class="nf">_loadDataValue</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="nb">dict</span><span class="p">,</span> <span class="n">structure</span><span class="p">,</span> <span class="n">key</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> Loads a data value.</span>
+<span class="sd"> """</span>
+ <span class="n">val</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_convertReferences</span><span class="p">(</span><span class="n">structure</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">template</span><span class="p">[</span><span class="s">"data"</span><span class="p">][</span><span class="n">key</span><span class="p">][</span><span class="s">"value"</span><span class="p">])</span>
+ <span class="k">if</span> <span class="s">"translate"</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">template</span><span class="p">[</span><span class="s">"data"</span><span class="p">][</span><span class="n">key</span><span class="p">]:</span>
+ <span class="k">if</span> <span class="n">val</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">template</span><span class="p">[</span><span class="s">"translations"</span><span class="p">][</span><span class="n">key</span><span class="p">]:</span>
+ <span class="n">val</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">template</span><span class="p">[</span><span class="s">"translations"</span><span class="p">][</span><span class="n">key</span><span class="p">][</span><span class="n">val</span><span class="p">]</span>
+ <span class="nb">dict</span><span class="p">[</span><span class="n">key</span><span class="p">]</span> <span class="o">=</span> <span class="n">val</span>
+ <span class="k">return</span>
+
+ <span class="k">def</span> <span class="nf">_loadDataDate</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="nb">dict</span><span class="p">,</span> <span class="n">structure</span><span class="p">,</span> <span class="n">key</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> Loads a date.</span>
+<span class="sd"> """</span>
+ <span class="n">val</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_convertReferences</span><span class="p">(</span><span class="n">structure</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">template</span><span class="p">[</span><span class="s">"data"</span><span class="p">][</span><span class="n">key</span><span class="p">][</span><span class="s">"value"</span><span class="p">])</span>
+ <span class="n">format</span> <span class="o">=</span> <span class="s">""</span><span class="o">.</span><span class="n">join</span><span class="p">([</span><span class="n">x</span><span class="o">.</span><span class="n">replace</span><span class="p">(</span><span class="n">x</span><span class="p">,</span> <span class="s">"%"</span> <span class="o">+</span> <span class="n">x</span><span class="p">)</span> <span class="k">if</span> <span class="n">x</span> <span class="ow">in</span> <span class="n">conf</span><span class="o">.</span><span class="n">dateFormat</span> <span class="k">else</span> <span class="n">x</span> <span class="k">for</span> <span class="n">x</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">template</span><span class="p">[</span><span class="s">"data"</span><span class="p">][</span><span class="n">key</span><span class="p">][</span><span class="s">"format"</span><span class="p">]])</span>
+ <span class="n">val</span> <span class="o">=</span> <span class="n">datetime</span><span class="o">.</span><span class="n">datetime</span><span class="o">.</span><span class="n">strptime</span><span class="p">(</span><span class="n">val</span><span class="p">,</span> <span class="n">format</span><span class="p">)</span><span class="o">.</span><span class="n">strftime</span><span class="p">(</span><span class="s">"%Y-%m-</span><span class="si">%d</span><span class="s">"</span><span class="p">)</span>
+ <span class="nb">dict</span><span class="p">[</span><span class="n">key</span><span class="p">]</span> <span class="o">=</span> <span class="n">val</span>
+ <span class="k">return</span>
+
+ <span class="k">def</span> <span class="nf">_convertReferences</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">structure</span><span class="p">,</span> <span class="n">val</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> Replaces all references ('%%') to actual values.</span>
+<span class="sd"> """</span>
+ <span class="n">idList</span> <span class="o">=</span> <span class="p">[</span><span class="n">x</span> <span class="k">for</span> <span class="n">x</span> <span class="ow">in</span> <span class="n">re</span><span class="o">.</span><span class="n">findall</span><span class="p">(</span><span class="s">r"%(\w+)%"</span><span class="p">,</span> <span class="n">val</span><span class="p">)</span> <span class="k">if</span> <span class="n">x</span> <span class="o">!=</span> <span class="s">"null"</span><span class="p">]</span>
+ <span class="k">for</span> <span class="n">identifier</span> <span class="ow">in</span> <span class="n">idList</span><span class="p">:</span>
+ <span class="k">if</span> <span class="n">identifier</span> <span class="ow">in</span> <span class="n">structure</span><span class="p">:</span>
+ <span class="n">val</span> <span class="o">=</span> <span class="n">val</span><span class="o">.</span><span class="n">replace</span><span class="p">(</span><span class="s">"%"</span> <span class="o">+</span> <span class="n">identifier</span> <span class="o">+</span> <span class="s">"%"</span><span class="p">,</span> <span class="n">structure</span><span class="p">[</span><span class="n">identifier</span><span class="p">])</span>
+ <span class="k">return</span> <span class="n">val</span>
+
+ <span class="k">def</span> <span class="nf">_loadData</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">path</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> Loads all data for a particular path.</span>
+<span class="sd"> """</span>
+ <span class="n">temp</span> <span class="o">=</span> <span class="p">{}</span>
+ <span class="n">final</span> <span class="o">=</span> <span class="p">{}</span>
+ <span class="n">splitPath</span> <span class="o">=</span> <span class="n">path</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s">"/"</span><span class="p">)</span>
+ <span class="n">structure</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_loadStructure</span><span class="p">(</span><span class="n">splitPath</span><span class="p">)</span>
+ <span class="k">for</span> <span class="n">key</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">template</span><span class="p">[</span><span class="s">"data"</span><span class="p">]:</span>
+ <span class="n">d</span> <span class="o">=</span> <span class="p">{</span>
+ <span class="s">"value"</span><span class="p">:</span> <span class="bp">self</span><span class="o">.</span><span class="n">_loadDataValue</span><span class="p">,</span>
+ <span class="s">"file"</span><span class="p">:</span> <span class="bp">self</span><span class="o">.</span><span class="n">_loadDataFile</span><span class="p">,</span>
+ <span class="s">"date"</span><span class="p">:</span> <span class="bp">self</span><span class="o">.</span><span class="n">_loadDataDate</span>
+ <span class="p">}[</span><span class="bp">self</span><span class="o">.</span><span class="n">template</span><span class="p">[</span><span class="s">"data"</span><span class="p">][</span><span class="n">key</span><span class="p">][</span><span class="s">"type"</span><span class="p">]](</span><span class="n">final</span><span class="p">,</span> <span class="n">structure</span><span class="p">,</span> <span class="n">key</span><span class="p">)</span>
+ <span class="n">final</span><span class="p">[</span><span class="s">"path"</span><span class="p">]</span> <span class="o">=</span> <span class="n">path</span>
+ <span class="k">if</span> <span class="n">final</span><span class="p">[</span><span class="s">"imtype"</span><span class="p">]</span> <span class="ow">not</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">count</span><span class="p">:</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">count</span><span class="p">[</span><span class="n">final</span><span class="p">[</span><span class="s">"imtype"</span><span class="p">]]</span> <span class="o">=</span> <span class="mi">1</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">count</span><span class="p">[</span><span class="n">final</span><span class="p">[</span><span class="s">"imtype"</span><span class="p">]]</span> <span class="o">+=</span> <span class="mi">1</span>
+ <span class="n">final</span><span class="p">[</span><span class="s">"pegasusid"</span><span class="p">]</span> <span class="o">=</span> <span class="n">final</span><span class="p">[</span><span class="s">"imtype"</span><span class="p">]</span> <span class="o">+</span> <span class="nb">str</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">count</span><span class="p">[</span><span class="n">final</span><span class="p">[</span><span class="s">"imtype"</span><span class="p">]])</span>
+ <span class="k">return</span> <span class="n">final</span>
+
+ <span class="k">def</span> <span class="nf">_loadFiles</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> Reads all data from all specified files.</span>
+<span class="sd"> """</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">filedata</span> <span class="o">=</span> <span class="p">{}</span>
+ <span class="k">for</span> <span class="n">key</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">template</span><span class="p">[</span><span class="s">"data"</span><span class="p">]:</span>
+ <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">template</span><span class="p">[</span><span class="s">"data"</span><span class="p">][</span><span class="n">key</span><span class="p">][</span><span class="s">"type"</span><span class="p">]</span> <span class="o">==</span> <span class="s">"file"</span><span class="p">:</span>
+ <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">template</span><span class="p">[</span><span class="s">"data"</span><span class="p">][</span><span class="n">key</span><span class="p">][</span><span class="s">"value"</span><span class="p">]</span> <span class="ow">not</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">filedata</span><span class="p">:</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">filedata</span><span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">template</span><span class="p">[</span><span class="s">"data"</span><span class="p">][</span><span class="n">key</span><span class="p">][</span><span class="s">"value"</span><span class="p">]]</span> <span class="o">=</span> <span class="p">{}</span>
+ <span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">template</span><span class="p">[</span><span class="s">"data"</span><span class="p">][</span><span class="n">key</span><span class="p">][</span><span class="s">"value"</span><span class="p">],</span> <span class="s">"r"</span><span class="p">)</span> <span class="k">as</span> <span class="n">rh</span><span class="p">:</span>
+ <span class="k">for</span> <span class="n">line</span> <span class="ow">in</span> <span class="n">rh</span><span class="o">.</span><span class="n">readlines</span><span class="p">():</span>
+ <span class="n">info</span> <span class="o">=</span> <span class="n">line</span><span class="o">.</span><span class="n">strip</span><span class="p">()</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s">","</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">filedata</span><span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">template</span><span class="p">[</span><span class="s">"data"</span><span class="p">][</span><span class="n">key</span><span class="p">][</span><span class="s">"value"</span><span class="p">]][</span><span class="n">info</span><span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">template</span><span class="p">[</span><span class="s">"data"</span><span class="p">][</span><span class="n">key</span><span class="p">][</span><span class="s">"keyColumn"</span><span class="p">]]]</span> <span class="o">=</span> <span class="n">info</span><span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">template</span><span class="p">[</span><span class="s">"data"</span><span class="p">][</span><span class="n">key</span><span class="p">][</span><span class="s">"valueColumn"</span><span class="p">]]</span>
+ <span class="k">return</span>
+
+<div class="viewcode-block" id="ImageLoader.crawl"><a class="viewcode-back" href="../../indexing.html#htpia.workflow.ImageLoader.crawl">[docs]</a> <span class="k">def</span> <span class="nf">crawl</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> Recursively walks through directories in base, and loads</span>
+<span class="sd"> the appropriate data.</span>
+<span class="sd"> """</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_loadFiles</span><span class="p">()</span>
+ <span class="k">for</span> <span class="n">root</span><span class="p">,</span> <span class="n">dirs</span><span class="p">,</span> <span class="n">files</span> <span class="ow">in</span> <span class="n">os</span><span class="o">.</span><span class="n">walk</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">template</span><span class="p">[</span><span class="s">"base"</span><span class="p">]):</span>
+ <span class="n">arr</span> <span class="o">=</span> <span class="n">root</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s">"/"</span><span class="p">)</span>
+ <span class="n">depth</span> <span class="o">=</span> <span class="nb">len</span><span class="p">(</span><span class="n">arr</span><span class="p">)</span>
+ <span class="k">if</span> <span class="p">(</span><span class="n">depth</span> <span class="o">==</span> <span class="bp">self</span><span class="o">.</span><span class="n">depth</span><span class="p">):</span>
+ <span class="k">for</span> <span class="nb">file</span> <span class="ow">in</span> <span class="n">files</span><span class="p">:</span>
+ <span class="k">if</span> <span class="nb">file</span><span class="p">[</span><span class="o">-</span><span class="nb">len</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">template</span><span class="p">[</span><span class="s">"filetype"</span><span class="p">]):]</span> <span class="o">==</span> <span class="bp">self</span><span class="o">.</span><span class="n">template</span><span class="p">[</span><span class="s">"filetype"</span><span class="p">]</span> <span class="ow">and</span> <span class="nb">file</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="o">!=</span> <span class="s">"."</span><span class="p">:</span>
+ <span class="n">d</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_loadData</span><span class="p">(</span><span class="n">root</span> <span class="o">+</span> <span class="s">"/"</span> <span class="o">+</span> <span class="nb">file</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">data</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">d</span><span class="p">)</span>
+ <span class="k">return</span>
+ </div>
+<div class="viewcode-block" id="ImageLoader.write"><a class="viewcode-back" href="../../indexing.html#htpia.workflow.ImageLoader.write">[docs]</a> <span class="k">def</span> <span class="nf">write</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> Writes the data loaded from crawl into csv format based on 'order'</span>
+<span class="sd"> """</span>
+ <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">data</span><span class="p">:</span>
+ <span class="n">conn</span> <span class="o">=</span> <span class="n">sqlite3</span><span class="o">.</span><span class="n">connect</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">output</span> <span class="o">+</span> <span class="s">"/images.db"</span><span class="p">)</span>
+ <span class="n">tablestr</span> <span class="o">=</span> <span class="s">"(pegasusid PRIMARY KEY"</span>
+ <span class="k">for</span> <span class="n">x</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">template</span><span class="p">[</span><span class="s">"order"</span><span class="p">]:</span>
+ <span class="k">if</span> <span class="n">x</span> <span class="o">!=</span> <span class="s">"pegasusid"</span><span class="p">:</span>
+ <span class="n">tablestr</span> <span class="o">+=</span> <span class="s">","</span> <span class="o">+</span> <span class="nb">str</span><span class="p">(</span><span class="n">x</span><span class="p">)</span>
+ <span class="n">tablestr</span> <span class="o">+=</span> <span class="s">")"</span>
+ <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">overwrite</span><span class="p">:</span>
+ <span class="n">conn</span><span class="o">.</span><span class="n">execute</span><span class="p">(</span><span class="s">"DROP TABLE IF EXISTS images"</span><span class="p">)</span>
+ <span class="n">conn</span><span class="o">.</span><span class="n">commit</span><span class="p">()</span>
+ <span class="n">conn</span><span class="o">.</span><span class="n">execute</span><span class="p">(</span><span class="s">"CREATE TABLE images "</span> <span class="o">+</span> <span class="n">tablestr</span><span class="p">)</span>
+ <span class="n">writedata</span> <span class="o">=</span> <span class="p">[]</span>
+ <span class="k">for</span> <span class="n">row</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">data</span><span class="p">:</span>
+ <span class="n">writedata</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="nb">tuple</span><span class="p">([</span><span class="nb">str</span><span class="p">(</span><span class="n">row</span><span class="p">[</span><span class="n">x</span><span class="p">])</span> <span class="k">for</span> <span class="n">x</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">template</span><span class="p">[</span><span class="s">"order"</span><span class="p">]]))</span>
+ <span class="n">query</span> <span class="o">=</span> <span class="s">"insert into images "</span> <span class="o">+</span> <span class="nb">str</span><span class="p">(</span><span class="nb">tuple</span><span class="p">([</span><span class="nb">str</span><span class="p">(</span><span class="n">x</span><span class="p">)</span> <span class="k">for</span> <span class="n">x</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">template</span><span class="p">[</span><span class="s">"order"</span><span class="p">]]))</span> <span class="o">+</span> <span class="s">" values ("</span> <span class="o">+</span> <span class="p">(</span><span class="s">"?,"</span> <span class="o">*</span> <span class="nb">len</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">template</span><span class="p">[</span><span class="s">"order"</span><span class="p">]))[:</span><span class="o">-</span><span class="mi">1</span><span class="p">]</span> <span class="o">+</span> <span class="s">")"</span>
+ <span class="n">conn</span><span class="o">.</span><span class="n">executemany</span><span class="p">(</span><span class="n">query</span><span class="p">,</span> <span class="n">writedata</span><span class="p">)</span>
+ <span class="n">conn</span><span class="o">.</span><span class="n">commit</span><span class="p">()</span>
+ <span class="k">if</span> <span class="ow">not</span> <span class="bp">self</span><span class="o">.</span><span class="n">overwrite</span><span class="p">:</span>
+ <span class="n">shutil</span><span class="o">.</span><span class="n">copyfile</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">templatePath</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">output</span> <span class="o">+</span> <span class="s">"/crawl.json"</span><span class="p">)</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="k">print</span> <span class="s">"Call crawl first!"</span>
+ <span class="k">return</span>
+ </div></div>
+<span class="k">class</span> <span class="nc">DirectorySetup</span><span class="p">:</span>
+
+ <span class="k">def</span> <span class="nf">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">jobhome</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> :param jobhome: The base directory to setup a job.</span>
+<span class="sd"> :type jobhome: str</span>
+<span class="sd"> """</span>
+ <span class="k">if</span> <span class="ow">not</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">isdir</span><span class="p">(</span><span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">dirname</span><span class="p">(</span><span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">dirname</span><span class="p">(</span><span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">abspath</span><span class="p">(</span><span class="n">jobhome</span><span class="p">)</span> <span class="o">+</span> <span class="s">"/"</span><span class="p">))):</span>
+ <span class="k">print</span> <span class="s">"Can't create job folder, path doesn't exist!"</span>
+ <span class="n">sys</span><span class="o">.</span><span class="n">exit</span><span class="p">()</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">jobhome</span> <span class="o">=</span> <span class="n">jobhome</span>
+ <span class="k">return</span>
+
+ <span class="k">def</span> <span class="nf">_makeDir</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">dirpath</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> Makes a directory if it doesn't exist. Catches and</span>
+<span class="sd"> prints out common errors.</span>
+<span class="sd"> """</span>
+ <span class="k">try</span><span class="p">:</span>
+ <span class="n">os</span><span class="o">.</span><span class="n">makedirs</span><span class="p">(</span><span class="n">dirpath</span><span class="p">)</span>
+ <span class="k">except</span> <span class="ne">OSError</span> <span class="k">as</span> <span class="n">e</span><span class="p">:</span>
+ <span class="k">raise</span> <span class="ne">Exception</span><span class="p">({</span>
+ <span class="n">errno</span><span class="o">.</span><span class="n">EEXIST</span><span class="p">:</span> <span class="s">"Directory "</span> <span class="o">+</span> <span class="n">dirpath</span> <span class="o">+</span> <span class="s">" already exists!"</span><span class="p">,</span>
+ <span class="n">errno</span><span class="o">.</span><span class="n">EACCES</span><span class="p">:</span> <span class="s">"You don't have permission to create directory "</span> <span class="o">+</span> <span class="n">dirpath</span> <span class="o">+</span> <span class="s">"."</span><span class="p">,</span>
+ <span class="p">}</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="n">e</span><span class="o">.</span><span class="n">errno</span><span class="p">,</span> <span class="s">"Error for directory "</span> <span class="o">+</span> <span class="n">dirpath</span> <span class="o">+</span> <span class="s">" error:"</span> <span class="o">+</span> <span class="nb">str</span><span class="p">(</span><span class="n">e</span><span class="p">)))</span>
+ <span class="k">return</span>
+
+ <span class="k">def</span> <span class="nf">_makeFile</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">filepath</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> Opens a file to create it, uses append mode</span>
+<span class="sd"> so it doesn't overwrite any existing files.</span>
+<span class="sd"> """</span>
+ <span class="k">try</span><span class="p">:</span>
+ <span class="nb">open</span><span class="p">(</span><span class="n">filepath</span><span class="p">,</span> <span class="s">"a"</span><span class="p">)</span>
+ <span class="k">except</span> <span class="ne">OSError</span> <span class="k">as</span> <span class="n">e</span><span class="p">:</span>
+ <span class="k">raise</span> <span class="ne">Exception</span><span class="p">({</span>
+
+ <span class="p">}</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="n">e</span><span class="p">,</span> <span class="s">"Unsepcified error for file "</span> <span class="o">+</span> <span class="n">filepath</span><span class="p">))</span>
+ <span class="k">return</span>
+
+ <span class="k">def</span> <span class="nf">setup</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> Creates the directory structure needed to submit jobs,</span>
+<span class="sd"> and creates empty template files needed for job submission.</span>
+<span class="sd"> """</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_makeDir</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">jobhome</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_makeDir</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">jobhome</span> <span class="o">+</span> <span class="s">"/input/"</span><span class="p">)</span>
+ <span class="k">for</span> <span class="n">fname</span> <span class="ow">in</span> <span class="n">conf</span><span class="o">.</span><span class="n">jobFiles</span><span class="p">:</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_makeFile</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">jobhome</span> <span class="o">+</span> <span class="s">"/input/"</span> <span class="o">+</span> <span class="n">fname</span><span class="p">)</span>
+ <span class="k">return</span>
+
+
+
+</pre></div>
+
+ </div>
+
+ </div>
+</div>
+<footer class="footer">
+ <div class="container">
+ <p class="pull-right">
+ <a href="#">Back to top</a>
+
+ </p>
+ <p>
+ © Copyright 2015, Avi Knecht.<br/>
+ Created using <a href="http://sphinx.pocoo.org/">Sphinx</a> 1.3a0.<br/>
+ </p>
+ </div>
+</footer>
+ </body>
+</html>
\ No newline at end of file
diff --git a/docs/build/html/_modules/ih/imgproc.html b/docs/build/html/_modules/ih/imgproc.html
new file mode 100644
index 0000000000000000000000000000000000000000..f4f4fe5971afe6f0ac56ff1d660011a446dfdf93
--- /dev/null
+++ b/docs/build/html/_modules/ih/imgproc.html
@@ -0,0 +1,1227 @@
+<!DOCTYPE html>
+
+
+<html xmlns="http://www.w3.org/1999/xhtml">
+ <head>
+ <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
+
+ <title>ih.imgproc — Image Harvest 1.0.1 documentation</title>
+
+ <link rel="stylesheet" href="../../_static/basic.css" type="text/css" />
+ <link rel="stylesheet" href="../../_static/pygments.css" type="text/css" />
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+
+ <script type="text/javascript">
+ var DOCUMENTATION_OPTIONS = {
+ URL_ROOT: '../../',
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+
+ <h1>Source code for ih.imgproc</h1><div class="highlight"><pre>
+<span class="sd">"""</span>
+<span class="sd">This file is part of Image Harvest.</span>
+
+<span class="sd">Image Harvest is free software: you can redistribute it and/or modify</span>
+<span class="sd">it under the terms of the GNU General Public License as published by</span>
+<span class="sd">the Free Software Foundation, either version 3 of the License, or</span>
+<span class="sd">(at your option) any later version.</span>
+
+<span class="sd">Image Harvest is distributed in the hope that it will be useful,</span>
+<span class="sd">but WITHOUT ANY WARRANTY; without even the implied warranty of</span>
+<span class="sd">MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the</span>
+<span class="sd">GNU General Public License for more details.</span>
+
+<span class="sd">You should have received a copy of the GNU General Public License</span>
+<span class="sd">along with Image Harvest. If not, see <http://www.gnu.org/licenses/>.</span>
+
+<span class="sd">.. module:: imgproc</span>
+<span class="sd"> :platform: Mac, Linux</span>
+<span class="sd"> :synopsis: Image processing function wrappers to opencv.</span>
+
+<span class="sd">.. moduleauthor:: Avi Knecht <avi@kurtknecht.com></span>
+
+<span class="sd">"""</span>
+
+<span class="kn">import</span> <span class="nn">os</span>
+<span class="kn">import</span> <span class="nn">cv2</span>
+<span class="kn">import</span> <span class="nn">numpy</span> <span class="kn">as</span> <span class="nn">np</span>
+<span class="kn">import</span> <span class="nn">math</span>
+<span class="kn">import</span> <span class="nn">conf</span>
+<span class="kn">import</span> <span class="nn">sqlite3</span>
+<span class="kn">import</span> <span class="nn">pymeanshift</span> <span class="kn">as</span> <span class="nn">pms</span>
+<span class="kn">import</span> <span class="nn">traceback</span>
+<span class="kn">import</span> <span class="nn">json</span>
+
+<span class="k">class</span> <span class="nc">ColorFilter</span><span class="p">(</span><span class="nb">object</span><span class="p">):</span>
+
+ <span class="sd">"""</span>
+<span class="sd"> Color Filtration logic container.</span>
+<span class="sd"> """</span>
+ <span class="k">def</span> <span class="nf">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="nb">filter</span><span class="p">):</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">tokens</span> <span class="o">=</span> <span class="p">{</span>
+ <span class="s">"True"</span><span class="p">:</span> <span class="bp">True</span><span class="p">,</span>
+ <span class="s">"False"</span><span class="p">:</span> <span class="bp">False</span><span class="p">,</span>
+ <span class="s">"and"</span><span class="p">:</span> <span class="k">lambda</span> <span class="n">left</span><span class="p">,</span> <span class="n">right</span><span class="p">:</span> <span class="n">np</span><span class="o">.</span><span class="n">logical_and</span><span class="p">(</span><span class="n">left</span><span class="p">,</span> <span class="n">right</span><span class="p">),</span>
+ <span class="s">"or"</span><span class="p">:</span> <span class="k">lambda</span> <span class="n">left</span><span class="p">,</span> <span class="n">right</span><span class="p">:</span> <span class="n">np</span><span class="o">.</span><span class="n">logical_or</span><span class="p">(</span><span class="n">left</span><span class="p">,</span> <span class="n">right</span><span class="p">),</span>
+ <span class="s">">"</span><span class="p">:</span> <span class="k">lambda</span> <span class="n">left</span><span class="p">,</span> <span class="n">right</span><span class="p">:</span> <span class="n">left</span> <span class="o">></span> <span class="n">right</span><span class="p">,</span>
+ <span class="s">"<"</span><span class="p">:</span> <span class="k">lambda</span> <span class="n">left</span><span class="p">,</span> <span class="n">right</span><span class="p">:</span> <span class="n">left</span> <span class="o"><</span> <span class="n">right</span><span class="p">,</span>
+ <span class="s">">="</span><span class="p">:</span> <span class="k">lambda</span> <span class="n">left</span><span class="p">,</span> <span class="n">right</span><span class="p">:</span> <span class="n">left</span> <span class="o">>=</span> <span class="n">right</span><span class="p">,</span>
+ <span class="s">"<="</span><span class="p">:</span> <span class="k">lambda</span> <span class="n">left</span><span class="p">,</span> <span class="n">right</span><span class="p">:</span> <span class="n">left</span> <span class="o"><=</span> <span class="n">right</span><span class="p">,</span>
+ <span class="s">"="</span><span class="p">:</span> <span class="k">lambda</span> <span class="n">left</span><span class="p">,</span> <span class="n">right</span><span class="p">:</span> <span class="n">left</span> <span class="o">==</span> <span class="n">right</span><span class="p">,</span>
+ <span class="s">"+"</span><span class="p">:</span> <span class="k">lambda</span> <span class="n">left</span><span class="p">,</span> <span class="n">right</span><span class="p">:</span> <span class="n">left</span> <span class="o">+</span> <span class="n">right</span><span class="p">,</span>
+ <span class="s">"-"</span><span class="p">:</span> <span class="k">lambda</span> <span class="n">left</span><span class="p">,</span> <span class="n">right</span><span class="p">:</span> <span class="n">left</span> <span class="o">-</span> <span class="n">right</span><span class="p">,</span>
+ <span class="s">"*"</span><span class="p">:</span> <span class="k">lambda</span> <span class="n">left</span><span class="p">,</span> <span class="n">right</span><span class="p">:</span> <span class="n">left</span> <span class="o">*</span> <span class="n">right</span><span class="p">,</span>
+ <span class="s">"/"</span><span class="p">:</span> <span class="k">lambda</span> <span class="n">left</span><span class="p">,</span> <span class="n">right</span><span class="p">:</span> <span class="n">left</span> <span class="o">/</span> <span class="n">right</span><span class="p">,</span>
+ <span class="s">"max"</span><span class="p">:</span> <span class="k">lambda</span> <span class="n">left</span><span class="p">,</span> <span class="n">right</span><span class="p">:</span> <span class="n">np</span><span class="o">.</span><span class="n">maximum</span><span class="p">(</span><span class="n">left</span><span class="p">,</span> <span class="n">right</span><span class="p">),</span>
+ <span class="s">"min"</span><span class="p">:</span> <span class="k">lambda</span> <span class="n">left</span><span class="p">,</span> <span class="n">right</span><span class="p">:</span> <span class="n">np</span><span class="o">.</span><span class="n">minimum</span><span class="p">(</span><span class="n">left</span><span class="p">,</span> <span class="n">right</span><span class="p">),</span>
+ <span class="s">"not"</span><span class="p">:</span> <span class="k">lambda</span> <span class="n">left</span><span class="p">,</span> <span class="n">right</span><span class="p">:</span> <span class="n">np</span><span class="o">.</span><span class="n">invert</span><span class="p">(</span><span class="n">left</span><span class="p">),</span>
+ <span class="s">"("</span><span class="p">:</span> <span class="s">"("</span><span class="p">,</span>
+ <span class="s">")"</span><span class="p">:</span> <span class="s">")"</span><span class="p">,</span>
+ <span class="p">}</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">filterString</span> <span class="o">=</span> <span class="nb">filter</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">emptyRes</span> <span class="o">=</span> <span class="bp">True</span>
+ <span class="k">return</span>
+
+ <span class="k">def</span> <span class="nf">_createArgList</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+ <span class="n">s</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">filterString</span><span class="o">.</span><span class="n">replace</span><span class="p">(</span><span class="s">"("</span><span class="p">,</span> <span class="s">" ( "</span><span class="p">)</span>
+ <span class="n">s</span> <span class="o">=</span> <span class="n">s</span><span class="o">.</span><span class="n">replace</span><span class="p">(</span><span class="s">")"</span><span class="p">,</span> <span class="s">" ) "</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">filter</span> <span class="o">=</span> <span class="p">[]</span>
+ <span class="k">for</span> <span class="n">item</span> <span class="ow">in</span> <span class="n">s</span><span class="o">.</span><span class="n">split</span><span class="p">():</span>
+ <span class="k">if</span> <span class="n">item</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">tokens</span><span class="p">:</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">filter</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">tokens</span><span class="p">[</span><span class="n">item</span><span class="p">])</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="k">try</span><span class="p">:</span>
+ <span class="n">val</span> <span class="o">=</span> <span class="nb">int</span><span class="p">(</span><span class="n">item</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">filter</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">val</span><span class="p">)</span>
+ <span class="k">except</span><span class="p">:</span>
+ <span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="s">"Invalid logic string."</span><span class="p">)</span>
+ <span class="c">#self.filter = [self.tokens[x] if x in self.tokens else int(x) for x in s.split()]</span>
+ <span class="k">return</span>
+
+ <span class="k">def</span> <span class="nf">_find</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">what</span><span class="p">,</span> <span class="n">start</span> <span class="o">=</span> <span class="mi">0</span><span class="p">):</span>
+ <span class="k">return</span> <span class="p">[</span><span class="n">i</span> <span class="k">for</span> <span class="n">i</span><span class="p">,</span><span class="n">x</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">filter</span><span class="p">)</span> <span class="k">if</span> <span class="n">x</span> <span class="o">==</span> <span class="n">what</span> <span class="ow">and</span> <span class="n">i</span> <span class="o">>=</span> <span class="n">start</span><span class="p">]</span>
+
+ <span class="k">def</span> <span class="nf">_parens</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+ <span class="n">left_1st</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_find</span><span class="p">(</span><span class="s">"("</span><span class="p">)</span>
+ <span class="k">if</span> <span class="ow">not</span> <span class="n">left_1st</span><span class="p">:</span>
+ <span class="k">return</span> <span class="bp">False</span><span class="p">,</span> <span class="o">-</span><span class="mi">1</span><span class="p">,</span> <span class="o">-</span><span class="mi">1</span>
+ <span class="n">left</span> <span class="o">=</span> <span class="n">left_1st</span><span class="p">[</span><span class="o">-</span><span class="mi">1</span><span class="p">]</span>
+ <span class="n">right</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_find</span><span class="p">(</span><span class="s">")"</span><span class="p">,</span> <span class="n">left</span> <span class="o">+</span> <span class="mi">2</span><span class="p">)[</span><span class="mi">0</span><span class="p">]</span>
+ <span class="k">return</span> <span class="bp">True</span><span class="p">,</span> <span class="n">left</span><span class="p">,</span> <span class="n">right</span>
+
+ <span class="k">def</span> <span class="nf">_eval</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="nb">filter</span><span class="p">):</span>
+ <span class="k">return</span> <span class="nb">filter</span><span class="p">[</span><span class="mi">1</span><span class="p">](</span><span class="nb">filter</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span> <span class="nb">filter</span><span class="p">[</span><span class="mi">2</span><span class="p">])</span>
+
+ <span class="k">def</span> <span class="nf">_formattedEval</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="nb">filter</span><span class="p">):</span>
+ <span class="k">if</span> <span class="ow">not</span> <span class="nb">filter</span><span class="p">:</span>
+ <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">emptyRes</span>
+ <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="nb">filter</span><span class="p">)</span> <span class="o">==</span> <span class="mi">1</span><span class="p">:</span>
+ <span class="k">return</span> <span class="nb">filter</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span>
+
+ <span class="n">has_parens</span><span class="p">,</span> <span class="n">l_paren</span><span class="p">,</span> <span class="n">r_paren</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_parens</span><span class="p">()</span>
+
+ <span class="k">if</span> <span class="ow">not</span> <span class="n">has_parens</span><span class="p">:</span>
+ <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">_eval</span><span class="p">(</span><span class="nb">filter</span><span class="p">)</span>
+
+ <span class="nb">filter</span><span class="p">[</span><span class="n">l_paren</span><span class="p">:</span><span class="n">r_paren</span> <span class="o">+</span> <span class="mi">1</span><span class="p">]</span> <span class="o">=</span> <span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">_eval</span><span class="p">(</span><span class="nb">filter</span><span class="p">[</span><span class="n">l_paren</span><span class="o">+</span><span class="mi">1</span><span class="p">:</span><span class="n">r_paren</span><span class="p">])]</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">emptyRes</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_eval</span>
+ <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">_formattedEval</span><span class="p">(</span><span class="nb">filter</span><span class="p">)</span>
+
+ <span class="k">def</span> <span class="nf">apply</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">image</span><span class="p">,</span> <span class="n">roi</span><span class="p">):</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">tokens</span><span class="p">[</span><span class="s">"r"</span><span class="p">]</span> <span class="o">=</span> <span class="n">image</span><span class="p">[:,:,</span><span class="mi">2</span><span class="p">]</span><span class="o">.</span><span class="n">astype</span><span class="p">(</span><span class="nb">float</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">tokens</span><span class="p">[</span><span class="s">"g"</span><span class="p">]</span> <span class="o">=</span> <span class="n">image</span><span class="p">[:,:,</span><span class="mi">1</span><span class="p">]</span><span class="o">.</span><span class="n">astype</span><span class="p">(</span><span class="nb">float</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">tokens</span><span class="p">[</span><span class="s">"b"</span><span class="p">]</span> <span class="o">=</span> <span class="n">image</span><span class="p">[:,:,</span><span class="mi">0</span><span class="p">]</span><span class="o">.</span><span class="n">astype</span><span class="p">(</span><span class="nb">float</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_createArgList</span><span class="p">()</span>
+ <span class="n">result</span> <span class="o">=</span> <span class="n">cv2</span><span class="o">.</span><span class="n">cvtColor</span><span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">where</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">_formattedEval</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">filter</span><span class="p">),</span> <span class="mi">255</span><span class="p">,</span> <span class="mi">0</span><span class="p">)</span><span class="o">.</span><span class="n">astype</span><span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">uint8</span><span class="p">),</span> <span class="n">cv2</span><span class="o">.</span><span class="n">COLOR_GRAY2BGR</span><span class="p">)</span>
+ <span class="n">image</span><span class="p">[</span><span class="n">roi</span><span class="p">[</span><span class="mi">0</span><span class="p">]:</span><span class="n">roi</span><span class="p">[</span><span class="mi">1</span><span class="p">],</span> <span class="n">roi</span><span class="p">[</span><span class="mi">2</span><span class="p">]:</span><span class="n">roi</span><span class="p">[</span><span class="mi">3</span><span class="p">]]</span> <span class="o">=</span> <span class="n">cv2</span><span class="o">.</span><span class="n">bitwise_and</span><span class="p">(</span><span class="n">image</span><span class="p">[</span><span class="n">roi</span><span class="p">[</span><span class="mi">0</span><span class="p">]:</span><span class="n">roi</span><span class="p">[</span><span class="mi">1</span><span class="p">],</span> <span class="n">roi</span><span class="p">[</span><span class="mi">2</span><span class="p">]:</span><span class="n">roi</span><span class="p">[</span><span class="mi">3</span><span class="p">]],</span> <span class="n">result</span><span class="p">[</span><span class="n">roi</span><span class="p">[</span><span class="mi">0</span><span class="p">]:</span><span class="n">roi</span><span class="p">[</span><span class="mi">1</span><span class="p">],</span> <span class="n">roi</span><span class="p">[</span><span class="mi">2</span><span class="p">]:</span><span class="n">roi</span><span class="p">[</span><span class="mi">3</span><span class="p">]])</span>
+ <span class="k">return</span> <span class="n">image</span>
+
+
+
+<div class="viewcode-block" id="Image"><a class="viewcode-back" href="../../processing.html#ih.imgproc.Image">[docs]</a><span class="k">class</span> <span class="nc">Image</span><span class="p">(</span><span class="nb">object</span><span class="p">):</span>
+
+ <span class="sd">"""</span>
+<span class="sd"> An individual image. Each image is loaded in as its own instance of the Image class for processing.</span>
+<span class="sd"> """</span>
+ <span class="k">def</span> <span class="nf">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="nb">input</span><span class="p">,</span> <span class="n">outputdir</span> <span class="o">=</span> <span class="s">"."</span><span class="p">,</span> <span class="n">writename</span> <span class="o">=</span> <span class="bp">None</span><span class="p">,</span> <span class="n">dev</span> <span class="o">=</span> <span class="bp">False</span><span class="p">,</span> <span class="n">db</span> <span class="o">=</span> <span class="bp">None</span><span class="p">,</span> <span class="n">dbid</span> <span class="o">=</span> <span class="bp">None</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> :param input: The input resource, either a path to an image or a raw numpy array.</span>
+<span class="sd"> :type resource: numpy.ndarray or str</span>
+<span class="sd"> :param outputdir: The directory to write output files</span>
+<span class="sd"> :type outputdir: str</span>
+<span class="sd"> :param writename: The name to write the output file as, should include extension.</span>
+<span class="sd"> :type writename: str</span>
+<span class="sd"> :param dev: Dev mode will do something...</span>
+<span class="sd"> :type dev: bool</span>
+<span class="sd"> """</span>
+ <span class="k">if</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">isdir</span><span class="p">(</span><span class="n">outputdir</span><span class="p">):</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">states</span> <span class="o">=</span> <span class="p">{}</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_loadDb</span><span class="p">(</span><span class="n">db</span><span class="p">,</span> <span class="n">dbid</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">input</span> <span class="o">=</span> <span class="nb">input</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">fname</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">image</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_loadResource</span><span class="p">(</span><span class="nb">input</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">y</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">image</span><span class="o">.</span><span class="n">shape</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">x</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">image</span><span class="o">.</span><span class="n">shape</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">outputdir</span> <span class="o">=</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">abspath</span><span class="p">(</span><span class="n">outputdir</span><span class="p">)</span>
+ <span class="k">if</span> <span class="n">writename</span><span class="p">:</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">writename</span> <span class="o">=</span> <span class="n">writename</span>
+ <span class="k">elif</span> <span class="nb">isinstance</span><span class="p">(</span><span class="nb">input</span><span class="p">,</span> <span class="n">np</span><span class="o">.</span><span class="n">ndarray</span><span class="p">):</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">writename</span> <span class="o">=</span> <span class="s">"out.png"</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">writename</span> <span class="o">=</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">basename</span><span class="p">(</span><span class="nb">input</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">dev</span> <span class="o">=</span> <span class="n">dev</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">window</span> <span class="o">=</span> <span class="mi">1</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="s">"Invalid output!"</span><span class="p">)</span>
+ <span class="k">return</span>
+
+ <span class="k">def</span> <span class="nf">_closeDb</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+ <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">conn</span><span class="p">:</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">conn</span><span class="o">.</span><span class="n">close</span><span class="p">()</span>
+ <span class="k">return</span>
+
+ <span class="k">def</span> <span class="nf">_loadDb</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">db</span><span class="p">,</span> <span class="n">dbid</span><span class="p">):</span>
+ <span class="k">if</span> <span class="n">db</span><span class="p">:</span>
+ <span class="k">if</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">isfile</span><span class="p">(</span><span class="n">db</span><span class="p">):</span>
+ <span class="k">if</span> <span class="n">dbid</span><span class="p">:</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">dbid</span> <span class="o">=</span> <span class="n">dbid</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">conn</span> <span class="o">=</span> <span class="n">sqlite3</span><span class="o">.</span><span class="n">connect</span><span class="p">(</span><span class="n">db</span><span class="p">,</span> <span class="n">check_same_thread</span> <span class="o">=</span> <span class="bp">False</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">conn</span><span class="o">.</span><span class="n">row_factory</span> <span class="o">=</span> <span class="n">sqlite3</span><span class="o">.</span><span class="n">Row</span>
+ <span class="n">result</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">conn</span><span class="o">.</span><span class="n">execute</span><span class="p">(</span><span class="s">"select pegasusid from images where pegasusid=?"</span><span class="p">,</span> <span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">dbid</span><span class="p">,))</span>
+ <span class="k">if</span> <span class="ow">not</span> <span class="n">result</span><span class="o">.</span><span class="n">fetchone</span><span class="p">():</span>
+ <span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="s">"Invalid pegasusid given!"</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_addColumn</span><span class="p">(</span><span class="s">"error"</span><span class="p">)</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="s">"A database id must be provided if you give a database."</span><span class="p">)</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="s">"Invalid database given!"</span><span class="p">)</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">conn</span> <span class="o">=</span> <span class="bp">False</span>
+ <span class="k">return</span>
+
+ <span class="k">def</span> <span class="nf">_addColumn</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">column</span><span class="p">,</span> <span class="n">tablename</span> <span class="o">=</span> <span class="s">"images"</span><span class="p">):</span>
+ <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">conn</span><span class="p">:</span>
+ <span class="k">if</span> <span class="n">column</span> <span class="ow">not</span> <span class="ow">in</span> <span class="p">[</span><span class="n">row</span><span class="p">[</span><span class="s">"name"</span><span class="p">]</span> <span class="k">for</span> <span class="n">row</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">conn</span><span class="o">.</span><span class="n">execute</span><span class="p">(</span><span class="s">"PRAGMA table_info("</span> <span class="o">+</span> <span class="n">tablename</span> <span class="o">+</span> <span class="s">");"</span><span class="p">)]:</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">conn</span><span class="o">.</span><span class="n">execute</span><span class="p">(</span><span class="s">"alter table "</span> <span class="o">+</span> <span class="n">tablename</span> <span class="o">+</span> <span class="s">" add column "</span> <span class="o">+</span> <span class="n">column</span> <span class="o">+</span> <span class="s">";"</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">conn</span><span class="o">.</span><span class="n">commit</span><span class="p">()</span>
+ <span class="k">return</span>
+
+ <span class="k">def</span> <span class="nf">_loadROIArg</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">arg</span><span class="p">,</span> <span class="n">i</span><span class="p">):</span>
+ <span class="n">vals</span> <span class="o">=</span> <span class="p">{</span>
+ <span class="mi">0</span><span class="p">:</span> <span class="mi">0</span><span class="p">,</span>
+ <span class="mi">1</span><span class="p">:</span> <span class="bp">self</span><span class="o">.</span><span class="n">y</span><span class="p">,</span>
+ <span class="mi">2</span><span class="p">:</span> <span class="mi">0</span><span class="p">,</span>
+ <span class="mi">3</span><span class="p">:</span> <span class="bp">self</span><span class="o">.</span><span class="n">x</span>
+ <span class="p">}</span>
+ <span class="n">arg</span> <span class="o">=</span> <span class="nb">str</span><span class="p">(</span><span class="n">arg</span><span class="p">)</span>
+ <span class="k">if</span> <span class="n">arg</span> <span class="o">==</span> <span class="s">"-1"</span><span class="p">:</span>
+ <span class="k">return</span> <span class="n">vals</span><span class="p">[</span><span class="n">i</span><span class="p">]</span>
+ <span class="n">arg</span> <span class="o">=</span> <span class="n">arg</span><span class="o">.</span><span class="n">replace</span><span class="p">(</span><span class="s">"x"</span><span class="p">,</span> <span class="nb">str</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">x</span><span class="p">))</span><span class="o">.</span><span class="n">replace</span><span class="p">(</span><span class="s">"y"</span><span class="p">,</span> <span class="nb">str</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">y</span><span class="p">))</span><span class="o">.</span><span class="n">replace</span><span class="p">(</span><span class="s">" "</span><span class="p">,</span><span class="s">""</span><span class="p">)</span>
+ <span class="k">if</span> <span class="s">"-"</span> <span class="ow">in</span> <span class="n">arg</span><span class="p">:</span>
+ <span class="k">try</span><span class="p">:</span>
+ <span class="n">left</span><span class="p">,</span> <span class="n">right</span> <span class="o">=</span> <span class="n">arg</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s">"-"</span><span class="p">)</span>
+ <span class="k">return</span> <span class="nb">int</span><span class="p">(</span><span class="n">left</span><span class="p">)</span> <span class="o">-</span> <span class="nb">int</span><span class="p">(</span><span class="n">right</span><span class="p">)</span>
+ <span class="k">except</span><span class="p">:</span>
+ <span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="s">"Could not load roi arg '</span><span class="si">%s</span><span class="s">'"</span> <span class="o">%</span> <span class="p">(</span><span class="n">arg</span><span class="p">,))</span>
+ <span class="k">elif</span> <span class="s">"+"</span> <span class="ow">in</span> <span class="n">arg</span><span class="p">:</span>
+ <span class="k">try</span><span class="p">:</span>
+ <span class="n">left</span><span class="p">,</span> <span class="n">right</span> <span class="o">=</span> <span class="n">arg</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s">"+"</span><span class="p">)</span>
+ <span class="k">return</span> <span class="nb">int</span><span class="p">(</span><span class="n">left</span><span class="p">)</span> <span class="o">+</span> <span class="nb">int</span><span class="p">(</span><span class="n">right</span><span class="p">)</span>
+ <span class="k">except</span><span class="p">:</span>
+ <span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="s">"Could not load roi arg '</span><span class="si">%s</span><span class="s">'"</span> <span class="o">%</span> <span class="p">(</span><span class="n">arg</span><span class="p">,))</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="k">return</span> <span class="nb">int</span><span class="p">(</span><span class="n">arg</span><span class="p">)</span>
+
+ <span class="k">def</span> <span class="nf">_loadROI</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">roi</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> :param roi: The region of interest to load.</span>
+<span class="sd"> :type roi: list or file</span>
+<span class="sd"> :return: The region of interest of form [ystart, yend, xstart, xend]</span>
+<span class="sd"> :rtype: list</span>
+<span class="sd"> :raises OSError: if the input path does not exist.</span>
+<span class="sd"> </span>
+<span class="sd"> Loads a region of interest, either a path to an roi or a raw list.</span>
+<span class="sd"> """</span>
+ <span class="k">if</span> <span class="ow">not</span> <span class="n">roi</span><span class="p">:</span>
+ <span class="n">roi</span> <span class="o">=</span> <span class="p">[</span><span class="o">-</span><span class="mi">1</span><span class="p">,</span> <span class="o">-</span><span class="mi">1</span><span class="p">,</span> <span class="o">-</span><span class="mi">1</span><span class="p">,</span> <span class="o">-</span><span class="mi">1</span><span class="p">]</span>
+ <span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">roi</span><span class="p">,</span> <span class="nb">list</span><span class="p">):</span>
+ <span class="k">return</span> <span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">_loadROIArg</span><span class="p">(</span><span class="n">z</span><span class="p">,</span> <span class="n">i</span><span class="p">)</span> <span class="k">for</span> <span class="n">i</span><span class="p">,</span><span class="n">z</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="n">roi</span><span class="p">)]</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="k">if</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">isfile</span><span class="p">(</span><span class="n">roi</span><span class="p">):</span>
+ <span class="k">try</span><span class="p">:</span>
+ <span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="n">roi</span><span class="p">,</span> <span class="s">"r"</span><span class="p">)</span> <span class="k">as</span> <span class="n">rh</span><span class="p">:</span>
+ <span class="n">r</span> <span class="o">=</span> <span class="n">json</span><span class="o">.</span><span class="n">load</span><span class="p">(</span><span class="n">rh</span><span class="p">)</span>
+ <span class="k">if</span> <span class="nb">all</span><span class="p">(</span><span class="n">x</span> <span class="ow">in</span> <span class="n">r</span> <span class="k">for</span> <span class="n">x</span> <span class="ow">in</span> <span class="p">[</span><span class="s">"xstart"</span><span class="p">,</span> <span class="s">"xend"</span><span class="p">,</span> <span class="s">"ystart"</span><span class="p">,</span> <span class="s">"yend"</span><span class="p">]):</span>
+ <span class="k">return</span> <span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">_loadROIArg</span><span class="p">(</span><span class="n">r</span><span class="p">[</span><span class="s">"ystart"</span><span class="p">],</span> <span class="mi">0</span><span class="p">),</span> <span class="bp">self</span><span class="o">.</span><span class="n">_loadROIArg</span><span class="p">(</span><span class="n">r</span><span class="p">[</span><span class="s">"yend"</span><span class="p">],</span> <span class="mi">1</span><span class="p">),</span> <span class="bp">self</span><span class="o">.</span><span class="n">_loadROIArg</span><span class="p">(</span><span class="n">r</span><span class="p">[</span><span class="s">"xstart"</span><span class="p">],</span> <span class="mi">2</span><span class="p">),</span> <span class="bp">self</span><span class="o">.</span><span class="n">_loadROIArg</span><span class="p">(</span><span class="n">r</span><span class="p">[</span><span class="s">"xend"</span><span class="p">],</span> <span class="mi">3</span><span class="p">)]</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="s">"Input roi file '</span><span class="si">%s</span><span class="s">' needs xstart, xend, ystart, and yend definitions!"</span> <span class="o">%</span> <span class="p">(</span><span class="n">roi</span><span class="p">,))</span>
+ <span class="k">except</span> <span class="ne">Exception</span> <span class="k">as</span> <span class="n">e</span><span class="p">:</span>
+ <span class="k">print</span> <span class="n">traceback</span><span class="o">.</span><span class="n">format_exc</span><span class="p">()</span>
+ <span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="s">"Input roi file '</span><span class="si">%s</span><span class="s">' is not valid json!"</span> <span class="o">%</span> <span class="p">(</span><span class="n">roi</span><span class="p">,))</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="s">"Input path to roi file '</span><span class="si">%s</span><span class="s">' does not exist!"</span> <span class="o">%</span> <span class="p">(</span><span class="n">roi</span><span class="p">,))</span>
+ <span class="k">return</span>
+
+ <span class="k">def</span> <span class="nf">_writeROI</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">roi</span><span class="p">,</span> <span class="n">output</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> :param roi: The region of interest to write.</span>
+<span class="sd"> :type roi: list</span>
+<span class="sd"> """</span>
+ <span class="k">try</span><span class="p">:</span>
+ <span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">outputdir</span> <span class="o">+</span> <span class="s">"/"</span> <span class="o">+</span> <span class="n">output</span><span class="p">,</span> <span class="s">"w"</span><span class="p">)</span> <span class="k">as</span> <span class="n">wh</span><span class="p">:</span>
+ <span class="n">wh</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="n">json</span><span class="o">.</span><span class="n">dumps</span><span class="p">({</span><span class="s">"ystart"</span><span class="p">:</span> <span class="n">roi</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span> <span class="s">"yend"</span><span class="p">:</span> <span class="n">roi</span><span class="p">[</span><span class="mi">1</span><span class="p">],</span> <span class="s">"xstart"</span><span class="p">:</span> <span class="n">roi</span><span class="p">[</span><span class="mi">2</span><span class="p">],</span> <span class="s">"xend"</span><span class="p">:</span> <span class="n">roi</span><span class="p">[</span><span class="mi">3</span><span class="p">]},</span> <span class="n">indent</span> <span class="o">=</span> <span class="mi">4</span><span class="p">))</span>
+ <span class="k">except</span><span class="p">:</span>
+ <span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="s">"Could not write roi."</span><span class="p">)</span>
+ <span class="k">return</span>
+
+ <span class="k">def</span> <span class="nf">_loadBins</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">binlist</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> :param bin: The bin to load</span>
+<span class="sd"> :type bin: list or file</span>
+<span class="sd"> """</span>
+
+ <span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">binlist</span><span class="p">,</span> <span class="nb">list</span><span class="p">):</span>
+ <span class="k">return</span> <span class="n">binlist</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="k">if</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">isfile</span><span class="p">(</span><span class="n">binlist</span><span class="p">):</span>
+ <span class="k">try</span><span class="p">:</span>
+ <span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="n">binlist</span><span class="p">,</span> <span class="s">"r"</span><span class="p">)</span> <span class="k">as</span> <span class="n">rh</span><span class="p">:</span>
+ <span class="k">return</span> <span class="n">json</span><span class="o">.</span><span class="n">load</span><span class="p">(</span><span class="n">rh</span><span class="p">)</span>
+ <span class="k">except</span><span class="p">:</span>
+ <span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="s">"Bin list not valid json!"</span><span class="p">)</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="s">"Bin file does not exist."</span><span class="p">)</span>
+ <span class="k">return</span>
+
+ <span class="k">def</span> <span class="nf">_loadResource</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">resource</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> :param resource: The resource to load.</span>
+<span class="sd"> :type resource: numpy.ndarray or file</span>
+<span class="sd"> :return: The image</span>
+<span class="sd"> :rtype: numpy.ndarray</span>
+<span class="sd"> :raises OSError: if the input path does not exist.</span>
+<span class="sd"> </span>
+<span class="sd"> Loads a resource, either a path to an image or a raw numpy array.</span>
+<span class="sd"> """</span>
+ <span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">resource</span><span class="p">,</span> <span class="n">np</span><span class="o">.</span><span class="n">ndarray</span><span class="p">):</span>
+ <span class="k">return</span> <span class="p">(</span><span class="s">"unknown"</span><span class="p">,</span> <span class="n">resource</span><span class="o">.</span><span class="n">copy</span><span class="p">())</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="k">if</span> <span class="n">resource</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">states</span><span class="p">:</span>
+ <span class="k">return</span> <span class="p">(</span><span class="n">resource</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">states</span><span class="p">[</span><span class="n">resource</span><span class="p">]</span><span class="o">.</span><span class="n">copy</span><span class="p">())</span>
+ <span class="k">elif</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">isfile</span><span class="p">(</span><span class="n">resource</span><span class="p">):</span>
+ <span class="n">image</span> <span class="o">=</span> <span class="n">cv2</span><span class="o">.</span><span class="n">imread</span><span class="p">(</span><span class="n">resource</span><span class="p">)</span>
+ <span class="k">if</span> <span class="n">image</span> <span class="ow">is</span> <span class="ow">not</span> <span class="bp">None</span><span class="p">:</span>
+ <span class="k">return</span> <span class="p">(</span><span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">basename</span><span class="p">(</span><span class="n">resource</span><span class="p">),</span> <span class="n">image</span><span class="p">)</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">conn</span><span class="p">:</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">conn</span><span class="o">.</span><span class="n">execute</span><span class="p">(</span><span class="s">"update images set error =? where pegasusid = ?"</span><span class="p">,</span> <span class="p">(</span><span class="s">"Load Error, input is not an image."</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">dbid</span><span class="p">))</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">conn</span><span class="o">.</span><span class="n">commit</span><span class="p">()</span>
+ <span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="s">"Input is not an image."</span><span class="p">)</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">conn</span><span class="p">:</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">conn</span><span class="o">.</span><span class="n">execute</span><span class="p">(</span><span class="s">"update images set error = ? where pegasusid = ?"</span><span class="p">,</span> <span class="p">(</span><span class="s">"Load Error, input path doesn't exist or specified resource is not a saved state."</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">dbid</span><span class="p">))</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">conn</span><span class="o">.</span><span class="n">commit</span><span class="p">()</span>
+ <span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="s">"Input path to resource does not exist."</span><span class="p">)</span>
+ <span class="k">return</span>
+
+ <span class="k">def</span> <span class="nf">_colorHistogram</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> :return: A list of histograms, corresponding to R, G, B.</span>
+<span class="sd"> :rtype: List of numpy arrays.</span>
+<span class="sd"> </span>
+<span class="sd"> Calculates a normalized colorHistogram of the current image. </span>
+<span class="sd"> The intensity is normalized between 0 and 255.</span>
+<span class="sd"> """</span>
+ <span class="n">returnhist</span> <span class="o">=</span> <span class="p">[]</span>
+
+ <span class="k">for</span> <span class="n">ch</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="mi">0</span><span class="p">,</span> <span class="mi">3</span><span class="p">):</span>
+ <span class="n">hist_item</span> <span class="o">=</span> <span class="n">cv2</span><span class="o">.</span><span class="n">calcHist</span><span class="p">([</span><span class="bp">self</span><span class="o">.</span><span class="n">image</span><span class="p">],</span> <span class="p">[</span><span class="n">ch</span><span class="p">],</span> <span class="bp">None</span><span class="p">,</span> <span class="p">[</span><span class="mi">256</span><span class="p">],</span> <span class="p">[</span><span class="mi">1</span><span class="p">,</span><span class="mi">255</span><span class="p">])</span>
+ <span class="n">cv2</span><span class="o">.</span><span class="n">normalize</span><span class="p">(</span><span class="n">hist_item</span><span class="p">,</span> <span class="n">hist_item</span><span class="p">,</span> <span class="mi">0</span><span class="p">,</span> <span class="mi">255</span><span class="p">,</span> <span class="n">cv2</span><span class="o">.</span><span class="n">NORM_MINMAX</span><span class="p">)</span>
+ <span class="n">hist</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">int32</span><span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">around</span><span class="p">(</span><span class="n">hist_item</span><span class="p">))</span>
+ <span class="n">returnhist</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">hist</span><span class="p">)</span>
+ <span class="k">return</span> <span class="n">returnhist</span>
+
+ <span class="k">def</span> <span class="nf">_isColor</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">image</span> <span class="o">=</span> <span class="bp">None</span><span class="p">):</span>
+ <span class="n">image</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">image</span> <span class="k">if</span> <span class="n">image</span> <span class="ow">is</span> <span class="bp">None</span> <span class="k">else</span> <span class="n">image</span>
+ <span class="k">return</span> <span class="nb">len</span><span class="p">(</span><span class="n">image</span><span class="o">.</span><span class="n">shape</span><span class="p">)</span> <span class="o">==</span> <span class="mi">3</span>
+
+<div class="viewcode-block" id="Image.save"><a class="viewcode-back" href="../../processing.html#ih.imgproc.Image.save">[docs]</a> <span class="k">def</span> <span class="nf">save</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">name</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> :param name: The name to save the image under.</span>
+<span class="sd"> :type name: str OR any hashable type.</span>
+<span class="sd"> </span>
+<span class="sd"> This function saves the current image in the 'states' variable under</span>
+<span class="sd"> the specified name. It can then be reloaded using the :py:meth:`~ih.imgproc.Image.restore`</span>
+<span class="sd"> method.</span>
+<span class="sd"> """</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">states</span><span class="p">[</span><span class="n">name</span><span class="p">]</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">image</span><span class="o">.</span><span class="n">copy</span><span class="p">()</span>
+ <span class="k">return</span>
+ </div>
+<div class="viewcode-block" id="Image.restore"><a class="viewcode-back" href="../../processing.html#ih.imgproc.Image.restore">[docs]</a> <span class="k">def</span> <span class="nf">restore</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">name</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> :param name: The name the image is saved under.</span>
+<span class="sd"> :type name: str OR any hashable type.</span>
+<span class="sd"> </span>
+<span class="sd"> Reloads a previously saved image from the 'states' variable.</span>
+<span class="sd"> """</span>
+ <span class="k">if</span> <span class="n">name</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">states</span><span class="p">:</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">image</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">states</span><span class="p">[</span><span class="n">name</span><span class="p">]</span><span class="o">.</span><span class="n">copy</span><span class="p">()</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">y</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">image</span><span class="o">.</span><span class="n">shape</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">x</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">image</span><span class="o">.</span><span class="n">shape</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="k">print</span> <span class="s">"Invalid state specified."</span>
+ <span class="k">return</span>
+ </div>
+<div class="viewcode-block" id="Image.list"><a class="viewcode-back" href="../../processing.html#ih.imgproc.Image.list">[docs]</a> <span class="k">def</span> <span class="nf">list</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> Lists all saved states.</span>
+<span class="sd"> """</span>
+ <span class="k">for</span> <span class="n">state</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">states</span><span class="p">:</span>
+ <span class="k">print</span> <span class="n">state</span>
+ <span class="k">return</span>
+ </div>
+<div class="viewcode-block" id="Image.destroy"><a class="viewcode-back" href="../../processing.html#ih.imgproc.Image.destroy">[docs]</a> <span class="k">def</span> <span class="nf">destroy</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> Destroys all currently open windows.</span>
+<span class="sd"> """</span>
+ <span class="n">cv2</span><span class="o">.</span><span class="n">destroyAllWindows</span><span class="p">()</span>
+ <span class="k">return</span>
+ </div>
+<div class="viewcode-block" id="Image.wait"><a class="viewcode-back" href="../../processing.html#ih.imgproc.Image.wait">[docs]</a> <span class="k">def</span> <span class="nf">wait</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> Waits until a key is pressed, then destroys all windows and</span>
+<span class="sd"> continues program execution.</span>
+<span class="sd"> """</span>
+ <span class="n">cv2</span><span class="o">.</span><span class="n">waitKey</span><span class="p">(</span><span class="mi">0</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">destroy</span><span class="p">()</span>
+ <span class="k">return</span>
+ </div>
+<div class="viewcode-block" id="Image.show"><a class="viewcode-back" href="../../processing.html#ih.imgproc.Image.show">[docs]</a> <span class="k">def</span> <span class="nf">show</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">title</span> <span class="o">=</span> <span class="bp">None</span><span class="p">):</span>
+ <span class="sd">""" </span>
+<span class="sd"> :param title: The title to give the display window, if left blank one will be created.</span>
+<span class="sd"> :type title: str</span>
+<span class="sd"> :return: None</span>
+<span class="sd"> </span>
+<span class="sd"> Displays the image in a window. Utilizes the :py:meth:`~ih.imgproc.Image.resize` function.</span>
+<span class="sd"> If a title is not specified, the window will be named 'windowX' where X is the number of times</span>
+<span class="sd"> show has been called.</span>
+<span class="sd"> </span>
+<span class="sd"> """</span>
+ <span class="n">cv2</span><span class="o">.</span><span class="n">imshow</span><span class="p">(</span><span class="n">title</span> <span class="k">if</span> <span class="n">title</span> <span class="k">else</span> <span class="s">"window "</span> <span class="o">+</span> <span class="nb">str</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">window</span><span class="p">),</span> <span class="bp">self</span><span class="o">.</span><span class="n">resize</span><span class="p">())</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">window</span> <span class="o">+=</span> <span class="mi">1</span>
+ <span class="k">return</span>
+ </div>
+<div class="viewcode-block" id="Image.resizeSelf"><a class="viewcode-back" href="../../processing.html#ih.imgproc.Image.resizeSelf">[docs]</a> <span class="k">def</span> <span class="nf">resizeSelf</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">scale</span> <span class="o">=</span> <span class="bp">None</span><span class="p">,</span> <span class="n">width</span> <span class="o">=</span> <span class="bp">None</span><span class="p">,</span> <span class="n">height</span> <span class="o">=</span> <span class="bp">None</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> :param scale: Value to scale image by.</span>
+<span class="sd"> :type scale: float</span>
+<span class="sd"> :param width: Target width of image.</span>
+<span class="sd"> :type width: int</span>
+<span class="sd"> :param height: Target height of image.</span>
+<span class="sd"> :type height: int</span>
+<span class="sd"> </span>
+<span class="sd"> Resizes the current image. If scale is set, it simply resizes the</span>
+<span class="sd"> width and height of the image based on the scale. If only one of width</span>
+<span class="sd"> or height is set, it scales the other accordingly. If both width</span>
+<span class="sd"> and height are set, it scales the image to the exact size specified.</span>
+<span class="sd"> """</span>
+ <span class="k">if</span> <span class="n">scale</span> <span class="ow">or</span> <span class="n">width</span> <span class="ow">or</span> <span class="n">height</span><span class="p">:</span>
+ <span class="k">if</span> <span class="n">scale</span><span class="p">:</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">image</span> <span class="o">=</span> <span class="n">cv2</span><span class="o">.</span><span class="n">resize</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">image</span><span class="p">,</span> <span class="p">(</span><span class="nb">int</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">x</span> <span class="o">*</span> <span class="n">scale</span><span class="p">),</span> <span class="nb">int</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">y</span> <span class="o">*</span> <span class="n">scale</span><span class="p">)))</span>
+ <span class="k">elif</span> <span class="n">width</span> <span class="ow">and</span> <span class="n">height</span><span class="p">:</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">image</span> <span class="o">=</span> <span class="n">cv2</span><span class="o">.</span><span class="n">resize</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">image</span><span class="p">,</span> <span class="n">height</span><span class="p">,</span> <span class="n">width</span><span class="p">)</span>
+ <span class="k">elif</span> <span class="n">width</span><span class="p">:</span>
+ <span class="n">scale</span> <span class="o">=</span> <span class="nb">float</span><span class="p">(</span><span class="n">width</span><span class="p">)</span> <span class="o">/</span> <span class="nb">float</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">x</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">image</span> <span class="o">=</span> <span class="n">cv2</span><span class="o">.</span><span class="n">resize</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">image</span><span class="p">,</span> <span class="p">(</span><span class="nb">int</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">x</span> <span class="o">*</span> <span class="n">scale</span><span class="p">),</span> <span class="nb">int</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">y</span> <span class="o">*</span> <span class="n">scale</span><span class="p">)))</span>
+ <span class="k">elif</span> <span class="n">height</span><span class="p">:</span>
+ <span class="n">scale</span> <span class="o">=</span> <span class="nb">float</span><span class="p">(</span><span class="n">height</span><span class="p">)</span> <span class="o">/</span> <span class="nb">float</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">y</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">image</span> <span class="o">=</span> <span class="n">cv2</span><span class="o">.</span><span class="n">resize</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">image</span><span class="p">,</span> <span class="p">(</span><span class="nb">int</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">x</span> <span class="o">*</span> <span class="n">scale</span><span class="p">),</span> <span class="nb">int</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">y</span> <span class="o">*</span> <span class="n">scale</span><span class="p">)))</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">y</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">image</span><span class="o">.</span><span class="n">shape</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">x</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">image</span><span class="o">.</span><span class="n">shape</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span>
+ <span class="k">return</span>
+ </div>
+<div class="viewcode-block" id="Image.resize"><a class="viewcode-back" href="../../processing.html#ih.imgproc.Image.resize">[docs]</a> <span class="k">def</span> <span class="nf">resize</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> If the image is large than conf.maxArea, resize its total area down to conf.maxArea.</span>
+<span class="sd"> This function is primarily used for viewing purposes, and as such, it does not resize</span>
+<span class="sd"> the base image, but creates a copy to resize instead.</span>
+<span class="sd"> """</span>
+ <span class="k">if</span> <span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">image</span><span class="o">.</span><span class="n">shape</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="o">*</span> <span class="bp">self</span><span class="o">.</span><span class="n">image</span><span class="o">.</span><span class="n">shape</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span> <span class="o">></span> <span class="n">conf</span><span class="o">.</span><span class="n">maxArea</span><span class="p">):</span>
+ <span class="n">scale</span> <span class="o">=</span> <span class="mi">1</span> <span class="o">/</span> <span class="n">math</span><span class="o">.</span><span class="n">sqrt</span><span class="p">((</span><span class="bp">self</span><span class="o">.</span><span class="n">image</span><span class="o">.</span><span class="n">shape</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span> <span class="o">*</span> <span class="bp">self</span><span class="o">.</span><span class="n">image</span><span class="o">.</span><span class="n">shape</span><span class="p">[</span><span class="mi">0</span><span class="p">])</span> <span class="o">/</span> <span class="n">conf</span><span class="o">.</span><span class="n">maxArea</span><span class="p">)</span>
+ <span class="k">return</span> <span class="n">cv2</span><span class="o">.</span><span class="n">resize</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">image</span><span class="o">.</span><span class="n">copy</span><span class="p">(),</span> <span class="p">(</span><span class="nb">int</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">x</span><span class="o">*</span><span class="n">scale</span><span class="p">),</span> <span class="nb">int</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">y</span><span class="o">*</span><span class="n">scale</span><span class="p">)))</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">image</span>
+ </div>
+<div class="viewcode-block" id="Image.write"><a class="viewcode-back" href="../../processing.html#ih.imgproc.Image.write">[docs]</a> <span class="k">def</span> <span class="nf">write</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">name</span> <span class="o">=</span> <span class="bp">None</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> Writes the current image to the given output directory, with the given name.</span>
+<span class="sd"> """</span>
+ <span class="n">writename</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">writename</span> <span class="k">if</span> <span class="ow">not</span> <span class="n">name</span> <span class="k">else</span> <span class="n">name</span>
+ <span class="n">cv2</span><span class="o">.</span><span class="n">imwrite</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">outputdir</span> <span class="o">+</span> <span class="s">"/"</span> <span class="o">+</span> <span class="n">writename</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">image</span><span class="p">)</span>
+ <span class="k">return</span>
+ </div>
+<div class="viewcode-block" id="Image.convertColor"><a class="viewcode-back" href="../../processing.html#ih.imgproc.Image.convertColor">[docs]</a> <span class="k">def</span> <span class="nf">convertColor</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">intype</span><span class="p">,</span> <span class="n">outtype</span><span class="p">):</span>
+ <span class="sd">""" </span>
+<span class="sd"> :param intype: The input image type</span>
+<span class="sd"> :type intype: str</span>
+<span class="sd"> :param outtype: The output image type</span>
+<span class="sd"> :type outtype: str</span>
+<span class="sd"> :return: The converted image.</span>
+<span class="sd"> :rtype: numpy.ndarray</span>
+<span class="sd"> :raises: KeyError</span>
+<span class="sd"> </span>
+<span class="sd"> Converts the given image between color spaces, based on the given types.</span>
+<span class="sd"> Supported types are: bgr, gray, hsv, lab, and ycrcb. Note, you cannot</span>
+<span class="sd"> restore color to a gray image with this function, for that you must use</span>
+<span class="sd"> bitwise_and with an appropriate mask + image. </span>
+<span class="sd"> """</span>
+ <span class="k">if</span> <span class="n">intype</span> <span class="ow">in</span> <span class="n">conf</span><span class="o">.</span><span class="n">colors</span><span class="p">:</span>
+ <span class="k">if</span> <span class="n">outtype</span> <span class="ow">in</span> <span class="n">conf</span><span class="o">.</span><span class="n">colors</span><span class="p">[</span><span class="n">intype</span><span class="p">]:</span>
+ <span class="k">for</span> <span class="n">code</span> <span class="ow">in</span> <span class="n">conf</span><span class="o">.</span><span class="n">colors</span><span class="p">[</span><span class="n">intype</span><span class="p">][</span><span class="n">outtype</span><span class="p">]:</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">image</span> <span class="o">=</span> <span class="n">cv2</span><span class="o">.</span><span class="n">cvtColor</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">image</span><span class="p">,</span> <span class="n">code</span><span class="p">)</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="k">raise</span> <span class="ne">KeyError</span><span class="p">(</span><span class="n">outtype</span> <span class="o">+</span> <span class="s">" is not a valid output type for the input type: "</span> <span class="o">+</span> <span class="n">intype</span><span class="p">)</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="k">raise</span> <span class="ne">KeyError</span><span class="p">(</span><span class="n">intype</span> <span class="o">+</span> <span class="s">" is not a valid image type."</span><span class="p">)</span>
+ <span class="k">return</span>
+ </div>
+<div class="viewcode-block" id="Image.threshold"><a class="viewcode-back" href="../../processing.html#ih.imgproc.Image.threshold">[docs]</a> <span class="k">def</span> <span class="nf">threshold</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">thresh</span><span class="p">,</span> <span class="nb">max</span> <span class="o">=</span> <span class="mi">255</span><span class="p">,</span> <span class="nb">type</span> <span class="o">=</span> <span class="s">"binary"</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> :param thresh: Threshold value.</span>
+<span class="sd"> :type thresh: int</span>
+<span class="sd"> :param max: Write value for binary threshold.</span>
+<span class="sd"> :type max: int</span>
+<span class="sd"> :param type: Threhsold type.</span>
+<span class="sd"> :type type: str</span>
+<span class="sd"> :return: The thresholded image.</span>
+<span class="sd"> :rtype: numpy.ndarray</span>
+<span class="sd"> :raises KeyError: if the specified threshold type doesn't exist.</span>
+<span class="sd"> </span>
+<span class="sd"> Thresholds the image based on the given type. The image must be </span>
+<span class="sd"> grayscale to be thresholded. If the image is of type 'bgr' it is</span>
+<span class="sd"> automatically converted to grayscale before thresholding.</span>
+<span class="sd"> Supported types are: binary, truncate, tozero, and otsu.</span>
+<span class="sd"> """</span>
+ <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">_isColor</span><span class="p">():</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">convertColor</span><span class="p">(</span><span class="s">"bgr"</span><span class="p">,</span> <span class="s">"gray"</span><span class="p">)</span>
+ <span class="k">if</span> <span class="nb">type</span> <span class="ow">in</span> <span class="n">conf</span><span class="o">.</span><span class="n">thresholds</span><span class="p">:</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">image</span> <span class="o">=</span> <span class="n">cv2</span><span class="o">.</span><span class="n">threshold</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">image</span><span class="p">,</span> <span class="n">thresh</span><span class="p">,</span> <span class="nb">max</span><span class="p">,</span> <span class="n">conf</span><span class="o">.</span><span class="n">thresholds</span><span class="p">[</span><span class="nb">type</span><span class="p">])[</span><span class="mi">1</span><span class="p">]</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="k">raise</span> <span class="ne">KeyError</span><span class="p">(</span><span class="nb">type</span> <span class="o">+</span> <span class="s">" is not a valid threshold type."</span><span class="p">)</span>
+ <span class="k">return</span>
+ </div>
+<div class="viewcode-block" id="Image.kmeans"><a class="viewcode-back" href="../../processing.html#ih.imgproc.Image.kmeans">[docs]</a> <span class="k">def</span> <span class="nf">kmeans</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">k</span><span class="p">,</span> <span class="n">criteria</span><span class="p">,</span> <span class="n">maxiter</span> <span class="o">=</span> <span class="mi">10</span><span class="p">,</span> <span class="n">accuracy</span> <span class="o">=</span> <span class="mf">1.0</span><span class="p">,</span> <span class="n">attempts</span> <span class="o">=</span> <span class="mi">10</span><span class="p">,</span> <span class="n">flags</span> <span class="o">=</span> <span class="s">"random"</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> :param k: Number of colors in final image.</span>
+<span class="sd"> :type k: int</span>
+<span class="sd"> :param criteria: Determination of how the algorithm stops execution. Should be one of 'accuracy', 'iteration', or 'either'.</span>
+<span class="sd"> :type criteria: str</span>
+<span class="sd"> :param maxiter: Maximum number of iterations of the algorithm.</span>
+<span class="sd"> :type maxiter: int</span>
+<span class="sd"> :param accuracy: Minimum accuracy before algorithm finishes executing.</span>
+<span class="sd"> :type accuracy: float</span>
+<span class="sd"> :param attempts: Number of times the algorithm is executed using different initial guesses.</span>
+<span class="sd"> :type attempts: int</span>
+<span class="sd"> :param flags: How to determine initial centers should be either 'random' or 'pp'.</span>
+<span class="sd"> :type flags: str</span>
+<span class="sd"> </span>
+<span class="sd"> This function is a wrapper to the OpenCV function `kmeans <http://docs.opencv.org/modules/core/doc/clustering.html>`_</span>
+<span class="sd"> Adjusts the colors in the image to find the most compact 'central' colors. The amount of colors</span>
+<span class="sd"> in the resulting image is the specified value 'k'. The colors are chosen based upon the minimum</span>
+<span class="sd"> amount of adjustment in the image necessary. The criteria parameter determines when the algorithm</span>
+<span class="sd"> stops. If 'accuracy' is specified, the algorithm runs until the specified accuracy is reached. If 'iteration'</span>
+<span class="sd"> is specified, the algorithm runs the specified number of iterations. If 'either' is specified, the algorithm</span>
+<span class="sd"> runs until one of the conditions is satisfied. The flags parameter determines the initial central colors,</span>
+<span class="sd"> and should be either 'random' -- to generate a random initial guess -- or 'pp' to use center initialization by Arthur and Vassilvitskii.</span>
+<span class="sd"> """</span>
+ <span class="k">if</span> <span class="n">flags</span> <span class="ow">in</span> <span class="n">conf</span><span class="o">.</span><span class="n">centers</span><span class="p">:</span>
+ <span class="k">if</span> <span class="n">criteria</span> <span class="ow">in</span> <span class="n">conf</span><span class="o">.</span><span class="n">ktermination</span><span class="p">:</span>
+ <span class="n">reshaped</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">image</span><span class="o">.</span><span class="n">reshape</span><span class="p">((</span><span class="o">-</span><span class="mi">1</span><span class="p">,</span><span class="mi">3</span><span class="p">))</span>
+ <span class="n">reshaped</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">float32</span><span class="p">(</span><span class="n">reshaped</span><span class="p">)</span>
+ <span class="n">ret</span><span class="p">,</span> <span class="n">label</span><span class="p">,</span> <span class="n">center</span> <span class="o">=</span> <span class="n">cv2</span><span class="o">.</span><span class="n">kmeans</span><span class="p">(</span><span class="n">reshaped</span><span class="p">,</span> <span class="n">k</span><span class="p">,</span> <span class="p">(</span><span class="n">conf</span><span class="o">.</span><span class="n">ktermination</span><span class="p">[</span><span class="n">criteria</span><span class="p">],</span> <span class="n">maxiter</span><span class="p">,</span> <span class="n">accuracy</span><span class="p">),</span> <span class="n">attempts</span><span class="p">,</span> <span class="n">conf</span><span class="o">.</span><span class="n">centers</span><span class="p">[</span><span class="n">flags</span><span class="p">])</span>
+ <span class="n">center</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">uint8</span><span class="p">(</span><span class="n">center</span><span class="p">)</span>
+ <span class="n">res</span> <span class="o">=</span> <span class="n">center</span><span class="p">[</span><span class="n">label</span><span class="o">.</span><span class="n">flatten</span><span class="p">()]</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">image</span> <span class="o">=</span> <span class="n">res</span><span class="o">.</span><span class="n">reshape</span><span class="p">((</span><span class="bp">self</span><span class="o">.</span><span class="n">image</span><span class="o">.</span><span class="n">shape</span><span class="p">))</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="k">raise</span> <span class="ne">KeyError</span><span class="p">(</span><span class="n">criteria</span> <span class="o">+</span> <span class="s">" is not a valid termination type. Should be one of 'accuracy', 'iteration', or 'either'"</span><span class="p">)</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="k">raise</span> <span class="ne">KeyError</span><span class="p">(</span><span class="n">flags</span> <span class="o">+</span> <span class="s">" is not a valid center type. Should be either 'random' or 'pp'."</span><span class="p">)</span>
+ <span class="k">return</span>
+
+ </div>
+<div class="viewcode-block" id="Image.meanshift"><a class="viewcode-back" href="../../processing.html#ih.imgproc.Image.meanshift">[docs]</a> <span class="k">def</span> <span class="nf">meanshift</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">spatial_radius</span><span class="p">,</span> <span class="n">range_radius</span><span class="p">,</span> <span class="n">min_density</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> :param spatial_radius: Spatial Radius</span>
+<span class="sd"> :type spatial_radius: float</span>
+<span class="sd"> :param range_radius: Range Radius.</span>
+<span class="sd"> :type range_radius: float</span>
+<span class="sd"> :param min_density: Minimum Density.</span>
+<span class="sd"> :type min_density: int</span>
+<span class="sd"> :return: The mean-shifted image.</span>
+<span class="sd"> :rtype: numpy.ndarray</span>
+<span class="sd"> </span>
+<span class="sd"> Segments the image into clusters based on nearest neighbors. This function</span>
+<span class="sd"> is a wrapper to the `pymeanshift <https://code.google.com/p/pymeanshift/>`_</span>
+<span class="sd"> module. For details on the algorithm itself: `Mean shift: A robust approach toward feature space analysis <http://dx.doi.org/10.1109/34.1000236>`_.</span>
+<span class="sd"> """</span>
+ <span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">image</span><span class="p">,</span> <span class="n">labels_image</span><span class="p">,</span> <span class="n">number_regions</span><span class="p">)</span> <span class="o">=</span> <span class="n">pms</span><span class="o">.</span><span class="n">segment</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">image</span><span class="p">,</span> <span class="n">spatial_radius</span> <span class="o">=</span> <span class="n">spatial_radius</span><span class="p">,</span> <span class="n">range_radius</span> <span class="o">=</span> <span class="n">range_radius</span><span class="p">,</span> <span class="n">min_density</span> <span class="o">=</span> <span class="n">min_density</span><span class="p">)</span>
+ <span class="k">return</span>
+ </div>
+<div class="viewcode-block" id="Image.adaptiveThreshold"><a class="viewcode-back" href="../../processing.html#ih.imgproc.Image.adaptiveThreshold">[docs]</a> <span class="k">def</span> <span class="nf">adaptiveThreshold</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">value</span><span class="p">,</span> <span class="n">adaptiveType</span><span class="p">,</span> <span class="n">thresholdType</span><span class="p">,</span> <span class="n">blockSize</span><span class="p">,</span> <span class="n">C</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> :param value: Intensity value for the pixels based on the thresholding conditions.</span>
+<span class="sd"> :type param: int</span>
+<span class="sd"> :param adaptiveType: Adaptive algorithm to use, should be either 'mean' or 'gaussian'.</span>
+<span class="sd"> :type adaptiveType: str</span>
+<span class="sd"> :param thresholdType: Threshold type, should be either 'binary' or 'inverse'.</span>
+<span class="sd"> :type thresholdType: str</span>
+<span class="sd"> :param blockSize: The window size to consider while thresholding, should only be an odd number.</span>
+<span class="sd"> :type blockSize: int</span>
+<span class="sd"> :param C: A constant subtracted from the calculated mean in each window.</span>
+<span class="sd"> :type C: int</span>
+<span class="sd"> </span>
+<span class="sd"> Thresholds an image by considering the image in several different windows instead of the image</span>
+<span class="sd"> as a whole. This function is a wrapper to the OpenCV function `adaptiveThreshold <http://docs.opencv.org/modules/imgproc/doc/miscellaneous_transformations.html#adaptivethreshold>`_.</span>
+<span class="sd"> Specifying 'mean' for adaptiveType calculates a simple mean of the area, wheras specifying 'gaussian' calculates a weighted sum</span>
+<span class="sd"> based upon a `Gaussian Kernel <http://docs.opencv.org/modules/imgproc/doc/filtering.html#Mat getGaussianKernel(int ksize, double sigma, int ktype)>`_.</span>
+<span class="sd"> Specifying 'binary' for thresholdType means that a particular intensity value must beat the threshold to be kept, whereas</span>
+<span class="sd"> specifying 'inverse' means that a particular intensity value must lose to the threshold to be kept.</span>
+<span class="sd"> Similar to a normal thresholding function, the image must be converted to grayscale first. This can be done using the</span>
+<span class="sd"> :meth:`~ih.imgproc.Image.convertColor` function, however, if your image is of type 'bgr', this is handled automatically.</span>
+<span class="sd"> """</span>
+ <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">_isColor</span><span class="p">():</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">convertColor</span><span class="p">(</span><span class="s">"bgr"</span><span class="p">,</span> <span class="s">"gray"</span><span class="p">)</span>
+ <span class="k">if</span> <span class="n">adaptiveType</span> <span class="ow">in</span> <span class="n">conf</span><span class="o">.</span><span class="n">adaptives</span><span class="p">:</span>
+ <span class="k">if</span> <span class="n">thresholdType</span> <span class="o">==</span> <span class="s">"binary"</span> <span class="ow">or</span> <span class="n">thresholdType</span> <span class="o">==</span> <span class="s">"inverse"</span><span class="p">:</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">image</span> <span class="o">=</span> <span class="n">cv2</span><span class="o">.</span><span class="n">adaptiveThreshold</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">image</span><span class="p">,</span> <span class="n">value</span><span class="p">,</span> <span class="n">conf</span><span class="o">.</span><span class="n">adaptives</span><span class="p">[</span><span class="n">adaptiveType</span><span class="p">],</span> <span class="n">conf</span><span class="o">.</span><span class="n">thresholds</span><span class="p">[</span><span class="n">thresholdType</span><span class="p">],</span> <span class="n">blockSize</span><span class="p">,</span> <span class="n">C</span><span class="p">)</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="s">"Threshold type: "</span> <span class="o">+</span> <span class="n">thresholdType</span> <span class="o">+</span> <span class="s">" must be either binary or inverse."</span><span class="p">)</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="s">"Adaptive type: "</span> <span class="o">+</span> <span class="n">adaptiveType</span> <span class="o">+</span> <span class="s">" is not a valid adaptive threshold type, should be either 'mean' or 'gaussian'"</span><span class="p">)</span>
+ <span class="k">return</span>
+ </div>
+<div class="viewcode-block" id="Image.blur"><a class="viewcode-back" href="../../processing.html#ih.imgproc.Image.blur">[docs]</a> <span class="k">def</span> <span class="nf">blur</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">ksize</span><span class="p">,</span> <span class="n">anchor</span> <span class="o">=</span> <span class="p">(</span><span class="o">-</span><span class="mi">1</span><span class="p">,</span> <span class="o">-</span><span class="mi">1</span><span class="p">),</span> <span class="n">borderType</span> <span class="o">=</span> <span class="s">"default"</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> :param ksize: The size of the kernel represented by a tuple (width, height). Both numbers should be odd and positive.</span>
+<span class="sd"> :type ksize: tuple</span>
+<span class="sd"> :param anchor: The anchor point for filtering. Default is (-1, -1) which is the center of the kernel.</span>
+<span class="sd"> :type anchor: tuple</span>
+<span class="sd"> :param borderType: The type of border mode used to extrapolate pixels outside the image.</span>
+<span class="sd"> :type borderType: str</span>
+<span class="sd"> </span>
+<span class="sd"> Smoothes an image using the normalized box filter. This function is a wrapper to the OpenCV function</span>
+<span class="sd"> `blur <http://docs.opencv.org/modules/imgproc/doc/filtering.html#blur>`_. Increasing the kernel size increase</span>
+<span class="sd"> the window considered when applying a blur. The anchor by default is the center of the kernel,</span>
+<span class="sd"> however you can alter the anchor to consider different areas of the kernel. When blurring on the edge</span>
+<span class="sd"> of the image, values for pixels that would be outside of the image are extrapolated. The method</span>
+<span class="sd"> of extrapolation depends on the specified 'borderType', and can be one of 'default', 'constant',</span>
+<span class="sd"> 'reflect', or 'replicate'.</span>
+<span class="sd"> """</span>
+ <span class="k">if</span> <span class="n">borderType</span> <span class="ow">in</span> <span class="n">conf</span><span class="o">.</span><span class="n">borders</span><span class="p">:</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">image</span> <span class="o">=</span> <span class="n">cv2</span><span class="o">.</span><span class="n">blur</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">image</span><span class="p">,</span> <span class="n">ksize</span><span class="p">,</span> <span class="n">anchor</span> <span class="o">=</span> <span class="n">anchor</span><span class="p">,</span> <span class="n">borderType</span> <span class="o">=</span> <span class="n">conf</span><span class="o">.</span><span class="n">borders</span><span class="p">[</span><span class="n">borderType</span><span class="p">])</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="s">"Invalid border type, should be one of: "</span> <span class="o">+</span> <span class="s">","</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">conf</span><span class="o">.</span><span class="n">borders</span><span class="o">.</span><span class="n">keys</span><span class="p">())</span> <span class="o">+</span> <span class="s">"."</span><span class="p">)</span>
+ <span class="k">return</span>
+ </div>
+<div class="viewcode-block" id="Image.medianBlur"><a class="viewcode-back" href="../../processing.html#ih.imgproc.Image.medianBlur">[docs]</a> <span class="k">def</span> <span class="nf">medianBlur</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">ksize</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> :param ksize: The size of the kernel (ksize x ksize). Should be odd and positive.</span>
+<span class="sd"> :type ksize: int</span>
+<span class="sd"> </span>
+<span class="sd"> This function smoothes an image using the median filter. The kernel is set to size (ksize, ksize).</span>
+<span class="sd"> The anchor position is assumed to be the center.</span>
+<span class="sd"> REFERENCE OPENCV MEDIAN BLUR</span>
+<span class="sd"> """</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">image</span> <span class="o">=</span> <span class="n">cv2</span><span class="o">.</span><span class="n">medianBlur</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">image</span><span class="p">,</span> <span class="n">ksize</span><span class="p">)</span>
+ <span class="k">return</span>
+ </div>
+<div class="viewcode-block" id="Image.gaussianBlur"><a class="viewcode-back" href="../../processing.html#ih.imgproc.Image.gaussianBlur">[docs]</a> <span class="k">def</span> <span class="nf">gaussianBlur</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">ksize</span><span class="p">,</span> <span class="n">sigmaX</span> <span class="o">=</span> <span class="mi">0</span><span class="p">,</span> <span class="n">sigmaY</span> <span class="o">=</span> <span class="mi">0</span><span class="p">,</span> <span class="n">borderType</span> <span class="o">=</span> <span class="s">"default"</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> :param ksize: The size of the kernel represented by a tuple (width, height). Both numers should be odd and positive.</span>
+<span class="sd"> :type ksize: tuple</span>
+<span class="sd"> :param sigmaX: The standard deviation in the x direction. If 0, the value is calculated based on the kernel size.</span>
+<span class="sd"> :type sigmaX: float</span>
+<span class="sd"> :param sigmaY: The standard deviation in the y direction. If 0, the value is equal to sigmaX.</span>
+<span class="sd"> :type sigmaY: float</span>
+<span class="sd"> :param borderType: The type of border mode used to extrapolate pixels outside the image.</span>
+<span class="sd"> :type borderType: str</span>
+<span class="sd"> </span>
+<span class="sd"> This function blurs an image based on a Gaussian kernel. When blurring on the edge</span>
+<span class="sd"> of the image, values for pixels that would be outside of the image are extrapolated. The method</span>
+<span class="sd"> of extrapolation depends on the specified 'borderType', and can be one of 'default', 'constant',</span>
+<span class="sd"> 'reflect', or 'replicate'. This function is a wrapper to the OpenCV function `GaussianBlur <http://docs.opencv.org/modules/imgproc/doc/filtering.html#gaussianblur>`_.</span>
+<span class="sd"> """</span>
+ <span class="k">if</span> <span class="n">borderType</span> <span class="ow">in</span> <span class="n">conf</span><span class="o">.</span><span class="n">borders</span><span class="p">:</span>
+ <span class="n">sigmaY</span> <span class="o">=</span> <span class="n">sigmaX</span> <span class="k">if</span> <span class="n">sigmaY</span> <span class="o">==</span> <span class="mi">0</span> <span class="k">else</span> <span class="n">sigmaY</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">image</span> <span class="o">=</span> <span class="n">cv2</span><span class="o">.</span><span class="n">GaussianBlur</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">image</span><span class="p">,</span> <span class="n">ksize</span><span class="p">,</span> <span class="n">sigmaX</span><span class="p">,</span> <span class="n">sigmaY</span><span class="p">,</span> <span class="n">borderType</span> <span class="o">=</span> <span class="n">conf</span><span class="o">.</span><span class="n">borders</span><span class="p">[</span><span class="n">borderType</span><span class="p">])</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="s">"Invalid border type, should be one of: "</span> <span class="o">+</span> <span class="s">","</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">conf</span><span class="o">.</span><span class="n">borders</span><span class="o">.</span><span class="n">keys</span><span class="p">())</span> <span class="o">+</span> <span class="s">"."</span><span class="p">)</span>
+ <span class="k">return</span>
+ </div>
+<div class="viewcode-block" id="Image.normalizeByIntensity"><a class="viewcode-back" href="../../processing.html#ih.imgproc.Image.normalizeByIntensity">[docs]</a> <span class="k">def</span> <span class="nf">normalizeByIntensity</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> Normalizes each channel of the pixel by its intensity. For each pixel, the intensity is defined as</span>
+<span class="sd"> :math:`I = R + G + B`, where :math:`R,G,B` are the color values for that pixel. We calculate new color values by </span>
+<span class="sd"> multiplying the original number by 255, and dividing by the intensity, that is, :math:`r = \\frac{255 \\cdot R}{I}</span>
+<span class="sd"> , g = \\frac{255 \\cdot G}{I}, b = \\frac{255 \\cdot B}{I}`.</span>
+<span class="sd"> """</span>
+ <span class="n">f</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">image</span><span class="o">.</span><span class="n">astype</span><span class="p">(</span><span class="nb">float</span><span class="p">)</span>
+ <span class="n">combined</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">add</span><span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">add</span><span class="p">(</span><span class="n">f</span><span class="p">[:,:,</span><span class="mi">0</span><span class="p">],</span> <span class="n">f</span><span class="p">[:,:,</span><span class="mi">1</span><span class="p">]),</span> <span class="n">f</span><span class="p">[:,:,</span><span class="mi">2</span><span class="p">])</span>
+ <span class="n">scaled</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">multiply</span><span class="p">(</span><span class="n">f</span><span class="p">,</span> <span class="p">[</span><span class="mi">255</span><span class="p">])</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">image</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">divide</span><span class="p">(</span><span class="n">scaled</span><span class="p">,</span> <span class="n">combined</span><span class="p">[:,:,</span><span class="bp">None</span><span class="p">])</span><span class="o">.</span><span class="n">astype</span><span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">uint8</span><span class="p">)</span>
+ <span class="k">return</span>
+ </div>
+<div class="viewcode-block" id="Image.morphology"><a class="viewcode-back" href="../../processing.html#ih.imgproc.Image.morphology">[docs]</a> <span class="k">def</span> <span class="nf">morphology</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">morphType</span><span class="p">,</span> <span class="n">ktype</span><span class="p">,</span> <span class="n">ksize</span><span class="p">,</span> <span class="n">anchor</span> <span class="o">=</span> <span class="p">(</span><span class="o">-</span><span class="mi">1</span><span class="p">,</span> <span class="o">-</span><span class="mi">1</span><span class="p">),</span> <span class="n">iterations</span> <span class="o">=</span> <span class="mi">1</span><span class="p">,</span> <span class="n">borderType</span> <span class="o">=</span> <span class="s">"default"</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> :param morphType: The type of morphology to perform. Should be dilate, erode, open, close, gradient, tophat, or blackhat.</span>
+<span class="sd"> :type morphType: str</span>
+<span class="sd"> :param ktype: the type of the kernel, should be rect, ellipse, or cross.</span>
+<span class="sd"> :type ktype: str</span>
+<span class="sd"> :param ksize: The size of the kernel represented by a tuple (width, height). Both numbers should be odd and positive.</span>
+<span class="sd"> :type ksize: tuple</span>
+<span class="sd"> :param anchor: The anchor point for filtering. Default is (-1, -1) which is the center of the kernel.</span>
+<span class="sd"> :type anchor: tuple</span>
+<span class="sd"> :param iterations: The number of times to perform the specified morphology.</span>
+<span class="sd"> :type iterations: int</span>
+<span class="sd"> :param borderType: The type of border mode used to extrapolate pixels outside the image.</span>
+<span class="sd"> :type borderType: str</span>
+<span class="sd"> </span>
+<span class="sd"> This function performs morphological operations based on the inputted values. This function is</span>
+<span class="sd"> a wrapper to the OpenCv function `morphologyEx <http://docs.opencv.org/modules/imgproc/doc/filtering.html#morphologyex>`_. When performing the morphology on the edges</span>
+<span class="sd"> of the image, values for pixels that would be outside of the image are extrapolated. The method</span>
+<span class="sd"> of extrapolation depends on the specified 'borderType', and can be one of 'default', 'constant',</span>
+<span class="sd"> 'reflect', or 'replicate'.</span>
+<span class="sd"> """</span>
+ <span class="k">if</span> <span class="n">morphType</span> <span class="ow">in</span> <span class="n">conf</span><span class="o">.</span><span class="n">morph</span><span class="p">:</span>
+ <span class="k">if</span> <span class="n">ktype</span> <span class="ow">in</span> <span class="n">conf</span><span class="o">.</span><span class="n">kernels</span><span class="p">:</span>
+ <span class="k">if</span> <span class="n">borderType</span> <span class="ow">in</span> <span class="n">conf</span><span class="o">.</span><span class="n">borders</span><span class="p">:</span>
+ <span class="n">kernel</span> <span class="o">=</span> <span class="n">cv2</span><span class="o">.</span><span class="n">getStructuringElement</span><span class="p">(</span><span class="n">conf</span><span class="o">.</span><span class="n">kernels</span><span class="p">[</span><span class="n">ktype</span><span class="p">],</span> <span class="n">ksize</span><span class="p">,</span> <span class="n">anchor</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">image</span> <span class="o">=</span> <span class="n">cv2</span><span class="o">.</span><span class="n">morphologyEx</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">image</span><span class="p">,</span> <span class="n">conf</span><span class="o">.</span><span class="n">morph</span><span class="p">[</span><span class="n">morphType</span><span class="p">],</span> <span class="n">kernel</span><span class="p">,</span> <span class="n">anchor</span> <span class="o">=</span> <span class="n">anchor</span><span class="p">,</span> <span class="n">iterations</span> <span class="o">=</span> <span class="n">iterations</span><span class="p">,</span> <span class="n">borderType</span> <span class="o">=</span> <span class="n">conf</span><span class="o">.</span><span class="n">borders</span><span class="p">[</span><span class="n">borderType</span><span class="p">])</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="s">"Invalid border type, should be one of: "</span> <span class="o">+</span> <span class="s">","</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">conf</span><span class="o">.</span><span class="n">borders</span><span class="o">.</span><span class="n">keys</span><span class="p">())</span> <span class="o">+</span> <span class="s">"."</span><span class="p">)</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="s">"Invalid kernel type, should be one of: "</span> <span class="o">+</span> <span class="s">","</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">conf</span><span class="o">.</span><span class="n">kernels</span><span class="o">.</span><span class="n">keys</span><span class="p">())</span> <span class="o">+</span> <span class="s">"."</span><span class="p">)</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="s">"Invalid morphology type, should be one of: "</span> <span class="o">+</span> <span class="s">","</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">conf</span><span class="o">.</span><span class="n">morph</span><span class="o">.</span><span class="n">keys</span><span class="p">())</span> <span class="o">+</span> <span class="s">"."</span><span class="p">)</span>
+ </div>
+<div class="viewcode-block" id="Image.crop"><a class="viewcode-back" href="../../processing.html#ih.imgproc.Image.crop">[docs]</a> <span class="k">def</span> <span class="nf">crop</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">roi</span><span class="p">,</span> <span class="n">resize</span> <span class="o">=</span> <span class="bp">False</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> :param roi: A list corresponding to the area of the image you want. List should be of the form [ystart, yend, xstart, xend]</span>
+<span class="sd"> :type roi: list or roi file</span>
+<span class="sd"> :param resize: If True, actually adjusts the size of the image, otherwise just draws over the part of the image not in the roi.</span>
+<span class="sd"> :type resize: bool</span>
+<span class="sd"> </span>
+<span class="sd"> This function crops the image based on the given roi [ystart, yend, xstart, xend]. There are two crop options,</span>
+<span class="sd"> by default, the function doesn't actually resize the image. Instead, it sets each pixel not in the roi to black.</span>
+<span class="sd"> If resize is set to True, the function will actually crop the image down to the roi.</span>
+<span class="sd"> """</span>
+ <span class="n">roi</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_loadROI</span><span class="p">(</span><span class="n">roi</span><span class="p">)</span>
+ <span class="n">ystart</span><span class="p">,</span> <span class="n">yend</span><span class="p">,</span> <span class="n">xstart</span><span class="p">,</span> <span class="n">xend</span> <span class="o">=</span> <span class="n">roi</span>
+ <span class="k">if</span> <span class="p">(</span><span class="n">resize</span><span class="p">):</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">image</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">image</span><span class="p">[</span><span class="n">ystart</span><span class="p">:</span> <span class="n">yend</span><span class="p">,</span> <span class="n">xstart</span><span class="p">:</span> <span class="n">xend</span><span class="p">]</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">x</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">image</span><span class="o">.</span><span class="n">shape</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">y</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">image</span><span class="o">.</span><span class="n">shape</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="n">maxx</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">x</span>
+ <span class="n">maxy</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">y</span>
+ <span class="n">off</span> <span class="o">=</span> <span class="p">[</span><span class="mi">0</span><span class="p">,</span> <span class="mi">0</span><span class="p">,</span> <span class="mi">0</span><span class="p">]</span> <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">_isColor</span><span class="p">()</span> <span class="k">else</span> <span class="p">[</span><span class="mi">0</span><span class="p">]</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">image</span><span class="p">[</span><span class="mi">0</span><span class="p">:</span><span class="n">ystart</span><span class="p">,</span> <span class="mi">0</span><span class="p">:</span><span class="n">maxx</span><span class="p">]</span> <span class="o">=</span> <span class="n">off</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">image</span><span class="p">[</span><span class="n">yend</span><span class="p">:</span><span class="n">maxy</span><span class="p">,</span> <span class="mi">0</span><span class="p">:</span><span class="n">maxx</span><span class="p">]</span> <span class="o">=</span> <span class="n">off</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">image</span><span class="p">[</span><span class="mi">0</span><span class="p">:</span><span class="n">maxy</span><span class="p">,</span> <span class="mi">0</span><span class="p">:</span><span class="n">xstart</span><span class="p">]</span> <span class="o">=</span> <span class="n">off</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">image</span><span class="p">[</span><span class="mi">0</span><span class="p">:</span><span class="n">maxy</span><span class="p">,</span> <span class="n">xend</span><span class="p">:</span><span class="n">maxx</span><span class="p">]</span> <span class="o">=</span> <span class="n">off</span>
+ <span class="k">return</span>
+ </div>
+<div class="viewcode-block" id="Image.contourCut"><a class="viewcode-back" href="../../processing.html#ih.imgproc.Image.contourCut">[docs]</a> <span class="k">def</span> <span class="nf">contourCut</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">binary</span><span class="p">,</span> <span class="n">basemin</span> <span class="o">=</span> <span class="mi">100</span><span class="p">,</span> <span class="n">padding</span> <span class="o">=</span> <span class="p">[</span><span class="mi">0</span><span class="p">,</span> <span class="mi">0</span><span class="p">,</span> <span class="mi">0</span><span class="p">,</span> <span class="mi">0</span><span class="p">],</span> <span class="n">resize</span> <span class="o">=</span> <span class="bp">False</span><span class="p">,</span> <span class="n">returnBound</span> <span class="o">=</span> <span class="bp">False</span><span class="p">,</span> <span class="n">roiwrite</span> <span class="o">=</span> <span class="s">"roi.json"</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> :param binary: The binary image to find contours of.</span>
+<span class="sd"> :type binary: str or np.ndarray</span>
+<span class="sd"> :param basemin: The minimum area a contour must have to be consider part of the foreground.</span>
+<span class="sd"> :type basemin: int</span>
+<span class="sd"> :param padding: Padding add to all sides of the final roi.</span>
+<span class="sd"> :type padding: int</span>
+<span class="sd"> :param returnBound: If set, instead of cropping the image, simply write the detected roi.</span>
+<span class="sd"> :type returnBound: bool</span>
+<span class="sd"> :param resize: Whether or not to resize the image.</span>
+<span class="sd"> :type resize: bool</span>
+<span class="sd"> </span>
+<span class="sd"> This function crops an image based on the size of detected contours in the image --</span>
+<span class="sd"> clusters of pixels in the image. The image is cropped such that all contours</span>
+<span class="sd"> that are greater than the specified area are included in the final output image.</span>
+<span class="sd"> image is cropped such that all contours that are greater than the specified area are</span>
+<span class="sd"> included in the final output image. If returnBound is set, instead of actually</span>
+<span class="sd"> cropping the image, the detected roi is written to a file instead. Otherwise,</span>
+<span class="sd"> the detected roi is passed into the :py:meth:`~ih.imgproc.Image.crop` function,</span>
+<span class="sd"> with the given resize value. This function is useful for getting accurate </span>
+<span class="sd"> height and width of a specific plant, as well as removing outlying clusters</span>
+<span class="sd"> of non-important pixels.</span>
+<span class="sd"> """</span>
+ <span class="n">bname</span><span class="p">,</span> <span class="n">binary</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_loadResource</span><span class="p">(</span><span class="n">binary</span><span class="p">)</span>
+ <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">_isColor</span><span class="p">(</span><span class="n">binary</span><span class="p">):</span>
+ <span class="n">binary</span> <span class="o">=</span> <span class="n">cv2</span><span class="o">.</span><span class="n">cvtColor</span><span class="p">(</span><span class="n">binary</span><span class="p">,</span> <span class="n">cv2</span><span class="o">.</span><span class="n">COLOR_BGR2GRAY</span><span class="p">)</span>
+ <span class="n">contours</span> <span class="o">=</span> <span class="n">cv2</span><span class="o">.</span><span class="n">findContours</span><span class="p">(</span><span class="n">binary</span><span class="p">,</span> <span class="n">cv2</span><span class="o">.</span><span class="n">RETR_TREE</span><span class="p">,</span> <span class="n">cv2</span><span class="o">.</span><span class="n">CHAIN_APPROX_SIMPLE</span><span class="p">)[</span><span class="mi">0</span><span class="p">]</span>
+ <span class="n">minx</span> <span class="o">=</span> <span class="n">binary</span><span class="o">.</span><span class="n">shape</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span>
+ <span class="n">miny</span> <span class="o">=</span> <span class="n">binary</span><span class="o">.</span><span class="n">shape</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span>
+ <span class="n">maxx</span> <span class="o">=</span> <span class="mi">0</span>
+ <span class="n">maxy</span> <span class="o">=</span> <span class="mi">0</span>
+ <span class="k">for</span> <span class="n">cnt</span> <span class="ow">in</span> <span class="n">contours</span><span class="p">:</span>
+ <span class="n">x</span><span class="p">,</span><span class="n">y</span><span class="p">,</span><span class="n">w</span><span class="p">,</span><span class="n">h</span> <span class="o">=</span> <span class="n">cv2</span><span class="o">.</span><span class="n">boundingRect</span><span class="p">(</span><span class="n">cnt</span><span class="p">)</span>
+ <span class="k">if</span> <span class="p">(</span><span class="n">basemin</span> <span class="o"><</span> <span class="n">cv2</span><span class="o">.</span><span class="n">contourArea</span><span class="p">(</span><span class="n">cnt</span><span class="p">)):</span>
+ <span class="k">if</span> <span class="p">(</span><span class="n">x</span> <span class="o"><</span> <span class="n">minx</span><span class="p">):</span>
+ <span class="n">minx</span> <span class="o">=</span> <span class="n">x</span>
+ <span class="k">if</span> <span class="p">(</span><span class="n">y</span> <span class="o"><</span> <span class="n">miny</span><span class="p">):</span>
+ <span class="n">miny</span> <span class="o">=</span> <span class="n">y</span>
+ <span class="k">if</span> <span class="p">(</span><span class="n">x</span> <span class="o">+</span> <span class="n">w</span> <span class="o">></span> <span class="n">maxx</span><span class="p">):</span>
+ <span class="n">maxx</span> <span class="o">=</span> <span class="n">x</span> <span class="o">+</span> <span class="n">w</span>
+ <span class="k">if</span> <span class="p">(</span><span class="n">y</span> <span class="o">+</span> <span class="n">h</span> <span class="o">></span> <span class="n">maxy</span><span class="p">):</span>
+ <span class="n">maxy</span> <span class="o">=</span> <span class="n">y</span> <span class="o">+</span> <span class="n">h</span>
+ <span class="n">roi</span> <span class="o">=</span> <span class="p">[</span><span class="mi">0</span> <span class="k">if</span> <span class="n">miny</span> <span class="o">-</span> <span class="n">padding</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="o"><</span> <span class="mi">0</span> <span class="k">else</span> <span class="n">miny</span> <span class="o">-</span> <span class="n">padding</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span> <span class="n">binary</span><span class="o">.</span><span class="n">shape</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="k">if</span> <span class="n">maxy</span> <span class="o">+</span> <span class="n">padding</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span> <span class="o">></span> <span class="n">binary</span><span class="o">.</span><span class="n">shape</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="k">else</span> <span class="n">maxy</span> <span class="o">+</span> <span class="n">padding</span><span class="p">[</span><span class="mi">1</span><span class="p">],</span> <span class="mi">0</span> <span class="k">if</span> <span class="n">minx</span> <span class="o">-</span> <span class="n">padding</span><span class="p">[</span><span class="mi">2</span><span class="p">]</span> <span class="o"><</span> <span class="mi">0</span> <span class="k">else</span> <span class="n">minx</span> <span class="o">-</span> <span class="n">padding</span><span class="p">[</span><span class="mi">2</span><span class="p">],</span> <span class="n">binary</span><span class="o">.</span><span class="n">shape</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span> <span class="k">if</span> <span class="n">maxx</span> <span class="o">+</span> <span class="n">padding</span><span class="p">[</span><span class="mi">3</span><span class="p">]</span> <span class="o">></span> <span class="n">binary</span><span class="o">.</span><span class="n">shape</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span> <span class="k">else</span> <span class="n">maxx</span> <span class="o">+</span> <span class="n">padding</span><span class="p">[</span><span class="mi">3</span><span class="p">]]</span>
+ <span class="k">if</span> <span class="n">returnBound</span><span class="p">:</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_writeROI</span><span class="p">(</span><span class="n">roi</span><span class="p">,</span> <span class="n">roiwrite</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">crop</span><span class="p">(</span><span class="n">roi</span><span class="p">,</span> <span class="n">resize</span><span class="p">)</span>
+ <span class="k">return</span>
+ </div>
+<div class="viewcode-block" id="Image.edges"><a class="viewcode-back" href="../../processing.html#ih.imgproc.Image.edges">[docs]</a> <span class="k">def</span> <span class="nf">edges</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">threshold1</span><span class="p">,</span> <span class="n">threshold2</span><span class="p">,</span> <span class="n">apertureSize</span> <span class="o">=</span> <span class="mi">3</span><span class="p">,</span> <span class="n">L2gradient</span> <span class="o">=</span> <span class="bp">False</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> :param threshold1: First threshold for the hysteresis procedure.</span>
+<span class="sd"> :type threshold1: int</span>
+<span class="sd"> :param threshold2: Second threshold for the hysteresis procedure.</span>
+<span class="sd"> :type threshold2: int</span>
+<span class="sd"> :param apertureSize: aperture size used for the Sobel algorithm. Must be odd, postive, and less than 8.</span>
+<span class="sd"> :type apertureSize: int</span>
+<span class="sd"> :L2gradient: Used to calculate Image gradient magnitude, if true then :math:`L = \sqrt{(dI/dx)^2 + (dI/dy)^2}`, if false then :math:`L = dI/dx + dI/dy`.</span>
+<span class="sd"> :type L2gradient: bool</span>
+<span class="sd"> </span>
+<span class="sd"> This function calculates the edges of an image using the Canny edge detection algorithm, which is built upon the Sobel</span>
+<span class="sd"> algorithm. This function is a wrapper to the OpenCV function `Canny <http://docs.opencv.org/modules/imgproc/doc/feature_detection.html#canny>`_.</span>
+<span class="sd"> """</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">image</span> <span class="o">=</span> <span class="n">cv2</span><span class="o">.</span><span class="n">Canny</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">image</span><span class="p">,</span> <span class="n">threshold1</span><span class="p">,</span> <span class="n">threshold2</span><span class="p">,</span> <span class="n">apertureSize</span> <span class="o">=</span> <span class="n">apertureSize</span><span class="p">,</span> <span class="n">L2gradient</span> <span class="o">=</span> <span class="n">L2gradient</span><span class="p">)</span>
+ <span class="k">return</span>
+ </div>
+<div class="viewcode-block" id="Image.colorFilter"><a class="viewcode-back" href="../../processing.html#ih.imgproc.Image.colorFilter">[docs]</a> <span class="k">def</span> <span class="nf">colorFilter</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">logic</span><span class="p">,</span> <span class="n">roi</span> <span class="o">=</span> <span class="bp">None</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> :param logic: The logic you want to run on the image.</span>
+<span class="sd"> :type logic: str</span>
+<span class="sd"> :param roi: The roi you want to apply the filter to</span>
+<span class="sd"> :type roi: list or roi file</span>
+<span class="sd"> </span>
+<span class="sd"> This function applies a color filter defined by the input logic, to a</span>
+<span class="sd"> targeted region defined by the input roi. The roi is defined the same,</span>
+<span class="sd"> [ystart, yend, xstart, xend]. The logic string itself is fairly complicated.</span>
+<span class="sd"> The string supports the following characters: '+', '-', '*', '/', '>', '>=',</span>
+<span class="sd"> '==', '<', '<=', 'and', 'or', '(', ')', 'r', 'g', 'b', 'max', and 'min' as well as any numeric</span>
+<span class="sd"> value. The logic string itself must be well formed -- each </span>
+<span class="sd"> operation, arg1 operator arg2, must be surrounded by parenthesis, and the entire statement</span>
+<span class="sd"> must be surrounded by parenthesis. For example,</span>
+<span class="sd"> if you want to check the intensity of the pixel, your logic string would be:</span>
+<span class="sd"> '(((r + g) + b) < 100)'. This string in particular will only keep pixels whose</span>
+<span class="sd"> intensity is less than 100. Similar rules apply for 'and' and 'or' operators.</span>
+<span class="sd"> Let's say we only want to keep pixels whose intensity is less than 100, OR both</span>
+<span class="sd"> the red and blue channels are greater than 150, the logic string would be: </span>
+<span class="sd"> '((((r + g) + b) < 100) or ((r > 150) and (b > 150)))'. The more complex</span>
+<span class="sd"> your logic is the harder it is to read, so you may want to consider breaking</span>
+<span class="sd"> up complex filtering into multiple steps for readability. Finally, despite</span>
+<span class="sd"> the fact this function solves arbitrary logic, it is very fast.</span>
+<span class="sd"> """</span>
+ <span class="nb">filter</span> <span class="o">=</span> <span class="n">ColorFilter</span><span class="p">(</span><span class="n">logic</span><span class="p">)</span>
+ <span class="n">roi</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_loadROI</span><span class="p">(</span><span class="n">roi</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">image</span> <span class="o">=</span> <span class="nb">filter</span><span class="o">.</span><span class="n">apply</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">image</span><span class="p">,</span> <span class="n">roi</span><span class="p">)</span>
+ <span class="k">return</span>
+ </div>
+<div class="viewcode-block" id="Image.bitwise_not"><a class="viewcode-back" href="../../processing.html#ih.imgproc.Image.bitwise_not">[docs]</a> <span class="k">def</span> <span class="nf">bitwise_not</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> Inverts the image. If the given image has multiple channels (i.e. is a color image) each channel is processed independently.</span>
+<span class="sd"> """</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">image</span> <span class="o">=</span> <span class="n">cv2</span><span class="o">.</span><span class="n">bitwise_not</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">image</span><span class="p">)</span>
+ <span class="k">return</span>
+ </div>
+<div class="viewcode-block" id="Image.bitwise_and"><a class="viewcode-back" href="../../processing.html#ih.imgproc.Image.bitwise_and">[docs]</a> <span class="k">def</span> <span class="nf">bitwise_and</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">comp</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> :param comp: The comparison image.</span>
+<span class="sd"> :type comp: str or np.ndarray</span>
+<span class="sd"> :return: The resulting mask.</span>
+<span class="sd"> :rtype: numpy.ndarray</span>
+<span class="sd"> </span>
+<span class="sd"> Performs logical AND between the input image and the comp image.</span>
+<span class="sd"> The comp input is very versatile, and can be one of three input types,</span>
+<span class="sd"> an image, a path, or a saved state. An image input is a raw numpy array,</span>
+<span class="sd"> and this input type will be passed through to the function without modification. </span>
+<span class="sd"> If a path is specified, ih attempts to load the file as an image, and pass it</span>
+<span class="sd"> to the function. Finally, the input is checked against the currently saved</span>
+<span class="sd"> image states. If it matches, the corresponding state is passed to the function.</span>
+<span class="sd"> The function assumes that the two input images are of matching type --</span>
+<span class="sd"> if they are not an error will be thrown. By default, images loaded from a</span>
+<span class="sd"> path are loaded as 'bgr' type images.</span>
+<span class="sd"> For more information on states, see :py:meth:`~ih.imgproc.Image.save`.</span>
+<span class="sd"> """</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">image</span> <span class="o">=</span> <span class="n">cv2</span><span class="o">.</span><span class="n">bitwise_and</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">image</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">_loadResource</span><span class="p">(</span><span class="n">comp</span><span class="p">)[</span><span class="mi">1</span><span class="p">])</span>
+ <span class="k">return</span>
+ </div>
+<div class="viewcode-block" id="Image.bitwise_or"><a class="viewcode-back" href="../../processing.html#ih.imgproc.Image.bitwise_or">[docs]</a> <span class="k">def</span> <span class="nf">bitwise_or</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">comp</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> :param comp: The comparison image.</span>
+<span class="sd"> :type comp: str or np.ndarray</span>
+<span class="sd"> :return: The resulting mask.</span>
+<span class="sd"> :rtype: numpy.ndarray</span>
+<span class="sd"> </span>
+<span class="sd"> Performs logical OR between the input image and the comp image.</span>
+<span class="sd"> The comp input is very versatile, and can be one of three input types,</span>
+<span class="sd"> an image, a path, or a saved state. An image input is a raw numpy array,</span>
+<span class="sd"> and this input type will be passed through to the function without modification. </span>
+<span class="sd"> If a path is specified, ih attempts to load the file as an image, and pass it</span>
+<span class="sd"> to the function. Finally, the input is checked against the currently saved</span>
+<span class="sd"> image states. If it matches, the corresponding state is passed to the function.</span>
+<span class="sd"> The function assumes that the two input images are of matching type --</span>
+<span class="sd"> if they are not an error will be thrown. By default, images loaded from a</span>
+<span class="sd"> path are loaded as 'bgr' type images.</span>
+<span class="sd"> For more information on states, see :py:meth:`~ih.imgproc.Image.save`.</span>
+<span class="sd"> """</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">image</span> <span class="o">=</span> <span class="n">cv2</span><span class="o">.</span><span class="n">bitwise_or</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">image</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">_loadResource</span><span class="p">(</span><span class="n">comp</span><span class="p">)[</span><span class="mi">1</span><span class="p">])</span>
+ <span class="k">return</span>
+ </div>
+<div class="viewcode-block" id="Image.bitwise_xor"><a class="viewcode-back" href="../../processing.html#ih.imgproc.Image.bitwise_xor">[docs]</a> <span class="k">def</span> <span class="nf">bitwise_xor</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">comp</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> :param comp: The comparison image.</span>
+<span class="sd"> :type comp: str or np.ndarray</span>
+<span class="sd"> :return: The resulting mask.</span>
+<span class="sd"> :rtype: numpy.ndarray</span>
+<span class="sd"> </span>
+<span class="sd"> Performs exclusive logical OR between the input image and the comp image.</span>
+<span class="sd"> The comp input is very versatile, and can be one of three input types,</span>
+<span class="sd"> an image, a path, or a saved state. An image input is a raw numpy array,</span>
+<span class="sd"> and this input type will be passed through to the function without modification. </span>
+<span class="sd"> If a path is specified, ih attempts to load the file as an image, and pass it</span>
+<span class="sd"> to the function. Finally, the input is checked against the currently saved</span>
+<span class="sd"> image states. If it matches, the corresponding state is passed to the function.</span>
+<span class="sd"> The function assumes that the two input images are of matching type --</span>
+<span class="sd"> if they are not an error will be thrown. By default, images loaded from a</span>
+<span class="sd"> path are loaded as 'bgr' type images.</span>
+<span class="sd"> For more information on states, see :py:meth:`~ih.imgproc.Image.save`.</span>
+<span class="sd"> """</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">image</span> <span class="o">=</span> <span class="n">cv2</span><span class="o">.</span><span class="n">bitwise_xor</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">image</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">_loadResource</span><span class="p">(</span><span class="n">comp</span><span class="p">)[</span><span class="mi">1</span><span class="p">])</span>
+ <span class="k">return</span>
+ </div>
+<div class="viewcode-block" id="Image.extractFinalPath"><a class="viewcode-back" href="../../processing.html#ih.imgproc.Image.extractFinalPath">[docs]</a> <span class="k">def</span> <span class="nf">extractFinalPath</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> This function writes the absolute path of the output file to the database.</span>
+<span class="sd"> """</span>
+ <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">conn</span><span class="p">:</span>
+ <span class="n">finalpath</span> <span class="o">=</span> <span class="s">"/"</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">abspath</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">input</span><span class="p">)</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s">"/"</span><span class="p">)[</span><span class="o">-</span><span class="mi">6</span><span class="p">:])</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_addColumn</span><span class="p">(</span><span class="s">"outputPath"</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">conn</span><span class="o">.</span><span class="n">execute</span><span class="p">(</span><span class="s">"update images set outputPath=? where pegasusid=?"</span><span class="p">,</span> <span class="p">(</span><span class="n">finalpath</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">dbid</span><span class="p">))</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">conn</span><span class="o">.</span><span class="n">commit</span><span class="p">()</span>
+ <span class="k">return</span>
+ </div>
+<div class="viewcode-block" id="Image.extractMoments"><a class="viewcode-back" href="../../processing.html#ih.imgproc.Image.extractMoments">[docs]</a> <span class="k">def</span> <span class="nf">extractMoments</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> :return: A dictionary corresponding to the different moments of the image.</span>
+<span class="sd"> :rtype: dict</span>
+<span class="sd"> </span>
+<span class="sd"> Calculates the moments of the image, and returns a dicitonary based on them.</span>
+<span class="sd"> Spatial moments are prefixed with 'm', central moments are prefixed with 'mu',</span>
+<span class="sd"> and central normalized moments are prefixed with 'nu'. This function</span>
+<span class="sd"> is a wrapper to the OpenCV function `moments <http://docs.opencv.org/modules/imgproc/doc/structural_analysis_and_shape_descriptors.html#moments>`_.</span>
+<span class="sd"> """</span>
+ <span class="n">moments</span> <span class="o">=</span> <span class="n">cv2</span><span class="o">.</span><span class="n">moments</span><span class="p">(</span><span class="n">cv2</span><span class="o">.</span><span class="n">inRange</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">image</span><span class="p">,</span> <span class="n">np</span><span class="o">.</span><span class="n">array</span><span class="p">([</span><span class="mi">1</span><span class="p">,</span> <span class="mi">1</span><span class="p">,</span> <span class="mi">1</span><span class="p">],</span> <span class="n">np</span><span class="o">.</span><span class="n">uint8</span><span class="p">),</span> <span class="n">np</span><span class="o">.</span><span class="n">array</span><span class="p">([</span><span class="mi">255</span><span class="p">,</span> <span class="mi">255</span><span class="p">,</span> <span class="mi">255</span><span class="p">],</span> <span class="n">np</span><span class="o">.</span><span class="n">uint8</span><span class="p">)))</span>
+ <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">conn</span><span class="p">:</span>
+ <span class="k">for</span> <span class="nb">id</span> <span class="ow">in</span> <span class="n">moments</span><span class="p">:</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_addColumn</span><span class="p">(</span><span class="nb">id</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">conn</span><span class="o">.</span><span class="n">execute</span><span class="p">(</span><span class="s">"update images set "</span> <span class="o">+</span> <span class="nb">id</span> <span class="o">+</span> <span class="s">"=? where pegasusid=?"</span><span class="p">,</span> <span class="p">(</span><span class="n">moments</span><span class="p">[</span><span class="nb">id</span><span class="p">],</span> <span class="bp">self</span><span class="o">.</span><span class="n">dbid</span><span class="p">))</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">conn</span><span class="o">.</span><span class="n">commit</span><span class="p">()</span>
+ <span class="k">return</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="k">return</span> <span class="n">moments</span>
+ </div>
+<div class="viewcode-block" id="Image.extractDimensions"><a class="viewcode-back" href="../../processing.html#ih.imgproc.Image.extractDimensions">[docs]</a> <span class="k">def</span> <span class="nf">extractDimensions</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> :return: A list corresponding to the height and width of the image.</span>
+<span class="sd"> :rtype: list</span>
+<span class="sd"> </span>
+<span class="sd"> Returns a list with the following form: [height, width]</span>
+<span class="sd"> """</span>
+ <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">conn</span><span class="p">:</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_addColumn</span><span class="p">(</span><span class="s">"height"</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_addColumn</span><span class="p">(</span><span class="s">"width"</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">conn</span><span class="o">.</span><span class="n">execute</span><span class="p">(</span><span class="s">"update images set height=?,width=? where pegasusid=?"</span><span class="p">,</span> <span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">y</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">x</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">dbid</span><span class="p">))</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">conn</span><span class="o">.</span><span class="n">commit</span><span class="p">()</span>
+ <span class="k">return</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="k">return</span> <span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">y</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">x</span><span class="p">]</span>
+ </div>
+<div class="viewcode-block" id="Image.extractPixels"><a class="viewcode-back" href="../../processing.html#ih.imgproc.Image.extractPixels">[docs]</a> <span class="k">def</span> <span class="nf">extractPixels</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> :return: The number of non-black pixels in the image.</span>
+<span class="sd"> :rtype: int</span>
+<span class="sd"> </span>
+<span class="sd"> Returns the number of non-black pixels in the image. Creates</span>
+<span class="sd"> a temporary binary image to do this. The point of this function</span>
+<span class="sd"> is not to threshold, so the binary image is created by all</span>
+<span class="sd"> pixels that fall into the range [1, 1, 1], [255, 255, 255].</span>
+<span class="sd"> """</span>
+ <span class="n">pixelCount</span> <span class="o">=</span> <span class="n">cv2</span><span class="o">.</span><span class="n">countNonZero</span><span class="p">(</span><span class="n">cv2</span><span class="o">.</span><span class="n">inRange</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">image</span><span class="p">,</span> <span class="n">np</span><span class="o">.</span><span class="n">array</span><span class="p">([</span><span class="mi">1</span><span class="p">,</span> <span class="mi">1</span><span class="p">,</span> <span class="mi">1</span><span class="p">],</span> <span class="n">np</span><span class="o">.</span><span class="n">uint8</span><span class="p">),</span> <span class="n">np</span><span class="o">.</span><span class="n">array</span><span class="p">([</span><span class="mi">255</span><span class="p">,</span> <span class="mi">255</span><span class="p">,</span> <span class="mi">255</span><span class="p">],</span> <span class="n">np</span><span class="o">.</span><span class="n">uint8</span><span class="p">)))</span>
+ <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">conn</span><span class="p">:</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_addColumn</span><span class="p">(</span><span class="s">"pixels"</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">conn</span><span class="o">.</span><span class="n">execute</span><span class="p">(</span><span class="s">"update images set pixels=? where pegasusid=?"</span><span class="p">,</span> <span class="p">(</span><span class="n">pixelCount</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">dbid</span><span class="p">))</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">conn</span><span class="o">.</span><span class="n">commit</span><span class="p">()</span>
+ <span class="k">return</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="k">return</span> <span class="n">pixelCount</span>
+ </div>
+<div class="viewcode-block" id="Image.extractColorData"><a class="viewcode-back" href="../../processing.html#ih.imgproc.Image.extractColorData">[docs]</a> <span class="k">def</span> <span class="nf">extractColorData</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">nonzero</span> <span class="o">=</span> <span class="bp">True</span><span class="p">,</span> <span class="n">returnhist</span> <span class="o">=</span> <span class="bp">False</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> :param nonzero: Whether or not to look at only nonzero pixels. Default true.</span>
+<span class="sd"> :type nonzero: bool</span>
+<span class="sd"> :return: Mean & median for each channel.</span>
+<span class="sd"> :rtype: list</span>
+<span class="sd"> </span>
+<span class="sd"> This function calculates a normalized histogram of each individual color channel of </span>
+<span class="sd"> the image, and returns the mean & median of the histograms for the channels</span>
+<span class="sd"> specified. Because images are imported with the channels ordered as B,G,R,</span>
+<span class="sd"> the output list is returned the same way. The returned list always looks like</span>
+<span class="sd"> this: [ [BlueMean, BlueMedian], [GreenMean, GreenMedian], [RedMean, RedMedian] ].</span>
+<span class="sd"> Mean values always come before median values. If nonzero is set to true (default)</span>
+<span class="sd"> the function will only calculate mediapytn and means based on the non-black pixels.</span>
+<span class="sd"> """</span>
+ <span class="n">hist</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_colorHistogram</span><span class="p">()</span>
+ <span class="k">if</span> <span class="n">returnhist</span><span class="p">:</span>
+ <span class="k">return</span> <span class="n">hist</span>
+ <span class="n">colors</span> <span class="o">=</span> <span class="p">[</span> <span class="p">[</span><span class="n">np</span><span class="o">.</span><span class="n">mean</span><span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">nonzero</span><span class="p">(</span><span class="n">hist</span><span class="p">[</span><span class="mi">0</span><span class="p">])</span> <span class="k">if</span> <span class="n">nonzero</span> <span class="k">else</span> <span class="n">hist</span><span class="p">[</span><span class="mi">0</span><span class="p">]),</span> <span class="n">np</span><span class="o">.</span><span class="n">median</span><span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">nonzero</span><span class="p">(</span><span class="n">hist</span><span class="p">[</span><span class="mi">0</span><span class="p">])</span> <span class="k">if</span> <span class="n">nonzero</span> <span class="k">else</span> <span class="n">hist</span><span class="p">[</span><span class="mi">0</span><span class="p">])],</span>
+ <span class="p">[</span><span class="n">np</span><span class="o">.</span><span class="n">mean</span><span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">nonzero</span><span class="p">(</span><span class="n">hist</span><span class="p">[</span><span class="mi">1</span><span class="p">])</span> <span class="k">if</span> <span class="n">nonzero</span> <span class="k">else</span> <span class="n">hist</span><span class="p">[</span><span class="mi">1</span><span class="p">]),</span> <span class="n">np</span><span class="o">.</span><span class="n">median</span><span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">nonzero</span><span class="p">(</span><span class="n">hist</span><span class="p">[</span><span class="mi">1</span><span class="p">])</span> <span class="k">if</span> <span class="n">nonzero</span> <span class="k">else</span> <span class="n">hist</span><span class="p">[</span><span class="mi">1</span><span class="p">])],</span>
+ <span class="p">[</span><span class="n">np</span><span class="o">.</span><span class="n">mean</span><span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">nonzero</span><span class="p">(</span><span class="n">hist</span><span class="p">[</span><span class="mi">2</span><span class="p">])</span> <span class="k">if</span> <span class="n">nonzero</span> <span class="k">else</span> <span class="n">hist</span><span class="p">[</span><span class="mi">2</span><span class="p">]),</span> <span class="n">np</span><span class="o">.</span><span class="n">median</span><span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">nonzero</span><span class="p">(</span><span class="n">hist</span><span class="p">[</span><span class="mi">2</span><span class="p">])</span> <span class="k">if</span> <span class="n">nonzero</span> <span class="k">else</span> <span class="n">hist</span><span class="p">[</span><span class="mi">2</span><span class="p">])]</span>
+ <span class="p">]</span>
+ <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">conn</span><span class="p">:</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_addColumn</span><span class="p">(</span><span class="s">"rmean"</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_addColumn</span><span class="p">(</span><span class="s">"rmed"</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_addColumn</span><span class="p">(</span><span class="s">"gmean"</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_addColumn</span><span class="p">(</span><span class="s">"gmed"</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_addColumn</span><span class="p">(</span><span class="s">"bmean"</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_addColumn</span><span class="p">(</span><span class="s">"bmed"</span><span class="p">)</span>
+ <span class="n">query</span> <span class="o">=</span> <span class="s">"update images set rmean=?,rmed=?,gmean=?,gmed=?,bmean=?,bmed=?"</span>
+ <span class="n">values</span> <span class="o">=</span> <span class="p">[</span><span class="n">colors</span><span class="p">[</span><span class="mi">2</span><span class="p">][</span><span class="mi">0</span><span class="p">],</span> <span class="n">colors</span><span class="p">[</span><span class="mi">2</span><span class="p">][</span><span class="mi">1</span><span class="p">],</span> <span class="n">colors</span><span class="p">[</span><span class="mi">1</span><span class="p">][</span><span class="mi">0</span><span class="p">],</span> <span class="n">colors</span><span class="p">[</span><span class="mi">1</span><span class="p">][</span><span class="mi">1</span><span class="p">],</span> <span class="n">colors</span><span class="p">[</span><span class="mi">0</span><span class="p">][</span><span class="mi">0</span><span class="p">],</span> <span class="n">colors</span><span class="p">[</span><span class="mi">0</span><span class="p">][</span><span class="mi">1</span><span class="p">]]</span>
+ <span class="k">for</span> <span class="n">x</span><span class="p">,</span><span class="n">c</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">([</span><span class="s">"bhist"</span><span class="p">,</span> <span class="s">"ghist"</span><span class="p">,</span> <span class="s">"rhist"</span><span class="p">]):</span>
+ <span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="mi">0</span><span class="p">,</span> <span class="mi">256</span><span class="p">):</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_addColumn</span><span class="p">(</span><span class="n">c</span> <span class="o">+</span> <span class="nb">str</span><span class="p">(</span><span class="n">i</span><span class="p">))</span>
+ <span class="n">query</span> <span class="o">+=</span> <span class="s">","</span> <span class="o">+</span> <span class="n">c</span> <span class="o">+</span> <span class="nb">str</span><span class="p">(</span><span class="n">i</span><span class="p">)</span> <span class="o">+</span> <span class="s">"=?"</span>
+ <span class="n">values</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="nb">int</span><span class="p">(</span><span class="n">hist</span><span class="p">[</span><span class="n">x</span><span class="p">][</span><span class="n">i</span><span class="p">]))</span>
+ <span class="n">query</span> <span class="o">+=</span> <span class="s">" where pegasusid=?"</span>
+ <span class="n">values</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">dbid</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">conn</span><span class="o">.</span><span class="n">execute</span><span class="p">(</span><span class="n">query</span><span class="p">,</span> <span class="nb">tuple</span><span class="p">(</span><span class="n">values</span><span class="p">))</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">conn</span><span class="o">.</span><span class="n">commit</span><span class="p">()</span>
+ <span class="k">return</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="k">return</span> <span class="n">colors</span>
+ </div>
+ <span class="k">def</span> <span class="nf">extractColorChannels</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+ <span class="n">b</span><span class="p">,</span> <span class="n">g</span><span class="p">,</span> <span class="n">r</span> <span class="o">=</span> <span class="n">cv2</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">image</span><span class="p">)</span>
+ <span class="n">bdata</span><span class="p">,</span> <span class="n">gdata</span><span class="p">,</span> <span class="n">rdata</span> <span class="o">=</span> <span class="p">[],</span> <span class="p">[],</span> <span class="p">[]</span>
+ <span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="mi">0</span><span class="p">,</span> <span class="mi">256</span><span class="p">):</span>
+ <span class="n">bdata</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">count_nonzero</span><span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">where</span><span class="p">(</span><span class="n">b</span> <span class="o">==</span> <span class="n">i</span><span class="p">,</span> <span class="bp">True</span><span class="p">,</span> <span class="bp">False</span><span class="p">)))</span>
+ <span class="n">gdata</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">count_nonzero</span><span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">where</span><span class="p">(</span><span class="n">g</span> <span class="o">==</span> <span class="n">i</span><span class="p">,</span> <span class="bp">True</span><span class="p">,</span> <span class="bp">False</span><span class="p">)))</span>
+ <span class="n">rdata</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">count_nonzero</span><span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">where</span><span class="p">(</span><span class="n">r</span> <span class="o">==</span> <span class="n">i</span><span class="p">,</span> <span class="bp">True</span><span class="p">,</span> <span class="bp">False</span><span class="p">)))</span>
+ <span class="n">data</span> <span class="o">=</span> <span class="p">[</span><span class="n">bdata</span><span class="p">,</span> <span class="n">gdata</span><span class="p">,</span> <span class="n">rdata</span><span class="p">]</span>
+ <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">conn</span><span class="p">:</span>
+ <span class="n">query</span> <span class="o">=</span> <span class="s">"update images set "</span>
+ <span class="n">values</span> <span class="o">=</span> <span class="p">[]</span>
+ <span class="k">for</span> <span class="n">x</span><span class="p">,</span><span class="n">c</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">([</span><span class="s">"b"</span><span class="p">,</span> <span class="s">"g"</span><span class="p">,</span> <span class="s">"r"</span><span class="p">]):</span>
+ <span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="mi">0</span><span class="p">,</span> <span class="mi">256</span><span class="p">):</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_addColumn</span><span class="p">(</span><span class="n">c</span> <span class="o">+</span> <span class="nb">str</span><span class="p">(</span><span class="n">i</span><span class="p">))</span>
+ <span class="k">if</span> <span class="n">i</span> <span class="o">==</span> <span class="mi">0</span><span class="p">:</span>
+ <span class="n">query</span> <span class="o">+=</span> <span class="n">c</span> <span class="o">+</span> <span class="nb">str</span><span class="p">(</span><span class="n">i</span><span class="p">)</span> <span class="o">+</span> <span class="s">"=?"</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="n">query</span> <span class="o">+=</span> <span class="s">","</span> <span class="o">+</span> <span class="n">c</span> <span class="o">+</span> <span class="nb">str</span><span class="p">(</span><span class="n">i</span><span class="p">)</span> <span class="o">+</span> <span class="s">"=?"</span>
+ <span class="n">values</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">data</span><span class="p">[</span><span class="n">x</span><span class="p">][</span><span class="n">i</span><span class="p">])</span>
+ <span class="n">query</span> <span class="o">+=</span> <span class="s">" where pegasusid=?"</span>
+ <span class="n">values</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">dbid</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">conn</span><span class="o">.</span><span class="n">execute</span><span class="p">(</span><span class="n">query</span><span class="p">,</span> <span class="nb">tuple</span><span class="p">(</span><span class="n">values</span><span class="p">))</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">conn</span><span class="o">.</span><span class="n">commit</span><span class="p">()</span>
+ <span class="k">return</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="k">return</span> <span class="p">(</span><span class="n">bdata</span><span class="p">,</span> <span class="n">gdata</span><span class="p">,</span> <span class="n">rdata</span><span class="p">)</span>
+
+<div class="viewcode-block" id="Image.extractBins"><a class="viewcode-back" href="../../processing.html#ih.imgproc.Image.extractBins">[docs]</a> <span class="k">def</span> <span class="nf">extractBins</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">binlist</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> :param binlist: The specified bins (color ranges) to count.</span>
+<span class="sd"> :type binlist: list</span>
+<span class="sd"> :return: The number of pixels that fall in each bin.</span>
+<span class="sd"> :rtype: list</span>
+<span class="sd"> </span>
+<span class="sd"> This function counts the number of pixels that fall into the range as</span>
+<span class="sd"> specified by each bin. This function expects the input to be a list of </span>
+<span class="sd"> dictionaries as follows:</span>
+<span class="sd"> </span>
+<span class="sd"> .. code-block:: python</span>
+<span class="sd"> </span>
+<span class="sd"> binlist = [</span>
+<span class="sd"> {"name": "bin1",</span>
+<span class="sd"> "min": [B, G, R],</span>
+<span class="sd"> "max": [B, G, R]</span>
+<span class="sd"> },</span>
+<span class="sd"> {"name": "bin2",</span>
+<span class="sd"> ...</span>
+<span class="sd"> ]</span>
+<span class="sd"> </span>
+<span class="sd"> Each range is defined by 6 values. A minimum and maximum blue,</span>
+<span class="sd"> green, and red value. The returned list is very similar to the </span>
+<span class="sd"> input list, except a 'count' key is added to each dictionary:</span>
+<span class="sd"> </span>
+<span class="sd"> .. code-block:: python</span>
+<span class="sd"> </span>
+<span class="sd"> returnlist = [</span>
+<span class="sd"> {"name": "bin1",</span>
+<span class="sd"> "min": [B, G, R],</span>
+<span class="sd"> "max": [B, G, R],</span>
+<span class="sd"> "count": VALUE</span>
+<span class="sd"> },</span>
+<span class="sd"> ...</span>
+<span class="sd"> ]</span>
+<span class="sd"> </span>
+<span class="sd"> Where 'VALUE' is the number of pixels that fall into the</span>
+<span class="sd"> corresponding range.</span>
+<span class="sd"> A list is used instead of a dictionary as the base structure</span>
+<span class="sd"> to maintain order for writing to the output database. When</span>
+<span class="sd"> using this function within a workflow, the order you specify</span>
+<span class="sd"> your bins is the order in which they will show up in the</span>
+<span class="sd"> database, and the name you specify for you bin will be</span>
+<span class="sd"> the column name in the database.</span>
+<span class="sd"> """</span>
+ <span class="n">binlist</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_loadBins</span><span class="p">(</span><span class="n">binlist</span><span class="p">)</span>
+ <span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="mi">0</span><span class="p">,</span> <span class="nb">len</span><span class="p">(</span><span class="n">binlist</span><span class="p">)):</span>
+ <span class="n">binlist</span><span class="p">[</span><span class="n">i</span><span class="p">][</span><span class="s">"count"</span><span class="p">]</span> <span class="o">=</span> <span class="n">cv2</span><span class="o">.</span><span class="n">countNonZero</span><span class="p">(</span><span class="n">cv2</span><span class="o">.</span><span class="n">inRange</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">image</span><span class="p">,</span> <span class="n">np</span><span class="o">.</span><span class="n">array</span><span class="p">(</span><span class="n">binlist</span><span class="p">[</span><span class="n">i</span><span class="p">][</span><span class="s">"min"</span><span class="p">],</span> <span class="n">np</span><span class="o">.</span><span class="n">uint8</span><span class="p">),</span> <span class="n">np</span><span class="o">.</span><span class="n">array</span><span class="p">(</span><span class="n">binlist</span><span class="p">[</span><span class="n">i</span><span class="p">][</span><span class="s">"max"</span><span class="p">],</span> <span class="n">np</span><span class="o">.</span><span class="n">uint8</span><span class="p">)))</span>
+ <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">conn</span><span class="p">:</span>
+ <span class="k">for</span> <span class="nb">bin</span> <span class="ow">in</span> <span class="n">binlist</span><span class="p">:</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_addColumn</span><span class="p">(</span><span class="nb">bin</span><span class="p">[</span><span class="s">"name"</span><span class="p">])</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">conn</span><span class="o">.</span><span class="n">execute</span><span class="p">(</span><span class="s">"update images set "</span> <span class="o">+</span> <span class="nb">bin</span><span class="p">[</span><span class="s">"name"</span><span class="p">]</span> <span class="o">+</span> <span class="s">"=? where pegasusid=?"</span><span class="p">,</span> <span class="p">(</span><span class="nb">bin</span><span class="p">[</span><span class="s">"count"</span><span class="p">],</span> <span class="bp">self</span><span class="o">.</span><span class="n">dbid</span><span class="p">))</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">conn</span><span class="o">.</span><span class="n">commit</span><span class="p">()</span>
+ <span class="k">return</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="k">return</span> <span class="n">binlist</span>
+
+ </div></div>
+</pre></div>
+
+ </div>
+
+ </div>
+</div>
+<footer class="footer">
+ <div class="container">
+ <p class="pull-right">
+ <a href="#">Back to top</a>
+
+ </p>
+ <p>
+ © Copyright 2015, Avi Knecht.<br/>
+ Created using <a href="http://sphinx.pocoo.org/">Sphinx</a> 1.3a0.<br/>
+ </p>
+ </div>
+</footer>
+ </body>
+</html>
\ No newline at end of file
diff --git a/docs/build/html/_modules/ih/statistics.html b/docs/build/html/_modules/ih/statistics.html
new file mode 100644
index 0000000000000000000000000000000000000000..7e3beec6cb913f916b90f6c37f8a2c2dc1b326fa
--- /dev/null
+++ b/docs/build/html/_modules/ih/statistics.html
@@ -0,0 +1,874 @@
+<!DOCTYPE html>
+
+
+<html xmlns="http://www.w3.org/1999/xhtml">
+ <head>
+ <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
+
+ <title>ih.statistics — Image Harvest 1.0.1 documentation</title>
+
+ <link rel="stylesheet" href="../../_static/basic.css" type="text/css" />
+ <link rel="stylesheet" href="../../_static/pygments.css" type="text/css" />
+ <link rel="stylesheet" href="../../_static/bootstrap-3.2.0/css/bootstrap.min.css" type="text/css" />
+ <link rel="stylesheet" href="../../_static/bootstrap-3.2.0/css/bootstrap-theme.min.css" type="text/css" />
+ <link rel="stylesheet" href="../../_static/bootstrap-sphinx.css" type="text/css" />
+
+ <script type="text/javascript">
+ var DOCUMENTATION_OPTIONS = {
+ URL_ROOT: '../../',
+ VERSION: '1.0.1',
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+ FILE_SUFFIX: '.html',
+ HAS_SOURCE: true
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+ <script type="text/javascript" src="../../_static/bootstrap-sphinx.js"></script>
+ <link rel="top" title="Image Harvest 1.0.1 documentation" href="../../index.html" />
+ <link rel="up" title="Module code" href="../index.html" />
+<meta charset='utf-8'>
+<meta http-equiv='X-UA-Compatible' content='IE=edge,chrome=1'>
+<meta name='viewport' content='width=device-width, initial-scale=1.0, maximum-scale=1'>
+<meta name="apple-mobile-web-app-capable" content="yes">
+
+ </head>
+ <body role="document">
+
+ <div id="navbar" class="navbar navbar-default navbar-fixed-top">
+ <div class="container">
+ <div class="navbar-header">
+ <!-- .btn-navbar is used as the toggle for collapsed navbar content -->
+ <button type="button" class="navbar-toggle" data-toggle="collapse" data-target=".nav-collapse">
+ <span class="icon-bar"></span>
+ <span class="icon-bar"></span>
+ <span class="icon-bar"></span>
+ </button>
+ <a class="navbar-brand" href="../../index.html">
+ Image Harvest</a>
+ <span class="navbar-text navbar-version pull-left"><b>1.0</b></span>
+ </div>
+
+ <div class="collapse navbar-collapse nav-collapse">
+ <ul class="nav navbar-nav">
+
+
+ <li class="dropdown globaltoc-container">
+ <a role="button"
+ id="dLabelGlobalToc"
+ data-toggle="dropdown"
+ data-target="#"
+ href="../../index.html">Site <b class="caret"></b></a>
+ <ul class="dropdown-menu globaltoc"
+ role="menu"
+ aria-labelledby="dLabelGlobalToc"><ul>
+<li class="toctree-l1"><a class="reference internal" href="../../introduction.html">Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../../installation.html">Installation</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../../start.html">Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../../ex_script_core1.html">Core Processing Example #1</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../../ex_script_core2.html">Core Processing Example #2</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../../ex_script_color1.html">Color Filter In Depth #1</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../../ex_workflow_1.html">Workflow Example #1</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../../examples.html">Examples</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../../processing.html">Image Processing</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../../viewer.html">Image Processing Viewer</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../../statistics.html">Statistics</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../../indexing.html">Image Loading</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../../workflowimage.html">Image Processing Workflows</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../../workflowstats.html">Statistics Workflows</a></li>
+</ul>
+</ul>
+</li>
+
+ <li class="dropdown">
+ <a role="button"
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+ data-toggle="dropdown"
+ data-target="#"
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+<div class="container">
+ <div class="row">
+ <div class="col-md-12">
+
+ <h1>Source code for ih.statistics</h1><div class="highlight"><pre>
+<span class="kn">import</span> <span class="nn">math</span>
+<span class="kn">import</span> <span class="nn">os</span>
+<span class="kn">import</span> <span class="nn">sqlite3</span>
+<span class="kn">import</span> <span class="nn">conf</span>
+<span class="kn">import</span> <span class="nn">datetime</span>
+<span class="kn">import</span> <span class="nn">numpy</span> <span class="kn">as</span> <span class="nn">np</span>
+<span class="kn">import</span> <span class="nn">pandas</span>
+<span class="kn">import</span> <span class="nn">ih.imgproc</span>
+<span class="kn">import</span> <span class="nn">cv2</span>
+<span class="kn">import</span> <span class="nn">json</span>
+<span class="kn">import</span> <span class="nn">traceback</span>
+<span class="kn">from</span> <span class="nn">scipy</span> <span class="kn">import</span> <span class="n">stats</span>
+
+<div class="viewcode-block" id="Stats"><a class="viewcode-back" href="../../statistics.html#ih.statistics.Stats">[docs]</a><span class="k">class</span> <span class="nc">Stats</span><span class="p">:</span>
+
+ <span class="k">def</span> <span class="nf">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">db</span><span class="p">):</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">db</span> <span class="o">=</span> <span class="n">db</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">conn</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_openConnection</span><span class="p">()</span>
+ <span class="k">return</span>
+
+ <span class="k">def</span> <span class="nf">_openConnection</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">db</span> <span class="o">=</span> <span class="bp">None</span><span class="p">):</span>
+ <span class="n">db</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">db</span> <span class="k">if</span> <span class="ow">not</span> <span class="n">db</span> <span class="k">else</span> <span class="n">db</span>
+ <span class="k">if</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">isfile</span><span class="p">(</span><span class="n">db</span><span class="p">):</span>
+ <span class="n">conn</span> <span class="o">=</span> <span class="n">sqlite3</span><span class="o">.</span><span class="n">connect</span><span class="p">(</span><span class="n">db</span><span class="p">,</span> <span class="n">check_same_thread</span> <span class="o">=</span> <span class="bp">False</span><span class="p">)</span>
+ <span class="n">conn</span><span class="o">.</span><span class="n">row_factory</span> <span class="o">=</span> <span class="n">sqlite3</span><span class="o">.</span><span class="n">Row</span>
+ <span class="n">result</span> <span class="o">=</span> <span class="n">conn</span><span class="o">.</span><span class="n">execute</span><span class="p">(</span><span class="s">"select pegasusid from images limit 0,1"</span><span class="p">)</span>
+ <span class="k">if</span> <span class="ow">not</span> <span class="n">result</span><span class="o">.</span><span class="n">fetchone</span><span class="p">():</span>
+ <span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="s">"Database '</span><span class="si">%s</span><span class="s">' has no entries!"</span> <span class="o">%</span> <span class="p">(</span><span class="n">db</span><span class="p">,))</span>
+ <span class="c"># Have to enable foreign keys EVERY time.</span>
+ <span class="n">conn</span><span class="o">.</span><span class="n">execute</span><span class="p">(</span><span class="s">"PRAGMA foreign_keys = ON"</span><span class="p">)</span>
+ <span class="n">conn</span><span class="o">.</span><span class="n">commit</span><span class="p">()</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="s">"Database file '</span><span class="si">%s</span><span class="s">' does not exist."</span> <span class="o">%</span> <span class="p">(</span><span class="n">db</span><span class="p">,))</span>
+ <span class="k">return</span> <span class="n">conn</span>
+
+ <span class="k">def</span> <span class="nf">_closeConnection</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">conn</span> <span class="o">=</span> <span class="bp">None</span><span class="p">):</span>
+ <span class="n">conn</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">conn</span> <span class="k">if</span> <span class="ow">not</span> <span class="n">conn</span> <span class="k">else</span> <span class="n">conn</span>
+ <span class="n">conn</span><span class="o">.</span><span class="n">close</span><span class="p">()</span>
+ <span class="k">return</span>
+
+ <span class="k">def</span> <span class="nf">_tableExists</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">tablename</span><span class="p">,</span> <span class="n">conn</span> <span class="o">=</span> <span class="bp">None</span><span class="p">):</span>
+ <span class="n">conn</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">conn</span> <span class="k">if</span> <span class="ow">not</span> <span class="n">conn</span> <span class="k">else</span> <span class="n">conn</span>
+ <span class="n">result</span> <span class="o">=</span> <span class="n">conn</span><span class="o">.</span><span class="n">execute</span><span class="p">(</span><span class="s">"select name from sqlite_master where type='table' and name=?"</span><span class="p">,</span> <span class="p">(</span><span class="n">tablename</span><span class="p">,))</span>
+ <span class="k">if</span> <span class="ow">not</span> <span class="n">result</span><span class="o">.</span><span class="n">fetchone</span><span class="p">():</span>
+ <span class="k">return</span> <span class="bp">False</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="k">return</span> <span class="bp">True</span>
+
+ <span class="k">def</span> <span class="nf">_validate</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">funcname</span><span class="p">,</span> <span class="n">intable</span><span class="p">,</span> <span class="n">outtable</span><span class="p">,</span> <span class="n">overwrite</span><span class="p">,</span> <span class="n">conn</span> <span class="o">=</span> <span class="bp">None</span><span class="p">):</span>
+ <span class="n">conn</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">conn</span> <span class="k">if</span> <span class="ow">not</span> <span class="n">conn</span> <span class="k">else</span> <span class="n">conn</span>
+ <span class="k">if</span> <span class="n">funcname</span> <span class="ow">in</span> <span class="n">conf</span><span class="o">.</span><span class="n">statsColumns</span><span class="p">:</span>
+ <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">_tableExists</span><span class="p">(</span><span class="n">intable</span><span class="p">):</span>
+ <span class="n">cols</span> <span class="o">=</span> <span class="p">[</span><span class="n">x</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span> <span class="k">for</span> <span class="n">x</span> <span class="ow">in</span> <span class="n">conn</span><span class="o">.</span><span class="n">execute</span><span class="p">(</span><span class="s">"PRAGMA table_info('"</span> <span class="o">+</span> <span class="n">intable</span> <span class="o">+</span> <span class="s">"')"</span><span class="p">)]</span>
+ <span class="k">if</span> <span class="nb">set</span><span class="p">(</span><span class="n">conf</span><span class="o">.</span><span class="n">statsColumns</span><span class="p">[</span><span class="n">funcname</span><span class="p">][</span><span class="s">"required"</span><span class="p">])</span> <span class="o"><=</span> <span class="nb">set</span><span class="p">(</span><span class="n">cols</span><span class="p">):</span>
+ <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">_tableExists</span><span class="p">(</span><span class="n">outtable</span><span class="p">,</span> <span class="n">conn</span><span class="p">)</span> <span class="ow">and</span> <span class="ow">not</span> <span class="n">overwrite</span><span class="p">:</span>
+ <span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="s">"Output table '"</span> <span class="o">+</span> <span class="n">outtable</span> <span class="o">+</span> <span class="s">"' already exists."</span><span class="p">)</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="s">"Table '"</span> <span class="o">+</span> <span class="n">intable</span> <span class="o">+</span> <span class="s">"' doesn't have all the required columns: '"</span> <span class="o">+</span> <span class="nb">str</span><span class="p">(</span><span class="n">conf</span><span class="o">.</span><span class="n">statsColumns</span><span class="p">[</span><span class="n">funcname</span><span class="p">][</span><span class="s">"required"</span><span class="p">])</span> <span class="o">+</span> <span class="s">"'."</span><span class="p">)</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="s">"Table '"</span> <span class="o">+</span> <span class="n">intable</span> <span class="o">+</span> <span class="s">"' doesn't exist."</span><span class="p">)</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="s">"Function '"</span> <span class="o">+</span> <span class="n">funcname</span> <span class="o">+</span> <span class="s">"' doesn't exist."</span><span class="p">)</span>
+ <span class="k">return</span>
+
+ <span class="k">def</span> <span class="nf">_massage</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">table</span><span class="p">,</span> <span class="n">headers</span><span class="p">,</span> <span class="n">imtypes</span> <span class="o">=</span> <span class="bp">None</span><span class="p">,</span> <span class="n">conn</span> <span class="o">=</span> <span class="bp">None</span><span class="p">):</span>
+ <span class="n">conn</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">conn</span> <span class="k">if</span> <span class="ow">not</span> <span class="n">conn</span> <span class="k">else</span> <span class="n">conn</span>
+ <span class="k">if</span> <span class="ow">not</span> <span class="n">imtypes</span><span class="p">:</span>
+ <span class="n">imtypes</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_getImageTypes</span><span class="p">(</span><span class="n">table</span><span class="p">,</span> <span class="n">conn</span><span class="p">)</span>
+ <span class="k">elif</span> <span class="ow">not</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">imtypes</span><span class="p">,</span> <span class="nb">list</span><span class="p">):</span>
+ <span class="n">imtypes</span> <span class="o">=</span> <span class="p">[</span><span class="n">imtypes</span><span class="p">]</span>
+
+ <span class="k">for</span> <span class="n">header</span> <span class="ow">in</span> <span class="n">headers</span><span class="p">:</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">conn</span><span class="o">.</span><span class="n">execute</span><span class="p">(</span><span class="s">"update "</span> <span class="o">+</span> <span class="n">table</span> <span class="o">+</span> <span class="s">" set "</span> <span class="o">+</span> <span class="n">header</span> <span class="o">+</span> <span class="s">"=? where "</span> <span class="o">+</span> <span class="n">header</span> <span class="o">+</span> <span class="s">" is null and ("</span> <span class="o">+</span> <span class="s">"or"</span><span class="o">.</span><span class="n">join</span><span class="p">([</span><span class="s">"imtype=?"</span> <span class="k">for</span> <span class="n">x</span> <span class="ow">in</span> <span class="n">imtypes</span><span class="p">])</span> <span class="o">+</span> <span class="s">")"</span><span class="p">,</span> <span class="p">(</span><span class="mi">0</span><span class="p">,)</span> <span class="o">+</span> <span class="nb">tuple</span><span class="p">(</span><span class="n">imtypes</span><span class="p">))</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">conn</span><span class="o">.</span><span class="n">commit</span><span class="p">()</span>
+ <span class="k">return</span>
+
+ <span class="k">def</span> <span class="nf">_columnExists</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">column</span><span class="p">,</span> <span class="n">tablename</span><span class="p">,</span> <span class="n">conn</span> <span class="o">=</span> <span class="bp">None</span><span class="p">):</span>
+ <span class="n">conn</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">conn</span> <span class="k">if</span> <span class="ow">not</span> <span class="n">conn</span> <span class="k">else</span> <span class="n">conn</span>
+ <span class="k">if</span> <span class="n">column</span> <span class="ow">in</span> <span class="p">[</span><span class="n">row</span><span class="p">[</span><span class="s">"name"</span><span class="p">]</span> <span class="k">for</span> <span class="n">row</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">conn</span><span class="o">.</span><span class="n">execute</span><span class="p">(</span><span class="s">"PRAGMA table_info('"</span> <span class="o">+</span> <span class="n">tablename</span> <span class="o">+</span> <span class="s">"')"</span><span class="p">)]:</span>
+ <span class="k">return</span> <span class="bp">True</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="k">return</span> <span class="bp">False</span>
+
+ <span class="k">def</span> <span class="nf">_addColumn</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">column</span><span class="p">,</span> <span class="n">tablename</span> <span class="o">=</span> <span class="s">"images"</span><span class="p">,</span> <span class="n">conn</span> <span class="o">=</span> <span class="bp">None</span><span class="p">):</span>
+ <span class="n">conn</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">conn</span> <span class="k">if</span> <span class="ow">not</span> <span class="n">conn</span> <span class="k">else</span> <span class="n">conn</span>
+ <span class="k">if</span> <span class="ow">not</span> <span class="bp">self</span><span class="o">.</span><span class="n">_columnExists</span><span class="p">(</span><span class="n">column</span><span class="p">,</span> <span class="n">tablename</span><span class="p">,</span> <span class="n">conn</span><span class="p">):</span>
+ <span class="n">conn</span><span class="o">.</span><span class="n">execute</span><span class="p">(</span><span class="s">"alter table '"</span> <span class="o">+</span> <span class="n">tablename</span> <span class="o">+</span> <span class="s">"' add column "</span> <span class="o">+</span> <span class="n">column</span> <span class="o">+</span> <span class="s">";"</span><span class="p">)</span>
+ <span class="n">conn</span><span class="o">.</span><span class="n">commit</span><span class="p">()</span>
+ <span class="k">return</span>
+
+ <span class="k">def</span> <span class="nf">_addKeyColumn</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">parent</span><span class="p">,</span> <span class="n">parentCol</span><span class="p">,</span> <span class="n">child</span><span class="p">,</span> <span class="n">childCol</span><span class="p">,</span> <span class="n">conn</span> <span class="o">=</span> <span class="bp">None</span><span class="p">):</span>
+ <span class="n">conn</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">conn</span> <span class="k">if</span> <span class="ow">not</span> <span class="n">conn</span> <span class="k">else</span> <span class="n">conn</span>
+ <span class="k">if</span> <span class="n">parentCol</span> <span class="ow">not</span> <span class="ow">in</span> <span class="p">[</span><span class="n">row</span><span class="p">[</span><span class="s">"name"</span><span class="p">]</span> <span class="k">for</span> <span class="n">row</span> <span class="ow">in</span> <span class="n">conn</span><span class="o">.</span><span class="n">execute</span><span class="p">(</span><span class="s">"PRAGMA table_info('"</span> <span class="o">+</span> <span class="n">parent</span> <span class="o">+</span> <span class="s">"');"</span><span class="p">)]</span> <span class="ow">and</span> <span class="n">childCol</span> <span class="ow">in</span> <span class="p">[</span><span class="n">row</span><span class="p">[</span><span class="s">"name"</span><span class="p">]</span> <span class="k">for</span> <span class="n">row</span> <span class="ow">in</span> <span class="n">conn</span><span class="o">.</span><span class="n">execute</span><span class="p">(</span><span class="s">"PRAGMA table_info('"</span> <span class="o">+</span> <span class="n">child</span> <span class="o">+</span> <span class="s">"');"</span><span class="p">)]:</span>
+ <span class="n">conn</span><span class="o">.</span><span class="n">execute</span><span class="p">(</span><span class="s">"alter table '"</span> <span class="o">+</span> <span class="n">parent</span> <span class="o">+</span> <span class="s">"' add column '"</span> <span class="o">+</span> <span class="n">parentCol</span> <span class="o">+</span> <span class="s">"' REFERENCES '"</span> <span class="o">+</span> <span class="n">child</span> <span class="o">+</span> <span class="s">"'('"</span> <span class="o">+</span> <span class="n">childCol</span> <span class="o">+</span> <span class="s">"');"</span><span class="p">)</span>
+ <span class="n">conn</span><span class="o">.</span><span class="n">commit</span><span class="p">()</span>
+ <span class="k">return</span>
+
+ <span class="k">def</span> <span class="nf">_createTable</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">funcname</span><span class="p">,</span> <span class="n">intable</span><span class="p">,</span> <span class="n">outtable</span><span class="p">,</span> <span class="n">overwrite</span><span class="p">,</span> <span class="n">conn</span> <span class="o">=</span> <span class="bp">None</span><span class="p">):</span>
+ <span class="n">conn</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">conn</span> <span class="k">if</span> <span class="ow">not</span> <span class="n">conn</span> <span class="k">else</span> <span class="n">conn</span>
+ <span class="n">tablestr</span> <span class="o">=</span> <span class="s">"(pegasusid INTEGER PRIMARY KEY"</span>
+ <span class="n">cols</span> <span class="o">=</span> <span class="p">[</span><span class="n">x</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span> <span class="k">for</span> <span class="n">x</span> <span class="ow">in</span> <span class="n">conn</span><span class="o">.</span><span class="n">execute</span><span class="p">(</span><span class="s">"pragma table_info('"</span> <span class="o">+</span> <span class="n">intable</span> <span class="o">+</span> <span class="s">"')"</span><span class="p">)]</span>
+ <span class="k">if</span> <span class="s">"all"</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">conf</span><span class="o">.</span><span class="n">statsColumns</span><span class="p">[</span><span class="n">funcname</span><span class="p">][</span><span class="s">"exclude"</span><span class="p">]:</span>
+ <span class="k">for</span> <span class="n">col</span> <span class="ow">in</span> <span class="n">cols</span><span class="p">:</span>
+ <span class="k">if</span> <span class="n">col</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">conf</span><span class="o">.</span><span class="n">statsColumns</span><span class="p">[</span><span class="n">funcname</span><span class="p">][</span><span class="s">"exclude"</span><span class="p">]</span> <span class="ow">and</span> <span class="n">col</span><span class="p">[:</span><span class="mi">3</span><span class="p">]</span> <span class="o">!=</span> <span class="s">"ref"</span><span class="p">:</span>
+ <span class="n">tablestr</span> <span class="o">+=</span> <span class="s">","</span> <span class="o">+</span> <span class="nb">str</span><span class="p">(</span><span class="n">col</span><span class="p">)</span>
+ <span class="k">for</span> <span class="n">col</span> <span class="ow">in</span> <span class="n">conf</span><span class="o">.</span><span class="n">statsColumns</span><span class="p">[</span><span class="n">funcname</span><span class="p">][</span><span class="s">"add"</span><span class="p">]:</span>
+ <span class="n">tablestr</span> <span class="o">+=</span> <span class="s">","</span> <span class="o">+</span> <span class="nb">str</span><span class="p">(</span><span class="n">col</span><span class="p">)</span>
+ <span class="n">tablestr</span> <span class="o">+=</span> <span class="s">")"</span>
+ <span class="k">if</span> <span class="n">overwrite</span><span class="p">:</span>
+ <span class="k">if</span> <span class="n">conf</span><span class="o">.</span><span class="n">statsColumns</span><span class="p">[</span><span class="n">funcname</span><span class="p">][</span><span class="s">"ref"</span><span class="p">]:</span>
+ <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">_columnExists</span><span class="p">(</span><span class="s">"ref_"</span> <span class="o">+</span> <span class="n">outtable</span><span class="p">,</span> <span class="n">intable</span><span class="p">,</span> <span class="n">conn</span><span class="p">):</span>
+ <span class="n">conn</span><span class="o">.</span><span class="n">execute</span><span class="p">(</span><span class="s">"update "</span> <span class="o">+</span> <span class="n">intable</span> <span class="o">+</span> <span class="s">" set ref_"</span> <span class="o">+</span> <span class="n">outtable</span> <span class="o">+</span> <span class="s">"=? where ref_"</span> <span class="o">+</span> <span class="n">outtable</span> <span class="o">+</span> <span class="s">" is not null"</span><span class="p">,</span> <span class="p">(</span><span class="bp">None</span><span class="p">,))</span>
+ <span class="n">conn</span><span class="o">.</span><span class="n">commit</span><span class="p">()</span>
+ <span class="n">conn</span><span class="o">.</span><span class="n">execute</span><span class="p">(</span><span class="s">"DROP TABLE IF EXISTS "</span> <span class="o">+</span> <span class="n">outtable</span><span class="p">)</span>
+ <span class="n">conn</span><span class="o">.</span><span class="n">commit</span><span class="p">()</span>
+ <span class="n">conn</span><span class="o">.</span><span class="n">execute</span><span class="p">(</span><span class="s">"CREATE TABLE "</span> <span class="o">+</span> <span class="n">outtable</span> <span class="o">+</span> <span class="s">" "</span> <span class="o">+</span> <span class="n">tablestr</span><span class="p">)</span>
+ <span class="n">conn</span><span class="o">.</span><span class="n">commit</span><span class="p">()</span>
+ <span class="k">if</span> <span class="n">conf</span><span class="o">.</span><span class="n">statsColumns</span><span class="p">[</span><span class="n">funcname</span><span class="p">][</span><span class="s">"ref"</span><span class="p">]:</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_addKeyColumn</span><span class="p">(</span><span class="n">intable</span><span class="p">,</span> <span class="s">"ref_"</span> <span class="o">+</span> <span class="n">outtable</span><span class="p">,</span> <span class="n">outtable</span><span class="p">,</span> <span class="s">"pegasusid"</span><span class="p">,</span> <span class="n">conn</span><span class="p">)</span>
+ <span class="k">return</span>
+
+ <span class="k">def</span> <span class="nf">_getHeaders</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">table</span><span class="p">,</span> <span class="n">conn</span> <span class="o">=</span> <span class="bp">None</span><span class="p">):</span>
+ <span class="n">conn</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">conn</span> <span class="k">if</span> <span class="ow">not</span> <span class="n">conn</span> <span class="k">else</span> <span class="n">conn</span>
+ <span class="k">return</span> <span class="p">[</span><span class="nb">str</span><span class="p">(</span><span class="n">x</span><span class="p">[</span><span class="mi">1</span><span class="p">])</span> <span class="k">for</span> <span class="n">x</span> <span class="ow">in</span> <span class="n">conn</span><span class="o">.</span><span class="n">execute</span><span class="p">(</span><span class="s">"pragma table_info("</span> <span class="o">+</span> <span class="n">table</span> <span class="o">+</span> <span class="s">")"</span><span class="p">)</span> <span class="k">if</span> <span class="n">x</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span> <span class="o">!=</span> <span class="s">"pegasusid"</span><span class="p">]</span>
+
+ <span class="k">def</span> <span class="nf">_getImageTypes</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">table</span><span class="p">,</span> <span class="n">conn</span> <span class="o">=</span> <span class="bp">None</span><span class="p">):</span>
+ <span class="n">conn</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">conn</span> <span class="k">if</span> <span class="ow">not</span> <span class="n">conn</span> <span class="k">else</span> <span class="n">conn</span>
+ <span class="k">return</span> <span class="p">[</span><span class="nb">str</span><span class="p">(</span><span class="n">x</span><span class="p">[</span><span class="mi">0</span><span class="p">])</span> <span class="k">for</span> <span class="n">x</span> <span class="ow">in</span> <span class="n">conn</span><span class="o">.</span><span class="n">execute</span><span class="p">(</span><span class="s">"select distinct imtype from "</span> <span class="o">+</span> <span class="n">table</span><span class="p">)]</span>
+
+ <span class="k">def</span> <span class="nf">_getDates</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">table</span><span class="p">,</span> <span class="n">conn</span> <span class="o">=</span> <span class="bp">None</span><span class="p">):</span>
+ <span class="n">conn</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">conn</span> <span class="k">if</span> <span class="ow">not</span> <span class="n">conn</span> <span class="k">else</span> <span class="n">conn</span>
+ <span class="k">return</span> <span class="p">[</span><span class="nb">str</span><span class="p">(</span><span class="n">x</span><span class="p">[</span><span class="mi">0</span><span class="p">])</span> <span class="k">for</span> <span class="n">x</span> <span class="ow">in</span> <span class="n">conn</span><span class="o">.</span><span class="n">execute</span><span class="p">(</span><span class="s">"select distinct date from "</span> <span class="o">+</span> <span class="n">table</span><span class="p">)]</span>
+
+ <span class="k">def</span> <span class="nf">_checkNull</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">value</span><span class="p">):</span>
+ <span class="k">return</span> <span class="bp">True</span> <span class="k">if</span> <span class="n">value</span> <span class="ow">is</span> <span class="bp">None</span> <span class="ow">or</span> <span class="nb">str</span><span class="p">(</span><span class="n">value</span><span class="p">)</span><span class="o">.</span><span class="n">lower</span><span class="p">()</span> <span class="o">==</span> <span class="s">"none"</span> <span class="k">else</span> <span class="bp">False</span>
+
+ <span class="k">def</span> <span class="nf">_loadLemnaData</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">dataFile</span><span class="p">,</span> <span class="n">dataHeaders</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> :param dataFile: The input dataFile</span>
+<span class="sd"> :type dataFile: str</span>
+<span class="sd"> :param dataHeaders: The input data headers</span>
+<span class="sd"> :type dataHeaders: dict</span>
+<span class="sd"> </span>
+<span class="sd"> dataHeaders should be:</span>
+<span class="sd"> { </span>
+<span class="sd"> "id": "Snapshot ID Tag",</span>
+<span class="sd"> "date": "Snapshot Time Stamp",</span>
+<span class="sd"> "dateFormat": "%m/%d/%y",</span>
+<span class="sd"> "metric": "Projected Shoot Area [pixels]"</span>
+<span class="sd"> }</span>
+<span class="sd"> """</span>
+ <span class="k">if</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">isfile</span><span class="p">(</span><span class="n">dataFile</span><span class="p">):</span>
+ <span class="k">if</span> <span class="nb">all</span><span class="p">(</span><span class="n">key</span> <span class="ow">in</span> <span class="n">dataHeaders</span> <span class="k">for</span> <span class="n">key</span> <span class="ow">in</span> <span class="p">[</span><span class="s">"id"</span><span class="p">,</span> <span class="s">"date"</span><span class="p">,</span> <span class="s">"dateFormat"</span><span class="p">,</span> <span class="s">"metric"</span><span class="p">]):</span>
+ <span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="n">dataFile</span><span class="p">)</span> <span class="k">as</span> <span class="n">rh</span><span class="p">:</span>
+ <span class="n">lines</span> <span class="o">=</span> <span class="n">rh</span><span class="o">.</span><span class="n">readlines</span><span class="p">()</span>
+ <span class="n">firstline</span> <span class="o">=</span> <span class="n">lines</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">.</span><span class="n">strip</span><span class="p">()</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s">","</span><span class="p">)</span>
+ <span class="k">if</span> <span class="n">dataHeaders</span><span class="p">[</span><span class="s">"id"</span><span class="p">]</span> <span class="ow">in</span> <span class="n">firstline</span><span class="p">:</span>
+ <span class="k">if</span> <span class="n">dataHeaders</span><span class="p">[</span><span class="s">"date"</span><span class="p">]</span> <span class="ow">in</span> <span class="n">firstline</span><span class="p">:</span>
+ <span class="k">if</span> <span class="n">dataHeaders</span><span class="p">[</span><span class="s">"metric"</span><span class="p">]</span> <span class="ow">in</span> <span class="n">firstline</span><span class="p">:</span>
+ <span class="n">idIndex</span> <span class="o">=</span> <span class="n">firstline</span><span class="o">.</span><span class="n">index</span><span class="p">(</span><span class="n">dataHeaders</span><span class="p">[</span><span class="s">"id"</span><span class="p">])</span>
+ <span class="n">dateIndex</span> <span class="o">=</span> <span class="n">firstline</span><span class="o">.</span><span class="n">index</span><span class="p">(</span><span class="n">dataHeaders</span><span class="p">[</span><span class="s">"date"</span><span class="p">])</span>
+ <span class="n">metricIndex</span> <span class="o">=</span> <span class="n">firstline</span><span class="o">.</span><span class="n">index</span><span class="p">(</span><span class="n">dataHeaders</span><span class="p">[</span><span class="s">"metric"</span><span class="p">])</span>
+ <span class="n">lemnaData</span> <span class="o">=</span> <span class="p">{}</span>
+ <span class="k">for</span> <span class="n">line</span> <span class="ow">in</span> <span class="n">lines</span><span class="p">[</span><span class="mi">1</span><span class="p">:]:</span>
+ <span class="n">info</span> <span class="o">=</span> <span class="n">line</span><span class="o">.</span><span class="n">strip</span><span class="p">()</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s">","</span><span class="p">)</span>
+ <span class="k">if</span> <span class="p">(</span><span class="n">info</span><span class="p">[</span><span class="n">metricIndex</span><span class="p">]</span> <span class="o">!=</span> <span class="s">"NA"</span><span class="p">):</span>
+ <span class="nb">id</span> <span class="o">=</span> <span class="n">info</span><span class="p">[</span><span class="n">idIndex</span><span class="p">][</span><span class="o">-</span><span class="mi">8</span><span class="p">:]</span>
+ <span class="n">date</span> <span class="o">=</span> <span class="n">datetime</span><span class="o">.</span><span class="n">datetime</span><span class="o">.</span><span class="n">strptime</span><span class="p">(</span><span class="n">info</span><span class="p">[</span><span class="n">dateIndex</span><span class="p">]</span><span class="o">.</span><span class="n">split</span><span class="p">()[</span><span class="mi">0</span><span class="p">],</span> <span class="n">dataHeaders</span><span class="p">[</span><span class="s">"dateFormat"</span><span class="p">])</span><span class="o">.</span><span class="n">strftime</span><span class="p">(</span><span class="s">"%Y-%m-</span><span class="si">%d</span><span class="s">"</span><span class="p">)</span>
+ <span class="k">try</span><span class="p">:</span>
+ <span class="n">metric</span> <span class="o">=</span> <span class="nb">float</span><span class="p">(</span><span class="n">info</span><span class="p">[</span><span class="n">metricIndex</span><span class="p">])</span>
+ <span class="k">if</span> <span class="nb">id</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">lemnaData</span><span class="p">:</span>
+ <span class="n">lemnaData</span><span class="p">[</span><span class="nb">id</span><span class="p">]</span> <span class="o">=</span> <span class="p">{}</span>
+ <span class="k">if</span> <span class="n">date</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">lemnaData</span><span class="p">[</span><span class="nb">id</span><span class="p">]:</span>
+ <span class="n">lemnaData</span><span class="p">[</span><span class="nb">id</span><span class="p">][</span><span class="n">date</span><span class="p">]</span> <span class="o">=</span> <span class="p">{}</span>
+ <span class="n">lemnaData</span><span class="p">[</span><span class="nb">id</span><span class="p">][</span><span class="n">date</span><span class="p">][</span><span class="s">"metric"</span><span class="p">]</span> <span class="o">=</span> <span class="n">metric</span>
+ <span class="k">except</span><span class="p">:</span>
+ <span class="k">pass</span>
+ <span class="k">return</span> <span class="n">lemnaData</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="s">"Metric Column: "</span><span class="p">,</span><span class="n">dataHeaders</span><span class="p">[</span><span class="s">"metric"</span><span class="p">],</span><span class="s">" does not exist."</span><span class="p">)</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="s">"Date Column: "</span><span class="p">,</span><span class="n">dataHeaders</span><span class="p">[</span><span class="s">"date"</span><span class="p">],</span><span class="s">" does not exist."</span><span class="p">)</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="s">"Id Column: "</span><span class="p">,</span><span class="n">dataHeaders</span><span class="p">[</span><span class="s">"id"</span><span class="p">],</span><span class="s">" does not exist."</span><span class="p">)</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="s">"Data Dictionary does not have all required keys ['id', 'date', 'dateFormat', 'metric']"</span><span class="p">)</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="s">"Data File: "</span> <span class="o">+</span> <span class="n">dataFile</span> <span class="o">+</span> <span class="s">" does not exist!"</span><span class="p">)</span>
+ <span class="k">return</span>
+
+ <span class="k">def</span> <span class="nf">loadSql</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">dblist</span><span class="p">):</span>
+ <span class="k">for</span> <span class="n">i</span><span class="p">,</span><span class="n">f</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="n">dblist</span><span class="p">):</span>
+ <span class="k">if</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">isfile</span><span class="p">(</span><span class="n">f</span><span class="p">):</span>
+ <span class="n">conn</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_openConnection</span><span class="p">(</span><span class="n">f</span><span class="p">)</span>
+ <span class="n">cols</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_getHeaders</span><span class="p">(</span><span class="s">"images"</span><span class="p">,</span> <span class="n">conn</span><span class="p">)</span>
+ <span class="k">for</span> <span class="n">col</span> <span class="ow">in</span> <span class="n">cols</span><span class="p">:</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_addColumn</span><span class="p">(</span><span class="n">col</span><span class="p">,</span> <span class="s">"images"</span><span class="p">)</span>
+ <span class="n">result</span> <span class="o">=</span> <span class="n">conn</span><span class="o">.</span><span class="n">execute</span><span class="p">(</span><span class="s">"select pegasusid,"</span> <span class="o">+</span> <span class="s">","</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">cols</span><span class="p">)</span> <span class="o">+</span> <span class="s">" from images"</span><span class="p">)</span>
+ <span class="n">query</span> <span class="o">=</span> <span class="s">"update images set "</span> <span class="o">+</span> <span class="s">","</span><span class="o">.</span><span class="n">join</span><span class="p">([</span><span class="n">col</span> <span class="o">+</span> <span class="s">"=?"</span> <span class="k">for</span> <span class="n">col</span> <span class="ow">in</span> <span class="n">cols</span><span class="p">])</span> <span class="o">+</span> <span class="s">" where pegasusid=?"</span>
+ <span class="n">values</span> <span class="o">=</span> <span class="p">[</span><span class="nb">tuple</span><span class="p">([</span><span class="n">row</span><span class="p">[</span><span class="n">col</span><span class="p">]</span> <span class="k">for</span> <span class="n">col</span> <span class="ow">in</span> <span class="n">cols</span><span class="p">]</span> <span class="o">+</span> <span class="p">[</span><span class="n">row</span><span class="p">[</span><span class="s">"pegasusid"</span><span class="p">]])</span> <span class="k">for</span> <span class="n">row</span> <span class="ow">in</span> <span class="n">result</span><span class="p">]</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">conn</span><span class="o">.</span><span class="n">executemany</span><span class="p">(</span><span class="n">query</span><span class="p">,</span> <span class="n">values</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">conn</span><span class="o">.</span><span class="n">commit</span><span class="p">()</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_closeConnection</span><span class="p">(</span><span class="n">conn</span><span class="p">)</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="k">print</span> <span class="s">"DB File: '</span><span class="si">%s</span><span class="s">' does not exist."</span> <span class="o">%</span> <span class="p">(</span><span class="n">f</span><span class="p">,)</span>
+ <span class="k">return</span>
+
+
+
+<div class="viewcode-block" id="Stats.logErrors"><a class="viewcode-back" href="../../statistics.html#ih.statistics.Stats.logErrors">[docs]</a> <span class="k">def</span> <span class="nf">logErrors</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">logfile</span><span class="p">,</span> <span class="n">table</span> <span class="o">=</span> <span class="s">"images"</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> :param logfile: The logfile to write errors to</span>
+<span class="sd"> :type logfile: str</span>
+<span class="sd"> :param table: The table to load errors from</span>
+<span class="sd"> :type table: str</span>
+<span class="sd"> </span>
+<span class="sd"> This function writes all errors from a given table to a log file,</span>
+<span class="sd"> usually used at the end of image processing to write all images that</span>
+<span class="sd"> did not process correctly.</span>
+<span class="sd"> """</span>
+ <span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="n">logfile</span><span class="p">,</span> <span class="s">"w"</span><span class="p">)</span> <span class="k">as</span> <span class="n">wh</span><span class="p">:</span>
+ <span class="n">wh</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s">"Image processing error log</span><span class="se">\n</span><span class="s">"</span><span class="p">)</span>
+ <span class="n">wh</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s">"==========================</span><span class="se">\n</span><span class="s">"</span><span class="p">)</span>
+ <span class="n">result</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">conn</span><span class="o">.</span><span class="n">execute</span><span class="p">(</span><span class="s">"select pegasusid,path,error from '"</span> <span class="o">+</span> <span class="n">table</span> <span class="o">+</span> <span class="s">"' where error is not null"</span><span class="p">)</span>
+ <span class="n">firstrow</span> <span class="o">=</span> <span class="n">result</span><span class="o">.</span><span class="n">fetchone</span><span class="p">()</span>
+ <span class="k">if</span> <span class="n">firstrow</span><span class="p">:</span>
+ <span class="n">wh</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s">"Image with id '</span><span class="si">%s</span><span class="s">' loaded from input path '</span><span class="si">%s</span><span class="s">' was not processed successfully.</span><span class="se">\n</span><span class="s">"</span> <span class="o">%</span> <span class="p">(</span><span class="n">firstrow</span><span class="p">[</span><span class="s">"pegasusid"</span><span class="p">],</span> <span class="n">firstrow</span><span class="p">[</span><span class="s">"path"</span><span class="p">]))</span>
+ <span class="k">for</span> <span class="n">row</span> <span class="ow">in</span> <span class="n">result</span><span class="p">:</span>
+ <span class="n">wh</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s">"Image with id '</span><span class="si">%s</span><span class="s">' loaded from input path '</span><span class="si">%s</span><span class="s">' was not processed successfully.</span><span class="se">\n</span><span class="s">"</span> <span class="o">%</span> <span class="p">(</span><span class="n">row</span><span class="p">[</span><span class="s">"pegasusid"</span><span class="p">],</span> <span class="n">row</span><span class="p">[</span><span class="s">"path"</span><span class="p">]))</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="n">wh</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s">"All images processed successfully! Nice job!</span><span class="se">\n</span><span class="s">"</span><span class="p">)</span>
+ <span class="k">return</span>
+ </div>
+<div class="viewcode-block" id="Stats.shootArea"><a class="viewcode-back" href="../../statistics.html#ih.statistics.Stats.shootArea">[docs]</a> <span class="k">def</span> <span class="nf">shootArea</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">intable</span><span class="p">,</span> <span class="n">outtable</span><span class="p">,</span> <span class="n">grouping</span><span class="p">,</span> <span class="n">overwrite</span> <span class="o">=</span> <span class="bp">False</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> :param intable: The input table to load information from</span>
+<span class="sd"> :type intable: str</span>
+<span class="sd"> :param outtable: The output table to write information to.</span>
+<span class="sd"> :type outtable: str</span>
+<span class="sd"> :param grouping: Which imtypes to group</span>
+<span class="sd"> :type grouping: list</span>
+<span class="sd"> </span>
+<span class="sd"> This function adds the numeric values of multiple image types together.</span>
+<span class="sd"> In general, it is used to combine side view + top view images of the same spectrum.</span>
+<span class="sd"> If you plan on correlating your data to lemnaTec's data, lemnaTec uses SV1 + SV2 + TV,</span>
+<span class="sd"> so you should aggregate your data likewise.</span>
+<span class="sd"> """</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_validate</span><span class="p">(</span><span class="s">"shootArea"</span><span class="p">,</span> <span class="n">intable</span><span class="p">,</span> <span class="n">outtable</span><span class="p">,</span> <span class="n">overwrite</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_createTable</span><span class="p">(</span><span class="s">"shootArea"</span><span class="p">,</span> <span class="n">intable</span><span class="p">,</span> <span class="n">outtable</span><span class="p">,</span> <span class="n">overwrite</span><span class="p">)</span>
+ <span class="n">headers</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_getHeaders</span><span class="p">(</span><span class="n">outtable</span><span class="p">)</span>
+ <span class="n">dataHeaders</span> <span class="o">=</span> <span class="p">[</span><span class="n">header</span> <span class="k">for</span> <span class="n">header</span> <span class="ow">in</span> <span class="n">headers</span> <span class="k">if</span> <span class="n">header</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">conf</span><span class="o">.</span><span class="n">allHeaders</span> <span class="ow">and</span> <span class="s">"ref"</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">header</span><span class="p">]</span>
+ <span class="n">start</span> <span class="o">=</span> <span class="nb">len</span><span class="p">(</span><span class="n">headers</span><span class="p">)</span> <span class="o">-</span> <span class="nb">len</span><span class="p">(</span><span class="n">dataHeaders</span><span class="p">)</span>
+ <span class="sd">"""</span>
+<span class="sd"> map = {</span>
+<span class="sd"> "genotype": {</span>
+<span class="sd"> "date": {</span>
+<span class="sd"> "treatment": {</span>
+<span class="sd"> "writeback": [],</span>
+<span class="sd"> "values": ()</span>
+<span class="sd"> }</span>
+<span class="sd"> }</span>
+<span class="sd"> }</span>
+<span class="sd"> }</span>
+<span class="sd"> """</span>
+ <span class="n">dataMap</span> <span class="o">=</span> <span class="p">{}</span>
+ <span class="n">result</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">conn</span><span class="o">.</span><span class="n">execute</span><span class="p">(</span><span class="s">"select pegasusid,"</span> <span class="o">+</span> <span class="s">","</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">headers</span><span class="p">)</span> <span class="o">+</span> <span class="s">" from "</span> <span class="o">+</span> <span class="n">intable</span> <span class="o">+</span> <span class="s">" where "</span> <span class="o">+</span> <span class="s">" or "</span><span class="o">.</span><span class="n">join</span><span class="p">([</span><span class="s">"imtype=?"</span> <span class="k">for</span> <span class="n">x</span> <span class="ow">in</span> <span class="n">grouping</span><span class="p">]),</span> <span class="nb">tuple</span><span class="p">([</span><span class="n">x</span> <span class="k">for</span> <span class="n">x</span> <span class="ow">in</span> <span class="n">grouping</span><span class="p">]))</span>
+ <span class="k">for</span> <span class="n">row</span> <span class="ow">in</span> <span class="n">result</span><span class="p">:</span>
+ <span class="k">if</span> <span class="n">row</span><span class="p">[</span><span class="s">"genotype"</span><span class="p">]</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">dataMap</span><span class="p">:</span>
+ <span class="n">dataMap</span><span class="p">[</span><span class="n">row</span><span class="p">[</span><span class="s">"genotype"</span><span class="p">]]</span> <span class="o">=</span> <span class="p">{}</span>
+ <span class="k">if</span> <span class="n">row</span><span class="p">[</span><span class="s">"date"</span><span class="p">]</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">dataMap</span><span class="p">[</span><span class="n">row</span><span class="p">[</span><span class="s">"genotype"</span><span class="p">]]:</span>
+ <span class="n">dataMap</span><span class="p">[</span><span class="n">row</span><span class="p">[</span><span class="s">"genotype"</span><span class="p">]][</span><span class="n">row</span><span class="p">[</span><span class="s">"date"</span><span class="p">]]</span> <span class="o">=</span> <span class="p">{}</span>
+ <span class="k">if</span> <span class="n">row</span><span class="p">[</span><span class="s">"treatment"</span><span class="p">]</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">dataMap</span><span class="p">[</span><span class="n">row</span><span class="p">[</span><span class="s">"genotype"</span><span class="p">]][</span><span class="n">row</span><span class="p">[</span><span class="s">"date"</span><span class="p">]]:</span>
+ <span class="n">dataMap</span><span class="p">[</span><span class="n">row</span><span class="p">[</span><span class="s">"genotype"</span><span class="p">]][</span><span class="n">row</span><span class="p">[</span><span class="s">"date"</span><span class="p">]][</span><span class="n">row</span><span class="p">[</span><span class="s">"treatment"</span><span class="p">]]</span> <span class="o">=</span> <span class="p">{</span><span class="s">"writeback"</span><span class="p">:</span> <span class="p">[</span><span class="n">row</span><span class="p">[</span><span class="s">"pegasusid"</span><span class="p">]],</span> <span class="s">"values"</span><span class="p">:</span> <span class="nb">tuple</span><span class="p">([</span><span class="n">row</span><span class="p">[</span><span class="n">x</span><span class="p">]</span> <span class="k">for</span> <span class="n">x</span> <span class="ow">in</span> <span class="n">headers</span><span class="p">])}</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="n">dataMap</span><span class="p">[</span><span class="n">row</span><span class="p">[</span><span class="s">"genotype"</span><span class="p">]][</span><span class="n">row</span><span class="p">[</span><span class="s">"date"</span><span class="p">]][</span><span class="n">row</span><span class="p">[</span><span class="s">"treatment"</span><span class="p">]][</span><span class="s">"writeback"</span><span class="p">]</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">row</span><span class="p">[</span><span class="s">"pegasusid"</span><span class="p">])</span>
+ <span class="n">values</span> <span class="o">=</span> <span class="p">[]</span>
+ <span class="k">for</span> <span class="n">i</span><span class="p">,(</span><span class="n">x</span><span class="p">,</span><span class="n">y</span><span class="p">)</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="nb">zip</span><span class="p">(</span><span class="n">dataMap</span><span class="p">[</span><span class="n">row</span><span class="p">[</span><span class="s">"genotype"</span><span class="p">]][</span><span class="n">row</span><span class="p">[</span><span class="s">"date"</span><span class="p">]][</span><span class="n">row</span><span class="p">[</span><span class="s">"treatment"</span><span class="p">]][</span><span class="s">"values"</span><span class="p">],</span> <span class="nb">tuple</span><span class="p">([</span><span class="n">row</span><span class="p">[</span><span class="n">x</span><span class="p">]</span> <span class="k">for</span> <span class="n">x</span> <span class="ow">in</span> <span class="n">headers</span><span class="p">]))):</span>
+ <span class="k">if</span> <span class="n">i</span> <span class="o"><</span> <span class="n">start</span><span class="p">:</span>
+ <span class="n">values</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">x</span><span class="p">)</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="k">try</span><span class="p">:</span>
+ <span class="n">values</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">x</span> <span class="o">+</span> <span class="n">y</span><span class="p">)</span>
+ <span class="k">except</span><span class="p">:</span>
+ <span class="n">values</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="bp">None</span><span class="p">)</span>
+ <span class="n">dataMap</span><span class="p">[</span><span class="n">row</span><span class="p">[</span><span class="s">"genotype"</span><span class="p">]][</span><span class="n">row</span><span class="p">[</span><span class="s">"date"</span><span class="p">]][</span><span class="n">row</span><span class="p">[</span><span class="s">"treatment"</span><span class="p">]][</span><span class="s">"values"</span><span class="p">]</span> <span class="o">=</span> <span class="nb">tuple</span><span class="p">(</span><span class="n">values</span><span class="p">)</span>
+
+ <span class="c">#Loop through dataMap, insert values and writeback accordingly</span>
+ <span class="k">for</span> <span class="n">genotype</span> <span class="ow">in</span> <span class="n">dataMap</span><span class="p">:</span>
+ <span class="k">for</span> <span class="n">date</span> <span class="ow">in</span> <span class="n">dataMap</span><span class="p">[</span><span class="n">genotype</span><span class="p">]:</span>
+ <span class="k">for</span> <span class="n">treatment</span> <span class="ow">in</span> <span class="n">dataMap</span><span class="p">[</span><span class="n">genotype</span><span class="p">][</span><span class="n">date</span><span class="p">]:</span>
+ <span class="n">lastid</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">conn</span><span class="o">.</span><span class="n">execute</span><span class="p">(</span><span class="s">"insert into "</span> <span class="o">+</span> <span class="n">outtable</span> <span class="o">+</span> <span class="s">" ("</span> <span class="o">+</span> <span class="s">","</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">headers</span><span class="p">)</span> <span class="o">+</span> <span class="s">") values ("</span> <span class="o">+</span> <span class="s">","</span><span class="o">.</span><span class="n">join</span><span class="p">([</span><span class="s">"?"</span><span class="p">]</span> <span class="o">*</span> <span class="nb">len</span><span class="p">(</span><span class="n">headers</span><span class="p">))</span> <span class="o">+</span> <span class="s">")"</span><span class="p">,</span> <span class="n">dataMap</span><span class="p">[</span><span class="n">genotype</span><span class="p">][</span><span class="n">date</span><span class="p">][</span><span class="n">treatment</span><span class="p">][</span><span class="s">"values"</span><span class="p">])</span><span class="o">.</span><span class="n">lastrowid</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">conn</span><span class="o">.</span><span class="n">executemany</span><span class="p">(</span><span class="s">"update "</span> <span class="o">+</span> <span class="n">intable</span> <span class="o">+</span> <span class="s">" set ref_"</span> <span class="o">+</span> <span class="n">outtable</span> <span class="o">+</span> <span class="s">"=? where pegasusid=?"</span><span class="p">,</span> <span class="nb">tuple</span><span class="p">([(</span><span class="n">lastid</span><span class="p">,</span> <span class="n">x</span><span class="p">)</span> <span class="k">for</span> <span class="n">x</span> <span class="ow">in</span> <span class="n">dataMap</span><span class="p">[</span><span class="n">row</span><span class="p">[</span><span class="s">"genotype"</span><span class="p">]][</span><span class="n">row</span><span class="p">[</span><span class="s">"date"</span><span class="p">]][</span><span class="n">row</span><span class="p">[</span><span class="s">"treatment"</span><span class="p">]][</span><span class="s">"writeback"</span><span class="p">]]))</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">conn</span><span class="o">.</span><span class="n">commit</span><span class="p">()</span>
+ <span class="k">return</span>
+ </div>
+<div class="viewcode-block" id="Stats.normalize"><a class="viewcode-back" href="../../statistics.html#ih.statistics.Stats.normalize">[docs]</a> <span class="k">def</span> <span class="nf">normalize</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">intable</span><span class="p">,</span> <span class="n">outtable</span><span class="p">,</span> <span class="n">column</span> <span class="o">=</span> <span class="s">"pixels"</span><span class="p">,</span> <span class="n">overwrite</span> <span class="o">=</span> <span class="bp">False</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> :param intable: The input table to load information from</span>
+<span class="sd"> :type intable: str</span>
+<span class="sd"> :param outtable: The output table to write information to.</span>
+<span class="sd"> :type outtable: str</span>
+<span class="sd"> :param column: The column to normalize information to</span>
+<span class="sd"> :type column: str</span>
+<span class="sd"> </span>
+<span class="sd"> Normalizes all numerical information to the specific column. This</span>
+<span class="sd"> function is usually used with 'pixels' as the specified column, which</span>
+<span class="sd"> expresses all numeric information as a percentage of the total pixels </span>
+<span class="sd"> in the image.</span>
+<span class="sd"> """</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_validate</span><span class="p">(</span><span class="s">"normalize"</span><span class="p">,</span> <span class="n">intable</span><span class="p">,</span> <span class="n">outtable</span><span class="p">,</span> <span class="n">overwrite</span><span class="p">)</span>
+ <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">_columnExists</span><span class="p">(</span><span class="n">column</span><span class="p">,</span> <span class="n">intable</span><span class="p">):</span>
+ <span class="n">conf</span><span class="o">.</span><span class="n">statsColumns</span><span class="p">[</span><span class="s">"normalize"</span><span class="p">][</span><span class="s">"exclude"</span><span class="p">]</span> <span class="o">+=</span> <span class="p">[</span><span class="n">column</span><span class="p">]</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_createTable</span><span class="p">(</span><span class="s">"normalize"</span><span class="p">,</span> <span class="n">intable</span><span class="p">,</span> <span class="n">outtable</span><span class="p">,</span> <span class="n">overwrite</span><span class="p">)</span>
+ <span class="n">headers</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_getHeaders</span><span class="p">(</span><span class="n">outtable</span><span class="p">)</span>
+ <span class="n">dataHeaders</span> <span class="o">=</span> <span class="p">[</span><span class="n">header</span> <span class="k">for</span> <span class="n">header</span> <span class="ow">in</span> <span class="n">headers</span> <span class="k">if</span> <span class="n">header</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">conf</span><span class="o">.</span><span class="n">allHeaders</span> <span class="ow">and</span> <span class="s">"ref"</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">header</span><span class="p">]</span>
+ <span class="n">result</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">conn</span><span class="o">.</span><span class="n">execute</span><span class="p">(</span><span class="s">"select pegasusid,"</span> <span class="o">+</span> <span class="n">column</span> <span class="o">+</span> <span class="s">","</span> <span class="o">+</span> <span class="s">","</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">headers</span><span class="p">)</span> <span class="o">+</span> <span class="s">" from "</span> <span class="o">+</span> <span class="n">intable</span><span class="p">)</span>
+ <span class="n">vals</span> <span class="o">=</span> <span class="p">()</span>
+ <span class="k">for</span> <span class="n">row</span> <span class="ow">in</span> <span class="n">result</span><span class="p">:</span>
+ <span class="n">vals</span> <span class="o">=</span> <span class="p">[]</span>
+ <span class="k">for</span> <span class="n">x</span> <span class="ow">in</span> <span class="n">headers</span><span class="p">:</span>
+ <span class="k">if</span> <span class="n">x</span> <span class="ow">in</span> <span class="n">conf</span><span class="o">.</span><span class="n">allHeaders</span><span class="p">:</span>
+ <span class="n">vals</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">row</span><span class="p">[</span><span class="n">x</span><span class="p">])</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="k">if</span> <span class="ow">not</span> <span class="bp">self</span><span class="o">.</span><span class="n">_checkNull</span><span class="p">(</span><span class="n">row</span><span class="p">[</span><span class="n">x</span><span class="p">]):</span>
+ <span class="k">if</span> <span class="ow">not</span> <span class="bp">self</span><span class="o">.</span><span class="n">_checkNull</span><span class="p">(</span><span class="n">row</span><span class="p">[</span><span class="n">column</span><span class="p">])</span> <span class="ow">and</span> <span class="n">row</span><span class="p">[</span><span class="n">column</span><span class="p">]:</span>
+ <span class="n">vals</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="nb">float</span><span class="p">(</span><span class="n">row</span><span class="p">[</span><span class="n">x</span><span class="p">])</span> <span class="o">/</span> <span class="nb">float</span><span class="p">(</span><span class="n">row</span><span class="p">[</span><span class="n">column</span><span class="p">]))</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="n">vals</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="bp">None</span><span class="p">)</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="n">vals</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="bp">None</span><span class="p">)</span>
+ <span class="n">lastid</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">conn</span><span class="o">.</span><span class="n">execute</span><span class="p">(</span><span class="s">"insert into "</span> <span class="o">+</span> <span class="n">outtable</span> <span class="o">+</span> <span class="s">" ("</span> <span class="o">+</span> <span class="s">","</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">headers</span><span class="p">)</span> <span class="o">+</span> <span class="s">") values ("</span> <span class="o">+</span> <span class="s">","</span><span class="o">.</span><span class="n">join</span><span class="p">([</span><span class="s">"?"</span><span class="p">]</span> <span class="o">*</span> <span class="nb">len</span><span class="p">(</span><span class="n">headers</span><span class="p">))</span> <span class="o">+</span> <span class="s">")"</span><span class="p">,</span> <span class="nb">tuple</span><span class="p">(</span><span class="n">vals</span><span class="p">))</span><span class="o">.</span><span class="n">lastrowid</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">conn</span><span class="o">.</span><span class="n">execute</span><span class="p">(</span><span class="s">"update "</span> <span class="o">+</span> <span class="n">intable</span> <span class="o">+</span> <span class="s">" set ref_"</span> <span class="o">+</span> <span class="n">outtable</span> <span class="o">+</span> <span class="s">"=? where pegasusid=?"</span><span class="p">,</span> <span class="p">(</span><span class="n">lastid</span><span class="p">,</span> <span class="n">row</span><span class="p">[</span><span class="s">"pegasusid"</span><span class="p">]))</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">conn</span><span class="o">.</span><span class="n">commit</span><span class="p">()</span>
+ <span class="k">return</span>
+ </div>
+ <span class="k">def</span> <span class="nf">extractAll</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">options</span><span class="p">):</span>
+ <span class="n">basepath</span> <span class="o">=</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">dirname</span><span class="p">(</span><span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">dirname</span><span class="p">(</span><span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">abspath</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">db</span><span class="p">)</span> <span class="o">+</span> <span class="s">"/"</span><span class="p">))</span>
+ <span class="k">if</span> <span class="s">"workflows"</span> <span class="ow">in</span> <span class="n">options</span><span class="p">:</span>
+ <span class="k">for</span> <span class="nb">type</span> <span class="ow">in</span> <span class="n">options</span><span class="p">[</span><span class="s">"workflows"</span><span class="p">]:</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_openConnection</span><span class="p">()</span>
+ <span class="n">tmp</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">conn</span><span class="o">.</span><span class="n">execute</span><span class="p">(</span><span class="s">"select pegasusid,experiment,id,date,imtype,imgname from images where imtype=?"</span><span class="p">,</span> <span class="p">(</span><span class="nb">type</span><span class="p">,))</span>
+ <span class="n">result</span> <span class="o">=</span> <span class="n">tmp</span><span class="o">.</span><span class="n">fetchall</span><span class="p">()</span>
+ <span class="k">for</span> <span class="n">row</span> <span class="ow">in</span> <span class="n">result</span><span class="p">:</span>
+ <span class="n">finalpath</span> <span class="o">=</span> <span class="n">row</span><span class="p">[</span><span class="s">"experiment"</span><span class="p">]</span><span class="o">.</span><span class="n">replace</span><span class="p">(</span><span class="s">" "</span><span class="p">,</span><span class="s">""</span><span class="p">)</span> <span class="o">+</span> <span class="s">"/"</span> <span class="o">+</span> <span class="n">row</span><span class="p">[</span><span class="s">"id"</span><span class="p">]</span><span class="o">.</span><span class="n">replace</span><span class="p">(</span><span class="s">" "</span><span class="p">,</span><span class="s">""</span><span class="p">)</span> <span class="o">+</span> <span class="s">"/"</span> <span class="o">+</span> <span class="n">row</span><span class="p">[</span><span class="s">"date"</span><span class="p">]</span><span class="o">.</span><span class="n">replace</span><span class="p">(</span><span class="s">" "</span><span class="p">,</span><span class="s">""</span><span class="p">)</span> <span class="o">+</span> <span class="s">"/"</span> <span class="o">+</span> <span class="n">row</span><span class="p">[</span><span class="s">"imtype"</span><span class="p">]</span><span class="o">.</span><span class="n">replace</span><span class="p">(</span><span class="s">" "</span><span class="p">,</span><span class="s">""</span><span class="p">)</span> <span class="o">+</span> <span class="s">"/"</span> <span class="o">+</span> <span class="n">row</span><span class="p">[</span><span class="s">"imgname"</span><span class="p">]</span><span class="o">.</span><span class="n">replace</span><span class="p">(</span><span class="s">" "</span><span class="p">,</span><span class="s">""</span><span class="p">)</span> <span class="o">+</span> <span class="s">"/"</span> <span class="o">+</span> <span class="n">row</span><span class="p">[</span><span class="s">"pegasusid"</span><span class="p">]</span> <span class="o">+</span> <span class="s">"_"</span> <span class="o">+</span> <span class="n">options</span><span class="p">[</span><span class="s">"workflows"</span><span class="p">][</span><span class="nb">type</span><span class="p">][</span><span class="s">"inputs"</span><span class="p">][</span><span class="mi">0</span><span class="p">]</span> <span class="o">+</span> <span class="s">".png"</span>
+ <span class="c">#finalpath = row["pegasusid"] + "_" + options["workflows"][type]["inputs"][0] + ".png"</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_closeConnection</span><span class="p">()</span>
+ <span class="k">if</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">isfile</span><span class="p">(</span><span class="n">finalpath</span><span class="p">):</span>
+ <span class="k">try</span><span class="p">:</span>
+ <span class="n">plant</span> <span class="o">=</span> <span class="n">ih</span><span class="o">.</span><span class="n">imgproc</span><span class="o">.</span><span class="n">Image</span><span class="p">(</span><span class="n">finalpath</span><span class="p">,</span> <span class="n">db</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">db</span><span class="p">,</span> <span class="n">dbid</span> <span class="o">=</span> <span class="n">row</span><span class="p">[</span><span class="s">"pegasusid"</span><span class="p">])</span>
+ <span class="n">plant</span><span class="o">.</span><span class="n">extractFinalPath</span><span class="p">()</span>
+ <span class="k">if</span> <span class="s">"--dimensions"</span> <span class="ow">in</span> <span class="n">options</span><span class="p">[</span><span class="s">"workflows"</span><span class="p">][</span><span class="nb">type</span><span class="p">][</span><span class="s">"arguments"</span><span class="p">]:</span>
+ <span class="n">plant</span><span class="o">.</span><span class="n">extractDimensions</span><span class="p">()</span>
+ <span class="k">if</span> <span class="s">"--pixels"</span> <span class="ow">in</span> <span class="n">options</span><span class="p">[</span><span class="s">"workflows"</span><span class="p">][</span><span class="nb">type</span><span class="p">][</span><span class="s">"arguments"</span><span class="p">]:</span>
+ <span class="n">plant</span><span class="o">.</span><span class="n">extractPixels</span><span class="p">()</span>
+ <span class="k">if</span> <span class="s">"--moments"</span> <span class="ow">in</span> <span class="n">options</span><span class="p">[</span><span class="s">"workflows"</span><span class="p">][</span><span class="nb">type</span><span class="p">][</span><span class="s">"arguments"</span><span class="p">]:</span>
+ <span class="n">plant</span><span class="o">.</span><span class="n">extractMoments</span><span class="p">()</span>
+ <span class="k">if</span> <span class="s">"--colors"</span> <span class="ow">in</span> <span class="n">options</span><span class="p">[</span><span class="s">"workflows"</span><span class="p">][</span><span class="nb">type</span><span class="p">][</span><span class="s">"arguments"</span><span class="p">]:</span>
+ <span class="n">plant</span><span class="o">.</span><span class="n">extractColorData</span><span class="p">()</span>
+ <span class="k">if</span> <span class="s">"--channels"</span> <span class="ow">in</span> <span class="n">options</span><span class="p">[</span><span class="s">"workflows"</span><span class="p">][</span><span class="nb">type</span><span class="p">][</span><span class="s">"arguments"</span><span class="p">]:</span>
+ <span class="n">plant</span><span class="o">.</span><span class="n">extractColorChannels</span><span class="p">()</span>
+ <span class="k">if</span> <span class="s">"--bins"</span> <span class="ow">in</span> <span class="n">options</span><span class="p">[</span><span class="s">"workflows"</span><span class="p">][</span><span class="nb">type</span><span class="p">][</span><span class="s">"arguments"</span><span class="p">]:</span>
+ <span class="n">plant</span><span class="o">.</span><span class="n">extractBins</span><span class="p">(</span><span class="n">options</span><span class="p">[</span><span class="s">"workflows"</span><span class="p">][</span><span class="nb">type</span><span class="p">][</span><span class="s">"arguments"</span><span class="p">][</span><span class="s">"--bins"</span><span class="p">])</span>
+ <span class="k">except</span> <span class="ne">Exception</span> <span class="k">as</span> <span class="n">e</span><span class="p">:</span>
+ <span class="k">print</span> <span class="n">traceback</span><span class="o">.</span><span class="n">format_exc</span><span class="p">()</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="k">print</span> <span class="s">"PATH DOES NOT EXIST: </span><span class="si">%s</span><span class="s">."</span> <span class="o">%</span> <span class="p">(</span><span class="n">finalpath</span><span class="p">,)</span>
+ <span class="k">if</span> <span class="s">"histogram-bin"</span> <span class="ow">in</span> <span class="n">options</span><span class="p">:</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_openConnection</span><span class="p">()</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">histogramBinning</span><span class="p">(</span><span class="s">"images"</span><span class="p">,</span> <span class="s">"histogramBins"</span><span class="p">,</span> <span class="nb">dict</span><span class="p">((</span><span class="nb">type</span><span class="p">,</span><span class="n">options</span><span class="p">[</span><span class="s">"workflows"</span><span class="p">][</span><span class="nb">type</span><span class="p">][</span><span class="s">"inputs"</span><span class="p">][</span><span class="mi">0</span><span class="p">])</span> <span class="k">for</span> <span class="nb">type</span> <span class="ow">in</span> <span class="n">options</span><span class="p">[</span><span class="s">"workflows"</span><span class="p">]),</span> <span class="n">options</span><span class="p">[</span><span class="s">"histogram-bin"</span><span class="p">][</span><span class="s">"--group"</span><span class="p">],</span> <span class="n">options</span><span class="p">[</span><span class="s">"histogram-bin"</span><span class="p">][</span><span class="s">"--chunks"</span><span class="p">],</span> <span class="n">options</span><span class="p">[</span><span class="s">"histogram-bin"</span><span class="p">][</span><span class="s">"--channels"</span><span class="p">],</span> <span class="bp">True</span><span class="p">)</span>
+ <span class="k">return</span>
+
+ <span class="k">def</span> <span class="nf">histogramBinning</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">intable</span><span class="p">,</span> <span class="n">outtable</span><span class="p">,</span> <span class="n">grouping</span><span class="p">,</span> <span class="n">chunks</span><span class="p">,</span> <span class="n">channels</span><span class="p">,</span> <span class="n">jsonwrite</span> <span class="o">=</span> <span class="bp">False</span><span class="p">,</span> <span class="n">overwrite</span> <span class="o">=</span> <span class="bp">False</span><span class="p">):</span>
+ <span class="n">color_vector</span> <span class="o">=</span> <span class="p">{}</span>
+ <span class="k">for</span> <span class="n">name</span> <span class="ow">in</span> <span class="n">grouping</span><span class="p">:</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_validate</span><span class="p">(</span><span class="s">"histogramBins"</span><span class="p">,</span> <span class="n">intable</span><span class="p">,</span> <span class="n">name</span> <span class="o">+</span> <span class="s">"_"</span> <span class="o">+</span> <span class="n">outtable</span><span class="p">,</span> <span class="n">overwrite</span><span class="p">)</span>
+ <span class="k">for</span> <span class="n">name</span> <span class="ow">in</span> <span class="n">grouping</span><span class="p">:</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_createTable</span><span class="p">(</span><span class="s">"histogramBins"</span><span class="p">,</span> <span class="n">intable</span><span class="p">,</span> <span class="n">name</span> <span class="o">+</span> <span class="s">"_"</span> <span class="o">+</span> <span class="n">outtable</span><span class="p">,</span> <span class="n">overwrite</span><span class="p">)</span>
+ <span class="n">color_vector</span><span class="p">[</span><span class="n">name</span><span class="p">]</span> <span class="o">=</span> <span class="p">[</span><span class="mi">0</span><span class="p">,</span> <span class="mi">0</span><span class="p">,</span> <span class="mi">0</span><span class="p">]</span>
+ <span class="nb">map</span> <span class="o">=</span> <span class="nb">dict</span><span class="p">((</span><span class="nb">type</span><span class="p">,</span> <span class="n">name</span><span class="p">)</span> <span class="k">for</span> <span class="n">name</span> <span class="ow">in</span> <span class="n">grouping</span> <span class="k">for</span> <span class="nb">type</span> <span class="ow">in</span> <span class="n">grouping</span><span class="p">[</span><span class="n">name</span><span class="p">])</span>
+ <span class="n">basequery</span> <span class="o">=</span> <span class="s">"select "</span>
+ <span class="k">for</span> <span class="n">x</span><span class="p">,</span><span class="n">c</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">([</span><span class="s">"bhist"</span><span class="p">,</span> <span class="s">"ghist"</span><span class="p">,</span> <span class="s">"rhist"</span><span class="p">]):</span>
+ <span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="mi">0</span><span class="p">,</span> <span class="mi">256</span><span class="p">):</span>
+ <span class="k">if</span> <span class="n">i</span> <span class="o">==</span> <span class="mi">0</span> <span class="ow">and</span> <span class="n">x</span> <span class="o">==</span> <span class="mi">0</span><span class="p">:</span>
+ <span class="n">basequery</span> <span class="o">+=</span> <span class="s">"SUM("</span> <span class="o">+</span> <span class="n">c</span> <span class="o">+</span> <span class="nb">str</span><span class="p">(</span><span class="n">i</span><span class="p">)</span> <span class="o">+</span> <span class="s">")"</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="n">basequery</span> <span class="o">+=</span> <span class="s">",SUM("</span> <span class="o">+</span> <span class="n">c</span> <span class="o">+</span> <span class="nb">str</span><span class="p">(</span><span class="n">i</span><span class="p">)</span> <span class="o">+</span> <span class="s">")"</span>
+ <span class="n">basequery</span> <span class="o">+=</span> <span class="s">" from images where "</span>
+ <span class="k">for</span> <span class="n">name</span> <span class="ow">in</span> <span class="n">grouping</span><span class="p">:</span>
+ <span class="n">query</span> <span class="o">=</span> <span class="n">basequery</span> <span class="o">+</span> <span class="s">" or "</span><span class="o">.</span><span class="n">join</span><span class="p">([</span><span class="s">"imtype=?"</span> <span class="k">for</span> <span class="n">x</span> <span class="ow">in</span> <span class="n">grouping</span><span class="p">[</span><span class="n">name</span><span class="p">]])</span>
+ <span class="n">result</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">conn</span><span class="o">.</span><span class="n">execute</span><span class="p">(</span><span class="n">query</span><span class="p">,</span> <span class="nb">tuple</span><span class="p">(</span><span class="n">grouping</span><span class="p">[</span><span class="n">name</span><span class="p">]))</span>
+ <span class="n">data</span> <span class="o">=</span> <span class="nb">list</span><span class="p">(</span><span class="n">result</span><span class="o">.</span><span class="n">fetchone</span><span class="p">())</span>
+ <span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="mi">0</span><span class="p">,</span> <span class="mi">3</span><span class="p">):</span>
+ <span class="n">color_vector</span><span class="p">[</span><span class="n">name</span><span class="p">][</span><span class="n">i</span><span class="p">]</span> <span class="o">=</span> <span class="n">data</span><span class="p">[</span><span class="n">i</span><span class="o">*</span><span class="mi">256</span><span class="p">:(</span><span class="n">i</span> <span class="o">+</span> <span class="mi">1</span><span class="p">)</span><span class="o">*</span><span class="mi">256</span><span class="p">]</span>
+ <span class="n">bins</span> <span class="o">=</span> <span class="p">{}</span>
+ <span class="k">for</span> <span class="n">name</span> <span class="ow">in</span> <span class="n">grouping</span><span class="p">:</span>
+ <span class="n">bins</span><span class="p">[</span><span class="n">name</span><span class="p">]</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_generateBins</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">_splitHist</span><span class="p">(</span><span class="n">color_vector</span><span class="p">[</span><span class="n">name</span><span class="p">],</span> <span class="n">chunks</span><span class="p">[</span><span class="n">name</span><span class="p">],</span> <span class="n">channels</span><span class="p">[</span><span class="n">name</span><span class="p">]),</span> <span class="n">name</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">conn</span><span class="o">.</span><span class="n">executemany</span><span class="p">(</span><span class="s">"insert into "</span> <span class="o">+</span> <span class="n">name</span> <span class="o">+</span> <span class="s">"_"</span> <span class="o">+</span> <span class="n">outtable</span> <span class="o">+</span> <span class="s">" (name, minr, ming, minb, maxr, maxg, maxb) values (?, ?, ?, ?, ?, ?, ?)"</span><span class="p">,</span> <span class="p">[(</span><span class="nb">bin</span><span class="p">[</span><span class="s">"name"</span><span class="p">],</span> <span class="nb">int</span><span class="p">(</span><span class="nb">bin</span><span class="p">[</span><span class="s">"min"</span><span class="p">][</span><span class="mi">2</span><span class="p">]),</span> <span class="nb">int</span><span class="p">(</span><span class="nb">bin</span><span class="p">[</span><span class="s">"min"</span><span class="p">][</span><span class="mi">1</span><span class="p">]),</span> <span class="nb">int</span><span class="p">(</span><span class="nb">bin</span><span class="p">[</span><span class="s">"min"</span><span class="p">][</span><span class="mi">0</span><span class="p">]),</span> <span class="nb">int</span><span class="p">(</span><span class="nb">bin</span><span class="p">[</span><span class="s">"max"</span><span class="p">][</span><span class="mi">2</span><span class="p">]),</span> <span class="nb">int</span><span class="p">(</span><span class="nb">bin</span><span class="p">[</span><span class="s">"max"</span><span class="p">][</span><span class="mi">1</span><span class="p">]),</span> <span class="nb">int</span><span class="p">(</span><span class="nb">bin</span><span class="p">[</span><span class="s">"max"</span><span class="p">][</span><span class="mi">0</span><span class="p">]))</span> <span class="k">for</span> <span class="nb">bin</span> <span class="ow">in</span> <span class="n">bins</span><span class="p">[</span><span class="n">name</span><span class="p">]])</span>
+<span class="c"># for bin in bins[name]:</span>
+<span class="c"># self.conn.execute("insert into " + name + "_" + outtable + " (name, minr, ming, minb, maxr, maxg, maxb) values (?, ?, ?, ?, ?, ?, ?)", (name + bin["name"], int(bin["min"][2]), int(bin["min"][1]), int(bin["min"][0]), int(bin["max"][2]), int(bin["max"][1]), int(bin["max"][0])))</span>
+<span class="c"># self.conn.commit()</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">conn</span><span class="o">.</span><span class="n">commit</span><span class="p">()</span>
+ <span class="k">if</span> <span class="n">jsonwrite</span><span class="p">:</span>
+ <span class="k">for</span> <span class="n">name</span> <span class="ow">in</span> <span class="n">grouping</span><span class="p">:</span>
+ <span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="n">name</span> <span class="o">+</span> <span class="s">"_hist_bins.json"</span><span class="p">,</span> <span class="s">"w"</span><span class="p">)</span> <span class="k">as</span> <span class="n">wh</span><span class="p">:</span>
+ <span class="n">json</span><span class="o">.</span><span class="n">dump</span><span class="p">(</span><span class="n">bins</span><span class="p">[</span><span class="n">name</span><span class="p">],</span> <span class="n">wh</span><span class="p">)</span>
+ <span class="k">return</span>
+
+
+ <span class="k">def</span> <span class="nf">_splitHist</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">hist</span><span class="p">,</span> <span class="n">chunks</span><span class="p">,</span> <span class="n">channels</span><span class="p">):</span>
+ <span class="n">returnlist</span> <span class="o">=</span> <span class="p">[</span> <span class="p">[</span><span class="mi">1</span><span class="p">],</span> <span class="p">[</span><span class="mi">1</span><span class="p">],</span> <span class="p">[</span><span class="mi">1</span><span class="p">]</span> <span class="p">]</span>
+ <span class="n">s</span> <span class="o">=</span> <span class="p">[</span><span class="nb">sum</span><span class="p">(</span><span class="n">x</span><span class="p">)</span> <span class="k">for</span> <span class="n">x</span> <span class="ow">in</span> <span class="n">hist</span><span class="p">]</span>
+ <span class="c">#s = [int(x) for x in np.sum(hist, axis = 1)]</span>
+ <span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="n">channels</span><span class="p">:</span>
+ <span class="n">tmp</span> <span class="o">=</span> <span class="mi">0</span>
+ <span class="n">integral</span> <span class="o">=</span> <span class="n">s</span><span class="p">[</span><span class="n">i</span><span class="p">]</span> <span class="o">/</span> <span class="n">chunks</span>
+ <span class="k">for</span> <span class="n">j</span><span class="p">,</span><span class="n">item</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="n">hist</span><span class="p">[</span><span class="n">i</span><span class="p">]):</span>
+ <span class="n">tmp</span> <span class="o">+=</span> <span class="n">item</span>
+ <span class="k">if</span> <span class="p">(</span><span class="n">tmp</span> <span class="o">></span> <span class="n">integral</span><span class="p">):</span>
+ <span class="n">returnlist</span><span class="p">[</span><span class="n">i</span><span class="p">]</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">j</span><span class="p">)</span>
+ <span class="n">tmp</span> <span class="o">=</span> <span class="mi">0</span>
+ <span class="n">returnlist</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="mi">255</span><span class="p">)</span>
+ <span class="n">returnlist</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="mi">255</span><span class="p">)</span>
+ <span class="n">returnlist</span><span class="p">[</span><span class="mi">2</span><span class="p">]</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="mi">255</span><span class="p">)</span>
+ <span class="k">return</span> <span class="n">returnlist</span>
+
+ <span class="k">def</span> <span class="nf">_generateBins</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">vector</span><span class="p">,</span> <span class="nb">type</span><span class="p">):</span>
+ <span class="n">bins</span> <span class="o">=</span> <span class="p">[]</span>
+ <span class="n">num</span> <span class="o">=</span> <span class="mi">1</span>
+ <span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="nb">range</span> <span class="p">(</span><span class="mi">0</span><span class="p">,</span> <span class="nb">len</span><span class="p">(</span><span class="n">vector</span><span class="p">[</span><span class="mi">0</span><span class="p">])</span> <span class="o">-</span> <span class="mi">1</span><span class="p">):</span>
+ <span class="k">for</span> <span class="n">j</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="mi">0</span><span class="p">,</span> <span class="nb">len</span><span class="p">(</span><span class="n">vector</span><span class="p">[</span><span class="mi">1</span><span class="p">])</span> <span class="o">-</span> <span class="mi">1</span><span class="p">):</span>
+ <span class="k">for</span> <span class="n">k</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="mi">0</span><span class="p">,</span> <span class="nb">len</span><span class="p">(</span><span class="n">vector</span><span class="p">[</span><span class="mi">2</span><span class="p">])</span> <span class="o">-</span> <span class="mi">1</span><span class="p">):</span>
+ <span class="n">bins</span><span class="o">.</span><span class="n">append</span><span class="p">({</span>
+ <span class="s">"name"</span><span class="p">:</span> <span class="nb">type</span> <span class="o">+</span> <span class="s">"_bin"</span> <span class="o">+</span> <span class="nb">str</span><span class="p">(</span><span class="n">num</span><span class="p">),</span>
+ <span class="s">"min"</span><span class="p">:</span> <span class="n">np</span><span class="o">.</span><span class="n">array</span><span class="p">([</span><span class="n">vector</span><span class="p">[</span><span class="mi">0</span><span class="p">][</span><span class="n">i</span><span class="p">],</span><span class="n">vector</span><span class="p">[</span><span class="mi">1</span><span class="p">][</span><span class="n">j</span><span class="p">],</span><span class="n">vector</span><span class="p">[</span><span class="mi">2</span><span class="p">][</span><span class="n">k</span><span class="p">]],</span> <span class="n">dtype</span><span class="o">=</span><span class="n">np</span><span class="o">.</span><span class="n">uint8</span><span class="p">)</span><span class="o">.</span><span class="n">tolist</span><span class="p">(),</span>
+ <span class="s">"max"</span><span class="p">:</span> <span class="n">np</span><span class="o">.</span><span class="n">array</span><span class="p">([</span><span class="n">vector</span><span class="p">[</span><span class="mi">0</span><span class="p">][</span><span class="n">i</span><span class="o">+</span><span class="mi">1</span><span class="p">],</span><span class="n">vector</span><span class="p">[</span><span class="mi">1</span><span class="p">][</span><span class="n">j</span><span class="o">+</span><span class="mi">1</span><span class="p">],</span><span class="n">vector</span><span class="p">[</span><span class="mi">2</span><span class="p">][</span><span class="n">k</span><span class="o">+</span><span class="mi">1</span><span class="p">]],</span> <span class="n">dtype</span><span class="o">=</span><span class="n">np</span><span class="o">.</span><span class="n">uint8</span><span class="p">)</span><span class="o">.</span><span class="n">tolist</span><span class="p">()</span>
+ <span class="p">})</span>
+ <span class="n">num</span> <span class="o">+=</span> <span class="mi">1</span>
+ <span class="k">return</span> <span class="n">bins</span>
+
+
+<div class="viewcode-block" id="Stats.correlation"><a class="viewcode-back" href="../../statistics.html#ih.statistics.Stats.correlation">[docs]</a> <span class="k">def</span> <span class="nf">correlation</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">intable</span><span class="p">,</span> <span class="n">outtable</span><span class="p">,</span> <span class="n">dataFile</span><span class="p">,</span> <span class="n">dataHeaders</span><span class="p">,</span> <span class="n">overwrite</span> <span class="o">=</span> <span class="bp">False</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> :param intable: The input table to load information from</span>
+<span class="sd"> :type intable: str</span>
+<span class="sd"> :param outtable: The output table to write information to.</span>
+<span class="sd"> :type outtable: str</span>
+<span class="sd"> :param dataFile: The csv data file to load</span>
+<span class="sd"> :type dataFile: str</span>
+<span class="sd"> :param dataHeaders: Column names for relevant table headers.</span>
+<span class="sd"> :type dataHeaders: str</span>
+<span class="sd"> </span>
+<span class="sd"> This function correlates all numeric values with values in the given file.</span>
+<span class="sd"> The input data file is assumed to be in csv format. In dataHeaders, you must</span>
+<span class="sd"> specify four keys, 'id', 'date', 'dateFormat', and 'metric'. Each of these should</span>
+<span class="sd"> be column names. Id corresponds to the lemnaTec style identifier ex: '023535-S'.</span>
+<span class="sd"> All dates are converted into Y-m-d form, you must provide a valid format in 'dateFormat',</span>
+<span class="sd"> that way the dates can be converted correctly. The 'metric' column is the actual value you</span>
+<span class="sd"> want to correlate to.</span>
+<span class="sd"> """</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_validate</span><span class="p">(</span><span class="s">"correlation"</span><span class="p">,</span> <span class="n">intable</span><span class="p">,</span> <span class="n">outtable</span><span class="p">,</span> <span class="n">overwrite</span><span class="p">)</span>
+ <span class="n">lemnaData</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_loadLemnaData</span><span class="p">(</span><span class="n">dataFile</span><span class="p">,</span> <span class="n">dataHeaders</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_createTable</span><span class="p">(</span><span class="s">"correlation"</span><span class="p">,</span> <span class="n">intable</span><span class="p">,</span> <span class="n">outtable</span><span class="p">,</span> <span class="n">overwrite</span><span class="p">)</span>
+ <span class="n">headers</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_getHeaders</span><span class="p">(</span><span class="n">outtable</span><span class="p">)</span>
+ <span class="n">numeric</span> <span class="o">=</span> <span class="p">[</span><span class="n">h</span> <span class="k">for</span> <span class="n">h</span> <span class="ow">in</span> <span class="n">headers</span> <span class="k">if</span> <span class="n">h</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">conf</span><span class="o">.</span><span class="n">allHeaders</span><span class="p">]</span>
+ <span class="k">for</span> <span class="nb">id</span> <span class="ow">in</span> <span class="n">lemnaData</span><span class="p">:</span>
+ <span class="k">for</span> <span class="n">imtype</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">_getImageTypes</span><span class="p">(</span><span class="n">intable</span><span class="p">):</span>
+ <span class="n">x</span> <span class="o">=</span> <span class="p">{}</span>
+ <span class="n">y</span> <span class="o">=</span> <span class="p">[]</span>
+ <span class="n">corr</span> <span class="o">=</span> <span class="p">{}</span>
+ <span class="n">result</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">conn</span><span class="o">.</span><span class="n">execute</span><span class="p">(</span><span class="s">"select pegasusid,"</span> <span class="o">+</span> <span class="s">","</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">headers</span> <span class="o">+</span> <span class="p">[</span><span class="s">"date"</span><span class="p">])</span> <span class="o">+</span> <span class="s">" from "</span> <span class="o">+</span> <span class="n">intable</span> <span class="o">+</span> <span class="s">" where id=? and imtype=? order by date"</span><span class="p">,</span> <span class="p">(</span><span class="nb">id</span><span class="p">,</span><span class="n">imtype</span><span class="p">))</span>
+ <span class="k">if</span> <span class="n">result</span><span class="o">.</span><span class="n">fetchone</span><span class="p">():</span>
+ <span class="k">for</span> <span class="n">row</span> <span class="ow">in</span> <span class="n">result</span><span class="p">:</span>
+ <span class="k">if</span> <span class="n">row</span><span class="p">[</span><span class="s">"date"</span><span class="p">]</span> <span class="ow">in</span> <span class="n">lemnaData</span><span class="p">[</span><span class="nb">id</span><span class="p">]:</span>
+ <span class="n">y</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">lemnaData</span><span class="p">[</span><span class="nb">id</span><span class="p">][</span><span class="n">row</span><span class="p">[</span><span class="s">"date"</span><span class="p">]][</span><span class="s">"metric"</span><span class="p">])</span>
+ <span class="k">for</span> <span class="n">header</span> <span class="ow">in</span> <span class="n">numeric</span><span class="p">:</span>
+ <span class="k">if</span> <span class="n">header</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">x</span><span class="p">:</span>
+ <span class="n">x</span><span class="p">[</span><span class="n">header</span><span class="p">]</span> <span class="o">=</span> <span class="p">[]</span>
+ <span class="k">try</span><span class="p">:</span>
+ <span class="n">x</span><span class="p">[</span><span class="n">header</span><span class="p">]</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="nb">float</span><span class="p">(</span><span class="n">row</span><span class="p">[</span><span class="n">header</span><span class="p">]))</span>
+ <span class="k">except</span><span class="p">:</span>
+ <span class="k">pass</span>
+ <span class="k">if</span> <span class="nb">any</span><span class="p">([</span><span class="n">x</span><span class="p">[</span><span class="n">header</span><span class="p">]</span> <span class="k">for</span> <span class="n">header</span> <span class="ow">in</span> <span class="n">numeric</span><span class="p">]):</span>
+ <span class="k">for</span> <span class="n">header</span> <span class="ow">in</span> <span class="n">numeric</span><span class="p">:</span>
+ <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">x</span><span class="p">[</span><span class="n">header</span><span class="p">])</span> <span class="o">==</span> <span class="nb">len</span><span class="p">(</span><span class="n">y</span><span class="p">):</span>
+ <span class="n">corr</span><span class="p">[</span><span class="n">header</span><span class="p">]</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">corrcoef</span><span class="p">(</span><span class="n">x</span><span class="p">[</span><span class="n">header</span><span class="p">],</span> <span class="n">y</span><span class="p">)[</span><span class="mi">0</span><span class="p">][</span><span class="mi">1</span><span class="p">]</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="n">corr</span><span class="p">[</span><span class="n">header</span><span class="p">]</span> <span class="o">=</span> <span class="bp">None</span>
+ <span class="n">lastid</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">conn</span><span class="o">.</span><span class="n">execute</span><span class="p">(</span><span class="s">"insert into "</span> <span class="o">+</span> <span class="n">outtable</span> <span class="o">+</span> <span class="s">" ("</span> <span class="o">+</span> <span class="s">","</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">headers</span><span class="p">)</span> <span class="o">+</span> <span class="s">") values ("</span> <span class="o">+</span> <span class="s">","</span><span class="o">.</span><span class="n">join</span><span class="p">([</span><span class="s">"?"</span><span class="p">]</span> <span class="o">*</span> <span class="nb">len</span><span class="p">(</span><span class="n">headers</span><span class="p">))</span> <span class="o">+</span> <span class="s">")"</span><span class="p">,</span> <span class="nb">tuple</span><span class="p">([</span><span class="n">row</span><span class="p">[</span><span class="n">header</span><span class="p">]</span> <span class="k">if</span> <span class="n">header</span> <span class="ow">in</span> <span class="n">conf</span><span class="o">.</span><span class="n">allHeaders</span> <span class="k">else</span> <span class="n">corr</span><span class="p">[</span><span class="n">header</span><span class="p">]</span> <span class="k">for</span> <span class="n">header</span> <span class="ow">in</span> <span class="n">headers</span><span class="p">]))</span><span class="o">.</span><span class="n">lastrowid</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">conn</span><span class="o">.</span><span class="n">execute</span><span class="p">(</span><span class="s">"update "</span> <span class="o">+</span> <span class="n">intable</span> <span class="o">+</span> <span class="s">" set ref_"</span> <span class="o">+</span> <span class="n">outtable</span> <span class="o">+</span> <span class="s">"=? where id=? and imtype=?"</span><span class="p">,</span> <span class="p">(</span><span class="n">lastid</span><span class="p">,</span> <span class="nb">id</span><span class="p">,</span> <span class="n">imtype</span><span class="p">))</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">conn</span><span class="o">.</span><span class="n">commit</span><span class="p">()</span>
+ <span class="k">return</span>
+ </div>
+<div class="viewcode-block" id="Stats.anova"><a class="viewcode-back" href="../../statistics.html#ih.statistics.Stats.anova">[docs]</a> <span class="k">def</span> <span class="nf">anova</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">intable</span><span class="p">,</span> <span class="n">outtable</span><span class="p">,</span> <span class="n">grouping</span><span class="p">,</span> <span class="n">overwrite</span> <span class="o">=</span> <span class="bp">False</span><span class="p">):</span>
+ <span class="sd">""" </span>
+<span class="sd"> :param intable: The input table to load information from</span>
+<span class="sd"> :type intable: str</span>
+<span class="sd"> :param outtable: The output table to write information to.</span>
+<span class="sd"> :type outtable: str</span>
+<span class="sd"> :param grouping: The list of image types to group by.</span>
+<span class="sd"> :type grouping: list</span>
+<span class="sd"> </span>
+<span class="sd"> Computes the analysis of variation of all numeric information based on 3 factors,</span>
+<span class="sd"> treatment, date, and the interaction between the two. Analysis of variation is</span>
+<span class="sd"> different than the rest of the stats functions, in that a lot of information is </span>
+<span class="sd"> lost after running it. The results themselves correspond to columns (pixels, rmed, binx...)</span>
+<span class="sd"> instead of actual images. </span>
+<span class="sd"> """</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_validate</span><span class="p">(</span><span class="s">"anova"</span><span class="p">,</span> <span class="n">intable</span><span class="p">,</span> <span class="n">outtable</span><span class="p">,</span> <span class="n">overwrite</span><span class="p">)</span>
+ <span class="n">headers</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_getHeaders</span><span class="p">(</span><span class="n">intable</span><span class="p">)</span>
+ <span class="n">numeric</span> <span class="o">=</span> <span class="p">[</span><span class="n">h</span> <span class="k">for</span> <span class="n">h</span> <span class="ow">in</span> <span class="n">headers</span> <span class="k">if</span> <span class="n">h</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">conf</span><span class="o">.</span><span class="n">allHeaders</span><span class="p">]</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_createTable</span><span class="p">(</span><span class="s">"anova"</span><span class="p">,</span> <span class="n">intable</span><span class="p">,</span> <span class="n">outtable</span><span class="p">,</span> <span class="n">overwrite</span><span class="p">)</span>
+ <span class="n">outHeaders</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_getHeaders</span><span class="p">(</span><span class="n">outtable</span><span class="p">)</span>
+ <span class="n">result</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">conn</span><span class="o">.</span><span class="n">execute</span><span class="p">(</span><span class="s">"select * from images"</span><span class="p">)</span>
+ <span class="n">rowdata</span> <span class="o">=</span> <span class="p">[]</span>
+ <span class="k">for</span> <span class="n">row</span> <span class="ow">in</span> <span class="n">result</span><span class="p">:</span>
+ <span class="n">rowdata</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="nb">dict</span><span class="p">(</span><span class="n">row</span><span class="p">))</span>
+ <span class="n">data</span> <span class="o">=</span> <span class="n">pandas</span><span class="o">.</span><span class="n">DataFrame</span><span class="p">(</span><span class="n">rowdata</span><span class="p">)</span><span class="o">.</span><span class="n">dropna</span><span class="p">()</span>
+ <span class="n">anova</span> <span class="o">=</span> <span class="p">{}</span>
+ <span class="k">for</span> <span class="n">col</span> <span class="ow">in</span> <span class="n">numeric</span><span class="p">:</span>
+ <span class="n">anova</span><span class="p">[</span><span class="n">col</span><span class="p">]</span> <span class="o">=</span> <span class="p">{}</span>
+ <span class="n">dateT</span> <span class="o">=</span> <span class="p">[]</span>
+ <span class="n">treatmentT</span> <span class="o">=</span> <span class="p">[]</span>
+ <span class="n">date_treatmentT</span> <span class="o">=</span> <span class="p">[]</span>
+ <span class="k">for</span> <span class="n">date</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">_getDates</span><span class="p">(</span><span class="n">intable</span><span class="p">):</span>
+ <span class="n">dateT</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">data</span><span class="p">[</span><span class="n">data</span><span class="p">[</span><span class="s">"date"</span><span class="p">]</span> <span class="o">==</span> <span class="n">date</span><span class="p">][</span><span class="n">col</span><span class="p">])</span>
+ <span class="k">for</span> <span class="n">treatment</span> <span class="ow">in</span> <span class="p">[</span><span class="s">"Control"</span><span class="p">,</span> <span class="s">"Stress"</span><span class="p">]:</span>
+ <span class="n">treatmentT</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">data</span><span class="p">[</span><span class="n">data</span><span class="p">[</span><span class="s">"treatment"</span><span class="p">]</span> <span class="o">==</span> <span class="n">treatment</span><span class="p">][</span><span class="n">col</span><span class="p">])</span>
+ <span class="n">date_treatmentT</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">data</span><span class="p">[</span><span class="n">np</span><span class="o">.</span><span class="n">where</span><span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">logical_and</span><span class="p">(</span><span class="n">data</span><span class="p">[</span><span class="s">"treatment"</span><span class="p">]</span> <span class="o">==</span> <span class="n">treatment</span><span class="p">,</span><span class="n">data</span><span class="p">[</span><span class="s">"date"</span><span class="p">]</span> <span class="o">==</span> <span class="n">date</span><span class="p">),</span> <span class="bp">True</span><span class="p">,</span> <span class="bp">False</span><span class="p">)][</span><span class="n">col</span><span class="p">])</span>
+ <span class="n">f_val</span><span class="p">,</span> <span class="n">d_pval</span> <span class="o">=</span> <span class="n">stats</span><span class="o">.</span><span class="n">f_oneway</span><span class="p">(</span><span class="o">*</span><span class="n">dateT</span><span class="p">)</span>
+ <span class="n">f_val</span><span class="p">,</span> <span class="n">t_pval</span> <span class="o">=</span> <span class="n">stats</span><span class="o">.</span><span class="n">f_oneway</span><span class="p">(</span><span class="o">*</span><span class="n">treatmentT</span><span class="p">)</span>
+ <span class="n">f_val</span><span class="p">,</span> <span class="n">dt_pval</span> <span class="o">=</span> <span class="n">stats</span><span class="o">.</span><span class="n">f_oneway</span><span class="p">(</span><span class="o">*</span><span class="n">date_treatmentT</span><span class="p">)</span>
+ <span class="n">anova</span><span class="p">[</span><span class="n">col</span><span class="p">][</span><span class="s">"date"</span><span class="p">]</span> <span class="o">=</span> <span class="n">d_pval</span>
+ <span class="n">anova</span><span class="p">[</span><span class="n">col</span><span class="p">][</span><span class="s">"treatment"</span><span class="p">]</span> <span class="o">=</span> <span class="n">t_pval</span>
+ <span class="n">anova</span><span class="p">[</span><span class="n">col</span><span class="p">][</span><span class="s">"date_treatment"</span><span class="p">]</span> <span class="o">=</span> <span class="n">dt_pval</span>
+ <span class="k">for</span> <span class="nb">type</span> <span class="ow">in</span> <span class="p">[</span><span class="s">"date"</span><span class="p">,</span> <span class="s">"treatment"</span><span class="p">,</span> <span class="s">"date_treatment"</span><span class="p">]:</span>
+ <span class="n">vals</span> <span class="o">=</span> <span class="p">[</span><span class="n">group</span><span class="p">]</span> <span class="o">+</span> <span class="p">[</span><span class="n">anova</span><span class="p">[</span><span class="n">x</span><span class="p">][</span><span class="nb">type</span><span class="p">]</span> <span class="k">for</span> <span class="n">x</span> <span class="ow">in</span> <span class="n">numeric</span><span class="p">]</span> <span class="o">+</span> <span class="p">[</span><span class="nb">type</span><span class="p">]</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">conn</span><span class="o">.</span><span class="n">execute</span><span class="p">(</span><span class="s">"insert into "</span> <span class="o">+</span> <span class="n">outtable</span> <span class="o">+</span> <span class="s">" ("</span> <span class="o">+</span> <span class="s">","</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">outHeaders</span><span class="p">)</span> <span class="o">+</span> <span class="s">") values ("</span> <span class="o">+</span> <span class="s">","</span><span class="o">.</span><span class="n">join</span><span class="p">([</span><span class="s">"?"</span><span class="p">]</span> <span class="o">*</span> <span class="nb">len</span><span class="p">(</span><span class="n">outHeaders</span><span class="p">))</span> <span class="o">+</span> <span class="s">")"</span><span class="p">,</span> <span class="nb">tuple</span><span class="p">(</span><span class="n">vals</span><span class="p">))</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">conn</span><span class="o">.</span><span class="n">commit</span><span class="p">()</span>
+ <span class="k">return</span>
+ </div>
+<div class="viewcode-block" id="Stats.tTest"><a class="viewcode-back" href="../../statistics.html#ih.statistics.Stats.tTest">[docs]</a> <span class="k">def</span> <span class="nf">tTest</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">intable</span><span class="p">,</span> <span class="n">outtable</span><span class="p">,</span> <span class="n">comp</span> <span class="o">=</span> <span class="s">"imtype"</span><span class="p">,</span> <span class="n">overwrite</span> <span class="o">=</span> <span class="bp">False</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> :param intable: The input table to perform the T test on.</span>
+<span class="sd"> :type intable: str</span>
+<span class="sd"> :param outtable: The output table to write the results to.</span>
+<span class="sd"> :type outtable: str</span>
+<span class="sd"> :param comp: Whether to compare image types or image names.</span>
+<span class="sd"> :type comp: str</span>
+<span class="sd"> :param overwrite: Whether or not to overwrite the output database</span>
+<span class="sd"> :type overwrite: bool</span>
+<span class="sd"> </span>
+<span class="sd"> This function computes a ttest of the input table for all numeric headers.</span>
+<span class="sd"> The comparison is either done based on image types or image names. Default</span>
+<span class="sd"> functionality is a comparison between image types, specify comp = 'imgname'</span>
+<span class="sd"> to compare image names.</span>
+<span class="sd"> """</span>
+
+ <span class="bp">self</span><span class="o">.</span><span class="n">_validate</span><span class="p">(</span><span class="s">"ttest"</span><span class="p">,</span> <span class="n">intable</span><span class="p">,</span> <span class="n">outtable</span><span class="p">,</span> <span class="n">overwrite</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_createTable</span><span class="p">(</span><span class="s">"ttest"</span><span class="p">,</span> <span class="n">intable</span><span class="p">,</span> <span class="n">outtable</span><span class="p">,</span> <span class="n">overwrite</span><span class="p">)</span>
+ <span class="n">comp</span> <span class="o">=</span> <span class="s">"imtype"</span> <span class="k">if</span> <span class="n">comp</span> <span class="o">==</span> <span class="s">"imtype"</span> <span class="k">else</span> <span class="s">"imgname"</span>
+ <span class="n">headers</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_getHeaders</span><span class="p">(</span><span class="n">outtable</span><span class="p">)</span>
+ <span class="n">numeric</span> <span class="o">=</span> <span class="p">[</span><span class="n">h</span> <span class="k">for</span> <span class="n">h</span> <span class="ow">in</span> <span class="n">headers</span> <span class="k">if</span> <span class="n">h</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">conf</span><span class="o">.</span><span class="n">allHeaders</span><span class="p">]</span>
+ <span class="n">meta</span> <span class="o">=</span> <span class="p">[</span><span class="n">h</span> <span class="k">for</span> <span class="n">h</span> <span class="ow">in</span> <span class="n">headers</span> <span class="k">if</span> <span class="n">h</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">numeric</span><span class="p">]</span>
+ <span class="n">data</span> <span class="o">=</span> <span class="p">{}</span>
+ <span class="n">result</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">conn</span><span class="o">.</span><span class="n">execute</span><span class="p">(</span><span class="s">"select pegasusid,treatment,"</span> <span class="o">+</span> <span class="s">","</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">headers</span><span class="p">)</span> <span class="o">+</span> <span class="s">" from "</span> <span class="o">+</span> <span class="n">intable</span><span class="p">)</span>
+ <span class="k">for</span> <span class="n">row</span> <span class="ow">in</span> <span class="n">result</span><span class="p">:</span>
+ <span class="k">if</span> <span class="n">row</span><span class="p">[</span><span class="n">comp</span><span class="p">]</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">data</span><span class="p">:</span>
+ <span class="n">data</span><span class="p">[</span><span class="n">row</span><span class="p">[</span><span class="n">comp</span><span class="p">]]</span> <span class="o">=</span> <span class="p">{}</span>
+ <span class="k">if</span> <span class="n">row</span><span class="p">[</span><span class="s">"date"</span><span class="p">]</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">data</span><span class="p">[</span><span class="n">row</span><span class="p">[</span><span class="n">comp</span><span class="p">]]:</span>
+ <span class="n">data</span><span class="p">[</span><span class="n">row</span><span class="p">[</span><span class="n">comp</span><span class="p">]][</span><span class="n">row</span><span class="p">[</span><span class="s">"date"</span><span class="p">]]</span> <span class="o">=</span> <span class="p">{</span><span class="s">"meta"</span><span class="p">:</span> <span class="nb">dict</span><span class="p">(</span><span class="n">row</span><span class="p">),</span> <span class="s">"id"</span><span class="p">:</span> <span class="p">[],</span> <span class="s">"values"</span><span class="p">:</span> <span class="p">{}}</span>
+ <span class="n">data</span><span class="p">[</span><span class="n">row</span><span class="p">[</span><span class="n">comp</span><span class="p">]][</span><span class="n">row</span><span class="p">[</span><span class="s">"date"</span><span class="p">]][</span><span class="s">"id"</span><span class="p">]</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">row</span><span class="p">[</span><span class="s">"pegasusid"</span><span class="p">])</span>
+ <span class="k">if</span> <span class="n">row</span><span class="p">[</span><span class="s">"treatment"</span><span class="p">]</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">data</span><span class="p">[</span><span class="n">row</span><span class="p">[</span><span class="n">comp</span><span class="p">]][</span><span class="n">row</span><span class="p">[</span><span class="s">"date"</span><span class="p">]][</span><span class="s">"values"</span><span class="p">]:</span>
+ <span class="n">data</span><span class="p">[</span><span class="n">row</span><span class="p">[</span><span class="n">comp</span><span class="p">]][</span><span class="n">row</span><span class="p">[</span><span class="s">"date"</span><span class="p">]][</span><span class="s">"values"</span><span class="p">][</span><span class="n">row</span><span class="p">[</span><span class="s">"treatment"</span><span class="p">]]</span> <span class="o">=</span> <span class="p">[[</span><span class="n">row</span><span class="p">[</span><span class="n">h</span><span class="p">]]</span> <span class="k">for</span> <span class="n">h</span> <span class="ow">in</span> <span class="n">numeric</span><span class="p">]</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="k">for</span> <span class="n">i</span><span class="p">,</span><span class="n">h</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="n">numeric</span><span class="p">):</span>
+ <span class="n">data</span><span class="p">[</span><span class="n">row</span><span class="p">[</span><span class="n">comp</span><span class="p">]][</span><span class="n">row</span><span class="p">[</span><span class="s">"date"</span><span class="p">]][</span><span class="s">"values"</span><span class="p">][</span><span class="n">row</span><span class="p">[</span><span class="s">"treatment"</span><span class="p">]][</span><span class="n">i</span><span class="p">]</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">row</span><span class="p">[</span><span class="n">h</span><span class="p">])</span>
+ <span class="k">for</span> <span class="n">comp</span> <span class="ow">in</span> <span class="n">data</span><span class="p">:</span>
+ <span class="k">for</span> <span class="n">date</span> <span class="ow">in</span> <span class="n">data</span><span class="p">[</span><span class="n">comp</span><span class="p">]:</span>
+ <span class="n">vals</span> <span class="o">=</span> <span class="p">[</span><span class="n">data</span><span class="p">[</span><span class="n">comp</span><span class="p">][</span><span class="n">date</span><span class="p">][</span><span class="s">"meta"</span><span class="p">][</span><span class="n">x</span><span class="p">]</span> <span class="k">for</span> <span class="n">x</span> <span class="ow">in</span> <span class="n">meta</span><span class="p">]</span>
+ <span class="k">for</span> <span class="n">a</span><span class="p">,</span><span class="n">b</span> <span class="ow">in</span> <span class="nb">zip</span><span class="p">(</span><span class="n">data</span><span class="p">[</span><span class="n">comp</span><span class="p">][</span><span class="n">date</span><span class="p">][</span><span class="s">"values"</span><span class="p">][</span><span class="s">"Control"</span><span class="p">],</span> <span class="n">data</span><span class="p">[</span><span class="n">comp</span><span class="p">][</span><span class="n">date</span><span class="p">][</span><span class="s">"values"</span><span class="p">][</span><span class="s">"Stress"</span><span class="p">]):</span>
+ <span class="k">try</span><span class="p">:</span>
+ <span class="n">res</span> <span class="o">=</span> <span class="n">stats</span><span class="o">.</span><span class="n">ttest_ind</span><span class="p">(</span><span class="n">a</span><span class="p">,</span> <span class="n">b</span><span class="p">)[</span><span class="mi">1</span><span class="p">]</span>
+ <span class="k">except</span><span class="p">:</span>
+ <span class="n">res</span> <span class="o">=</span> <span class="bp">None</span>
+ <span class="n">vals</span> <span class="o">+=</span> <span class="p">[</span><span class="n">res</span><span class="p">]</span>
+ <span class="n">lastid</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">conn</span><span class="o">.</span><span class="n">execute</span><span class="p">(</span><span class="s">"insert into "</span> <span class="o">+</span> <span class="n">outtable</span> <span class="o">+</span> <span class="s">" ("</span> <span class="o">+</span> <span class="s">","</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">headers</span><span class="p">)</span> <span class="o">+</span> <span class="s">") values ("</span> <span class="o">+</span> <span class="s">","</span><span class="o">.</span><span class="n">join</span><span class="p">([</span><span class="s">"?"</span><span class="p">]</span> <span class="o">*</span> <span class="nb">len</span><span class="p">(</span><span class="n">headers</span><span class="p">))</span> <span class="o">+</span> <span class="s">")"</span><span class="p">,</span> <span class="n">vals</span><span class="p">)</span><span class="o">.</span><span class="n">lastrowid</span>
+ <span class="n">updateVals</span> <span class="o">=</span> <span class="p">(</span><span class="n">lastid</span><span class="p">,)</span> <span class="o">+</span> <span class="nb">tuple</span><span class="p">(</span><span class="n">data</span><span class="p">[</span><span class="n">comp</span><span class="p">][</span><span class="n">date</span><span class="p">][</span><span class="s">"id"</span><span class="p">])</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">conn</span><span class="o">.</span><span class="n">execute</span><span class="p">(</span><span class="s">"update "</span> <span class="o">+</span> <span class="n">intable</span> <span class="o">+</span> <span class="s">" set ref_"</span> <span class="o">+</span> <span class="n">outtable</span> <span class="o">+</span> <span class="s">"=? where id in ("</span> <span class="o">+</span> <span class="s">","</span><span class="o">.</span><span class="n">join</span><span class="p">([</span><span class="s">"?"</span><span class="p">]</span> <span class="o">*</span> <span class="nb">len</span><span class="p">(</span><span class="n">data</span><span class="p">[</span><span class="n">comp</span><span class="p">][</span><span class="n">date</span><span class="p">][</span><span class="s">"id"</span><span class="p">]))</span> <span class="o">+</span> <span class="s">")"</span><span class="p">,</span> <span class="n">updateVals</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">conn</span><span class="o">.</span><span class="n">commit</span><span class="p">()</span>
+ <span class="k">return</span>
+ </div>
+<div class="viewcode-block" id="Stats.treatmentComp"><a class="viewcode-back" href="../../statistics.html#ih.statistics.Stats.treatmentComp">[docs]</a> <span class="k">def</span> <span class="nf">treatmentComp</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">intable</span><span class="p">,</span> <span class="n">outtable</span><span class="p">,</span> <span class="nb">type</span> <span class="o">=</span> <span class="s">"ratio"</span><span class="p">,</span> <span class="n">direction</span> <span class="o">=</span> <span class="s">"Control"</span><span class="p">,</span> <span class="n">comp</span> <span class="o">=</span> <span class="s">"imtype"</span><span class="p">,</span> <span class="n">overwrite</span> <span class="o">=</span> <span class="bp">False</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> :param intable: The input table to load information from</span>
+<span class="sd"> :type intable: str</span>
+<span class="sd"> :param outtable: The output table to write information to.</span>
+<span class="sd"> :type outtable: str</span>
+<span class="sd"> :param type: The type of calculation to do between treatments. Should be ratio or difference.</span>
+<span class="sd"> :type type: str</span>
+<span class="sd"> :param direction: Whether to compute C ~ S, or S ~ C, default is Control first.</span>
+<span class="sd"> :type direction: str</span>
+<span class="sd"> :param comp: Whether to compare by imtype or imgname</span>
+<span class="sd"> :type comp: str</span>
+<span class="sd"> </span>
+<span class="sd"> This function compares information between treatments -- It finds plants that are identical</span>
+<span class="sd"> except for treatment, and computes either a ratio or difference between them. Direction</span>
+<span class="sd"> is specified as the column you want first, so direction = "Control" will compute C ~ S, and </span>
+<span class="sd"> direction = "Stress" will compute S ~ C. If you have already normalized your table, difference</span>
+<span class="sd"> will provide better information than ratio.</span>
+<span class="sd"> """</span>
+ <span class="n">t1</span> <span class="o">=</span> <span class="s">"Stress"</span> <span class="k">if</span> <span class="n">direction</span> <span class="o">==</span> <span class="s">"Stress"</span> <span class="k">else</span> <span class="s">"Control"</span>
+ <span class="n">t2</span> <span class="o">=</span> <span class="s">"Stress"</span> <span class="k">if</span> <span class="n">direction</span> <span class="o">==</span> <span class="s">"Control"</span> <span class="k">else</span> <span class="s">"Control"</span>
+ <span class="k">if</span> <span class="nb">type</span> <span class="o">==</span> <span class="s">"ratio"</span><span class="p">:</span>
+ <span class="n">op</span> <span class="o">=</span> <span class="k">lambda</span> <span class="n">left</span><span class="p">,</span> <span class="n">right</span><span class="p">:</span> <span class="p">(</span><span class="n">left</span> <span class="o">/</span> <span class="n">right</span><span class="p">)</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="n">op</span> <span class="o">=</span> <span class="k">lambda</span> <span class="n">left</span><span class="p">,</span> <span class="n">right</span><span class="p">:</span> <span class="p">(</span><span class="n">left</span> <span class="o">-</span> <span class="n">right</span><span class="p">)</span>
+ <span class="n">comp</span> <span class="o">=</span> <span class="s">"imtype"</span> <span class="k">if</span> <span class="n">comp</span> <span class="o">==</span> <span class="s">"imtype"</span> <span class="k">else</span> <span class="s">"imgname"</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_validate</span><span class="p">(</span><span class="s">"treatmentComp"</span><span class="p">,</span> <span class="n">intable</span><span class="p">,</span> <span class="n">outtable</span><span class="p">,</span> <span class="n">overwrite</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_createTable</span><span class="p">(</span><span class="s">"treatmentComp"</span><span class="p">,</span> <span class="n">intable</span><span class="p">,</span> <span class="n">outtable</span><span class="p">,</span> <span class="n">overwrite</span><span class="p">)</span>
+ <span class="n">headers</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_getHeaders</span><span class="p">(</span><span class="n">outtable</span><span class="p">)</span>
+ <span class="n">numeric</span> <span class="o">=</span> <span class="p">[</span><span class="n">h</span> <span class="k">for</span> <span class="n">h</span> <span class="ow">in</span> <span class="n">headers</span> <span class="k">if</span> <span class="n">h</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">conf</span><span class="o">.</span><span class="n">allHeaders</span><span class="p">]</span>
+ <span class="n">meta</span> <span class="o">=</span> <span class="p">[</span><span class="n">h</span> <span class="k">for</span> <span class="n">h</span> <span class="ow">in</span> <span class="n">headers</span> <span class="k">if</span> <span class="n">h</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">numeric</span><span class="p">]</span>
+ <span class="n">data</span> <span class="o">=</span> <span class="p">{}</span>
+ <span class="n">result</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">conn</span><span class="o">.</span><span class="n">execute</span><span class="p">(</span><span class="s">"select pegasusid,"</span> <span class="o">+</span> <span class="s">","</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">headers</span><span class="p">)</span> <span class="o">+</span> <span class="s">" from "</span> <span class="o">+</span> <span class="n">intable</span><span class="p">)</span>
+ <span class="k">for</span> <span class="n">row</span> <span class="ow">in</span> <span class="n">result</span><span class="p">:</span>
+ <span class="k">if</span> <span class="n">row</span><span class="p">[</span><span class="s">"genotype"</span><span class="p">]</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">data</span><span class="p">:</span>
+ <span class="n">data</span><span class="p">[</span><span class="n">row</span><span class="p">[</span><span class="s">"genotype"</span><span class="p">]]</span> <span class="o">=</span> <span class="p">{</span><span class="s">"id"</span><span class="p">:</span> <span class="p">[],</span> <span class="s">"values"</span><span class="p">:</span> <span class="p">{},</span> <span class="s">"meta"</span><span class="p">:</span> <span class="p">{}}</span>
+ <span class="n">data</span><span class="p">[</span><span class="n">row</span><span class="p">[</span><span class="s">"genotype"</span><span class="p">]][</span><span class="s">"meta"</span><span class="p">][</span><span class="n">row</span><span class="p">[</span><span class="n">comp</span><span class="p">]]</span> <span class="o">=</span> <span class="nb">dict</span><span class="p">(</span><span class="n">row</span><span class="p">)</span>
+ <span class="n">data</span><span class="p">[</span><span class="n">row</span><span class="p">[</span><span class="s">"genotype"</span><span class="p">]][</span><span class="s">"id"</span><span class="p">]</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">row</span><span class="p">[</span><span class="s">"pegasusid"</span><span class="p">])</span>
+ <span class="k">if</span> <span class="n">row</span><span class="p">[</span><span class="n">comp</span><span class="p">]</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">data</span><span class="p">[</span><span class="n">row</span><span class="p">[</span><span class="s">"genotype"</span><span class="p">]][</span><span class="s">"values"</span><span class="p">]:</span>
+ <span class="n">data</span><span class="p">[</span><span class="n">row</span><span class="p">[</span><span class="s">"genotype"</span><span class="p">]][</span><span class="s">"values"</span><span class="p">][</span><span class="n">row</span><span class="p">[</span><span class="n">comp</span><span class="p">]]</span> <span class="o">=</span> <span class="p">{}</span>
+ <span class="k">if</span> <span class="n">row</span><span class="p">[</span><span class="s">"date"</span><span class="p">]</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">data</span><span class="p">[</span><span class="n">row</span><span class="p">[</span><span class="s">"genotype"</span><span class="p">]][</span><span class="s">"values"</span><span class="p">][</span><span class="n">row</span><span class="p">[</span><span class="n">comp</span><span class="p">]]:</span>
+ <span class="n">data</span><span class="p">[</span><span class="n">row</span><span class="p">[</span><span class="s">"genotype"</span><span class="p">]][</span><span class="s">"values"</span><span class="p">][</span><span class="n">row</span><span class="p">[</span><span class="n">comp</span><span class="p">]][</span><span class="n">row</span><span class="p">[</span><span class="s">"date"</span><span class="p">]]</span> <span class="o">=</span> <span class="p">{}</span>
+ <span class="k">if</span> <span class="n">row</span><span class="p">[</span><span class="s">"treatment"</span><span class="p">]</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">data</span><span class="p">[</span><span class="n">row</span><span class="p">[</span><span class="s">"genotype"</span><span class="p">]][</span><span class="s">"values"</span><span class="p">][</span><span class="n">row</span><span class="p">[</span><span class="n">comp</span><span class="p">]][</span><span class="n">row</span><span class="p">[</span><span class="s">"date"</span><span class="p">]]:</span>
+ <span class="n">data</span><span class="p">[</span><span class="n">row</span><span class="p">[</span><span class="s">"genotype"</span><span class="p">]][</span><span class="s">"values"</span><span class="p">][</span><span class="n">row</span><span class="p">[</span><span class="n">comp</span><span class="p">]][</span><span class="n">row</span><span class="p">[</span><span class="s">"date"</span><span class="p">]][</span><span class="n">row</span><span class="p">[</span><span class="s">"treatment"</span><span class="p">]]</span> <span class="o">=</span> <span class="p">[</span><span class="n">row</span><span class="p">[</span><span class="n">h</span><span class="p">]</span> <span class="k">for</span> <span class="n">h</span> <span class="ow">in</span> <span class="n">numeric</span><span class="p">]</span>
+ <span class="k">for</span> <span class="n">genotype</span> <span class="ow">in</span> <span class="n">data</span><span class="p">:</span>
+ <span class="k">for</span> <span class="n">comp</span> <span class="ow">in</span> <span class="n">data</span><span class="p">[</span><span class="n">genotype</span><span class="p">][</span><span class="s">"values"</span><span class="p">]:</span>
+ <span class="k">for</span> <span class="n">date</span> <span class="ow">in</span> <span class="n">data</span><span class="p">[</span><span class="n">genotype</span><span class="p">][</span><span class="s">"values"</span><span class="p">][</span><span class="n">comp</span><span class="p">]:</span>
+ <span class="n">vals</span> <span class="o">=</span> <span class="p">[</span><span class="n">data</span><span class="p">[</span><span class="n">genotype</span><span class="p">][</span><span class="s">"meta"</span><span class="p">][</span><span class="n">comp</span><span class="p">][</span><span class="n">x</span><span class="p">]</span> <span class="k">for</span> <span class="n">x</span> <span class="ow">in</span> <span class="n">meta</span><span class="p">]</span>
+ <span class="k">for</span> <span class="n">a</span><span class="p">,</span><span class="n">b</span> <span class="ow">in</span> <span class="nb">zip</span><span class="p">(</span><span class="n">data</span><span class="p">[</span><span class="n">genotype</span><span class="p">][</span><span class="s">"values"</span><span class="p">][</span><span class="n">comp</span><span class="p">][</span><span class="n">date</span><span class="p">][</span><span class="n">t1</span><span class="p">],</span> <span class="n">data</span><span class="p">[</span><span class="n">genotype</span><span class="p">][</span><span class="s">"values"</span><span class="p">][</span><span class="n">comp</span><span class="p">][</span><span class="n">date</span><span class="p">][</span><span class="n">t2</span><span class="p">]):</span>
+ <span class="k">try</span><span class="p">:</span>
+ <span class="n">res</span> <span class="o">=</span> <span class="n">op</span><span class="p">(</span><span class="nb">float</span><span class="p">(</span><span class="n">a</span><span class="p">),</span> <span class="nb">float</span><span class="p">(</span><span class="n">b</span><span class="p">))</span>
+ <span class="k">except</span><span class="p">:</span>
+ <span class="n">res</span> <span class="o">=</span> <span class="bp">None</span>
+ <span class="n">vals</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">res</span><span class="p">)</span>
+ <span class="n">lastid</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">conn</span><span class="o">.</span><span class="n">execute</span><span class="p">(</span><span class="s">"insert into "</span> <span class="o">+</span> <span class="n">outtable</span> <span class="o">+</span> <span class="s">" ("</span> <span class="o">+</span> <span class="s">","</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">headers</span><span class="p">)</span> <span class="o">+</span> <span class="s">") values ("</span> <span class="o">+</span> <span class="s">","</span><span class="o">.</span><span class="n">join</span><span class="p">([</span><span class="s">"?"</span><span class="p">]</span> <span class="o">*</span> <span class="nb">len</span><span class="p">(</span><span class="n">headers</span><span class="p">))</span> <span class="o">+</span> <span class="s">")"</span><span class="p">,</span> <span class="n">vals</span><span class="p">)</span><span class="o">.</span><span class="n">lastrowid</span>
+ <span class="n">updateVals</span> <span class="o">=</span> <span class="p">(</span><span class="n">lastid</span><span class="p">,)</span> <span class="o">+</span> <span class="nb">tuple</span><span class="p">(</span><span class="n">data</span><span class="p">[</span><span class="n">genotype</span><span class="p">][</span><span class="s">"id"</span><span class="p">])</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">conn</span><span class="o">.</span><span class="n">execute</span><span class="p">(</span><span class="s">"update "</span> <span class="o">+</span> <span class="n">intable</span> <span class="o">+</span> <span class="s">" set ref_"</span> <span class="o">+</span> <span class="n">outtable</span> <span class="o">+</span> <span class="s">"=? where id in ("</span> <span class="o">+</span> <span class="s">","</span><span class="o">.</span><span class="n">join</span><span class="p">([</span><span class="s">"?"</span><span class="p">]</span> <span class="o">*</span> <span class="nb">len</span><span class="p">(</span><span class="n">data</span><span class="p">[</span><span class="n">genotype</span><span class="p">][</span><span class="s">"id"</span><span class="p">]))</span> <span class="o">+</span> <span class="s">")"</span><span class="p">,</span> <span class="n">updateVals</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">conn</span><span class="o">.</span><span class="n">commit</span><span class="p">()</span>
+ <span class="k">return</span>
+ </div>
+<div class="viewcode-block" id="Stats.threshold"><a class="viewcode-back" href="../../statistics.html#ih.statistics.Stats.threshold">[docs]</a> <span class="k">def</span> <span class="nf">threshold</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">intable</span><span class="p">,</span> <span class="n">outtable</span><span class="p">,</span> <span class="n">thresh</span> <span class="o">=</span> <span class="mf">0.01</span><span class="p">,</span> <span class="n">overwrite</span> <span class="o">=</span> <span class="bp">False</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> :param intable: The input table to load information from</span>
+<span class="sd"> :type intable: str</span>
+<span class="sd"> :param outtable: The output table to write information to.</span>
+<span class="sd"> :type outtable: str</span>
+<span class="sd"> :param thresh: The threshold value.</span>
+<span class="sd"> :type thresh: float</span>
+<span class="sd"> </span>
+<span class="sd"> This function thresholds the table based on the given value. All values</span>
+<span class="sd"> that fall below the threhsold are 'updated' in place with 'null'. Normalize</span>
+<span class="sd"> is often called before thresholding.</span>
+<span class="sd"> """</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_validate</span><span class="p">(</span><span class="s">"threshold"</span><span class="p">,</span> <span class="n">intable</span><span class="p">,</span> <span class="n">outtable</span><span class="p">,</span> <span class="n">overwrite</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_createTable</span><span class="p">(</span><span class="s">"threshold"</span><span class="p">,</span> <span class="n">intable</span><span class="p">,</span> <span class="n">outtable</span><span class="p">,</span> <span class="n">overwrite</span><span class="p">)</span>
+ <span class="n">headers</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_getHeaders</span><span class="p">(</span><span class="n">outtable</span><span class="p">)</span>
+ <span class="n">numeric</span> <span class="o">=</span> <span class="p">[</span><span class="n">h</span> <span class="k">for</span> <span class="n">h</span> <span class="ow">in</span> <span class="n">headers</span> <span class="k">if</span> <span class="n">h</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">conf</span><span class="o">.</span><span class="n">allHeaders</span><span class="p">]</span>
+ <span class="n">result</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">conn</span><span class="o">.</span><span class="n">execute</span><span class="p">(</span><span class="s">"select pegasusid,"</span> <span class="o">+</span> <span class="s">","</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">headers</span><span class="p">)</span> <span class="o">+</span> <span class="s">" from "</span> <span class="o">+</span> <span class="n">intable</span><span class="p">)</span>
+ <span class="k">for</span> <span class="n">row</span> <span class="ow">in</span> <span class="n">result</span><span class="p">:</span>
+ <span class="n">vals</span> <span class="o">=</span> <span class="p">[]</span>
+ <span class="k">for</span> <span class="n">x</span> <span class="ow">in</span> <span class="n">headers</span><span class="p">:</span>
+ <span class="k">if</span> <span class="n">x</span> <span class="ow">in</span> <span class="n">conf</span><span class="o">.</span><span class="n">allHeaders</span><span class="p">:</span>
+ <span class="n">vals</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">row</span><span class="p">[</span><span class="n">x</span><span class="p">])</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="k">if</span> <span class="ow">not</span> <span class="bp">self</span><span class="o">.</span><span class="n">_checkNull</span><span class="p">(</span><span class="n">row</span><span class="p">[</span><span class="n">x</span><span class="p">]):</span>
+ <span class="k">if</span> <span class="nb">float</span><span class="p">(</span><span class="n">row</span><span class="p">[</span><span class="n">x</span><span class="p">])</span> <span class="o">></span> <span class="n">thresh</span><span class="p">:</span>
+ <span class="n">vals</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">row</span><span class="p">[</span><span class="n">x</span><span class="p">])</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="n">vals</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="bp">None</span><span class="p">)</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="n">vals</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="bp">None</span><span class="p">)</span>
+ <span class="n">lastid</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">conn</span><span class="o">.</span><span class="n">execute</span><span class="p">(</span><span class="s">"insert into "</span> <span class="o">+</span> <span class="n">outtable</span> <span class="o">+</span> <span class="s">" ("</span> <span class="o">+</span> <span class="s">","</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">headers</span><span class="p">)</span> <span class="o">+</span> <span class="s">") values ("</span> <span class="o">+</span> <span class="s">","</span><span class="o">.</span><span class="n">join</span><span class="p">([</span><span class="s">"?"</span><span class="p">]</span> <span class="o">*</span> <span class="nb">len</span><span class="p">(</span><span class="n">headers</span><span class="p">))</span> <span class="o">+</span> <span class="s">")"</span><span class="p">,</span> <span class="nb">tuple</span><span class="p">(</span><span class="n">vals</span><span class="p">))</span><span class="o">.</span><span class="n">lastrowid</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">conn</span><span class="o">.</span><span class="n">execute</span><span class="p">(</span><span class="s">"update "</span> <span class="o">+</span> <span class="n">intable</span> <span class="o">+</span> <span class="s">" set ref_"</span> <span class="o">+</span> <span class="n">outtable</span> <span class="o">+</span> <span class="s">"=? where pegasusid=?"</span><span class="p">,</span> <span class="p">(</span><span class="n">lastid</span><span class="p">,</span> <span class="n">row</span><span class="p">[</span><span class="s">"pegasusid"</span><span class="p">]))</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">conn</span><span class="o">.</span><span class="n">commit</span><span class="p">()</span>
+ <span class="k">return</span>
+ </div>
+ <span class="k">def</span> <span class="nf">SOMANYGRAPHINGFUNCTIONS</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+ <span class="k">return</span>
+
+<div class="viewcode-block" id="Stats.export"><a class="viewcode-back" href="../../statistics.html#ih.statistics.Stats.export">[docs]</a> <span class="k">def</span> <span class="nf">export</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">table</span><span class="p">,</span> <span class="n">processed</span> <span class="o">=</span> <span class="bp">True</span><span class="p">,</span> <span class="n">group</span> <span class="o">=</span> <span class="bp">None</span><span class="p">,</span> <span class="n">fname</span> <span class="o">=</span> <span class="bp">None</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> :param table: The table to write to csv</span>
+<span class="sd"> :type table: str</span>
+<span class="sd"> :param processed: Whether or not to extract processed data</span>
+<span class="sd"> :type processed: bool</span>
+<span class="sd"> :param group: Which image types to extract from the database.</span>
+<span class="sd"> :type group: list</span>
+<span class="sd"> :param fname: The file name to write to.</span>
+<span class="sd"> :type fname: str</span>
+<span class="sd"> </span>
+<span class="sd"> This function simply extracts data from a database and writes it to csv format.</span>
+<span class="sd"> Default functionality is to extract only data that has been processed. This is</span>
+<span class="sd"> checked by finding if an outputPath has been set. Additionally,</span>
+<span class="sd"> you can specify a list of image types to extract, if not, the default list contains</span>
+<span class="sd"> all rgb and fluo images. Finally, if no file name is specified, the name</span>
+<span class="sd"> of the table is used as the filename.</span>
+<span class="sd"> """</span>
+ <span class="n">group</span> <span class="o">=</span> <span class="n">group</span> <span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">group</span><span class="p">,</span> <span class="nb">list</span><span class="p">)</span> <span class="k">else</span> <span class="bp">self</span><span class="o">.</span><span class="n">_getImageTypes</span><span class="p">(</span><span class="n">table</span><span class="p">)</span>
+ <span class="n">fname</span> <span class="o">=</span> <span class="n">fname</span> <span class="k">if</span> <span class="n">fname</span> <span class="k">else</span> <span class="n">table</span> <span class="o">+</span> <span class="s">".csv"</span>
+ <span class="n">query</span> <span class="o">=</span> <span class="s">"select * from "</span> <span class="o">+</span> <span class="n">table</span>
+ <span class="n">values</span> <span class="o">=</span> <span class="nb">tuple</span><span class="p">()</span>
+ <span class="k">if</span> <span class="n">processed</span><span class="p">:</span>
+ <span class="n">query</span> <span class="o">+=</span> <span class="s">" where outputPath is not null"</span>
+ <span class="k">if</span> <span class="n">group</span><span class="p">:</span>
+ <span class="n">query</span> <span class="o">+=</span> <span class="s">" and ("</span> <span class="o">+</span> <span class="s">" or "</span><span class="o">.</span><span class="n">join</span><span class="p">([</span><span class="s">"imtype=?"</span> <span class="k">for</span> <span class="n">x</span> <span class="ow">in</span> <span class="n">group</span><span class="p">])</span>
+ <span class="n">values</span> <span class="o">=</span> <span class="nb">tuple</span><span class="p">([</span><span class="n">x</span> <span class="k">for</span> <span class="n">x</span> <span class="ow">in</span> <span class="n">group</span><span class="p">])</span>
+ <span class="k">elif</span> <span class="n">group</span><span class="p">:</span>
+ <span class="n">query</span> <span class="o">+=</span> <span class="s">" where "</span> <span class="o">+</span> <span class="s">" or "</span><span class="o">.</span><span class="n">join</span><span class="p">([</span><span class="s">"imtype=?"</span> <span class="k">for</span> <span class="n">x</span> <span class="ow">in</span> <span class="n">group</span><span class="p">])</span>
+ <span class="n">values</span> <span class="o">=</span> <span class="nb">tuple</span><span class="p">([</span><span class="n">x</span> <span class="k">for</span> <span class="n">x</span> <span class="ow">in</span> <span class="n">group</span><span class="p">])</span>
+ <span class="n">table</span> <span class="o">=</span> <span class="n">pandas</span><span class="o">.</span><span class="n">io</span><span class="o">.</span><span class="n">sql</span><span class="o">.</span><span class="n">read_sql</span><span class="p">(</span><span class="n">sql</span> <span class="o">=</span> <span class="n">query</span><span class="p">,</span> <span class="n">params</span> <span class="o">=</span> <span class="n">values</span><span class="p">,</span> <span class="n">con</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">conn</span><span class="p">)</span>
+ <span class="n">table</span><span class="o">.</span><span class="n">to_csv</span><span class="p">(</span><span class="n">fname</span><span class="p">)</span>
+ <span class="k">return</span></div></div>
+</pre></div>
+
+ </div>
+
+ </div>
+</div>
+<footer class="footer">
+ <div class="container">
+ <p class="pull-right">
+ <a href="#">Back to top</a>
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+ </div>
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+</html>
\ No newline at end of file
diff --git a/docs/build/html/_modules/ih/workflow.html b/docs/build/html/_modules/ih/workflow.html
new file mode 100644
index 0000000000000000000000000000000000000000..86c18cb785b0ae4b0e2a3052e05ffa063ac4c305
--- /dev/null
+++ b/docs/build/html/_modules/ih/workflow.html
@@ -0,0 +1,1182 @@
+<!DOCTYPE html>
+
+
+<html xmlns="http://www.w3.org/1999/xhtml">
+ <head>
+ <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
+
+ <title>ih.workflow — Image Harvest 1.0.1 documentation</title>
+
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+ </button>
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+ Image Harvest</a>
+ <span class="navbar-text navbar-version pull-left"><b>1.0</b></span>
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+<li class="toctree-l1"><a class="reference internal" href="../../introduction.html">Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../../installation.html">Installation</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../../start.html">Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../../ex_script_core1.html">Core Processing Example #1</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../../ex_script_core2.html">Core Processing Example #2</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../../ex_script_color1.html">Color Filter In Depth #1</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../../ex_workflow_1.html">Workflow Example #1</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../../examples.html">Examples</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../../processing.html">Image Processing</a></li>
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+<li class="toctree-l1"><a class="reference internal" href="../../statistics.html">Statistics</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../../indexing.html">Image Loading</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../../workflowimage.html">Image Processing Workflows</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../../workflowstats.html">Statistics Workflows</a></li>
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+ <div class="col-md-12">
+
+ <h1>Source code for ih.workflow</h1><div class="highlight"><pre>
+<span class="sd">"""</span>
+<span class="sd">This file is part of Image Harvest.</span>
+
+<span class="sd">Image Harvest is free software: you can redistribute it and/or modify</span>
+<span class="sd">it under the terms of the GNU General Public License as published by</span>
+<span class="sd">the Free Software Foundation, either version 3 of the License, or</span>
+<span class="sd">(at your option) any later version.</span>
+
+<span class="sd">Image Harvest is distributed in the hope that it will be useful,</span>
+<span class="sd">but WITHOUT ANY WARRANTY; without even the implied warranty of</span>
+<span class="sd">MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the</span>
+<span class="sd">GNU General Public License for more details.</span>
+
+<span class="sd">You should have received a copy of the GNU General Public License</span>
+<span class="sd">along with Image Harvest. If not, see <http://www.gnu.org/licenses/>.</span>
+<span class="sd">"""</span>
+
+<span class="kn">import</span> <span class="nn">os</span>
+<span class="kn">import</span> <span class="nn">conf</span>
+<span class="kn">import</span> <span class="nn">sys</span>
+<span class="kn">import</span> <span class="nn">json</span>
+<span class="kn">import</span> <span class="nn">re</span>
+<span class="kn">import</span> <span class="nn">csv</span>
+<span class="kn">import</span> <span class="nn">datetime</span>
+<span class="kn">import</span> <span class="nn">sqlite3</span>
+<span class="kn">import</span> <span class="nn">shutil</span>
+<span class="kn">import</span> <span class="nn">errno</span>
+<span class="kn">import</span> <span class="nn">textwrap</span>
+<span class="kn">import</span> <span class="nn">copy</span>
+<span class="kn">import</span> <span class="nn">ih.validator</span>
+<span class="kn">import</span> <span class="nn">xml.dom.minidom</span>
+<span class="kn">from</span> <span class="nn">Pegasus.DAX3</span> <span class="kn">import</span> <span class="o">*</span>
+
+
+<span class="k">class</span> <span class="nc">Workflow</span><span class="p">(</span><span class="nb">object</span><span class="p">):</span>
+
+ <span class="sd">"""</span>
+<span class="sd"> Generic workflow creation class.</span>
+<span class="sd"> """</span>
+
+ <span class="k">def</span> <span class="nf">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">jobhome</span><span class="p">,</span> <span class="n">basename</span> <span class="o">=</span> <span class="bp">None</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> :param jobhome: The base directory for job submission.</span>
+<span class="sd"> :type jobhome: str</span>
+<span class="sd"> </span>
+<span class="sd"> Creates a Workflow class based on the input directory. Only loads and </span>
+<span class="sd"> validates the config file by default.</span>
+<span class="sd"> """</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">err</span> <span class="o">=</span> <span class="s">""</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">jobhome</span> <span class="o">=</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">abspath</span><span class="p">(</span><span class="n">jobhome</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">jobname</span> <span class="o">=</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">basename</span><span class="p">(</span><span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">dirname</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">jobhome</span> <span class="o">+</span> <span class="s">"/"</span><span class="p">))</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">basename</span> <span class="o">=</span> <span class="n">basename</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">dax</span> <span class="o">=</span> <span class="n">ADAG</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">jobname</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">executables</span> <span class="o">=</span> <span class="p">{}</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">files</span> <span class="o">=</span> <span class="p">{</span><span class="bp">self</span><span class="o">.</span><span class="n">dax</span><span class="p">:</span> <span class="p">{}}</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">jobs</span> <span class="o">=</span> <span class="p">{</span><span class="bp">self</span><span class="o">.</span><span class="n">dax</span><span class="p">:</span> <span class="p">{}}</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">deps</span> <span class="o">=</span> <span class="p">{}</span>
+ <span class="k">return</span>
+
+ <span class="k">def</span> <span class="nf">_loadInputFiles</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> Loads the input files into the appropriate variables</span>
+<span class="sd"> This should be overloaded.</span>
+<span class="sd"> """</span>
+ <span class="k">return</span>
+
+ <span class="k">def</span> <span class="nf">_isFile</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">name</span><span class="p">,</span> <span class="n">dax</span><span class="p">,</span> <span class="n">imtype</span><span class="p">,</span> <span class="n">inout</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> Convenience function to check if a given file exists.</span>
+<span class="sd"> """</span>
+ <span class="k">if</span> <span class="n">name</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">files</span><span class="p">[</span><span class="n">dax</span><span class="p">][</span><span class="n">imtype</span><span class="p">][</span><span class="n">inout</span><span class="p">]:</span>
+ <span class="k">return</span> <span class="bp">True</span>
+ <span class="k">return</span> <span class="bp">False</span>
+
+ <span class="k">def</span> <span class="nf">_isJob</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">name</span><span class="p">,</span> <span class="n">dax</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> Convenience function to check if a given job exists.</span>
+<span class="sd"> """</span>
+ <span class="k">if</span> <span class="n">name</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">jobs</span><span class="p">[</span><span class="n">dax</span><span class="p">]:</span>
+ <span class="k">return</span> <span class="bp">True</span>
+ <span class="k">return</span> <span class="bp">False</span>
+
+ <span class="k">def</span> <span class="nf">_isExecutable</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">name</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> Convenience function to check if a given executable exists.</span>
+<span class="sd"> """</span>
+ <span class="k">if</span> <span class="n">name</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">executables</span><span class="p">:</span>
+ <span class="k">return</span> <span class="bp">True</span>
+ <span class="k">return</span> <span class="bp">False</span>
+
+ <span class="k">def</span> <span class="nf">_createSetup</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> Creates the base structure for job submission. Everything is contained </span>
+<span class="sd"> within a folder based on the current timestamp.</span>
+<span class="sd"> """</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">basepath</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">jobhome</span> <span class="o">+</span> <span class="s">"/"</span> <span class="o">+</span> <span class="bp">self</span><span class="o">.</span><span class="n">basename</span> <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">basename</span> <span class="k">else</span> <span class="bp">self</span><span class="o">.</span><span class="n">jobhome</span> <span class="o">+</span> <span class="s">"/"</span> <span class="o">+</span> <span class="n">datetime</span><span class="o">.</span><span class="n">datetime</span><span class="o">.</span><span class="n">now</span><span class="p">()</span><span class="o">.</span><span class="n">strftime</span><span class="p">(</span><span class="s">"%Y-%m-</span><span class="si">%d</span><span class="s">_%H%M%S"</span><span class="p">)</span>
+ <span class="k">if</span> <span class="ow">not</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">exists</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">basepath</span><span class="p">):</span>
+ <span class="n">os</span><span class="o">.</span><span class="n">makedirs</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">basepath</span><span class="p">)</span>
+ <span class="k">if</span> <span class="ow">not</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">exists</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">basepath</span> <span class="o">+</span> <span class="s">"/input"</span><span class="p">):</span>
+ <span class="n">os</span><span class="o">.</span><span class="n">makedirs</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">basepath</span> <span class="o">+</span> <span class="s">"/input"</span><span class="p">)</span>
+ <span class="k">if</span> <span class="ow">not</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">exists</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">basepath</span> <span class="o">+</span> <span class="s">"/output"</span><span class="p">):</span>
+ <span class="n">os</span><span class="o">.</span><span class="n">makedirs</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">basepath</span> <span class="o">+</span> <span class="s">"/output"</span><span class="p">)</span>
+ <span class="k">if</span> <span class="ow">not</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">exists</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">basepath</span> <span class="o">+</span> <span class="s">"input/templates"</span><span class="p">):</span>
+ <span class="n">os</span><span class="o">.</span><span class="n">makedirs</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">basepath</span> <span class="o">+</span> <span class="s">"/input/templates"</span><span class="p">)</span>
+ <span class="k">if</span> <span class="ow">not</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">exists</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">basepath</span> <span class="o">+</span> <span class="s">"/input/rawfiles"</span><span class="p">):</span>
+ <span class="n">os</span><span class="o">.</span><span class="n">makedirs</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">basepath</span> <span class="o">+</span> <span class="s">"/input/rawfiles"</span><span class="p">)</span>
+ <span class="k">return</span>
+
+ <span class="k">def</span> <span class="nf">_addFile</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">name</span><span class="p">,</span> <span class="n">imtype</span><span class="p">,</span> <span class="n">inout</span><span class="p">,</span> <span class="n">path</span> <span class="o">=</span> <span class="bp">None</span><span class="p">,</span> <span class="n">dax</span> <span class="o">=</span> <span class="bp">None</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> Adds the inputted file to the dax, as well as the internal variable self.files</span>
+<span class="sd"> """</span>
+ <span class="n">dax</span> <span class="o">=</span> <span class="n">dax</span> <span class="k">if</span> <span class="n">dax</span> <span class="k">else</span> <span class="bp">self</span><span class="o">.</span><span class="n">dax</span>
+ <span class="k">if</span> <span class="ow">not</span> <span class="bp">self</span><span class="o">.</span><span class="n">_isFile</span><span class="p">(</span><span class="n">name</span><span class="p">,</span> <span class="n">dax</span><span class="p">,</span> <span class="n">imtype</span><span class="p">,</span> <span class="n">inout</span><span class="p">):</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">files</span><span class="p">[</span><span class="n">dax</span><span class="p">][</span><span class="n">imtype</span><span class="p">][</span><span class="n">inout</span><span class="p">][</span><span class="n">name</span><span class="p">]</span> <span class="o">=</span> <span class="p">{</span><span class="s">"file"</span><span class="p">:</span> <span class="n">File</span><span class="p">(</span><span class="n">name</span><span class="p">),</span> <span class="s">"path"</span><span class="p">:</span> <span class="s">""</span><span class="p">}</span>
+ <span class="k">if</span> <span class="n">inout</span> <span class="o">==</span> <span class="s">"input"</span><span class="p">:</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">files</span><span class="p">[</span><span class="n">dax</span><span class="p">][</span><span class="n">imtype</span><span class="p">][</span><span class="n">inout</span><span class="p">][</span><span class="n">name</span><span class="p">][</span><span class="s">"path"</span><span class="p">]</span> <span class="o">=</span> <span class="n">path</span> <span class="k">if</span> <span class="n">path</span> <span class="k">else</span> <span class="n">name</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">files</span><span class="p">[</span><span class="n">dax</span><span class="p">][</span><span class="n">imtype</span><span class="p">][</span><span class="n">inout</span><span class="p">][</span><span class="n">name</span><span class="p">][</span><span class="s">"file"</span><span class="p">]</span><span class="o">.</span><span class="n">addPFN</span><span class="p">(</span><span class="n">PFN</span><span class="p">(</span><span class="s">"file://"</span> <span class="o">+</span> <span class="n">path</span><span class="o">.</span><span class="n">replace</span><span class="p">(</span><span class="s">" "</span><span class="p">,</span><span class="s">"%20"</span><span class="p">),</span> <span class="s">"local"</span><span class="p">))</span>
+ <span class="n">dax</span><span class="o">.</span><span class="n">addFile</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">files</span><span class="p">[</span><span class="n">dax</span><span class="p">][</span><span class="n">imtype</span><span class="p">][</span><span class="n">inout</span><span class="p">][</span><span class="n">name</span><span class="p">][</span><span class="s">"file"</span><span class="p">])</span>
+ <span class="k">return</span>
+
+ <span class="k">def</span> <span class="nf">_addJob</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">jobname</span><span class="p">,</span> <span class="n">executable</span><span class="p">,</span> <span class="n">inputs</span><span class="p">,</span> <span class="n">outputs</span><span class="p">,</span> <span class="n">arguments</span><span class="p">,</span> <span class="n">dependencies</span> <span class="o">=</span> <span class="bp">None</span><span class="p">,</span> <span class="n">dax</span> <span class="o">=</span> <span class="bp">None</span><span class="p">,</span> <span class="n">label</span> <span class="o">=</span> <span class="bp">None</span><span class="p">,</span> <span class="n">walltime</span> <span class="o">=</span> <span class="bp">None</span><span class="p">):</span>
+ <span class="n">dax</span> <span class="o">=</span> <span class="n">dax</span> <span class="k">if</span> <span class="n">dax</span> <span class="k">else</span> <span class="bp">self</span><span class="o">.</span><span class="n">dax</span>
+ <span class="k">if</span> <span class="ow">not</span> <span class="bp">self</span><span class="o">.</span><span class="n">_isJob</span><span class="p">(</span><span class="n">jobname</span><span class="p">,</span> <span class="n">dax</span><span class="p">):</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">jobs</span><span class="p">[</span><span class="n">dax</span><span class="p">][</span><span class="n">jobname</span><span class="p">]</span> <span class="o">=</span> <span class="n">Job</span><span class="p">(</span><span class="n">executable</span><span class="p">)</span>
+ <span class="n">dax</span><span class="o">.</span><span class="n">addJob</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">jobs</span><span class="p">[</span><span class="n">dax</span><span class="p">][</span><span class="n">jobname</span><span class="p">])</span>
+ <span class="k">for</span> <span class="n">key</span> <span class="ow">in</span> <span class="n">inputs</span><span class="p">:</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">jobs</span><span class="p">[</span><span class="n">dax</span><span class="p">][</span><span class="n">jobname</span><span class="p">]</span><span class="o">.</span><span class="n">uses</span><span class="p">(</span><span class="n">inputs</span><span class="p">[</span><span class="n">key</span><span class="p">][</span><span class="s">"file"</span><span class="p">],</span> <span class="n">link</span> <span class="o">=</span> <span class="n">Link</span><span class="o">.</span><span class="n">INPUT</span><span class="p">)</span>
+ <span class="k">for</span> <span class="n">key</span> <span class="ow">in</span> <span class="n">outputs</span><span class="p">:</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">jobs</span><span class="p">[</span><span class="n">dax</span><span class="p">][</span><span class="n">jobname</span><span class="p">]</span><span class="o">.</span><span class="n">uses</span><span class="p">(</span><span class="n">outputs</span><span class="p">[</span><span class="n">key</span><span class="p">][</span><span class="s">"file"</span><span class="p">],</span> <span class="n">link</span> <span class="o">=</span> <span class="n">Link</span><span class="o">.</span><span class="n">OUTPUT</span><span class="p">,</span> <span class="n">transfer</span> <span class="o">=</span> <span class="n">outputs</span><span class="p">[</span><span class="n">key</span><span class="p">][</span><span class="s">"transfer"</span><span class="p">])</span>
+ <span class="n">arglist</span> <span class="o">=</span> <span class="p">[]</span>
+ <span class="k">for</span> <span class="n">arg</span> <span class="ow">in</span> <span class="n">arguments</span><span class="p">:</span>
+ <span class="n">arglist</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">arg</span><span class="p">)</span>
+ <span class="k">if</span> <span class="nb">str</span><span class="p">(</span><span class="n">arguments</span><span class="p">[</span><span class="n">arg</span><span class="p">])</span> <span class="ow">in</span> <span class="n">inputs</span><span class="p">:</span>
+ <span class="n">arglist</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">inputs</span><span class="p">[</span><span class="nb">str</span><span class="p">(</span><span class="n">arguments</span><span class="p">[</span><span class="n">arg</span><span class="p">])][</span><span class="s">"file"</span><span class="p">])</span>
+ <span class="k">elif</span> <span class="nb">str</span><span class="p">(</span><span class="n">arguments</span><span class="p">[</span><span class="n">arg</span><span class="p">])</span> <span class="ow">in</span> <span class="n">outputs</span><span class="p">:</span>
+ <span class="n">arglist</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">outputs</span><span class="p">[</span><span class="nb">str</span><span class="p">(</span><span class="n">arguments</span><span class="p">[</span><span class="n">arg</span><span class="p">])][</span><span class="s">"file"</span><span class="p">])</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="n">arglist</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="nb">str</span><span class="p">(</span><span class="n">arguments</span><span class="p">[</span><span class="n">arg</span><span class="p">]))</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">jobs</span><span class="p">[</span><span class="n">dax</span><span class="p">][</span><span class="n">jobname</span><span class="p">]</span><span class="o">.</span><span class="n">addArguments</span><span class="p">(</span><span class="o">*</span><span class="n">arglist</span><span class="p">)</span>
+ <span class="k">if</span> <span class="n">dependencies</span><span class="p">:</span>
+ <span class="k">for</span> <span class="n">depend</span> <span class="ow">in</span> <span class="n">dependencies</span><span class="p">:</span>
+ <span class="n">dax</span><span class="o">.</span><span class="n">depends</span><span class="p">(</span><span class="n">child</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">jobs</span><span class="p">[</span><span class="n">dax</span><span class="p">][</span><span class="n">jobname</span><span class="p">],</span> <span class="n">parent</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">jobs</span><span class="p">[</span><span class="n">dax</span><span class="p">][</span><span class="n">depend</span><span class="p">])</span>
+ <span class="k">if</span> <span class="n">label</span><span class="p">:</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">jobs</span><span class="p">[</span><span class="n">dax</span><span class="p">][</span><span class="n">jobname</span><span class="p">]</span><span class="o">.</span><span class="n">profile</span><span class="p">(</span><span class="n">Namespace</span><span class="o">.</span><span class="n">PEGASUS</span><span class="p">,</span> <span class="s">"label"</span><span class="p">,</span> <span class="n">label</span><span class="p">)</span>
+ <span class="k">if</span> <span class="n">walltime</span><span class="p">:</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">jobs</span><span class="p">[</span><span class="n">dax</span><span class="p">][</span><span class="n">jobname</span><span class="p">]</span><span class="o">.</span><span class="n">profile</span><span class="p">(</span><span class="n">Namespace</span><span class="o">.</span><span class="n">GLOBUS</span><span class="p">,</span> <span class="s">"maxwalltime"</span><span class="p">,</span> <span class="n">walltime</span><span class="p">)</span>
+ <span class="k">return</span>
+
+ <span class="k">def</span> <span class="nf">create</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> Creates a new pegasus submission directory based on the current timestamp,</span>
+<span class="sd"> and populates it with all required information to submit a pegasus job.</span>
+<span class="sd"> This function should be overloaded.</span>
+<span class="sd"> """</span>
+ <span class="k">return</span>
+
+
+<div class="viewcode-block" id="Statistics"><a class="viewcode-back" href="../../workflowstats.html#ih.workflow.Statistics">[docs]</a><span class="k">class</span> <span class="nc">Statistics</span><span class="p">(</span><span class="n">Workflow</span><span class="p">):</span>
+
+ <span class="sd">"""</span>
+<span class="sd"> A class specifically for statistics workflow</span>
+<span class="sd"> validation and submission.</span>
+<span class="sd"> """</span>
+
+ <span class="k">def</span> <span class="nf">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">jobhome</span><span class="p">,</span> <span class="n">basename</span><span class="p">,</span> <span class="n">validOnly</span> <span class="o">=</span> <span class="bp">False</span><span class="p">):</span>
+ <span class="nb">super</span><span class="p">(</span><span class="n">Statistics</span><span class="p">,</span> <span class="bp">self</span><span class="p">)</span><span class="o">.</span><span class="n">__init__</span><span class="p">(</span><span class="n">jobhome</span><span class="p">,</span> <span class="n">basename</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">configfile</span> <span class="o">=</span> <span class="n">jobhome</span> <span class="o">+</span> <span class="s">"/input/"</span> <span class="o">+</span> <span class="n">conf</span><span class="o">.</span><span class="n">configFile</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">statsfile</span> <span class="o">=</span> <span class="n">jobhome</span> <span class="o">+</span> <span class="s">"/input/"</span> <span class="o">+</span> <span class="n">conf</span><span class="o">.</span><span class="n">statsFile</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">dbfile</span> <span class="o">=</span> <span class="n">jobhome</span> <span class="o">+</span> <span class="s">"/"</span> <span class="o">+</span> <span class="n">basename</span> <span class="o">+</span> <span class="s">"/output/"</span> <span class="o">+</span> <span class="n">conf</span><span class="o">.</span><span class="n">outputdb</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">validOnly</span> <span class="o">=</span> <span class="n">validOnly</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">rawFiles</span> <span class="o">=</span> <span class="p">{}</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_loadInputFiles</span><span class="p">()</span>
+ <span class="k">return</span>
+
+ <span class="k">def</span> <span class="nf">_getImageTypes</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+ <span class="k">return</span> <span class="p">[</span><span class="n">x</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="k">for</span> <span class="n">x</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">db</span><span class="o">.</span><span class="n">execute</span><span class="p">(</span><span class="s">"select distinct imtype from images"</span><span class="p">)]</span>
+
+
+ <span class="k">def</span> <span class="nf">_loadInputFiles</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">validator</span> <span class="o">=</span> <span class="n">ih</span><span class="o">.</span><span class="n">validator</span><span class="o">.</span><span class="n">Statistics</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">statsfile</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">configfile</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">dbfile</span><span class="p">)</span>
+ <span class="k">if</span> <span class="ow">not</span> <span class="bp">self</span><span class="o">.</span><span class="n">validator</span><span class="o">.</span><span class="n">isValid</span><span class="p">()</span> <span class="ow">or</span> <span class="bp">self</span><span class="o">.</span><span class="n">validOnly</span><span class="p">:</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">validator</span><span class="o">.</span><span class="n">printErrors</span><span class="p">()</span>
+ <span class="n">sys</span><span class="o">.</span><span class="n">exit</span><span class="p">()</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">stats</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">validator</span><span class="o">.</span><span class="n">workflow</span><span class="o">.</span><span class="n">data</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">db</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">validator</span><span class="o">.</span><span class="n">db</span><span class="o">.</span><span class="n">conn</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">config</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">validator</span><span class="o">.</span><span class="n">config</span><span class="o">.</span><span class="n">data</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">rawFiles</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">validator</span><span class="o">.</span><span class="n">workflow</span><span class="o">.</span><span class="n">rawFiles</span>
+ <span class="k">return</span>
+
+ <span class="k">def</span> <span class="nf">_copyFiles</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> Copies all input files to the correct location.</span>
+<span class="sd"> """</span>
+ <span class="k">if</span> <span class="ow">not</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">exists</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">basepath</span> <span class="o">+</span> <span class="s">"/input/stats"</span><span class="p">):</span>
+ <span class="n">os</span><span class="o">.</span><span class="n">makedirs</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">basepath</span> <span class="o">+</span> <span class="s">"/input/stats"</span><span class="p">)</span>
+ <span class="n">shutil</span><span class="o">.</span><span class="n">copyfile</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">statsfile</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">basepath</span> <span class="o">+</span> <span class="s">"/input/templates/"</span> <span class="o">+</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">basename</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">statsfile</span><span class="p">))</span>
+ <span class="k">return</span>
+
+ <span class="k">def</span> <span class="nf">_loadFiles</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">loc</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> Loads all files (input and output) into the dax and the self.files variable</span>
+<span class="sd"> """</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">files</span><span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">dax</span><span class="p">]</span> <span class="o">=</span> <span class="p">{}</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">files</span><span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">dax</span><span class="p">][</span><span class="s">"raw"</span><span class="p">]</span> <span class="o">=</span> <span class="p">{</span><span class="s">"input"</span><span class="p">:</span> <span class="p">{},</span> <span class="s">"output"</span><span class="p">:</span> <span class="p">{}}</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_addFile</span><span class="p">(</span><span class="s">"output.db"</span><span class="p">,</span> <span class="s">"raw"</span><span class="p">,</span> <span class="s">"input"</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">basepath</span> <span class="o">+</span> <span class="s">"/output/output.db"</span><span class="p">)</span>
+ <span class="k">for</span> <span class="nb">type</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">stats</span><span class="p">[</span><span class="s">"workflows"</span><span class="p">]:</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">files</span><span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">dax</span><span class="p">][</span><span class="nb">type</span><span class="p">]</span> <span class="o">=</span> <span class="p">{</span><span class="s">"input"</span><span class="p">:</span> <span class="p">{},</span> <span class="s">"output"</span><span class="p">:</span> <span class="p">{}}</span>
+ <span class="k">for</span> <span class="n">f</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">rawFiles</span><span class="p">[</span><span class="nb">type</span><span class="p">]:</span>
+ <span class="n">shutil</span><span class="o">.</span><span class="n">copyfile</span><span class="p">(</span><span class="n">f</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">basepath</span> <span class="o">+</span> <span class="s">"/input/rawfiles/"</span> <span class="o">+</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">basename</span><span class="p">(</span><span class="n">f</span><span class="p">))</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_addFile</span><span class="p">(</span><span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">basename</span><span class="p">(</span><span class="n">f</span><span class="p">),</span> <span class="nb">type</span><span class="p">,</span> <span class="s">"input"</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">basepath</span> <span class="o">+</span> <span class="s">"/input/rawfiles/"</span> <span class="o">+</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">basename</span><span class="p">(</span><span class="n">f</span><span class="p">))</span>
+ <span class="k">return</span>
+
+ <span class="k">def</span> <span class="nf">_loadExecutables</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">os</span><span class="o">=</span><span class="s">"linux"</span><span class="p">,</span> <span class="n">arch</span><span class="o">=</span><span class="s">"x86_64"</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> Loads all executables (as specified in the conf) into</span>
+<span class="sd"> the dax, as well as the internal self.executables variable</span>
+<span class="sd"> """</span>
+ <span class="k">for</span> <span class="n">ex</span> <span class="ow">in</span> <span class="n">conf</span><span class="o">.</span><span class="n">valid</span><span class="p">:</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">executables</span><span class="p">[</span><span class="n">ex</span><span class="p">]</span> <span class="o">=</span> <span class="n">Executable</span><span class="p">(</span><span class="n">name</span><span class="o">=</span><span class="n">ex</span><span class="p">,</span> <span class="n">os</span><span class="o">=</span><span class="n">os</span><span class="p">,</span> <span class="n">arch</span><span class="o">=</span><span class="n">arch</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">executables</span><span class="p">[</span><span class="n">ex</span><span class="p">]</span><span class="o">.</span><span class="n">addPFN</span><span class="p">(</span><span class="n">PFN</span><span class="p">(</span><span class="s">"file://"</span> <span class="o">+</span> <span class="bp">self</span><span class="o">.</span><span class="n">config</span><span class="p">[</span><span class="s">"installdir"</span><span class="p">]</span> <span class="o">+</span> <span class="s">"/"</span> <span class="o">+</span> <span class="n">ex</span><span class="p">,</span> <span class="s">"local"</span><span class="p">))</span>
+ <span class="c">#if "cluster" in self.config:</span>
+ <span class="c"># self.executables[ex].addProfile(Profile(Namespace.PEGASUS, "clusters.size", self.config["cluster"]))</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">dax</span><span class="o">.</span><span class="n">addExecutable</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">executables</span><span class="p">[</span><span class="n">ex</span><span class="p">])</span>
+ <span class="k">return</span>
+
+ <span class="k">def</span> <span class="nf">_loadNotify</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+ <span class="k">if</span> <span class="s">"notify"</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">config</span><span class="p">:</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">dax</span><span class="o">.</span><span class="n">invoke</span><span class="p">(</span><span class="n">When</span><span class="o">.</span><span class="n">AT_END</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">basepath</span> <span class="o">+</span> <span class="s">"/input/stats/notify.sh"</span><span class="p">)</span>
+ <span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">basepath</span> <span class="o">+</span> <span class="s">"/input/stats/notify.sh"</span><span class="p">,</span> <span class="s">"w"</span><span class="p">)</span> <span class="k">as</span> <span class="n">wh</span><span class="p">:</span>
+ <span class="n">notify</span> <span class="o">=</span> <span class="n">textwrap</span><span class="o">.</span><span class="n">dedent</span><span class="p">(</span><span class="s">"""</span><span class="se">\</span>
+<span class="s"> #!/bin/bash</span>
+<span class="s"> </span><span class="si">%s</span><span class="s">/email -t </span><span class="si">%s</span><span class="s"> --report=pegasus-analyzer</span>
+<span class="s"> """</span> <span class="o">%</span> <span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">config</span><span class="p">[</span><span class="s">"notify"</span><span class="p">][</span><span class="s">"pegasus_home"</span><span class="p">],</span> <span class="bp">self</span><span class="o">.</span><span class="n">config</span><span class="p">[</span><span class="s">"notify"</span><span class="p">][</span><span class="s">"email"</span><span class="p">]))</span>
+ <span class="n">wh</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="n">notify</span><span class="p">)</span>
+ <span class="n">os</span><span class="o">.</span><span class="n">chmod</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">basepath</span> <span class="o">+</span> <span class="s">"/input/stats/notify.sh"</span><span class="p">,</span> <span class="mo">0755</span><span class="p">)</span>
+ <span class="k">return</span>
+
+ <span class="k">def</span> <span class="nf">_loadJobInputs</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">job</span><span class="p">,</span> <span class="nb">type</span><span class="p">,</span> <span class="n">basename</span><span class="p">,</span> <span class="n">extension</span><span class="p">,</span> <span class="n">save</span> <span class="o">=</span> <span class="bp">False</span><span class="p">):</span>
+ <span class="n">inputs</span> <span class="o">=</span> <span class="p">{}</span>
+ <span class="k">for</span> <span class="n">i</span><span class="p">,</span><span class="nb">input</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="n">job</span><span class="p">[</span><span class="s">"inputs"</span><span class="p">]):</span>
+ <span class="n">ftype</span> <span class="o">=</span> <span class="n">conf</span><span class="o">.</span><span class="n">valid</span><span class="p">[</span><span class="n">job</span><span class="p">[</span><span class="s">"executable"</span><span class="p">]][</span><span class="s">"inputs"</span><span class="p">][</span><span class="n">i</span><span class="p">]</span>
+ <span class="k">if</span> <span class="nb">input</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">rawFiles</span><span class="p">[</span><span class="nb">type</span><span class="p">]:</span>
+ <span class="n">inputs</span><span class="p">[</span><span class="nb">input</span><span class="p">]</span> <span class="o">=</span> <span class="p">{</span><span class="s">"file"</span><span class="p">:</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">basename</span><span class="p">(</span><span class="nb">input</span><span class="p">),</span> <span class="s">"transfer"</span><span class="p">:</span> <span class="n">save</span><span class="p">}</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="n">ex</span> <span class="o">=</span> <span class="n">extension</span> <span class="k">if</span> <span class="n">job</span><span class="p">[</span><span class="s">"name"</span><span class="p">]</span> <span class="o">==</span> <span class="bp">self</span><span class="o">.</span><span class="n">workflow</span><span class="p">[</span><span class="s">"workflows"</span><span class="p">][</span><span class="nb">type</span><span class="p">][</span><span class="mi">0</span><span class="p">][</span><span class="s">"name"</span><span class="p">]</span> <span class="k">else</span> <span class="n">conf</span><span class="o">.</span><span class="n">fileExtensions</span><span class="p">[</span><span class="n">ftype</span><span class="p">]</span>
+ <span class="n">inputs</span><span class="p">[</span><span class="nb">input</span><span class="p">]</span> <span class="o">=</span> <span class="p">{</span><span class="s">"file"</span><span class="p">:</span> <span class="n">basename</span> <span class="o">+</span> <span class="s">"_"</span> <span class="o">+</span> <span class="nb">input</span> <span class="o">+</span> <span class="n">ex</span><span class="p">,</span> <span class="s">"transfer"</span><span class="p">:</span> <span class="n">save</span><span class="p">}</span>
+ <span class="k">return</span> <span class="n">inputs</span>
+
+ <span class="k">def</span> <span class="nf">_loadJobInputs</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">job</span><span class="p">,</span> <span class="nb">type</span><span class="p">,</span> <span class="n">save</span> <span class="o">=</span> <span class="bp">False</span><span class="p">):</span>
+ <span class="n">inputs</span> <span class="o">=</span> <span class="p">{</span><span class="s">"output.db"</span><span class="p">:</span> <span class="p">{</span><span class="s">"file"</span><span class="p">:</span> <span class="s">"output.db"</span><span class="p">,</span> <span class="s">"transfer"</span><span class="p">:</span> <span class="bp">True</span><span class="p">}}</span>
+ <span class="k">for</span> <span class="n">i</span><span class="p">,</span><span class="nb">input</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="n">job</span><span class="p">[</span><span class="s">"inputs"</span><span class="p">]):</span>
+ <span class="n">ftype</span> <span class="o">=</span> <span class="n">conf</span><span class="o">.</span><span class="n">valid</span><span class="p">[</span><span class="n">job</span><span class="p">[</span><span class="s">"executable"</span><span class="p">]][</span><span class="s">"inputs"</span><span class="p">][</span><span class="n">i</span><span class="p">]</span>
+ <span class="k">if</span> <span class="nb">input</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">rawFiles</span><span class="p">[</span><span class="nb">type</span><span class="p">]:</span>
+ <span class="n">inputs</span><span class="p">[</span><span class="nb">input</span><span class="p">]</span> <span class="o">=</span> <span class="p">{</span><span class="s">"file"</span><span class="p">:</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">basename</span><span class="p">(</span><span class="nb">input</span><span class="p">),</span> <span class="s">"transfer"</span><span class="p">:</span> <span class="n">save</span><span class="p">}</span>
+ <span class="k">return</span> <span class="n">inputs</span>
+
+ <span class="k">def</span> <span class="nf">_createDax</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">loc</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> Loads all jobs into the dax, and then writes the dax</span>
+<span class="sd"> to input/loc/stats.dax</span>
+<span class="sd"> """</span>
+ <span class="n">serial</span> <span class="o">=</span> <span class="p">[]</span>
+ <span class="k">if</span> <span class="s">"maxwalltime"</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">config</span><span class="p">:</span>
+ <span class="k">if</span> <span class="s">"stats"</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">config</span><span class="p">[</span><span class="s">"maxwalltime"</span><span class="p">]:</span>
+ <span class="n">maxwalltime</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">config</span><span class="p">[</span><span class="s">"maxwalltime"</span><span class="p">][</span><span class="s">"stats"</span><span class="p">]</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="n">maxwalltime</span> <span class="o">=</span> <span class="bp">None</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="n">maxwalltime</span> <span class="o">=</span> <span class="bp">None</span>
+ <span class="k">for</span> <span class="nb">type</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">stats</span><span class="p">[</span><span class="s">"workflows"</span><span class="p">]:</span>
+ <span class="k">for</span> <span class="n">job</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">stats</span><span class="p">[</span><span class="s">"workflows"</span><span class="p">][</span><span class="nb">type</span><span class="p">]:</span>
+ <span class="n">jobname</span> <span class="o">=</span> <span class="nb">type</span> <span class="o">+</span> <span class="s">"_"</span> <span class="o">+</span> <span class="n">job</span><span class="p">[</span><span class="s">"name"</span><span class="p">]</span>
+ <span class="n">job</span><span class="p">[</span><span class="s">"arguments"</span><span class="p">][</span><span class="s">"--intable"</span><span class="p">]</span> <span class="o">=</span> <span class="nb">type</span> <span class="o">+</span> <span class="s">"_"</span> <span class="o">+</span> <span class="n">job</span><span class="p">[</span><span class="s">"arguments"</span><span class="p">][</span><span class="s">"--intable"</span><span class="p">]</span> <span class="k">if</span> <span class="n">job</span><span class="p">[</span><span class="s">"arguments"</span><span class="p">][</span><span class="s">"--intable"</span><span class="p">]</span> <span class="o">!=</span> <span class="s">"images"</span> <span class="k">else</span> <span class="n">job</span><span class="p">[</span><span class="s">"arguments"</span><span class="p">][</span><span class="s">"--intable"</span><span class="p">]</span>
+ <span class="n">job</span><span class="p">[</span><span class="s">"arguments"</span><span class="p">][</span><span class="s">"--outtable"</span><span class="p">]</span> <span class="o">=</span> <span class="nb">type</span> <span class="o">+</span> <span class="s">"_"</span> <span class="o">+</span> <span class="n">job</span><span class="p">[</span><span class="s">"arguments"</span><span class="p">][</span><span class="s">"--outtable"</span><span class="p">]</span>
+ <span class="n">job</span><span class="p">[</span><span class="s">"arguments"</span><span class="p">][</span><span class="s">"--db"</span><span class="p">]</span> <span class="o">=</span> <span class="s">"output.db"</span>
+ <span class="n">inputs</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_loadJobInputs</span><span class="p">(</span><span class="n">job</span><span class="p">,</span> <span class="nb">type</span><span class="p">)</span>
+ <span class="n">outputs</span> <span class="o">=</span> <span class="p">{}</span>
+ <span class="n">depends</span> <span class="o">=</span> <span class="p">[</span><span class="nb">type</span> <span class="o">+</span> <span class="s">"_"</span> <span class="o">+</span> <span class="n">depend</span> <span class="k">for</span> <span class="n">depend</span> <span class="ow">in</span> <span class="n">job</span><span class="p">[</span><span class="s">"depends"</span><span class="p">]]</span> <span class="k">if</span> <span class="s">"depends"</span> <span class="ow">in</span> <span class="n">job</span> <span class="k">else</span> <span class="n">serial</span>
+ <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">stats</span><span class="p">[</span><span class="s">"workflows"</span><span class="p">][</span><span class="nb">type</span><span class="p">]</span><span class="o">.</span><span class="n">index</span><span class="p">(</span><span class="n">job</span><span class="p">)</span> <span class="o">==</span> <span class="nb">len</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">stats</span><span class="p">[</span><span class="s">"workflows"</span><span class="p">][</span><span class="nb">type</span><span class="p">])</span> <span class="o">-</span> <span class="mi">1</span><span class="p">:</span>
+ <span class="n">serial</span> <span class="o">=</span> <span class="p">[</span><span class="n">jobname</span><span class="p">]</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="n">serial</span> <span class="o">=</span> <span class="p">[]</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_addJob</span><span class="p">(</span><span class="n">jobname</span><span class="p">,</span> <span class="n">job</span><span class="p">[</span><span class="s">"executable"</span><span class="p">],</span> <span class="n">inputs</span><span class="p">,</span> <span class="n">outputs</span><span class="p">,</span> <span class="n">job</span><span class="p">[</span><span class="s">"arguments"</span><span class="p">],</span> <span class="n">depends</span><span class="p">,</span> <span class="n">walltime</span> <span class="o">=</span> <span class="n">maxwalltime</span><span class="p">)</span>
+ <span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">basepath</span> <span class="o">+</span> <span class="s">"/"</span> <span class="o">+</span> <span class="n">loc</span> <span class="o">+</span> <span class="s">"/stats.dax"</span><span class="p">,</span> <span class="s">"w"</span><span class="p">)</span> <span class="k">as</span> <span class="n">wh</span><span class="p">:</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">dax</span><span class="o">.</span><span class="n">writeXML</span><span class="p">(</span><span class="n">wh</span><span class="p">)</span>
+ <span class="k">return</span>
+
+ <span class="k">def</span> <span class="nf">_createReplica</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">loc</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> Creates the pegasus configuration replica catalog. input/conf.rc</span>
+<span class="sd"> """</span>
+ <span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">basepath</span> <span class="o">+</span> <span class="s">"/"</span> <span class="o">+</span> <span class="n">loc</span> <span class="o">+</span> <span class="s">"/conf.rc"</span><span class="p">,</span> <span class="s">"w"</span><span class="p">)</span> <span class="k">as</span> <span class="n">wh</span><span class="p">:</span>
+ <span class="n">pegasusrc</span> <span class="o">=</span> <span class="n">textwrap</span><span class="o">.</span><span class="n">dedent</span><span class="p">(</span><span class="s">"""</span><span class="se">\</span>
+<span class="s"> pegasus.catalog.site = XML</span>
+<span class="s"> pegasus.catalog.site.file = </span><span class="si">%s</span><span class="s">/sites.xml</span>
+<span class="s"> </span>
+<span class="s"> pegasus.condor.logs.symlink = false</span>
+<span class="s"> </span>
+<span class="s"> pegasus.transfer.links = true</span>
+<span class="s"> </span>
+<span class="s"> pegasus.data.configuration = sharedfs</span>
+<span class="s"> </span>
+<span class="s"> """</span> <span class="o">%</span> <span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">basepath</span> <span class="o">+</span> <span class="s">"/"</span> <span class="o">+</span> <span class="n">loc</span><span class="p">))</span>
+ <span class="n">wh</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="n">pegasusrc</span><span class="p">)</span>
+ <span class="k">return</span>
+
+ <span class="k">def</span> <span class="nf">_createSites</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">loc</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> Creates the pegasus site catalog. input/sites.xml</span>
+<span class="sd"> """</span>
+ <span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">basepath</span> <span class="o">+</span> <span class="s">"/"</span> <span class="o">+</span> <span class="n">loc</span> <span class="o">+</span> <span class="s">"/sites.xml"</span><span class="p">,</span> <span class="s">"w"</span><span class="p">)</span> <span class="k">as</span> <span class="n">wh</span><span class="p">:</span>
+ <span class="n">sites</span> <span class="o">=</span> <span class="s">"""</span><span class="se">\</span>
+<span class="s"> <sitecatalog xmlns="http://pegasus.isi.edu/schema/sitecatalog" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://pegasus.isi.edu/schema/sitecatalog http://pegasus.isi.edu/schema/sc-4.0.xsd" version="4.0"></span>
+<span class="s"> </span>
+<span class="s"> <site handle="local" arch="x86_64" os="LINUX"></span>
+<span class="s"> <directory type="shared-scratch" path="</span><span class="si">%s</span><span class="s">"></span>
+<span class="s"> <file-server operation="all" url="file://</span><span class="si">%s</span><span class="s">" /></span>
+<span class="s"> </directory></span>
+<span class="s"> <directory type="local-storage" path="</span><span class="si">%s</span><span class="s">"></span>
+<span class="s"> <file-server operation="all" url="file://</span><span class="si">%s</span><span class="s">" /></span>
+<span class="s"> </directory></span>
+<span class="s"> """</span> <span class="o">%</span> <span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">basepath</span> <span class="o">+</span> <span class="s">"/work/stats/"</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">basepath</span> <span class="o">+</span> <span class="s">"/work/stats/"</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">basepath</span> <span class="o">+</span> <span class="s">"/output/"</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">basepath</span> <span class="o">+</span> <span class="s">"/output/"</span><span class="p">)</span>
+ <span class="k">for</span> <span class="n">namespace</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">config</span><span class="p">[</span><span class="s">"profile"</span><span class="p">]:</span>
+ <span class="k">for</span> <span class="n">key</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">config</span><span class="p">[</span><span class="s">"profile"</span><span class="p">][</span><span class="n">namespace</span><span class="p">]:</span>
+ <span class="n">val</span> <span class="o">=</span> <span class="s">":"</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">config</span><span class="p">[</span><span class="s">"profile"</span><span class="p">][</span><span class="n">namespace</span><span class="p">][</span><span class="n">key</span><span class="p">])</span> <span class="k">if</span> <span class="s">"path"</span> <span class="ow">in</span> <span class="n">key</span><span class="o">.</span><span class="n">lower</span><span class="p">()</span> <span class="k">else</span> <span class="bp">self</span><span class="o">.</span><span class="n">config</span><span class="p">[</span><span class="s">"profile"</span><span class="p">][</span><span class="n">namespace</span><span class="p">][</span><span class="n">key</span><span class="p">]</span>
+ <span class="n">sites</span> <span class="o">+=</span> <span class="s">"""</span><span class="se">\n\t</span><span class="s"><profile namespace="</span><span class="si">%s</span><span class="s">" key="</span><span class="si">%s</span><span class="s">"></span><span class="si">%s</span><span class="s"></profile> """</span> <span class="o">%</span> <span class="p">(</span><span class="n">namespace</span><span class="p">,</span> <span class="n">key</span><span class="p">,</span> <span class="n">val</span><span class="p">)</span>
+ <span class="n">sites</span> <span class="o">+=</span> <span class="s">"</site></sitecatalog>"</span>
+ <span class="n">sites</span> <span class="o">=</span> <span class="n">sites</span><span class="o">.</span><span class="n">replace</span><span class="p">(</span><span class="s">"</span><span class="se">\n</span><span class="s">"</span><span class="p">,</span><span class="s">""</span><span class="p">)</span>
+ <span class="n">wh</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s">"</span><span class="se">\n</span><span class="s">"</span><span class="o">.</span><span class="n">join</span><span class="p">([</span><span class="n">line</span> <span class="k">for</span> <span class="n">line</span> <span class="ow">in</span> <span class="n">xml</span><span class="o">.</span><span class="n">dom</span><span class="o">.</span><span class="n">minidom</span><span class="o">.</span><span class="n">parseString</span><span class="p">(</span><span class="n">sites</span><span class="p">)</span><span class="o">.</span><span class="n">toprettyxml</span><span class="p">()</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s">'</span><span class="se">\n</span><span class="s">'</span><span class="p">)</span> <span class="k">if</span> <span class="n">line</span><span class="o">.</span><span class="n">strip</span><span class="p">()]))</span>
+ <span class="k">return</span>
+
+ <span class="k">def</span> <span class="nf">_createSubmit</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">loc</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> Creates the pegasus submit script. submit.sh</span>
+<span class="sd"> """</span>
+ <span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">basepath</span> <span class="o">+</span> <span class="s">"/"</span> <span class="o">+</span> <span class="n">loc</span> <span class="o">+</span> <span class="s">"/submit.sh"</span><span class="p">,</span> <span class="s">"w"</span><span class="p">)</span> <span class="k">as</span> <span class="n">wh</span><span class="p">:</span>
+ <span class="n">submit</span> <span class="o">=</span> <span class="n">textwrap</span><span class="o">.</span><span class="n">dedent</span><span class="p">(</span><span class="s">"""</span><span class="se">\</span>
+<span class="s"> #!/bin/bash</span>
+<span class="s"> </span>
+<span class="s"> plan=`pegasus-plan </span><span class="se">\\</span><span class="s"></span>
+<span class="s"> --conf "</span><span class="si">%s</span><span class="s">" </span><span class="se">\\</span><span class="s"></span>
+<span class="s"> --sites local </span><span class="se">\\</span><span class="s"></span>
+<span class="s"> --dir "</span><span class="si">%s</span><span class="s">" </span><span class="se">\\</span><span class="s"></span>
+<span class="s"> --output-site local </span><span class="se">\\</span><span class="s"></span>
+<span class="s"> --dax "</span><span class="si">%s</span><span class="s">" </span><span class="se">\\</span><span class="s"></span>
+<span class="s"> --randomdir </span><span class="se">\\</span><span class="s">"""</span> <span class="o">%</span> <span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">basepath</span> <span class="o">+</span> <span class="s">"/"</span> <span class="o">+</span> <span class="n">loc</span> <span class="o">+</span> <span class="s">"/conf.rc"</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">basepath</span> <span class="o">+</span> <span class="s">"/work/stats"</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">basepath</span> <span class="o">+</span> <span class="s">"/"</span> <span class="o">+</span> <span class="n">loc</span> <span class="o">+</span> <span class="s">"/stats.dax"</span><span class="p">))</span>
+ <span class="k">if</span> <span class="s">"cluster"</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">config</span><span class="p">:</span>
+ <span class="n">submit</span> <span class="o">+=</span> <span class="s">"""--cluster horizontal </span><span class="se">\\\n</span><span class="s">"""</span>
+ <span class="n">submit</span> <span class="o">+=</span> <span class="n">textwrap</span><span class="o">.</span><span class="n">dedent</span><span class="p">(</span><span class="s">"""</span><span class="se">\</span>
+<span class="s"> --submit`</span>
+<span class="s"> </span>
+<span class="s"> status=`echo "$plan" | grep pegasus-status | tr -s ' '| cut -d ' ' -f 6`</span>
+<span class="s"> echo -e "#!/bin/bash</span>
+<span class="s"> pegasus-status -l $status" > status.sh</span>
+<span class="s"> chmod 744 status.sh</span>
+<span class="s"> </span>
+<span class="s"> remove=`echo "$plan" | grep pegasus-remove | tr -s ' '| cut -d ' ' -f 5`</span>
+<span class="s"> echo -e "#!/bin/bash</span>
+<span class="s"> pegasus-remove $remove" > remove.sh </span>
+<span class="s"> chmod 744 remove.sh</span>
+<span class="s"> </span>
+<span class="s"> echo "$plan"</span>
+<span class="s"> echo "Alternatively, you can use the status & remove scripts in the current directory!"</span>
+<span class="s"> </span>
+<span class="s"> """</span><span class="p">)</span>
+ <span class="n">wh</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="n">submit</span><span class="p">)</span>
+ <span class="n">os</span><span class="o">.</span><span class="n">chmod</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">basepath</span> <span class="o">+</span> <span class="s">"/"</span> <span class="o">+</span> <span class="n">loc</span> <span class="o">+</span> <span class="s">"/submit.sh"</span><span class="p">,</span> <span class="mo">0755</span><span class="p">)</span>
+ <span class="k">return</span>
+
+<div class="viewcode-block" id="Statistics.create"><a class="viewcode-back" href="../../workflowstats.html#ih.workflow.Statistics.create">[docs]</a> <span class="k">def</span> <span class="nf">create</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> Creates a new pegasus submission directory based on the current timestamp,</span>
+<span class="sd"> and populates it with all required information to submit a pegasus job.</span>
+<span class="sd"> """</span>
+ <span class="n">loc</span> <span class="o">=</span> <span class="s">"/input/stats/"</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_createSetup</span><span class="p">()</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_copyFiles</span><span class="p">()</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_loadFiles</span><span class="p">(</span><span class="n">loc</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_loadExecutables</span><span class="p">()</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_loadNotify</span><span class="p">()</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_createDax</span><span class="p">(</span><span class="n">loc</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_createReplica</span><span class="p">(</span><span class="n">loc</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_createSites</span><span class="p">(</span><span class="n">loc</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_createSubmit</span><span class="p">(</span><span class="n">loc</span><span class="p">)</span>
+ <span class="k">return</span>
+
+
+
+
+ </div></div>
+<div class="viewcode-block" id="ImageProcessor"><a class="viewcode-back" href="../../workflowimage.html#ih.workflow.ImageProcessor">[docs]</a><span class="k">class</span> <span class="nc">ImageProcessor</span><span class="p">(</span><span class="n">Workflow</span><span class="p">):</span>
+
+ <span class="sd">"""</span>
+<span class="sd"> A class specifically for image processing workflow</span>
+<span class="sd"> validation and submission.</span>
+<span class="sd"> """</span>
+
+ <span class="k">def</span> <span class="nf">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">jobhome</span><span class="p">,</span> <span class="n">basename</span> <span class="o">=</span> <span class="bp">None</span><span class="p">,</span> <span class="n">validOnly</span> <span class="o">=</span> <span class="bp">False</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> :param jobhome: The base directory for job submission.</span>
+<span class="sd"> :type jobhome: str</span>
+<span class="sd"> </span>
+<span class="sd"> Creates a Workflow class based on the input directory. Loads and validates all input files,</span>
+<span class="sd"> and quits out if something doesn't exist or is defined innapropriately.</span>
+<span class="sd"> """</span>
+ <span class="nb">super</span><span class="p">(</span><span class="n">ImageProcessor</span><span class="p">,</span> <span class="bp">self</span><span class="p">)</span><span class="o">.</span><span class="n">__init__</span><span class="p">(</span><span class="n">jobhome</span><span class="p">,</span> <span class="n">basename</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">validOnly</span> <span class="o">=</span> <span class="n">validOnly</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">workfile</span> <span class="o">=</span> <span class="n">jobhome</span> <span class="o">+</span> <span class="s">"/input/"</span> <span class="o">+</span> <span class="n">conf</span><span class="o">.</span><span class="n">workflowFile</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">metafile</span> <span class="o">=</span> <span class="n">jobhome</span> <span class="o">+</span> <span class="s">"/input/"</span> <span class="o">+</span> <span class="n">conf</span><span class="o">.</span><span class="n">dbFile</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">configfile</span> <span class="o">=</span> <span class="n">jobhome</span> <span class="o">+</span> <span class="s">"/input/"</span> <span class="o">+</span> <span class="n">conf</span><span class="o">.</span><span class="n">configFile</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_loadInputFiles</span><span class="p">()</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">exdax</span> <span class="o">=</span> <span class="n">ADAG</span><span class="p">(</span><span class="s">"extract-"</span> <span class="o">+</span> <span class="bp">self</span><span class="o">.</span><span class="n">jobname</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">jobs</span><span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">exdax</span><span class="p">]</span> <span class="o">=</span> <span class="p">{}</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">files</span><span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">exdax</span><span class="p">]</span> <span class="o">=</span> <span class="p">{}</span>
+ <span class="k">return</span>
+
+ <span class="k">def</span> <span class="nf">_loadInputFiles</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> Loads the input files into the appropriate variables</span>
+<span class="sd"> """</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">validator</span> <span class="o">=</span> <span class="n">ih</span><span class="o">.</span><span class="n">validator</span><span class="o">.</span><span class="n">ImageProcessor</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">workfile</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">configfile</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">metafile</span><span class="p">)</span>
+ <span class="k">if</span> <span class="ow">not</span> <span class="bp">self</span><span class="o">.</span><span class="n">validator</span><span class="o">.</span><span class="n">isValid</span><span class="p">()</span> <span class="ow">or</span> <span class="bp">self</span><span class="o">.</span><span class="n">validOnly</span><span class="p">:</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">validator</span><span class="o">.</span><span class="n">printErrors</span><span class="p">()</span>
+ <span class="n">sys</span><span class="o">.</span><span class="n">exit</span><span class="p">()</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">workflow</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">validator</span><span class="o">.</span><span class="n">workflow</span><span class="o">.</span><span class="n">data</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">metadata</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">validator</span><span class="o">.</span><span class="n">db</span><span class="o">.</span><span class="n">conn</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">config</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">validator</span><span class="o">.</span><span class="n">config</span><span class="o">.</span><span class="n">data</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">rawFiles</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">validator</span><span class="o">.</span><span class="n">workflow</span><span class="o">.</span><span class="n">rawFiles</span>
+ <span class="k">return</span>
+
+ <span class="k">def</span> <span class="nf">_getImageTypes</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> Convenience function to get all image types from the database.</span>
+<span class="sd"> """</span>
+ <span class="k">return</span> <span class="p">[</span><span class="n">x</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="k">for</span> <span class="n">x</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">metadata</span><span class="o">.</span><span class="n">execute</span><span class="p">(</span><span class="s">"select distinct imtype from images"</span><span class="p">)]</span>
+
+ <span class="k">def</span> <span class="nf">_copyFiles</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> Copies all input files to the correct location.</span>
+<span class="sd"> """</span>
+ <span class="k">if</span> <span class="ow">not</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">exists</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">basepath</span> <span class="o">+</span> <span class="s">"/input/imgproc"</span><span class="p">):</span>
+ <span class="n">os</span><span class="o">.</span><span class="n">makedirs</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">basepath</span> <span class="o">+</span> <span class="s">"/input/imgproc"</span><span class="p">)</span>
+ <span class="n">shutil</span><span class="o">.</span><span class="n">copyfile</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">workfile</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">basepath</span> <span class="o">+</span> <span class="s">"/input/templates/"</span> <span class="o">+</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">basename</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">workfile</span><span class="p">))</span>
+ <span class="n">shutil</span><span class="o">.</span><span class="n">copyfile</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">configfile</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">basepath</span> <span class="o">+</span> <span class="s">"/input/templates/"</span> <span class="o">+</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">basename</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">configfile</span><span class="p">))</span>
+ <span class="n">shutil</span><span class="o">.</span><span class="n">copyfile</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">metafile</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">basepath</span> <span class="o">+</span> <span class="s">"/output/output.db"</span><span class="p">)</span>
+ <span class="k">for</span> <span class="nb">type</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">rawFiles</span><span class="p">:</span>
+ <span class="k">for</span> <span class="nb">input</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">rawFiles</span><span class="p">[</span><span class="nb">type</span><span class="p">]:</span>
+ <span class="n">shutil</span><span class="o">.</span><span class="n">copyfile</span><span class="p">(</span><span class="nb">input</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">basepath</span> <span class="o">+</span> <span class="s">"/input/rawfiles/"</span> <span class="o">+</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">basename</span><span class="p">(</span><span class="nb">input</span><span class="p">))</span>
+ <span class="k">return</span>
+
+ <span class="k">def</span> <span class="nf">_loadFiles</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">loc</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> Loads all files (input and output) into the dax and the self.files variable</span>
+<span class="sd"> """</span>
+ <span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">basepath</span> <span class="o">+</span> <span class="s">"/input/rawfiles/extract.json"</span><span class="p">,</span> <span class="s">"w"</span><span class="p">)</span> <span class="k">as</span> <span class="n">wh</span><span class="p">:</span>
+ <span class="n">json</span><span class="o">.</span><span class="n">dump</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">workflow</span><span class="p">[</span><span class="s">"extract"</span><span class="p">],</span> <span class="n">wh</span><span class="p">)</span>
+ <span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">basepath</span> <span class="o">+</span> <span class="s">"/"</span> <span class="o">+</span> <span class="n">loc</span> <span class="o">+</span> <span class="s">"/map.rc"</span><span class="p">,</span> <span class="s">"w"</span><span class="p">)</span> <span class="k">as</span> <span class="n">wh</span><span class="p">:</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">exInput</span> <span class="o">=</span> <span class="p">{</span><span class="s">"db"</span><span class="p">:</span> <span class="s">"img.db"</span><span class="p">,</span> <span class="s">"extract.json"</span><span class="p">:</span> <span class="s">"extract.json"</span><span class="p">}</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">files</span><span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">dax</span><span class="p">]</span> <span class="o">=</span> <span class="p">{}</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">files</span><span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">exdax</span><span class="p">]</span> <span class="o">=</span> <span class="p">{}</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">files</span><span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">exdax</span><span class="p">][</span><span class="s">"all"</span><span class="p">]</span> <span class="o">=</span> <span class="p">{</span><span class="s">"input"</span><span class="p">:</span> <span class="p">{},</span> <span class="s">"output"</span><span class="p">:</span> <span class="p">{}}</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">files</span><span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">dax</span><span class="p">][</span><span class="s">"raw"</span><span class="p">]</span> <span class="o">=</span> <span class="p">{</span><span class="s">"input"</span><span class="p">:</span> <span class="p">{},</span> <span class="s">"output"</span><span class="p">:</span> <span class="p">{}}</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_addFile</span><span class="p">(</span><span class="s">"img.db"</span><span class="p">,</span> <span class="s">"raw"</span><span class="p">,</span> <span class="s">"input"</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">basepath</span> <span class="o">+</span> <span class="s">"/output/output.db"</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_addFile</span><span class="p">(</span><span class="s">"img.db"</span><span class="p">,</span> <span class="s">"all"</span><span class="p">,</span> <span class="s">"input"</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">basepath</span> <span class="o">+</span> <span class="s">"/output/output.db"</span><span class="p">,</span> <span class="n">dax</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">exdax</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_addFile</span><span class="p">(</span><span class="s">"img.log"</span><span class="p">,</span> <span class="s">"raw"</span><span class="p">,</span> <span class="s">"output"</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">basepath</span> <span class="o">+</span> <span class="s">"/output/imgproc.log"</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_addFile</span><span class="p">(</span><span class="s">"extract.json"</span><span class="p">,</span> <span class="s">"raw"</span><span class="p">,</span> <span class="s">"input"</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">basepath</span> <span class="o">+</span> <span class="s">"/input/rawfiles/extract.json"</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_addFile</span><span class="p">(</span><span class="s">"extract.json"</span><span class="p">,</span> <span class="s">"all"</span><span class="p">,</span> <span class="s">"input"</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">basepath</span> <span class="o">+</span> <span class="s">"/input/rawfiles/extract.json"</span><span class="p">,</span> <span class="n">dax</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">exdax</span><span class="p">)</span>
+ <span class="k">for</span> <span class="nb">type</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">workflow</span><span class="p">[</span><span class="s">"workflows"</span><span class="p">]:</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">files</span><span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">dax</span><span class="p">][</span><span class="nb">type</span><span class="p">]</span> <span class="o">=</span> <span class="p">{</span><span class="s">"input"</span><span class="p">:</span> <span class="p">{},</span> <span class="s">"output"</span><span class="p">:</span> <span class="p">{}}</span>
+ <span class="k">for</span> <span class="nb">input</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">rawFiles</span><span class="p">[</span><span class="nb">type</span><span class="p">]:</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_addFile</span><span class="p">(</span><span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">basename</span><span class="p">(</span><span class="nb">input</span><span class="p">),</span> <span class="nb">type</span><span class="p">,</span> <span class="s">"input"</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">basepath</span> <span class="o">+</span> <span class="s">"/input/rawfiles/"</span> <span class="o">+</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">basename</span><span class="p">(</span><span class="nb">input</span><span class="p">))</span>
+ <span class="n">wh</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s">"img.log file://"</span> <span class="o">+</span> <span class="bp">self</span><span class="o">.</span><span class="n">basepath</span> <span class="o">+</span> <span class="s">"/output/imgproc.log pool=</span><span class="se">\"</span><span class="s">local</span><span class="se">\"\n</span><span class="s">"</span><span class="p">)</span>
+ <span class="n">inputImages</span> <span class="o">=</span> <span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">workflow</span><span class="p">[</span><span class="s">"workflows"</span><span class="p">][</span><span class="nb">type</span><span class="p">][</span><span class="mi">0</span><span class="p">][</span><span class="s">"inputs"</span><span class="p">][</span><span class="n">i</span><span class="p">]</span> <span class="k">for</span> <span class="n">i</span><span class="p">,</span><span class="n">x</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="n">conf</span><span class="o">.</span><span class="n">valid</span><span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">workflow</span><span class="p">[</span><span class="s">"workflows"</span><span class="p">][</span><span class="nb">type</span><span class="p">][</span><span class="mi">0</span><span class="p">][</span><span class="s">"executable"</span><span class="p">]][</span><span class="s">"inputs"</span><span class="p">])</span> <span class="k">if</span> <span class="n">x</span> <span class="o">==</span> <span class="s">"image"</span><span class="p">]</span>
+ <span class="n">outputImages</span> <span class="o">=</span> <span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">workflow</span><span class="p">[</span><span class="s">"workflows"</span><span class="p">][</span><span class="nb">type</span><span class="p">][</span><span class="n">z</span><span class="p">][</span><span class="s">"outputs"</span><span class="p">][</span><span class="n">i</span><span class="p">]</span> <span class="k">for</span> <span class="n">z</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="mi">0</span><span class="p">,</span> <span class="nb">len</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">workflow</span><span class="p">[</span><span class="s">"workflows"</span><span class="p">][</span><span class="nb">type</span><span class="p">]))</span> <span class="k">for</span> <span class="n">i</span><span class="p">,</span><span class="n">x</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="n">conf</span><span class="o">.</span><span class="n">valid</span><span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">workflow</span><span class="p">[</span><span class="s">"workflows"</span><span class="p">][</span><span class="nb">type</span><span class="p">][</span><span class="n">z</span><span class="p">][</span><span class="s">"executable"</span><span class="p">]][</span><span class="s">"outputs"</span><span class="p">])</span> <span class="k">if</span> <span class="n">x</span> <span class="o">==</span> <span class="s">"image"</span><span class="p">]</span>
+ <span class="n">outputFiles</span> <span class="o">=</span> <span class="nb">dict</span><span class="p">((</span><span class="bp">self</span><span class="o">.</span><span class="n">workflow</span><span class="p">[</span><span class="s">"workflows"</span><span class="p">][</span><span class="nb">type</span><span class="p">][</span><span class="n">z</span><span class="p">][</span><span class="s">"outputs"</span><span class="p">][</span><span class="n">i</span><span class="p">],</span> <span class="n">conf</span><span class="o">.</span><span class="n">fileExtensions</span><span class="p">[</span><span class="n">conf</span><span class="o">.</span><span class="n">valid</span><span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">workflow</span><span class="p">[</span><span class="s">"workflows"</span><span class="p">][</span><span class="nb">type</span><span class="p">][</span><span class="n">z</span><span class="p">][</span><span class="s">"executable"</span><span class="p">]][</span><span class="s">"outputs"</span><span class="p">][</span><span class="n">i</span><span class="p">]])</span> <span class="k">for</span> <span class="n">z</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="mi">0</span><span class="p">,</span> <span class="nb">len</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">workflow</span><span class="p">[</span><span class="s">"workflows"</span><span class="p">][</span><span class="nb">type</span><span class="p">]))</span> <span class="k">for</span> <span class="n">i</span><span class="p">,</span><span class="n">x</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="n">conf</span><span class="o">.</span><span class="n">valid</span><span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">workflow</span><span class="p">[</span><span class="s">"workflows"</span><span class="p">][</span><span class="nb">type</span><span class="p">][</span><span class="n">z</span><span class="p">][</span><span class="s">"executable"</span><span class="p">]][</span><span class="s">"outputs"</span><span class="p">])</span> <span class="k">if</span> <span class="n">x</span> <span class="o">!=</span> <span class="s">"image"</span> <span class="ow">and</span> <span class="n">x</span> <span class="o">!=</span> <span class="s">"none"</span> <span class="ow">and</span> <span class="nb">len</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">workflow</span><span class="p">[</span><span class="s">"workflows"</span><span class="p">][</span><span class="nb">type</span><span class="p">][</span><span class="n">z</span><span class="p">][</span><span class="s">"outputs"</span><span class="p">])</span> <span class="o">></span> <span class="n">i</span><span class="p">)</span>
+ <span class="k">for</span> <span class="n">row</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">metadata</span><span class="o">.</span><span class="n">execute</span><span class="p">(</span><span class="s">"select pegasusid, experiment, id, date, imgname, path from images where imtype=?"</span><span class="p">,</span> <span class="p">(</span><span class="nb">type</span><span class="p">,)):</span>
+ <span class="n">realname</span> <span class="o">=</span> <span class="n">row</span><span class="p">[</span><span class="s">"path"</span><span class="p">]</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s">"/"</span><span class="p">)[</span><span class="o">-</span><span class="mi">1</span><span class="p">]</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s">"."</span><span class="p">)[</span><span class="mi">0</span><span class="p">]</span>
+ <span class="c">#derivedPath = row["experiment"].replace(" ","%20") + "/" + row["id"].replace(" ","%20") + "/" + row["date"].replace(" ","%20") + "/" + type + "/" + row["imgname"].replace(" ","%20") + "/"</span>
+ <span class="n">derivedPath</span> <span class="o">=</span> <span class="n">row</span><span class="p">[</span><span class="s">"experiment"</span><span class="p">]</span><span class="o">.</span><span class="n">replace</span><span class="p">(</span><span class="s">" "</span><span class="p">,</span><span class="s">""</span><span class="p">)</span> <span class="o">+</span> <span class="s">"/"</span> <span class="o">+</span> <span class="n">row</span><span class="p">[</span><span class="s">"id"</span><span class="p">]</span><span class="o">.</span><span class="n">replace</span><span class="p">(</span><span class="s">" "</span><span class="p">,</span><span class="s">""</span><span class="p">)</span> <span class="o">+</span> <span class="s">"/"</span> <span class="o">+</span> <span class="n">row</span><span class="p">[</span><span class="s">"date"</span><span class="p">]</span><span class="o">.</span><span class="n">replace</span><span class="p">(</span><span class="s">" "</span><span class="p">,</span><span class="s">""</span><span class="p">)</span> <span class="o">+</span> <span class="s">"/"</span> <span class="o">+</span> <span class="nb">type</span> <span class="o">+</span> <span class="s">"/"</span> <span class="o">+</span> <span class="n">row</span><span class="p">[</span><span class="s">"imgname"</span><span class="p">]</span><span class="o">.</span><span class="n">replace</span><span class="p">(</span><span class="s">" "</span><span class="p">,</span><span class="s">""</span><span class="p">)</span> <span class="o">+</span> <span class="s">"/"</span>
+ <span class="k">for</span> <span class="nb">input</span> <span class="ow">in</span> <span class="n">inputImages</span><span class="p">:</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_addFile</span><span class="p">(</span><span class="n">derivedPath</span> <span class="o">+</span> <span class="n">row</span><span class="p">[</span><span class="s">"pegasusid"</span><span class="p">]</span> <span class="o">+</span> <span class="s">"_"</span> <span class="o">+</span> <span class="nb">input</span> <span class="o">+</span> <span class="s">"."</span> <span class="o">+</span> <span class="n">row</span><span class="p">[</span><span class="s">"path"</span><span class="p">]</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s">"."</span><span class="p">)[</span><span class="mi">1</span><span class="p">],</span> <span class="nb">type</span><span class="p">,</span> <span class="s">"input"</span><span class="p">,</span> <span class="n">row</span><span class="p">[</span><span class="s">"path"</span><span class="p">])</span>
+ <span class="k">for</span> <span class="n">output</span> <span class="ow">in</span> <span class="n">outputImages</span><span class="p">:</span>
+ <span class="k">if</span> <span class="n">output</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">workflow</span><span class="p">[</span><span class="s">"extract"</span><span class="p">][</span><span class="s">"workflows"</span><span class="p">][</span><span class="nb">type</span><span class="p">][</span><span class="s">"inputs"</span><span class="p">]:</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">exInput</span><span class="p">[</span><span class="n">derivedPath</span> <span class="o">+</span> <span class="n">row</span><span class="p">[</span><span class="s">"pegasusid"</span><span class="p">]</span> <span class="o">+</span> <span class="s">"_"</span> <span class="o">+</span> <span class="n">output</span> <span class="o">+</span> <span class="s">".png"</span><span class="p">]</span> <span class="o">=</span> <span class="n">derivedPath</span> <span class="o">+</span> <span class="n">row</span><span class="p">[</span><span class="s">"pegasusid"</span><span class="p">]</span> <span class="o">+</span> <span class="s">"_"</span> <span class="o">+</span> <span class="n">output</span> <span class="o">+</span> <span class="s">".png"</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_addFile</span><span class="p">(</span><span class="n">derivedPath</span> <span class="o">+</span> <span class="n">row</span><span class="p">[</span><span class="s">"pegasusid"</span><span class="p">]</span> <span class="o">+</span> <span class="s">"_"</span> <span class="o">+</span> <span class="n">output</span> <span class="o">+</span> <span class="s">".png"</span><span class="p">,</span> <span class="s">"all"</span><span class="p">,</span> <span class="s">"input"</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">basepath</span> <span class="o">+</span> <span class="s">"/output/"</span> <span class="o">+</span> <span class="n">derivedPath</span> <span class="o">+</span> <span class="n">row</span><span class="p">[</span><span class="s">"pegasusid"</span><span class="p">]</span> <span class="o">+</span> <span class="s">"_"</span> <span class="o">+</span> <span class="n">output</span> <span class="o">+</span> <span class="s">".png"</span><span class="p">,</span> <span class="n">dax</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">exdax</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_addFile</span><span class="p">(</span><span class="n">derivedPath</span> <span class="o">+</span> <span class="n">row</span><span class="p">[</span><span class="s">"pegasusid"</span><span class="p">]</span> <span class="o">+</span> <span class="s">"_"</span> <span class="o">+</span> <span class="n">output</span> <span class="o">+</span> <span class="s">".png"</span><span class="p">,</span> <span class="nb">type</span><span class="p">,</span> <span class="s">"output"</span><span class="p">)</span>
+ <span class="n">wh</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="n">derivedPath</span> <span class="o">+</span> <span class="n">row</span><span class="p">[</span><span class="s">"pegasusid"</span><span class="p">]</span> <span class="o">+</span> <span class="s">"_"</span> <span class="o">+</span> <span class="n">output</span> <span class="o">+</span> <span class="s">".png file://"</span> <span class="o">+</span> <span class="bp">self</span><span class="o">.</span><span class="n">basepath</span> <span class="o">+</span> <span class="s">"/output/"</span> <span class="o">+</span> <span class="n">derivedPath</span> <span class="o">+</span> <span class="n">row</span><span class="p">[</span><span class="s">"pegasusid"</span><span class="p">]</span><span class="o">.</span><span class="n">replace</span><span class="p">(</span><span class="s">" "</span><span class="p">,</span><span class="s">"%20"</span><span class="p">)</span> <span class="o">+</span> <span class="s">"_"</span> <span class="o">+</span> <span class="n">output</span> <span class="o">+</span> <span class="s">".png pool=</span><span class="se">\"</span><span class="s">local</span><span class="se">\"\n</span><span class="s">"</span><span class="p">)</span>
+ <span class="k">for</span> <span class="n">output</span> <span class="ow">in</span> <span class="n">outputFiles</span><span class="p">:</span>
+ <span class="n">outname</span> <span class="o">=</span> <span class="n">output</span> <span class="o">+</span> <span class="n">outputFiles</span><span class="p">[</span><span class="n">output</span><span class="p">]</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_addFile</span><span class="p">(</span><span class="n">derivedPath</span> <span class="o">+</span> <span class="n">row</span><span class="p">[</span><span class="s">"pegasusid"</span><span class="p">]</span> <span class="o">+</span> <span class="s">"_"</span> <span class="o">+</span> <span class="n">outname</span><span class="p">,</span> <span class="nb">type</span><span class="p">,</span> <span class="s">"output"</span><span class="p">)</span>
+ <span class="n">wh</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="n">derivedPath</span> <span class="o">+</span> <span class="n">row</span><span class="p">[</span><span class="s">"pegasusid"</span><span class="p">]</span> <span class="o">+</span> <span class="s">"_"</span> <span class="o">+</span> <span class="n">outname</span> <span class="o">+</span> <span class="s">" file://"</span> <span class="o">+</span> <span class="bp">self</span><span class="o">.</span><span class="n">basepath</span> <span class="o">+</span> <span class="s">"/output/"</span> <span class="o">+</span> <span class="n">derivedPath</span><span class="o">.</span><span class="n">replace</span><span class="p">(</span><span class="s">"_"</span><span class="p">,</span><span class="s">"%20"</span><span class="p">)</span> <span class="o">+</span> <span class="n">outname</span> <span class="o">+</span> <span class="s">" pool=</span><span class="se">\"</span><span class="s">local</span><span class="se">\"\n</span><span class="s">"</span><span class="p">)</span>
+ <span class="k">return</span>
+
+ <span class="k">def</span> <span class="nf">_loadNotify</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+ <span class="k">if</span> <span class="s">"notify"</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">config</span><span class="p">:</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">dax</span><span class="o">.</span><span class="n">invoke</span><span class="p">(</span><span class="n">When</span><span class="o">.</span><span class="n">AT_END</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">basepath</span> <span class="o">+</span> <span class="s">"/input/imgproc/notify.sh"</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">exdax</span><span class="o">.</span><span class="n">invoke</span><span class="p">(</span><span class="n">When</span><span class="o">.</span><span class="n">AT_END</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">basepath</span> <span class="o">+</span> <span class="s">"/input/imgproc/notify.sh"</span><span class="p">)</span>
+ <span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">basepath</span> <span class="o">+</span> <span class="s">"/input/imgproc/notify.sh"</span><span class="p">,</span> <span class="s">"w"</span><span class="p">)</span> <span class="k">as</span> <span class="n">wh</span><span class="p">:</span>
+ <span class="n">notify</span> <span class="o">=</span> <span class="n">textwrap</span><span class="o">.</span><span class="n">dedent</span><span class="p">(</span><span class="s">"""</span><span class="se">\</span>
+<span class="s"> #!/bin/bash</span>
+<span class="s"> </span><span class="si">%s</span><span class="s">/email -t </span><span class="si">%s</span><span class="s"> --report=pegasus-analyzer</span>
+<span class="s"> """</span> <span class="o">%</span> <span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">config</span><span class="p">[</span><span class="s">"notify"</span><span class="p">][</span><span class="s">"pegasus_home"</span><span class="p">],</span> <span class="bp">self</span><span class="o">.</span><span class="n">config</span><span class="p">[</span><span class="s">"notify"</span><span class="p">][</span><span class="s">"email"</span><span class="p">]))</span>
+ <span class="n">wh</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="n">notify</span><span class="p">)</span>
+ <span class="n">os</span><span class="o">.</span><span class="n">chmod</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">basepath</span> <span class="o">+</span> <span class="s">"/input/imgproc/notify.sh"</span><span class="p">,</span> <span class="mo">0755</span><span class="p">)</span>
+ <span class="k">return</span>
+
+ <span class="k">def</span> <span class="nf">_loadExecutables</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">os</span><span class="o">=</span><span class="s">"linux"</span><span class="p">,</span> <span class="n">arch</span><span class="o">=</span><span class="s">"x86_64"</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> Loads all executables (as specified in the conf) into</span>
+<span class="sd"> the dax, as well as the internal self.executables variable</span>
+<span class="sd"> """</span>
+ <span class="k">for</span> <span class="n">ex</span> <span class="ow">in</span> <span class="n">conf</span><span class="o">.</span><span class="n">valid</span><span class="p">:</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">executables</span><span class="p">[</span><span class="n">ex</span><span class="p">]</span> <span class="o">=</span> <span class="n">Executable</span><span class="p">(</span><span class="n">name</span><span class="o">=</span><span class="n">ex</span><span class="p">,</span> <span class="n">os</span><span class="o">=</span><span class="n">os</span><span class="p">,</span> <span class="n">arch</span><span class="o">=</span><span class="n">arch</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">executables</span><span class="p">[</span><span class="n">ex</span><span class="p">]</span><span class="o">.</span><span class="n">addPFN</span><span class="p">(</span><span class="n">PFN</span><span class="p">(</span><span class="s">"file://"</span> <span class="o">+</span> <span class="bp">self</span><span class="o">.</span><span class="n">config</span><span class="p">[</span><span class="s">"installdir"</span><span class="p">]</span> <span class="o">+</span> <span class="s">"/"</span> <span class="o">+</span> <span class="n">ex</span><span class="p">,</span> <span class="s">"local"</span><span class="p">))</span>
+ <span class="c">#if "cluster" in self.config:</span>
+ <span class="c"># val = int(self.config["cluster"] * conf.valid[ex]["weight"]) if "weight" in conf.valid[ex] else self.config["cluster"]</span>
+ <span class="c"># self.executables[ex].addProfile(Profile(Namespace.PEGASUS, "clusters.size", val))</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">dax</span><span class="o">.</span><span class="n">addExecutable</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">executables</span><span class="p">[</span><span class="n">ex</span><span class="p">])</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">exdax</span><span class="o">.</span><span class="n">addExecutable</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">executables</span><span class="p">[</span><span class="n">ex</span><span class="p">])</span>
+ <span class="k">return</span>
+
+ <span class="k">def</span> <span class="nf">_loadJobInputs</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">job</span><span class="p">,</span> <span class="nb">type</span><span class="p">,</span> <span class="n">basename</span><span class="p">,</span> <span class="n">extension</span><span class="p">,</span> <span class="n">save</span> <span class="o">=</span> <span class="bp">False</span><span class="p">):</span>
+ <span class="n">inputs</span> <span class="o">=</span> <span class="p">{}</span>
+ <span class="k">for</span> <span class="n">i</span><span class="p">,</span><span class="nb">input</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="n">job</span><span class="p">[</span><span class="s">"inputs"</span><span class="p">]):</span>
+ <span class="n">ftype</span> <span class="o">=</span> <span class="n">conf</span><span class="o">.</span><span class="n">valid</span><span class="p">[</span><span class="n">job</span><span class="p">[</span><span class="s">"executable"</span><span class="p">]][</span><span class="s">"inputs"</span><span class="p">][</span><span class="n">i</span><span class="p">]</span>
+ <span class="k">if</span> <span class="nb">input</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">rawFiles</span><span class="p">[</span><span class="nb">type</span><span class="p">]:</span>
+ <span class="n">inputs</span><span class="p">[</span><span class="nb">input</span><span class="p">]</span> <span class="o">=</span> <span class="p">{</span><span class="s">"file"</span><span class="p">:</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">basename</span><span class="p">(</span><span class="nb">input</span><span class="p">),</span> <span class="s">"transfer"</span><span class="p">:</span> <span class="n">save</span><span class="p">}</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="n">ex</span> <span class="o">=</span> <span class="n">extension</span> <span class="k">if</span> <span class="n">job</span><span class="p">[</span><span class="s">"name"</span><span class="p">]</span> <span class="o">==</span> <span class="bp">self</span><span class="o">.</span><span class="n">workflow</span><span class="p">[</span><span class="s">"workflows"</span><span class="p">][</span><span class="nb">type</span><span class="p">][</span><span class="mi">0</span><span class="p">][</span><span class="s">"name"</span><span class="p">]</span> <span class="k">else</span> <span class="n">conf</span><span class="o">.</span><span class="n">fileExtensions</span><span class="p">[</span><span class="n">ftype</span><span class="p">]</span>
+ <span class="n">inputs</span><span class="p">[</span><span class="nb">input</span><span class="p">]</span> <span class="o">=</span> <span class="p">{</span><span class="s">"file"</span><span class="p">:</span> <span class="n">basename</span> <span class="o">+</span> <span class="s">"_"</span> <span class="o">+</span> <span class="nb">input</span> <span class="o">+</span> <span class="n">ex</span><span class="p">,</span> <span class="s">"transfer"</span><span class="p">:</span> <span class="n">save</span><span class="p">}</span>
+ <span class="k">return</span> <span class="n">inputs</span>
+
+ <span class="k">def</span> <span class="nf">_loadJobOutputs</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">job</span><span class="p">,</span> <span class="nb">type</span><span class="p">,</span> <span class="n">basename</span><span class="p">,</span> <span class="n">save</span><span class="p">):</span>
+ <span class="n">outputs</span> <span class="o">=</span> <span class="p">{}</span>
+ <span class="k">for</span> <span class="n">i</span><span class="p">,</span><span class="n">output</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="n">job</span><span class="p">[</span><span class="s">"outputs"</span><span class="p">]):</span>
+ <span class="k">if</span> <span class="n">output</span> <span class="o">!=</span> <span class="s">"none"</span><span class="p">:</span>
+ <span class="n">outputs</span><span class="p">[</span><span class="n">output</span><span class="p">]</span> <span class="o">=</span> <span class="p">{</span><span class="s">"file"</span><span class="p">:</span> <span class="n">basename</span> <span class="o">+</span> <span class="s">"_"</span> <span class="o">+</span> <span class="n">output</span> <span class="o">+</span> <span class="n">conf</span><span class="o">.</span><span class="n">fileExtensions</span><span class="p">[</span><span class="n">conf</span><span class="o">.</span><span class="n">valid</span><span class="p">[</span><span class="n">job</span><span class="p">[</span><span class="s">"executable"</span><span class="p">]][</span><span class="s">"outputs"</span><span class="p">][</span><span class="n">i</span><span class="p">]],</span> <span class="s">"transfer"</span><span class="p">:</span> <span class="n">save</span><span class="p">}</span>
+ <span class="k">return</span> <span class="n">outputs</span>
+
+ <span class="c">#def _loadJobOutputs(self, job, type, basename):</span>
+ <span class="c"># return dict((output, basename + "_" + output + conf.fileExtensions[conf.valid[job["executable"]]["outputs"][i]]) for i,output in enumerate(job["outputs"]) if output != "none")</span>
+
+ <span class="k">def</span> <span class="nf">_createDax</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">loc</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> Loads all jobs into the dax, and then writes the dax</span>
+<span class="sd"> to input/workflow.dax</span>
+<span class="sd"> """</span>
+ <span class="n">exDep</span> <span class="o">=</span> <span class="p">{}</span>
+ <span class="n">exInput</span> <span class="o">=</span> <span class="p">{}</span>
+ <span class="n">clusternum</span> <span class="o">=</span> <span class="p">{}</span>
+ <span class="n">meancluster</span> <span class="o">=</span> <span class="p">{}</span>
+
+ <span class="k">if</span> <span class="s">"maxwalltime"</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">config</span><span class="p">:</span>
+ <span class="k">if</span> <span class="s">"images"</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">config</span><span class="p">[</span><span class="s">"maxwalltime"</span><span class="p">]:</span>
+ <span class="n">maxwalltime</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">config</span><span class="p">[</span><span class="s">"maxwalltime"</span><span class="p">][</span><span class="s">"images"</span><span class="p">]</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="n">maxwalltime</span> <span class="o">=</span> <span class="bp">None</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="n">maxwalltime</span> <span class="o">=</span> <span class="bp">None</span>
+
+ <span class="n">save</span> <span class="o">=</span> <span class="bp">True</span> <span class="k">if</span> <span class="s">"save-steps"</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">workflow</span><span class="p">[</span><span class="s">"options"</span><span class="p">]</span> <span class="k">else</span> <span class="bp">False</span>
+ <span class="k">for</span> <span class="nb">type</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">workflow</span><span class="p">[</span><span class="s">"workflows"</span><span class="p">]:</span>
+ <span class="n">exDep</span><span class="p">[</span><span class="nb">type</span><span class="p">]</span> <span class="o">=</span> <span class="p">[[]]</span>
+ <span class="n">exInput</span><span class="p">[</span><span class="nb">type</span><span class="p">]</span> <span class="o">=</span> <span class="p">[{}]</span>
+ <span class="n">jobnum</span> <span class="o">=</span> <span class="o">-</span><span class="mi">1</span>
+ <span class="n">clusternum</span><span class="p">[</span><span class="nb">type</span><span class="p">]</span> <span class="o">=</span> <span class="mi">0</span>
+ <span class="n">meancluster</span><span class="p">[</span><span class="nb">type</span><span class="p">]</span> <span class="o">=</span> <span class="mi">0</span>
+ <span class="n">exNames</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">workflow</span><span class="p">[</span><span class="s">"extract"</span><span class="p">][</span><span class="s">"workflows"</span><span class="p">][</span><span class="nb">type</span><span class="p">][</span><span class="s">"depends"</span><span class="p">]</span>
+ <span class="k">for</span> <span class="n">infile</span> <span class="ow">in</span> <span class="p">[</span><span class="n">x</span> <span class="k">for</span> <span class="n">x</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">files</span><span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">dax</span><span class="p">][</span><span class="nb">type</span><span class="p">][</span><span class="s">"input"</span><span class="p">]</span> <span class="k">if</span> <span class="s">"."</span> <span class="o">+</span> <span class="n">x</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s">"."</span><span class="p">)[</span><span class="mi">1</span><span class="p">]</span> <span class="ow">in</span> <span class="n">conf</span><span class="o">.</span><span class="n">imageExtensions</span><span class="p">]:</span>
+ <span class="k">if</span> <span class="s">"cluster"</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">config</span><span class="p">:</span>
+ <span class="n">jobnum</span> <span class="o">+=</span> <span class="mi">1</span>
+ <span class="k">if</span> <span class="n">jobnum</span> <span class="o">==</span> <span class="bp">self</span><span class="o">.</span><span class="n">config</span><span class="p">[</span><span class="s">"cluster"</span><span class="p">]:</span>
+ <span class="n">jobnum</span> <span class="o">=</span> <span class="mi">0</span>
+ <span class="n">clusternum</span><span class="p">[</span><span class="nb">type</span><span class="p">]</span> <span class="o">+=</span> <span class="mi">1</span>
+ <span class="n">exDep</span><span class="p">[</span><span class="nb">type</span><span class="p">]</span><span class="o">.</span><span class="n">append</span><span class="p">([])</span>
+ <span class="n">exInput</span><span class="p">[</span><span class="nb">type</span><span class="p">]</span><span class="o">.</span><span class="n">append</span><span class="p">({})</span>
+ <span class="k">elif</span> <span class="p">((</span><span class="n">clusternum</span><span class="p">[</span><span class="nb">type</span><span class="p">]</span> <span class="o">*</span> <span class="mi">100</span> <span class="o">+</span> <span class="n">jobnum</span><span class="p">)</span> <span class="o">%</span> <span class="nb">int</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">config</span><span class="p">[</span><span class="s">"cluster"</span><span class="p">]</span> <span class="o">*</span> <span class="mf">0.3</span><span class="p">))</span> <span class="o">==</span> <span class="mi">0</span><span class="p">:</span>
+ <span class="n">meancluster</span><span class="p">[</span><span class="nb">type</span><span class="p">]</span> <span class="o">+=</span> <span class="mi">1</span>
+ <span class="n">extension</span> <span class="o">=</span> <span class="s">"."</span> <span class="o">+</span> <span class="n">infile</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s">"."</span><span class="p">)[</span><span class="mi">1</span><span class="p">]</span>
+ <span class="n">derivedPath</span> <span class="o">=</span> <span class="n">infile</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s">"_"</span><span class="p">)[</span><span class="mi">0</span><span class="p">]</span>
+ <span class="n">realname</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">files</span><span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">dax</span><span class="p">][</span><span class="nb">type</span><span class="p">][</span><span class="s">"input"</span><span class="p">][</span><span class="n">infile</span><span class="p">][</span><span class="s">"path"</span><span class="p">]</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s">"/"</span><span class="p">)[</span><span class="o">-</span><span class="mi">1</span><span class="p">]</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s">"."</span><span class="p">)[</span><span class="mi">0</span><span class="p">]</span>
+ <span class="k">for</span> <span class="n">stepnum</span><span class="p">,</span><span class="n">job</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">workflow</span><span class="p">[</span><span class="s">"workflows"</span><span class="p">][</span><span class="nb">type</span><span class="p">]):</span>
+ <span class="n">jobname</span> <span class="o">=</span> <span class="n">derivedPath</span> <span class="o">+</span> <span class="s">"_"</span> <span class="o">+</span> <span class="n">job</span><span class="p">[</span><span class="s">"name"</span><span class="p">]</span>
+ <span class="n">inputs</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_loadJobInputs</span><span class="p">(</span><span class="n">job</span><span class="p">,</span> <span class="nb">type</span><span class="p">,</span> <span class="n">derivedPath</span><span class="p">,</span> <span class="n">extension</span><span class="p">)</span>
+ <span class="k">if</span> <span class="n">job</span><span class="p">[</span><span class="s">"name"</span><span class="p">]</span> <span class="ow">in</span> <span class="n">exNames</span><span class="p">:</span>
+ <span class="n">outputs</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_loadJobOutputs</span><span class="p">(</span><span class="n">job</span><span class="p">,</span> <span class="nb">type</span><span class="p">,</span> <span class="n">derivedPath</span><span class="p">,</span> <span class="bp">True</span><span class="p">)</span>
+ <span class="n">exDep</span><span class="p">[</span><span class="nb">type</span><span class="p">][</span><span class="n">clusternum</span><span class="p">[</span><span class="nb">type</span><span class="p">]]</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">jobname</span><span class="p">)</span>
+ <span class="n">reqFile</span> <span class="o">=</span> <span class="n">derivedPath</span> <span class="o">+</span> <span class="s">"_"</span> <span class="o">+</span> <span class="bp">self</span><span class="o">.</span><span class="n">workflow</span><span class="p">[</span><span class="s">"extract"</span><span class="p">][</span><span class="s">"workflows"</span><span class="p">][</span><span class="nb">type</span><span class="p">][</span><span class="s">"inputs"</span><span class="p">][</span><span class="mi">0</span><span class="p">]</span> <span class="o">+</span> <span class="s">".png"</span>
+ <span class="n">exInput</span><span class="p">[</span><span class="nb">type</span><span class="p">][</span><span class="n">clusternum</span><span class="p">[</span><span class="nb">type</span><span class="p">]][</span><span class="n">reqFile</span><span class="p">]</span> <span class="o">=</span> <span class="p">{</span><span class="s">"file"</span><span class="p">:</span> <span class="n">reqFile</span><span class="p">,</span> <span class="s">"transfer"</span><span class="p">:</span> <span class="n">save</span><span class="p">}</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="n">outputs</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_loadJobOutputs</span><span class="p">(</span><span class="n">job</span><span class="p">,</span> <span class="nb">type</span><span class="p">,</span> <span class="n">derivedPath</span><span class="p">,</span> <span class="n">save</span><span class="p">)</span>
+ <span class="n">depends</span> <span class="o">=</span> <span class="p">[</span><span class="n">derivedPath</span> <span class="o">+</span> <span class="s">"_"</span> <span class="o">+</span> <span class="n">depend</span> <span class="k">for</span> <span class="n">depend</span> <span class="ow">in</span> <span class="n">job</span><span class="p">[</span><span class="s">"depends"</span><span class="p">]]</span> <span class="k">if</span> <span class="s">"depends"</span> <span class="ow">in</span> <span class="n">job</span> <span class="k">else</span> <span class="p">[]</span>
+ <span class="k">if</span> <span class="n">job</span><span class="p">[</span><span class="s">"executable"</span><span class="p">]</span> <span class="o">==</span> <span class="s">"ih-meanshift"</span><span class="p">:</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_addJob</span><span class="p">(</span><span class="n">jobname</span><span class="p">,</span> <span class="n">job</span><span class="p">[</span><span class="s">"executable"</span><span class="p">],</span> <span class="n">inputs</span><span class="p">,</span> <span class="n">outputs</span><span class="p">,</span> <span class="n">job</span><span class="p">[</span><span class="s">"arguments"</span><span class="p">],</span> <span class="n">depends</span><span class="p">,</span> <span class="n">label</span> <span class="o">=</span> <span class="nb">type</span> <span class="o">+</span> <span class="s">"_step"</span> <span class="o">+</span> <span class="nb">str</span><span class="p">(</span><span class="n">stepnum</span><span class="p">)</span> <span class="o">+</span> <span class="s">"_cluster"</span> <span class="o">+</span> <span class="nb">str</span><span class="p">(</span><span class="n">meancluster</span><span class="p">[</span><span class="nb">type</span><span class="p">])</span> <span class="k">if</span> <span class="s">"cluster"</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">config</span> <span class="k">else</span> <span class="bp">None</span><span class="p">,</span> <span class="n">walltime</span> <span class="o">=</span> <span class="n">maxwalltime</span><span class="p">)</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_addJob</span><span class="p">(</span><span class="n">jobname</span><span class="p">,</span> <span class="n">job</span><span class="p">[</span><span class="s">"executable"</span><span class="p">],</span> <span class="n">inputs</span><span class="p">,</span> <span class="n">outputs</span><span class="p">,</span> <span class="n">job</span><span class="p">[</span><span class="s">"arguments"</span><span class="p">],</span> <span class="n">depends</span><span class="p">,</span> <span class="n">label</span> <span class="o">=</span> <span class="nb">type</span> <span class="o">+</span> <span class="s">"_step"</span> <span class="o">+</span> <span class="nb">str</span><span class="p">(</span><span class="n">stepnum</span><span class="p">)</span> <span class="o">+</span> <span class="s">"_cluster"</span> <span class="o">+</span> <span class="nb">str</span><span class="p">(</span><span class="n">clusternum</span><span class="p">[</span><span class="nb">type</span><span class="p">])</span> <span class="k">if</span> <span class="s">"cluster"</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">config</span> <span class="k">else</span> <span class="bp">None</span><span class="p">,</span> <span class="n">walltime</span> <span class="o">=</span> <span class="n">maxwalltime</span><span class="p">)</span>
+
+
+ <span class="n">maprc</span> <span class="o">=</span> <span class="nb">open</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">basepath</span> <span class="o">+</span> <span class="s">"/"</span> <span class="o">+</span> <span class="n">loc</span> <span class="o">+</span> <span class="s">"/map.rc"</span><span class="p">,</span> <span class="s">"a"</span><span class="p">)</span>
+ <span class="n">binDep</span> <span class="o">=</span> <span class="p">[]</span>
+ <span class="n">aggIn</span> <span class="o">=</span> <span class="p">{}</span>
+ <span class="k">for</span> <span class="nb">type</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">workflow</span><span class="p">[</span><span class="s">"workflows"</span><span class="p">]:</span>
+ <span class="k">for</span> <span class="n">q</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="mi">0</span><span class="p">,</span> <span class="n">clusternum</span><span class="p">[</span><span class="nb">type</span><span class="p">]</span> <span class="o">+</span> <span class="mi">1</span><span class="p">):</span>
+ <span class="n">arguments</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">workflow</span><span class="p">[</span><span class="s">"extract"</span><span class="p">][</span><span class="s">"workflows"</span><span class="p">][</span><span class="nb">type</span><span class="p">][</span><span class="s">"arguments"</span><span class="p">]</span>
+ <span class="k">if</span> <span class="s">"--input"</span> <span class="ow">in</span> <span class="n">arguments</span><span class="p">:</span>
+ <span class="k">del</span> <span class="n">arguments</span><span class="p">[</span><span class="s">"--input"</span><span class="p">]</span>
+ <span class="k">if</span> <span class="s">"histogram-bin"</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">workflow</span><span class="p">[</span><span class="s">"extract"</span><span class="p">]:</span>
+ <span class="k">if</span> <span class="nb">type</span> <span class="ow">in</span> <span class="p">[</span><span class="n">imtype</span> <span class="k">for</span> <span class="n">key</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">workflow</span><span class="p">[</span><span class="s">"extract"</span><span class="p">][</span><span class="s">"histogram-bin"</span><span class="p">][</span><span class="s">"--group"</span><span class="p">]</span> <span class="k">for</span> <span class="n">imtype</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">workflow</span><span class="p">[</span><span class="s">"extract"</span><span class="p">][</span><span class="s">"histogram-bin"</span><span class="p">][</span><span class="s">"--group"</span><span class="p">][</span><span class="n">key</span><span class="p">]]:</span>
+ <span class="n">arguments</span><span class="p">[</span><span class="s">"--colors"</span><span class="p">]</span> <span class="o">=</span> <span class="s">""</span>
+ <span class="n">arguments</span><span class="p">[</span><span class="s">"--db"</span><span class="p">]</span> <span class="o">=</span> <span class="s">"db"</span>
+ <span class="n">arguments</span><span class="p">[</span><span class="s">"--createdb"</span><span class="p">]</span> <span class="o">=</span> <span class="s">""</span>
+ <span class="n">arguments</span><span class="p">[</span><span class="s">"--inputs"</span><span class="p">]</span> <span class="o">=</span> <span class="s">" "</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">exInput</span><span class="p">[</span><span class="nb">type</span><span class="p">][</span><span class="n">q</span><span class="p">]</span><span class="o">.</span><span class="n">keys</span><span class="p">())</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_addFile</span><span class="p">(</span><span class="nb">type</span> <span class="o">+</span> <span class="nb">str</span><span class="p">(</span><span class="n">q</span><span class="p">)</span> <span class="o">+</span> <span class="s">".db"</span><span class="p">,</span> <span class="nb">type</span><span class="p">,</span> <span class="s">"output"</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_addJob</span><span class="p">(</span><span class="nb">type</span> <span class="o">+</span> <span class="s">"_extract"</span> <span class="o">+</span> <span class="nb">str</span><span class="p">(</span><span class="n">q</span><span class="p">),</span> <span class="s">"ih-extract-multi"</span><span class="p">,</span> <span class="n">exInput</span><span class="p">[</span><span class="nb">type</span><span class="p">][</span><span class="n">q</span><span class="p">],</span> <span class="p">{</span><span class="s">"db"</span><span class="p">:</span> <span class="p">{</span><span class="s">"file"</span><span class="p">:</span> <span class="nb">type</span> <span class="o">+</span> <span class="nb">str</span><span class="p">(</span><span class="n">q</span><span class="p">)</span> <span class="o">+</span> <span class="s">".db"</span><span class="p">,</span> <span class="s">"transfer"</span><span class="p">:</span> <span class="bp">False</span><span class="p">}},</span> <span class="n">arguments</span><span class="p">,</span> <span class="n">exDep</span><span class="p">[</span><span class="nb">type</span><span class="p">][</span><span class="n">q</span><span class="p">])</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_addJob</span><span class="p">(</span><span class="nb">type</span> <span class="o">+</span> <span class="s">"_extract"</span> <span class="o">+</span> <span class="nb">str</span><span class="p">(</span><span class="n">q</span><span class="p">),</span> <span class="s">"ih-extract-multi"</span><span class="p">,</span> <span class="n">exInput</span><span class="p">[</span><span class="nb">type</span><span class="p">][</span><span class="n">q</span><span class="p">],</span> <span class="p">{</span><span class="s">"db"</span><span class="p">:</span> <span class="p">{</span><span class="s">"file"</span><span class="p">:</span> <span class="nb">type</span> <span class="o">+</span> <span class="nb">str</span><span class="p">(</span><span class="n">q</span><span class="p">)</span> <span class="o">+</span> <span class="s">".db"</span><span class="p">,</span> <span class="s">"transfer"</span><span class="p">:</span> <span class="bp">False</span><span class="p">}},</span> <span class="n">arguments</span><span class="p">,</span> <span class="p">[],</span> <span class="n">dax</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">exdax</span><span class="p">)</span>
+ <span class="n">maprc</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="nb">type</span> <span class="o">+</span> <span class="nb">str</span><span class="p">(</span><span class="n">q</span><span class="p">)</span> <span class="o">+</span> <span class="s">".db"</span> <span class="o">+</span> <span class="s">" file://"</span> <span class="o">+</span> <span class="bp">self</span><span class="o">.</span><span class="n">basepath</span> <span class="o">+</span> <span class="s">"/output/"</span> <span class="o">+</span> <span class="nb">type</span> <span class="o">+</span> <span class="nb">str</span><span class="p">(</span><span class="n">q</span><span class="p">)</span> <span class="o">+</span> <span class="s">".db"</span> <span class="o">+</span> <span class="s">" pool=</span><span class="se">\"</span><span class="s">local</span><span class="se">\"\n</span><span class="s">"</span><span class="p">)</span>
+ <span class="n">binDep</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="nb">type</span> <span class="o">+</span> <span class="s">"_extract"</span> <span class="o">+</span> <span class="nb">str</span><span class="p">(</span><span class="n">q</span><span class="p">))</span>
+ <span class="n">aggIn</span><span class="p">[</span><span class="nb">type</span> <span class="o">+</span> <span class="nb">str</span><span class="p">(</span><span class="n">q</span><span class="p">)</span> <span class="o">+</span> <span class="s">".db"</span><span class="p">]</span> <span class="o">=</span> <span class="p">{</span><span class="s">"file"</span><span class="p">:</span> <span class="nb">type</span> <span class="o">+</span> <span class="nb">str</span><span class="p">(</span><span class="n">q</span><span class="p">)</span> <span class="o">+</span> <span class="s">".db"</span><span class="p">,</span> <span class="s">"transfer"</span><span class="p">:</span> <span class="bp">False</span><span class="p">}</span>
+ <span class="n">aggIn</span><span class="p">[</span><span class="s">"db"</span><span class="p">]</span> <span class="o">=</span> <span class="p">{</span><span class="s">"file"</span><span class="p">:</span> <span class="s">"img.db"</span><span class="p">,</span> <span class="s">"transfer"</span><span class="p">:</span> <span class="bp">False</span><span class="p">}</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_addJob</span><span class="p">(</span><span class="s">"sql_aggregate1"</span><span class="p">,</span> <span class="s">"ih-sql-aggregate"</span><span class="p">,</span> <span class="n">aggIn</span><span class="p">,</span> <span class="p">{},</span> <span class="p">{</span><span class="s">"--db"</span><span class="p">:</span> <span class="s">"db"</span><span class="p">,</span> <span class="s">"--inputs"</span><span class="p">:</span> <span class="s">" "</span><span class="o">.</span><span class="n">join</span><span class="p">([</span><span class="n">aggIn</span><span class="p">[</span><span class="n">x</span><span class="p">][</span><span class="s">"file"</span><span class="p">]</span> <span class="k">for</span> <span class="n">x</span> <span class="ow">in</span> <span class="n">aggIn</span> <span class="k">if</span> <span class="n">x</span> <span class="o">!=</span> <span class="s">"db"</span><span class="p">])},</span> <span class="n">binDep</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_addJob</span><span class="p">(</span><span class="s">"sql_aggregate1"</span><span class="p">,</span> <span class="s">"ih-sql-aggregate"</span><span class="p">,</span> <span class="n">aggIn</span><span class="p">,</span> <span class="p">{},</span> <span class="p">{</span><span class="s">"--db"</span><span class="p">:</span> <span class="s">"db"</span><span class="p">,</span> <span class="s">"--inputs"</span><span class="p">:</span> <span class="s">" "</span><span class="o">.</span><span class="n">join</span><span class="p">([</span><span class="n">aggIn</span><span class="p">[</span><span class="n">x</span><span class="p">][</span><span class="s">"file"</span><span class="p">]</span> <span class="k">for</span> <span class="n">x</span> <span class="ow">in</span> <span class="n">aggIn</span> <span class="k">if</span> <span class="n">x</span> <span class="o">!=</span> <span class="s">"db"</span><span class="p">])},</span> <span class="n">binDep</span><span class="p">,</span> <span class="n">dax</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">exdax</span><span class="p">)</span>
+
+ <span class="k">if</span> <span class="s">"histogram-bin"</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">workflow</span><span class="p">[</span><span class="s">"extract"</span><span class="p">]:</span>
+ <span class="n">outputs</span> <span class="o">=</span> <span class="p">{}</span>
+ <span class="k">for</span> <span class="n">name</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">workflow</span><span class="p">[</span><span class="s">"extract"</span><span class="p">][</span><span class="s">"histogram-bin"</span><span class="p">][</span><span class="s">"--group"</span><span class="p">]:</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_addFile</span><span class="p">(</span><span class="n">name</span> <span class="o">+</span> <span class="s">"_hist_bins.json"</span><span class="p">,</span> <span class="s">"raw"</span><span class="p">,</span> <span class="s">"output"</span><span class="p">)</span>
+ <span class="n">maprc</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="n">name</span> <span class="o">+</span> <span class="s">"_hist_bins.json"</span> <span class="o">+</span> <span class="s">" file://"</span> <span class="o">+</span> <span class="bp">self</span><span class="o">.</span><span class="n">basepath</span> <span class="o">+</span> <span class="s">"/output/"</span> <span class="o">+</span> <span class="n">name</span> <span class="o">+</span> <span class="s">"_hist_bins.json"</span> <span class="o">+</span> <span class="s">" pool=</span><span class="se">\"</span><span class="s">local</span><span class="se">\"\n</span><span class="s">"</span><span class="p">)</span>
+ <span class="n">outputs</span><span class="p">[</span><span class="n">name</span> <span class="o">+</span> <span class="s">"_hist_bins.json"</span><span class="p">]</span> <span class="o">=</span> <span class="p">{</span><span class="s">"file"</span><span class="p">:</span> <span class="n">name</span> <span class="o">+</span> <span class="s">"_hist_bins.json"</span><span class="p">,</span> <span class="s">"transfer"</span><span class="p">:</span> <span class="bp">True</span><span class="p">}</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_addJob</span><span class="p">(</span><span class="s">"bin_creation"</span><span class="p">,</span> <span class="s">"ih-stats-histogram-bin"</span><span class="p">,</span> <span class="p">{</span><span class="s">"db"</span><span class="p">:</span> <span class="p">{</span><span class="s">"file"</span><span class="p">:</span> <span class="s">"img.db"</span><span class="p">,</span> <span class="s">"transfer"</span><span class="p">:</span> <span class="bp">True</span><span class="p">},</span> <span class="s">"extract.json"</span><span class="p">:</span> <span class="p">{</span><span class="s">"file"</span><span class="p">:</span> <span class="s">"extract.json"</span><span class="p">,</span> <span class="s">"transfer"</span><span class="p">:</span> <span class="bp">False</span><span class="p">}},</span> <span class="n">outputs</span><span class="p">,</span> <span class="p">{</span><span class="s">"--db"</span><span class="p">:</span> <span class="s">"db"</span><span class="p">,</span> <span class="s">"--options"</span><span class="p">:</span> <span class="s">"extract.json"</span><span class="p">,</span> <span class="s">"--intable"</span><span class="p">:</span> <span class="s">"images"</span><span class="p">,</span> <span class="s">"--outtable"</span><span class="p">:</span> <span class="s">"histogramBins"</span><span class="p">,</span> <span class="s">"--jsonwrite"</span><span class="p">:</span> <span class="s">""</span><span class="p">,</span> <span class="s">"--overwrite"</span><span class="p">:</span> <span class="s">""</span><span class="p">},</span> <span class="p">[</span><span class="s">"sql_aggregate1"</span><span class="p">])</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_addJob</span><span class="p">(</span><span class="s">"bin_creation"</span><span class="p">,</span> <span class="s">"ih-stats-histogram-bin"</span><span class="p">,</span> <span class="p">{</span><span class="s">"db"</span><span class="p">:</span> <span class="p">{</span><span class="s">"file"</span><span class="p">:</span> <span class="s">"img.db"</span><span class="p">,</span> <span class="s">"transfer"</span><span class="p">:</span> <span class="bp">True</span><span class="p">},</span> <span class="s">"extract.json"</span><span class="p">:</span> <span class="p">{</span><span class="s">"file"</span><span class="p">:</span> <span class="s">"extract.json"</span><span class="p">,</span> <span class="s">"transfer"</span><span class="p">:</span> <span class="bp">False</span><span class="p">}},</span> <span class="n">outputs</span><span class="p">,</span> <span class="p">{</span><span class="s">"--db"</span><span class="p">:</span> <span class="s">"db"</span><span class="p">,</span> <span class="s">"--options"</span><span class="p">:</span> <span class="s">"extract.json"</span><span class="p">,</span> <span class="s">"--intable"</span><span class="p">:</span> <span class="s">"images"</span><span class="p">,</span> <span class="s">"--outtable"</span><span class="p">:</span> <span class="s">"histogramBins"</span><span class="p">,</span> <span class="s">"--jsonwrite"</span><span class="p">:</span> <span class="s">""</span><span class="p">,</span> <span class="s">"--overwrite"</span><span class="p">:</span> <span class="s">""</span><span class="p">},</span> <span class="p">[</span><span class="s">"sql_aggregate1"</span><span class="p">],</span> <span class="n">dax</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">exdax</span><span class="p">)</span>
+
+ <span class="n">binDep</span> <span class="o">=</span> <span class="p">[]</span>
+ <span class="nb">map</span> <span class="o">=</span> <span class="p">{}</span>
+
+ <span class="k">for</span> <span class="n">group</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">workflow</span><span class="p">[</span><span class="s">"extract"</span><span class="p">][</span><span class="s">"histogram-bin"</span><span class="p">][</span><span class="s">"--group"</span><span class="p">]:</span>
+ <span class="k">for</span> <span class="nb">type</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">workflow</span><span class="p">[</span><span class="s">"extract"</span><span class="p">][</span><span class="s">"histogram-bin"</span><span class="p">][</span><span class="s">"--group"</span><span class="p">][</span><span class="n">group</span><span class="p">]:</span>
+ <span class="nb">map</span><span class="p">[</span><span class="nb">type</span><span class="p">]</span> <span class="o">=</span> <span class="n">group</span>
+
+ <span class="k">for</span> <span class="nb">type</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">workflow</span><span class="p">[</span><span class="s">"workflows"</span><span class="p">]:</span>
+ <span class="k">for</span> <span class="n">q</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="mi">0</span><span class="p">,</span> <span class="n">clusternum</span><span class="p">[</span><span class="nb">type</span><span class="p">]</span> <span class="o">+</span> <span class="mi">1</span><span class="p">):</span>
+ <span class="n">arguments</span> <span class="o">=</span> <span class="p">{}</span>
+ <span class="n">arguments</span><span class="p">[</span><span class="s">"--db"</span><span class="p">]</span> <span class="o">=</span> <span class="s">"db"</span>
+ <span class="n">arguments</span><span class="p">[</span><span class="s">"--inputs"</span><span class="p">]</span> <span class="o">=</span> <span class="s">" "</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">exInput</span><span class="p">[</span><span class="nb">type</span><span class="p">][</span><span class="n">q</span><span class="p">]</span><span class="o">.</span><span class="n">keys</span><span class="p">())</span>
+ <span class="n">exInput</span><span class="p">[</span><span class="nb">type</span><span class="p">][</span><span class="n">q</span><span class="p">][</span><span class="s">"db"</span><span class="p">]</span> <span class="o">=</span> <span class="p">{</span><span class="s">"file"</span><span class="p">:</span> <span class="nb">type</span> <span class="o">+</span> <span class="nb">str</span><span class="p">(</span><span class="n">q</span><span class="p">)</span> <span class="o">+</span> <span class="s">".db"</span><span class="p">,</span> <span class="s">"transfer"</span><span class="p">:</span> <span class="bp">False</span><span class="p">}</span>
+ <span class="n">exInput</span><span class="p">[</span><span class="nb">type</span><span class="p">][</span><span class="n">q</span><span class="p">][</span><span class="s">"binfile"</span><span class="p">]</span> <span class="o">=</span> <span class="p">{</span><span class="s">"file"</span><span class="p">:</span> <span class="nb">map</span><span class="p">[</span><span class="nb">type</span><span class="p">]</span> <span class="o">+</span> <span class="s">"_hist_bins.json"</span><span class="p">,</span> <span class="s">"transfer"</span><span class="p">:</span> <span class="bp">False</span><span class="p">}</span>
+ <span class="n">arguments</span><span class="p">[</span><span class="s">"--bins"</span><span class="p">]</span> <span class="o">=</span> <span class="s">"binfile"</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_addJob</span><span class="p">(</span><span class="nb">type</span> <span class="o">+</span> <span class="s">"_extractBins"</span> <span class="o">+</span> <span class="nb">str</span><span class="p">(</span><span class="n">q</span><span class="p">),</span> <span class="s">"ih-extract-multi"</span><span class="p">,</span> <span class="n">exInput</span><span class="p">[</span><span class="nb">type</span><span class="p">][</span><span class="n">q</span><span class="p">],</span> <span class="p">{},</span> <span class="n">arguments</span><span class="p">,</span> <span class="p">[</span><span class="s">"bin_creation"</span><span class="p">])</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_addJob</span><span class="p">(</span><span class="nb">type</span> <span class="o">+</span> <span class="s">"_extractBins"</span> <span class="o">+</span> <span class="nb">str</span><span class="p">(</span><span class="n">q</span><span class="p">),</span> <span class="s">"ih-extract-multi"</span><span class="p">,</span> <span class="n">exInput</span><span class="p">[</span><span class="nb">type</span><span class="p">][</span><span class="n">q</span><span class="p">],</span> <span class="p">{},</span> <span class="n">arguments</span><span class="p">,</span> <span class="p">[</span><span class="s">"bin_creation"</span><span class="p">],</span> <span class="n">dax</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">exdax</span><span class="p">)</span>
+ <span class="n">binDep</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="nb">type</span> <span class="o">+</span> <span class="s">"_extractBins"</span> <span class="o">+</span> <span class="nb">str</span><span class="p">(</span><span class="n">q</span><span class="p">))</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_addJob</span><span class="p">(</span><span class="s">"sql_aggregate2"</span><span class="p">,</span> <span class="s">"ih-sql-aggregate"</span><span class="p">,</span> <span class="n">aggIn</span><span class="p">,</span> <span class="p">{},</span> <span class="p">{</span><span class="s">"--db"</span><span class="p">:</span> <span class="s">"db"</span><span class="p">,</span> <span class="s">"--inputs"</span><span class="p">:</span> <span class="s">" "</span><span class="o">.</span><span class="n">join</span><span class="p">([</span><span class="n">aggIn</span><span class="p">[</span><span class="n">x</span><span class="p">][</span><span class="s">"file"</span><span class="p">]</span> <span class="k">for</span> <span class="n">x</span> <span class="ow">in</span> <span class="n">aggIn</span> <span class="k">if</span> <span class="n">x</span> <span class="o">!=</span> <span class="s">"db"</span><span class="p">])},</span> <span class="n">binDep</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_addJob</span><span class="p">(</span><span class="s">"sql_aggregate2"</span><span class="p">,</span> <span class="s">"ih-sql-aggregate"</span><span class="p">,</span> <span class="n">aggIn</span><span class="p">,</span> <span class="p">{},</span> <span class="p">{</span><span class="s">"--db"</span><span class="p">:</span> <span class="s">"db"</span><span class="p">,</span> <span class="s">"--inputs"</span><span class="p">:</span> <span class="s">" "</span><span class="o">.</span><span class="n">join</span><span class="p">([</span><span class="n">aggIn</span><span class="p">[</span><span class="n">x</span><span class="p">][</span><span class="s">"file"</span><span class="p">]</span> <span class="k">for</span> <span class="n">x</span> <span class="ow">in</span> <span class="n">aggIn</span> <span class="k">if</span> <span class="n">x</span> <span class="o">!=</span> <span class="s">"db"</span><span class="p">])},</span> <span class="n">binDep</span><span class="p">,</span> <span class="n">dax</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">exdax</span><span class="p">)</span>
+
+ <span class="n">z</span> <span class="o">=</span> <span class="mi">2</span> <span class="k">if</span> <span class="s">"histogram-bin"</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">workflow</span><span class="p">[</span><span class="s">"extract"</span><span class="p">]</span> <span class="k">else</span> <span class="mi">1</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_addJob</span><span class="p">(</span><span class="s">"error-log"</span><span class="p">,</span> <span class="s">"ih-error-log"</span><span class="p">,</span> <span class="p">{</span><span class="s">"db"</span><span class="p">:</span> <span class="p">{</span><span class="s">"file"</span><span class="p">:</span> <span class="s">"img.db"</span><span class="p">,</span> <span class="s">"transfer"</span><span class="p">:</span> <span class="bp">False</span><span class="p">}},</span> <span class="p">{</span><span class="s">"output"</span><span class="p">:</span> <span class="p">{</span><span class="s">"file"</span><span class="p">:</span> <span class="s">"img.log"</span><span class="p">,</span> <span class="s">"transfer"</span><span class="p">:</span> <span class="bp">True</span><span class="p">}},</span> <span class="p">{</span><span class="s">"--db"</span><span class="p">:</span> <span class="s">"db"</span><span class="p">,</span> <span class="s">"--output"</span><span class="p">:</span> <span class="s">"output"</span><span class="p">},</span> <span class="p">[</span><span class="s">"sql_aggregate"</span> <span class="o">+</span> <span class="nb">str</span><span class="p">(</span><span class="n">z</span><span class="p">)])</span>
+ <span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">basepath</span> <span class="o">+</span> <span class="s">"/"</span> <span class="o">+</span> <span class="n">loc</span> <span class="o">+</span> <span class="s">"/workflow.dax"</span><span class="p">,</span> <span class="s">"w"</span><span class="p">)</span> <span class="k">as</span> <span class="n">wh</span><span class="p">:</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">dax</span><span class="o">.</span><span class="n">writeXML</span><span class="p">(</span><span class="n">wh</span><span class="p">)</span>
+ <span class="k">return</span>
+
+ <span class="k">def</span> <span class="nf">_createExtract</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">loc</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> Creates the extraction step only dax!</span>
+<span class="sd"> """</span>
+ <span class="c">#self._addJob("extractOnly", "ih-extract-all", self.exInput, {}, {"--db": "db", "--options": "extract.json"}, dax = self.exdax)</span>
+ <span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">basepath</span> <span class="o">+</span> <span class="s">"/"</span> <span class="o">+</span> <span class="n">loc</span> <span class="o">+</span> <span class="s">"/extract.dax"</span><span class="p">,</span> <span class="s">"w"</span><span class="p">)</span> <span class="k">as</span> <span class="n">wh</span><span class="p">:</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">exdax</span><span class="o">.</span><span class="n">writeXML</span><span class="p">(</span><span class="n">wh</span><span class="p">)</span>
+ <span class="k">return</span>
+
+ <span class="k">def</span> <span class="nf">_createReplica</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">loc</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> Creates the pegasus configuration replica catalog. input/conf.rc</span>
+<span class="sd"> """</span>
+ <span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">basepath</span> <span class="o">+</span> <span class="s">"/"</span> <span class="o">+</span> <span class="n">loc</span> <span class="o">+</span> <span class="s">"/conf.rc"</span><span class="p">,</span> <span class="s">"w"</span><span class="p">)</span> <span class="k">as</span> <span class="n">wh</span><span class="p">:</span>
+ <span class="n">pegasusrc</span> <span class="o">=</span> <span class="n">textwrap</span><span class="o">.</span><span class="n">dedent</span><span class="p">(</span><span class="s">"""</span><span class="se">\</span>
+<span class="s"> pegasus.catalog.site = XML</span>
+<span class="s"> pegasus.catalog.site.file = </span><span class="si">%s</span><span class="s">/sites.xml</span>
+<span class="s"> </span>
+<span class="s"> pegasus.condor.logs.symlink = false</span>
+<span class="s"> </span>
+<span class="s"> pegasus.transfer.links = true</span>
+<span class="s"> </span>
+<span class="s"> pegasus.data.configuration = sharedfs</span>
+<span class="s"> </span>
+<span class="s"> pegasus.dir.storage.mapper = Replica</span>
+<span class="s"> pegasus.dir.storage.mapper.replica = File</span>
+<span class="s"> pegasus.dir.storage.mapper.replica.file = </span><span class="si">%s</span><span class="s">/map.rc</span>
+<span class="s"> """</span> <span class="o">%</span> <span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">basepath</span> <span class="o">+</span> <span class="s">"/"</span> <span class="o">+</span> <span class="n">loc</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">basepath</span> <span class="o">+</span> <span class="s">"/"</span> <span class="o">+</span> <span class="n">loc</span><span class="p">))</span>
+ <span class="n">wh</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="n">pegasusrc</span><span class="p">)</span>
+ <span class="k">return</span>
+
+ <span class="k">def</span> <span class="nf">_createSites</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">loc</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> Creates the pegasus site catalog. input/sites.xml</span>
+<span class="sd"> """</span>
+ <span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">basepath</span> <span class="o">+</span> <span class="s">"/"</span> <span class="o">+</span> <span class="n">loc</span> <span class="o">+</span> <span class="s">"/sites.xml"</span><span class="p">,</span> <span class="s">"w"</span><span class="p">)</span> <span class="k">as</span> <span class="n">wh</span><span class="p">:</span>
+ <span class="n">sites</span> <span class="o">=</span> <span class="s">"""</span><span class="se">\</span>
+<span class="s"> <sitecatalog xmlns="http://pegasus.isi.edu/schema/sitecatalog" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://pegasus.isi.edu/schema/sitecatalog http://pegasus.isi.edu/schema/sc-4.0.xsd" version="4.0"></span>
+<span class="s"> </span>
+<span class="s"> <site handle="local" arch="x86_64" os="LINUX"></span>
+<span class="s"> <directory type="shared-scratch" path="</span><span class="si">%s</span><span class="s">"></span>
+<span class="s"> <file-server operation="all" url="file://</span><span class="si">%s</span><span class="s">" /></span>
+<span class="s"> </directory></span>
+<span class="s"> <directory type="local-storage" path="</span><span class="si">%s</span><span class="s">"></span>
+<span class="s"> <file-server operation="all" url="file://</span><span class="si">%s</span><span class="s">" /></span>
+<span class="s"> </directory></span>
+<span class="s"> """</span> <span class="o">%</span> <span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">basepath</span> <span class="o">+</span> <span class="s">"/work/imgproc/"</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">basepath</span> <span class="o">+</span> <span class="s">"/work/imgproc/"</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">basepath</span> <span class="o">+</span> <span class="s">"/output/"</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">basepath</span> <span class="o">+</span> <span class="s">"/output/"</span><span class="p">)</span>
+ <span class="k">for</span> <span class="n">namespace</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">config</span><span class="p">[</span><span class="s">"profile"</span><span class="p">]:</span>
+ <span class="k">for</span> <span class="n">key</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">config</span><span class="p">[</span><span class="s">"profile"</span><span class="p">][</span><span class="n">namespace</span><span class="p">]:</span>
+ <span class="n">val</span> <span class="o">=</span> <span class="s">":"</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">config</span><span class="p">[</span><span class="s">"profile"</span><span class="p">][</span><span class="n">namespace</span><span class="p">][</span><span class="n">key</span><span class="p">])</span> <span class="k">if</span> <span class="s">"path"</span> <span class="ow">in</span> <span class="n">key</span><span class="o">.</span><span class="n">lower</span><span class="p">()</span> <span class="k">else</span> <span class="bp">self</span><span class="o">.</span><span class="n">config</span><span class="p">[</span><span class="s">"profile"</span><span class="p">][</span><span class="n">namespace</span><span class="p">][</span><span class="n">key</span><span class="p">]</span>
+ <span class="n">sites</span> <span class="o">+=</span> <span class="s">"""</span><span class="se">\n\t</span><span class="s"><profile namespace="</span><span class="si">%s</span><span class="s">" key="</span><span class="si">%s</span><span class="s">"></span><span class="si">%s</span><span class="s"></profile> """</span> <span class="o">%</span> <span class="p">(</span><span class="n">namespace</span><span class="p">,</span> <span class="n">key</span><span class="p">,</span> <span class="n">val</span><span class="p">)</span>
+ <span class="n">sites</span> <span class="o">+=</span> <span class="s">"</site></sitecatalog>"</span>
+ <span class="n">sites</span> <span class="o">=</span> <span class="n">sites</span><span class="o">.</span><span class="n">replace</span><span class="p">(</span><span class="s">"</span><span class="se">\n</span><span class="s">"</span><span class="p">,</span><span class="s">""</span><span class="p">)</span>
+ <span class="n">wh</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s">"</span><span class="se">\n</span><span class="s">"</span><span class="o">.</span><span class="n">join</span><span class="p">([</span><span class="n">line</span> <span class="k">for</span> <span class="n">line</span> <span class="ow">in</span> <span class="n">xml</span><span class="o">.</span><span class="n">dom</span><span class="o">.</span><span class="n">minidom</span><span class="o">.</span><span class="n">parseString</span><span class="p">(</span><span class="n">sites</span><span class="p">)</span><span class="o">.</span><span class="n">toprettyxml</span><span class="p">()</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s">'</span><span class="se">\n</span><span class="s">'</span><span class="p">)</span> <span class="k">if</span> <span class="n">line</span><span class="o">.</span><span class="n">strip</span><span class="p">()]))</span>
+ <span class="k">return</span>
+
+ <span class="k">def</span> <span class="nf">_createSubmit</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">loc</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> Creates the pegasus submit script. submit.sh</span>
+<span class="sd"> """</span>
+ <span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">basepath</span> <span class="o">+</span> <span class="s">"/"</span> <span class="o">+</span> <span class="n">loc</span> <span class="o">+</span> <span class="s">"/submit.sh"</span><span class="p">,</span> <span class="s">"w"</span><span class="p">)</span> <span class="k">as</span> <span class="n">wh</span><span class="p">:</span>
+ <span class="n">submit</span> <span class="o">=</span> <span class="n">textwrap</span><span class="o">.</span><span class="n">dedent</span><span class="p">(</span><span class="s">"""</span><span class="se">\</span>
+<span class="s"> #!/bin/bash</span>
+<span class="s"> if [ "$1" = "--extract-only" ] || [ "$1" = "--extract" ] || [ "$1" = "-e" ]; then</span>
+<span class="s"> DAX="</span><span class="si">%s</span><span class="s">"</span>
+<span class="s"> else</span>
+<span class="s"> DAX="</span><span class="si">%s</span><span class="s">"</span>
+<span class="s"> fi</span>
+<span class="s"> plan=`pegasus-plan </span><span class="se">\\</span><span class="s"></span>
+<span class="s"> --conf "</span><span class="si">%s</span><span class="s">" </span><span class="se">\\</span><span class="s"></span>
+<span class="s"> --sites local </span><span class="se">\\</span><span class="s"></span>
+<span class="s"> --dir "</span><span class="si">%s</span><span class="s">" </span><span class="se">\\</span><span class="s"></span>
+<span class="s"> --output-site local </span><span class="se">\\</span><span class="s"></span>
+<span class="s"> --dax "$DAX" </span><span class="se">\\</span><span class="s"></span>
+<span class="s"> --randomdir </span><span class="se">\\</span><span class="s"></span>
+<span class="s"> """</span> <span class="o">%</span> <span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">basepath</span> <span class="o">+</span> <span class="s">"/"</span> <span class="o">+</span> <span class="n">loc</span> <span class="o">+</span> <span class="s">"/extract.dax"</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">basepath</span> <span class="o">+</span> <span class="s">"/"</span> <span class="o">+</span> <span class="n">loc</span> <span class="o">+</span> <span class="s">"/workflow.dax"</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">basepath</span> <span class="o">+</span> <span class="s">"/"</span> <span class="o">+</span> <span class="n">loc</span> <span class="o">+</span> <span class="s">"/conf.rc"</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">basepath</span> <span class="o">+</span> <span class="s">"/work/imgproc"</span><span class="p">))</span>
+ <span class="k">if</span> <span class="s">"cluster"</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">config</span><span class="p">:</span>
+ <span class="n">submit</span> <span class="o">+=</span> <span class="s">"""--cluster label </span><span class="se">\\\n</span><span class="s">"""</span>
+ <span class="n">submit</span> <span class="o">+=</span> <span class="n">textwrap</span><span class="o">.</span><span class="n">dedent</span><span class="p">(</span><span class="s">"""</span><span class="se">\</span>
+<span class="s"> --submit`</span>
+<span class="s"> </span>
+<span class="s"> status=`echo "$plan" | grep pegasus-status | tr -s ' '| cut -d ' ' -f 6`</span>
+<span class="s"> echo -e "#!/bin/bash</span>
+<span class="s"> pegasus-status -l $status" > status.sh</span>
+<span class="s"> chmod 744 status.sh</span>
+<span class="s"> </span>
+<span class="s"> remove=`echo "$plan" | grep pegasus-remove | tr -s ' '| cut -d ' ' -f 5`</span>
+<span class="s"> echo -e "#!/bin/bash</span>
+<span class="s"> pegasus-remove $remove" > remove.sh </span>
+<span class="s"> chmod 744 remove.sh</span>
+<span class="s"> </span>
+<span class="s"> echo "$plan"</span>
+<span class="s"> echo "Alternatively, you can use the status & remove scripts in the current directory!"</span>
+<span class="s"> </span>
+<span class="s"> """</span><span class="p">)</span>
+ <span class="n">wh</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="n">submit</span><span class="p">)</span>
+ <span class="n">os</span><span class="o">.</span><span class="n">chmod</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">basepath</span> <span class="o">+</span> <span class="s">"/"</span> <span class="o">+</span> <span class="n">loc</span> <span class="o">+</span> <span class="s">"/submit.sh"</span><span class="p">,</span> <span class="mo">0755</span><span class="p">)</span>
+ <span class="k">return</span>
+
+<div class="viewcode-block" id="ImageProcessor.create"><a class="viewcode-back" href="../../workflowimage.html#ih.workflow.ImageProcessor.create">[docs]</a> <span class="k">def</span> <span class="nf">create</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> Creates a new pegasus submission directory based on the current timestamp,</span>
+<span class="sd"> and populates it with all required information to submit a pegasus job.</span>
+<span class="sd"> """</span>
+ <span class="k">print</span> <span class="s">"Generating workflow. Please wait."</span>
+ <span class="n">loc</span> <span class="o">=</span> <span class="s">"/input/imgproc/"</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_createSetup</span><span class="p">()</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_copyFiles</span><span class="p">()</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_loadFiles</span><span class="p">(</span><span class="n">loc</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_loadExecutables</span><span class="p">()</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_loadNotify</span><span class="p">()</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_createDax</span><span class="p">(</span><span class="n">loc</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_createExtract</span><span class="p">(</span><span class="n">loc</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_createReplica</span><span class="p">(</span><span class="n">loc</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_createSites</span><span class="p">(</span><span class="n">loc</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_createSubmit</span><span class="p">(</span><span class="n">loc</span><span class="p">)</span>
+ <span class="k">return</span>
+
+</div></div>
+<div class="viewcode-block" id="ImageLoader"><a class="viewcode-back" href="../../indexing.html#ih.workflow.ImageLoader">[docs]</a><span class="k">class</span> <span class="nc">ImageLoader</span><span class="p">:</span>
+ <span class="sd">"""</span>
+<span class="sd"> This should handle all meta-data definitions</span>
+<span class="sd"> """</span>
+
+ <span class="k">def</span> <span class="nf">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">template</span><span class="p">,</span> <span class="n">output</span><span class="p">,</span> <span class="n">validOnly</span> <span class="o">=</span> <span class="bp">False</span><span class="p">,</span> <span class="n">overwrite</span> <span class="o">=</span> <span class="bp">False</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> :param template: Path to input template file, should be valid json.</span>
+<span class="sd"> :type template: str</span>
+<span class="sd"> """</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">templatePath</span> <span class="o">=</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">abspath</span><span class="p">(</span><span class="n">template</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">err</span> <span class="o">=</span> <span class="s">""</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">output</span> <span class="o">=</span> <span class="n">output</span> <span class="o">+</span> <span class="s">"/input/"</span>
+ <span class="k">try</span><span class="p">:</span>
+ <span class="nb">open</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">output</span> <span class="o">+</span> <span class="s">"/images.db"</span><span class="p">)</span>
+ <span class="k">except</span> <span class="ne">IOError</span><span class="p">:</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">err</span> <span class="o">+=</span> <span class="s">"Path Error: Cannot open output db file. </span><span class="se">\n</span><span class="s">"</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">validator</span> <span class="o">=</span> <span class="n">ih</span><span class="o">.</span><span class="n">validator</span><span class="o">.</span><span class="n">ImageLoader</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">templatePath</span><span class="p">)</span>
+ <span class="k">if</span> <span class="ow">not</span> <span class="bp">self</span><span class="o">.</span><span class="n">validator</span><span class="o">.</span><span class="n">isValid</span><span class="p">()</span> <span class="ow">or</span> <span class="n">validOnly</span><span class="p">:</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">validator</span><span class="o">.</span><span class="n">printErrors</span><span class="p">()</span>
+ <span class="n">sys</span><span class="o">.</span><span class="n">exit</span><span class="p">()</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">overwrite</span> <span class="o">=</span> <span class="n">overwrite</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">template</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">validator</span><span class="o">.</span><span class="n">data</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">template</span><span class="p">[</span><span class="s">"order"</span><span class="p">]</span><span class="o">.</span><span class="n">insert</span><span class="p">(</span><span class="mi">0</span><span class="p">,</span> <span class="s">"pegasusid"</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">count</span> <span class="o">=</span> <span class="p">{}</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">depth</span> <span class="o">=</span> <span class="nb">len</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">template</span><span class="p">[</span><span class="s">"path"</span><span class="p">]</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s">"/"</span><span class="p">))</span> <span class="o">-</span> <span class="mi">1</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">structure</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_dictTemplate</span><span class="p">()</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">data</span> <span class="o">=</span> <span class="p">[]</span>
+ <span class="k">return</span>
+
+ <span class="k">def</span> <span class="nf">_success</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+ <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">overwrite</span><span class="p">:</span>
+ <span class="k">print</span> <span class="s">"Directory re-crawled!"</span>
+ <span class="k">print</span> <span class="s">"Use ih-run to submit your jobs."</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="k">print</span> <span class="s">"Directory setup successful!"</span>
+ <span class="k">print</span> <span class="s">"Define the required templates in "</span> <span class="o">+</span> <span class="bp">self</span><span class="o">.</span><span class="n">output</span> <span class="o">+</span> <span class="s">"."</span>
+ <span class="k">print</span> <span class="s">"Then use ih-run to submit your jobs."</span>
+ <span class="k">return</span>
+
+ <span class="k">def</span> <span class="nf">_dictTemplate</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> Creates the first of two intermediary dictionaries for crawling. This relates</span>
+<span class="sd"> identifiers in the path, to a specified depth, as well as operators to split</span>
+<span class="sd"> the value at that depth.</span>
+<span class="sd"> """</span>
+ <span class="n">m</span> <span class="o">=</span> <span class="p">[</span><span class="n">x</span> <span class="k">for</span> <span class="n">x</span> <span class="ow">in</span> <span class="n">re</span><span class="o">.</span><span class="n">findall</span><span class="p">(</span><span class="s">r"%(\w+)%"</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">template</span><span class="p">[</span><span class="s">"path"</span><span class="p">])</span> <span class="k">if</span> <span class="n">x</span> <span class="o">!=</span> <span class="s">"null"</span><span class="p">]</span>
+ <span class="n">sp</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">template</span><span class="p">[</span><span class="s">"path"</span><span class="p">]</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s">"/"</span><span class="p">)</span>
+ <span class="n">d</span> <span class="o">=</span> <span class="p">{}</span>
+ <span class="k">for</span> <span class="n">key</span> <span class="ow">in</span> <span class="n">m</span><span class="p">:</span>
+ <span class="n">d</span><span class="p">[</span><span class="n">key</span><span class="p">]</span> <span class="o">=</span> <span class="p">{}</span>
+ <span class="n">d</span><span class="p">[</span><span class="n">key</span><span class="p">][</span><span class="s">"depth"</span><span class="p">]</span> <span class="o">=</span> <span class="p">[</span><span class="n">n</span> <span class="k">for</span> <span class="n">n</span><span class="p">,</span><span class="n">x</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="n">sp</span><span class="p">)</span> <span class="k">if</span> <span class="n">key</span> <span class="ow">in</span> <span class="n">x</span><span class="p">][</span><span class="mi">0</span><span class="p">]</span>
+ <span class="n">d</span><span class="p">[</span><span class="n">key</span><span class="p">][</span><span class="s">"split"</span><span class="p">]</span> <span class="o">=</span> <span class="p">[]</span>
+ <span class="n">val</span> <span class="o">=</span> <span class="n">sp</span><span class="p">[</span><span class="n">d</span><span class="p">[</span><span class="n">key</span><span class="p">][</span><span class="s">"depth"</span><span class="p">]]</span>
+ <span class="k">for</span> <span class="n">operator</span> <span class="ow">in</span> <span class="p">[</span><span class="s">" "</span><span class="p">,</span> <span class="s">"_"</span><span class="p">,</span> <span class="s">"-"</span><span class="p">]:</span>
+ <span class="k">if</span> <span class="n">operator</span> <span class="ow">in</span> <span class="n">val</span><span class="p">:</span>
+ <span class="n">b</span> <span class="o">=</span> <span class="n">val</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="n">operator</span><span class="p">)</span>
+ <span class="n">x</span> <span class="o">=</span> <span class="p">[</span><span class="n">n</span> <span class="k">for</span> <span class="n">n</span><span class="p">,</span><span class="n">x</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="n">b</span><span class="p">)</span> <span class="k">if</span> <span class="n">key</span> <span class="ow">in</span> <span class="n">x</span><span class="p">][</span><span class="mi">0</span><span class="p">]</span>
+ <span class="n">d</span><span class="p">[</span><span class="n">key</span><span class="p">][</span><span class="s">"split"</span><span class="p">]</span><span class="o">.</span><span class="n">append</span><span class="p">({</span><span class="s">"operator"</span><span class="p">:</span> <span class="n">operator</span><span class="p">,</span> <span class="s">"index"</span><span class="p">:</span> <span class="n">x</span><span class="p">})</span>
+ <span class="n">val</span> <span class="o">=</span> <span class="n">b</span><span class="p">[</span><span class="n">x</span><span class="p">]</span>
+ <span class="k">return</span> <span class="n">d</span>
+
+ <span class="k">def</span> <span class="nf">_loadStructure</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">splitPath</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> Creates the second of two intermediary dictionaries for crawling.</span>
+<span class="sd"> This utilizes the template created in _dictTemplate, and creates</span>
+<span class="sd"> a dictionary with actual values instead of structure.</span>
+<span class="sd"> """</span>
+ <span class="n">d</span> <span class="o">=</span><span class="p">{}</span>
+ <span class="k">for</span> <span class="n">key</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">structure</span><span class="p">:</span>
+ <span class="n">val</span> <span class="o">=</span> <span class="n">splitPath</span><span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">structure</span><span class="p">[</span><span class="n">key</span><span class="p">][</span><span class="s">"depth"</span><span class="p">]]</span>
+ <span class="k">for</span> <span class="n">operator</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">structure</span><span class="p">[</span><span class="n">key</span><span class="p">][</span><span class="s">"split"</span><span class="p">]:</span>
+ <span class="n">val</span> <span class="o">=</span> <span class="n">val</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="n">operator</span><span class="p">[</span><span class="s">"operator"</span><span class="p">])[</span><span class="n">operator</span><span class="p">[</span><span class="s">"index"</span><span class="p">]]</span>
+ <span class="n">d</span><span class="p">[</span><span class="n">key</span><span class="p">]</span> <span class="o">=</span> <span class="n">val</span>
+ <span class="k">return</span> <span class="n">d</span>
+
+ <span class="k">def</span> <span class="nf">_loadDataFile</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="nb">dict</span><span class="p">,</span> <span class="n">structure</span><span class="p">,</span> <span class="n">key</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> Loads data from a data file. If the specified key isn't in the file,</span>
+<span class="sd"> write 'UNKNOWN' instead.</span>
+<span class="sd"> """</span>
+ <span class="n">keyVal</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_convertReferences</span><span class="p">(</span><span class="n">structure</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">template</span><span class="p">[</span><span class="s">"data"</span><span class="p">][</span><span class="n">key</span><span class="p">][</span><span class="s">"key"</span><span class="p">])</span>
+ <span class="k">if</span> <span class="n">keyVal</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">filedata</span><span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">template</span><span class="p">[</span><span class="s">"data"</span><span class="p">][</span><span class="n">key</span><span class="p">][</span><span class="s">"value"</span><span class="p">]]:</span>
+ <span class="nb">dict</span><span class="p">[</span><span class="n">key</span><span class="p">]</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">filedata</span><span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">template</span><span class="p">[</span><span class="s">"data"</span><span class="p">][</span><span class="n">key</span><span class="p">][</span><span class="s">"value"</span><span class="p">]][</span><span class="n">keyVal</span><span class="p">]</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="nb">dict</span><span class="p">[</span><span class="n">key</span><span class="p">]</span> <span class="o">=</span> <span class="s">"UNKNOWN"</span>
+ <span class="k">return</span>
+
+ <span class="k">def</span> <span class="nf">_loadDataValue</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="nb">dict</span><span class="p">,</span> <span class="n">structure</span><span class="p">,</span> <span class="n">key</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> Loads a data value.</span>
+<span class="sd"> """</span>
+ <span class="n">val</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_convertReferences</span><span class="p">(</span><span class="n">structure</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">template</span><span class="p">[</span><span class="s">"data"</span><span class="p">][</span><span class="n">key</span><span class="p">][</span><span class="s">"value"</span><span class="p">])</span>
+ <span class="k">if</span> <span class="s">"translate"</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">template</span><span class="p">[</span><span class="s">"data"</span><span class="p">][</span><span class="n">key</span><span class="p">]:</span>
+ <span class="k">if</span> <span class="n">val</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">template</span><span class="p">[</span><span class="s">"translations"</span><span class="p">][</span><span class="n">key</span><span class="p">]:</span>
+ <span class="n">val</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">template</span><span class="p">[</span><span class="s">"translations"</span><span class="p">][</span><span class="n">key</span><span class="p">][</span><span class="n">val</span><span class="p">]</span>
+ <span class="nb">dict</span><span class="p">[</span><span class="n">key</span><span class="p">]</span> <span class="o">=</span> <span class="n">val</span>
+ <span class="k">return</span>
+
+ <span class="k">def</span> <span class="nf">_loadDataDate</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="nb">dict</span><span class="p">,</span> <span class="n">structure</span><span class="p">,</span> <span class="n">key</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> Loads a date.</span>
+<span class="sd"> """</span>
+ <span class="n">val</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_convertReferences</span><span class="p">(</span><span class="n">structure</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">template</span><span class="p">[</span><span class="s">"data"</span><span class="p">][</span><span class="n">key</span><span class="p">][</span><span class="s">"value"</span><span class="p">])</span>
+ <span class="n">format</span> <span class="o">=</span> <span class="s">""</span><span class="o">.</span><span class="n">join</span><span class="p">([</span><span class="n">x</span><span class="o">.</span><span class="n">replace</span><span class="p">(</span><span class="n">x</span><span class="p">,</span> <span class="s">"%"</span> <span class="o">+</span> <span class="n">x</span><span class="p">)</span> <span class="k">if</span> <span class="n">x</span> <span class="ow">in</span> <span class="n">conf</span><span class="o">.</span><span class="n">dateFormat</span> <span class="k">else</span> <span class="n">x</span> <span class="k">for</span> <span class="n">x</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">template</span><span class="p">[</span><span class="s">"data"</span><span class="p">][</span><span class="n">key</span><span class="p">][</span><span class="s">"format"</span><span class="p">]])</span>
+ <span class="n">val</span> <span class="o">=</span> <span class="n">datetime</span><span class="o">.</span><span class="n">datetime</span><span class="o">.</span><span class="n">strptime</span><span class="p">(</span><span class="n">val</span><span class="p">,</span> <span class="n">format</span><span class="p">)</span><span class="o">.</span><span class="n">strftime</span><span class="p">(</span><span class="s">"%Y-%m-</span><span class="si">%d</span><span class="s">"</span><span class="p">)</span>
+ <span class="nb">dict</span><span class="p">[</span><span class="n">key</span><span class="p">]</span> <span class="o">=</span> <span class="n">val</span>
+ <span class="k">return</span>
+
+ <span class="k">def</span> <span class="nf">_convertReferences</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">structure</span><span class="p">,</span> <span class="n">val</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> Replaces all references ('%%') to actual values.</span>
+<span class="sd"> """</span>
+ <span class="n">idList</span> <span class="o">=</span> <span class="p">[</span><span class="n">x</span> <span class="k">for</span> <span class="n">x</span> <span class="ow">in</span> <span class="n">re</span><span class="o">.</span><span class="n">findall</span><span class="p">(</span><span class="s">r"%(\w+)%"</span><span class="p">,</span> <span class="n">val</span><span class="p">)</span> <span class="k">if</span> <span class="n">x</span> <span class="o">!=</span> <span class="s">"null"</span><span class="p">]</span>
+ <span class="k">for</span> <span class="n">identifier</span> <span class="ow">in</span> <span class="n">idList</span><span class="p">:</span>
+ <span class="k">if</span> <span class="n">identifier</span> <span class="ow">in</span> <span class="n">structure</span><span class="p">:</span>
+ <span class="n">val</span> <span class="o">=</span> <span class="n">val</span><span class="o">.</span><span class="n">replace</span><span class="p">(</span><span class="s">"%"</span> <span class="o">+</span> <span class="n">identifier</span> <span class="o">+</span> <span class="s">"%"</span><span class="p">,</span> <span class="n">structure</span><span class="p">[</span><span class="n">identifier</span><span class="p">])</span>
+ <span class="k">return</span> <span class="n">val</span>
+
+ <span class="k">def</span> <span class="nf">_loadData</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">path</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> Loads all data for a particular path.</span>
+<span class="sd"> """</span>
+ <span class="n">temp</span> <span class="o">=</span> <span class="p">{}</span>
+ <span class="n">final</span> <span class="o">=</span> <span class="p">{}</span>
+ <span class="n">splitPath</span> <span class="o">=</span> <span class="n">path</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s">"/"</span><span class="p">)</span>
+ <span class="n">structure</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_loadStructure</span><span class="p">(</span><span class="n">splitPath</span><span class="p">)</span>
+ <span class="k">for</span> <span class="n">key</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">template</span><span class="p">[</span><span class="s">"data"</span><span class="p">]:</span>
+ <span class="n">d</span> <span class="o">=</span> <span class="p">{</span>
+ <span class="s">"value"</span><span class="p">:</span> <span class="bp">self</span><span class="o">.</span><span class="n">_loadDataValue</span><span class="p">,</span>
+ <span class="s">"file"</span><span class="p">:</span> <span class="bp">self</span><span class="o">.</span><span class="n">_loadDataFile</span><span class="p">,</span>
+ <span class="s">"date"</span><span class="p">:</span> <span class="bp">self</span><span class="o">.</span><span class="n">_loadDataDate</span>
+ <span class="p">}[</span><span class="bp">self</span><span class="o">.</span><span class="n">template</span><span class="p">[</span><span class="s">"data"</span><span class="p">][</span><span class="n">key</span><span class="p">][</span><span class="s">"type"</span><span class="p">]](</span><span class="n">final</span><span class="p">,</span> <span class="n">structure</span><span class="p">,</span> <span class="n">key</span><span class="p">)</span>
+ <span class="n">final</span><span class="p">[</span><span class="s">"path"</span><span class="p">]</span> <span class="o">=</span> <span class="n">path</span>
+ <span class="k">if</span> <span class="n">final</span><span class="p">[</span><span class="s">"imtype"</span><span class="p">]</span> <span class="ow">not</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">count</span><span class="p">:</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">count</span><span class="p">[</span><span class="n">final</span><span class="p">[</span><span class="s">"imtype"</span><span class="p">]]</span> <span class="o">=</span> <span class="mi">1</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">count</span><span class="p">[</span><span class="n">final</span><span class="p">[</span><span class="s">"imtype"</span><span class="p">]]</span> <span class="o">+=</span> <span class="mi">1</span>
+ <span class="n">final</span><span class="p">[</span><span class="s">"pegasusid"</span><span class="p">]</span> <span class="o">=</span> <span class="n">final</span><span class="p">[</span><span class="s">"imtype"</span><span class="p">]</span> <span class="o">+</span> <span class="nb">str</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">count</span><span class="p">[</span><span class="n">final</span><span class="p">[</span><span class="s">"imtype"</span><span class="p">]])</span>
+ <span class="k">return</span> <span class="n">final</span>
+
+ <span class="k">def</span> <span class="nf">_loadFiles</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> Reads all data from all specified files.</span>
+<span class="sd"> """</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">filedata</span> <span class="o">=</span> <span class="p">{}</span>
+ <span class="k">for</span> <span class="n">key</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">template</span><span class="p">[</span><span class="s">"data"</span><span class="p">]:</span>
+ <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">template</span><span class="p">[</span><span class="s">"data"</span><span class="p">][</span><span class="n">key</span><span class="p">][</span><span class="s">"type"</span><span class="p">]</span> <span class="o">==</span> <span class="s">"file"</span><span class="p">:</span>
+ <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">template</span><span class="p">[</span><span class="s">"data"</span><span class="p">][</span><span class="n">key</span><span class="p">][</span><span class="s">"value"</span><span class="p">]</span> <span class="ow">not</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">filedata</span><span class="p">:</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">filedata</span><span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">template</span><span class="p">[</span><span class="s">"data"</span><span class="p">][</span><span class="n">key</span><span class="p">][</span><span class="s">"value"</span><span class="p">]]</span> <span class="o">=</span> <span class="p">{}</span>
+ <span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">template</span><span class="p">[</span><span class="s">"data"</span><span class="p">][</span><span class="n">key</span><span class="p">][</span><span class="s">"value"</span><span class="p">],</span> <span class="s">"r"</span><span class="p">)</span> <span class="k">as</span> <span class="n">rh</span><span class="p">:</span>
+ <span class="k">for</span> <span class="n">line</span> <span class="ow">in</span> <span class="n">rh</span><span class="o">.</span><span class="n">readlines</span><span class="p">():</span>
+ <span class="n">info</span> <span class="o">=</span> <span class="n">line</span><span class="o">.</span><span class="n">strip</span><span class="p">()</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s">","</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">filedata</span><span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">template</span><span class="p">[</span><span class="s">"data"</span><span class="p">][</span><span class="n">key</span><span class="p">][</span><span class="s">"value"</span><span class="p">]][</span><span class="n">info</span><span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">template</span><span class="p">[</span><span class="s">"data"</span><span class="p">][</span><span class="n">key</span><span class="p">][</span><span class="s">"keyColumn"</span><span class="p">]]]</span> <span class="o">=</span> <span class="n">info</span><span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">template</span><span class="p">[</span><span class="s">"data"</span><span class="p">][</span><span class="n">key</span><span class="p">][</span><span class="s">"valueColumn"</span><span class="p">]]</span>
+ <span class="k">return</span>
+
+<div class="viewcode-block" id="ImageLoader.crawl"><a class="viewcode-back" href="../../indexing.html#ih.workflow.ImageLoader.crawl">[docs]</a> <span class="k">def</span> <span class="nf">crawl</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> Recursively walks through directories in base, and loads</span>
+<span class="sd"> the appropriate data.</span>
+<span class="sd"> """</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_loadFiles</span><span class="p">()</span>
+ <span class="k">for</span> <span class="n">root</span><span class="p">,</span> <span class="n">dirs</span><span class="p">,</span> <span class="n">files</span> <span class="ow">in</span> <span class="n">os</span><span class="o">.</span><span class="n">walk</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">template</span><span class="p">[</span><span class="s">"base"</span><span class="p">]):</span>
+ <span class="n">arr</span> <span class="o">=</span> <span class="n">root</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s">"/"</span><span class="p">)</span>
+ <span class="n">depth</span> <span class="o">=</span> <span class="nb">len</span><span class="p">(</span><span class="n">arr</span><span class="p">)</span>
+ <span class="k">if</span> <span class="p">(</span><span class="n">depth</span> <span class="o">==</span> <span class="bp">self</span><span class="o">.</span><span class="n">depth</span><span class="p">):</span>
+ <span class="k">for</span> <span class="nb">file</span> <span class="ow">in</span> <span class="n">files</span><span class="p">:</span>
+ <span class="k">if</span> <span class="nb">file</span><span class="p">[</span><span class="o">-</span><span class="nb">len</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">template</span><span class="p">[</span><span class="s">"filetype"</span><span class="p">]):]</span> <span class="o">==</span> <span class="bp">self</span><span class="o">.</span><span class="n">template</span><span class="p">[</span><span class="s">"filetype"</span><span class="p">]</span> <span class="ow">and</span> <span class="nb">file</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="o">!=</span> <span class="s">"."</span><span class="p">:</span>
+ <span class="n">d</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_loadData</span><span class="p">(</span><span class="n">root</span> <span class="o">+</span> <span class="s">"/"</span> <span class="o">+</span> <span class="nb">file</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">data</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">d</span><span class="p">)</span>
+ <span class="k">return</span>
+ </div>
+<div class="viewcode-block" id="ImageLoader.write"><a class="viewcode-back" href="../../indexing.html#ih.workflow.ImageLoader.write">[docs]</a> <span class="k">def</span> <span class="nf">write</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> Writes the data loaded from crawl into csv format based on 'order'</span>
+<span class="sd"> """</span>
+ <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">data</span><span class="p">:</span>
+ <span class="n">conn</span> <span class="o">=</span> <span class="n">sqlite3</span><span class="o">.</span><span class="n">connect</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">output</span> <span class="o">+</span> <span class="s">"/images.db"</span><span class="p">)</span>
+ <span class="n">tablestr</span> <span class="o">=</span> <span class="s">"(pegasusid PRIMARY KEY"</span>
+ <span class="k">for</span> <span class="n">x</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">template</span><span class="p">[</span><span class="s">"order"</span><span class="p">]:</span>
+ <span class="k">if</span> <span class="n">x</span> <span class="o">!=</span> <span class="s">"pegasusid"</span><span class="p">:</span>
+ <span class="n">tablestr</span> <span class="o">+=</span> <span class="s">","</span> <span class="o">+</span> <span class="nb">str</span><span class="p">(</span><span class="n">x</span><span class="p">)</span>
+ <span class="n">tablestr</span> <span class="o">+=</span> <span class="s">")"</span>
+ <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">overwrite</span><span class="p">:</span>
+ <span class="n">conn</span><span class="o">.</span><span class="n">execute</span><span class="p">(</span><span class="s">"DROP TABLE IF EXISTS images"</span><span class="p">)</span>
+ <span class="n">conn</span><span class="o">.</span><span class="n">commit</span><span class="p">()</span>
+ <span class="n">conn</span><span class="o">.</span><span class="n">execute</span><span class="p">(</span><span class="s">"CREATE TABLE images "</span> <span class="o">+</span> <span class="n">tablestr</span><span class="p">)</span>
+ <span class="n">writedata</span> <span class="o">=</span> <span class="p">[]</span>
+ <span class="k">for</span> <span class="n">row</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">data</span><span class="p">:</span>
+ <span class="n">writedata</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="nb">tuple</span><span class="p">([</span><span class="nb">str</span><span class="p">(</span><span class="n">row</span><span class="p">[</span><span class="n">x</span><span class="p">])</span> <span class="k">for</span> <span class="n">x</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">template</span><span class="p">[</span><span class="s">"order"</span><span class="p">]]))</span>
+ <span class="n">query</span> <span class="o">=</span> <span class="s">"insert into images "</span> <span class="o">+</span> <span class="nb">str</span><span class="p">(</span><span class="nb">tuple</span><span class="p">([</span><span class="nb">str</span><span class="p">(</span><span class="n">x</span><span class="p">)</span> <span class="k">for</span> <span class="n">x</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">template</span><span class="p">[</span><span class="s">"order"</span><span class="p">]]))</span> <span class="o">+</span> <span class="s">" values ("</span> <span class="o">+</span> <span class="p">(</span><span class="s">"?,"</span> <span class="o">*</span> <span class="nb">len</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">template</span><span class="p">[</span><span class="s">"order"</span><span class="p">]))[:</span><span class="o">-</span><span class="mi">1</span><span class="p">]</span> <span class="o">+</span> <span class="s">")"</span>
+ <span class="n">conn</span><span class="o">.</span><span class="n">executemany</span><span class="p">(</span><span class="n">query</span><span class="p">,</span> <span class="n">writedata</span><span class="p">)</span>
+ <span class="n">conn</span><span class="o">.</span><span class="n">commit</span><span class="p">()</span>
+ <span class="k">if</span> <span class="ow">not</span> <span class="bp">self</span><span class="o">.</span><span class="n">overwrite</span><span class="p">:</span>
+ <span class="n">shutil</span><span class="o">.</span><span class="n">copyfile</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">templatePath</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">output</span> <span class="o">+</span> <span class="s">"/crawl.json"</span><span class="p">)</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="k">print</span> <span class="s">"Call crawl first!"</span>
+ <span class="k">return</span>
+ </div></div>
+<span class="k">class</span> <span class="nc">DirectorySetup</span><span class="p">:</span>
+
+ <span class="k">def</span> <span class="nf">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">jobhome</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> :param jobhome: The base directory to setup a job.</span>
+<span class="sd"> :type jobhome: str</span>
+<span class="sd"> """</span>
+ <span class="k">if</span> <span class="ow">not</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">isdir</span><span class="p">(</span><span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">dirname</span><span class="p">(</span><span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">dirname</span><span class="p">(</span><span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">abspath</span><span class="p">(</span><span class="n">jobhome</span><span class="p">)</span> <span class="o">+</span> <span class="s">"/"</span><span class="p">))):</span>
+ <span class="k">print</span> <span class="s">"Can't create job folder, path doesn't exist!"</span>
+ <span class="n">sys</span><span class="o">.</span><span class="n">exit</span><span class="p">()</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">jobhome</span> <span class="o">=</span> <span class="n">jobhome</span>
+ <span class="k">return</span>
+
+ <span class="k">def</span> <span class="nf">_makeDir</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">dirpath</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> Makes a directory if it doesn't exist. Catches and</span>
+<span class="sd"> prints out common errors.</span>
+<span class="sd"> """</span>
+ <span class="k">try</span><span class="p">:</span>
+ <span class="n">os</span><span class="o">.</span><span class="n">makedirs</span><span class="p">(</span><span class="n">dirpath</span><span class="p">)</span>
+ <span class="k">except</span> <span class="ne">OSError</span> <span class="k">as</span> <span class="n">e</span><span class="p">:</span>
+ <span class="k">raise</span> <span class="ne">Exception</span><span class="p">({</span>
+ <span class="n">errno</span><span class="o">.</span><span class="n">EEXIST</span><span class="p">:</span> <span class="s">"Directory "</span> <span class="o">+</span> <span class="n">dirpath</span> <span class="o">+</span> <span class="s">" already exists!"</span><span class="p">,</span>
+ <span class="n">errno</span><span class="o">.</span><span class="n">EACCES</span><span class="p">:</span> <span class="s">"You don't have permission to create directory "</span> <span class="o">+</span> <span class="n">dirpath</span> <span class="o">+</span> <span class="s">"."</span><span class="p">,</span>
+ <span class="p">}</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="n">e</span><span class="o">.</span><span class="n">errno</span><span class="p">,</span> <span class="s">"Error for directory "</span> <span class="o">+</span> <span class="n">dirpath</span> <span class="o">+</span> <span class="s">" error:"</span> <span class="o">+</span> <span class="nb">str</span><span class="p">(</span><span class="n">e</span><span class="p">)))</span>
+ <span class="k">return</span>
+
+ <span class="k">def</span> <span class="nf">_makeFile</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">filepath</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> Opens a file to create it, uses append mode</span>
+<span class="sd"> so it doesn't overwrite any existing files.</span>
+<span class="sd"> """</span>
+ <span class="k">try</span><span class="p">:</span>
+ <span class="nb">open</span><span class="p">(</span><span class="n">filepath</span><span class="p">,</span> <span class="s">"a"</span><span class="p">)</span>
+ <span class="k">except</span> <span class="ne">OSError</span> <span class="k">as</span> <span class="n">e</span><span class="p">:</span>
+ <span class="k">raise</span> <span class="ne">Exception</span><span class="p">({</span>
+
+ <span class="p">}</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="n">e</span><span class="p">,</span> <span class="s">"Unsepcified error for file "</span> <span class="o">+</span> <span class="n">filepath</span><span class="p">))</span>
+ <span class="k">return</span>
+
+ <span class="k">def</span> <span class="nf">setup</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> Creates the directory structure needed to submit jobs,</span>
+<span class="sd"> and creates empty template files needed for job submission.</span>
+<span class="sd"> """</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_makeDir</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">jobhome</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_makeDir</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">jobhome</span> <span class="o">+</span> <span class="s">"/input/"</span><span class="p">)</span>
+ <span class="k">for</span> <span class="n">fname</span> <span class="ow">in</span> <span class="n">conf</span><span class="o">.</span><span class="n">jobFiles</span><span class="p">:</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_makeFile</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">jobhome</span> <span class="o">+</span> <span class="s">"/input/"</span> <span class="o">+</span> <span class="n">fname</span><span class="p">)</span>
+ <span class="k">return</span>
+
+
+
+</pre></div>
+
+ </div>
+
+ </div>
+</div>
+<footer class="footer">
+ <div class="container">
+ <p class="pull-right">
+ <a href="#">Back to top</a>
+
+ </p>
+ <p>
+ © Copyright 2015, Avi Knecht.<br/>
+ Created using <a href="http://sphinx.pocoo.org/">Sphinx</a> 1.3a0.<br/>
+ </p>
+ </div>
+</footer>
+ </body>
+</html>
\ No newline at end of file
diff --git a/docs/build/html/_modules/index.html b/docs/build/html/_modules/index.html
new file mode 100644
index 0000000000000000000000000000000000000000..32ababe99bd774195a65949f91c28ac4480af48b
--- /dev/null
+++ b/docs/build/html/_modules/index.html
@@ -0,0 +1,158 @@
+<!DOCTYPE html>
+
+
+<html xmlns="http://www.w3.org/1999/xhtml">
+ <head>
+ <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
+
+ <title>Overview: module code — Image Harvest 1.0.1 documentation</title>
+
+ <link rel="stylesheet" href="../_static/basic.css" type="text/css" />
+ <link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
+ <link rel="stylesheet" href="../_static/bootstrap-3.2.0/css/bootstrap.min.css" type="text/css" />
+ <link rel="stylesheet" href="../_static/bootstrap-3.2.0/css/bootstrap-theme.min.css" type="text/css" />
+ <link rel="stylesheet" href="../_static/bootstrap-sphinx.css" type="text/css" />
+
+ <script type="text/javascript">
+ var DOCUMENTATION_OPTIONS = {
+ URL_ROOT: '../',
+ VERSION: '1.0.1',
+ COLLAPSE_INDEX: false,
+ FILE_SUFFIX: '.html',
+ HAS_SOURCE: true
+ };
+ </script>
+ <script type="text/javascript" src="../_static/jquery.js"></script>
+ <script type="text/javascript" src="../_static/underscore.js"></script>
+ <script type="text/javascript" src="../_static/doctools.js"></script>
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+ <script type="text/javascript" src="../_static/js/jquery-1.11.0.min.js"></script>
+ <script type="text/javascript" src="../_static/js/jquery-fix.js"></script>
+ <script type="text/javascript" src="../_static/bootstrap-3.2.0/js/bootstrap.min.js"></script>
+ <script type="text/javascript" src="../_static/bootstrap-sphinx.js"></script>
+ <link rel="top" title="Image Harvest 1.0.1 documentation" href="../index.html" />
+<meta charset='utf-8'>
+<meta http-equiv='X-UA-Compatible' content='IE=edge,chrome=1'>
+<meta name='viewport' content='width=device-width, initial-scale=1.0, maximum-scale=1'>
+<meta name="apple-mobile-web-app-capable" content="yes">
+
+ </head>
+ <body role="document">
+
+ <div id="navbar" class="navbar navbar-default navbar-fixed-top">
+ <div class="container">
+ <div class="navbar-header">
+ <!-- .btn-navbar is used as the toggle for collapsed navbar content -->
+ <button type="button" class="navbar-toggle" data-toggle="collapse" data-target=".nav-collapse">
+ <span class="icon-bar"></span>
+ <span class="icon-bar"></span>
+ <span class="icon-bar"></span>
+ </button>
+ <a class="navbar-brand" href="../index.html">
+ Image Harvest</a>
+ <span class="navbar-text navbar-version pull-left"><b>1.0</b></span>
+ </div>
+
+ <div class="collapse navbar-collapse nav-collapse">
+ <ul class="nav navbar-nav">
+
+
+ <li class="dropdown globaltoc-container">
+ <a role="button"
+ id="dLabelGlobalToc"
+ data-toggle="dropdown"
+ data-target="#"
+ href="../index.html">Site <b class="caret"></b></a>
+ <ul class="dropdown-menu globaltoc"
+ role="menu"
+ aria-labelledby="dLabelGlobalToc"><ul>
+<li class="toctree-l1"><a class="reference internal" href="../introduction.html">Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../installation.html">Installation</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../start.html">Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../ex_script_core1.html">Core Processing Example #1</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../ex_script_core2.html">Core Processing Example #2</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../ex_script_color1.html">Color Filter In Depth #1</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../ex_workflow_1.html">Workflow Example #1</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../examples.html">Examples</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../processing.html">Image Processing</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../viewer.html">Image Processing Viewer</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../statistics.html">Statistics</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../indexing.html">Image Loading</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../workflowimage.html">Image Processing Workflows</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../workflowstats.html">Statistics Workflows</a></li>
+</ul>
+</ul>
+</li>
+
+ <li class="dropdown">
+ <a role="button"
+ id="dLabelLocalToc"
+ data-toggle="dropdown"
+ data-target="#"
+ href="#">Page <b class="caret"></b></a>
+ <ul class="dropdown-menu localtoc"
+ role="menu"
+ aria-labelledby="dLabelLocalToc"></ul>
+</li>
+
+
+
+
+
+
+
+
+
+
+ <li class="hidden-sm"></li>
+
+ </ul>
+
+
+
+<form class="navbar-form navbar-right" action="../search.html" method="get">
+ <div class="form-group">
+ <input type="text" name="q" class="form-control" placeholder="Search" />
+ </div>
+ <input type="hidden" name="check_keywords" value="yes" />
+ <input type="hidden" name="area" value="default" />
+</form>
+
+ </div>
+ </div>
+ </div>
+
+<div class="container">
+ <div class="row">
+ <div class="col-md-12">
+
+ <h1>All modules for which code is available</h1>
+<ul><li><a href="htpia/imgproc.html">htpia.imgproc</a></li>
+<li><a href="htpia/statistics.html">htpia.statistics</a></li>
+<li><a href="htpia/workflow.html">htpia.workflow</a></li>
+<li><a href="ih/imgproc.html">ih.imgproc</a></li>
+<li><a href="ih/statistics.html">ih.statistics</a></li>
+<li><a href="ih/workflow.html">ih.workflow</a></li>
+<li><a href="plantcv/imgproc.html">plantcv.imgproc</a></li>
+<li><a href="plantcv/statistics.html">plantcv.statistics</a></li>
+<li><a href="plantcv/workflow.html">plantcv.workflow</a></li>
+</ul>
+
+ </div>
+
+ </div>
+</div>
+<footer class="footer">
+ <div class="container">
+ <p class="pull-right">
+ <a href="#">Back to top</a>
+
+ </p>
+ <p>
+ © Copyright 2015, Avi Knecht.<br/>
+ Created using <a href="http://sphinx.pocoo.org/">Sphinx</a> 1.3a0.<br/>
+ </p>
+ </div>
+</footer>
+ </body>
+</html>
\ No newline at end of file
diff --git a/docs/build/html/_modules/plantcv/imgproc.html b/docs/build/html/_modules/plantcv/imgproc.html
new file mode 100644
index 0000000000000000000000000000000000000000..750778867323855a8ead882328883dca13a7ad7d
--- /dev/null
+++ b/docs/build/html/_modules/plantcv/imgproc.html
@@ -0,0 +1,1091 @@
+<!DOCTYPE html>
+
+
+<html xmlns="http://www.w3.org/1999/xhtml">
+ <head>
+ <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
+
+ <title>plantcv.imgproc — Image Harvest 1.0.1 documentation</title>
+
+ <link rel="stylesheet" href="../../_static/basic.css" type="text/css" />
+ <link rel="stylesheet" href="../../_static/pygments.css" type="text/css" />
+ <link rel="stylesheet" href="../../_static/bootstrap-3.2.0/css/bootstrap.min.css" type="text/css" />
+ <link rel="stylesheet" href="../../_static/bootstrap-3.2.0/css/bootstrap-theme.min.css" type="text/css" />
+ <link rel="stylesheet" href="../../_static/bootstrap-sphinx.css" type="text/css" />
+
+ <script type="text/javascript">
+ var DOCUMENTATION_OPTIONS = {
+ URL_ROOT: '../../',
+ VERSION: '1.0.1',
+ COLLAPSE_INDEX: false,
+ FILE_SUFFIX: '.html',
+ HAS_SOURCE: true
+ };
+ </script>
+ <script type="text/javascript" src="../../_static/jquery.js"></script>
+ <script type="text/javascript" src="../../_static/underscore.js"></script>
+ <script type="text/javascript" src="../../_static/doctools.js"></script>
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+ <script type="text/javascript" src="../../_static/js/jquery-fix.js"></script>
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+ <script type="text/javascript" src="../../_static/bootstrap-sphinx.js"></script>
+ <link rel="top" title="Image Harvest 1.0.1 documentation" href="../../index.html" />
+ <link rel="up" title="Module code" href="../index.html" />
+<meta charset='utf-8'>
+<meta http-equiv='X-UA-Compatible' content='IE=edge,chrome=1'>
+<meta name='viewport' content='width=device-width, initial-scale=1.0, maximum-scale=1'>
+<meta name="apple-mobile-web-app-capable" content="yes">
+
+ </head>
+ <body role="document">
+
+ <div id="navbar" class="navbar navbar-default navbar-fixed-top">
+ <div class="container">
+ <div class="navbar-header">
+ <!-- .btn-navbar is used as the toggle for collapsed navbar content -->
+ <button type="button" class="navbar-toggle" data-toggle="collapse" data-target=".nav-collapse">
+ <span class="icon-bar"></span>
+ <span class="icon-bar"></span>
+ <span class="icon-bar"></span>
+ </button>
+ <a class="navbar-brand" href="../../index.html">
+ Image Harvest</a>
+ <span class="navbar-text navbar-version pull-left"><b>1.0</b></span>
+ </div>
+
+ <div class="collapse navbar-collapse nav-collapse">
+ <ul class="nav navbar-nav">
+
+
+ <li class="dropdown globaltoc-container">
+ <a role="button"
+ id="dLabelGlobalToc"
+ data-toggle="dropdown"
+ data-target="#"
+ href="../../index.html">Site <b class="caret"></b></a>
+ <ul class="dropdown-menu globaltoc"
+ role="menu"
+ aria-labelledby="dLabelGlobalToc"><ul>
+<li class="toctree-l1"><a class="reference internal" href="../../introduction.html">Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../../installation.html">Installation</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../../start.html">Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../../ex_script_core1.html">Core Processing Example #1</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../../ex_script_core2.html">Core Processing Example #2</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../../ex_script_color1.html">Color Filter In Depth #1</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../../ex_workflow_1.html">Workflow Example #1</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../../examples.html">Examples</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../../processing.html">Image Processing</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../../viewer.html">Image Processing Viewer</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../../statistics.html">Statistics</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../../indexing.html">Image Loading</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../../workflowimage.html">Image Processing Workflows</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../../workflowstats.html">Statistics Workflows</a></li>
+</ul>
+</ul>
+</li>
+
+ <li class="dropdown">
+ <a role="button"
+ id="dLabelLocalToc"
+ data-toggle="dropdown"
+ data-target="#"
+ href="#">Page <b class="caret"></b></a>
+ <ul class="dropdown-menu localtoc"
+ role="menu"
+ aria-labelledby="dLabelLocalToc"></ul>
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+ <h1>Source code for plantcv.imgproc</h1><div class="highlight"><pre>
+<span class="sd">"""</span>
+
+<span class="sd">.. module:: imgproc</span>
+<span class="sd"> :platform: Mac, Linux</span>
+<span class="sd"> :synopsis: Image processing function wrappers to opencv.</span>
+
+<span class="sd">.. moduleauthor:: Avi Knecht <avi@kurtknecht.com></span>
+
+<span class="sd">"""</span>
+
+<span class="kn">import</span> <span class="nn">os</span>
+<span class="kn">import</span> <span class="nn">cv2</span>
+<span class="kn">import</span> <span class="nn">numpy</span> <span class="kn">as</span> <span class="nn">np</span>
+<span class="kn">import</span> <span class="nn">math</span>
+<span class="kn">import</span> <span class="nn">conf</span>
+<span class="kn">import</span> <span class="nn">sqlite3</span>
+<span class="kn">import</span> <span class="nn">pymeanshift</span> <span class="kn">as</span> <span class="nn">pms</span>
+<span class="kn">import</span> <span class="nn">traceback</span>
+<span class="kn">import</span> <span class="nn">json</span>
+
+<span class="k">class</span> <span class="nc">ColorFilter</span><span class="p">(</span><span class="nb">object</span><span class="p">):</span>
+
+ <span class="sd">"""</span>
+<span class="sd"> Color Filtration logic container.</span>
+<span class="sd"> """</span>
+ <span class="k">def</span> <span class="nf">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="nb">filter</span><span class="p">):</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">tokens</span> <span class="o">=</span> <span class="p">{</span>
+ <span class="s">"True"</span><span class="p">:</span> <span class="bp">True</span><span class="p">,</span>
+ <span class="s">"False"</span><span class="p">:</span> <span class="bp">False</span><span class="p">,</span>
+ <span class="s">"and"</span><span class="p">:</span> <span class="k">lambda</span> <span class="n">left</span><span class="p">,</span> <span class="n">right</span><span class="p">:</span> <span class="n">np</span><span class="o">.</span><span class="n">logical_and</span><span class="p">(</span><span class="n">left</span><span class="p">,</span> <span class="n">right</span><span class="p">),</span>
+ <span class="s">"or"</span><span class="p">:</span> <span class="k">lambda</span> <span class="n">left</span><span class="p">,</span> <span class="n">right</span><span class="p">:</span> <span class="n">np</span><span class="o">.</span><span class="n">logical_or</span><span class="p">(</span><span class="n">left</span><span class="p">,</span> <span class="n">right</span><span class="p">),</span>
+ <span class="s">">"</span><span class="p">:</span> <span class="k">lambda</span> <span class="n">left</span><span class="p">,</span> <span class="n">right</span><span class="p">:</span> <span class="n">left</span> <span class="o">></span> <span class="n">right</span><span class="p">,</span>
+ <span class="s">"<"</span><span class="p">:</span> <span class="k">lambda</span> <span class="n">left</span><span class="p">,</span> <span class="n">right</span><span class="p">:</span> <span class="n">left</span> <span class="o"><</span> <span class="n">right</span><span class="p">,</span>
+ <span class="s">">="</span><span class="p">:</span> <span class="k">lambda</span> <span class="n">left</span><span class="p">,</span> <span class="n">right</span><span class="p">:</span> <span class="n">left</span> <span class="o">>=</span> <span class="n">right</span><span class="p">,</span>
+ <span class="s">"<="</span><span class="p">:</span> <span class="k">lambda</span> <span class="n">left</span><span class="p">,</span> <span class="n">right</span><span class="p">:</span> <span class="n">left</span> <span class="o"><=</span> <span class="n">right</span><span class="p">,</span>
+ <span class="s">"="</span><span class="p">:</span> <span class="k">lambda</span> <span class="n">left</span><span class="p">,</span> <span class="n">right</span><span class="p">:</span> <span class="n">left</span> <span class="o">==</span> <span class="n">right</span><span class="p">,</span>
+ <span class="s">"+"</span><span class="p">:</span> <span class="k">lambda</span> <span class="n">left</span><span class="p">,</span> <span class="n">right</span><span class="p">:</span> <span class="n">left</span> <span class="o">+</span> <span class="n">right</span><span class="p">,</span>
+ <span class="s">"-"</span><span class="p">:</span> <span class="k">lambda</span> <span class="n">left</span><span class="p">,</span> <span class="n">right</span><span class="p">:</span> <span class="n">left</span> <span class="o">-</span> <span class="n">right</span><span class="p">,</span>
+ <span class="s">"*"</span><span class="p">:</span> <span class="k">lambda</span> <span class="n">left</span><span class="p">,</span> <span class="n">right</span><span class="p">:</span> <span class="n">left</span> <span class="o">*</span> <span class="n">right</span><span class="p">,</span>
+ <span class="s">"/"</span><span class="p">:</span> <span class="k">lambda</span> <span class="n">left</span><span class="p">,</span> <span class="n">right</span><span class="p">:</span> <span class="n">left</span> <span class="o">/</span> <span class="n">right</span><span class="p">,</span>
+ <span class="s">"max"</span><span class="p">:</span> <span class="k">lambda</span> <span class="n">left</span><span class="p">,</span> <span class="n">right</span><span class="p">:</span> <span class="n">np</span><span class="o">.</span><span class="n">maximum</span><span class="p">(</span><span class="n">left</span><span class="p">,</span> <span class="n">right</span><span class="p">),</span>
+ <span class="s">"min"</span><span class="p">:</span> <span class="k">lambda</span> <span class="n">left</span><span class="p">,</span> <span class="n">right</span><span class="p">:</span> <span class="n">np</span><span class="o">.</span><span class="n">minimum</span><span class="p">(</span><span class="n">left</span><span class="p">,</span> <span class="n">right</span><span class="p">),</span>
+ <span class="s">"not"</span><span class="p">:</span> <span class="k">lambda</span> <span class="n">left</span><span class="p">,</span> <span class="n">right</span><span class="p">:</span> <span class="n">np</span><span class="o">.</span><span class="n">invert</span><span class="p">(</span><span class="n">left</span><span class="p">),</span>
+ <span class="s">"("</span><span class="p">:</span> <span class="s">"("</span><span class="p">,</span>
+ <span class="s">")"</span><span class="p">:</span> <span class="s">")"</span><span class="p">,</span>
+ <span class="p">}</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">filterString</span> <span class="o">=</span> <span class="nb">filter</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">emptyRes</span> <span class="o">=</span> <span class="bp">True</span>
+ <span class="k">return</span>
+
+ <span class="k">def</span> <span class="nf">_createArgList</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+ <span class="n">s</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">filterString</span><span class="o">.</span><span class="n">replace</span><span class="p">(</span><span class="s">"("</span><span class="p">,</span> <span class="s">" ( "</span><span class="p">)</span>
+ <span class="n">s</span> <span class="o">=</span> <span class="n">s</span><span class="o">.</span><span class="n">replace</span><span class="p">(</span><span class="s">")"</span><span class="p">,</span> <span class="s">" ) "</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">filter</span> <span class="o">=</span> <span class="p">[]</span>
+ <span class="k">for</span> <span class="n">item</span> <span class="ow">in</span> <span class="n">s</span><span class="o">.</span><span class="n">split</span><span class="p">():</span>
+ <span class="k">if</span> <span class="n">item</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">tokens</span><span class="p">:</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">filter</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">tokens</span><span class="p">[</span><span class="n">item</span><span class="p">])</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="k">try</span><span class="p">:</span>
+ <span class="n">val</span> <span class="o">=</span> <span class="nb">int</span><span class="p">(</span><span class="n">item</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">filter</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">val</span><span class="p">)</span>
+ <span class="k">except</span><span class="p">:</span>
+ <span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="s">"Invalid logic string."</span><span class="p">)</span>
+ <span class="c">#self.filter = [self.tokens[x] if x in self.tokens else int(x) for x in s.split()]</span>
+ <span class="k">return</span>
+
+ <span class="k">def</span> <span class="nf">_find</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">what</span><span class="p">,</span> <span class="n">start</span> <span class="o">=</span> <span class="mi">0</span><span class="p">):</span>
+ <span class="k">return</span> <span class="p">[</span><span class="n">i</span> <span class="k">for</span> <span class="n">i</span><span class="p">,</span><span class="n">x</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">filter</span><span class="p">)</span> <span class="k">if</span> <span class="n">x</span> <span class="o">==</span> <span class="n">what</span> <span class="ow">and</span> <span class="n">i</span> <span class="o">>=</span> <span class="n">start</span><span class="p">]</span>
+
+ <span class="k">def</span> <span class="nf">_parens</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+ <span class="n">left_1st</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_find</span><span class="p">(</span><span class="s">"("</span><span class="p">)</span>
+ <span class="k">if</span> <span class="ow">not</span> <span class="n">left_1st</span><span class="p">:</span>
+ <span class="k">return</span> <span class="bp">False</span><span class="p">,</span> <span class="o">-</span><span class="mi">1</span><span class="p">,</span> <span class="o">-</span><span class="mi">1</span>
+ <span class="n">left</span> <span class="o">=</span> <span class="n">left_1st</span><span class="p">[</span><span class="o">-</span><span class="mi">1</span><span class="p">]</span>
+ <span class="n">right</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_find</span><span class="p">(</span><span class="s">")"</span><span class="p">,</span> <span class="n">left</span> <span class="o">+</span> <span class="mi">2</span><span class="p">)[</span><span class="mi">0</span><span class="p">]</span>
+ <span class="k">return</span> <span class="bp">True</span><span class="p">,</span> <span class="n">left</span><span class="p">,</span> <span class="n">right</span>
+
+ <span class="k">def</span> <span class="nf">_eval</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="nb">filter</span><span class="p">):</span>
+ <span class="k">return</span> <span class="nb">filter</span><span class="p">[</span><span class="mi">1</span><span class="p">](</span><span class="nb">filter</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span> <span class="nb">filter</span><span class="p">[</span><span class="mi">2</span><span class="p">])</span>
+
+ <span class="k">def</span> <span class="nf">_formattedEval</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="nb">filter</span><span class="p">):</span>
+ <span class="k">if</span> <span class="ow">not</span> <span class="nb">filter</span><span class="p">:</span>
+ <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">emptyRes</span>
+ <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="nb">filter</span><span class="p">)</span> <span class="o">==</span> <span class="mi">1</span><span class="p">:</span>
+ <span class="k">return</span> <span class="nb">filter</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span>
+
+ <span class="n">has_parens</span><span class="p">,</span> <span class="n">l_paren</span><span class="p">,</span> <span class="n">r_paren</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_parens</span><span class="p">()</span>
+
+ <span class="k">if</span> <span class="ow">not</span> <span class="n">has_parens</span><span class="p">:</span>
+ <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">_eval</span><span class="p">(</span><span class="nb">filter</span><span class="p">)</span>
+
+ <span class="nb">filter</span><span class="p">[</span><span class="n">l_paren</span><span class="p">:</span><span class="n">r_paren</span> <span class="o">+</span> <span class="mi">1</span><span class="p">]</span> <span class="o">=</span> <span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">_eval</span><span class="p">(</span><span class="nb">filter</span><span class="p">[</span><span class="n">l_paren</span><span class="o">+</span><span class="mi">1</span><span class="p">:</span><span class="n">r_paren</span><span class="p">])]</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">emptyRes</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_eval</span>
+ <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">_formattedEval</span><span class="p">(</span><span class="nb">filter</span><span class="p">)</span>
+
+ <span class="k">def</span> <span class="nf">apply</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">image</span><span class="p">,</span> <span class="n">roi</span><span class="p">):</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">tokens</span><span class="p">[</span><span class="s">"r"</span><span class="p">]</span> <span class="o">=</span> <span class="n">image</span><span class="p">[:,:,</span><span class="mi">2</span><span class="p">]</span><span class="o">.</span><span class="n">astype</span><span class="p">(</span><span class="nb">float</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">tokens</span><span class="p">[</span><span class="s">"g"</span><span class="p">]</span> <span class="o">=</span> <span class="n">image</span><span class="p">[:,:,</span><span class="mi">1</span><span class="p">]</span><span class="o">.</span><span class="n">astype</span><span class="p">(</span><span class="nb">float</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">tokens</span><span class="p">[</span><span class="s">"b"</span><span class="p">]</span> <span class="o">=</span> <span class="n">image</span><span class="p">[:,:,</span><span class="mi">0</span><span class="p">]</span><span class="o">.</span><span class="n">astype</span><span class="p">(</span><span class="nb">float</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_createArgList</span><span class="p">()</span>
+ <span class="n">result</span> <span class="o">=</span> <span class="n">cv2</span><span class="o">.</span><span class="n">cvtColor</span><span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">where</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">_formattedEval</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">filter</span><span class="p">),</span> <span class="mi">255</span><span class="p">,</span> <span class="mi">0</span><span class="p">)</span><span class="o">.</span><span class="n">astype</span><span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">uint8</span><span class="p">),</span> <span class="n">cv2</span><span class="o">.</span><span class="n">COLOR_GRAY2BGR</span><span class="p">)</span>
+ <span class="n">image</span><span class="p">[</span><span class="n">roi</span><span class="p">[</span><span class="mi">0</span><span class="p">]:</span><span class="n">roi</span><span class="p">[</span><span class="mi">1</span><span class="p">],</span> <span class="n">roi</span><span class="p">[</span><span class="mi">2</span><span class="p">]:</span><span class="n">roi</span><span class="p">[</span><span class="mi">3</span><span class="p">]]</span> <span class="o">=</span> <span class="n">cv2</span><span class="o">.</span><span class="n">bitwise_and</span><span class="p">(</span><span class="n">image</span><span class="p">[</span><span class="n">roi</span><span class="p">[</span><span class="mi">0</span><span class="p">]:</span><span class="n">roi</span><span class="p">[</span><span class="mi">1</span><span class="p">],</span> <span class="n">roi</span><span class="p">[</span><span class="mi">2</span><span class="p">]:</span><span class="n">roi</span><span class="p">[</span><span class="mi">3</span><span class="p">]],</span> <span class="n">result</span><span class="p">[</span><span class="n">roi</span><span class="p">[</span><span class="mi">0</span><span class="p">]:</span><span class="n">roi</span><span class="p">[</span><span class="mi">1</span><span class="p">],</span> <span class="n">roi</span><span class="p">[</span><span class="mi">2</span><span class="p">]:</span><span class="n">roi</span><span class="p">[</span><span class="mi">3</span><span class="p">]])</span>
+ <span class="k">return</span> <span class="n">image</span>
+
+
+
+<div class="viewcode-block" id="Image"><a class="viewcode-back" href="../../processing.html#plantcv.imgproc.Image">[docs]</a><span class="k">class</span> <span class="nc">Image</span><span class="p">(</span><span class="nb">object</span><span class="p">):</span>
+
+ <span class="sd">"""</span>
+<span class="sd"> Each image is instantiated as a class</span>
+<span class="sd"> """</span>
+ <span class="k">def</span> <span class="nf">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="nb">input</span><span class="p">,</span> <span class="n">outputdir</span> <span class="o">=</span> <span class="s">"."</span><span class="p">,</span> <span class="n">writename</span> <span class="o">=</span> <span class="bp">None</span><span class="p">,</span> <span class="n">dev</span> <span class="o">=</span> <span class="bp">False</span><span class="p">,</span> <span class="n">db</span> <span class="o">=</span> <span class="bp">None</span><span class="p">,</span> <span class="n">dbid</span> <span class="o">=</span> <span class="bp">None</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> :param input: The input resource, either a path to an image or a raw numpy array.</span>
+<span class="sd"> :type resource: numpy.ndarray or str</span>
+<span class="sd"> :param outputdir: The directory to write output files</span>
+<span class="sd"> :type outputdir: str</span>
+<span class="sd"> :param writename: The name to write the output file as, should include extension.</span>
+<span class="sd"> :type writename: str</span>
+<span class="sd"> :param dev: Dev mode will do something...</span>
+<span class="sd"> :type dev: bool</span>
+<span class="sd"> """</span>
+ <span class="k">if</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">isdir</span><span class="p">(</span><span class="n">outputdir</span><span class="p">):</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">states</span> <span class="o">=</span> <span class="p">{}</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_loadDb</span><span class="p">(</span><span class="n">db</span><span class="p">,</span> <span class="n">dbid</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">input</span> <span class="o">=</span> <span class="nb">input</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">fname</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">image</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_loadResource</span><span class="p">(</span><span class="nb">input</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">y</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">image</span><span class="o">.</span><span class="n">shape</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">x</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">image</span><span class="o">.</span><span class="n">shape</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">outputdir</span> <span class="o">=</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">abspath</span><span class="p">(</span><span class="n">outputdir</span><span class="p">)</span>
+ <span class="k">if</span> <span class="n">writename</span><span class="p">:</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">writename</span> <span class="o">=</span> <span class="n">writename</span>
+ <span class="k">elif</span> <span class="nb">isinstance</span><span class="p">(</span><span class="nb">input</span><span class="p">,</span> <span class="n">np</span><span class="o">.</span><span class="n">ndarray</span><span class="p">):</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">writename</span> <span class="o">=</span> <span class="s">"out.png"</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">writename</span> <span class="o">=</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">basename</span><span class="p">(</span><span class="nb">input</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">dev</span> <span class="o">=</span> <span class="n">dev</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">window</span> <span class="o">=</span> <span class="mi">1</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="s">"Invalid output!"</span><span class="p">)</span>
+ <span class="k">return</span>
+
+ <span class="k">def</span> <span class="nf">_loadDb</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">db</span><span class="p">,</span> <span class="n">dbid</span><span class="p">):</span>
+ <span class="k">if</span> <span class="n">db</span><span class="p">:</span>
+ <span class="k">if</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">isfile</span><span class="p">(</span><span class="n">db</span><span class="p">):</span>
+ <span class="k">if</span> <span class="n">dbid</span><span class="p">:</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">dbid</span> <span class="o">=</span> <span class="n">dbid</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">conn</span> <span class="o">=</span> <span class="n">sqlite3</span><span class="o">.</span><span class="n">connect</span><span class="p">(</span><span class="n">db</span><span class="p">,</span> <span class="n">check_same_thread</span> <span class="o">=</span> <span class="bp">False</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">conn</span><span class="o">.</span><span class="n">row_factory</span> <span class="o">=</span> <span class="n">sqlite3</span><span class="o">.</span><span class="n">Row</span>
+ <span class="n">result</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">conn</span><span class="o">.</span><span class="n">execute</span><span class="p">(</span><span class="s">"select pegasusid from images where pegasusid=?"</span><span class="p">,</span> <span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">dbid</span><span class="p">,))</span>
+ <span class="k">if</span> <span class="ow">not</span> <span class="n">result</span><span class="o">.</span><span class="n">fetchone</span><span class="p">():</span>
+ <span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="s">"Invalid pegasusid given!"</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_addColumn</span><span class="p">(</span><span class="s">"error"</span><span class="p">)</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="s">"A database id must be provided if you give a database."</span><span class="p">)</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="s">"Invalid database given!"</span><span class="p">)</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">conn</span> <span class="o">=</span> <span class="bp">False</span>
+ <span class="k">return</span>
+
+ <span class="k">def</span> <span class="nf">_addColumn</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">column</span><span class="p">,</span> <span class="n">tablename</span> <span class="o">=</span> <span class="s">"images"</span><span class="p">):</span>
+ <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">conn</span><span class="p">:</span>
+ <span class="k">if</span> <span class="n">column</span> <span class="ow">not</span> <span class="ow">in</span> <span class="p">[</span><span class="n">row</span><span class="p">[</span><span class="s">"name"</span><span class="p">]</span> <span class="k">for</span> <span class="n">row</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">conn</span><span class="o">.</span><span class="n">execute</span><span class="p">(</span><span class="s">"PRAGMA table_info("</span> <span class="o">+</span> <span class="n">tablename</span> <span class="o">+</span> <span class="s">");"</span><span class="p">)]:</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">conn</span><span class="o">.</span><span class="n">execute</span><span class="p">(</span><span class="s">"alter table "</span> <span class="o">+</span> <span class="n">tablename</span> <span class="o">+</span> <span class="s">" add column "</span> <span class="o">+</span> <span class="n">column</span> <span class="o">+</span> <span class="s">";"</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">conn</span><span class="o">.</span><span class="n">commit</span><span class="p">()</span>
+ <span class="k">return</span>
+
+ <span class="k">def</span> <span class="nf">_loadROIArg</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">arg</span><span class="p">,</span> <span class="n">i</span><span class="p">):</span>
+ <span class="n">vals</span> <span class="o">=</span> <span class="p">{</span>
+ <span class="mi">0</span><span class="p">:</span> <span class="s">"0"</span><span class="p">,</span>
+ <span class="mi">1</span><span class="p">:</span> <span class="nb">str</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">y</span><span class="p">),</span>
+ <span class="mi">2</span><span class="p">:</span> <span class="s">"0"</span><span class="p">,</span>
+ <span class="mi">3</span><span class="p">:</span> <span class="nb">str</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">x</span><span class="p">)</span>
+ <span class="p">}</span>
+ <span class="n">arg</span> <span class="o">=</span> <span class="nb">str</span><span class="p">(</span><span class="n">arg</span><span class="p">)</span>
+ <span class="n">arg</span> <span class="o">=</span> <span class="n">arg</span><span class="o">.</span><span class="n">replace</span><span class="p">(</span><span class="s">"x"</span><span class="p">,</span> <span class="nb">str</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">x</span><span class="p">))</span><span class="o">.</span><span class="n">replace</span><span class="p">(</span><span class="s">"y"</span><span class="p">,</span> <span class="nb">str</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">y</span><span class="p">))</span><span class="o">.</span><span class="n">replace</span><span class="p">(</span><span class="s">" "</span><span class="p">,</span><span class="s">""</span><span class="p">)</span><span class="o">.</span><span class="n">replace</span><span class="p">(</span><span class="s">"-1"</span><span class="p">,</span><span class="n">vals</span><span class="p">[</span><span class="n">i</span><span class="p">])</span>
+ <span class="k">if</span> <span class="s">"-"</span> <span class="ow">in</span> <span class="n">arg</span><span class="p">:</span>
+ <span class="k">try</span><span class="p">:</span>
+ <span class="n">left</span><span class="p">,</span> <span class="n">right</span> <span class="o">=</span> <span class="n">arg</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s">"-"</span><span class="p">)</span>
+ <span class="k">return</span> <span class="nb">int</span><span class="p">(</span><span class="n">left</span><span class="p">)</span> <span class="o">-</span> <span class="nb">int</span><span class="p">(</span><span class="n">right</span><span class="p">)</span>
+ <span class="k">except</span><span class="p">:</span>
+ <span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="s">"Could not load roi arg '</span><span class="si">%s</span><span class="s">'"</span> <span class="o">%</span> <span class="p">(</span><span class="n">arg</span><span class="p">,))</span>
+ <span class="k">elif</span> <span class="s">"+"</span> <span class="ow">in</span> <span class="n">arg</span><span class="p">:</span>
+ <span class="k">try</span><span class="p">:</span>
+ <span class="n">left</span><span class="p">,</span> <span class="n">right</span> <span class="o">=</span> <span class="n">arg</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s">"+"</span><span class="p">)</span>
+ <span class="k">return</span> <span class="nb">int</span><span class="p">(</span><span class="n">left</span><span class="p">)</span> <span class="o">+</span> <span class="nb">int</span><span class="p">(</span><span class="n">right</span><span class="p">)</span>
+ <span class="k">except</span><span class="p">:</span>
+ <span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="s">"Could not load roi arg '</span><span class="si">%s</span><span class="s">'"</span> <span class="o">%</span> <span class="p">(</span><span class="n">arg</span><span class="p">,))</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="k">return</span> <span class="nb">int</span><span class="p">(</span><span class="n">arg</span><span class="p">)</span>
+
+ <span class="k">def</span> <span class="nf">_loadROI</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">roi</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> :param roi: The region of interest to load.</span>
+<span class="sd"> :type roi: list or file</span>
+<span class="sd"> :return: The region of interest of form [ystart, yend, xstart, xend]</span>
+<span class="sd"> :rtype: list</span>
+<span class="sd"> :raises OSError: if the input path does not exist.</span>
+<span class="sd"> </span>
+<span class="sd"> Loads a region of interest, either a path to an roi or a raw list.</span>
+<span class="sd"> """</span>
+ <span class="k">if</span> <span class="ow">not</span> <span class="n">roi</span><span class="p">:</span>
+ <span class="n">roi</span> <span class="o">=</span> <span class="p">[</span><span class="o">-</span><span class="mi">1</span><span class="p">,</span> <span class="o">-</span><span class="mi">1</span><span class="p">,</span> <span class="o">-</span><span class="mi">1</span><span class="p">,</span> <span class="o">-</span><span class="mi">1</span><span class="p">]</span>
+ <span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">roi</span><span class="p">,</span> <span class="nb">list</span><span class="p">):</span>
+ <span class="k">return</span> <span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">_loadROIArg</span><span class="p">(</span><span class="n">z</span><span class="p">,</span> <span class="n">i</span><span class="p">)</span> <span class="k">for</span> <span class="n">i</span><span class="p">,</span><span class="n">z</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="n">roi</span><span class="p">)]</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="k">if</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">isfile</span><span class="p">(</span><span class="n">roi</span><span class="p">):</span>
+ <span class="k">try</span><span class="p">:</span>
+ <span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="n">roi</span><span class="p">,</span> <span class="s">"r"</span><span class="p">)</span> <span class="k">as</span> <span class="n">rh</span><span class="p">:</span>
+ <span class="n">r</span> <span class="o">=</span> <span class="n">json</span><span class="o">.</span><span class="n">load</span><span class="p">(</span><span class="n">rh</span><span class="p">)</span>
+ <span class="k">print</span> <span class="s">"json is loading"</span>
+ <span class="k">if</span> <span class="nb">all</span><span class="p">(</span><span class="n">x</span> <span class="ow">in</span> <span class="n">r</span> <span class="k">for</span> <span class="n">x</span> <span class="ow">in</span> <span class="p">[</span><span class="s">"xstart"</span><span class="p">,</span> <span class="s">"xend"</span><span class="p">,</span> <span class="s">"ystart"</span><span class="p">,</span> <span class="s">"yend"</span><span class="p">]):</span>
+ <span class="k">return</span> <span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">_loadROIArg</span><span class="p">(</span><span class="n">r</span><span class="p">[</span><span class="s">"ystart"</span><span class="p">],</span> <span class="mi">0</span><span class="p">),</span> <span class="bp">self</span><span class="o">.</span><span class="n">_loadROIArg</span><span class="p">(</span><span class="n">r</span><span class="p">[</span><span class="s">"yend"</span><span class="p">],</span> <span class="mi">1</span><span class="p">),</span> <span class="bp">self</span><span class="o">.</span><span class="n">_loadROIArg</span><span class="p">(</span><span class="n">r</span><span class="p">[</span><span class="s">"xstart"</span><span class="p">],</span> <span class="mi">2</span><span class="p">),</span> <span class="bp">self</span><span class="o">.</span><span class="n">_loadROIArg</span><span class="p">(</span><span class="n">r</span><span class="p">[</span><span class="s">"xend"</span><span class="p">],</span> <span class="mi">3</span><span class="p">)]</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="s">"Input roi file '</span><span class="si">%s</span><span class="s">' needs xstart, xend, ystart, and yend definitions!"</span> <span class="o">%</span> <span class="p">(</span><span class="n">roi</span><span class="p">,))</span>
+ <span class="k">except</span> <span class="ne">Exception</span> <span class="k">as</span> <span class="n">e</span><span class="p">:</span>
+ <span class="k">print</span> <span class="n">traceback</span><span class="o">.</span><span class="n">format_exc</span><span class="p">()</span>
+ <span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="s">"Input roi file '</span><span class="si">%s</span><span class="s">' is not valid json!"</span> <span class="o">%</span> <span class="p">(</span><span class="n">roi</span><span class="p">,))</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="s">"Input path to roi file '</span><span class="si">%s</span><span class="s">' does not exist!"</span> <span class="o">%</span> <span class="p">(</span><span class="n">roi</span><span class="p">,))</span>
+ <span class="k">return</span>
+
+ <span class="k">def</span> <span class="nf">_writeROI</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">roi</span><span class="p">,</span> <span class="n">output</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> :param roi: The region of interest to write.</span>
+<span class="sd"> :type roi: list</span>
+<span class="sd"> """</span>
+ <span class="k">try</span><span class="p">:</span>
+ <span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">outputdir</span> <span class="o">+</span> <span class="s">"/"</span> <span class="o">+</span> <span class="n">output</span><span class="p">,</span> <span class="s">"w"</span><span class="p">)</span> <span class="k">as</span> <span class="n">wh</span><span class="p">:</span>
+ <span class="n">wh</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="n">json</span><span class="o">.</span><span class="n">dumps</span><span class="p">({</span><span class="s">"ystart"</span><span class="p">:</span> <span class="n">roi</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span> <span class="s">"yend"</span><span class="p">:</span> <span class="n">roi</span><span class="p">[</span><span class="mi">1</span><span class="p">],</span> <span class="s">"xstart"</span><span class="p">:</span> <span class="n">roi</span><span class="p">[</span><span class="mi">2</span><span class="p">],</span> <span class="s">"xend"</span><span class="p">:</span> <span class="n">roi</span><span class="p">[</span><span class="mi">3</span><span class="p">]},</span> <span class="n">indent</span> <span class="o">=</span> <span class="mi">4</span><span class="p">))</span>
+ <span class="k">except</span><span class="p">:</span>
+ <span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="s">"Could not write roi."</span><span class="p">)</span>
+ <span class="k">return</span>
+
+ <span class="k">def</span> <span class="nf">_loadBins</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">binlist</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> :param bin: The bin to load</span>
+<span class="sd"> :type bin: list or file</span>
+<span class="sd"> """</span>
+
+ <span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">binlist</span><span class="p">,</span> <span class="nb">list</span><span class="p">):</span>
+ <span class="k">return</span> <span class="n">binlist</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="k">if</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">isfile</span><span class="p">(</span><span class="n">binlist</span><span class="p">):</span>
+ <span class="k">try</span><span class="p">:</span>
+ <span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="n">binlist</span><span class="p">,</span> <span class="s">"r"</span><span class="p">)</span> <span class="k">as</span> <span class="n">rh</span><span class="p">:</span>
+ <span class="k">return</span> <span class="n">json</span><span class="o">.</span><span class="n">load</span><span class="p">(</span><span class="n">rh</span><span class="p">)</span>
+ <span class="k">except</span><span class="p">:</span>
+ <span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="s">"Bin list not valid json!"</span><span class="p">)</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="s">"Bin file does not exist."</span><span class="p">)</span>
+ <span class="k">return</span>
+
+ <span class="k">def</span> <span class="nf">_loadResource</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">resource</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> :param resource: The resource to load.</span>
+<span class="sd"> :type resource: numpy.ndarray or file</span>
+<span class="sd"> :return: The image</span>
+<span class="sd"> :rtype: numpy.ndarray</span>
+<span class="sd"> :raises OSError: if the input path does not exist.</span>
+<span class="sd"> </span>
+<span class="sd"> Loads a resource, either a path to an image or a raw numpy array.</span>
+<span class="sd"> """</span>
+ <span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">resource</span><span class="p">,</span> <span class="n">np</span><span class="o">.</span><span class="n">ndarray</span><span class="p">):</span>
+ <span class="k">return</span> <span class="p">(</span><span class="s">"unknown"</span><span class="p">,</span> <span class="n">resource</span><span class="o">.</span><span class="n">copy</span><span class="p">())</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="k">if</span> <span class="n">resource</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">states</span><span class="p">:</span>
+ <span class="k">return</span> <span class="p">(</span><span class="n">resource</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">states</span><span class="p">[</span><span class="n">resource</span><span class="p">]</span><span class="o">.</span><span class="n">copy</span><span class="p">())</span>
+ <span class="k">elif</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">isfile</span><span class="p">(</span><span class="n">resource</span><span class="p">):</span>
+ <span class="n">image</span> <span class="o">=</span> <span class="n">cv2</span><span class="o">.</span><span class="n">imread</span><span class="p">(</span><span class="n">resource</span><span class="p">)</span>
+ <span class="k">if</span> <span class="n">image</span> <span class="ow">is</span> <span class="ow">not</span> <span class="bp">None</span><span class="p">:</span>
+ <span class="k">return</span> <span class="p">(</span><span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">basename</span><span class="p">(</span><span class="n">resource</span><span class="p">),</span> <span class="n">image</span><span class="p">)</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">conn</span><span class="p">:</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">conn</span><span class="o">.</span><span class="n">execute</span><span class="p">(</span><span class="s">"update images set error =? where pegasusid = ?"</span><span class="p">,</span> <span class="p">(</span><span class="s">"Load Error, input is not an image."</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">dbid</span><span class="p">))</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">conn</span><span class="o">.</span><span class="n">commit</span><span class="p">()</span>
+ <span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="s">"Input is not an image."</span><span class="p">)</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">conn</span><span class="p">:</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">conn</span><span class="o">.</span><span class="n">execute</span><span class="p">(</span><span class="s">"update images set error = ? where pegasusid = ?"</span><span class="p">,</span> <span class="p">(</span><span class="s">"Load Error, input path doesn't exist or specified resource is not a saved state."</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">dbid</span><span class="p">))</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">conn</span><span class="o">.</span><span class="n">commit</span><span class="p">()</span>
+ <span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="s">"Input path to resource does not exist."</span><span class="p">)</span>
+ <span class="k">return</span>
+
+ <span class="k">def</span> <span class="nf">_colorHistogram</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> :return: A list of histograms, corresponding to R, G, B.</span>
+<span class="sd"> :rtype: List of numpy arrays.</span>
+<span class="sd"> </span>
+<span class="sd"> Calculates a normalized colorHistogram of the current image. </span>
+<span class="sd"> The intensity is normalized between 0 and 255.</span>
+<span class="sd"> """</span>
+ <span class="n">returnhist</span> <span class="o">=</span> <span class="p">[]</span>
+
+ <span class="k">for</span> <span class="n">ch</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="mi">0</span><span class="p">,</span> <span class="mi">3</span><span class="p">):</span>
+ <span class="n">hist_item</span> <span class="o">=</span> <span class="n">cv2</span><span class="o">.</span><span class="n">calcHist</span><span class="p">([</span><span class="bp">self</span><span class="o">.</span><span class="n">image</span><span class="p">],</span> <span class="p">[</span><span class="n">ch</span><span class="p">],</span> <span class="bp">None</span><span class="p">,</span> <span class="p">[</span><span class="mi">256</span><span class="p">],</span> <span class="p">[</span><span class="mi">1</span><span class="p">,</span><span class="mi">255</span><span class="p">])</span>
+ <span class="n">cv2</span><span class="o">.</span><span class="n">normalize</span><span class="p">(</span><span class="n">hist_item</span><span class="p">,</span> <span class="n">hist_item</span><span class="p">,</span> <span class="mi">0</span><span class="p">,</span> <span class="mi">255</span><span class="p">,</span> <span class="n">cv2</span><span class="o">.</span><span class="n">NORM_MINMAX</span><span class="p">)</span>
+ <span class="n">hist</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">int32</span><span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">around</span><span class="p">(</span><span class="n">hist_item</span><span class="p">))</span>
+ <span class="n">returnhist</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">hist</span><span class="p">)</span>
+ <span class="k">return</span> <span class="n">returnhist</span>
+
+ <span class="k">def</span> <span class="nf">_isColor</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">image</span> <span class="o">=</span> <span class="bp">None</span><span class="p">):</span>
+ <span class="n">image</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">image</span> <span class="k">if</span> <span class="n">image</span> <span class="ow">is</span> <span class="bp">None</span> <span class="k">else</span> <span class="n">image</span>
+ <span class="k">return</span> <span class="nb">len</span><span class="p">(</span><span class="n">image</span><span class="o">.</span><span class="n">shape</span><span class="p">)</span> <span class="o">==</span> <span class="mi">3</span>
+
+<div class="viewcode-block" id="Image.save"><a class="viewcode-back" href="../../processing.html#plantcv.imgproc.Image.save">[docs]</a> <span class="k">def</span> <span class="nf">save</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">name</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> :param name: The name to save the image under.</span>
+<span class="sd"> :type name: str OR any hashable type.</span>
+<span class="sd"> </span>
+<span class="sd"> This function saves the current image in the 'states' variable under</span>
+<span class="sd"> the specified name. It can then be reloaded using the :py:meth:`~plantcv.imgproc.Image.restore`</span>
+<span class="sd"> method.</span>
+<span class="sd"> """</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">states</span><span class="p">[</span><span class="n">name</span><span class="p">]</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">image</span><span class="o">.</span><span class="n">copy</span><span class="p">()</span>
+ <span class="k">return</span>
+ </div>
+<div class="viewcode-block" id="Image.restore"><a class="viewcode-back" href="../../processing.html#plantcv.imgproc.Image.restore">[docs]</a> <span class="k">def</span> <span class="nf">restore</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">name</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> :param name: The name the image is saved under.</span>
+<span class="sd"> :type name: str OR any hashable type.</span>
+<span class="sd"> </span>
+<span class="sd"> Reloads a previously saved image from the 'states' variable.</span>
+<span class="sd"> """</span>
+ <span class="k">if</span> <span class="n">name</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">states</span><span class="p">:</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">image</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">states</span><span class="p">[</span><span class="n">name</span><span class="p">]</span><span class="o">.</span><span class="n">copy</span><span class="p">()</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="k">print</span> <span class="s">"Invalid state specified."</span>
+ <span class="k">return</span>
+ </div>
+<div class="viewcode-block" id="Image.list"><a class="viewcode-back" href="../../processing.html#plantcv.imgproc.Image.list">[docs]</a> <span class="k">def</span> <span class="nf">list</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> Lists all saved states.</span>
+<span class="sd"> """</span>
+ <span class="k">for</span> <span class="n">state</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">states</span><span class="p">:</span>
+ <span class="k">print</span> <span class="n">state</span>
+ <span class="k">return</span>
+ </div>
+<div class="viewcode-block" id="Image.destroy"><a class="viewcode-back" href="../../processing.html#plantcv.imgproc.Image.destroy">[docs]</a> <span class="k">def</span> <span class="nf">destroy</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> Destroys all currently open windows.</span>
+<span class="sd"> """</span>
+ <span class="n">cv2</span><span class="o">.</span><span class="n">destroyAllWindows</span><span class="p">()</span>
+ <span class="k">return</span>
+ </div>
+<div class="viewcode-block" id="Image.wait"><a class="viewcode-back" href="../../processing.html#plantcv.imgproc.Image.wait">[docs]</a> <span class="k">def</span> <span class="nf">wait</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> Waits until a key is pressed, then destroys all windows and</span>
+<span class="sd"> continues program execution.</span>
+<span class="sd"> """</span>
+ <span class="n">cv2</span><span class="o">.</span><span class="n">waitKey</span><span class="p">(</span><span class="mi">0</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">destroy</span><span class="p">()</span>
+ <span class="k">return</span>
+ </div>
+<div class="viewcode-block" id="Image.show"><a class="viewcode-back" href="../../processing.html#plantcv.imgproc.Image.show">[docs]</a> <span class="k">def</span> <span class="nf">show</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">title</span> <span class="o">=</span> <span class="bp">None</span><span class="p">):</span>
+ <span class="sd">""" </span>
+<span class="sd"> :param title: The title to give the display window, if left blank one will be created.</span>
+<span class="sd"> :type title: str</span>
+<span class="sd"> :return: None</span>
+<span class="sd"> </span>
+<span class="sd"> Displays the image in a window. Utilizes the :py:meth:`~plantcv.ImageProcessor.Image.resize` function.</span>
+<span class="sd"> If a title is not specified, the window will be named 'windowX' where X is the number of times</span>
+<span class="sd"> show has been called.</span>
+<span class="sd"> </span>
+<span class="sd"> """</span>
+ <span class="n">cv2</span><span class="o">.</span><span class="n">imshow</span><span class="p">(</span><span class="n">title</span> <span class="k">if</span> <span class="n">title</span> <span class="k">else</span> <span class="s">"window "</span> <span class="o">+</span> <span class="nb">str</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">window</span><span class="p">),</span> <span class="bp">self</span><span class="o">.</span><span class="n">resize</span><span class="p">())</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">window</span> <span class="o">+=</span> <span class="mi">1</span>
+ <span class="k">return</span>
+ </div>
+<div class="viewcode-block" id="Image.resize"><a class="viewcode-back" href="../../processing.html#plantcv.imgproc.Image.resize">[docs]</a> <span class="k">def</span> <span class="nf">resize</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> If the image is large than conf.maxArea, resize its total area down to conf.maxArea.</span>
+<span class="sd"> This function is primarily used for viewing purposes, and as such, it does not resize</span>
+<span class="sd"> the base image, but creates a copy to resize instead.</span>
+<span class="sd"> """</span>
+ <span class="k">if</span> <span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">image</span><span class="o">.</span><span class="n">shape</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="o">*</span> <span class="bp">self</span><span class="o">.</span><span class="n">image</span><span class="o">.</span><span class="n">shape</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span> <span class="o">></span> <span class="n">conf</span><span class="o">.</span><span class="n">maxArea</span><span class="p">):</span>
+ <span class="n">scale</span> <span class="o">=</span> <span class="mi">1</span> <span class="o">/</span> <span class="n">math</span><span class="o">.</span><span class="n">sqrt</span><span class="p">((</span><span class="bp">self</span><span class="o">.</span><span class="n">image</span><span class="o">.</span><span class="n">shape</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span> <span class="o">*</span> <span class="bp">self</span><span class="o">.</span><span class="n">image</span><span class="o">.</span><span class="n">shape</span><span class="p">[</span><span class="mi">0</span><span class="p">])</span> <span class="o">/</span> <span class="n">conf</span><span class="o">.</span><span class="n">maxArea</span><span class="p">)</span>
+ <span class="k">return</span> <span class="n">cv2</span><span class="o">.</span><span class="n">resize</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">image</span><span class="o">.</span><span class="n">copy</span><span class="p">(),</span> <span class="p">(</span><span class="nb">int</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">image</span><span class="o">.</span><span class="n">shape</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span><span class="o">*</span><span class="n">scale</span><span class="p">),</span> <span class="nb">int</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">image</span><span class="o">.</span><span class="n">shape</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">*</span><span class="n">scale</span><span class="p">)))</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">image</span>
+ </div>
+<div class="viewcode-block" id="Image.write"><a class="viewcode-back" href="../../processing.html#plantcv.imgproc.Image.write">[docs]</a> <span class="k">def</span> <span class="nf">write</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">name</span> <span class="o">=</span> <span class="bp">None</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> Writes the current image to the given output directory, with the given name.</span>
+<span class="sd"> """</span>
+ <span class="n">writename</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">writename</span> <span class="k">if</span> <span class="ow">not</span> <span class="n">name</span> <span class="k">else</span> <span class="n">name</span>
+ <span class="n">cv2</span><span class="o">.</span><span class="n">imwrite</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">outputdir</span> <span class="o">+</span> <span class="s">"/"</span> <span class="o">+</span> <span class="n">writename</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">image</span><span class="p">)</span>
+ <span class="k">return</span>
+ </div>
+<div class="viewcode-block" id="Image.convertColor"><a class="viewcode-back" href="../../processing.html#plantcv.imgproc.Image.convertColor">[docs]</a> <span class="k">def</span> <span class="nf">convertColor</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">intype</span><span class="p">,</span> <span class="n">outtype</span><span class="p">):</span>
+ <span class="sd">""" </span>
+<span class="sd"> :param intype: The input image type</span>
+<span class="sd"> :type intype: str</span>
+<span class="sd"> :param outtype: The output image type</span>
+<span class="sd"> :type outtype: str</span>
+<span class="sd"> :return: The converted image.</span>
+<span class="sd"> :rtype: numpy.ndarray</span>
+<span class="sd"> :raises: KeyError</span>
+<span class="sd"> </span>
+<span class="sd"> Converts the given image between color spaces, based on the given types.</span>
+<span class="sd"> Supported types are: rgb, bgr, gray, hsv, lab, and ycrcb</span>
+<span class="sd"> """</span>
+ <span class="k">if</span> <span class="n">intype</span> <span class="ow">in</span> <span class="n">conf</span><span class="o">.</span><span class="n">colors</span><span class="p">:</span>
+ <span class="k">if</span> <span class="n">outtype</span> <span class="ow">in</span> <span class="n">conf</span><span class="o">.</span><span class="n">colors</span><span class="p">[</span><span class="n">intype</span><span class="p">]:</span>
+ <span class="k">for</span> <span class="n">code</span> <span class="ow">in</span> <span class="n">conf</span><span class="o">.</span><span class="n">colors</span><span class="p">[</span><span class="n">intype</span><span class="p">][</span><span class="n">outtype</span><span class="p">]:</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">image</span> <span class="o">=</span> <span class="n">cv2</span><span class="o">.</span><span class="n">cvtColor</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">image</span><span class="p">,</span> <span class="n">code</span><span class="p">)</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="k">raise</span> <span class="ne">KeyError</span><span class="p">(</span><span class="n">outtype</span> <span class="o">+</span> <span class="s">" is not a valid image type."</span><span class="p">)</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="k">raise</span> <span class="ne">KeyError</span><span class="p">(</span><span class="n">intype</span> <span class="o">+</span> <span class="s">" is not a valid image type."</span><span class="p">)</span>
+ <span class="k">return</span>
+ </div>
+<div class="viewcode-block" id="Image.threshold"><a class="viewcode-back" href="../../processing.html#plantcv.imgproc.Image.threshold">[docs]</a> <span class="k">def</span> <span class="nf">threshold</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">thresh</span><span class="p">,</span> <span class="nb">max</span> <span class="o">=</span> <span class="mi">255</span><span class="p">,</span> <span class="nb">type</span> <span class="o">=</span> <span class="s">"binary"</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> :param thresh: Threshold value.</span>
+<span class="sd"> :type thresh: int</span>
+<span class="sd"> :param max: Write value for binary threshold.</span>
+<span class="sd"> :type max: int</span>
+<span class="sd"> :param type: Threhsold type.</span>
+<span class="sd"> :type type: str</span>
+<span class="sd"> :return: The thresholded image.</span>
+<span class="sd"> :rtype: numpy.ndarray</span>
+<span class="sd"> :raises KeyError: if the specified threshold type doesn't exist.</span>
+<span class="sd"> </span>
+<span class="sd"> Thresholds the image based on the given type.</span>
+<span class="sd"> Supported types are: binary, truncate, tozero, and otsu.</span>
+<span class="sd"> """</span>
+ <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">_isColor</span><span class="p">():</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">convertColor</span><span class="p">(</span><span class="s">"bgr"</span><span class="p">,</span> <span class="s">"gray"</span><span class="p">)</span>
+ <span class="k">if</span> <span class="nb">type</span> <span class="ow">in</span> <span class="n">conf</span><span class="o">.</span><span class="n">thresholds</span><span class="p">:</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">image</span> <span class="o">=</span> <span class="n">cv2</span><span class="o">.</span><span class="n">threshold</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">image</span><span class="p">,</span> <span class="n">thresh</span><span class="p">,</span> <span class="nb">max</span><span class="p">,</span> <span class="n">conf</span><span class="o">.</span><span class="n">thresholds</span><span class="p">[</span><span class="nb">type</span><span class="p">])[</span><span class="mi">1</span><span class="p">]</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="k">raise</span> <span class="ne">KeyError</span><span class="p">(</span><span class="nb">type</span> <span class="o">+</span> <span class="s">" is not a valid threshold type."</span><span class="p">)</span>
+ <span class="k">return</span>
+ </div>
+<div class="viewcode-block" id="Image.meanshift"><a class="viewcode-back" href="../../processing.html#plantcv.imgproc.Image.meanshift">[docs]</a> <span class="k">def</span> <span class="nf">meanshift</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">spatial_radius</span><span class="p">,</span> <span class="n">range_radius</span><span class="p">,</span> <span class="n">min_density</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> :param spatial_radius: Spatial Radius</span>
+<span class="sd"> :type spatial_radius: float</span>
+<span class="sd"> :param range_radius: Range Radius.</span>
+<span class="sd"> :type range_radius: float</span>
+<span class="sd"> :param min_density: Minimum Density.</span>
+<span class="sd"> :type min_density: int</span>
+<span class="sd"> :return: The mean-shifted image.</span>
+<span class="sd"> :rtype: numpy.ndarray</span>
+<span class="sd"> </span>
+<span class="sd"> Reference to paper HERE: http://dx.doi.org/10.1109/34.1000236</span>
+<span class="sd"> Reference to pymeanshift HERE: https://code.google.com/p/pymeanshift/</span>
+<span class="sd"> Segments the image into clusters based on nearest neighbors.</span>
+<span class="sd"> """</span>
+ <span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">image</span><span class="p">,</span> <span class="n">labels_image</span><span class="p">,</span> <span class="n">number_regions</span><span class="p">)</span> <span class="o">=</span> <span class="n">pms</span><span class="o">.</span><span class="n">segment</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">image</span><span class="p">,</span> <span class="n">spatial_radius</span> <span class="o">=</span> <span class="n">spatial_radius</span><span class="p">,</span> <span class="n">range_radius</span> <span class="o">=</span> <span class="n">range_radius</span><span class="p">,</span> <span class="n">min_density</span> <span class="o">=</span> <span class="n">min_density</span><span class="p">)</span>
+ <span class="k">return</span>
+ </div>
+<div class="viewcode-block" id="Image.adaptiveThreshold"><a class="viewcode-back" href="../../processing.html#plantcv.imgproc.Image.adaptiveThreshold">[docs]</a> <span class="k">def</span> <span class="nf">adaptiveThreshold</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">value</span><span class="p">,</span> <span class="n">adaptiveType</span><span class="p">,</span> <span class="n">thresholdType</span><span class="p">,</span> <span class="n">blockSize</span><span class="p">,</span> <span class="n">C</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> :param value: Write value for the pixels based on the conditions.</span>
+<span class="sd"> :type param: int</span>
+<span class="sd"> :param adaptiveType: Adaptive algorithm to use, should be either 'mean' or 'gaussian'.</span>
+<span class="sd"> :type adaptiveType: str</span>
+<span class="sd"> :param thresholdType: Threshold type, should be either 'binary' or 'inverse'.</span>
+<span class="sd"> :type thresholdType: str</span>
+<span class="sd"> :param blockSize: The window size to consider while thresholding, should only be an odd number.</span>
+<span class="sd"> :type blockSize: int</span>
+<span class="sd"> :param C: A constant subtracted from the calculated mean in each window.</span>
+<span class="sd"> :type C: int</span>
+<span class="sd"> </span>
+<span class="sd"> Thresholds an image by considering the image in several different windows instead of the image</span>
+<span class="sd"> as a whole. MATH HERE, REFERENCE OPENCV DOCS.</span>
+<span class="sd"> """</span>
+ <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">_isColor</span><span class="p">():</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">convertColor</span><span class="p">(</span><span class="s">"bgr"</span><span class="p">,</span> <span class="s">"gray"</span><span class="p">)</span>
+ <span class="k">if</span> <span class="n">adaptiveType</span> <span class="ow">in</span> <span class="n">conf</span><span class="o">.</span><span class="n">adaptives</span><span class="p">:</span>
+ <span class="k">if</span> <span class="n">thresholdType</span> <span class="o">==</span> <span class="s">"binary"</span> <span class="ow">or</span> <span class="n">thresholdType</span> <span class="o">==</span> <span class="s">"inverse"</span><span class="p">:</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">image</span> <span class="o">=</span> <span class="n">cv2</span><span class="o">.</span><span class="n">adaptiveThreshold</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">image</span><span class="p">,</span> <span class="n">value</span><span class="p">,</span> <span class="n">conf</span><span class="o">.</span><span class="n">adaptives</span><span class="p">[</span><span class="n">adaptiveType</span><span class="p">],</span> <span class="n">conf</span><span class="o">.</span><span class="n">thresholds</span><span class="p">[</span><span class="n">thresholdType</span><span class="p">],</span> <span class="n">blockSize</span><span class="p">,</span> <span class="n">C</span><span class="p">)</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="s">"Threshold type: "</span> <span class="o">+</span> <span class="n">thresholdType</span> <span class="o">+</span> <span class="s">" must be either binary or inverse."</span><span class="p">)</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="s">"Adaptive type: "</span> <span class="o">+</span> <span class="n">adaptiveType</span> <span class="o">+</span> <span class="s">" is not a valid adaptive threshold type, should be either 'mean' or 'gaussian'"</span><span class="p">)</span>
+ <span class="k">return</span>
+ </div>
+<div class="viewcode-block" id="Image.blur"><a class="viewcode-back" href="../../processing.html#plantcv.imgproc.Image.blur">[docs]</a> <span class="k">def</span> <span class="nf">blur</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">ksize</span><span class="p">,</span> <span class="n">anchor</span> <span class="o">=</span> <span class="p">(</span><span class="o">-</span><span class="mi">1</span><span class="p">,</span> <span class="o">-</span><span class="mi">1</span><span class="p">),</span> <span class="n">borderType</span> <span class="o">=</span> <span class="s">"default"</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> :param ksize: The size of the kernel represented by a tuple (width, height). Both numbers should be odd and positive.</span>
+<span class="sd"> :type ksize: tuple</span>
+<span class="sd"> :param anchor: The anchor point for filtering. Default is (-1, -1) which is the center of the kernel.</span>
+<span class="sd"> :type anchor: tuple</span>
+<span class="sd"> :param borderType: The type of border mode used to extrapolate pixels outside the image. Literally no information on this.</span>
+<span class="sd"> :type borderType: str</span>
+<span class="sd"> </span>
+<span class="sd"> This function smoothes an image using the following kernel: MATH HERE.</span>
+<span class="sd"> </span>
+<span class="sd"> Changing the anchor point changes the location considered by the kernel. If you have</span>
+<span class="sd"> the kernel: MATH, when the anchor point is in the center, you consider 1 pixel in each</span>
+<span class="sd"> direciton around your target pixel. If you move the anchor point to the top, you consider</span>
+<span class="sd"> no pixels above, and more below. MORE MATH.</span>
+<span class="sd"> REFERENCE OPENCV DOCS.</span>
+<span class="sd"> """</span>
+ <span class="k">if</span> <span class="n">borderType</span> <span class="ow">in</span> <span class="n">conf</span><span class="o">.</span><span class="n">borders</span><span class="p">:</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">image</span> <span class="o">=</span> <span class="n">cv2</span><span class="o">.</span><span class="n">blur</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">image</span><span class="p">,</span> <span class="n">anchor</span> <span class="o">=</span> <span class="n">anchor</span><span class="p">,</span> <span class="n">borderType</span> <span class="o">=</span> <span class="n">conf</span><span class="o">.</span><span class="n">borders</span><span class="p">[</span><span class="n">borderType</span><span class="p">])</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="s">"Invalid border type, should be one of: "</span> <span class="o">+</span> <span class="s">","</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">conf</span><span class="o">.</span><span class="n">borders</span><span class="o">.</span><span class="n">keys</span><span class="p">())</span> <span class="o">+</span> <span class="s">"."</span><span class="p">)</span>
+ <span class="k">return</span>
+ </div>
+<div class="viewcode-block" id="Image.medianBlur"><a class="viewcode-back" href="../../processing.html#plantcv.imgproc.Image.medianBlur">[docs]</a> <span class="k">def</span> <span class="nf">medianBlur</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">ksize</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> :param ksize: The size of the kernel (ksize x ksize). Should be odd and positive.</span>
+<span class="sd"> :type ksize: int</span>
+<span class="sd"> </span>
+<span class="sd"> This function smoothes an image using the median filter. The kernel is set to size (ksize, ksize).</span>
+<span class="sd"> The anchor position is assumed to be the center.</span>
+<span class="sd"> REFERENCE OPENCV MEDIAN BLUR</span>
+<span class="sd"> """</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">image</span> <span class="o">=</span> <span class="n">cv2</span><span class="o">.</span><span class="n">medianBlur</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">image</span><span class="p">,</span> <span class="n">ksize</span><span class="p">)</span>
+ <span class="k">return</span>
+ </div>
+<div class="viewcode-block" id="Image.gaussianBlur"><a class="viewcode-back" href="../../processing.html#plantcv.imgproc.Image.gaussianBlur">[docs]</a> <span class="k">def</span> <span class="nf">gaussianBlur</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">ksize</span><span class="p">,</span> <span class="n">sigmaX</span> <span class="o">=</span> <span class="mi">0</span><span class="p">,</span> <span class="n">sigmaY</span> <span class="o">=</span> <span class="mi">0</span><span class="p">,</span> <span class="n">borderType</span> <span class="o">=</span> <span class="s">"default"</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> :param ksize: The size of the kernel represented by a tuple (width, height). Both numers should be odd and positive.</span>
+<span class="sd"> :type ksize: tuple</span>
+<span class="sd"> :param sigmaX: The standard deviation in the x direction. If 0, the value is calculated based on the kernel size.</span>
+<span class="sd"> :type sigmaX: float</span>
+<span class="sd"> :param sigmaY: The standard deviation in the y direction. If 0, the value is equal to sigmaX.</span>
+<span class="sd"> :type sigmaY: float</span>
+<span class="sd"> :param borderType: The type of border mode used to extrapolate pixels outside the image. Literally no information on this.</span>
+<span class="sd"> :type borderType: str</span>
+<span class="sd"> </span>
+<span class="sd"> This function blurs an image based on a Gaussian kernel -- which is defined as: MATH.</span>
+<span class="sd"> REFERENCE to OPENCV GAUSSIAN BLUR</span>
+<span class="sd"> REFERENCE OPENCV GAUSSIAN KERNEL</span>
+<span class="sd"> """</span>
+ <span class="k">if</span> <span class="n">borderType</span> <span class="ow">in</span> <span class="n">conf</span><span class="o">.</span><span class="n">borders</span><span class="p">:</span>
+ <span class="n">sigmaY</span> <span class="o">=</span> <span class="n">sigmaX</span> <span class="k">if</span> <span class="n">sigmaY</span> <span class="o">==</span> <span class="mi">0</span> <span class="k">else</span> <span class="n">sigmaY</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">image</span> <span class="o">=</span> <span class="n">cv2</span><span class="o">.</span><span class="n">GaussianBlur</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">image</span><span class="p">,</span> <span class="n">ksize</span><span class="p">,</span> <span class="n">sigmaX</span><span class="p">,</span> <span class="n">sigmaY</span><span class="p">,</span> <span class="n">borderType</span> <span class="o">=</span> <span class="n">conf</span><span class="o">.</span><span class="n">borders</span><span class="p">[</span><span class="n">borderType</span><span class="p">])</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="s">"Invalid border type, should be one of: "</span> <span class="o">+</span> <span class="s">","</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">conf</span><span class="o">.</span><span class="n">borders</span><span class="o">.</span><span class="n">keys</span><span class="p">())</span> <span class="o">+</span> <span class="s">"."</span><span class="p">)</span>
+ <span class="k">return</span>
+ </div>
+<div class="viewcode-block" id="Image.normalizeByIntensity"><a class="viewcode-back" href="../../processing.html#plantcv.imgproc.Image.normalizeByIntensity">[docs]</a> <span class="k">def</span> <span class="nf">normalizeByIntensity</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> Normalizes each channel of by pixel intensity. That is, for each pixel:</span>
+<span class="sd"> I = R + G + B</span>
+<span class="sd"> newr = R * 255 / I</span>
+<span class="sd"> newg = G * 255 / I</span>
+<span class="sd"> newb = B * 255 / I</span>
+<span class="sd"> """</span>
+ <span class="n">f</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">image</span><span class="o">.</span><span class="n">astype</span><span class="p">(</span><span class="nb">float</span><span class="p">)</span>
+ <span class="n">combined</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">add</span><span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">add</span><span class="p">(</span><span class="n">f</span><span class="p">[:,:,</span><span class="mi">0</span><span class="p">],</span> <span class="n">f</span><span class="p">[:,:,</span><span class="mi">1</span><span class="p">]),</span> <span class="n">f</span><span class="p">[:,:,</span><span class="mi">2</span><span class="p">])</span>
+ <span class="n">scaled</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">multiply</span><span class="p">(</span><span class="n">f</span><span class="p">,</span> <span class="p">[</span><span class="mi">255</span><span class="p">])</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">image</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">divide</span><span class="p">(</span><span class="n">scaled</span><span class="p">,</span> <span class="n">combined</span><span class="p">[:,:,</span><span class="bp">None</span><span class="p">])</span><span class="o">.</span><span class="n">astype</span><span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">uint8</span><span class="p">)</span>
+ <span class="k">return</span>
+ </div>
+<div class="viewcode-block" id="Image.morphology"><a class="viewcode-back" href="../../processing.html#plantcv.imgproc.Image.morphology">[docs]</a> <span class="k">def</span> <span class="nf">morphology</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">morphType</span><span class="p">,</span> <span class="n">ktype</span><span class="p">,</span> <span class="n">ksize</span><span class="p">,</span> <span class="n">anchor</span> <span class="o">=</span> <span class="p">(</span><span class="o">-</span><span class="mi">1</span><span class="p">,</span> <span class="o">-</span><span class="mi">1</span><span class="p">),</span> <span class="n">iterations</span> <span class="o">=</span> <span class="mi">1</span><span class="p">,</span> <span class="n">borderType</span> <span class="o">=</span> <span class="s">"default"</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> :param morphType: The type of morphology to perform. Should be dilate, erode, open, close, gradient, tophat, or blackhat.</span>
+<span class="sd"> :type morphType: str</span>
+<span class="sd"> :param ktype: the type of the kernel, should be rect, ellipse, or cross.</span>
+<span class="sd"> :type ktype: str</span>
+<span class="sd"> :param ksize: The size of the kernel represented by a tuple (width, height). Both numbers should be odd and positive.</span>
+<span class="sd"> :type ksize: tuple</span>
+<span class="sd"> :param anchor: The anchor point for filtering. Default is (-1, -1) which is the center of the kernel.</span>
+<span class="sd"> :type anchor: tuple</span>
+<span class="sd"> :param iterations: The number of times to perform the specified morphology.</span>
+<span class="sd"> :type iterations: int</span>
+<span class="sd"> :param borderType: The type of border mode used to extrapolate pixels outside the image. Literally no information on this.</span>
+<span class="sd"> :type borderType: str</span>
+<span class="sd"> </span>
+<span class="sd"> This function performs morphological operations based on the inputted values.</span>
+<span class="sd"> REFERENCE to OPENCV MORPHOLOGY</span>
+<span class="sd"> SHOW MORPHOLOGY EXAMPLES</span>
+<span class="sd"> """</span>
+ <span class="k">if</span> <span class="n">morphType</span> <span class="ow">in</span> <span class="n">conf</span><span class="o">.</span><span class="n">morph</span><span class="p">:</span>
+ <span class="k">if</span> <span class="n">ktype</span> <span class="ow">in</span> <span class="n">conf</span><span class="o">.</span><span class="n">kernels</span><span class="p">:</span>
+ <span class="k">if</span> <span class="n">borderType</span> <span class="ow">in</span> <span class="n">conf</span><span class="o">.</span><span class="n">borders</span><span class="p">:</span>
+ <span class="n">kernel</span> <span class="o">=</span> <span class="n">cv2</span><span class="o">.</span><span class="n">getStructuringElement</span><span class="p">(</span><span class="n">conf</span><span class="o">.</span><span class="n">kernels</span><span class="p">[</span><span class="n">ktype</span><span class="p">],</span> <span class="n">ksize</span><span class="p">,</span> <span class="n">anchor</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">image</span> <span class="o">=</span> <span class="n">cv2</span><span class="o">.</span><span class="n">morphologyEx</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">image</span><span class="p">,</span> <span class="n">conf</span><span class="o">.</span><span class="n">morph</span><span class="p">[</span><span class="n">morphType</span><span class="p">],</span> <span class="n">kernel</span><span class="p">,</span> <span class="n">anchor</span> <span class="o">=</span> <span class="n">anchor</span><span class="p">,</span> <span class="n">iterations</span> <span class="o">=</span> <span class="n">iterations</span><span class="p">,</span> <span class="n">borderType</span> <span class="o">=</span> <span class="n">conf</span><span class="o">.</span><span class="n">borders</span><span class="p">[</span><span class="n">borderType</span><span class="p">])</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="s">"Invalid border type, should be one of: "</span> <span class="o">+</span> <span class="s">","</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">conf</span><span class="o">.</span><span class="n">borders</span><span class="o">.</span><span class="n">keys</span><span class="p">())</span> <span class="o">+</span> <span class="s">"."</span><span class="p">)</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="s">"Invalid kernel type, should be one of: "</span> <span class="o">+</span> <span class="s">","</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">conf</span><span class="o">.</span><span class="n">kernels</span><span class="o">.</span><span class="n">keys</span><span class="p">())</span> <span class="o">+</span> <span class="s">"."</span><span class="p">)</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="s">"Invalid morphology type, should be one of: "</span> <span class="o">+</span> <span class="s">","</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">conf</span><span class="o">.</span><span class="n">morph</span><span class="o">.</span><span class="n">keys</span><span class="p">())</span> <span class="o">+</span> <span class="s">"."</span><span class="p">)</span>
+ </div>
+<div class="viewcode-block" id="Image.crop"><a class="viewcode-back" href="../../processing.html#plantcv.imgproc.Image.crop">[docs]</a> <span class="k">def</span> <span class="nf">crop</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">roi</span><span class="p">,</span> <span class="n">resize</span> <span class="o">=</span> <span class="bp">False</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> :param roi: A list corresponding to the area of the image you want. List should be of the form [ystart, yend, xstart, xend]</span>
+<span class="sd"> :type roi: list or roi file</span>
+<span class="sd"> :param resize: If True, actually adjusts the size of the image, otherwise just draws over the part of the image not in the roi.</span>
+<span class="sd"> :type resize: bool</span>
+<span class="sd"> </span>
+<span class="sd"> This function crops the image based on the given roi [ystart, yend, xstart, xend]. There are two crop options,</span>
+<span class="sd"> by default, the function doesn't actually resize the image. Instead, it sets each pixel not in the roi to black.</span>
+<span class="sd"> If resize is set to True, the function will actually crop the image down to the roi.</span>
+<span class="sd"> """</span>
+ <span class="n">roi</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_loadROI</span><span class="p">(</span><span class="n">roi</span><span class="p">)</span>
+ <span class="n">ystart</span><span class="p">,</span> <span class="n">yend</span><span class="p">,</span> <span class="n">xstart</span><span class="p">,</span> <span class="n">xend</span> <span class="o">=</span> <span class="n">roi</span>
+ <span class="k">if</span> <span class="p">(</span><span class="n">resize</span><span class="p">):</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">image</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">image</span><span class="p">[</span><span class="n">ystart</span><span class="p">:</span> <span class="n">yend</span><span class="p">,</span> <span class="n">xstart</span><span class="p">:</span> <span class="n">xend</span><span class="p">]</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">x</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">image</span><span class="o">.</span><span class="n">shape</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">y</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">image</span><span class="o">.</span><span class="n">shape</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="n">maxx</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">x</span>
+ <span class="n">maxy</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">y</span>
+ <span class="n">off</span> <span class="o">=</span> <span class="p">[</span><span class="mi">0</span><span class="p">,</span> <span class="mi">0</span><span class="p">,</span> <span class="mi">0</span><span class="p">]</span> <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">_isColor</span><span class="p">()</span> <span class="k">else</span> <span class="p">[</span><span class="mi">0</span><span class="p">]</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">image</span><span class="p">[</span><span class="mi">0</span><span class="p">:</span><span class="n">ystart</span><span class="p">,</span> <span class="mi">0</span><span class="p">:</span><span class="n">maxx</span><span class="p">]</span> <span class="o">=</span> <span class="n">off</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">image</span><span class="p">[</span><span class="n">yend</span><span class="p">:</span><span class="n">maxy</span><span class="p">,</span> <span class="mi">0</span><span class="p">:</span><span class="n">maxx</span><span class="p">]</span> <span class="o">=</span> <span class="n">off</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">image</span><span class="p">[</span><span class="mi">0</span><span class="p">:</span><span class="n">maxy</span><span class="p">,</span> <span class="mi">0</span><span class="p">:</span><span class="n">xstart</span><span class="p">]</span> <span class="o">=</span> <span class="n">off</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">image</span><span class="p">[</span><span class="mi">0</span><span class="p">:</span><span class="n">maxy</span><span class="p">,</span> <span class="n">xend</span><span class="p">:</span><span class="n">maxx</span><span class="p">]</span> <span class="o">=</span> <span class="n">off</span>
+ <span class="k">return</span>
+ </div>
+<div class="viewcode-block" id="Image.contourCut"><a class="viewcode-back" href="../../processing.html#plantcv.imgproc.Image.contourCut">[docs]</a> <span class="k">def</span> <span class="nf">contourCut</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">binary</span><span class="p">,</span> <span class="n">basemin</span> <span class="o">=</span> <span class="mi">100</span><span class="p">,</span> <span class="n">padding</span> <span class="o">=</span> <span class="p">[</span><span class="mi">0</span><span class="p">,</span> <span class="mi">0</span><span class="p">,</span> <span class="mi">0</span><span class="p">,</span> <span class="mi">0</span><span class="p">],</span> <span class="n">resize</span> <span class="o">=</span> <span class="bp">False</span><span class="p">,</span> <span class="n">returnBound</span> <span class="o">=</span> <span class="bp">False</span><span class="p">,</span> <span class="n">roiwrite</span> <span class="o">=</span> <span class="s">"roi.json"</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> :param binary: The binary image to find contours of.</span>
+<span class="sd"> :type binary: str or np.ndarray</span>
+<span class="sd"> :param basemin: The minimum area a contour must have to be consider part of the foreground.</span>
+<span class="sd"> :type basemin: int</span>
+<span class="sd"> :param padding: Padding add to all sides of the final roi.</span>
+<span class="sd"> :type padding: int</span>
+<span class="sd"> :param returnBound: If set, instead of cropping the image, simply write the detected roi.</span>
+<span class="sd"> :type returnBound: bool</span>
+<span class="sd"> :param resize: Whether or not to resize the image.</span>
+<span class="sd"> :type resize: bool</span>
+<span class="sd"> </span>
+<span class="sd"> This function crops an image based on the size of detected contours in the image. The</span>
+<span class="sd"> image is cropped such that all contours that are greater than the specified area are</span>
+<span class="sd"> included in the final output image. If returnBound is set, instead of actually</span>
+<span class="sd"> cropping the image, the detected roi is written to a file instead. Otherwise,</span>
+<span class="sd"> the detected roi is passed into the :py:meth:`~plantcv.imgproc.crop` function,</span>
+<span class="sd"> with the given resize value.</span>
+<span class="sd"> """</span>
+ <span class="n">bname</span><span class="p">,</span> <span class="n">binary</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_loadResource</span><span class="p">(</span><span class="n">binary</span><span class="p">)</span>
+ <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">_isColor</span><span class="p">(</span><span class="n">binary</span><span class="p">):</span>
+ <span class="n">binary</span> <span class="o">=</span> <span class="n">cv2</span><span class="o">.</span><span class="n">cvtColor</span><span class="p">(</span><span class="n">binary</span><span class="p">,</span> <span class="n">cv2</span><span class="o">.</span><span class="n">COLOR_BGR2GRAY</span><span class="p">)</span>
+ <span class="n">contours</span> <span class="o">=</span> <span class="n">cv2</span><span class="o">.</span><span class="n">findContours</span><span class="p">(</span><span class="n">binary</span><span class="p">,</span> <span class="n">cv2</span><span class="o">.</span><span class="n">RETR_TREE</span><span class="p">,</span> <span class="n">cv2</span><span class="o">.</span><span class="n">CHAIN_APPROX_SIMPLE</span><span class="p">)[</span><span class="mi">0</span><span class="p">]</span>
+ <span class="n">minx</span> <span class="o">=</span> <span class="n">binary</span><span class="o">.</span><span class="n">shape</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span>
+ <span class="n">miny</span> <span class="o">=</span> <span class="n">binary</span><span class="o">.</span><span class="n">shape</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span>
+ <span class="n">maxx</span> <span class="o">=</span> <span class="mi">0</span>
+ <span class="n">maxy</span> <span class="o">=</span> <span class="mi">0</span>
+ <span class="k">for</span> <span class="n">cnt</span> <span class="ow">in</span> <span class="n">contours</span><span class="p">:</span>
+ <span class="n">x</span><span class="p">,</span><span class="n">y</span><span class="p">,</span><span class="n">w</span><span class="p">,</span><span class="n">h</span> <span class="o">=</span> <span class="n">cv2</span><span class="o">.</span><span class="n">boundingRect</span><span class="p">(</span><span class="n">cnt</span><span class="p">)</span>
+ <span class="k">if</span> <span class="p">(</span><span class="n">basemin</span> <span class="o"><</span> <span class="n">cv2</span><span class="o">.</span><span class="n">contourArea</span><span class="p">(</span><span class="n">cnt</span><span class="p">)):</span>
+ <span class="k">if</span> <span class="p">(</span><span class="n">x</span> <span class="o"><</span> <span class="n">minx</span><span class="p">):</span>
+ <span class="n">minx</span> <span class="o">=</span> <span class="n">x</span>
+ <span class="k">if</span> <span class="p">(</span><span class="n">y</span> <span class="o"><</span> <span class="n">miny</span><span class="p">):</span>
+ <span class="n">miny</span> <span class="o">=</span> <span class="n">y</span>
+ <span class="k">if</span> <span class="p">(</span><span class="n">x</span> <span class="o">+</span> <span class="n">w</span> <span class="o">></span> <span class="n">maxx</span><span class="p">):</span>
+ <span class="n">maxx</span> <span class="o">=</span> <span class="n">x</span> <span class="o">+</span> <span class="n">w</span>
+ <span class="k">if</span> <span class="p">(</span><span class="n">y</span> <span class="o">+</span> <span class="n">h</span> <span class="o">></span> <span class="n">maxy</span><span class="p">):</span>
+ <span class="n">maxy</span> <span class="o">=</span> <span class="n">y</span> <span class="o">+</span> <span class="n">h</span>
+ <span class="n">roi</span> <span class="o">=</span> <span class="p">[</span><span class="mi">0</span> <span class="k">if</span> <span class="n">miny</span> <span class="o">-</span> <span class="n">padding</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="o"><</span> <span class="mi">0</span> <span class="k">else</span> <span class="n">miny</span> <span class="o">-</span> <span class="n">padding</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span> <span class="n">binary</span><span class="o">.</span><span class="n">shape</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="k">if</span> <span class="n">maxy</span> <span class="o">+</span> <span class="n">padding</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span> <span class="o">></span> <span class="n">binary</span><span class="o">.</span><span class="n">shape</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="k">else</span> <span class="n">maxy</span> <span class="o">+</span> <span class="n">padding</span><span class="p">[</span><span class="mi">1</span><span class="p">],</span> <span class="mi">0</span> <span class="k">if</span> <span class="n">minx</span> <span class="o">-</span> <span class="n">padding</span><span class="p">[</span><span class="mi">2</span><span class="p">]</span> <span class="o"><</span> <span class="mi">0</span> <span class="k">else</span> <span class="n">minx</span> <span class="o">-</span> <span class="n">padding</span><span class="p">[</span><span class="mi">2</span><span class="p">],</span> <span class="n">binary</span><span class="o">.</span><span class="n">shape</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span> <span class="k">if</span> <span class="n">maxx</span> <span class="o">+</span> <span class="n">padding</span><span class="p">[</span><span class="mi">3</span><span class="p">]</span> <span class="o">></span> <span class="n">binary</span><span class="o">.</span><span class="n">shape</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span> <span class="k">else</span> <span class="n">maxx</span> <span class="o">+</span> <span class="n">padding</span><span class="p">[</span><span class="mi">3</span><span class="p">]]</span>
+ <span class="k">if</span> <span class="n">returnBound</span><span class="p">:</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_writeROI</span><span class="p">(</span><span class="n">roi</span><span class="p">,</span> <span class="n">roiwrite</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">crop</span><span class="p">(</span><span class="n">roi</span><span class="p">,</span> <span class="n">resize</span><span class="p">)</span>
+ <span class="k">return</span>
+ </div>
+<div class="viewcode-block" id="Image.edges"><a class="viewcode-back" href="../../processing.html#plantcv.imgproc.Image.edges">[docs]</a> <span class="k">def</span> <span class="nf">edges</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">threshold1</span><span class="p">,</span> <span class="n">threshold2</span><span class="p">,</span> <span class="n">apertureSize</span> <span class="o">=</span> <span class="mi">3</span><span class="p">,</span> <span class="n">L2gradient</span> <span class="o">=</span> <span class="bp">False</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> :param threshold1: First threshold for the hysteresis procedure.</span>
+<span class="sd"> :type threshold1: int</span>
+<span class="sd"> :param threshold2: Second threshold for the hysteresis procedure.</span>
+<span class="sd"> :type threshold2: int</span>
+<span class="sd"> :param apertureSize: aperture size used for the Sobel algorithm.</span>
+<span class="sd"> :type apertureSize: int</span>
+<span class="sd"> :L2gradient: Used to calculate Image gradient magnitude, if true then :math:`L = \sqrt{(dI/dx)^2 + (dI/dy)^2}`, if false then :math:`L = dI/dx + dI/dy`.</span>
+<span class="sd"> :type L2gradient: bool</span>
+<span class="sd"> </span>
+<span class="sd"> This function calculates the edges of an image using the Canny edge detection algorithm, which is built upon the Sobel</span>
+<span class="sd"> algorithm, which calculates derivatives of an image. REFERENCE TO OPENCV HERE.</span>
+<span class="sd"> """</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">image</span> <span class="o">=</span> <span class="n">cv2</span><span class="o">.</span><span class="n">Canny</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">image</span><span class="p">,</span> <span class="n">threshold1</span><span class="p">,</span> <span class="n">threshold2</span><span class="p">,</span> <span class="n">apertureSize</span> <span class="o">=</span> <span class="n">apertureSize</span><span class="p">,</span> <span class="n">L2gradient</span> <span class="o">=</span> <span class="n">L2gradient</span><span class="p">)</span>
+ <span class="k">return</span>
+ </div>
+<div class="viewcode-block" id="Image.colorFilter"><a class="viewcode-back" href="../../processing.html#plantcv.imgproc.Image.colorFilter">[docs]</a> <span class="k">def</span> <span class="nf">colorFilter</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">logic</span><span class="p">,</span> <span class="n">roi</span> <span class="o">=</span> <span class="bp">None</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> :param logic: The logic you want to run on the image.</span>
+<span class="sd"> :type logic: str</span>
+<span class="sd"> :param roi: The roi you want to apply the filter to</span>
+<span class="sd"> :type roi: list or roi file</span>
+<span class="sd"> </span>
+<span class="sd"> This function applies a color filter defined by the input logic, to a</span>
+<span class="sd"> targeted region defined by the input roi. The roi is defined the same,</span>
+<span class="sd"> [ystart, yend, xstart, xend]. The logic string itself is fairly complicated.</span>
+<span class="sd"> The string supports the following operators: '+', '-', '*', '/', '>', '>=',</span>
+<span class="sd"> '==', '<', '<=', 'and', 'or', '(', ')', 'r', 'g', 'b', as well as any numeric</span>
+<span class="sd"> value. The logic string itself is confined to symbolic logic rules -- each </span>
+<span class="sd"> operation, arg1 operator arg2, must be surrounded by parenthesis. For example,</span>
+<span class="sd"> if you want to check the intensity of the pixel, your logic string would be:</span>
+<span class="sd"> '(((r + g) + b) < 100)'. This string in particular will only keep pixels whose</span>
+<span class="sd"> intensity is less than 100. Similar rules apply for 'and' and 'or' operators.</span>
+<span class="sd"> Let's say we only want to keep pixels whose intensity is less than 100, OR both</span>
+<span class="sd"> the red and blue channels are greater than 150, the logic string would be: </span>
+<span class="sd"> '((((r + g) + b) < 100) or ((r > 150) and (b > 150)))'.</span>
+<span class="sd"> """</span>
+ <span class="nb">filter</span> <span class="o">=</span> <span class="n">ColorFilter</span><span class="p">(</span><span class="n">logic</span><span class="p">)</span>
+ <span class="n">roi</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_loadROI</span><span class="p">(</span><span class="n">roi</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">image</span> <span class="o">=</span> <span class="nb">filter</span><span class="o">.</span><span class="n">apply</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">image</span><span class="p">,</span> <span class="n">roi</span><span class="p">)</span>
+ <span class="k">return</span>
+ </div>
+<div class="viewcode-block" id="Image.bitwise_not"><a class="viewcode-back" href="../../processing.html#plantcv.imgproc.Image.bitwise_not">[docs]</a> <span class="k">def</span> <span class="nf">bitwise_not</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> Inverts the image. If the given image has multiple channels (i.e. is a color image) each channel is processed independently.</span>
+<span class="sd"> """</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">image</span> <span class="o">=</span> <span class="n">cv2</span><span class="o">.</span><span class="n">bitwise_not</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">image</span><span class="p">)</span>
+ <span class="k">return</span>
+ </div>
+<div class="viewcode-block" id="Image.bitwise_and"><a class="viewcode-back" href="../../processing.html#plantcv.imgproc.Image.bitwise_and">[docs]</a> <span class="k">def</span> <span class="nf">bitwise_and</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">comp</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> :param comp: The comparison image.</span>
+<span class="sd"> :type comp: str or np.ndarray</span>
+<span class="sd"> :return: The resulting mask.</span>
+<span class="sd"> :rtype: numpy.ndarray</span>
+<span class="sd"> </span>
+<span class="sd"> Performs logical and on the class image, and reference image.</span>
+<span class="sd"> Assumes the two images are the correct type.</span>
+<span class="sd"> """</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">image</span> <span class="o">=</span> <span class="n">cv2</span><span class="o">.</span><span class="n">bitwise_and</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">image</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">_loadResource</span><span class="p">(</span><span class="n">comp</span><span class="p">)[</span><span class="mi">1</span><span class="p">])</span>
+ <span class="k">return</span>
+ </div>
+<div class="viewcode-block" id="Image.bitwise_or"><a class="viewcode-back" href="../../processing.html#plantcv.imgproc.Image.bitwise_or">[docs]</a> <span class="k">def</span> <span class="nf">bitwise_or</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">comp</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> :param comp: The comparison image.</span>
+<span class="sd"> :type comp: str or np.ndarray</span>
+<span class="sd"> :return: The resulting mask.</span>
+<span class="sd"> :rtype: numpy.ndarray</span>
+<span class="sd"> </span>
+<span class="sd"> Performs bitwise or logic on the class image, and reference image.</span>
+<span class="sd"> Assumes the two images are the correct type.</span>
+<span class="sd"> """</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">image</span> <span class="o">=</span> <span class="n">cv2</span><span class="o">.</span><span class="n">bitwise_or</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">image</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">_loadResource</span><span class="p">(</span><span class="n">comp</span><span class="p">)[</span><span class="mi">1</span><span class="p">])</span>
+ <span class="k">return</span>
+ </div>
+<div class="viewcode-block" id="Image.bitwise_xor"><a class="viewcode-back" href="../../processing.html#plantcv.imgproc.Image.bitwise_xor">[docs]</a> <span class="k">def</span> <span class="nf">bitwise_xor</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">comp</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> :param comp: The comparison image.</span>
+<span class="sd"> :type comp: str or np.ndarray</span>
+<span class="sd"> :return: The resulting mask.</span>
+<span class="sd"> :rtype: numpy.ndarray</span>
+<span class="sd"> </span>
+<span class="sd"> Performs bitwise exclusive or logic on the class image, and reference image.</span>
+<span class="sd"> Assumes the two images are the correct type.</span>
+<span class="sd"> """</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">image</span> <span class="o">=</span> <span class="n">cv2</span><span class="o">.</span><span class="n">bitwise_xor</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">image</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">_loadResource</span><span class="p">(</span><span class="n">comp</span><span class="p">)[</span><span class="mi">1</span><span class="p">])</span>
+ <span class="k">return</span>
+ </div>
+<div class="viewcode-block" id="Image.extractFinalPath"><a class="viewcode-back" href="../../processing.html#plantcv.imgproc.Image.extractFinalPath">[docs]</a> <span class="k">def</span> <span class="nf">extractFinalPath</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> This function writes the absolute path of the output file to the database.</span>
+<span class="sd"> """</span>
+ <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">conn</span><span class="p">:</span>
+ <span class="n">finalpath</span> <span class="o">=</span> <span class="s">"/"</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">abspath</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">input</span><span class="p">)</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s">"/"</span><span class="p">)[</span><span class="o">-</span><span class="mi">6</span><span class="p">:])</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_addColumn</span><span class="p">(</span><span class="s">"outputPath"</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">conn</span><span class="o">.</span><span class="n">execute</span><span class="p">(</span><span class="s">"update images set outputPath=? where pegasusid=?"</span><span class="p">,</span> <span class="p">(</span><span class="n">finalpath</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">dbid</span><span class="p">))</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">conn</span><span class="o">.</span><span class="n">commit</span><span class="p">()</span>
+ <span class="k">return</span>
+ </div>
+<div class="viewcode-block" id="Image.extractMoments"><a class="viewcode-back" href="../../processing.html#plantcv.imgproc.Image.extractMoments">[docs]</a> <span class="k">def</span> <span class="nf">extractMoments</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> :return: A dictionary corresponding to the different moments of the image.</span>
+<span class="sd"> :rtype: dict</span>
+<span class="sd"> </span>
+<span class="sd"> Calculates the moments of the image, and returns a dicitonary based on them.</span>
+<span class="sd"> Spatial moments are prefixed with 'm', central moments are prefixed with 'mu',</span>
+<span class="sd"> and central normalized moments are prefixed with 'nu'.</span>
+<span class="sd"> REFERENCE TO OPENCV DOCUMENTATION</span>
+<span class="sd"> REFERENCE TO GREEN'S THEOREM</span>
+<span class="sd"> """</span>
+ <span class="n">moments</span> <span class="o">=</span> <span class="n">cv2</span><span class="o">.</span><span class="n">moments</span><span class="p">(</span><span class="n">cv2</span><span class="o">.</span><span class="n">inRange</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">image</span><span class="p">,</span> <span class="n">np</span><span class="o">.</span><span class="n">array</span><span class="p">([</span><span class="mi">1</span><span class="p">,</span> <span class="mi">1</span><span class="p">,</span> <span class="mi">1</span><span class="p">],</span> <span class="n">np</span><span class="o">.</span><span class="n">uint8</span><span class="p">),</span> <span class="n">np</span><span class="o">.</span><span class="n">array</span><span class="p">([</span><span class="mi">255</span><span class="p">,</span> <span class="mi">255</span><span class="p">,</span> <span class="mi">255</span><span class="p">],</span> <span class="n">np</span><span class="o">.</span><span class="n">uint8</span><span class="p">)))</span>
+ <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">conn</span><span class="p">:</span>
+ <span class="k">for</span> <span class="nb">id</span> <span class="ow">in</span> <span class="n">moments</span><span class="p">:</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_addColumn</span><span class="p">(</span><span class="nb">id</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">conn</span><span class="o">.</span><span class="n">execute</span><span class="p">(</span><span class="s">"update images set "</span> <span class="o">+</span> <span class="nb">id</span> <span class="o">+</span> <span class="s">"=? where pegasusid=?"</span><span class="p">,</span> <span class="p">(</span><span class="n">moments</span><span class="p">[</span><span class="nb">id</span><span class="p">],</span> <span class="bp">self</span><span class="o">.</span><span class="n">dbid</span><span class="p">))</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">conn</span><span class="o">.</span><span class="n">commit</span><span class="p">()</span>
+ <span class="k">return</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="k">return</span> <span class="n">moments</span>
+ </div>
+<div class="viewcode-block" id="Image.extractDimensions"><a class="viewcode-back" href="../../processing.html#plantcv.imgproc.Image.extractDimensions">[docs]</a> <span class="k">def</span> <span class="nf">extractDimensions</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> :return: A list corresponding to the height and width of the image.</span>
+<span class="sd"> :rtype: list</span>
+<span class="sd"> </span>
+<span class="sd"> Returns a list with the following form: [height, width]</span>
+<span class="sd"> """</span>
+ <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">conn</span><span class="p">:</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_addColumn</span><span class="p">(</span><span class="s">"height"</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_addColumn</span><span class="p">(</span><span class="s">"width"</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">conn</span><span class="o">.</span><span class="n">execute</span><span class="p">(</span><span class="s">"update images set height=?,width=? where pegasusid=?"</span><span class="p">,</span> <span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">y</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">x</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">dbid</span><span class="p">))</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">conn</span><span class="o">.</span><span class="n">commit</span><span class="p">()</span>
+ <span class="k">return</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="k">return</span> <span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">y</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">x</span><span class="p">]</span>
+ </div>
+<div class="viewcode-block" id="Image.extractPixels"><a class="viewcode-back" href="../../processing.html#plantcv.imgproc.Image.extractPixels">[docs]</a> <span class="k">def</span> <span class="nf">extractPixels</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> :return: The number of non-black pixels in the image.</span>
+<span class="sd"> :rtype: int</span>
+<span class="sd"> </span>
+<span class="sd"> Returns the number of non-black pixels in the image. Creates</span>
+<span class="sd"> a temporary binary image to do this. The point of this function</span>
+<span class="sd"> is not to threshold, so the binary image is created by all</span>
+<span class="sd"> pixels that fall into the range [1, 1, 1], [255, 255, 255].</span>
+<span class="sd"> """</span>
+ <span class="n">pixelCount</span> <span class="o">=</span> <span class="n">cv2</span><span class="o">.</span><span class="n">countNonZero</span><span class="p">(</span><span class="n">cv2</span><span class="o">.</span><span class="n">inRange</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">image</span><span class="p">,</span> <span class="n">np</span><span class="o">.</span><span class="n">array</span><span class="p">([</span><span class="mi">1</span><span class="p">,</span> <span class="mi">1</span><span class="p">,</span> <span class="mi">1</span><span class="p">],</span> <span class="n">np</span><span class="o">.</span><span class="n">uint8</span><span class="p">),</span> <span class="n">np</span><span class="o">.</span><span class="n">array</span><span class="p">([</span><span class="mi">255</span><span class="p">,</span> <span class="mi">255</span><span class="p">,</span> <span class="mi">255</span><span class="p">],</span> <span class="n">np</span><span class="o">.</span><span class="n">uint8</span><span class="p">)))</span>
+ <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">conn</span><span class="p">:</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_addColumn</span><span class="p">(</span><span class="s">"pixels"</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">conn</span><span class="o">.</span><span class="n">execute</span><span class="p">(</span><span class="s">"update images set pixels=? where pegasusid=?"</span><span class="p">,</span> <span class="p">(</span><span class="n">pixelCount</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">dbid</span><span class="p">))</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">conn</span><span class="o">.</span><span class="n">commit</span><span class="p">()</span>
+ <span class="k">return</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="k">return</span> <span class="n">pixelCount</span>
+ </div>
+<div class="viewcode-block" id="Image.extractColorData"><a class="viewcode-back" href="../../processing.html#plantcv.imgproc.Image.extractColorData">[docs]</a> <span class="k">def</span> <span class="nf">extractColorData</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">nonzero</span> <span class="o">=</span> <span class="bp">True</span><span class="p">,</span> <span class="n">returnhist</span> <span class="o">=</span> <span class="bp">False</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> :param nonzero: Whether or not to look at only nonzero pixels. Default true.</span>
+<span class="sd"> :type nonzero: bool</span>
+<span class="sd"> :return: Mean & median for each channel.</span>
+<span class="sd"> :rtype: list</span>
+<span class="sd"> </span>
+<span class="sd"> This function calculates a normalized histogram of each individual color channel of </span>
+<span class="sd"> the image, and returns the mean & median of the histograms for the channels</span>
+<span class="sd"> specified. Because images are imported with the channels ordered as B,G,R,</span>
+<span class="sd"> the output list is returned the same way. The returned list always looks like</span>
+<span class="sd"> this: [ [BlueMean, BlueMedian], [GreenMean, GreenMedian], [RedMean, RedMedian] ].</span>
+<span class="sd"> Mean values always come before median values. If nonzero is set to true (default)</span>
+<span class="sd"> the function will only calculate mediapytn and means based on the non-black pixels.</span>
+<span class="sd"> """</span>
+ <span class="n">hist</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_colorHistogram</span><span class="p">()</span>
+ <span class="k">if</span> <span class="n">returnhist</span><span class="p">:</span>
+ <span class="k">return</span> <span class="n">hist</span>
+ <span class="n">colors</span> <span class="o">=</span> <span class="p">[</span> <span class="p">[</span><span class="n">np</span><span class="o">.</span><span class="n">mean</span><span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">nonzero</span><span class="p">(</span><span class="n">hist</span><span class="p">[</span><span class="mi">0</span><span class="p">])</span> <span class="k">if</span> <span class="n">nonzero</span> <span class="k">else</span> <span class="n">hist</span><span class="p">[</span><span class="mi">0</span><span class="p">]),</span> <span class="n">np</span><span class="o">.</span><span class="n">median</span><span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">nonzero</span><span class="p">(</span><span class="n">hist</span><span class="p">[</span><span class="mi">0</span><span class="p">])</span> <span class="k">if</span> <span class="n">nonzero</span> <span class="k">else</span> <span class="n">hist</span><span class="p">[</span><span class="mi">0</span><span class="p">])],</span>
+ <span class="p">[</span><span class="n">np</span><span class="o">.</span><span class="n">mean</span><span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">nonzero</span><span class="p">(</span><span class="n">hist</span><span class="p">[</span><span class="mi">1</span><span class="p">])</span> <span class="k">if</span> <span class="n">nonzero</span> <span class="k">else</span> <span class="n">hist</span><span class="p">[</span><span class="mi">1</span><span class="p">]),</span> <span class="n">np</span><span class="o">.</span><span class="n">median</span><span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">nonzero</span><span class="p">(</span><span class="n">hist</span><span class="p">[</span><span class="mi">1</span><span class="p">])</span> <span class="k">if</span> <span class="n">nonzero</span> <span class="k">else</span> <span class="n">hist</span><span class="p">[</span><span class="mi">1</span><span class="p">])],</span>
+ <span class="p">[</span><span class="n">np</span><span class="o">.</span><span class="n">mean</span><span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">nonzero</span><span class="p">(</span><span class="n">hist</span><span class="p">[</span><span class="mi">2</span><span class="p">])</span> <span class="k">if</span> <span class="n">nonzero</span> <span class="k">else</span> <span class="n">hist</span><span class="p">[</span><span class="mi">2</span><span class="p">]),</span> <span class="n">np</span><span class="o">.</span><span class="n">median</span><span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">nonzero</span><span class="p">(</span><span class="n">hist</span><span class="p">[</span><span class="mi">2</span><span class="p">])</span> <span class="k">if</span> <span class="n">nonzero</span> <span class="k">else</span> <span class="n">hist</span><span class="p">[</span><span class="mi">2</span><span class="p">])]</span>
+ <span class="p">]</span>
+ <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">conn</span><span class="p">:</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_addColumn</span><span class="p">(</span><span class="s">"rmean"</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_addColumn</span><span class="p">(</span><span class="s">"rmed"</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_addColumn</span><span class="p">(</span><span class="s">"gmean"</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_addColumn</span><span class="p">(</span><span class="s">"gmed"</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_addColumn</span><span class="p">(</span><span class="s">"bmean"</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_addColumn</span><span class="p">(</span><span class="s">"bmed"</span><span class="p">)</span>
+ <span class="n">query</span> <span class="o">=</span> <span class="s">"update images set rmean=?,rmed=?,gmean=?,gmed=?,bmean=?,bmed=?"</span>
+ <span class="n">values</span> <span class="o">=</span> <span class="p">[</span><span class="n">colors</span><span class="p">[</span><span class="mi">2</span><span class="p">][</span><span class="mi">0</span><span class="p">],</span> <span class="n">colors</span><span class="p">[</span><span class="mi">2</span><span class="p">][</span><span class="mi">1</span><span class="p">],</span> <span class="n">colors</span><span class="p">[</span><span class="mi">1</span><span class="p">][</span><span class="mi">0</span><span class="p">],</span> <span class="n">colors</span><span class="p">[</span><span class="mi">1</span><span class="p">][</span><span class="mi">1</span><span class="p">],</span> <span class="n">colors</span><span class="p">[</span><span class="mi">0</span><span class="p">][</span><span class="mi">0</span><span class="p">],</span> <span class="n">colors</span><span class="p">[</span><span class="mi">0</span><span class="p">][</span><span class="mi">1</span><span class="p">]]</span>
+ <span class="k">for</span> <span class="n">x</span><span class="p">,</span><span class="n">c</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">([</span><span class="s">"bhist"</span><span class="p">,</span> <span class="s">"ghist"</span><span class="p">,</span> <span class="s">"rhist"</span><span class="p">]):</span>
+ <span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="mi">0</span><span class="p">,</span> <span class="mi">256</span><span class="p">):</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_addColumn</span><span class="p">(</span><span class="n">c</span> <span class="o">+</span> <span class="nb">str</span><span class="p">(</span><span class="n">i</span><span class="p">))</span>
+ <span class="n">query</span> <span class="o">+=</span> <span class="s">","</span> <span class="o">+</span> <span class="n">c</span> <span class="o">+</span> <span class="nb">str</span><span class="p">(</span><span class="n">i</span><span class="p">)</span> <span class="o">+</span> <span class="s">"=?"</span>
+ <span class="n">values</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="nb">int</span><span class="p">(</span><span class="n">hist</span><span class="p">[</span><span class="n">x</span><span class="p">][</span><span class="n">i</span><span class="p">]))</span>
+ <span class="n">query</span> <span class="o">+=</span> <span class="s">" where pegasusid=?"</span>
+ <span class="n">values</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">dbid</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">conn</span><span class="o">.</span><span class="n">execute</span><span class="p">(</span><span class="n">query</span><span class="p">,</span> <span class="nb">tuple</span><span class="p">(</span><span class="n">values</span><span class="p">))</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">conn</span><span class="o">.</span><span class="n">commit</span><span class="p">()</span>
+ <span class="k">return</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="k">return</span> <span class="n">colors</span>
+ </div>
+ <span class="k">def</span> <span class="nf">extractColorChannels</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+ <span class="n">b</span><span class="p">,</span> <span class="n">g</span><span class="p">,</span> <span class="n">r</span> <span class="o">=</span> <span class="n">cv2</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">image</span><span class="p">)</span>
+ <span class="n">bdata</span><span class="p">,</span> <span class="n">gdata</span><span class="p">,</span> <span class="n">rdata</span> <span class="o">=</span> <span class="p">[],</span> <span class="p">[],</span> <span class="p">[]</span>
+ <span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="mi">0</span><span class="p">,</span> <span class="mi">256</span><span class="p">):</span>
+ <span class="n">bdata</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">count_nonzero</span><span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">where</span><span class="p">(</span><span class="n">b</span> <span class="o">==</span> <span class="n">i</span><span class="p">,</span> <span class="bp">True</span><span class="p">,</span> <span class="bp">False</span><span class="p">)))</span>
+ <span class="n">gdata</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">count_nonzero</span><span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">where</span><span class="p">(</span><span class="n">g</span> <span class="o">==</span> <span class="n">i</span><span class="p">,</span> <span class="bp">True</span><span class="p">,</span> <span class="bp">False</span><span class="p">)))</span>
+ <span class="n">rdata</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">count_nonzero</span><span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">where</span><span class="p">(</span><span class="n">r</span> <span class="o">==</span> <span class="n">i</span><span class="p">,</span> <span class="bp">True</span><span class="p">,</span> <span class="bp">False</span><span class="p">)))</span>
+ <span class="n">data</span> <span class="o">=</span> <span class="p">[</span><span class="n">bdata</span><span class="p">,</span> <span class="n">gdata</span><span class="p">,</span> <span class="n">rdata</span><span class="p">]</span>
+ <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">conn</span><span class="p">:</span>
+ <span class="n">query</span> <span class="o">=</span> <span class="s">"update images set "</span>
+ <span class="n">values</span> <span class="o">=</span> <span class="p">[]</span>
+ <span class="k">for</span> <span class="n">x</span><span class="p">,</span><span class="n">c</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">([</span><span class="s">"b"</span><span class="p">,</span> <span class="s">"g"</span><span class="p">,</span> <span class="s">"r"</span><span class="p">]):</span>
+ <span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="mi">0</span><span class="p">,</span> <span class="mi">256</span><span class="p">):</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_addColumn</span><span class="p">(</span><span class="n">c</span> <span class="o">+</span> <span class="nb">str</span><span class="p">(</span><span class="n">i</span><span class="p">))</span>
+ <span class="k">if</span> <span class="n">i</span> <span class="o">==</span> <span class="mi">0</span><span class="p">:</span>
+ <span class="n">query</span> <span class="o">+=</span> <span class="n">c</span> <span class="o">+</span> <span class="nb">str</span><span class="p">(</span><span class="n">i</span><span class="p">)</span> <span class="o">+</span> <span class="s">"=?"</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="n">query</span> <span class="o">+=</span> <span class="s">","</span> <span class="o">+</span> <span class="n">c</span> <span class="o">+</span> <span class="nb">str</span><span class="p">(</span><span class="n">i</span><span class="p">)</span> <span class="o">+</span> <span class="s">"=?"</span>
+ <span class="n">values</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">data</span><span class="p">[</span><span class="n">x</span><span class="p">][</span><span class="n">i</span><span class="p">])</span>
+ <span class="n">query</span> <span class="o">+=</span> <span class="s">" where pegasusid=?"</span>
+ <span class="n">values</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">dbid</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">conn</span><span class="o">.</span><span class="n">execute</span><span class="p">(</span><span class="n">query</span><span class="p">,</span> <span class="nb">tuple</span><span class="p">(</span><span class="n">values</span><span class="p">))</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">conn</span><span class="o">.</span><span class="n">commit</span><span class="p">()</span>
+ <span class="k">return</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="k">return</span> <span class="p">(</span><span class="n">bdata</span><span class="p">,</span> <span class="n">gdata</span><span class="p">,</span> <span class="n">rdata</span><span class="p">)</span>
+
+<div class="viewcode-block" id="Image.extractBins"><a class="viewcode-back" href="../../processing.html#plantcv.imgproc.Image.extractBins">[docs]</a> <span class="k">def</span> <span class="nf">extractBins</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">binlist</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> :param binlist: The specified bins (color ranges) to count.</span>
+<span class="sd"> :type binlist: list</span>
+<span class="sd"> :return: The number of pixels that fall in each bin.</span>
+<span class="sd"> :rtype: list</span>
+<span class="sd"> </span>
+<span class="sd"> This function counts the number of pixels that fall into the range as</span>
+<span class="sd"> specified by each bin. This function expects the input to be a list of </span>
+<span class="sd"> dictionaries as follows:</span>
+<span class="sd"> </span>
+<span class="sd"> .. code-block:: python</span>
+<span class="sd"> </span>
+<span class="sd"> binlist = [</span>
+<span class="sd"> {"name": "bin1",</span>
+<span class="sd"> "min": [B, G, R],</span>
+<span class="sd"> "max": [B, G, R]</span>
+<span class="sd"> },</span>
+<span class="sd"> {"name": "bin2",</span>
+<span class="sd"> ...</span>
+<span class="sd"> ]</span>
+<span class="sd"> </span>
+<span class="sd"> Each range is defined by 6 values. A minimum and maximum blue,</span>
+<span class="sd"> green, and red value. The returned list is very similar to the </span>
+<span class="sd"> input list, except a 'count' key is added to each dictionary:</span>
+<span class="sd"> </span>
+<span class="sd"> .. code-block:: python</span>
+<span class="sd"> </span>
+<span class="sd"> returnlist = [</span>
+<span class="sd"> {"name": "bin1",</span>
+<span class="sd"> "min": [B, G, R],</span>
+<span class="sd"> "max": [B, G, R],</span>
+<span class="sd"> "count": VALUE</span>
+<span class="sd"> },</span>
+<span class="sd"> ...</span>
+<span class="sd"> ]</span>
+<span class="sd"> </span>
+<span class="sd"> Where 'VALUE' is the number of pixels that fall into the</span>
+<span class="sd"> corresponding range.</span>
+<span class="sd"> A list is used instead of a dictionary as the base structure</span>
+<span class="sd"> to maintain order for writing to the output database. When</span>
+<span class="sd"> using this function within a workflow, the order you specify</span>
+<span class="sd"> your bins is the order in which they will show up in the</span>
+<span class="sd"> database, and the name you specify for you bin will be</span>
+<span class="sd"> the column name in the database.</span>
+<span class="sd"> """</span>
+ <span class="n">binlist</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_loadBins</span><span class="p">(</span><span class="n">binlist</span><span class="p">)</span>
+ <span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="mi">0</span><span class="p">,</span> <span class="nb">len</span><span class="p">(</span><span class="n">binlist</span><span class="p">)):</span>
+ <span class="n">binlist</span><span class="p">[</span><span class="n">i</span><span class="p">][</span><span class="s">"count"</span><span class="p">]</span> <span class="o">=</span> <span class="n">cv2</span><span class="o">.</span><span class="n">countNonZero</span><span class="p">(</span><span class="n">cv2</span><span class="o">.</span><span class="n">inRange</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">image</span><span class="p">,</span> <span class="n">np</span><span class="o">.</span><span class="n">array</span><span class="p">(</span><span class="n">binlist</span><span class="p">[</span><span class="n">i</span><span class="p">][</span><span class="s">"min"</span><span class="p">],</span> <span class="n">np</span><span class="o">.</span><span class="n">uint8</span><span class="p">),</span> <span class="n">np</span><span class="o">.</span><span class="n">array</span><span class="p">(</span><span class="n">binlist</span><span class="p">[</span><span class="n">i</span><span class="p">][</span><span class="s">"max"</span><span class="p">],</span> <span class="n">np</span><span class="o">.</span><span class="n">uint8</span><span class="p">)))</span>
+ <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">conn</span><span class="p">:</span>
+ <span class="k">for</span> <span class="nb">bin</span> <span class="ow">in</span> <span class="n">binlist</span><span class="p">:</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_addColumn</span><span class="p">(</span><span class="nb">bin</span><span class="p">[</span><span class="s">"name"</span><span class="p">])</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">conn</span><span class="o">.</span><span class="n">execute</span><span class="p">(</span><span class="s">"update images set "</span> <span class="o">+</span> <span class="nb">bin</span><span class="p">[</span><span class="s">"name"</span><span class="p">]</span> <span class="o">+</span> <span class="s">"=? where pegasusid=?"</span><span class="p">,</span> <span class="p">(</span><span class="nb">bin</span><span class="p">[</span><span class="s">"count"</span><span class="p">],</span> <span class="bp">self</span><span class="o">.</span><span class="n">dbid</span><span class="p">))</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">conn</span><span class="o">.</span><span class="n">commit</span><span class="p">()</span>
+ <span class="k">return</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="k">return</span> <span class="n">binlist</span>
+
+ </div></div>
+</pre></div>
+
+ </div>
+
+ </div>
+</div>
+<footer class="footer">
+ <div class="container">
+ <p class="pull-right">
+ <a href="#">Back to top</a>
+
+ </p>
+ <p>
+ © Copyright 2015, Avi Knecht.<br/>
+ Created using <a href="http://sphinx.pocoo.org/">Sphinx</a> 1.3a0.<br/>
+ </p>
+ </div>
+</footer>
+ </body>
+</html>
\ No newline at end of file
diff --git a/docs/build/html/_modules/plantcv/statistics.html b/docs/build/html/_modules/plantcv/statistics.html
new file mode 100644
index 0000000000000000000000000000000000000000..8da0a4c2d44a559451d884600801f9fb67ed8c6f
--- /dev/null
+++ b/docs/build/html/_modules/plantcv/statistics.html
@@ -0,0 +1,802 @@
+<!DOCTYPE html>
+
+
+<html xmlns="http://www.w3.org/1999/xhtml">
+ <head>
+ <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
+
+ <title>plantcv.statistics — Image Harvest 1.0.1 documentation</title>
+
+ <link rel="stylesheet" href="../../_static/basic.css" type="text/css" />
+ <link rel="stylesheet" href="../../_static/pygments.css" type="text/css" />
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+ URL_ROOT: '../../',
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+ <script type="text/javascript" src="../../_static/bootstrap-sphinx.js"></script>
+ <link rel="top" title="Image Harvest 1.0.1 documentation" href="../../index.html" />
+ <link rel="up" title="Module code" href="../index.html" />
+<meta charset='utf-8'>
+<meta http-equiv='X-UA-Compatible' content='IE=edge,chrome=1'>
+<meta name='viewport' content='width=device-width, initial-scale=1.0, maximum-scale=1'>
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+
+ <div id="navbar" class="navbar navbar-default navbar-fixed-top">
+ <div class="container">
+ <div class="navbar-header">
+ <!-- .btn-navbar is used as the toggle for collapsed navbar content -->
+ <button type="button" class="navbar-toggle" data-toggle="collapse" data-target=".nav-collapse">
+ <span class="icon-bar"></span>
+ <span class="icon-bar"></span>
+ <span class="icon-bar"></span>
+ </button>
+ <a class="navbar-brand" href="../../index.html">
+ Image Harvest</a>
+ <span class="navbar-text navbar-version pull-left"><b>1.0</b></span>
+ </div>
+
+ <div class="collapse navbar-collapse nav-collapse">
+ <ul class="nav navbar-nav">
+
+
+ <li class="dropdown globaltoc-container">
+ <a role="button"
+ id="dLabelGlobalToc"
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+ data-target="#"
+ href="../../index.html">Site <b class="caret"></b></a>
+ <ul class="dropdown-menu globaltoc"
+ role="menu"
+ aria-labelledby="dLabelGlobalToc"><ul>
+<li class="toctree-l1"><a class="reference internal" href="../../introduction.html">Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../../installation.html">Installation</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../../start.html">Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../../ex_script_core1.html">Core Processing Example #1</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../../ex_script_core2.html">Core Processing Example #2</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../../ex_script_color1.html">Color Filter In Depth #1</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../../ex_workflow_1.html">Workflow Example #1</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../../examples.html">Examples</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../../processing.html">Image Processing</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../../viewer.html">Image Processing Viewer</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../../statistics.html">Statistics</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../../indexing.html">Image Loading</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../../workflowimage.html">Image Processing Workflows</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../../workflowstats.html">Statistics Workflows</a></li>
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+</li>
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+ <div class="col-md-12">
+
+ <h1>Source code for plantcv.statistics</h1><div class="highlight"><pre>
+<span class="kn">import</span> <span class="nn">math</span>
+<span class="kn">import</span> <span class="nn">os</span>
+<span class="kn">import</span> <span class="nn">sqlite3</span>
+<span class="kn">import</span> <span class="nn">conf</span>
+<span class="kn">import</span> <span class="nn">datetime</span>
+<span class="kn">import</span> <span class="nn">numpy</span> <span class="kn">as</span> <span class="nn">np</span>
+<span class="kn">import</span> <span class="nn">pandas</span>
+<span class="kn">import</span> <span class="nn">plantcv.imgproc</span>
+<span class="kn">import</span> <span class="nn">cv2</span>
+<span class="kn">import</span> <span class="nn">json</span>
+<span class="kn">import</span> <span class="nn">traceback</span>
+<span class="kn">from</span> <span class="nn">scipy</span> <span class="kn">import</span> <span class="n">stats</span>
+
+<div class="viewcode-block" id="Stats"><a class="viewcode-back" href="../../statistics.html#plantcv.statistics.Stats">[docs]</a><span class="k">class</span> <span class="nc">Stats</span><span class="p">:</span>
+
+ <span class="k">def</span> <span class="nf">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">db</span><span class="p">):</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">db</span> <span class="o">=</span> <span class="n">db</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">conn</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_openConnection</span><span class="p">()</span>
+ <span class="k">return</span>
+
+ <span class="k">def</span> <span class="nf">_openConnection</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">db</span> <span class="o">=</span> <span class="bp">None</span><span class="p">):</span>
+ <span class="n">db</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">db</span> <span class="k">if</span> <span class="ow">not</span> <span class="n">db</span> <span class="k">else</span> <span class="n">db</span>
+ <span class="k">if</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">isfile</span><span class="p">(</span><span class="n">db</span><span class="p">):</span>
+ <span class="n">conn</span> <span class="o">=</span> <span class="n">sqlite3</span><span class="o">.</span><span class="n">connect</span><span class="p">(</span><span class="n">db</span><span class="p">,</span> <span class="n">check_same_thread</span> <span class="o">=</span> <span class="bp">False</span><span class="p">)</span>
+ <span class="n">conn</span><span class="o">.</span><span class="n">row_factory</span> <span class="o">=</span> <span class="n">sqlite3</span><span class="o">.</span><span class="n">Row</span>
+ <span class="n">result</span> <span class="o">=</span> <span class="n">conn</span><span class="o">.</span><span class="n">execute</span><span class="p">(</span><span class="s">"select pegasusid from images limit 0,1"</span><span class="p">)</span>
+ <span class="k">if</span> <span class="ow">not</span> <span class="n">result</span><span class="o">.</span><span class="n">fetchone</span><span class="p">():</span>
+ <span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="s">"Database '</span><span class="si">%s</span><span class="s">' has no entries!"</span> <span class="o">%</span> <span class="p">(</span><span class="n">db</span><span class="p">,))</span>
+ <span class="c"># Have to enable foreign keys EVERY time.</span>
+ <span class="n">conn</span><span class="o">.</span><span class="n">execute</span><span class="p">(</span><span class="s">"PRAGMA foreign_keys = ON"</span><span class="p">)</span>
+ <span class="n">conn</span><span class="o">.</span><span class="n">commit</span><span class="p">()</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="s">"Database file '</span><span class="si">%s</span><span class="s">' does not exist."</span> <span class="o">%</span> <span class="p">(</span><span class="n">db</span><span class="p">,))</span>
+ <span class="k">return</span> <span class="n">conn</span>
+
+ <span class="k">def</span> <span class="nf">_closeConnection</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">conn</span> <span class="o">=</span> <span class="bp">None</span><span class="p">):</span>
+ <span class="n">conn</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">conn</span> <span class="k">if</span> <span class="ow">not</span> <span class="n">conn</span> <span class="k">else</span> <span class="n">conn</span>
+ <span class="n">conn</span><span class="o">.</span><span class="n">close</span><span class="p">()</span>
+ <span class="k">return</span>
+
+ <span class="k">def</span> <span class="nf">_tableExists</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">tablename</span><span class="p">,</span> <span class="n">conn</span> <span class="o">=</span> <span class="bp">None</span><span class="p">):</span>
+ <span class="n">conn</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">conn</span> <span class="k">if</span> <span class="ow">not</span> <span class="n">conn</span> <span class="k">else</span> <span class="n">conn</span>
+ <span class="n">result</span> <span class="o">=</span> <span class="n">conn</span><span class="o">.</span><span class="n">execute</span><span class="p">(</span><span class="s">"select name from sqlite_master where type='table' and name=?"</span><span class="p">,</span> <span class="p">(</span><span class="n">tablename</span><span class="p">,))</span>
+ <span class="k">if</span> <span class="ow">not</span> <span class="n">result</span><span class="o">.</span><span class="n">fetchone</span><span class="p">():</span>
+ <span class="k">return</span> <span class="bp">False</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="k">return</span> <span class="bp">True</span>
+
+ <span class="k">def</span> <span class="nf">_validate</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">funcname</span><span class="p">,</span> <span class="n">intable</span><span class="p">,</span> <span class="n">outtable</span><span class="p">,</span> <span class="n">overwrite</span><span class="p">,</span> <span class="n">conn</span> <span class="o">=</span> <span class="bp">None</span><span class="p">):</span>
+ <span class="n">conn</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">conn</span> <span class="k">if</span> <span class="ow">not</span> <span class="n">conn</span> <span class="k">else</span> <span class="n">conn</span>
+ <span class="k">if</span> <span class="n">funcname</span> <span class="ow">in</span> <span class="n">conf</span><span class="o">.</span><span class="n">statsColumns</span><span class="p">:</span>
+ <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">_tableExists</span><span class="p">(</span><span class="n">intable</span><span class="p">):</span>
+ <span class="n">cols</span> <span class="o">=</span> <span class="p">[</span><span class="n">x</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span> <span class="k">for</span> <span class="n">x</span> <span class="ow">in</span> <span class="n">conn</span><span class="o">.</span><span class="n">execute</span><span class="p">(</span><span class="s">"PRAGMA table_info('"</span> <span class="o">+</span> <span class="n">intable</span> <span class="o">+</span> <span class="s">"')"</span><span class="p">)]</span>
+ <span class="k">if</span> <span class="nb">set</span><span class="p">(</span><span class="n">conf</span><span class="o">.</span><span class="n">statsColumns</span><span class="p">[</span><span class="n">funcname</span><span class="p">][</span><span class="s">"required"</span><span class="p">])</span> <span class="o"><=</span> <span class="nb">set</span><span class="p">(</span><span class="n">cols</span><span class="p">):</span>
+ <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">_tableExists</span><span class="p">(</span><span class="n">outtable</span><span class="p">,</span> <span class="n">conn</span><span class="p">)</span> <span class="ow">and</span> <span class="ow">not</span> <span class="n">overwrite</span><span class="p">:</span>
+ <span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="s">"Output table '"</span> <span class="o">+</span> <span class="n">outtable</span> <span class="o">+</span> <span class="s">"' already exists."</span><span class="p">)</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="s">"Table '"</span> <span class="o">+</span> <span class="n">intable</span> <span class="o">+</span> <span class="s">"' doesn't have all the required columns: '"</span> <span class="o">+</span> <span class="nb">str</span><span class="p">(</span><span class="n">conf</span><span class="o">.</span><span class="n">statsColumns</span><span class="p">[</span><span class="n">funcname</span><span class="p">][</span><span class="s">"required"</span><span class="p">])</span> <span class="o">+</span> <span class="s">"'."</span><span class="p">)</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="s">"Table '"</span> <span class="o">+</span> <span class="n">intable</span> <span class="o">+</span> <span class="s">"' doesn't exist."</span><span class="p">)</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="s">"Function '"</span> <span class="o">+</span> <span class="n">funcname</span> <span class="o">+</span> <span class="s">"' doesn't exist."</span><span class="p">)</span>
+ <span class="k">return</span>
+
+ <span class="k">def</span> <span class="nf">_columnExists</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">column</span><span class="p">,</span> <span class="n">tablename</span><span class="p">,</span> <span class="n">conn</span> <span class="o">=</span> <span class="bp">None</span><span class="p">):</span>
+ <span class="n">conn</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">conn</span> <span class="k">if</span> <span class="ow">not</span> <span class="n">conn</span> <span class="k">else</span> <span class="n">conn</span>
+ <span class="k">if</span> <span class="n">column</span> <span class="ow">in</span> <span class="p">[</span><span class="n">row</span><span class="p">[</span><span class="s">"name"</span><span class="p">]</span> <span class="k">for</span> <span class="n">row</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">conn</span><span class="o">.</span><span class="n">execute</span><span class="p">(</span><span class="s">"PRAGMA table_info('"</span> <span class="o">+</span> <span class="n">tablename</span> <span class="o">+</span> <span class="s">"')"</span><span class="p">)]:</span>
+ <span class="k">return</span> <span class="bp">True</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="k">return</span> <span class="bp">False</span>
+
+ <span class="k">def</span> <span class="nf">_addColumn</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">column</span><span class="p">,</span> <span class="n">tablename</span> <span class="o">=</span> <span class="s">"images"</span><span class="p">,</span> <span class="n">conn</span> <span class="o">=</span> <span class="bp">None</span><span class="p">):</span>
+ <span class="n">conn</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">conn</span> <span class="k">if</span> <span class="ow">not</span> <span class="n">conn</span> <span class="k">else</span> <span class="n">conn</span>
+ <span class="k">if</span> <span class="ow">not</span> <span class="bp">self</span><span class="o">.</span><span class="n">_columnExists</span><span class="p">(</span><span class="n">column</span><span class="p">,</span> <span class="n">tablename</span><span class="p">,</span> <span class="n">conn</span><span class="p">):</span>
+ <span class="n">conn</span><span class="o">.</span><span class="n">execute</span><span class="p">(</span><span class="s">"alter table '"</span> <span class="o">+</span> <span class="n">tablename</span> <span class="o">+</span> <span class="s">"' add column "</span> <span class="o">+</span> <span class="n">column</span> <span class="o">+</span> <span class="s">";"</span><span class="p">)</span>
+ <span class="n">conn</span><span class="o">.</span><span class="n">commit</span><span class="p">()</span>
+ <span class="k">return</span>
+
+ <span class="k">def</span> <span class="nf">_addKeyColumn</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">parent</span><span class="p">,</span> <span class="n">parentCol</span><span class="p">,</span> <span class="n">child</span><span class="p">,</span> <span class="n">childCol</span><span class="p">,</span> <span class="n">conn</span> <span class="o">=</span> <span class="bp">None</span><span class="p">):</span>
+ <span class="n">conn</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">conn</span> <span class="k">if</span> <span class="ow">not</span> <span class="n">conn</span> <span class="k">else</span> <span class="n">conn</span>
+ <span class="k">if</span> <span class="n">parentCol</span> <span class="ow">not</span> <span class="ow">in</span> <span class="p">[</span><span class="n">row</span><span class="p">[</span><span class="s">"name"</span><span class="p">]</span> <span class="k">for</span> <span class="n">row</span> <span class="ow">in</span> <span class="n">conn</span><span class="o">.</span><span class="n">execute</span><span class="p">(</span><span class="s">"PRAGMA table_info('"</span> <span class="o">+</span> <span class="n">parent</span> <span class="o">+</span> <span class="s">"');"</span><span class="p">)]</span> <span class="ow">and</span> <span class="n">childCol</span> <span class="ow">in</span> <span class="p">[</span><span class="n">row</span><span class="p">[</span><span class="s">"name"</span><span class="p">]</span> <span class="k">for</span> <span class="n">row</span> <span class="ow">in</span> <span class="n">conn</span><span class="o">.</span><span class="n">execute</span><span class="p">(</span><span class="s">"PRAGMA table_info('"</span> <span class="o">+</span> <span class="n">child</span> <span class="o">+</span> <span class="s">"');"</span><span class="p">)]:</span>
+ <span class="n">conn</span><span class="o">.</span><span class="n">execute</span><span class="p">(</span><span class="s">"alter table '"</span> <span class="o">+</span> <span class="n">parent</span> <span class="o">+</span> <span class="s">"' add column '"</span> <span class="o">+</span> <span class="n">parentCol</span> <span class="o">+</span> <span class="s">"' REFERENCES '"</span> <span class="o">+</span> <span class="n">child</span> <span class="o">+</span> <span class="s">"'('"</span> <span class="o">+</span> <span class="n">childCol</span> <span class="o">+</span> <span class="s">"');"</span><span class="p">)</span>
+ <span class="n">conn</span><span class="o">.</span><span class="n">commit</span><span class="p">()</span>
+ <span class="k">return</span>
+
+ <span class="k">def</span> <span class="nf">_createTable</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">funcname</span><span class="p">,</span> <span class="n">intable</span><span class="p">,</span> <span class="n">outtable</span><span class="p">,</span> <span class="n">overwrite</span><span class="p">,</span> <span class="n">conn</span> <span class="o">=</span> <span class="bp">None</span><span class="p">):</span>
+ <span class="n">conn</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">conn</span> <span class="k">if</span> <span class="ow">not</span> <span class="n">conn</span> <span class="k">else</span> <span class="n">conn</span>
+ <span class="n">tablestr</span> <span class="o">=</span> <span class="s">"(pegasusid INTEGER PRIMARY KEY"</span>
+ <span class="n">cols</span> <span class="o">=</span> <span class="p">[</span><span class="n">x</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span> <span class="k">for</span> <span class="n">x</span> <span class="ow">in</span> <span class="n">conn</span><span class="o">.</span><span class="n">execute</span><span class="p">(</span><span class="s">"pragma table_info('"</span> <span class="o">+</span> <span class="n">intable</span> <span class="o">+</span> <span class="s">"')"</span><span class="p">)]</span>
+ <span class="k">if</span> <span class="s">"all"</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">conf</span><span class="o">.</span><span class="n">statsColumns</span><span class="p">[</span><span class="n">funcname</span><span class="p">][</span><span class="s">"exclude"</span><span class="p">]:</span>
+ <span class="k">for</span> <span class="n">col</span> <span class="ow">in</span> <span class="n">cols</span><span class="p">:</span>
+ <span class="k">if</span> <span class="n">col</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">conf</span><span class="o">.</span><span class="n">statsColumns</span><span class="p">[</span><span class="n">funcname</span><span class="p">][</span><span class="s">"exclude"</span><span class="p">]</span> <span class="ow">and</span> <span class="n">col</span><span class="p">[:</span><span class="mi">3</span><span class="p">]</span> <span class="o">!=</span> <span class="s">"ref"</span><span class="p">:</span>
+ <span class="n">tablestr</span> <span class="o">+=</span> <span class="s">","</span> <span class="o">+</span> <span class="nb">str</span><span class="p">(</span><span class="n">col</span><span class="p">)</span>
+ <span class="k">for</span> <span class="n">col</span> <span class="ow">in</span> <span class="n">conf</span><span class="o">.</span><span class="n">statsColumns</span><span class="p">[</span><span class="n">funcname</span><span class="p">][</span><span class="s">"add"</span><span class="p">]:</span>
+ <span class="n">tablestr</span> <span class="o">+=</span> <span class="s">","</span> <span class="o">+</span> <span class="nb">str</span><span class="p">(</span><span class="n">col</span><span class="p">)</span>
+ <span class="n">tablestr</span> <span class="o">+=</span> <span class="s">")"</span>
+ <span class="k">if</span> <span class="n">overwrite</span><span class="p">:</span>
+ <span class="n">conn</span><span class="o">.</span><span class="n">execute</span><span class="p">(</span><span class="s">"DROP TABLE IF EXISTS "</span> <span class="o">+</span> <span class="n">outtable</span><span class="p">)</span>
+ <span class="n">conn</span><span class="o">.</span><span class="n">commit</span><span class="p">()</span>
+ <span class="n">conn</span><span class="o">.</span><span class="n">execute</span><span class="p">(</span><span class="s">"CREATE TABLE "</span> <span class="o">+</span> <span class="n">outtable</span> <span class="o">+</span> <span class="s">" "</span> <span class="o">+</span> <span class="n">tablestr</span><span class="p">)</span>
+ <span class="n">conn</span><span class="o">.</span><span class="n">commit</span><span class="p">()</span>
+ <span class="k">if</span> <span class="n">conf</span><span class="o">.</span><span class="n">statsColumns</span><span class="p">[</span><span class="n">funcname</span><span class="p">][</span><span class="s">"ref"</span><span class="p">]:</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_addKeyColumn</span><span class="p">(</span><span class="n">intable</span><span class="p">,</span> <span class="s">"ref_"</span> <span class="o">+</span> <span class="n">outtable</span><span class="p">,</span> <span class="n">outtable</span><span class="p">,</span> <span class="s">"pegasusid"</span><span class="p">,</span> <span class="n">conn</span><span class="p">)</span>
+ <span class="k">return</span>
+
+ <span class="k">def</span> <span class="nf">_getHeaders</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">table</span><span class="p">,</span> <span class="n">conn</span> <span class="o">=</span> <span class="bp">None</span><span class="p">):</span>
+ <span class="n">conn</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">conn</span> <span class="k">if</span> <span class="ow">not</span> <span class="n">conn</span> <span class="k">else</span> <span class="n">conn</span>
+ <span class="k">return</span> <span class="p">[</span><span class="nb">str</span><span class="p">(</span><span class="n">x</span><span class="p">[</span><span class="mi">1</span><span class="p">])</span> <span class="k">for</span> <span class="n">x</span> <span class="ow">in</span> <span class="n">conn</span><span class="o">.</span><span class="n">execute</span><span class="p">(</span><span class="s">"pragma table_info("</span> <span class="o">+</span> <span class="n">table</span> <span class="o">+</span> <span class="s">")"</span><span class="p">)</span> <span class="k">if</span> <span class="n">x</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span> <span class="o">!=</span> <span class="s">"pegasusid"</span><span class="p">]</span>
+
+ <span class="k">def</span> <span class="nf">_getImageTypes</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">table</span><span class="p">,</span> <span class="n">conn</span> <span class="o">=</span> <span class="bp">None</span><span class="p">):</span>
+ <span class="n">conn</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">conn</span> <span class="k">if</span> <span class="ow">not</span> <span class="n">conn</span> <span class="k">else</span> <span class="n">conn</span>
+ <span class="k">return</span> <span class="p">[</span><span class="nb">str</span><span class="p">(</span><span class="n">x</span><span class="p">[</span><span class="mi">0</span><span class="p">])</span> <span class="k">for</span> <span class="n">x</span> <span class="ow">in</span> <span class="n">conn</span><span class="o">.</span><span class="n">execute</span><span class="p">(</span><span class="s">"select distinct imtype from "</span> <span class="o">+</span> <span class="n">table</span><span class="p">)]</span>
+
+ <span class="k">def</span> <span class="nf">_getDates</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">table</span><span class="p">,</span> <span class="n">conn</span> <span class="o">=</span> <span class="bp">None</span><span class="p">):</span>
+ <span class="n">conn</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">conn</span> <span class="k">if</span> <span class="ow">not</span> <span class="n">conn</span> <span class="k">else</span> <span class="n">conn</span>
+ <span class="k">return</span> <span class="p">[</span><span class="nb">str</span><span class="p">(</span><span class="n">x</span><span class="p">[</span><span class="mi">0</span><span class="p">])</span> <span class="k">for</span> <span class="n">x</span> <span class="ow">in</span> <span class="n">conn</span><span class="o">.</span><span class="n">execute</span><span class="p">(</span><span class="s">"select distinct date from "</span> <span class="o">+</span> <span class="n">table</span><span class="p">)]</span>
+
+ <span class="k">def</span> <span class="nf">_loadLemnaData</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">dataFile</span><span class="p">,</span> <span class="n">dataHeaders</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> :param dataFile: The input dataFile</span>
+<span class="sd"> :type dataFile: str</span>
+<span class="sd"> :param dataHeaders: The input data headers</span>
+<span class="sd"> :type dataHeaders: dict</span>
+<span class="sd"> </span>
+<span class="sd"> dataHeaders should be:</span>
+<span class="sd"> { </span>
+<span class="sd"> "id": "Snapshot ID Tag",</span>
+<span class="sd"> "date": "Snapshot Time Stamp",</span>
+<span class="sd"> "dateFormat": "%m/%d/%y",</span>
+<span class="sd"> "metric": "Projected Shoot Area [pixels]"</span>
+<span class="sd"> }</span>
+<span class="sd"> """</span>
+ <span class="k">if</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">isfile</span><span class="p">(</span><span class="n">dataFile</span><span class="p">):</span>
+ <span class="k">if</span> <span class="nb">all</span><span class="p">(</span><span class="n">key</span> <span class="ow">in</span> <span class="n">dataHeaders</span> <span class="k">for</span> <span class="n">key</span> <span class="ow">in</span> <span class="p">[</span><span class="s">"id"</span><span class="p">,</span> <span class="s">"date"</span><span class="p">,</span> <span class="s">"dateFormat"</span><span class="p">,</span> <span class="s">"metric"</span><span class="p">]):</span>
+ <span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="n">dataFile</span><span class="p">)</span> <span class="k">as</span> <span class="n">rh</span><span class="p">:</span>
+ <span class="n">lines</span> <span class="o">=</span> <span class="n">rh</span><span class="o">.</span><span class="n">readlines</span><span class="p">()</span>
+ <span class="n">firstline</span> <span class="o">=</span> <span class="n">lines</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">.</span><span class="n">strip</span><span class="p">()</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s">","</span><span class="p">)</span>
+ <span class="k">if</span> <span class="n">dataHeaders</span><span class="p">[</span><span class="s">"id"</span><span class="p">]</span> <span class="ow">in</span> <span class="n">firstline</span><span class="p">:</span>
+ <span class="k">if</span> <span class="n">dataHeaders</span><span class="p">[</span><span class="s">"date"</span><span class="p">]</span> <span class="ow">in</span> <span class="n">firstline</span><span class="p">:</span>
+ <span class="k">if</span> <span class="n">dataHeaders</span><span class="p">[</span><span class="s">"metric"</span><span class="p">]</span> <span class="ow">in</span> <span class="n">firstline</span><span class="p">:</span>
+ <span class="n">idIndex</span> <span class="o">=</span> <span class="n">firstline</span><span class="o">.</span><span class="n">index</span><span class="p">(</span><span class="n">dataHeaders</span><span class="p">[</span><span class="s">"id"</span><span class="p">])</span>
+ <span class="n">dateIndex</span> <span class="o">=</span> <span class="n">firstline</span><span class="o">.</span><span class="n">index</span><span class="p">(</span><span class="n">dataHeaders</span><span class="p">[</span><span class="s">"date"</span><span class="p">])</span>
+ <span class="n">metricIndex</span> <span class="o">=</span> <span class="n">firstline</span><span class="o">.</span><span class="n">index</span><span class="p">(</span><span class="n">dataHeaders</span><span class="p">[</span><span class="s">"metric"</span><span class="p">])</span>
+ <span class="n">lemnaData</span> <span class="o">=</span> <span class="p">{}</span>
+ <span class="k">for</span> <span class="n">line</span> <span class="ow">in</span> <span class="n">lines</span><span class="p">[</span><span class="mi">1</span><span class="p">:]:</span>
+ <span class="n">info</span> <span class="o">=</span> <span class="n">line</span><span class="o">.</span><span class="n">strip</span><span class="p">()</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s">","</span><span class="p">)</span>
+ <span class="k">if</span> <span class="p">(</span><span class="n">info</span><span class="p">[</span><span class="n">metricIndex</span><span class="p">]</span> <span class="o">!=</span> <span class="s">"NA"</span><span class="p">):</span>
+ <span class="nb">id</span> <span class="o">=</span> <span class="n">info</span><span class="p">[</span><span class="n">idIndex</span><span class="p">][</span><span class="o">-</span><span class="mi">8</span><span class="p">:]</span>
+ <span class="n">date</span> <span class="o">=</span> <span class="n">datetime</span><span class="o">.</span><span class="n">datetime</span><span class="o">.</span><span class="n">strptime</span><span class="p">(</span><span class="n">info</span><span class="p">[</span><span class="n">dateIndex</span><span class="p">]</span><span class="o">.</span><span class="n">split</span><span class="p">()[</span><span class="mi">0</span><span class="p">],</span> <span class="n">dataHeaders</span><span class="p">[</span><span class="s">"dateFormat"</span><span class="p">])</span><span class="o">.</span><span class="n">strftime</span><span class="p">(</span><span class="s">"%Y-%m-</span><span class="si">%d</span><span class="s">"</span><span class="p">)</span>
+ <span class="k">try</span><span class="p">:</span>
+ <span class="n">metric</span> <span class="o">=</span> <span class="nb">float</span><span class="p">(</span><span class="n">info</span><span class="p">[</span><span class="n">metricIndex</span><span class="p">])</span>
+ <span class="k">if</span> <span class="nb">id</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">lemnaData</span><span class="p">:</span>
+ <span class="n">lemnaData</span><span class="p">[</span><span class="nb">id</span><span class="p">]</span> <span class="o">=</span> <span class="p">{}</span>
+ <span class="k">if</span> <span class="n">date</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">lemnaData</span><span class="p">[</span><span class="nb">id</span><span class="p">]:</span>
+ <span class="n">lemnaData</span><span class="p">[</span><span class="nb">id</span><span class="p">][</span><span class="n">date</span><span class="p">]</span> <span class="o">=</span> <span class="p">{}</span>
+ <span class="n">lemnaData</span><span class="p">[</span><span class="nb">id</span><span class="p">][</span><span class="n">date</span><span class="p">][</span><span class="s">"metric"</span><span class="p">]</span> <span class="o">=</span> <span class="n">metric</span>
+ <span class="k">except</span><span class="p">:</span>
+ <span class="k">pass</span>
+ <span class="k">return</span> <span class="n">lemnaData</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="s">"Metric Column: "</span><span class="p">,</span><span class="n">dataHeaders</span><span class="p">[</span><span class="s">"metric"</span><span class="p">],</span><span class="s">" does not exist."</span><span class="p">)</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="s">"Date Column: "</span><span class="p">,</span><span class="n">dataHeaders</span><span class="p">[</span><span class="s">"date"</span><span class="p">],</span><span class="s">" does not exist."</span><span class="p">)</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="s">"Id Column: "</span><span class="p">,</span><span class="n">dataHeaders</span><span class="p">[</span><span class="s">"id"</span><span class="p">],</span><span class="s">" does not exist."</span><span class="p">)</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="s">"Data Dictionary does not have all required keys ['id', 'date', 'dateFormat', 'metric']"</span><span class="p">)</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="s">"Data File: "</span> <span class="o">+</span> <span class="n">dataFile</span> <span class="o">+</span> <span class="s">" does not exist!"</span><span class="p">)</span>
+ <span class="k">return</span>
+
+ <span class="k">def</span> <span class="nf">loadSql</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">dblist</span><span class="p">):</span>
+ <span class="k">for</span> <span class="n">i</span><span class="p">,</span><span class="n">f</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="n">dblist</span><span class="p">):</span>
+ <span class="k">if</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">isfile</span><span class="p">(</span><span class="n">f</span><span class="p">):</span>
+ <span class="n">conn</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_openConnection</span><span class="p">(</span><span class="n">f</span><span class="p">)</span>
+ <span class="n">cols</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_getHeaders</span><span class="p">(</span><span class="s">"images"</span><span class="p">,</span> <span class="n">conn</span><span class="p">)</span>
+ <span class="k">for</span> <span class="n">col</span> <span class="ow">in</span> <span class="n">cols</span><span class="p">:</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_addColumn</span><span class="p">(</span><span class="n">col</span><span class="p">,</span> <span class="s">"images"</span><span class="p">)</span>
+ <span class="n">result</span> <span class="o">=</span> <span class="n">conn</span><span class="o">.</span><span class="n">execute</span><span class="p">(</span><span class="s">"select pegasusid,"</span> <span class="o">+</span> <span class="s">","</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">cols</span><span class="p">)</span> <span class="o">+</span> <span class="s">" from images"</span><span class="p">)</span>
+ <span class="n">query</span> <span class="o">=</span> <span class="s">"update images set "</span> <span class="o">+</span> <span class="s">","</span><span class="o">.</span><span class="n">join</span><span class="p">([</span><span class="n">col</span> <span class="o">+</span> <span class="s">"=?"</span> <span class="k">for</span> <span class="n">col</span> <span class="ow">in</span> <span class="n">cols</span><span class="p">])</span> <span class="o">+</span> <span class="s">" where pegasusid=?"</span>
+ <span class="n">values</span> <span class="o">=</span> <span class="p">[</span><span class="nb">tuple</span><span class="p">([</span><span class="n">row</span><span class="p">[</span><span class="n">col</span><span class="p">]</span> <span class="k">for</span> <span class="n">col</span> <span class="ow">in</span> <span class="n">cols</span><span class="p">]</span> <span class="o">+</span> <span class="p">[</span><span class="n">row</span><span class="p">[</span><span class="s">"pegasusid"</span><span class="p">]])</span> <span class="k">for</span> <span class="n">row</span> <span class="ow">in</span> <span class="n">result</span><span class="p">]</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">conn</span><span class="o">.</span><span class="n">executemany</span><span class="p">(</span><span class="n">query</span><span class="p">,</span> <span class="n">values</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">conn</span><span class="o">.</span><span class="n">commit</span><span class="p">()</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_closeConnection</span><span class="p">(</span><span class="n">conn</span><span class="p">)</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="k">print</span> <span class="s">"DB File: '</span><span class="si">%s</span><span class="s">' does not exist."</span> <span class="o">%</span> <span class="p">(</span><span class="n">f</span><span class="p">,)</span>
+ <span class="k">return</span>
+
+
+
+<div class="viewcode-block" id="Stats.logErrors"><a class="viewcode-back" href="../../statistics.html#plantcv.statistics.Stats.logErrors">[docs]</a> <span class="k">def</span> <span class="nf">logErrors</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">logfile</span><span class="p">,</span> <span class="n">table</span> <span class="o">=</span> <span class="s">"images"</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> :param logfile: The logfile to write errors to</span>
+<span class="sd"> :type logfile: str</span>
+<span class="sd"> :param table: The table to load errors from</span>
+<span class="sd"> :type table: str</span>
+<span class="sd"> </span>
+<span class="sd"> This function writes all errors from a given table to a log file,</span>
+<span class="sd"> usually used at the end of image processing to write all images that</span>
+<span class="sd"> did not process correctly.</span>
+<span class="sd"> """</span>
+ <span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="n">logfile</span><span class="p">,</span> <span class="s">"w"</span><span class="p">)</span> <span class="k">as</span> <span class="n">wh</span><span class="p">:</span>
+ <span class="n">wh</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s">"Image processing error log</span><span class="se">\n</span><span class="s">"</span><span class="p">)</span>
+ <span class="n">wh</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s">"==========================</span><span class="se">\n</span><span class="s">"</span><span class="p">)</span>
+ <span class="n">result</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">conn</span><span class="o">.</span><span class="n">execute</span><span class="p">(</span><span class="s">"select pegasusid,path,error from '"</span> <span class="o">+</span> <span class="n">table</span> <span class="o">+</span> <span class="s">"' where error is not null"</span><span class="p">)</span>
+ <span class="n">firstrow</span> <span class="o">=</span> <span class="n">result</span><span class="o">.</span><span class="n">fetchone</span><span class="p">()</span>
+ <span class="k">if</span> <span class="n">firstrow</span><span class="p">:</span>
+ <span class="n">wh</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s">"Error with image id '"</span> <span class="o">+</span> <span class="n">firstrow</span><span class="p">[</span><span class="s">"pegasusid"</span><span class="p">]</span> <span class="o">+</span> <span class="s">"', located at path '"</span> <span class="o">+</span> <span class="n">row</span><span class="p">[</span><span class="s">"path"</span><span class="p">]</span> <span class="o">+</span> <span class="s">"', error: '"</span> <span class="o">+</span> <span class="n">row</span><span class="p">[</span><span class="s">"error"</span><span class="p">]</span> <span class="o">+</span> <span class="s">"'. </span><span class="se">\n</span><span class="s">"</span><span class="p">)</span>
+ <span class="k">for</span> <span class="n">row</span> <span class="ow">in</span> <span class="n">result</span><span class="p">:</span>
+ <span class="n">wh</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s">"Error with image id '"</span> <span class="o">+</span> <span class="n">row</span><span class="p">[</span><span class="s">"pegasusid"</span><span class="p">]</span> <span class="o">+</span> <span class="s">"', located at path '"</span> <span class="o">+</span> <span class="n">row</span><span class="p">[</span><span class="s">"path"</span><span class="p">]</span> <span class="o">+</span> <span class="s">"', error: '"</span> <span class="o">+</span> <span class="n">row</span><span class="p">[</span><span class="s">"error"</span><span class="p">]</span> <span class="o">+</span> <span class="s">"'. </span><span class="se">\n</span><span class="s">"</span><span class="p">)</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="n">wh</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s">"All images processed successfully! Nice job!</span><span class="se">\n</span><span class="s">"</span><span class="p">)</span>
+ <span class="k">return</span>
+ </div>
+<div class="viewcode-block" id="Stats.shootArea"><a class="viewcode-back" href="../../statistics.html#plantcv.statistics.Stats.shootArea">[docs]</a> <span class="k">def</span> <span class="nf">shootArea</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">intable</span><span class="p">,</span> <span class="n">outtable</span><span class="p">,</span> <span class="n">grouping</span><span class="p">,</span> <span class="n">overwrite</span> <span class="o">=</span> <span class="bp">False</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> :param intable: The input table to load information from</span>
+<span class="sd"> :type intable: str</span>
+<span class="sd"> :param outtable: The output table to write information to.</span>
+<span class="sd"> :type outtable: str</span>
+<span class="sd"> :param grouping: Which imtypes to group</span>
+<span class="sd"> :type grouping: list</span>
+<span class="sd"> </span>
+<span class="sd"> This function adds the numeric values of multiple image types together.</span>
+<span class="sd"> In general, it is used to combine side view + top view images of the same spectrum.</span>
+<span class="sd"> If you plan on correlating your data to lemnaTec's data, lemnaTec uses SV1 + SV2 + TV,</span>
+<span class="sd"> so you should aggregate your data likewise.</span>
+<span class="sd"> """</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_validate</span><span class="p">(</span><span class="s">"shootArea"</span><span class="p">,</span> <span class="n">intable</span><span class="p">,</span> <span class="n">outtable</span><span class="p">,</span> <span class="n">overwrite</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_createTable</span><span class="p">(</span><span class="s">"shootArea"</span><span class="p">,</span> <span class="n">intable</span><span class="p">,</span> <span class="n">outtable</span><span class="p">,</span> <span class="n">overwrite</span><span class="p">)</span>
+ <span class="n">headers</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_getHeaders</span><span class="p">(</span><span class="n">outtable</span><span class="p">)</span>
+ <span class="n">result</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">conn</span><span class="o">.</span><span class="n">execute</span><span class="p">(</span><span class="s">"select pegasusid,"</span> <span class="o">+</span> <span class="s">","</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">headers</span><span class="p">)</span> <span class="o">+</span> <span class="s">" from "</span> <span class="o">+</span> <span class="n">intable</span> <span class="o">+</span> <span class="s">" where "</span> <span class="o">+</span> <span class="s">" or "</span><span class="o">.</span><span class="n">join</span><span class="p">([</span><span class="s">"imtype=?"</span> <span class="k">for</span> <span class="n">x</span> <span class="ow">in</span> <span class="n">grouping</span><span class="p">]),</span> <span class="nb">tuple</span><span class="p">([</span><span class="n">x</span> <span class="k">for</span> <span class="n">x</span> <span class="ow">in</span> <span class="n">grouping</span><span class="p">]))</span>
+ <span class="k">for</span> <span class="n">row</span> <span class="ow">in</span> <span class="n">result</span><span class="p">:</span>
+ <span class="n">exists</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">conn</span><span class="o">.</span><span class="n">execute</span><span class="p">(</span><span class="s">"select * from "</span> <span class="o">+</span> <span class="n">outtable</span> <span class="o">+</span> <span class="s">" where experiment=? and id=? and genotype=? and date=? and treatment=? and imtype=?"</span><span class="p">,</span> <span class="p">(</span><span class="n">row</span><span class="p">[</span><span class="s">"experiment"</span><span class="p">],</span> <span class="n">row</span><span class="p">[</span><span class="s">"id"</span><span class="p">],</span> <span class="n">row</span><span class="p">[</span><span class="s">"genotype"</span><span class="p">],</span> <span class="n">row</span><span class="p">[</span><span class="s">"date"</span><span class="p">],</span> <span class="n">row</span><span class="p">[</span><span class="s">"treatment"</span><span class="p">],</span> <span class="n">conf</span><span class="o">.</span><span class="n">typeMap</span><span class="p">[</span><span class="n">row</span><span class="p">[</span><span class="s">"imtype"</span><span class="p">]]))</span>
+ <span class="n">outrow</span> <span class="o">=</span> <span class="n">exists</span><span class="o">.</span><span class="n">fetchone</span><span class="p">()</span>
+ <span class="k">if</span> <span class="ow">not</span> <span class="n">outrow</span><span class="p">:</span>
+ <span class="n">lastid</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">conn</span><span class="o">.</span><span class="n">execute</span><span class="p">(</span><span class="s">"insert into "</span> <span class="o">+</span> <span class="n">outtable</span> <span class="o">+</span> <span class="s">" ("</span> <span class="o">+</span> <span class="s">","</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">headers</span><span class="p">)</span> <span class="o">+</span> <span class="s">") values ("</span> <span class="o">+</span> <span class="s">","</span><span class="o">.</span><span class="n">join</span><span class="p">([</span><span class="s">"?"</span><span class="p">]</span> <span class="o">*</span> <span class="nb">len</span><span class="p">(</span><span class="n">headers</span><span class="p">))</span> <span class="o">+</span> <span class="s">")"</span><span class="p">,</span> <span class="nb">tuple</span><span class="p">([</span><span class="nb">str</span><span class="p">(</span><span class="n">row</span><span class="p">[</span><span class="n">x</span><span class="p">])</span> <span class="k">if</span> <span class="n">x</span> <span class="o">!=</span> <span class="s">"imtype"</span> <span class="k">else</span> <span class="n">conf</span><span class="o">.</span><span class="n">typeMap</span><span class="p">[</span><span class="n">row</span><span class="p">[</span><span class="n">x</span><span class="p">]]</span> <span class="k">for</span> <span class="n">x</span> <span class="ow">in</span> <span class="n">headers</span><span class="p">]))</span><span class="o">.</span><span class="n">lastrowid</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="n">lastid</span> <span class="o">=</span> <span class="n">outrow</span><span class="p">[</span><span class="s">"pegasusid"</span><span class="p">]</span>
+ <span class="n">vals</span> <span class="o">=</span> <span class="nb">dict</span><span class="p">((</span><span class="n">header</span><span class="p">,</span> <span class="nb">float</span><span class="p">(</span><span class="n">row</span><span class="p">[</span><span class="n">header</span><span class="p">])</span> <span class="o">+</span> <span class="nb">float</span><span class="p">(</span><span class="n">outrow</span><span class="p">[</span><span class="n">header</span><span class="p">]))</span> <span class="k">for</span> <span class="n">header</span> <span class="ow">in</span> <span class="n">headers</span> <span class="k">if</span> <span class="n">header</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">conf</span><span class="o">.</span><span class="n">allHeaders</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">conn</span><span class="o">.</span><span class="n">execute</span><span class="p">(</span><span class="s">"update "</span> <span class="o">+</span> <span class="n">outtable</span> <span class="o">+</span> <span class="s">" set "</span> <span class="o">+</span> <span class="s">","</span><span class="o">.</span><span class="n">join</span><span class="p">([</span><span class="nb">str</span><span class="p">(</span><span class="n">x</span><span class="p">)</span> <span class="o">+</span> <span class="s">"="</span> <span class="o">+</span> <span class="nb">str</span><span class="p">(</span><span class="n">vals</span><span class="p">[</span><span class="n">x</span><span class="p">])</span> <span class="k">for</span> <span class="n">x</span> <span class="ow">in</span> <span class="n">vals</span><span class="p">])</span> <span class="o">+</span> <span class="s">" where pegasusid=?"</span><span class="p">,</span> <span class="p">(</span><span class="n">outrow</span><span class="p">[</span><span class="s">"pegasusid"</span><span class="p">],))</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">conn</span><span class="o">.</span><span class="n">execute</span><span class="p">(</span><span class="s">"update "</span> <span class="o">+</span> <span class="n">intable</span> <span class="o">+</span> <span class="s">" set ref_"</span> <span class="o">+</span> <span class="n">outtable</span> <span class="o">+</span> <span class="s">"=? where pegasusid=?"</span><span class="p">,</span> <span class="p">(</span><span class="n">lastid</span><span class="p">,</span> <span class="n">row</span><span class="p">[</span><span class="s">"pegasusid"</span><span class="p">]))</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">conn</span><span class="o">.</span><span class="n">commit</span><span class="p">()</span>
+ <span class="k">return</span>
+ </div>
+<div class="viewcode-block" id="Stats.normalize"><a class="viewcode-back" href="../../statistics.html#plantcv.statistics.Stats.normalize">[docs]</a> <span class="k">def</span> <span class="nf">normalize</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">intable</span><span class="p">,</span> <span class="n">outtable</span><span class="p">,</span> <span class="n">column</span> <span class="o">=</span> <span class="s">"pixels"</span><span class="p">,</span> <span class="n">overwrite</span> <span class="o">=</span> <span class="bp">False</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> :param intable: The input table to load information from</span>
+<span class="sd"> :type intable: str</span>
+<span class="sd"> :param outtable: The output table to write information to.</span>
+<span class="sd"> :type outtable: str</span>
+<span class="sd"> :param column: The column to normalize information to</span>
+<span class="sd"> :type column: str</span>
+<span class="sd"> </span>
+<span class="sd"> Normalizes all numerical information to the specific column. This</span>
+<span class="sd"> function is usually used with 'pixels' as the specified column, which</span>
+<span class="sd"> expresses all numeric information as a percentage of the total pixels </span>
+<span class="sd"> in the image.</span>
+<span class="sd"> """</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_validate</span><span class="p">(</span><span class="s">"normalize"</span><span class="p">,</span> <span class="n">intable</span><span class="p">,</span> <span class="n">outtable</span><span class="p">,</span> <span class="n">overwrite</span><span class="p">)</span>
+ <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">_columnExists</span><span class="p">(</span><span class="n">column</span><span class="p">,</span> <span class="n">intable</span><span class="p">):</span>
+ <span class="n">conf</span><span class="o">.</span><span class="n">statsColumns</span><span class="p">[</span><span class="s">"normalize"</span><span class="p">][</span><span class="s">"exclude"</span><span class="p">]</span> <span class="o">+=</span> <span class="p">[</span><span class="n">column</span><span class="p">]</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_createTable</span><span class="p">(</span><span class="s">"normalize"</span><span class="p">,</span> <span class="n">intable</span><span class="p">,</span> <span class="n">outtable</span><span class="p">,</span> <span class="n">overwrite</span><span class="p">)</span>
+ <span class="n">headers</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_getHeaders</span><span class="p">(</span><span class="n">outtable</span><span class="p">)</span>
+ <span class="n">result</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">conn</span><span class="o">.</span><span class="n">execute</span><span class="p">(</span><span class="s">"select pegasusid,"</span> <span class="o">+</span> <span class="n">column</span> <span class="o">+</span> <span class="s">","</span> <span class="o">+</span> <span class="s">","</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">headers</span><span class="p">)</span> <span class="o">+</span> <span class="s">" from "</span> <span class="o">+</span> <span class="n">intable</span><span class="p">)</span>
+ <span class="k">for</span> <span class="n">row</span> <span class="ow">in</span> <span class="n">result</span><span class="p">:</span>
+ <span class="k">if</span> <span class="nb">all</span><span class="p">([</span><span class="n">row</span><span class="p">[</span><span class="n">x</span><span class="p">]</span> <span class="ow">is</span> <span class="ow">not</span> <span class="bp">None</span> <span class="k">for</span> <span class="n">x</span> <span class="ow">in</span> <span class="n">headers</span> <span class="k">if</span> <span class="n">x</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">conf</span><span class="o">.</span><span class="n">allHeaders</span><span class="p">]):</span>
+ <span class="n">vals</span> <span class="o">=</span> <span class="nb">tuple</span><span class="p">([</span><span class="n">row</span><span class="p">[</span><span class="n">x</span><span class="p">]</span> <span class="k">if</span> <span class="n">x</span> <span class="ow">in</span> <span class="n">conf</span><span class="o">.</span><span class="n">allHeaders</span> <span class="k">else</span> <span class="nb">float</span><span class="p">(</span><span class="n">row</span><span class="p">[</span><span class="n">x</span><span class="p">])</span> <span class="o">/</span> <span class="nb">float</span><span class="p">(</span><span class="n">row</span><span class="p">[</span><span class="n">column</span><span class="p">])</span> <span class="k">for</span> <span class="n">x</span> <span class="ow">in</span> <span class="n">headers</span><span class="p">])</span>
+ <span class="n">lastid</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">conn</span><span class="o">.</span><span class="n">execute</span><span class="p">(</span><span class="s">"insert into "</span> <span class="o">+</span> <span class="n">outtable</span> <span class="o">+</span> <span class="s">" ("</span> <span class="o">+</span> <span class="s">","</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">headers</span><span class="p">)</span> <span class="o">+</span> <span class="s">") values ("</span> <span class="o">+</span> <span class="s">","</span><span class="o">.</span><span class="n">join</span><span class="p">([</span><span class="s">"?"</span><span class="p">]</span> <span class="o">*</span> <span class="nb">len</span><span class="p">(</span><span class="n">headers</span><span class="p">))</span> <span class="o">+</span> <span class="s">")"</span><span class="p">,</span> <span class="n">vals</span><span class="p">)</span><span class="o">.</span><span class="n">lastrowid</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">conn</span><span class="o">.</span><span class="n">execute</span><span class="p">(</span><span class="s">"update "</span> <span class="o">+</span> <span class="n">intable</span> <span class="o">+</span> <span class="s">" set ref_"</span> <span class="o">+</span> <span class="n">outtable</span> <span class="o">+</span> <span class="s">"=? where pegasusid=?"</span><span class="p">,</span> <span class="p">(</span><span class="n">lastid</span><span class="p">,</span> <span class="n">row</span><span class="p">[</span><span class="s">"pegasusid"</span><span class="p">]))</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">conn</span><span class="o">.</span><span class="n">commit</span><span class="p">()</span>
+ <span class="k">return</span>
+ </div>
+ <span class="k">def</span> <span class="nf">extractAll</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">options</span><span class="p">):</span>
+ <span class="n">basepath</span> <span class="o">=</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">dirname</span><span class="p">(</span><span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">dirname</span><span class="p">(</span><span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">abspath</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">db</span><span class="p">)</span> <span class="o">+</span> <span class="s">"/"</span><span class="p">))</span>
+ <span class="k">if</span> <span class="s">"workflows"</span> <span class="ow">in</span> <span class="n">options</span><span class="p">:</span>
+ <span class="k">for</span> <span class="nb">type</span> <span class="ow">in</span> <span class="n">options</span><span class="p">[</span><span class="s">"workflows"</span><span class="p">]:</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_openConnection</span><span class="p">()</span>
+ <span class="n">tmp</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">conn</span><span class="o">.</span><span class="n">execute</span><span class="p">(</span><span class="s">"select pegasusid,experiment,id,date,imtype,imgname from images where imtype=?"</span><span class="p">,</span> <span class="p">(</span><span class="nb">type</span><span class="p">,))</span>
+ <span class="n">result</span> <span class="o">=</span> <span class="n">tmp</span><span class="o">.</span><span class="n">fetchall</span><span class="p">()</span>
+ <span class="k">for</span> <span class="n">row</span> <span class="ow">in</span> <span class="n">result</span><span class="p">:</span>
+ <span class="n">finalpath</span> <span class="o">=</span> <span class="n">row</span><span class="p">[</span><span class="s">"experiment"</span><span class="p">]</span><span class="o">.</span><span class="n">replace</span><span class="p">(</span><span class="s">" "</span><span class="p">,</span><span class="s">""</span><span class="p">)</span> <span class="o">+</span> <span class="s">"/"</span> <span class="o">+</span> <span class="n">row</span><span class="p">[</span><span class="s">"id"</span><span class="p">]</span><span class="o">.</span><span class="n">replace</span><span class="p">(</span><span class="s">" "</span><span class="p">,</span><span class="s">""</span><span class="p">)</span> <span class="o">+</span> <span class="s">"/"</span> <span class="o">+</span> <span class="n">row</span><span class="p">[</span><span class="s">"date"</span><span class="p">]</span><span class="o">.</span><span class="n">replace</span><span class="p">(</span><span class="s">" "</span><span class="p">,</span><span class="s">""</span><span class="p">)</span> <span class="o">+</span> <span class="s">"/"</span> <span class="o">+</span> <span class="n">row</span><span class="p">[</span><span class="s">"imtype"</span><span class="p">]</span><span class="o">.</span><span class="n">replace</span><span class="p">(</span><span class="s">" "</span><span class="p">,</span><span class="s">""</span><span class="p">)</span> <span class="o">+</span> <span class="s">"/"</span> <span class="o">+</span> <span class="n">row</span><span class="p">[</span><span class="s">"imgname"</span><span class="p">]</span><span class="o">.</span><span class="n">replace</span><span class="p">(</span><span class="s">" "</span><span class="p">,</span><span class="s">""</span><span class="p">)</span> <span class="o">+</span> <span class="s">"/"</span> <span class="o">+</span> <span class="n">row</span><span class="p">[</span><span class="s">"pegasusid"</span><span class="p">]</span> <span class="o">+</span> <span class="s">"_"</span> <span class="o">+</span> <span class="n">options</span><span class="p">[</span><span class="s">"workflows"</span><span class="p">][</span><span class="nb">type</span><span class="p">][</span><span class="s">"inputs"</span><span class="p">][</span><span class="mi">0</span><span class="p">]</span> <span class="o">+</span> <span class="s">".png"</span>
+ <span class="c">#finalpath = row["pegasusid"] + "_" + options["workflows"][type]["inputs"][0] + ".png"</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_closeConnection</span><span class="p">()</span>
+ <span class="k">if</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">isfile</span><span class="p">(</span><span class="n">finalpath</span><span class="p">):</span>
+ <span class="k">try</span><span class="p">:</span>
+ <span class="n">plant</span> <span class="o">=</span> <span class="n">plantcv</span><span class="o">.</span><span class="n">imgproc</span><span class="o">.</span><span class="n">Image</span><span class="p">(</span><span class="n">finalpath</span><span class="p">,</span> <span class="n">db</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">db</span><span class="p">,</span> <span class="n">dbid</span> <span class="o">=</span> <span class="n">row</span><span class="p">[</span><span class="s">"pegasusid"</span><span class="p">])</span>
+ <span class="n">plant</span><span class="o">.</span><span class="n">extractFinalPath</span><span class="p">()</span>
+ <span class="k">if</span> <span class="s">"--dimensions"</span> <span class="ow">in</span> <span class="n">options</span><span class="p">[</span><span class="s">"workflows"</span><span class="p">][</span><span class="nb">type</span><span class="p">][</span><span class="s">"arguments"</span><span class="p">]:</span>
+ <span class="n">plant</span><span class="o">.</span><span class="n">extractDimensions</span><span class="p">()</span>
+ <span class="k">if</span> <span class="s">"--pixels"</span> <span class="ow">in</span> <span class="n">options</span><span class="p">[</span><span class="s">"workflows"</span><span class="p">][</span><span class="nb">type</span><span class="p">][</span><span class="s">"arguments"</span><span class="p">]:</span>
+ <span class="n">plant</span><span class="o">.</span><span class="n">extractPixels</span><span class="p">()</span>
+ <span class="k">if</span> <span class="s">"--moments"</span> <span class="ow">in</span> <span class="n">options</span><span class="p">[</span><span class="s">"workflows"</span><span class="p">][</span><span class="nb">type</span><span class="p">][</span><span class="s">"arguments"</span><span class="p">]:</span>
+ <span class="n">plant</span><span class="o">.</span><span class="n">extractMoments</span><span class="p">()</span>
+ <span class="k">if</span> <span class="s">"--colors"</span> <span class="ow">in</span> <span class="n">options</span><span class="p">[</span><span class="s">"workflows"</span><span class="p">][</span><span class="nb">type</span><span class="p">][</span><span class="s">"arguments"</span><span class="p">]:</span>
+ <span class="n">plant</span><span class="o">.</span><span class="n">extractColorData</span><span class="p">()</span>
+ <span class="k">if</span> <span class="s">"--channels"</span> <span class="ow">in</span> <span class="n">options</span><span class="p">[</span><span class="s">"workflows"</span><span class="p">][</span><span class="nb">type</span><span class="p">][</span><span class="s">"arguments"</span><span class="p">]:</span>
+ <span class="n">plant</span><span class="o">.</span><span class="n">extractColorChannels</span><span class="p">()</span>
+ <span class="k">if</span> <span class="s">"--bins"</span> <span class="ow">in</span> <span class="n">options</span><span class="p">[</span><span class="s">"workflows"</span><span class="p">][</span><span class="nb">type</span><span class="p">][</span><span class="s">"arguments"</span><span class="p">]:</span>
+ <span class="n">plant</span><span class="o">.</span><span class="n">extractBins</span><span class="p">(</span><span class="n">options</span><span class="p">[</span><span class="s">"workflows"</span><span class="p">][</span><span class="nb">type</span><span class="p">][</span><span class="s">"arguments"</span><span class="p">][</span><span class="s">"--bins"</span><span class="p">])</span>
+ <span class="k">except</span> <span class="ne">Exception</span> <span class="k">as</span> <span class="n">e</span><span class="p">:</span>
+ <span class="k">print</span> <span class="n">traceback</span><span class="o">.</span><span class="n">format_exc</span><span class="p">()</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="k">print</span> <span class="s">"PATH DOES NOT EXIST: </span><span class="si">%s</span><span class="s">."</span> <span class="o">%</span> <span class="p">(</span><span class="n">finalpath</span><span class="p">,)</span>
+ <span class="k">if</span> <span class="s">"histogram-bin"</span> <span class="ow">in</span> <span class="n">options</span><span class="p">:</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_openConnection</span><span class="p">()</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">histogramBinning</span><span class="p">(</span><span class="s">"images"</span><span class="p">,</span> <span class="s">"histogramBins"</span><span class="p">,</span> <span class="nb">dict</span><span class="p">((</span><span class="nb">type</span><span class="p">,</span><span class="n">options</span><span class="p">[</span><span class="s">"workflows"</span><span class="p">][</span><span class="nb">type</span><span class="p">][</span><span class="s">"inputs"</span><span class="p">][</span><span class="mi">0</span><span class="p">])</span> <span class="k">for</span> <span class="nb">type</span> <span class="ow">in</span> <span class="n">options</span><span class="p">[</span><span class="s">"workflows"</span><span class="p">]),</span> <span class="n">options</span><span class="p">[</span><span class="s">"histogram-bin"</span><span class="p">][</span><span class="s">"--group"</span><span class="p">],</span> <span class="n">options</span><span class="p">[</span><span class="s">"histogram-bin"</span><span class="p">][</span><span class="s">"--chunks"</span><span class="p">],</span> <span class="n">options</span><span class="p">[</span><span class="s">"histogram-bin"</span><span class="p">][</span><span class="s">"--channels"</span><span class="p">],</span> <span class="bp">True</span><span class="p">)</span>
+ <span class="k">return</span>
+
+ <span class="k">def</span> <span class="nf">histogramBinning</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">intable</span><span class="p">,</span> <span class="n">outtable</span><span class="p">,</span> <span class="n">grouping</span><span class="p">,</span> <span class="n">chunks</span><span class="p">,</span> <span class="n">channels</span><span class="p">,</span> <span class="n">jsonwrite</span> <span class="o">=</span> <span class="bp">False</span><span class="p">,</span> <span class="n">overwrite</span> <span class="o">=</span> <span class="bp">False</span><span class="p">):</span>
+ <span class="n">color_vector</span> <span class="o">=</span> <span class="p">{}</span>
+ <span class="k">for</span> <span class="n">name</span> <span class="ow">in</span> <span class="n">grouping</span><span class="p">:</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_validate</span><span class="p">(</span><span class="s">"histogramBins"</span><span class="p">,</span> <span class="n">intable</span><span class="p">,</span> <span class="n">name</span> <span class="o">+</span> <span class="s">"_"</span> <span class="o">+</span> <span class="n">outtable</span><span class="p">,</span> <span class="n">overwrite</span><span class="p">)</span>
+ <span class="k">for</span> <span class="n">name</span> <span class="ow">in</span> <span class="n">grouping</span><span class="p">:</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_createTable</span><span class="p">(</span><span class="s">"histogramBins"</span><span class="p">,</span> <span class="n">intable</span><span class="p">,</span> <span class="n">name</span> <span class="o">+</span> <span class="s">"_"</span> <span class="o">+</span> <span class="n">outtable</span><span class="p">,</span> <span class="n">overwrite</span><span class="p">)</span>
+ <span class="n">color_vector</span><span class="p">[</span><span class="n">name</span><span class="p">]</span> <span class="o">=</span> <span class="p">[</span><span class="mi">0</span><span class="p">,</span> <span class="mi">0</span><span class="p">,</span> <span class="mi">0</span><span class="p">]</span>
+ <span class="nb">map</span> <span class="o">=</span> <span class="nb">dict</span><span class="p">((</span><span class="nb">type</span><span class="p">,</span> <span class="n">name</span><span class="p">)</span> <span class="k">for</span> <span class="n">name</span> <span class="ow">in</span> <span class="n">grouping</span> <span class="k">for</span> <span class="nb">type</span> <span class="ow">in</span> <span class="n">grouping</span><span class="p">[</span><span class="n">name</span><span class="p">])</span>
+ <span class="n">basequery</span> <span class="o">=</span> <span class="s">"select "</span>
+ <span class="k">for</span> <span class="n">x</span><span class="p">,</span><span class="n">c</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">([</span><span class="s">"bhist"</span><span class="p">,</span> <span class="s">"ghist"</span><span class="p">,</span> <span class="s">"rhist"</span><span class="p">]):</span>
+ <span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="mi">0</span><span class="p">,</span> <span class="mi">256</span><span class="p">):</span>
+ <span class="k">if</span> <span class="n">i</span> <span class="o">==</span> <span class="mi">0</span> <span class="ow">and</span> <span class="n">x</span> <span class="o">==</span> <span class="mi">0</span><span class="p">:</span>
+ <span class="n">basequery</span> <span class="o">+=</span> <span class="s">"SUM("</span> <span class="o">+</span> <span class="n">c</span> <span class="o">+</span> <span class="nb">str</span><span class="p">(</span><span class="n">i</span><span class="p">)</span> <span class="o">+</span> <span class="s">")"</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="n">basequery</span> <span class="o">+=</span> <span class="s">",SUM("</span> <span class="o">+</span> <span class="n">c</span> <span class="o">+</span> <span class="nb">str</span><span class="p">(</span><span class="n">i</span><span class="p">)</span> <span class="o">+</span> <span class="s">")"</span>
+ <span class="n">basequery</span> <span class="o">+=</span> <span class="s">" from images where "</span>
+ <span class="k">for</span> <span class="n">name</span> <span class="ow">in</span> <span class="n">grouping</span><span class="p">:</span>
+ <span class="n">query</span> <span class="o">=</span> <span class="n">basequery</span> <span class="o">+</span> <span class="s">" or "</span><span class="o">.</span><span class="n">join</span><span class="p">([</span><span class="s">"imtype=?"</span> <span class="k">for</span> <span class="n">x</span> <span class="ow">in</span> <span class="n">grouping</span><span class="p">[</span><span class="n">name</span><span class="p">]])</span>
+ <span class="n">result</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">conn</span><span class="o">.</span><span class="n">execute</span><span class="p">(</span><span class="n">query</span><span class="p">,</span> <span class="nb">tuple</span><span class="p">(</span><span class="n">grouping</span><span class="p">[</span><span class="n">name</span><span class="p">]))</span>
+ <span class="n">data</span> <span class="o">=</span> <span class="nb">list</span><span class="p">(</span><span class="n">result</span><span class="o">.</span><span class="n">fetchone</span><span class="p">())</span>
+ <span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="mi">0</span><span class="p">,</span> <span class="mi">3</span><span class="p">):</span>
+ <span class="n">color_vector</span><span class="p">[</span><span class="n">name</span><span class="p">][</span><span class="n">i</span><span class="p">]</span> <span class="o">=</span> <span class="n">data</span><span class="p">[</span><span class="n">i</span><span class="o">*</span><span class="mi">256</span><span class="p">:(</span><span class="n">i</span> <span class="o">+</span> <span class="mi">1</span><span class="p">)</span><span class="o">*</span><span class="mi">256</span><span class="p">]</span>
+ <span class="n">bins</span> <span class="o">=</span> <span class="p">{}</span>
+ <span class="k">for</span> <span class="n">name</span> <span class="ow">in</span> <span class="n">grouping</span><span class="p">:</span>
+ <span class="n">bins</span><span class="p">[</span><span class="n">name</span><span class="p">]</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_generateBins</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">_splitHist</span><span class="p">(</span><span class="n">color_vector</span><span class="p">[</span><span class="n">name</span><span class="p">],</span> <span class="n">chunks</span><span class="p">[</span><span class="n">name</span><span class="p">],</span> <span class="n">channels</span><span class="p">[</span><span class="n">name</span><span class="p">]),</span> <span class="n">name</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">conn</span><span class="o">.</span><span class="n">executemany</span><span class="p">(</span><span class="s">"insert into "</span> <span class="o">+</span> <span class="n">name</span> <span class="o">+</span> <span class="s">"_"</span> <span class="o">+</span> <span class="n">outtable</span> <span class="o">+</span> <span class="s">" (name, minr, ming, minb, maxr, maxg, maxb) values (?, ?, ?, ?, ?, ?, ?)"</span><span class="p">,</span> <span class="p">[(</span><span class="nb">bin</span><span class="p">[</span><span class="s">"name"</span><span class="p">],</span> <span class="nb">int</span><span class="p">(</span><span class="nb">bin</span><span class="p">[</span><span class="s">"min"</span><span class="p">][</span><span class="mi">2</span><span class="p">]),</span> <span class="nb">int</span><span class="p">(</span><span class="nb">bin</span><span class="p">[</span><span class="s">"min"</span><span class="p">][</span><span class="mi">1</span><span class="p">]),</span> <span class="nb">int</span><span class="p">(</span><span class="nb">bin</span><span class="p">[</span><span class="s">"min"</span><span class="p">][</span><span class="mi">0</span><span class="p">]),</span> <span class="nb">int</span><span class="p">(</span><span class="nb">bin</span><span class="p">[</span><span class="s">"max"</span><span class="p">][</span><span class="mi">2</span><span class="p">]),</span> <span class="nb">int</span><span class="p">(</span><span class="nb">bin</span><span class="p">[</span><span class="s">"max"</span><span class="p">][</span><span class="mi">1</span><span class="p">]),</span> <span class="nb">int</span><span class="p">(</span><span class="nb">bin</span><span class="p">[</span><span class="s">"max"</span><span class="p">][</span><span class="mi">0</span><span class="p">]))</span> <span class="k">for</span> <span class="nb">bin</span> <span class="ow">in</span> <span class="n">bins</span><span class="p">[</span><span class="n">name</span><span class="p">]])</span>
+<span class="c"># for bin in bins[name]:</span>
+<span class="c"># self.conn.execute("insert into " + name + "_" + outtable + " (name, minr, ming, minb, maxr, maxg, maxb) values (?, ?, ?, ?, ?, ?, ?)", (name + bin["name"], int(bin["min"][2]), int(bin["min"][1]), int(bin["min"][0]), int(bin["max"][2]), int(bin["max"][1]), int(bin["max"][0])))</span>
+<span class="c"># self.conn.commit()</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">conn</span><span class="o">.</span><span class="n">commit</span><span class="p">()</span>
+ <span class="k">if</span> <span class="n">jsonwrite</span><span class="p">:</span>
+ <span class="k">for</span> <span class="n">name</span> <span class="ow">in</span> <span class="n">grouping</span><span class="p">:</span>
+ <span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="n">name</span> <span class="o">+</span> <span class="s">"_hist_bins.json"</span><span class="p">,</span> <span class="s">"w"</span><span class="p">)</span> <span class="k">as</span> <span class="n">wh</span><span class="p">:</span>
+ <span class="n">json</span><span class="o">.</span><span class="n">dump</span><span class="p">(</span><span class="n">bins</span><span class="p">[</span><span class="n">name</span><span class="p">],</span> <span class="n">wh</span><span class="p">)</span>
+ <span class="k">return</span>
+
+
+ <span class="k">def</span> <span class="nf">_splitHist</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">hist</span><span class="p">,</span> <span class="n">chunks</span><span class="p">,</span> <span class="n">channels</span><span class="p">):</span>
+ <span class="n">returnlist</span> <span class="o">=</span> <span class="p">[</span> <span class="p">[</span><span class="mi">1</span><span class="p">],</span> <span class="p">[</span><span class="mi">1</span><span class="p">],</span> <span class="p">[</span><span class="mi">1</span><span class="p">]</span> <span class="p">]</span>
+ <span class="n">s</span> <span class="o">=</span> <span class="p">[</span><span class="nb">sum</span><span class="p">(</span><span class="n">x</span><span class="p">)</span> <span class="k">for</span> <span class="n">x</span> <span class="ow">in</span> <span class="n">hist</span><span class="p">]</span>
+ <span class="c">#s = [int(x) for x in np.sum(hist, axis = 1)]</span>
+ <span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="n">channels</span><span class="p">:</span>
+ <span class="n">tmp</span> <span class="o">=</span> <span class="mi">0</span>
+ <span class="n">integral</span> <span class="o">=</span> <span class="n">s</span><span class="p">[</span><span class="n">i</span><span class="p">]</span> <span class="o">/</span> <span class="n">chunks</span>
+ <span class="k">for</span> <span class="n">j</span><span class="p">,</span><span class="n">item</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="n">hist</span><span class="p">[</span><span class="n">i</span><span class="p">]):</span>
+ <span class="n">tmp</span> <span class="o">+=</span> <span class="n">item</span>
+ <span class="k">if</span> <span class="p">(</span><span class="n">tmp</span> <span class="o">></span> <span class="n">integral</span><span class="p">):</span>
+ <span class="n">returnlist</span><span class="p">[</span><span class="n">i</span><span class="p">]</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">j</span><span class="p">)</span>
+ <span class="n">tmp</span> <span class="o">=</span> <span class="mi">0</span>
+ <span class="n">returnlist</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="mi">255</span><span class="p">)</span>
+ <span class="n">returnlist</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="mi">255</span><span class="p">)</span>
+ <span class="n">returnlist</span><span class="p">[</span><span class="mi">2</span><span class="p">]</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="mi">255</span><span class="p">)</span>
+ <span class="k">return</span> <span class="n">returnlist</span>
+
+ <span class="k">def</span> <span class="nf">_generateBins</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">vector</span><span class="p">,</span> <span class="nb">type</span><span class="p">):</span>
+ <span class="n">bins</span> <span class="o">=</span> <span class="p">[]</span>
+ <span class="n">num</span> <span class="o">=</span> <span class="mi">1</span>
+ <span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="nb">range</span> <span class="p">(</span><span class="mi">0</span><span class="p">,</span> <span class="nb">len</span><span class="p">(</span><span class="n">vector</span><span class="p">[</span><span class="mi">0</span><span class="p">])</span> <span class="o">-</span> <span class="mi">1</span><span class="p">):</span>
+ <span class="k">for</span> <span class="n">j</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="mi">0</span><span class="p">,</span> <span class="nb">len</span><span class="p">(</span><span class="n">vector</span><span class="p">[</span><span class="mi">1</span><span class="p">])</span> <span class="o">-</span> <span class="mi">1</span><span class="p">):</span>
+ <span class="k">for</span> <span class="n">k</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="mi">0</span><span class="p">,</span> <span class="nb">len</span><span class="p">(</span><span class="n">vector</span><span class="p">[</span><span class="mi">2</span><span class="p">])</span> <span class="o">-</span> <span class="mi">1</span><span class="p">):</span>
+ <span class="n">bins</span><span class="o">.</span><span class="n">append</span><span class="p">({</span>
+ <span class="s">"name"</span><span class="p">:</span> <span class="nb">type</span> <span class="o">+</span> <span class="s">"_bin"</span> <span class="o">+</span> <span class="nb">str</span><span class="p">(</span><span class="n">num</span><span class="p">),</span>
+ <span class="s">"min"</span><span class="p">:</span> <span class="n">np</span><span class="o">.</span><span class="n">array</span><span class="p">([</span><span class="n">vector</span><span class="p">[</span><span class="mi">0</span><span class="p">][</span><span class="n">i</span><span class="p">],</span><span class="n">vector</span><span class="p">[</span><span class="mi">1</span><span class="p">][</span><span class="n">j</span><span class="p">],</span><span class="n">vector</span><span class="p">[</span><span class="mi">2</span><span class="p">][</span><span class="n">k</span><span class="p">]],</span> <span class="n">dtype</span><span class="o">=</span><span class="n">np</span><span class="o">.</span><span class="n">uint8</span><span class="p">)</span><span class="o">.</span><span class="n">tolist</span><span class="p">(),</span>
+ <span class="s">"max"</span><span class="p">:</span> <span class="n">np</span><span class="o">.</span><span class="n">array</span><span class="p">([</span><span class="n">vector</span><span class="p">[</span><span class="mi">0</span><span class="p">][</span><span class="n">i</span><span class="o">+</span><span class="mi">1</span><span class="p">],</span><span class="n">vector</span><span class="p">[</span><span class="mi">1</span><span class="p">][</span><span class="n">j</span><span class="o">+</span><span class="mi">1</span><span class="p">],</span><span class="n">vector</span><span class="p">[</span><span class="mi">2</span><span class="p">][</span><span class="n">k</span><span class="o">+</span><span class="mi">1</span><span class="p">]],</span> <span class="n">dtype</span><span class="o">=</span><span class="n">np</span><span class="o">.</span><span class="n">uint8</span><span class="p">)</span><span class="o">.</span><span class="n">tolist</span><span class="p">()</span>
+ <span class="p">})</span>
+ <span class="n">num</span> <span class="o">+=</span> <span class="mi">1</span>
+ <span class="k">return</span> <span class="n">bins</span>
+
+
+<div class="viewcode-block" id="Stats.correlation"><a class="viewcode-back" href="../../statistics.html#plantcv.statistics.Stats.correlation">[docs]</a> <span class="k">def</span> <span class="nf">correlation</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">intable</span><span class="p">,</span> <span class="n">outtable</span><span class="p">,</span> <span class="n">dataFile</span><span class="p">,</span> <span class="n">dataHeaders</span><span class="p">,</span> <span class="n">overwrite</span> <span class="o">=</span> <span class="bp">False</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> :param intable: The input table to load information from</span>
+<span class="sd"> :type intable: str</span>
+<span class="sd"> :param outtable: The output table to write information to.</span>
+<span class="sd"> :type outtable: str</span>
+<span class="sd"> :param dataFile: The csv data file to load</span>
+<span class="sd"> :type dataFile: str</span>
+<span class="sd"> :param dataHeaders: Column names for relevant table headers.</span>
+<span class="sd"> :type dataHeaders: str</span>
+<span class="sd"> </span>
+<span class="sd"> This function correlates all numeric values with values in the given file.</span>
+<span class="sd"> The input data file is assumed to be in csv format. In dataHeaders, you must</span>
+<span class="sd"> specify four keys, 'id', 'date', 'dateFormat', and 'metric'. Each of these should</span>
+<span class="sd"> be column names. Id corresponds to the lemnaTec style identifier ex: '023535-S'.</span>
+<span class="sd"> All dates are converted into Y-m-d form, you must provide a valid format in 'dateFormat',</span>
+<span class="sd"> that way the dates can be converted correctly. The 'metric' column is the actual value you</span>
+<span class="sd"> want to correlate to.</span>
+<span class="sd"> """</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_validate</span><span class="p">(</span><span class="s">"correlation"</span><span class="p">,</span> <span class="n">intable</span><span class="p">,</span> <span class="n">outtable</span><span class="p">,</span> <span class="n">overwrite</span><span class="p">)</span>
+ <span class="n">lemnaData</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_loadLemnaData</span><span class="p">(</span><span class="n">dataFile</span><span class="p">,</span> <span class="n">dataHeaders</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_createTable</span><span class="p">(</span><span class="s">"correlation"</span><span class="p">,</span> <span class="n">intable</span><span class="p">,</span> <span class="n">outtable</span><span class="p">,</span> <span class="n">overwrite</span><span class="p">)</span>
+ <span class="n">headers</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_getHeaders</span><span class="p">(</span><span class="n">outtable</span><span class="p">)</span>
+ <span class="n">numeric</span> <span class="o">=</span> <span class="p">[</span><span class="n">h</span> <span class="k">for</span> <span class="n">h</span> <span class="ow">in</span> <span class="n">headers</span> <span class="k">if</span> <span class="n">h</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">conf</span><span class="o">.</span><span class="n">allHeaders</span><span class="p">]</span>
+ <span class="k">for</span> <span class="nb">id</span> <span class="ow">in</span> <span class="n">lemnaData</span><span class="p">:</span>
+ <span class="k">for</span> <span class="n">imtype</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">_getImageTypes</span><span class="p">(</span><span class="n">intable</span><span class="p">):</span>
+ <span class="n">x</span> <span class="o">=</span> <span class="p">{}</span>
+ <span class="n">y</span> <span class="o">=</span> <span class="p">[]</span>
+ <span class="n">corr</span> <span class="o">=</span> <span class="p">{}</span>
+ <span class="n">result</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">conn</span><span class="o">.</span><span class="n">execute</span><span class="p">(</span><span class="s">"select pegasusid,"</span> <span class="o">+</span> <span class="s">","</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">headers</span> <span class="o">+</span> <span class="p">[</span><span class="s">"date"</span><span class="p">])</span> <span class="o">+</span> <span class="s">" from "</span> <span class="o">+</span> <span class="n">intable</span> <span class="o">+</span> <span class="s">" where id=? and imtype=? order by date"</span><span class="p">,</span> <span class="p">(</span><span class="nb">id</span><span class="p">,</span><span class="n">imtype</span><span class="p">))</span>
+ <span class="k">if</span> <span class="n">result</span><span class="o">.</span><span class="n">fetchone</span><span class="p">():</span>
+ <span class="k">for</span> <span class="n">row</span> <span class="ow">in</span> <span class="n">result</span><span class="p">:</span>
+ <span class="k">if</span> <span class="n">row</span><span class="p">[</span><span class="s">"date"</span><span class="p">]</span> <span class="ow">in</span> <span class="n">lemnaData</span><span class="p">[</span><span class="nb">id</span><span class="p">]:</span>
+ <span class="n">y</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">lemnaData</span><span class="p">[</span><span class="nb">id</span><span class="p">][</span><span class="n">row</span><span class="p">[</span><span class="s">"date"</span><span class="p">]][</span><span class="s">"metric"</span><span class="p">])</span>
+ <span class="k">for</span> <span class="n">header</span> <span class="ow">in</span> <span class="n">numeric</span><span class="p">:</span>
+ <span class="k">if</span> <span class="n">header</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">x</span><span class="p">:</span>
+ <span class="n">x</span><span class="p">[</span><span class="n">header</span><span class="p">]</span> <span class="o">=</span> <span class="p">[]</span>
+ <span class="k">try</span><span class="p">:</span>
+ <span class="n">x</span><span class="p">[</span><span class="n">header</span><span class="p">]</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="nb">float</span><span class="p">(</span><span class="n">row</span><span class="p">[</span><span class="n">header</span><span class="p">]))</span>
+ <span class="k">except</span><span class="p">:</span>
+ <span class="k">pass</span>
+ <span class="k">if</span> <span class="nb">any</span><span class="p">([</span><span class="n">x</span><span class="p">[</span><span class="n">header</span><span class="p">]</span> <span class="k">for</span> <span class="n">header</span> <span class="ow">in</span> <span class="n">numeric</span><span class="p">]):</span>
+ <span class="k">for</span> <span class="n">header</span> <span class="ow">in</span> <span class="n">numeric</span><span class="p">:</span>
+ <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">x</span><span class="p">[</span><span class="n">header</span><span class="p">])</span> <span class="o">==</span> <span class="nb">len</span><span class="p">(</span><span class="n">y</span><span class="p">):</span>
+ <span class="n">corr</span><span class="p">[</span><span class="n">header</span><span class="p">]</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">corrcoef</span><span class="p">(</span><span class="n">x</span><span class="p">[</span><span class="n">header</span><span class="p">],</span> <span class="n">y</span><span class="p">)[</span><span class="mi">0</span><span class="p">][</span><span class="mi">1</span><span class="p">]</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="n">corr</span><span class="p">[</span><span class="n">header</span><span class="p">]</span> <span class="o">=</span> <span class="s">"na"</span>
+ <span class="n">lastid</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">conn</span><span class="o">.</span><span class="n">execute</span><span class="p">(</span><span class="s">"insert into "</span> <span class="o">+</span> <span class="n">outtable</span> <span class="o">+</span> <span class="s">" ("</span> <span class="o">+</span> <span class="s">","</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">headers</span><span class="p">)</span> <span class="o">+</span> <span class="s">") values ("</span> <span class="o">+</span> <span class="s">","</span><span class="o">.</span><span class="n">join</span><span class="p">([</span><span class="s">"?"</span><span class="p">]</span> <span class="o">*</span> <span class="nb">len</span><span class="p">(</span><span class="n">headers</span><span class="p">))</span> <span class="o">+</span> <span class="s">")"</span><span class="p">,</span> <span class="nb">tuple</span><span class="p">([</span><span class="n">row</span><span class="p">[</span><span class="n">header</span><span class="p">]</span> <span class="k">if</span> <span class="n">header</span> <span class="ow">in</span> <span class="n">conf</span><span class="o">.</span><span class="n">allHeaders</span> <span class="k">else</span> <span class="n">corr</span><span class="p">[</span><span class="n">header</span><span class="p">]</span> <span class="k">for</span> <span class="n">header</span> <span class="ow">in</span> <span class="n">headers</span><span class="p">]))</span><span class="o">.</span><span class="n">lastrowid</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">conn</span><span class="o">.</span><span class="n">execute</span><span class="p">(</span><span class="s">"update "</span> <span class="o">+</span> <span class="n">intable</span> <span class="o">+</span> <span class="s">" set ref_"</span> <span class="o">+</span> <span class="n">outtable</span> <span class="o">+</span> <span class="s">"=? where id=? and imtype=?"</span><span class="p">,</span> <span class="p">(</span><span class="n">lastid</span><span class="p">,</span> <span class="nb">id</span><span class="p">,</span> <span class="n">imtype</span><span class="p">))</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">conn</span><span class="o">.</span><span class="n">commit</span><span class="p">()</span>
+ <span class="k">return</span>
+ </div>
+<div class="viewcode-block" id="Stats.anova"><a class="viewcode-back" href="../../statistics.html#plantcv.statistics.Stats.anova">[docs]</a> <span class="k">def</span> <span class="nf">anova</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">intable</span><span class="p">,</span> <span class="n">outtable</span><span class="p">,</span> <span class="n">grouping</span><span class="p">,</span> <span class="n">overwrite</span> <span class="o">=</span> <span class="bp">False</span><span class="p">):</span>
+ <span class="sd">""" </span>
+<span class="sd"> :param intable: The input table to load information from</span>
+<span class="sd"> :type intable: str</span>
+<span class="sd"> :param outtable: The output table to write information to.</span>
+<span class="sd"> :type outtable: str</span>
+<span class="sd"> :param grouping: The list of image types to group by.</span>
+<span class="sd"> :type grouping: list</span>
+<span class="sd"> </span>
+<span class="sd"> Computes the analysis of variation of all numeric information based on 3 factors,</span>
+<span class="sd"> treatment, date, and the interaction between the two. Analysis of variation is</span>
+<span class="sd"> different than the rest of the stats functions, in that a lot of information is </span>
+<span class="sd"> lost after running it. The results themselves correspond to columns (pixels, rmed, binx...)</span>
+<span class="sd"> instead of actual images. </span>
+<span class="sd"> """</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_validate</span><span class="p">(</span><span class="s">"anova"</span><span class="p">,</span> <span class="n">intable</span><span class="p">,</span> <span class="n">outtable</span><span class="p">,</span> <span class="n">overwrite</span><span class="p">)</span>
+ <span class="n">headers</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_getHeaders</span><span class="p">(</span><span class="n">intable</span><span class="p">)</span>
+ <span class="n">numeric</span> <span class="o">=</span> <span class="p">[</span><span class="n">h</span> <span class="k">for</span> <span class="n">h</span> <span class="ow">in</span> <span class="n">headers</span> <span class="k">if</span> <span class="n">h</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">conf</span><span class="o">.</span><span class="n">allHeaders</span><span class="p">]</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_createTable</span><span class="p">(</span><span class="s">"anova"</span><span class="p">,</span> <span class="n">intable</span><span class="p">,</span> <span class="n">outtable</span><span class="p">,</span> <span class="n">overwrite</span><span class="p">)</span>
+ <span class="n">outHeaders</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_getHeaders</span><span class="p">(</span><span class="n">outtable</span><span class="p">)</span>
+ <span class="n">result</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">conn</span><span class="o">.</span><span class="n">execute</span><span class="p">(</span><span class="s">"select * from images"</span><span class="p">)</span>
+ <span class="n">rowdata</span> <span class="o">=</span> <span class="p">[]</span>
+ <span class="k">for</span> <span class="n">row</span> <span class="ow">in</span> <span class="n">result</span><span class="p">:</span>
+ <span class="n">rowdata</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="nb">dict</span><span class="p">(</span><span class="n">row</span><span class="p">))</span>
+ <span class="n">data</span> <span class="o">=</span> <span class="n">pandas</span><span class="o">.</span><span class="n">DataFrame</span><span class="p">(</span><span class="n">rowdata</span><span class="p">)</span><span class="o">.</span><span class="n">dropna</span><span class="p">()</span>
+ <span class="n">anova</span> <span class="o">=</span> <span class="p">{}</span>
+ <span class="k">for</span> <span class="n">col</span> <span class="ow">in</span> <span class="n">numeric</span><span class="p">:</span>
+ <span class="n">anova</span><span class="p">[</span><span class="n">col</span><span class="p">]</span> <span class="o">=</span> <span class="p">{}</span>
+ <span class="n">dateT</span> <span class="o">=</span> <span class="p">[]</span>
+ <span class="n">treatmentT</span> <span class="o">=</span> <span class="p">[]</span>
+ <span class="n">date_treatmentT</span> <span class="o">=</span> <span class="p">[]</span>
+ <span class="k">for</span> <span class="n">date</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">_getDates</span><span class="p">(</span><span class="n">intable</span><span class="p">):</span>
+ <span class="n">dateT</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">data</span><span class="p">[</span><span class="n">data</span><span class="p">[</span><span class="s">"date"</span><span class="p">]</span> <span class="o">==</span> <span class="n">date</span><span class="p">][</span><span class="n">col</span><span class="p">])</span>
+ <span class="k">for</span> <span class="n">treatment</span> <span class="ow">in</span> <span class="p">[</span><span class="s">"Control"</span><span class="p">,</span> <span class="s">"Stress"</span><span class="p">]:</span>
+ <span class="n">treatmentT</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">data</span><span class="p">[</span><span class="n">data</span><span class="p">[</span><span class="s">"treatment"</span><span class="p">]</span> <span class="o">==</span> <span class="n">treatment</span><span class="p">][</span><span class="n">col</span><span class="p">])</span>
+ <span class="n">date_treatmentT</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">data</span><span class="p">[</span><span class="n">np</span><span class="o">.</span><span class="n">where</span><span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">logical_and</span><span class="p">(</span><span class="n">data</span><span class="p">[</span><span class="s">"treatment"</span><span class="p">]</span> <span class="o">==</span> <span class="n">treatment</span><span class="p">,</span><span class="n">data</span><span class="p">[</span><span class="s">"date"</span><span class="p">]</span> <span class="o">==</span> <span class="n">date</span><span class="p">),</span> <span class="bp">True</span><span class="p">,</span> <span class="bp">False</span><span class="p">)][</span><span class="n">col</span><span class="p">])</span>
+ <span class="n">f_val</span><span class="p">,</span> <span class="n">d_pval</span> <span class="o">=</span> <span class="n">stats</span><span class="o">.</span><span class="n">f_oneway</span><span class="p">(</span><span class="o">*</span><span class="n">dateT</span><span class="p">)</span>
+ <span class="n">f_val</span><span class="p">,</span> <span class="n">t_pval</span> <span class="o">=</span> <span class="n">stats</span><span class="o">.</span><span class="n">f_oneway</span><span class="p">(</span><span class="o">*</span><span class="n">treatmentT</span><span class="p">)</span>
+ <span class="n">f_val</span><span class="p">,</span> <span class="n">dt_pval</span> <span class="o">=</span> <span class="n">stats</span><span class="o">.</span><span class="n">f_oneway</span><span class="p">(</span><span class="o">*</span><span class="n">date_treatmentT</span><span class="p">)</span>
+ <span class="n">anova</span><span class="p">[</span><span class="n">col</span><span class="p">][</span><span class="s">"date"</span><span class="p">]</span> <span class="o">=</span> <span class="n">d_pval</span>
+ <span class="n">anova</span><span class="p">[</span><span class="n">col</span><span class="p">][</span><span class="s">"treatment"</span><span class="p">]</span> <span class="o">=</span> <span class="n">t_pval</span>
+ <span class="n">anova</span><span class="p">[</span><span class="n">col</span><span class="p">][</span><span class="s">"date_treatment"</span><span class="p">]</span> <span class="o">=</span> <span class="n">dt_pval</span>
+ <span class="k">for</span> <span class="nb">type</span> <span class="ow">in</span> <span class="p">[</span><span class="s">"date"</span><span class="p">,</span> <span class="s">"treatment"</span><span class="p">,</span> <span class="s">"date_treatment"</span><span class="p">]:</span>
+ <span class="n">vals</span> <span class="o">=</span> <span class="p">[</span><span class="n">group</span><span class="p">]</span> <span class="o">+</span> <span class="p">[</span><span class="n">anova</span><span class="p">[</span><span class="n">x</span><span class="p">][</span><span class="nb">type</span><span class="p">]</span> <span class="k">for</span> <span class="n">x</span> <span class="ow">in</span> <span class="n">numeric</span><span class="p">]</span> <span class="o">+</span> <span class="p">[</span><span class="nb">type</span><span class="p">]</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">conn</span><span class="o">.</span><span class="n">execute</span><span class="p">(</span><span class="s">"insert into "</span> <span class="o">+</span> <span class="n">outtable</span> <span class="o">+</span> <span class="s">" ("</span> <span class="o">+</span> <span class="s">","</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">outHeaders</span><span class="p">)</span> <span class="o">+</span> <span class="s">") values ("</span> <span class="o">+</span> <span class="s">","</span><span class="o">.</span><span class="n">join</span><span class="p">([</span><span class="s">"?"</span><span class="p">]</span> <span class="o">*</span> <span class="nb">len</span><span class="p">(</span><span class="n">outHeaders</span><span class="p">))</span> <span class="o">+</span> <span class="s">")"</span><span class="p">,</span> <span class="nb">tuple</span><span class="p">(</span><span class="n">vals</span><span class="p">))</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">conn</span><span class="o">.</span><span class="n">commit</span><span class="p">()</span>
+ <span class="k">return</span>
+ </div>
+<div class="viewcode-block" id="Stats.tTest"><a class="viewcode-back" href="../../statistics.html#plantcv.statistics.Stats.tTest">[docs]</a> <span class="k">def</span> <span class="nf">tTest</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">intable</span><span class="p">,</span> <span class="n">outtable</span><span class="p">,</span> <span class="n">comp</span> <span class="o">=</span> <span class="s">"imtype"</span><span class="p">,</span> <span class="n">overwrite</span> <span class="o">=</span> <span class="bp">False</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> :param intable: The input table to perform the T test on.</span>
+<span class="sd"> :type intable: str</span>
+<span class="sd"> :param outtable: The output table to write the results to.</span>
+<span class="sd"> :type outtable: str</span>
+<span class="sd"> :param comp: Whether to compare image types or image names.</span>
+<span class="sd"> :type comp: str</span>
+<span class="sd"> :param overwrite: Whether or not to overwrite the output database</span>
+<span class="sd"> :type overwrite: bool</span>
+<span class="sd"> </span>
+<span class="sd"> This function computes a ttest of the input table for all numeric headers.</span>
+<span class="sd"> The comparison is either done based on image types or image names. Default</span>
+<span class="sd"> functionality is a comparison between image types, specify comp = 'imgname'</span>
+<span class="sd"> to compare image names.</span>
+<span class="sd"> """</span>
+
+ <span class="bp">self</span><span class="o">.</span><span class="n">_validate</span><span class="p">(</span><span class="s">"ttest"</span><span class="p">,</span> <span class="n">intable</span><span class="p">,</span> <span class="n">outtable</span><span class="p">,</span> <span class="n">overwrite</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_createTable</span><span class="p">(</span><span class="s">"ttest"</span><span class="p">,</span> <span class="n">intable</span><span class="p">,</span> <span class="n">outtable</span><span class="p">,</span> <span class="n">overwrite</span><span class="p">)</span>
+ <span class="n">comp</span> <span class="o">=</span> <span class="s">"imtype"</span> <span class="k">if</span> <span class="n">comp</span> <span class="o">==</span> <span class="s">"imtype"</span> <span class="k">else</span> <span class="s">"imgname"</span>
+ <span class="n">headers</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_getHeaders</span><span class="p">(</span><span class="n">outtable</span><span class="p">)</span>
+ <span class="n">numeric</span> <span class="o">=</span> <span class="p">[</span><span class="n">h</span> <span class="k">for</span> <span class="n">h</span> <span class="ow">in</span> <span class="n">headers</span> <span class="k">if</span> <span class="n">h</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">conf</span><span class="o">.</span><span class="n">allHeaders</span><span class="p">]</span>
+ <span class="n">meta</span> <span class="o">=</span> <span class="p">[</span><span class="n">h</span> <span class="k">for</span> <span class="n">h</span> <span class="ow">in</span> <span class="n">headers</span> <span class="k">if</span> <span class="n">h</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">numeric</span><span class="p">]</span>
+ <span class="n">data</span> <span class="o">=</span> <span class="p">{}</span>
+ <span class="n">result</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">conn</span><span class="o">.</span><span class="n">execute</span><span class="p">(</span><span class="s">"select pegasusid,treatment,"</span> <span class="o">+</span> <span class="s">","</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">headers</span><span class="p">)</span> <span class="o">+</span> <span class="s">" from "</span> <span class="o">+</span> <span class="n">intable</span><span class="p">)</span>
+ <span class="k">for</span> <span class="n">row</span> <span class="ow">in</span> <span class="n">result</span><span class="p">:</span>
+ <span class="k">if</span> <span class="n">row</span><span class="p">[</span><span class="n">comp</span><span class="p">]</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">data</span><span class="p">:</span>
+ <span class="n">data</span><span class="p">[</span><span class="n">row</span><span class="p">[</span><span class="n">comp</span><span class="p">]]</span> <span class="o">=</span> <span class="p">{}</span>
+ <span class="k">if</span> <span class="n">row</span><span class="p">[</span><span class="s">"date"</span><span class="p">]</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">data</span><span class="p">[</span><span class="n">row</span><span class="p">[</span><span class="n">comp</span><span class="p">]]:</span>
+ <span class="n">data</span><span class="p">[</span><span class="n">row</span><span class="p">[</span><span class="n">comp</span><span class="p">]][</span><span class="n">row</span><span class="p">[</span><span class="s">"date"</span><span class="p">]]</span> <span class="o">=</span> <span class="p">{</span><span class="s">"meta"</span><span class="p">:</span> <span class="nb">dict</span><span class="p">(</span><span class="n">row</span><span class="p">),</span> <span class="s">"id"</span><span class="p">:</span> <span class="p">[],</span> <span class="s">"values"</span><span class="p">:</span> <span class="p">{}}</span>
+ <span class="n">data</span><span class="p">[</span><span class="n">row</span><span class="p">[</span><span class="n">comp</span><span class="p">]][</span><span class="n">row</span><span class="p">[</span><span class="s">"date"</span><span class="p">]][</span><span class="s">"id"</span><span class="p">]</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">row</span><span class="p">[</span><span class="s">"pegasusid"</span><span class="p">])</span>
+ <span class="k">if</span> <span class="n">row</span><span class="p">[</span><span class="s">"treatment"</span><span class="p">]</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">data</span><span class="p">[</span><span class="n">row</span><span class="p">[</span><span class="n">comp</span><span class="p">]][</span><span class="n">row</span><span class="p">[</span><span class="s">"date"</span><span class="p">]][</span><span class="s">"values"</span><span class="p">]:</span>
+ <span class="n">data</span><span class="p">[</span><span class="n">row</span><span class="p">[</span><span class="n">comp</span><span class="p">]][</span><span class="n">row</span><span class="p">[</span><span class="s">"date"</span><span class="p">]][</span><span class="s">"values"</span><span class="p">][</span><span class="n">row</span><span class="p">[</span><span class="s">"treatment"</span><span class="p">]]</span> <span class="o">=</span> <span class="p">[[</span><span class="n">row</span><span class="p">[</span><span class="n">h</span><span class="p">]]</span> <span class="k">for</span> <span class="n">h</span> <span class="ow">in</span> <span class="n">numeric</span><span class="p">]</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="k">for</span> <span class="n">i</span><span class="p">,</span><span class="n">h</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="n">numeric</span><span class="p">):</span>
+ <span class="n">data</span><span class="p">[</span><span class="n">row</span><span class="p">[</span><span class="n">comp</span><span class="p">]][</span><span class="n">row</span><span class="p">[</span><span class="s">"date"</span><span class="p">]][</span><span class="s">"values"</span><span class="p">][</span><span class="n">row</span><span class="p">[</span><span class="s">"treatment"</span><span class="p">]][</span><span class="n">i</span><span class="p">]</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">row</span><span class="p">[</span><span class="n">h</span><span class="p">])</span>
+ <span class="k">for</span> <span class="n">comp</span> <span class="ow">in</span> <span class="n">data</span><span class="p">:</span>
+ <span class="k">for</span> <span class="n">date</span> <span class="ow">in</span> <span class="n">data</span><span class="p">[</span><span class="n">comp</span><span class="p">]:</span>
+ <span class="n">vals</span> <span class="o">=</span> <span class="p">[</span><span class="n">data</span><span class="p">[</span><span class="n">comp</span><span class="p">][</span><span class="n">date</span><span class="p">][</span><span class="s">"meta"</span><span class="p">][</span><span class="n">x</span><span class="p">]</span> <span class="k">for</span> <span class="n">x</span> <span class="ow">in</span> <span class="n">meta</span><span class="p">]</span>
+ <span class="k">for</span> <span class="n">a</span><span class="p">,</span><span class="n">b</span> <span class="ow">in</span> <span class="nb">zip</span><span class="p">(</span><span class="n">data</span><span class="p">[</span><span class="n">comp</span><span class="p">][</span><span class="n">date</span><span class="p">][</span><span class="s">"values"</span><span class="p">][</span><span class="s">"Control"</span><span class="p">],</span> <span class="n">data</span><span class="p">[</span><span class="n">comp</span><span class="p">][</span><span class="n">date</span><span class="p">][</span><span class="s">"values"</span><span class="p">][</span><span class="s">"Stress"</span><span class="p">]):</span>
+ <span class="k">try</span><span class="p">:</span>
+ <span class="n">res</span> <span class="o">=</span> <span class="n">stats</span><span class="o">.</span><span class="n">ttest_ind</span><span class="p">(</span><span class="n">a</span><span class="p">,</span> <span class="n">b</span><span class="p">)[</span><span class="mi">1</span><span class="p">]</span>
+ <span class="k">except</span><span class="p">:</span>
+ <span class="n">res</span> <span class="o">=</span> <span class="s">"null"</span>
+ <span class="n">vals</span> <span class="o">+=</span> <span class="p">[</span><span class="n">res</span><span class="p">]</span>
+ <span class="n">lastid</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">conn</span><span class="o">.</span><span class="n">execute</span><span class="p">(</span><span class="s">"insert into "</span> <span class="o">+</span> <span class="n">outtable</span> <span class="o">+</span> <span class="s">" ("</span> <span class="o">+</span> <span class="s">","</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">headers</span><span class="p">)</span> <span class="o">+</span> <span class="s">") values ("</span> <span class="o">+</span> <span class="s">","</span><span class="o">.</span><span class="n">join</span><span class="p">([</span><span class="s">"?"</span><span class="p">]</span> <span class="o">*</span> <span class="nb">len</span><span class="p">(</span><span class="n">headers</span><span class="p">))</span> <span class="o">+</span> <span class="s">")"</span><span class="p">,</span> <span class="n">vals</span><span class="p">)</span><span class="o">.</span><span class="n">lastrowid</span>
+ <span class="n">updateVals</span> <span class="o">=</span> <span class="p">(</span><span class="n">lastid</span><span class="p">,)</span> <span class="o">+</span> <span class="nb">tuple</span><span class="p">(</span><span class="n">data</span><span class="p">[</span><span class="n">comp</span><span class="p">][</span><span class="n">date</span><span class="p">][</span><span class="s">"id"</span><span class="p">])</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">conn</span><span class="o">.</span><span class="n">execute</span><span class="p">(</span><span class="s">"update "</span> <span class="o">+</span> <span class="n">intable</span> <span class="o">+</span> <span class="s">" set ref_"</span> <span class="o">+</span> <span class="n">outtable</span> <span class="o">+</span> <span class="s">"=? where id in ("</span> <span class="o">+</span> <span class="s">","</span><span class="o">.</span><span class="n">join</span><span class="p">([</span><span class="s">"?"</span><span class="p">]</span> <span class="o">*</span> <span class="nb">len</span><span class="p">(</span><span class="n">data</span><span class="p">[</span><span class="n">comp</span><span class="p">][</span><span class="n">date</span><span class="p">][</span><span class="s">"id"</span><span class="p">]))</span> <span class="o">+</span> <span class="s">")"</span><span class="p">,</span> <span class="n">updateVals</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">conn</span><span class="o">.</span><span class="n">commit</span><span class="p">()</span>
+ <span class="k">return</span>
+ </div>
+<div class="viewcode-block" id="Stats.treatmentComp"><a class="viewcode-back" href="../../statistics.html#plantcv.statistics.Stats.treatmentComp">[docs]</a> <span class="k">def</span> <span class="nf">treatmentComp</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">intable</span><span class="p">,</span> <span class="n">outtable</span><span class="p">,</span> <span class="nb">type</span> <span class="o">=</span> <span class="s">"ratio"</span><span class="p">,</span> <span class="n">direction</span> <span class="o">=</span> <span class="s">"Control"</span><span class="p">,</span> <span class="n">comp</span> <span class="o">=</span> <span class="s">"imtype"</span><span class="p">,</span> <span class="n">overwrite</span> <span class="o">=</span> <span class="bp">False</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> :param intable: The input table to load information from</span>
+<span class="sd"> :type intable: str</span>
+<span class="sd"> :param outtable: The output table to write information to.</span>
+<span class="sd"> :type outtable: str</span>
+<span class="sd"> :param type: The type of calculation to do between treatments. Should be ratio or difference.</span>
+<span class="sd"> :type type: str</span>
+<span class="sd"> :param direction: Whether to compute C ~ S, or S ~ C, default is Control first.</span>
+<span class="sd"> :type direction: str</span>
+<span class="sd"> :param comp: Whether to compare by imtype or imgname</span>
+<span class="sd"> :type comp: str</span>
+<span class="sd"> </span>
+<span class="sd"> This function compares information between treatments -- It finds plants that are identical</span>
+<span class="sd"> except for treatment, and computes either a ratio or difference between them. Direction</span>
+<span class="sd"> is specified as the column you want first, so direction = "Control" will compute C ~ S, and </span>
+<span class="sd"> direction = "Stress" will compute S ~ C. If you have already normalized your table, difference</span>
+<span class="sd"> will provide better information than ratio.</span>
+<span class="sd"> """</span>
+ <span class="n">t1</span> <span class="o">=</span> <span class="s">"Stress"</span> <span class="k">if</span> <span class="n">direction</span> <span class="o">==</span> <span class="s">"Stress"</span> <span class="k">else</span> <span class="s">"Control"</span>
+ <span class="n">t2</span> <span class="o">=</span> <span class="s">"Stress"</span> <span class="k">if</span> <span class="n">direction</span> <span class="o">==</span> <span class="s">"Control"</span> <span class="k">else</span> <span class="s">"Control"</span>
+ <span class="k">if</span> <span class="nb">type</span> <span class="o">==</span> <span class="s">"ratio"</span><span class="p">:</span>
+ <span class="n">op</span> <span class="o">=</span> <span class="k">lambda</span> <span class="n">left</span><span class="p">,</span> <span class="n">right</span><span class="p">:</span> <span class="p">(</span><span class="n">left</span> <span class="o">/</span> <span class="n">right</span><span class="p">)</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="n">op</span> <span class="o">=</span> <span class="k">lambda</span> <span class="n">left</span><span class="p">,</span> <span class="n">right</span><span class="p">:</span> <span class="p">(</span><span class="n">left</span> <span class="o">-</span> <span class="n">right</span><span class="p">)</span>
+ <span class="n">comp</span> <span class="o">=</span> <span class="s">"imtype"</span> <span class="k">if</span> <span class="n">comp</span> <span class="o">==</span> <span class="s">"imtype"</span> <span class="k">else</span> <span class="s">"imgname"</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_validate</span><span class="p">(</span><span class="s">"treatmentComp"</span><span class="p">,</span> <span class="n">intable</span><span class="p">,</span> <span class="n">outtable</span><span class="p">,</span> <span class="n">overwrite</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_createTable</span><span class="p">(</span><span class="s">"treatmentComp"</span><span class="p">,</span> <span class="n">intable</span><span class="p">,</span> <span class="n">outtable</span><span class="p">,</span> <span class="n">overwrite</span><span class="p">)</span>
+ <span class="n">headers</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_getHeaders</span><span class="p">(</span><span class="n">outtable</span><span class="p">)</span>
+ <span class="n">numeric</span> <span class="o">=</span> <span class="p">[</span><span class="n">h</span> <span class="k">for</span> <span class="n">h</span> <span class="ow">in</span> <span class="n">headers</span> <span class="k">if</span> <span class="n">h</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">conf</span><span class="o">.</span><span class="n">allHeaders</span><span class="p">]</span>
+ <span class="n">meta</span> <span class="o">=</span> <span class="p">[</span><span class="n">h</span> <span class="k">for</span> <span class="n">h</span> <span class="ow">in</span> <span class="n">headers</span> <span class="k">if</span> <span class="n">h</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">numeric</span><span class="p">]</span>
+ <span class="n">data</span> <span class="o">=</span> <span class="p">{}</span>
+ <span class="n">result</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">conn</span><span class="o">.</span><span class="n">execute</span><span class="p">(</span><span class="s">"select pegasusid,"</span> <span class="o">+</span> <span class="s">","</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">headers</span><span class="p">)</span> <span class="o">+</span> <span class="s">" from "</span> <span class="o">+</span> <span class="n">intable</span><span class="p">)</span>
+ <span class="k">for</span> <span class="n">row</span> <span class="ow">in</span> <span class="n">result</span><span class="p">:</span>
+ <span class="k">if</span> <span class="n">row</span><span class="p">[</span><span class="s">"genotype"</span><span class="p">]</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">data</span><span class="p">:</span>
+ <span class="n">data</span><span class="p">[</span><span class="n">row</span><span class="p">[</span><span class="s">"genotype"</span><span class="p">]]</span> <span class="o">=</span> <span class="p">{</span><span class="s">"id"</span><span class="p">:</span> <span class="p">[],</span> <span class="s">"values"</span><span class="p">:</span> <span class="p">{},</span> <span class="s">"meta"</span><span class="p">:</span> <span class="p">{}}</span>
+ <span class="n">data</span><span class="p">[</span><span class="n">row</span><span class="p">[</span><span class="s">"genotype"</span><span class="p">]][</span><span class="s">"meta"</span><span class="p">][</span><span class="n">row</span><span class="p">[</span><span class="n">comp</span><span class="p">]]</span> <span class="o">=</span> <span class="nb">dict</span><span class="p">(</span><span class="n">row</span><span class="p">)</span>
+ <span class="n">data</span><span class="p">[</span><span class="n">row</span><span class="p">[</span><span class="s">"genotype"</span><span class="p">]][</span><span class="s">"id"</span><span class="p">]</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">row</span><span class="p">[</span><span class="s">"pegasusid"</span><span class="p">])</span>
+ <span class="k">if</span> <span class="n">row</span><span class="p">[</span><span class="n">comp</span><span class="p">]</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">data</span><span class="p">[</span><span class="n">row</span><span class="p">[</span><span class="s">"genotype"</span><span class="p">]][</span><span class="s">"values"</span><span class="p">]:</span>
+ <span class="n">data</span><span class="p">[</span><span class="n">row</span><span class="p">[</span><span class="s">"genotype"</span><span class="p">]][</span><span class="s">"values"</span><span class="p">][</span><span class="n">row</span><span class="p">[</span><span class="n">comp</span><span class="p">]]</span> <span class="o">=</span> <span class="p">{}</span>
+ <span class="k">if</span> <span class="n">row</span><span class="p">[</span><span class="s">"date"</span><span class="p">]</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">data</span><span class="p">[</span><span class="n">row</span><span class="p">[</span><span class="s">"genotype"</span><span class="p">]][</span><span class="s">"values"</span><span class="p">][</span><span class="n">row</span><span class="p">[</span><span class="n">comp</span><span class="p">]]:</span>
+ <span class="n">data</span><span class="p">[</span><span class="n">row</span><span class="p">[</span><span class="s">"genotype"</span><span class="p">]][</span><span class="s">"values"</span><span class="p">][</span><span class="n">row</span><span class="p">[</span><span class="n">comp</span><span class="p">]][</span><span class="n">row</span><span class="p">[</span><span class="s">"date"</span><span class="p">]]</span> <span class="o">=</span> <span class="p">{}</span>
+ <span class="k">if</span> <span class="n">row</span><span class="p">[</span><span class="s">"treatment"</span><span class="p">]</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">data</span><span class="p">[</span><span class="n">row</span><span class="p">[</span><span class="s">"genotype"</span><span class="p">]][</span><span class="s">"values"</span><span class="p">][</span><span class="n">row</span><span class="p">[</span><span class="n">comp</span><span class="p">]][</span><span class="n">row</span><span class="p">[</span><span class="s">"date"</span><span class="p">]]:</span>
+ <span class="n">data</span><span class="p">[</span><span class="n">row</span><span class="p">[</span><span class="s">"genotype"</span><span class="p">]][</span><span class="s">"values"</span><span class="p">][</span><span class="n">row</span><span class="p">[</span><span class="n">comp</span><span class="p">]][</span><span class="n">row</span><span class="p">[</span><span class="s">"date"</span><span class="p">]][</span><span class="n">row</span><span class="p">[</span><span class="s">"treatment"</span><span class="p">]]</span> <span class="o">=</span> <span class="p">[</span><span class="n">row</span><span class="p">[</span><span class="n">h</span><span class="p">]</span> <span class="k">for</span> <span class="n">h</span> <span class="ow">in</span> <span class="n">numeric</span><span class="p">]</span>
+ <span class="k">for</span> <span class="n">genotype</span> <span class="ow">in</span> <span class="n">data</span><span class="p">:</span>
+ <span class="k">for</span> <span class="n">comp</span> <span class="ow">in</span> <span class="n">data</span><span class="p">[</span><span class="n">genotype</span><span class="p">][</span><span class="s">"values"</span><span class="p">]:</span>
+ <span class="k">for</span> <span class="n">date</span> <span class="ow">in</span> <span class="n">data</span><span class="p">[</span><span class="n">genotype</span><span class="p">][</span><span class="s">"values"</span><span class="p">][</span><span class="n">comp</span><span class="p">]:</span>
+ <span class="n">vals</span> <span class="o">=</span> <span class="p">[</span><span class="n">data</span><span class="p">[</span><span class="n">genotype</span><span class="p">][</span><span class="s">"meta"</span><span class="p">][</span><span class="n">comp</span><span class="p">][</span><span class="n">x</span><span class="p">]</span> <span class="k">for</span> <span class="n">x</span> <span class="ow">in</span> <span class="n">meta</span><span class="p">]</span>
+ <span class="k">for</span> <span class="n">a</span><span class="p">,</span><span class="n">b</span> <span class="ow">in</span> <span class="nb">zip</span><span class="p">(</span><span class="n">data</span><span class="p">[</span><span class="n">genotype</span><span class="p">][</span><span class="s">"values"</span><span class="p">][</span><span class="n">comp</span><span class="p">][</span><span class="n">date</span><span class="p">][</span><span class="n">t1</span><span class="p">],</span> <span class="n">data</span><span class="p">[</span><span class="n">genotype</span><span class="p">][</span><span class="s">"values"</span><span class="p">][</span><span class="n">comp</span><span class="p">][</span><span class="n">date</span><span class="p">][</span><span class="n">t2</span><span class="p">]):</span>
+ <span class="k">try</span><span class="p">:</span>
+ <span class="n">res</span> <span class="o">=</span> <span class="n">op</span><span class="p">(</span><span class="nb">float</span><span class="p">(</span><span class="n">a</span><span class="p">),</span> <span class="nb">float</span><span class="p">(</span><span class="n">b</span><span class="p">))</span>
+ <span class="k">except</span><span class="p">:</span>
+ <span class="n">res</span> <span class="o">=</span> <span class="s">"null"</span>
+ <span class="n">vals</span> <span class="o">+=</span> <span class="p">[</span><span class="n">res</span><span class="p">]</span>
+ <span class="n">lastid</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">conn</span><span class="o">.</span><span class="n">execute</span><span class="p">(</span><span class="s">"insert into "</span> <span class="o">+</span> <span class="n">outtable</span> <span class="o">+</span> <span class="s">" ("</span> <span class="o">+</span> <span class="s">","</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">headers</span><span class="p">)</span> <span class="o">+</span> <span class="s">") values ("</span> <span class="o">+</span> <span class="s">","</span><span class="o">.</span><span class="n">join</span><span class="p">([</span><span class="s">"?"</span><span class="p">]</span> <span class="o">*</span> <span class="nb">len</span><span class="p">(</span><span class="n">headers</span><span class="p">))</span> <span class="o">+</span> <span class="s">")"</span><span class="p">,</span> <span class="n">vals</span><span class="p">)</span><span class="o">.</span><span class="n">lastrowid</span>
+ <span class="n">updateVals</span> <span class="o">=</span> <span class="p">(</span><span class="n">lastid</span><span class="p">,)</span> <span class="o">+</span> <span class="nb">tuple</span><span class="p">(</span><span class="n">data</span><span class="p">[</span><span class="n">genotype</span><span class="p">][</span><span class="s">"id"</span><span class="p">])</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">conn</span><span class="o">.</span><span class="n">execute</span><span class="p">(</span><span class="s">"update "</span> <span class="o">+</span> <span class="n">intable</span> <span class="o">+</span> <span class="s">" set ref_"</span> <span class="o">+</span> <span class="n">outtable</span> <span class="o">+</span> <span class="s">"=? where id in ("</span> <span class="o">+</span> <span class="s">","</span><span class="o">.</span><span class="n">join</span><span class="p">([</span><span class="s">"?"</span><span class="p">]</span> <span class="o">*</span> <span class="nb">len</span><span class="p">(</span><span class="n">data</span><span class="p">[</span><span class="n">genotype</span><span class="p">][</span><span class="s">"id"</span><span class="p">]))</span> <span class="o">+</span> <span class="s">")"</span><span class="p">,</span> <span class="n">updateVals</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">conn</span><span class="o">.</span><span class="n">commit</span><span class="p">()</span>
+ <span class="k">return</span>
+ </div>
+<div class="viewcode-block" id="Stats.threshold"><a class="viewcode-back" href="../../statistics.html#plantcv.statistics.Stats.threshold">[docs]</a> <span class="k">def</span> <span class="nf">threshold</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">intable</span><span class="p">,</span> <span class="n">outtable</span><span class="p">,</span> <span class="n">thresh</span> <span class="o">=</span> <span class="mf">0.01</span><span class="p">,</span> <span class="n">overwrite</span> <span class="o">=</span> <span class="bp">False</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> :param intable: The input table to load information from</span>
+<span class="sd"> :type intable: str</span>
+<span class="sd"> :param outtable: The output table to write information to.</span>
+<span class="sd"> :type outtable: str</span>
+<span class="sd"> :param thresh: The threshold value.</span>
+<span class="sd"> :type thresh: float</span>
+<span class="sd"> </span>
+<span class="sd"> This function thresholds the table based on the given value. All values</span>
+<span class="sd"> that fall below the threhsold are 'updated' in place with 'null'. Normalize</span>
+<span class="sd"> is often called before thresholding.</span>
+<span class="sd"> """</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_validate</span><span class="p">(</span><span class="s">"threshold"</span><span class="p">,</span> <span class="n">intable</span><span class="p">,</span> <span class="n">outtable</span><span class="p">,</span> <span class="n">overwrite</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_createTable</span><span class="p">(</span><span class="s">"threshold"</span><span class="p">,</span> <span class="n">intable</span><span class="p">,</span> <span class="n">outtable</span><span class="p">,</span> <span class="n">overwrite</span><span class="p">)</span>
+ <span class="n">headers</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_getHeaders</span><span class="p">(</span><span class="n">outtable</span><span class="p">)</span>
+ <span class="n">numeric</span> <span class="o">=</span> <span class="p">[</span><span class="n">h</span> <span class="k">for</span> <span class="n">h</span> <span class="ow">in</span> <span class="n">headers</span> <span class="k">if</span> <span class="n">h</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">conf</span><span class="o">.</span><span class="n">allHeaders</span><span class="p">]</span>
+ <span class="n">result</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">conn</span><span class="o">.</span><span class="n">execute</span><span class="p">(</span><span class="s">"select pegasusid,"</span> <span class="o">+</span> <span class="s">","</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">headers</span><span class="p">)</span> <span class="o">+</span> <span class="s">" from "</span> <span class="o">+</span> <span class="n">intable</span><span class="p">)</span>
+ <span class="k">for</span> <span class="n">row</span> <span class="ow">in</span> <span class="n">result</span><span class="p">:</span>
+ <span class="n">vals</span> <span class="o">=</span> <span class="nb">tuple</span><span class="p">([</span><span class="n">row</span><span class="p">[</span><span class="n">h</span><span class="p">]</span> <span class="k">if</span> <span class="n">h</span> <span class="ow">in</span> <span class="n">conf</span><span class="o">.</span><span class="n">allHeaders</span> <span class="k">else</span> <span class="n">row</span><span class="p">[</span><span class="n">h</span><span class="p">]</span> <span class="k">if</span> <span class="nb">float</span><span class="p">(</span><span class="n">row</span><span class="p">[</span><span class="n">h</span><span class="p">])</span> <span class="o">></span> <span class="n">thresh</span> <span class="k">else</span> <span class="s">"null"</span> <span class="k">for</span> <span class="n">h</span> <span class="ow">in</span> <span class="n">headers</span><span class="p">])</span>
+ <span class="n">lastid</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">conn</span><span class="o">.</span><span class="n">execute</span><span class="p">(</span><span class="s">"insert into "</span> <span class="o">+</span> <span class="n">outtable</span> <span class="o">+</span> <span class="s">" ("</span> <span class="o">+</span> <span class="s">","</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">headers</span><span class="p">)</span> <span class="o">+</span> <span class="s">") values ("</span> <span class="o">+</span> <span class="s">","</span><span class="o">.</span><span class="n">join</span><span class="p">([</span><span class="s">"?"</span><span class="p">]</span> <span class="o">*</span> <span class="nb">len</span><span class="p">(</span><span class="n">headers</span><span class="p">))</span> <span class="o">+</span> <span class="s">")"</span><span class="p">,</span> <span class="n">vals</span><span class="p">)</span><span class="o">.</span><span class="n">lastrowid</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">conn</span><span class="o">.</span><span class="n">execute</span><span class="p">(</span><span class="s">"update "</span> <span class="o">+</span> <span class="n">intable</span> <span class="o">+</span> <span class="s">" set ref_"</span> <span class="o">+</span> <span class="n">outtable</span> <span class="o">+</span> <span class="s">"=? where pegasusid=?"</span><span class="p">,</span> <span class="p">(</span><span class="n">lastid</span><span class="p">,</span> <span class="n">row</span><span class="p">[</span><span class="s">"pegasusid"</span><span class="p">]))</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">conn</span><span class="o">.</span><span class="n">commit</span><span class="p">()</span>
+ <span class="k">return</span>
+ </div>
+ <span class="k">def</span> <span class="nf">SOMANYGRAPHINGFUNCTIONS</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+ <span class="k">return</span>
+
+<div class="viewcode-block" id="Stats.export"><a class="viewcode-back" href="../../statistics.html#plantcv.statistics.Stats.export">[docs]</a> <span class="k">def</span> <span class="nf">export</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">table</span><span class="p">,</span> <span class="n">processed</span> <span class="o">=</span> <span class="bp">True</span><span class="p">,</span> <span class="n">grouping</span> <span class="o">=</span> <span class="bp">None</span><span class="p">,</span> <span class="n">fname</span> <span class="o">=</span> <span class="bp">None</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> :param table: The table to write to csv</span>
+<span class="sd"> :type table: str</span>
+<span class="sd"> :param processed: Whether or not to extract processed data</span>
+<span class="sd"> :type processed: bool</span>
+<span class="sd"> :param grouping: Which image types to extract from the database.</span>
+<span class="sd"> :type grouping: list</span>
+<span class="sd"> :param fname: The file name to write to.</span>
+<span class="sd"> :type fname: str</span>
+<span class="sd"> </span>
+<span class="sd"> This function simply extracts data from a database and writes it to csv format.</span>
+<span class="sd"> Default functionality is to extract only data that has been processed. This is</span>
+<span class="sd"> checked by finding if an outputPath has been set. Additionally,</span>
+<span class="sd"> you can specify a list of image types to extract, if not, the default list contains</span>
+<span class="sd"> all rgb and fluo images. Finally, if no file name is specified, the name</span>
+<span class="sd"> of the table is used as the filename.</span>
+<span class="sd"> """</span>
+
+ <span class="n">grouping</span> <span class="o">=</span> <span class="n">grouping</span> <span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">grouping</span><span class="p">,</span> <span class="nb">list</span><span class="p">)</span> <span class="k">else</span> <span class="bp">self</span><span class="o">.</span><span class="n">_getImageTypes</span><span class="p">(</span><span class="n">table</span><span class="p">)</span>
+ <span class="n">fname</span> <span class="o">=</span> <span class="n">fname</span> <span class="k">if</span> <span class="n">fname</span> <span class="k">else</span> <span class="n">table</span> <span class="o">+</span> <span class="s">".csv"</span>
+ <span class="n">query</span> <span class="o">=</span> <span class="s">"select * from "</span> <span class="o">+</span> <span class="n">table</span>
+ <span class="n">values</span> <span class="o">=</span> <span class="nb">tuple</span><span class="p">()</span>
+ <span class="k">if</span> <span class="n">processed</span><span class="p">:</span>
+ <span class="n">query</span> <span class="o">+=</span> <span class="s">" where outputPath is not null"</span>
+ <span class="k">if</span> <span class="n">grouping</span><span class="p">:</span>
+ <span class="n">query</span> <span class="o">+=</span> <span class="s">" and ("</span> <span class="o">+</span> <span class="s">" or "</span><span class="o">.</span><span class="n">join</span><span class="p">([</span><span class="s">"imtype=?"</span> <span class="k">for</span> <span class="n">x</span> <span class="ow">in</span> <span class="n">grouping</span><span class="p">])</span>
+ <span class="n">values</span> <span class="o">=</span> <span class="nb">tuple</span><span class="p">([</span><span class="n">x</span> <span class="k">for</span> <span class="n">x</span> <span class="ow">in</span> <span class="n">grouping</span><span class="p">])</span>
+ <span class="k">elif</span> <span class="n">grouping</span><span class="p">:</span>
+ <span class="n">query</span> <span class="o">+=</span> <span class="s">" "</span> <span class="o">+</span> <span class="s">" or "</span><span class="o">.</span><span class="n">join</span><span class="p">([</span><span class="s">"imtype=?"</span> <span class="k">for</span> <span class="n">x</span> <span class="ow">in</span> <span class="n">grouping</span><span class="p">])</span>
+ <span class="n">values</span> <span class="o">=</span> <span class="nb">tuple</span><span class="p">([</span><span class="n">x</span> <span class="k">for</span> <span class="n">x</span> <span class="ow">in</span> <span class="n">grouping</span><span class="p">])</span>
+ <span class="n">table</span> <span class="o">=</span> <span class="n">pandas</span><span class="o">.</span><span class="n">io</span><span class="o">.</span><span class="n">sql</span><span class="o">.</span><span class="n">read_frame</span><span class="p">(</span><span class="n">query</span><span class="p">,</span> <span class="n">values</span><span class="p">)</span>
+ <span class="n">table</span><span class="o">.</span><span class="n">to_csv</span><span class="p">(</span><span class="n">fname</span><span class="p">)</span>
+ <span class="k">return</span></div></div>
+</pre></div>
+
+ </div>
+
+ </div>
+</div>
+<footer class="footer">
+ <div class="container">
+ <p class="pull-right">
+ <a href="#">Back to top</a>
+
+ </p>
+ <p>
+ © Copyright 2015, Avi Knecht.<br/>
+ Created using <a href="http://sphinx.pocoo.org/">Sphinx</a> 1.3a0.<br/>
+ </p>
+ </div>
+</footer>
+ </body>
+</html>
\ No newline at end of file
diff --git a/docs/build/html/_modules/plantcv/workflow.html b/docs/build/html/_modules/plantcv/workflow.html
new file mode 100644
index 0000000000000000000000000000000000000000..b4d1731aa6cbcf3b9b75339f0a90fc00d4656cf7
--- /dev/null
+++ b/docs/build/html/_modules/plantcv/workflow.html
@@ -0,0 +1,1135 @@
+<!DOCTYPE html>
+
+
+<html xmlns="http://www.w3.org/1999/xhtml">
+ <head>
+ <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
+
+ <title>plantcv.workflow — Image Harvest 1.0.1 documentation</title>
+
+ <link rel="stylesheet" href="../../_static/basic.css" type="text/css" />
+ <link rel="stylesheet" href="../../_static/pygments.css" type="text/css" />
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+ var DOCUMENTATION_OPTIONS = {
+ URL_ROOT: '../../',
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+ <link rel="top" title="Image Harvest 1.0.1 documentation" href="../../index.html" />
+ <link rel="up" title="Module code" href="../index.html" />
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+<meta name='viewport' content='width=device-width, initial-scale=1.0, maximum-scale=1'>
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+
+ <div id="navbar" class="navbar navbar-default navbar-fixed-top">
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+ <div class="navbar-header">
+ <!-- .btn-navbar is used as the toggle for collapsed navbar content -->
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+ <span class="icon-bar"></span>
+ <span class="icon-bar"></span>
+ </button>
+ <a class="navbar-brand" href="../../index.html">
+ Image Harvest</a>
+ <span class="navbar-text navbar-version pull-left"><b>1.0</b></span>
+ </div>
+
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+ <ul class="nav navbar-nav">
+
+
+ <li class="dropdown globaltoc-container">
+ <a role="button"
+ id="dLabelGlobalToc"
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+ href="../../index.html">Site <b class="caret"></b></a>
+ <ul class="dropdown-menu globaltoc"
+ role="menu"
+ aria-labelledby="dLabelGlobalToc"><ul>
+<li class="toctree-l1"><a class="reference internal" href="../../introduction.html">Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../../installation.html">Installation</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../../start.html">Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../../ex_script_core1.html">Core Processing Example #1</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../../ex_script_core2.html">Core Processing Example #2</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../../ex_script_color1.html">Color Filter In Depth #1</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../../ex_workflow_1.html">Workflow Example #1</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../../examples.html">Examples</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../../processing.html">Image Processing</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../../viewer.html">Image Processing Viewer</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../../statistics.html">Statistics</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../../indexing.html">Image Loading</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../../workflowimage.html">Image Processing Workflows</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../../workflowstats.html">Statistics Workflows</a></li>
+</ul>
+</ul>
+</li>
+
+ <li class="dropdown">
+ <a role="button"
+ id="dLabelLocalToc"
+ data-toggle="dropdown"
+ data-target="#"
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+ </div>
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+ </div>
+
+<div class="container">
+ <div class="row">
+ <div class="col-md-12">
+
+ <h1>Source code for plantcv.workflow</h1><div class="highlight"><pre>
+<span class="sd">"""</span>
+
+<span class="sd">.. module:: workflow</span>
+<span class="sd"> :platform: Mac, Linux</span>
+<span class="sd"> :synopsis: Custom workflow creation, and workflow submission.</span>
+
+<span class="sd">.. moduleauthor:: Avi Knecht <avi@kurtknecht.com></span>
+
+<span class="sd">"""</span>
+
+<span class="kn">import</span> <span class="nn">os</span>
+<span class="kn">import</span> <span class="nn">conf</span>
+<span class="kn">import</span> <span class="nn">sys</span>
+<span class="kn">import</span> <span class="nn">json</span>
+<span class="kn">import</span> <span class="nn">re</span>
+<span class="kn">import</span> <span class="nn">csv</span>
+<span class="kn">import</span> <span class="nn">datetime</span>
+<span class="kn">import</span> <span class="nn">sqlite3</span>
+<span class="kn">import</span> <span class="nn">shutil</span>
+<span class="kn">import</span> <span class="nn">errno</span>
+<span class="kn">import</span> <span class="nn">textwrap</span>
+<span class="kn">import</span> <span class="nn">copy</span>
+<span class="kn">import</span> <span class="nn">plantcv.validator</span>
+<span class="kn">import</span> <span class="nn">xml.dom.minidom</span>
+<span class="kn">from</span> <span class="nn">Pegasus.DAX3</span> <span class="kn">import</span> <span class="o">*</span>
+
+
+<span class="k">class</span> <span class="nc">Workflow</span><span class="p">(</span><span class="nb">object</span><span class="p">):</span>
+
+ <span class="sd">"""</span>
+<span class="sd"> Generic workflow creation class.</span>
+<span class="sd"> """</span>
+
+ <span class="k">def</span> <span class="nf">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">jobhome</span><span class="p">,</span> <span class="n">basename</span> <span class="o">=</span> <span class="bp">None</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> :param jobhome: The base directory for job submission.</span>
+<span class="sd"> :type jobhome: str</span>
+<span class="sd"> </span>
+<span class="sd"> Creates a Workflow class based on the input directory. Only loads and </span>
+<span class="sd"> validates the config file by default.</span>
+<span class="sd"> """</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">err</span> <span class="o">=</span> <span class="s">""</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">jobhome</span> <span class="o">=</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">abspath</span><span class="p">(</span><span class="n">jobhome</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">jobname</span> <span class="o">=</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">basename</span><span class="p">(</span><span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">dirname</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">jobhome</span> <span class="o">+</span> <span class="s">"/"</span><span class="p">))</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">basename</span> <span class="o">=</span> <span class="n">basename</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">dax</span> <span class="o">=</span> <span class="n">ADAG</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">jobname</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">executables</span> <span class="o">=</span> <span class="p">{}</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">files</span> <span class="o">=</span> <span class="p">{</span><span class="bp">self</span><span class="o">.</span><span class="n">dax</span><span class="p">:</span> <span class="p">{}}</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">jobs</span> <span class="o">=</span> <span class="p">{</span><span class="bp">self</span><span class="o">.</span><span class="n">dax</span><span class="p">:</span> <span class="p">{}}</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">deps</span> <span class="o">=</span> <span class="p">{}</span>
+ <span class="k">return</span>
+
+ <span class="k">def</span> <span class="nf">_loadInputFiles</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> Loads the input files into the appropriate variables</span>
+<span class="sd"> This should be overloaded.</span>
+<span class="sd"> """</span>
+ <span class="k">return</span>
+
+ <span class="k">def</span> <span class="nf">_isFile</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">name</span><span class="p">,</span> <span class="n">dax</span><span class="p">,</span> <span class="n">imtype</span><span class="p">,</span> <span class="n">inout</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> Convenience function to check if a given file exists.</span>
+<span class="sd"> """</span>
+ <span class="k">if</span> <span class="n">name</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">files</span><span class="p">[</span><span class="n">dax</span><span class="p">][</span><span class="n">imtype</span><span class="p">][</span><span class="n">inout</span><span class="p">]:</span>
+ <span class="k">return</span> <span class="bp">True</span>
+ <span class="k">return</span> <span class="bp">False</span>
+
+ <span class="k">def</span> <span class="nf">_isJob</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">name</span><span class="p">,</span> <span class="n">dax</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> Convenience function to check if a given job exists.</span>
+<span class="sd"> """</span>
+ <span class="k">if</span> <span class="n">name</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">jobs</span><span class="p">[</span><span class="n">dax</span><span class="p">]:</span>
+ <span class="k">return</span> <span class="bp">True</span>
+ <span class="k">return</span> <span class="bp">False</span>
+
+ <span class="k">def</span> <span class="nf">_isExecutable</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">name</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> Convenience function to check if a given executable exists.</span>
+<span class="sd"> """</span>
+ <span class="k">if</span> <span class="n">name</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">executables</span><span class="p">:</span>
+ <span class="k">return</span> <span class="bp">True</span>
+ <span class="k">return</span> <span class="bp">False</span>
+
+ <span class="k">def</span> <span class="nf">_createSetup</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> Creates the base structure for job submission. Everything is contained </span>
+<span class="sd"> within a folder based on the current timestamp.</span>
+<span class="sd"> """</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">basepath</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">jobhome</span> <span class="o">+</span> <span class="s">"/"</span> <span class="o">+</span> <span class="bp">self</span><span class="o">.</span><span class="n">basename</span> <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">basename</span> <span class="k">else</span> <span class="bp">self</span><span class="o">.</span><span class="n">jobhome</span> <span class="o">+</span> <span class="s">"/"</span> <span class="o">+</span> <span class="n">datetime</span><span class="o">.</span><span class="n">datetime</span><span class="o">.</span><span class="n">now</span><span class="p">()</span><span class="o">.</span><span class="n">strftime</span><span class="p">(</span><span class="s">"%Y-%m-</span><span class="si">%d</span><span class="s">_%H%M%S"</span><span class="p">)</span>
+ <span class="k">if</span> <span class="ow">not</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">exists</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">basepath</span><span class="p">):</span>
+ <span class="n">os</span><span class="o">.</span><span class="n">makedirs</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">basepath</span><span class="p">)</span>
+ <span class="k">if</span> <span class="ow">not</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">exists</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">basepath</span> <span class="o">+</span> <span class="s">"/input"</span><span class="p">):</span>
+ <span class="n">os</span><span class="o">.</span><span class="n">makedirs</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">basepath</span> <span class="o">+</span> <span class="s">"/input"</span><span class="p">)</span>
+ <span class="k">if</span> <span class="ow">not</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">exists</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">basepath</span> <span class="o">+</span> <span class="s">"/output"</span><span class="p">):</span>
+ <span class="n">os</span><span class="o">.</span><span class="n">makedirs</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">basepath</span> <span class="o">+</span> <span class="s">"/output"</span><span class="p">)</span>
+ <span class="k">if</span> <span class="ow">not</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">exists</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">basepath</span> <span class="o">+</span> <span class="s">"input/templates"</span><span class="p">):</span>
+ <span class="n">os</span><span class="o">.</span><span class="n">makedirs</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">basepath</span> <span class="o">+</span> <span class="s">"/input/templates"</span><span class="p">)</span>
+ <span class="k">if</span> <span class="ow">not</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">exists</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">basepath</span> <span class="o">+</span> <span class="s">"/input/rawfiles"</span><span class="p">):</span>
+ <span class="n">os</span><span class="o">.</span><span class="n">makedirs</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">basepath</span> <span class="o">+</span> <span class="s">"/input/rawfiles"</span><span class="p">)</span>
+ <span class="k">return</span>
+
+ <span class="k">def</span> <span class="nf">_addFile</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">name</span><span class="p">,</span> <span class="n">imtype</span><span class="p">,</span> <span class="n">inout</span><span class="p">,</span> <span class="n">path</span> <span class="o">=</span> <span class="bp">None</span><span class="p">,</span> <span class="n">dax</span> <span class="o">=</span> <span class="bp">None</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> Adds the inputted file to the dax, as well as the internal variable self.files</span>
+<span class="sd"> """</span>
+ <span class="n">dax</span> <span class="o">=</span> <span class="n">dax</span> <span class="k">if</span> <span class="n">dax</span> <span class="k">else</span> <span class="bp">self</span><span class="o">.</span><span class="n">dax</span>
+ <span class="k">if</span> <span class="ow">not</span> <span class="bp">self</span><span class="o">.</span><span class="n">_isFile</span><span class="p">(</span><span class="n">name</span><span class="p">,</span> <span class="n">dax</span><span class="p">,</span> <span class="n">imtype</span><span class="p">,</span> <span class="n">inout</span><span class="p">):</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">files</span><span class="p">[</span><span class="n">dax</span><span class="p">][</span><span class="n">imtype</span><span class="p">][</span><span class="n">inout</span><span class="p">][</span><span class="n">name</span><span class="p">]</span> <span class="o">=</span> <span class="p">{</span><span class="s">"file"</span><span class="p">:</span> <span class="n">File</span><span class="p">(</span><span class="n">name</span><span class="p">),</span> <span class="s">"path"</span><span class="p">:</span> <span class="s">""</span><span class="p">}</span>
+ <span class="k">if</span> <span class="n">inout</span> <span class="o">==</span> <span class="s">"input"</span><span class="p">:</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">files</span><span class="p">[</span><span class="n">dax</span><span class="p">][</span><span class="n">imtype</span><span class="p">][</span><span class="n">inout</span><span class="p">][</span><span class="n">name</span><span class="p">][</span><span class="s">"path"</span><span class="p">]</span> <span class="o">=</span> <span class="n">path</span> <span class="k">if</span> <span class="n">path</span> <span class="k">else</span> <span class="n">name</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">files</span><span class="p">[</span><span class="n">dax</span><span class="p">][</span><span class="n">imtype</span><span class="p">][</span><span class="n">inout</span><span class="p">][</span><span class="n">name</span><span class="p">][</span><span class="s">"file"</span><span class="p">]</span><span class="o">.</span><span class="n">addPFN</span><span class="p">(</span><span class="n">PFN</span><span class="p">(</span><span class="s">"file://"</span> <span class="o">+</span> <span class="n">path</span><span class="o">.</span><span class="n">replace</span><span class="p">(</span><span class="s">" "</span><span class="p">,</span><span class="s">"%20"</span><span class="p">),</span> <span class="s">"local"</span><span class="p">))</span>
+ <span class="n">dax</span><span class="o">.</span><span class="n">addFile</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">files</span><span class="p">[</span><span class="n">dax</span><span class="p">][</span><span class="n">imtype</span><span class="p">][</span><span class="n">inout</span><span class="p">][</span><span class="n">name</span><span class="p">][</span><span class="s">"file"</span><span class="p">])</span>
+ <span class="k">return</span>
+
+ <span class="k">def</span> <span class="nf">_addJob</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">jobname</span><span class="p">,</span> <span class="n">executable</span><span class="p">,</span> <span class="n">inputs</span><span class="p">,</span> <span class="n">outputs</span><span class="p">,</span> <span class="n">arguments</span><span class="p">,</span> <span class="n">dependencies</span> <span class="o">=</span> <span class="bp">None</span><span class="p">,</span> <span class="n">dax</span> <span class="o">=</span> <span class="bp">None</span><span class="p">,</span> <span class="n">label</span> <span class="o">=</span> <span class="bp">None</span><span class="p">):</span>
+ <span class="n">dax</span> <span class="o">=</span> <span class="n">dax</span> <span class="k">if</span> <span class="n">dax</span> <span class="k">else</span> <span class="bp">self</span><span class="o">.</span><span class="n">dax</span>
+ <span class="k">if</span> <span class="ow">not</span> <span class="bp">self</span><span class="o">.</span><span class="n">_isJob</span><span class="p">(</span><span class="n">jobname</span><span class="p">,</span> <span class="n">dax</span><span class="p">):</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">jobs</span><span class="p">[</span><span class="n">dax</span><span class="p">][</span><span class="n">jobname</span><span class="p">]</span> <span class="o">=</span> <span class="n">Job</span><span class="p">(</span><span class="n">executable</span><span class="p">)</span>
+ <span class="n">dax</span><span class="o">.</span><span class="n">addJob</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">jobs</span><span class="p">[</span><span class="n">dax</span><span class="p">][</span><span class="n">jobname</span><span class="p">])</span>
+ <span class="k">for</span> <span class="n">key</span> <span class="ow">in</span> <span class="n">inputs</span><span class="p">:</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">jobs</span><span class="p">[</span><span class="n">dax</span><span class="p">][</span><span class="n">jobname</span><span class="p">]</span><span class="o">.</span><span class="n">uses</span><span class="p">(</span><span class="n">inputs</span><span class="p">[</span><span class="n">key</span><span class="p">][</span><span class="s">"file"</span><span class="p">],</span> <span class="n">link</span> <span class="o">=</span> <span class="n">Link</span><span class="o">.</span><span class="n">INPUT</span><span class="p">)</span>
+ <span class="k">for</span> <span class="n">key</span> <span class="ow">in</span> <span class="n">outputs</span><span class="p">:</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">jobs</span><span class="p">[</span><span class="n">dax</span><span class="p">][</span><span class="n">jobname</span><span class="p">]</span><span class="o">.</span><span class="n">uses</span><span class="p">(</span><span class="n">outputs</span><span class="p">[</span><span class="n">key</span><span class="p">][</span><span class="s">"file"</span><span class="p">],</span> <span class="n">link</span> <span class="o">=</span> <span class="n">Link</span><span class="o">.</span><span class="n">OUTPUT</span><span class="p">,</span> <span class="n">transfer</span> <span class="o">=</span> <span class="n">outputs</span><span class="p">[</span><span class="n">key</span><span class="p">][</span><span class="s">"transfer"</span><span class="p">])</span>
+ <span class="n">arglist</span> <span class="o">=</span> <span class="p">[]</span>
+ <span class="k">for</span> <span class="n">arg</span> <span class="ow">in</span> <span class="n">arguments</span><span class="p">:</span>
+ <span class="n">arglist</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">arg</span><span class="p">)</span>
+ <span class="k">if</span> <span class="nb">str</span><span class="p">(</span><span class="n">arguments</span><span class="p">[</span><span class="n">arg</span><span class="p">])</span> <span class="ow">in</span> <span class="n">inputs</span><span class="p">:</span>
+ <span class="n">arglist</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">inputs</span><span class="p">[</span><span class="nb">str</span><span class="p">(</span><span class="n">arguments</span><span class="p">[</span><span class="n">arg</span><span class="p">])][</span><span class="s">"file"</span><span class="p">])</span>
+ <span class="k">elif</span> <span class="nb">str</span><span class="p">(</span><span class="n">arguments</span><span class="p">[</span><span class="n">arg</span><span class="p">])</span> <span class="ow">in</span> <span class="n">outputs</span><span class="p">:</span>
+ <span class="n">arglist</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">outputs</span><span class="p">[</span><span class="nb">str</span><span class="p">(</span><span class="n">arguments</span><span class="p">[</span><span class="n">arg</span><span class="p">])][</span><span class="s">"file"</span><span class="p">])</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="n">arglist</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="nb">str</span><span class="p">(</span><span class="n">arguments</span><span class="p">[</span><span class="n">arg</span><span class="p">]))</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">jobs</span><span class="p">[</span><span class="n">dax</span><span class="p">][</span><span class="n">jobname</span><span class="p">]</span><span class="o">.</span><span class="n">addArguments</span><span class="p">(</span><span class="o">*</span><span class="n">arglist</span><span class="p">)</span>
+ <span class="k">if</span> <span class="n">dependencies</span><span class="p">:</span>
+ <span class="k">for</span> <span class="n">depend</span> <span class="ow">in</span> <span class="n">dependencies</span><span class="p">:</span>
+ <span class="n">dax</span><span class="o">.</span><span class="n">depends</span><span class="p">(</span><span class="n">child</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">jobs</span><span class="p">[</span><span class="n">dax</span><span class="p">][</span><span class="n">jobname</span><span class="p">],</span> <span class="n">parent</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">jobs</span><span class="p">[</span><span class="n">dax</span><span class="p">][</span><span class="n">depend</span><span class="p">])</span>
+ <span class="k">if</span> <span class="n">label</span><span class="p">:</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">jobs</span><span class="p">[</span><span class="n">dax</span><span class="p">][</span><span class="n">jobname</span><span class="p">]</span><span class="o">.</span><span class="n">profile</span><span class="p">(</span><span class="n">Namespace</span><span class="o">.</span><span class="n">PEGASUS</span><span class="p">,</span> <span class="s">"label"</span><span class="p">,</span> <span class="n">label</span><span class="p">)</span>
+ <span class="k">return</span>
+
+ <span class="k">def</span> <span class="nf">create</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> Creates a new pegasus submission directory based on the current timestamp,</span>
+<span class="sd"> and populates it with all required information to submit a pegasus job.</span>
+<span class="sd"> This function should be overloaded.</span>
+<span class="sd"> """</span>
+ <span class="k">return</span>
+
+
+<div class="viewcode-block" id="Statistics"><a class="viewcode-back" href="../../workflowstats.html#plantcv.workflow.Statistics">[docs]</a><span class="k">class</span> <span class="nc">Statistics</span><span class="p">(</span><span class="n">Workflow</span><span class="p">):</span>
+
+ <span class="sd">"""</span>
+<span class="sd"> A class specifically for statistics workflow</span>
+<span class="sd"> validation and submission.</span>
+<span class="sd"> """</span>
+
+ <span class="k">def</span> <span class="nf">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">jobhome</span><span class="p">,</span> <span class="n">basename</span><span class="p">,</span> <span class="n">validOnly</span> <span class="o">=</span> <span class="bp">False</span><span class="p">):</span>
+ <span class="nb">super</span><span class="p">(</span><span class="n">Statistics</span><span class="p">,</span> <span class="bp">self</span><span class="p">)</span><span class="o">.</span><span class="n">__init__</span><span class="p">(</span><span class="n">jobhome</span><span class="p">,</span> <span class="n">basename</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">configfile</span> <span class="o">=</span> <span class="n">jobhome</span> <span class="o">+</span> <span class="s">"/input/"</span> <span class="o">+</span> <span class="n">conf</span><span class="o">.</span><span class="n">configFile</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">statsfile</span> <span class="o">=</span> <span class="n">jobhome</span> <span class="o">+</span> <span class="s">"/input/"</span> <span class="o">+</span> <span class="n">conf</span><span class="o">.</span><span class="n">statsFile</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">dbfile</span> <span class="o">=</span> <span class="n">jobhome</span> <span class="o">+</span> <span class="s">"/"</span> <span class="o">+</span> <span class="n">basename</span> <span class="o">+</span> <span class="s">"/output/"</span> <span class="o">+</span> <span class="n">conf</span><span class="o">.</span><span class="n">outputdb</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">validOnly</span> <span class="o">=</span> <span class="n">validOnly</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">rawFiles</span> <span class="o">=</span> <span class="p">{}</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_loadInputFiles</span><span class="p">()</span>
+ <span class="k">return</span>
+
+ <span class="k">def</span> <span class="nf">_getImageTypes</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+ <span class="k">return</span> <span class="p">[</span><span class="n">x</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="k">for</span> <span class="n">x</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">db</span><span class="o">.</span><span class="n">execute</span><span class="p">(</span><span class="s">"select distinct imtype from images"</span><span class="p">)]</span>
+
+
+ <span class="k">def</span> <span class="nf">_loadInputFiles</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">validator</span> <span class="o">=</span> <span class="n">plantcv</span><span class="o">.</span><span class="n">validator</span><span class="o">.</span><span class="n">Statistics</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">statsfile</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">configfile</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">dbfile</span><span class="p">)</span>
+ <span class="k">if</span> <span class="ow">not</span> <span class="bp">self</span><span class="o">.</span><span class="n">validator</span><span class="o">.</span><span class="n">isValid</span><span class="p">()</span> <span class="ow">or</span> <span class="bp">self</span><span class="o">.</span><span class="n">validOnly</span><span class="p">:</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">validator</span><span class="o">.</span><span class="n">printErrors</span><span class="p">()</span>
+ <span class="n">sys</span><span class="o">.</span><span class="n">exit</span><span class="p">()</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">stats</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">validator</span><span class="o">.</span><span class="n">workflow</span><span class="o">.</span><span class="n">data</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">db</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">validator</span><span class="o">.</span><span class="n">db</span><span class="o">.</span><span class="n">conn</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">config</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">validator</span><span class="o">.</span><span class="n">config</span><span class="o">.</span><span class="n">data</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">rawFiles</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">validator</span><span class="o">.</span><span class="n">workflow</span><span class="o">.</span><span class="n">rawFiles</span>
+ <span class="k">return</span>
+
+ <span class="k">def</span> <span class="nf">_copyFiles</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> Copies all input files to the correct location.</span>
+<span class="sd"> """</span>
+ <span class="k">if</span> <span class="ow">not</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">exists</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">basepath</span> <span class="o">+</span> <span class="s">"/input/stats"</span><span class="p">):</span>
+ <span class="n">os</span><span class="o">.</span><span class="n">makedirs</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">basepath</span> <span class="o">+</span> <span class="s">"/input/stats"</span><span class="p">)</span>
+ <span class="n">shutil</span><span class="o">.</span><span class="n">copyfile</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">statsfile</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">basepath</span> <span class="o">+</span> <span class="s">"/input/templates/"</span> <span class="o">+</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">basename</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">statsfile</span><span class="p">))</span>
+ <span class="k">return</span>
+
+ <span class="k">def</span> <span class="nf">_loadFiles</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">loc</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> Loads all files (input and output) into the dax and the self.files variable</span>
+<span class="sd"> """</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">files</span><span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">dax</span><span class="p">]</span> <span class="o">=</span> <span class="p">{}</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">files</span><span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">dax</span><span class="p">][</span><span class="s">"raw"</span><span class="p">]</span> <span class="o">=</span> <span class="p">{</span><span class="s">"input"</span><span class="p">:</span> <span class="p">{},</span> <span class="s">"output"</span><span class="p">:</span> <span class="p">{}}</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_addFile</span><span class="p">(</span><span class="s">"output.db"</span><span class="p">,</span> <span class="s">"raw"</span><span class="p">,</span> <span class="s">"input"</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">basepath</span> <span class="o">+</span> <span class="s">"/output/output.db"</span><span class="p">)</span>
+ <span class="k">for</span> <span class="nb">type</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">stats</span><span class="p">[</span><span class="s">"workflows"</span><span class="p">]:</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">files</span><span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">dax</span><span class="p">][</span><span class="nb">type</span><span class="p">]</span> <span class="o">=</span> <span class="p">{</span><span class="s">"input"</span><span class="p">:</span> <span class="p">{},</span> <span class="s">"output"</span><span class="p">:</span> <span class="p">{}}</span>
+ <span class="k">for</span> <span class="n">f</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">rawFiles</span><span class="p">[</span><span class="nb">type</span><span class="p">]:</span>
+ <span class="n">shutil</span><span class="o">.</span><span class="n">copyfile</span><span class="p">(</span><span class="n">f</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">basepath</span> <span class="o">+</span> <span class="s">"/input/rawfiles/"</span> <span class="o">+</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">basename</span><span class="p">(</span><span class="n">f</span><span class="p">))</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_addFile</span><span class="p">(</span><span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">basename</span><span class="p">(</span><span class="n">f</span><span class="p">),</span> <span class="nb">type</span><span class="p">,</span> <span class="s">"input"</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">basepath</span> <span class="o">+</span> <span class="s">"/input/rawfiles/"</span> <span class="o">+</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">basename</span><span class="p">(</span><span class="n">f</span><span class="p">))</span>
+ <span class="k">return</span>
+
+ <span class="k">def</span> <span class="nf">_loadExecutables</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">os</span><span class="o">=</span><span class="s">"linux"</span><span class="p">,</span> <span class="n">arch</span><span class="o">=</span><span class="s">"x86_64"</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> Loads all executables (as specified in the conf) into</span>
+<span class="sd"> the dax, as well as the internal self.executables variable</span>
+<span class="sd"> """</span>
+ <span class="k">for</span> <span class="n">ex</span> <span class="ow">in</span> <span class="n">conf</span><span class="o">.</span><span class="n">valid</span><span class="p">:</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">executables</span><span class="p">[</span><span class="n">ex</span><span class="p">]</span> <span class="o">=</span> <span class="n">Executable</span><span class="p">(</span><span class="n">name</span><span class="o">=</span><span class="n">ex</span><span class="p">,</span> <span class="n">os</span><span class="o">=</span><span class="n">os</span><span class="p">,</span> <span class="n">arch</span><span class="o">=</span><span class="n">arch</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">executables</span><span class="p">[</span><span class="n">ex</span><span class="p">]</span><span class="o">.</span><span class="n">addPFN</span><span class="p">(</span><span class="n">PFN</span><span class="p">(</span><span class="s">"file://"</span> <span class="o">+</span> <span class="bp">self</span><span class="o">.</span><span class="n">config</span><span class="p">[</span><span class="s">"installdir"</span><span class="p">]</span> <span class="o">+</span> <span class="s">"/"</span> <span class="o">+</span> <span class="n">ex</span><span class="p">,</span> <span class="s">"local"</span><span class="p">))</span>
+ <span class="c">#if "cluster" in self.config:</span>
+ <span class="c"># self.executables[ex].addProfile(Profile(Namespace.PEGASUS, "clusters.size", self.config["cluster"]))</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">dax</span><span class="o">.</span><span class="n">addExecutable</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">executables</span><span class="p">[</span><span class="n">ex</span><span class="p">])</span>
+ <span class="k">return</span>
+
+ <span class="k">def</span> <span class="nf">_loadJobInputs</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">job</span><span class="p">,</span> <span class="nb">type</span><span class="p">):</span>
+ <span class="n">inputs</span> <span class="o">=</span> <span class="p">{</span><span class="s">"output.db"</span><span class="p">:</span> <span class="s">"output.db"</span><span class="p">}</span>
+ <span class="k">for</span> <span class="n">i</span><span class="p">,</span><span class="nb">input</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="n">job</span><span class="p">[</span><span class="s">"inputs"</span><span class="p">]):</span>
+ <span class="n">ftype</span> <span class="o">=</span> <span class="n">conf</span><span class="o">.</span><span class="n">valid</span><span class="p">[</span><span class="n">job</span><span class="p">[</span><span class="s">"executable"</span><span class="p">]][</span><span class="s">"inputs"</span><span class="p">][</span><span class="n">i</span><span class="p">]</span>
+ <span class="k">if</span> <span class="nb">input</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">rawFiles</span><span class="p">[</span><span class="nb">type</span><span class="p">]:</span>
+ <span class="n">inputs</span><span class="p">[</span><span class="nb">input</span><span class="p">]</span> <span class="o">=</span> <span class="nb">input</span>
+ <span class="k">return</span> <span class="n">inputs</span>
+
+ <span class="k">def</span> <span class="nf">_createDax</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">loc</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> Loads all jobs into the dax, and then writes the dax</span>
+<span class="sd"> to input/loc/stats.dax</span>
+<span class="sd"> """</span>
+ <span class="n">serial</span> <span class="o">=</span> <span class="p">[]</span>
+ <span class="k">for</span> <span class="nb">type</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">stats</span><span class="p">[</span><span class="s">"workflows"</span><span class="p">]:</span>
+ <span class="k">for</span> <span class="n">job</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">stats</span><span class="p">[</span><span class="s">"workflows"</span><span class="p">][</span><span class="nb">type</span><span class="p">]:</span>
+ <span class="n">jobname</span> <span class="o">=</span> <span class="nb">type</span> <span class="o">+</span> <span class="s">"_"</span> <span class="o">+</span> <span class="n">job</span><span class="p">[</span><span class="s">"name"</span><span class="p">]</span>
+ <span class="n">job</span><span class="p">[</span><span class="s">"arguments"</span><span class="p">][</span><span class="s">"--intable"</span><span class="p">]</span> <span class="o">=</span> <span class="nb">type</span> <span class="o">+</span> <span class="s">"_"</span> <span class="o">+</span> <span class="n">job</span><span class="p">[</span><span class="s">"arguments"</span><span class="p">][</span><span class="s">"--intable"</span><span class="p">]</span> <span class="k">if</span> <span class="n">job</span><span class="p">[</span><span class="s">"arguments"</span><span class="p">][</span><span class="s">"--intable"</span><span class="p">]</span> <span class="o">!=</span> <span class="s">"images"</span> <span class="k">else</span> <span class="n">job</span><span class="p">[</span><span class="s">"arguments"</span><span class="p">][</span><span class="s">"--intable"</span><span class="p">]</span>
+ <span class="n">job</span><span class="p">[</span><span class="s">"arguments"</span><span class="p">][</span><span class="s">"--outtable"</span><span class="p">]</span> <span class="o">=</span> <span class="nb">type</span> <span class="o">+</span> <span class="s">"_"</span> <span class="o">+</span> <span class="n">job</span><span class="p">[</span><span class="s">"arguments"</span><span class="p">][</span><span class="s">"--outtable"</span><span class="p">]</span>
+ <span class="n">job</span><span class="p">[</span><span class="s">"arguments"</span><span class="p">][</span><span class="s">"--db"</span><span class="p">]</span> <span class="o">=</span> <span class="s">"output.db"</span>
+ <span class="n">inputs</span> <span class="o">=</span> <span class="p">{</span><span class="s">"output.db"</span><span class="p">:</span> <span class="s">"output.db"</span><span class="p">}</span>
+ <span class="n">inputs</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_loadJobInputs</span><span class="p">(</span><span class="n">job</span><span class="p">,</span> <span class="nb">type</span><span class="p">)</span>
+ <span class="n">outputs</span> <span class="o">=</span> <span class="p">{}</span>
+ <span class="n">depends</span> <span class="o">=</span> <span class="p">[</span><span class="nb">type</span> <span class="o">+</span> <span class="s">"_"</span> <span class="o">+</span> <span class="n">depend</span> <span class="k">for</span> <span class="n">depend</span> <span class="ow">in</span> <span class="n">job</span><span class="p">[</span><span class="s">"depends"</span><span class="p">]]</span> <span class="k">if</span> <span class="s">"depends"</span> <span class="ow">in</span> <span class="n">job</span> <span class="k">else</span> <span class="n">serial</span>
+ <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">stats</span><span class="p">[</span><span class="s">"workflows"</span><span class="p">][</span><span class="nb">type</span><span class="p">]</span><span class="o">.</span><span class="n">index</span><span class="p">(</span><span class="n">job</span><span class="p">)</span> <span class="o">==</span> <span class="nb">len</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">stats</span><span class="p">[</span><span class="s">"workflows"</span><span class="p">][</span><span class="nb">type</span><span class="p">])</span> <span class="o">-</span> <span class="mi">1</span><span class="p">:</span>
+ <span class="n">serial</span> <span class="o">=</span> <span class="p">[</span><span class="n">jobname</span><span class="p">]</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="n">serial</span> <span class="o">=</span> <span class="p">[]</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_addJob</span><span class="p">(</span><span class="n">jobname</span><span class="p">,</span> <span class="n">job</span><span class="p">[</span><span class="s">"executable"</span><span class="p">],</span> <span class="n">inputs</span><span class="p">,</span> <span class="n">outputs</span><span class="p">,</span> <span class="n">job</span><span class="p">[</span><span class="s">"arguments"</span><span class="p">],</span> <span class="n">depends</span><span class="p">)</span>
+ <span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">basepath</span> <span class="o">+</span> <span class="s">"/"</span> <span class="o">+</span> <span class="n">loc</span> <span class="o">+</span> <span class="s">"/stats.dax"</span><span class="p">,</span> <span class="s">"w"</span><span class="p">)</span> <span class="k">as</span> <span class="n">wh</span><span class="p">:</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">dax</span><span class="o">.</span><span class="n">writeXML</span><span class="p">(</span><span class="n">wh</span><span class="p">)</span>
+ <span class="k">return</span>
+
+ <span class="k">def</span> <span class="nf">_createReplica</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">loc</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> Creates the pegasus configuration replica catalog. input/conf.rc</span>
+<span class="sd"> """</span>
+ <span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">basepath</span> <span class="o">+</span> <span class="s">"/"</span> <span class="o">+</span> <span class="n">loc</span> <span class="o">+</span> <span class="s">"/conf.rc"</span><span class="p">,</span> <span class="s">"w"</span><span class="p">)</span> <span class="k">as</span> <span class="n">wh</span><span class="p">:</span>
+ <span class="n">pegasusrc</span> <span class="o">=</span> <span class="n">textwrap</span><span class="o">.</span><span class="n">dedent</span><span class="p">(</span><span class="s">"""</span><span class="se">\</span>
+<span class="s"> pegasus.catalog.site = XML</span>
+<span class="s"> pegasus.catalog.site.file = </span><span class="si">%s</span><span class="s">/sites.xml</span>
+<span class="s"> </span>
+<span class="s"> pegasus.condor.logs.symlink = false</span>
+<span class="s"> </span>
+<span class="s"> pegasus.transfer.links = true</span>
+<span class="s"> </span>
+<span class="s"> pegasus.data.configuration = sharedfs</span>
+<span class="s"> </span>
+<span class="s"> """</span> <span class="o">%</span> <span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">basepath</span> <span class="o">+</span> <span class="s">"/"</span> <span class="o">+</span> <span class="n">loc</span><span class="p">))</span>
+ <span class="n">wh</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="n">pegasusrc</span><span class="p">)</span>
+ <span class="k">return</span>
+
+ <span class="k">def</span> <span class="nf">_createSites</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">loc</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> Creates the pegasus site catalog. input/sites.xml</span>
+<span class="sd"> """</span>
+ <span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">basepath</span> <span class="o">+</span> <span class="s">"/"</span> <span class="o">+</span> <span class="n">loc</span> <span class="o">+</span> <span class="s">"/sites.xml"</span><span class="p">,</span> <span class="s">"w"</span><span class="p">)</span> <span class="k">as</span> <span class="n">wh</span><span class="p">:</span>
+ <span class="n">sites</span> <span class="o">=</span> <span class="s">"""</span><span class="se">\</span>
+<span class="s"> <sitecatalog xmlns="http://pegasus.isi.edu/schema/sitecatalog" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://pegasus.isi.edu/schema/sitecatalog http://pegasus.isi.edu/schema/sc-4.0.xsd" version="4.0"></span>
+<span class="s"> </span>
+<span class="s"> <site handle="local" arch="x86_64" os="LINUX"></span>
+<span class="s"> <directory type="shared-scratch" path="</span><span class="si">%s</span><span class="s">"></span>
+<span class="s"> <file-server operation="all" url="file://</span><span class="si">%s</span><span class="s">" /></span>
+<span class="s"> </directory></span>
+<span class="s"> <directory type="local-storage" path="</span><span class="si">%s</span><span class="s">"></span>
+<span class="s"> <file-server operation="all" url="file://</span><span class="si">%s</span><span class="s">" /></span>
+<span class="s"> </directory></span>
+<span class="s"> """</span> <span class="o">%</span> <span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">basepath</span> <span class="o">+</span> <span class="s">"/work/stats/"</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">basepath</span> <span class="o">+</span> <span class="s">"/work/stats/"</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">basepath</span> <span class="o">+</span> <span class="s">"/output/"</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">basepath</span> <span class="o">+</span> <span class="s">"/output/"</span><span class="p">)</span>
+ <span class="k">for</span> <span class="n">namespace</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">config</span><span class="p">[</span><span class="s">"profile"</span><span class="p">]:</span>
+ <span class="k">for</span> <span class="n">key</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">config</span><span class="p">[</span><span class="s">"profile"</span><span class="p">][</span><span class="n">namespace</span><span class="p">]:</span>
+ <span class="n">val</span> <span class="o">=</span> <span class="s">":"</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">config</span><span class="p">[</span><span class="s">"profile"</span><span class="p">][</span><span class="n">namespace</span><span class="p">][</span><span class="n">key</span><span class="p">])</span> <span class="k">if</span> <span class="s">"path"</span> <span class="ow">in</span> <span class="n">key</span><span class="o">.</span><span class="n">lower</span><span class="p">()</span> <span class="k">else</span> <span class="bp">self</span><span class="o">.</span><span class="n">config</span><span class="p">[</span><span class="s">"profile"</span><span class="p">][</span><span class="n">namespace</span><span class="p">][</span><span class="n">key</span><span class="p">]</span>
+ <span class="n">sites</span> <span class="o">+=</span> <span class="s">"""</span><span class="se">\n\t</span><span class="s"><profile namespace="</span><span class="si">%s</span><span class="s">" key="</span><span class="si">%s</span><span class="s">"></span><span class="si">%s</span><span class="s"></profile> """</span> <span class="o">%</span> <span class="p">(</span><span class="n">namespace</span><span class="p">,</span> <span class="n">key</span><span class="p">,</span> <span class="n">val</span><span class="p">)</span>
+ <span class="n">sites</span> <span class="o">+=</span> <span class="s">"</site></sitecatalog>"</span>
+ <span class="n">sites</span> <span class="o">=</span> <span class="n">sites</span><span class="o">.</span><span class="n">replace</span><span class="p">(</span><span class="s">"</span><span class="se">\n</span><span class="s">"</span><span class="p">,</span><span class="s">""</span><span class="p">)</span>
+ <span class="n">wh</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s">"</span><span class="se">\n</span><span class="s">"</span><span class="o">.</span><span class="n">join</span><span class="p">([</span><span class="n">line</span> <span class="k">for</span> <span class="n">line</span> <span class="ow">in</span> <span class="n">xml</span><span class="o">.</span><span class="n">dom</span><span class="o">.</span><span class="n">minidom</span><span class="o">.</span><span class="n">parseString</span><span class="p">(</span><span class="n">sites</span><span class="p">)</span><span class="o">.</span><span class="n">toprettyxml</span><span class="p">()</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s">'</span><span class="se">\n</span><span class="s">'</span><span class="p">)</span> <span class="k">if</span> <span class="n">line</span><span class="o">.</span><span class="n">strip</span><span class="p">()]))</span>
+ <span class="k">return</span>
+
+ <span class="k">def</span> <span class="nf">_createSubmit</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">loc</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> Creates the pegasus submit script. submit.sh</span>
+<span class="sd"> """</span>
+ <span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">basepath</span> <span class="o">+</span> <span class="s">"/"</span> <span class="o">+</span> <span class="n">loc</span> <span class="o">+</span> <span class="s">"/submit.sh"</span><span class="p">,</span> <span class="s">"w"</span><span class="p">)</span> <span class="k">as</span> <span class="n">wh</span><span class="p">:</span>
+ <span class="n">submit</span> <span class="o">=</span> <span class="n">textwrap</span><span class="o">.</span><span class="n">dedent</span><span class="p">(</span><span class="s">"""</span><span class="se">\</span>
+<span class="s"> #!/bin/bash</span>
+<span class="s"> </span>
+<span class="s"> plan=`pegasus-plan </span><span class="se">\\</span><span class="s"></span>
+<span class="s"> --conf "</span><span class="si">%s</span><span class="s">" </span><span class="se">\\</span><span class="s"></span>
+<span class="s"> --sites local </span><span class="se">\\</span><span class="s"></span>
+<span class="s"> --dir "</span><span class="si">%s</span><span class="s">" </span><span class="se">\\</span><span class="s"></span>
+<span class="s"> --output-site local </span><span class="se">\\</span><span class="s"></span>
+<span class="s"> --dax "</span><span class="si">%s</span><span class="s">" </span><span class="se">\\</span><span class="s"></span>
+<span class="s"> --randomdir </span><span class="se">\\</span><span class="s">"""</span> <span class="o">%</span> <span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">basepath</span> <span class="o">+</span> <span class="s">"/"</span> <span class="o">+</span> <span class="n">loc</span> <span class="o">+</span> <span class="s">"/conf.rc"</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">basepath</span> <span class="o">+</span> <span class="s">"/work/stats"</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">basepath</span> <span class="o">+</span> <span class="s">"/"</span> <span class="o">+</span> <span class="n">loc</span> <span class="o">+</span> <span class="s">"/stats.dax"</span><span class="p">))</span>
+ <span class="k">if</span> <span class="s">"cluster"</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">config</span><span class="p">:</span>
+ <span class="n">submit</span> <span class="o">+=</span> <span class="s">"""--cluster horizontal </span><span class="se">\\\n</span><span class="s">"""</span>
+ <span class="n">submit</span> <span class="o">+=</span> <span class="n">textwrap</span><span class="o">.</span><span class="n">dedent</span><span class="p">(</span><span class="s">"""</span><span class="se">\</span>
+<span class="s"> --submit`</span>
+<span class="s"> </span>
+<span class="s"> status=`echo "$plan" | grep pegasus-status | tr -s ' '| cut -d ' ' -f 6`</span>
+<span class="s"> echo -e "#!/bin/bash</span>
+<span class="s"> pegasus-status -l $status" > status.sh</span>
+<span class="s"> chmod 744 status.sh</span>
+<span class="s"> </span>
+<span class="s"> remove=`echo "$plan" | grep pegasus-remove | tr -s ' '| cut -d ' ' -f 5`</span>
+<span class="s"> echo -e "#!/bin/bash</span>
+<span class="s"> pegasus-remove $remove" > remove.sh </span>
+<span class="s"> chmod 744 remove.sh</span>
+<span class="s"> </span>
+<span class="s"> echo "$plan"</span>
+<span class="s"> echo "Alternatively, you can use the status & remove scripts in the current directory!"</span>
+<span class="s"> </span>
+<span class="s"> """</span><span class="p">)</span>
+ <span class="n">wh</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="n">submit</span><span class="p">)</span>
+ <span class="n">os</span><span class="o">.</span><span class="n">chmod</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">basepath</span> <span class="o">+</span> <span class="s">"/"</span> <span class="o">+</span> <span class="n">loc</span> <span class="o">+</span> <span class="s">"/submit.sh"</span><span class="p">,</span> <span class="mo">0755</span><span class="p">)</span>
+ <span class="k">return</span>
+
+<div class="viewcode-block" id="Statistics.create"><a class="viewcode-back" href="../../workflowstats.html#plantcv.workflow.Statistics.create">[docs]</a> <span class="k">def</span> <span class="nf">create</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> Creates a new pegasus submission directory based on the current timestamp,</span>
+<span class="sd"> and populates it with all required information to submit a pegasus job.</span>
+<span class="sd"> """</span>
+ <span class="n">loc</span> <span class="o">=</span> <span class="s">"/input/stats/"</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_createSetup</span><span class="p">()</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_copyFiles</span><span class="p">()</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_loadFiles</span><span class="p">(</span><span class="n">loc</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_loadExecutables</span><span class="p">()</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_createDax</span><span class="p">(</span><span class="n">loc</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_createReplica</span><span class="p">(</span><span class="n">loc</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_createSites</span><span class="p">(</span><span class="n">loc</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_createSubmit</span><span class="p">(</span><span class="n">loc</span><span class="p">)</span>
+ <span class="k">return</span>
+
+
+
+
+ </div></div>
+<div class="viewcode-block" id="ImageProcessor"><a class="viewcode-back" href="../../workflowimage.html#plantcv.workflow.ImageProcessor">[docs]</a><span class="k">class</span> <span class="nc">ImageProcessor</span><span class="p">(</span><span class="n">Workflow</span><span class="p">):</span>
+
+ <span class="sd">"""</span>
+<span class="sd"> A class specifically for image processing workflow</span>
+<span class="sd"> validation and submission.</span>
+<span class="sd"> """</span>
+
+ <span class="k">def</span> <span class="nf">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">jobhome</span><span class="p">,</span> <span class="n">basename</span> <span class="o">=</span> <span class="bp">None</span><span class="p">,</span> <span class="n">validOnly</span> <span class="o">=</span> <span class="bp">False</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> :param jobhome: The base directory for job submission.</span>
+<span class="sd"> :type jobhome: str</span>
+<span class="sd"> </span>
+<span class="sd"> Creates a Workflow class based on the input directory. Loads and validates all input files,</span>
+<span class="sd"> and quits out if something doesn't exist or is defined innapropriately.</span>
+<span class="sd"> """</span>
+ <span class="nb">super</span><span class="p">(</span><span class="n">ImageProcessor</span><span class="p">,</span> <span class="bp">self</span><span class="p">)</span><span class="o">.</span><span class="n">__init__</span><span class="p">(</span><span class="n">jobhome</span><span class="p">,</span> <span class="n">basename</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">validOnly</span> <span class="o">=</span> <span class="n">validOnly</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">workfile</span> <span class="o">=</span> <span class="n">jobhome</span> <span class="o">+</span> <span class="s">"/input/"</span> <span class="o">+</span> <span class="n">conf</span><span class="o">.</span><span class="n">workflowFile</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">metafile</span> <span class="o">=</span> <span class="n">jobhome</span> <span class="o">+</span> <span class="s">"/input/"</span> <span class="o">+</span> <span class="n">conf</span><span class="o">.</span><span class="n">dbFile</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">configfile</span> <span class="o">=</span> <span class="n">jobhome</span> <span class="o">+</span> <span class="s">"/input/"</span> <span class="o">+</span> <span class="n">conf</span><span class="o">.</span><span class="n">configFile</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_loadInputFiles</span><span class="p">()</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">exdax</span> <span class="o">=</span> <span class="n">ADAG</span><span class="p">(</span><span class="s">"extract-"</span> <span class="o">+</span> <span class="bp">self</span><span class="o">.</span><span class="n">jobname</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">jobs</span><span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">exdax</span><span class="p">]</span> <span class="o">=</span> <span class="p">{}</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">files</span><span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">exdax</span><span class="p">]</span> <span class="o">=</span> <span class="p">{}</span>
+ <span class="k">return</span>
+
+ <span class="k">def</span> <span class="nf">_loadInputFiles</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> Loads the input files into the appropriate variables</span>
+<span class="sd"> """</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">validator</span> <span class="o">=</span> <span class="n">plantcv</span><span class="o">.</span><span class="n">validator</span><span class="o">.</span><span class="n">ImageProcessor</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">workfile</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">configfile</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">metafile</span><span class="p">)</span>
+ <span class="k">if</span> <span class="ow">not</span> <span class="bp">self</span><span class="o">.</span><span class="n">validator</span><span class="o">.</span><span class="n">isValid</span><span class="p">()</span> <span class="ow">or</span> <span class="bp">self</span><span class="o">.</span><span class="n">validOnly</span><span class="p">:</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">validator</span><span class="o">.</span><span class="n">printErrors</span><span class="p">()</span>
+ <span class="n">sys</span><span class="o">.</span><span class="n">exit</span><span class="p">()</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">workflow</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">validator</span><span class="o">.</span><span class="n">workflow</span><span class="o">.</span><span class="n">data</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">metadata</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">validator</span><span class="o">.</span><span class="n">db</span><span class="o">.</span><span class="n">conn</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">config</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">validator</span><span class="o">.</span><span class="n">config</span><span class="o">.</span><span class="n">data</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">rawFiles</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">validator</span><span class="o">.</span><span class="n">workflow</span><span class="o">.</span><span class="n">rawFiles</span>
+ <span class="k">return</span>
+
+ <span class="k">def</span> <span class="nf">_getImageTypes</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> Convenience function to get all image types from the database.</span>
+<span class="sd"> """</span>
+ <span class="k">return</span> <span class="p">[</span><span class="n">x</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="k">for</span> <span class="n">x</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">metadata</span><span class="o">.</span><span class="n">execute</span><span class="p">(</span><span class="s">"select distinct imtype from images"</span><span class="p">)]</span>
+
+ <span class="k">def</span> <span class="nf">_copyFiles</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> Copies all input files to the correct location.</span>
+<span class="sd"> """</span>
+ <span class="k">if</span> <span class="ow">not</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">exists</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">basepath</span> <span class="o">+</span> <span class="s">"/input/imgproc"</span><span class="p">):</span>
+ <span class="n">os</span><span class="o">.</span><span class="n">makedirs</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">basepath</span> <span class="o">+</span> <span class="s">"/input/imgproc"</span><span class="p">)</span>
+ <span class="n">shutil</span><span class="o">.</span><span class="n">copyfile</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">workfile</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">basepath</span> <span class="o">+</span> <span class="s">"/input/templates/"</span> <span class="o">+</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">basename</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">workfile</span><span class="p">))</span>
+ <span class="n">shutil</span><span class="o">.</span><span class="n">copyfile</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">configfile</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">basepath</span> <span class="o">+</span> <span class="s">"/input/templates/"</span> <span class="o">+</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">basename</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">configfile</span><span class="p">))</span>
+ <span class="n">shutil</span><span class="o">.</span><span class="n">copyfile</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">metafile</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">basepath</span> <span class="o">+</span> <span class="s">"/output/output.db"</span><span class="p">)</span>
+ <span class="k">for</span> <span class="nb">type</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">rawFiles</span><span class="p">:</span>
+ <span class="k">for</span> <span class="nb">input</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">rawFiles</span><span class="p">[</span><span class="nb">type</span><span class="p">]:</span>
+ <span class="n">shutil</span><span class="o">.</span><span class="n">copyfile</span><span class="p">(</span><span class="nb">input</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">basepath</span> <span class="o">+</span> <span class="s">"/input/rawfiles/"</span> <span class="o">+</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">basename</span><span class="p">(</span><span class="nb">input</span><span class="p">))</span>
+ <span class="k">return</span>
+
+ <span class="k">def</span> <span class="nf">_loadFiles</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">loc</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> Loads all files (input and output) into the dax and the self.files variable</span>
+<span class="sd"> """</span>
+ <span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">basepath</span> <span class="o">+</span> <span class="s">"/input/rawfiles/extract.json"</span><span class="p">,</span> <span class="s">"w"</span><span class="p">)</span> <span class="k">as</span> <span class="n">wh</span><span class="p">:</span>
+ <span class="n">json</span><span class="o">.</span><span class="n">dump</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">workflow</span><span class="p">[</span><span class="s">"extract"</span><span class="p">],</span> <span class="n">wh</span><span class="p">)</span>
+ <span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">basepath</span> <span class="o">+</span> <span class="s">"/"</span> <span class="o">+</span> <span class="n">loc</span> <span class="o">+</span> <span class="s">"/map.rc"</span><span class="p">,</span> <span class="s">"w"</span><span class="p">)</span> <span class="k">as</span> <span class="n">wh</span><span class="p">:</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">exInput</span> <span class="o">=</span> <span class="p">{</span><span class="s">"db"</span><span class="p">:</span> <span class="s">"img.db"</span><span class="p">,</span> <span class="s">"extract.json"</span><span class="p">:</span> <span class="s">"extract.json"</span><span class="p">}</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">files</span><span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">dax</span><span class="p">]</span> <span class="o">=</span> <span class="p">{}</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">files</span><span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">exdax</span><span class="p">]</span> <span class="o">=</span> <span class="p">{}</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">files</span><span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">exdax</span><span class="p">][</span><span class="s">"all"</span><span class="p">]</span> <span class="o">=</span> <span class="p">{</span><span class="s">"input"</span><span class="p">:</span> <span class="p">{},</span> <span class="s">"output"</span><span class="p">:</span> <span class="p">{}}</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">files</span><span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">dax</span><span class="p">][</span><span class="s">"raw"</span><span class="p">]</span> <span class="o">=</span> <span class="p">{</span><span class="s">"input"</span><span class="p">:</span> <span class="p">{},</span> <span class="s">"output"</span><span class="p">:</span> <span class="p">{}}</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_addFile</span><span class="p">(</span><span class="s">"img.db"</span><span class="p">,</span> <span class="s">"raw"</span><span class="p">,</span> <span class="s">"input"</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">basepath</span> <span class="o">+</span> <span class="s">"/output/output.db"</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_addFile</span><span class="p">(</span><span class="s">"img.db"</span><span class="p">,</span> <span class="s">"all"</span><span class="p">,</span> <span class="s">"input"</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">basepath</span> <span class="o">+</span> <span class="s">"/output/output.db"</span><span class="p">,</span> <span class="n">dax</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">exdax</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_addFile</span><span class="p">(</span><span class="s">"img.log"</span><span class="p">,</span> <span class="s">"raw"</span><span class="p">,</span> <span class="s">"output"</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">basepath</span> <span class="o">+</span> <span class="s">"/output/imgproc.log"</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_addFile</span><span class="p">(</span><span class="s">"extract.json"</span><span class="p">,</span> <span class="s">"raw"</span><span class="p">,</span> <span class="s">"input"</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">basepath</span> <span class="o">+</span> <span class="s">"/input/rawfiles/extract.json"</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_addFile</span><span class="p">(</span><span class="s">"extract.json"</span><span class="p">,</span> <span class="s">"all"</span><span class="p">,</span> <span class="s">"input"</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">basepath</span> <span class="o">+</span> <span class="s">"/input/rawfiles/extract.json"</span><span class="p">,</span> <span class="n">dax</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">exdax</span><span class="p">)</span>
+ <span class="k">for</span> <span class="nb">type</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">workflow</span><span class="p">[</span><span class="s">"workflows"</span><span class="p">]:</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">files</span><span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">dax</span><span class="p">][</span><span class="nb">type</span><span class="p">]</span> <span class="o">=</span> <span class="p">{</span><span class="s">"input"</span><span class="p">:</span> <span class="p">{},</span> <span class="s">"output"</span><span class="p">:</span> <span class="p">{}}</span>
+ <span class="k">for</span> <span class="nb">input</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">rawFiles</span><span class="p">[</span><span class="nb">type</span><span class="p">]:</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_addFile</span><span class="p">(</span><span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">basename</span><span class="p">(</span><span class="nb">input</span><span class="p">),</span> <span class="nb">type</span><span class="p">,</span> <span class="s">"input"</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">basepath</span> <span class="o">+</span> <span class="s">"/input/rawfiles/"</span> <span class="o">+</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">basename</span><span class="p">(</span><span class="nb">input</span><span class="p">))</span>
+ <span class="n">wh</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s">"img.log file://"</span> <span class="o">+</span> <span class="bp">self</span><span class="o">.</span><span class="n">basepath</span> <span class="o">+</span> <span class="s">"/output/imgproc.log pool=</span><span class="se">\"</span><span class="s">local</span><span class="se">\"\n</span><span class="s">"</span><span class="p">)</span>
+ <span class="n">inputImages</span> <span class="o">=</span> <span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">workflow</span><span class="p">[</span><span class="s">"workflows"</span><span class="p">][</span><span class="nb">type</span><span class="p">][</span><span class="mi">0</span><span class="p">][</span><span class="s">"inputs"</span><span class="p">][</span><span class="n">i</span><span class="p">]</span> <span class="k">for</span> <span class="n">i</span><span class="p">,</span><span class="n">x</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="n">conf</span><span class="o">.</span><span class="n">valid</span><span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">workflow</span><span class="p">[</span><span class="s">"workflows"</span><span class="p">][</span><span class="nb">type</span><span class="p">][</span><span class="mi">0</span><span class="p">][</span><span class="s">"executable"</span><span class="p">]][</span><span class="s">"inputs"</span><span class="p">])</span> <span class="k">if</span> <span class="n">x</span> <span class="o">==</span> <span class="s">"image"</span><span class="p">]</span>
+ <span class="n">outputImages</span> <span class="o">=</span> <span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">workflow</span><span class="p">[</span><span class="s">"workflows"</span><span class="p">][</span><span class="nb">type</span><span class="p">][</span><span class="n">z</span><span class="p">][</span><span class="s">"outputs"</span><span class="p">][</span><span class="n">i</span><span class="p">]</span> <span class="k">for</span> <span class="n">z</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="mi">0</span><span class="p">,</span> <span class="nb">len</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">workflow</span><span class="p">[</span><span class="s">"workflows"</span><span class="p">][</span><span class="nb">type</span><span class="p">]))</span> <span class="k">for</span> <span class="n">i</span><span class="p">,</span><span class="n">x</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="n">conf</span><span class="o">.</span><span class="n">valid</span><span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">workflow</span><span class="p">[</span><span class="s">"workflows"</span><span class="p">][</span><span class="nb">type</span><span class="p">][</span><span class="n">z</span><span class="p">][</span><span class="s">"executable"</span><span class="p">]][</span><span class="s">"outputs"</span><span class="p">])</span> <span class="k">if</span> <span class="n">x</span> <span class="o">==</span> <span class="s">"image"</span><span class="p">]</span>
+ <span class="n">outputFiles</span> <span class="o">=</span> <span class="nb">dict</span><span class="p">((</span><span class="bp">self</span><span class="o">.</span><span class="n">workflow</span><span class="p">[</span><span class="s">"workflows"</span><span class="p">][</span><span class="nb">type</span><span class="p">][</span><span class="n">z</span><span class="p">][</span><span class="s">"outputs"</span><span class="p">][</span><span class="n">i</span><span class="p">],</span> <span class="n">conf</span><span class="o">.</span><span class="n">fileExtensions</span><span class="p">[</span><span class="n">conf</span><span class="o">.</span><span class="n">valid</span><span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">workflow</span><span class="p">[</span><span class="s">"workflows"</span><span class="p">][</span><span class="nb">type</span><span class="p">][</span><span class="n">z</span><span class="p">][</span><span class="s">"executable"</span><span class="p">]][</span><span class="s">"outputs"</span><span class="p">][</span><span class="n">i</span><span class="p">]])</span> <span class="k">for</span> <span class="n">z</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="mi">0</span><span class="p">,</span> <span class="nb">len</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">workflow</span><span class="p">[</span><span class="s">"workflows"</span><span class="p">][</span><span class="nb">type</span><span class="p">]))</span> <span class="k">for</span> <span class="n">i</span><span class="p">,</span><span class="n">x</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="n">conf</span><span class="o">.</span><span class="n">valid</span><span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">workflow</span><span class="p">[</span><span class="s">"workflows"</span><span class="p">][</span><span class="nb">type</span><span class="p">][</span><span class="n">z</span><span class="p">][</span><span class="s">"executable"</span><span class="p">]][</span><span class="s">"outputs"</span><span class="p">])</span> <span class="k">if</span> <span class="n">x</span> <span class="o">!=</span> <span class="s">"image"</span> <span class="ow">and</span> <span class="n">x</span> <span class="o">!=</span> <span class="s">"none"</span> <span class="ow">and</span> <span class="nb">len</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">workflow</span><span class="p">[</span><span class="s">"workflows"</span><span class="p">][</span><span class="nb">type</span><span class="p">][</span><span class="n">z</span><span class="p">][</span><span class="s">"outputs"</span><span class="p">])</span> <span class="o">></span> <span class="n">i</span><span class="p">)</span>
+ <span class="k">for</span> <span class="n">row</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">metadata</span><span class="o">.</span><span class="n">execute</span><span class="p">(</span><span class="s">"select pegasusid, experiment, id, date, imgname, path from images where imtype=?"</span><span class="p">,</span> <span class="p">(</span><span class="nb">type</span><span class="p">,)):</span>
+ <span class="n">realname</span> <span class="o">=</span> <span class="n">row</span><span class="p">[</span><span class="s">"path"</span><span class="p">]</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s">"/"</span><span class="p">)[</span><span class="o">-</span><span class="mi">1</span><span class="p">]</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s">"."</span><span class="p">)[</span><span class="mi">0</span><span class="p">]</span>
+ <span class="c">#derivedPath = row["experiment"].replace(" ","%20") + "/" + row["id"].replace(" ","%20") + "/" + row["date"].replace(" ","%20") + "/" + type + "/" + row["imgname"].replace(" ","%20") + "/"</span>
+ <span class="n">derivedPath</span> <span class="o">=</span> <span class="n">row</span><span class="p">[</span><span class="s">"experiment"</span><span class="p">]</span><span class="o">.</span><span class="n">replace</span><span class="p">(</span><span class="s">" "</span><span class="p">,</span><span class="s">""</span><span class="p">)</span> <span class="o">+</span> <span class="s">"/"</span> <span class="o">+</span> <span class="n">row</span><span class="p">[</span><span class="s">"id"</span><span class="p">]</span><span class="o">.</span><span class="n">replace</span><span class="p">(</span><span class="s">" "</span><span class="p">,</span><span class="s">""</span><span class="p">)</span> <span class="o">+</span> <span class="s">"/"</span> <span class="o">+</span> <span class="n">row</span><span class="p">[</span><span class="s">"date"</span><span class="p">]</span><span class="o">.</span><span class="n">replace</span><span class="p">(</span><span class="s">" "</span><span class="p">,</span><span class="s">""</span><span class="p">)</span> <span class="o">+</span> <span class="s">"/"</span> <span class="o">+</span> <span class="nb">type</span> <span class="o">+</span> <span class="s">"/"</span> <span class="o">+</span> <span class="n">row</span><span class="p">[</span><span class="s">"imgname"</span><span class="p">]</span><span class="o">.</span><span class="n">replace</span><span class="p">(</span><span class="s">" "</span><span class="p">,</span><span class="s">""</span><span class="p">)</span> <span class="o">+</span> <span class="s">"/"</span>
+ <span class="k">for</span> <span class="nb">input</span> <span class="ow">in</span> <span class="n">inputImages</span><span class="p">:</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_addFile</span><span class="p">(</span><span class="n">derivedPath</span> <span class="o">+</span> <span class="n">row</span><span class="p">[</span><span class="s">"pegasusid"</span><span class="p">]</span> <span class="o">+</span> <span class="s">"_"</span> <span class="o">+</span> <span class="nb">input</span> <span class="o">+</span> <span class="s">"."</span> <span class="o">+</span> <span class="n">row</span><span class="p">[</span><span class="s">"path"</span><span class="p">]</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s">"."</span><span class="p">)[</span><span class="mi">1</span><span class="p">],</span> <span class="nb">type</span><span class="p">,</span> <span class="s">"input"</span><span class="p">,</span> <span class="n">row</span><span class="p">[</span><span class="s">"path"</span><span class="p">])</span>
+ <span class="k">for</span> <span class="n">output</span> <span class="ow">in</span> <span class="n">outputImages</span><span class="p">:</span>
+ <span class="k">if</span> <span class="n">output</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">workflow</span><span class="p">[</span><span class="s">"extract"</span><span class="p">][</span><span class="s">"workflows"</span><span class="p">][</span><span class="nb">type</span><span class="p">][</span><span class="s">"inputs"</span><span class="p">]:</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">exInput</span><span class="p">[</span><span class="n">derivedPath</span> <span class="o">+</span> <span class="n">row</span><span class="p">[</span><span class="s">"pegasusid"</span><span class="p">]</span> <span class="o">+</span> <span class="s">"_"</span> <span class="o">+</span> <span class="n">output</span> <span class="o">+</span> <span class="s">".png"</span><span class="p">]</span> <span class="o">=</span> <span class="n">derivedPath</span> <span class="o">+</span> <span class="n">row</span><span class="p">[</span><span class="s">"pegasusid"</span><span class="p">]</span> <span class="o">+</span> <span class="s">"_"</span> <span class="o">+</span> <span class="n">output</span> <span class="o">+</span> <span class="s">".png"</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_addFile</span><span class="p">(</span><span class="n">derivedPath</span> <span class="o">+</span> <span class="n">row</span><span class="p">[</span><span class="s">"pegasusid"</span><span class="p">]</span> <span class="o">+</span> <span class="s">"_"</span> <span class="o">+</span> <span class="n">output</span> <span class="o">+</span> <span class="s">".png"</span><span class="p">,</span> <span class="s">"all"</span><span class="p">,</span> <span class="s">"input"</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">basepath</span> <span class="o">+</span> <span class="s">"/output/"</span> <span class="o">+</span> <span class="n">derivedPath</span> <span class="o">+</span> <span class="n">row</span><span class="p">[</span><span class="s">"pegasusid"</span><span class="p">]</span> <span class="o">+</span> <span class="s">"_"</span> <span class="o">+</span> <span class="n">output</span> <span class="o">+</span> <span class="s">".png"</span><span class="p">,</span> <span class="n">dax</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">exdax</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_addFile</span><span class="p">(</span><span class="n">derivedPath</span> <span class="o">+</span> <span class="n">row</span><span class="p">[</span><span class="s">"pegasusid"</span><span class="p">]</span> <span class="o">+</span> <span class="s">"_"</span> <span class="o">+</span> <span class="n">output</span> <span class="o">+</span> <span class="s">".png"</span><span class="p">,</span> <span class="nb">type</span><span class="p">,</span> <span class="s">"output"</span><span class="p">)</span>
+ <span class="n">wh</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="n">derivedPath</span> <span class="o">+</span> <span class="n">row</span><span class="p">[</span><span class="s">"pegasusid"</span><span class="p">]</span> <span class="o">+</span> <span class="s">"_"</span> <span class="o">+</span> <span class="n">output</span> <span class="o">+</span> <span class="s">".png file://"</span> <span class="o">+</span> <span class="bp">self</span><span class="o">.</span><span class="n">basepath</span> <span class="o">+</span> <span class="s">"/output/"</span> <span class="o">+</span> <span class="n">derivedPath</span> <span class="o">+</span> <span class="n">row</span><span class="p">[</span><span class="s">"pegasusid"</span><span class="p">]</span><span class="o">.</span><span class="n">replace</span><span class="p">(</span><span class="s">" "</span><span class="p">,</span><span class="s">"%20"</span><span class="p">)</span> <span class="o">+</span> <span class="s">"_"</span> <span class="o">+</span> <span class="n">output</span> <span class="o">+</span> <span class="s">".png pool=</span><span class="se">\"</span><span class="s">local</span><span class="se">\"\n</span><span class="s">"</span><span class="p">)</span>
+ <span class="k">for</span> <span class="n">output</span> <span class="ow">in</span> <span class="n">outputFiles</span><span class="p">:</span>
+ <span class="n">outname</span> <span class="o">=</span> <span class="n">output</span> <span class="o">+</span> <span class="n">outputFiles</span><span class="p">[</span><span class="n">output</span><span class="p">]</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_addFile</span><span class="p">(</span><span class="n">derivedPath</span> <span class="o">+</span> <span class="n">row</span><span class="p">[</span><span class="s">"pegasusid"</span><span class="p">]</span> <span class="o">+</span> <span class="s">"_"</span> <span class="o">+</span> <span class="n">outname</span><span class="p">,</span> <span class="nb">type</span><span class="p">,</span> <span class="s">"output"</span><span class="p">)</span>
+ <span class="n">wh</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="n">derivedPath</span> <span class="o">+</span> <span class="n">row</span><span class="p">[</span><span class="s">"pegasusid"</span><span class="p">]</span> <span class="o">+</span> <span class="s">"_"</span> <span class="o">+</span> <span class="n">outname</span> <span class="o">+</span> <span class="s">" file://"</span> <span class="o">+</span> <span class="bp">self</span><span class="o">.</span><span class="n">basepath</span> <span class="o">+</span> <span class="s">"/output/"</span> <span class="o">+</span> <span class="n">derivedPath</span><span class="o">.</span><span class="n">replace</span><span class="p">(</span><span class="s">"_"</span><span class="p">,</span><span class="s">"%20"</span><span class="p">)</span> <span class="o">+</span> <span class="n">outname</span> <span class="o">+</span> <span class="s">" pool=</span><span class="se">\"</span><span class="s">local</span><span class="se">\"\n</span><span class="s">"</span><span class="p">)</span>
+ <span class="k">return</span>
+
+ <span class="k">def</span> <span class="nf">_loadNotify</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+ <span class="k">if</span> <span class="s">"email"</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">config</span><span class="p">:</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">dax</span><span class="o">.</span><span class="n">invoke</span><span class="p">(</span><span class="s">"at_end"</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">basepath</span> <span class="o">+</span> <span class="s">"/input/imgproc/notify.sh"</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">exdax</span><span class="o">.</span><span class="n">invoke</span><span class="p">(</span><span class="s">"at_end"</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">basepath</span> <span class="o">+</span> <span class="s">"/input/imgproc/notify.sh"</span><span class="p">)</span>
+ <span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">basepath</span> <span class="o">+</span> <span class="s">"/input/imgproc/notify.sh"</span><span class="p">,</span> <span class="s">"w"</span><span class="p">)</span> <span class="k">as</span> <span class="n">wh</span><span class="p">:</span>
+ <span class="n">notify</span> <span class="o">=</span> <span class="n">textwrap</span><span class="o">.</span><span class="n">dedent</span><span class="p">(</span><span class="s">"""</span><span class="se">\</span>
+<span class="s"> #!/bin/bash</span>
+<span class="s"> $PEGASUS_HOME/notification/email -t </span><span class="si">%s</span><span class="s"></span>
+<span class="s"> """</span> <span class="o">%</span> <span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">config</span><span class="p">[</span><span class="s">"email"</span><span class="p">],))</span>
+ <span class="n">wh</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="n">notify</span><span class="p">)</span>
+ <span class="n">os</span><span class="o">.</span><span class="n">chmod</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">basepath</span> <span class="o">+</span> <span class="s">"/input/imgproc/notify.sh"</span><span class="p">,</span> <span class="mo">0755</span><span class="p">)</span>
+ <span class="k">return</span>
+
+ <span class="k">def</span> <span class="nf">_loadExecutables</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">os</span><span class="o">=</span><span class="s">"linux"</span><span class="p">,</span> <span class="n">arch</span><span class="o">=</span><span class="s">"x86_64"</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> Loads all executables (as specified in the conf) into</span>
+<span class="sd"> the dax, as well as the internal self.executables variable</span>
+<span class="sd"> """</span>
+ <span class="k">for</span> <span class="n">ex</span> <span class="ow">in</span> <span class="n">conf</span><span class="o">.</span><span class="n">valid</span><span class="p">:</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">executables</span><span class="p">[</span><span class="n">ex</span><span class="p">]</span> <span class="o">=</span> <span class="n">Executable</span><span class="p">(</span><span class="n">name</span><span class="o">=</span><span class="n">ex</span><span class="p">,</span> <span class="n">os</span><span class="o">=</span><span class="n">os</span><span class="p">,</span> <span class="n">arch</span><span class="o">=</span><span class="n">arch</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">executables</span><span class="p">[</span><span class="n">ex</span><span class="p">]</span><span class="o">.</span><span class="n">addPFN</span><span class="p">(</span><span class="n">PFN</span><span class="p">(</span><span class="s">"file://"</span> <span class="o">+</span> <span class="bp">self</span><span class="o">.</span><span class="n">config</span><span class="p">[</span><span class="s">"installdir"</span><span class="p">]</span> <span class="o">+</span> <span class="s">"/"</span> <span class="o">+</span> <span class="n">ex</span><span class="p">,</span> <span class="s">"local"</span><span class="p">))</span>
+ <span class="c">#if "cluster" in self.config:</span>
+ <span class="c"># val = int(self.config["cluster"] * conf.valid[ex]["weight"]) if "weight" in conf.valid[ex] else self.config["cluster"]</span>
+ <span class="c"># self.executables[ex].addProfile(Profile(Namespace.PEGASUS, "clusters.size", val))</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">dax</span><span class="o">.</span><span class="n">addExecutable</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">executables</span><span class="p">[</span><span class="n">ex</span><span class="p">])</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">exdax</span><span class="o">.</span><span class="n">addExecutable</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">executables</span><span class="p">[</span><span class="n">ex</span><span class="p">])</span>
+ <span class="k">return</span>
+
+ <span class="k">def</span> <span class="nf">_loadJobInputs</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">job</span><span class="p">,</span> <span class="nb">type</span><span class="p">,</span> <span class="n">basename</span><span class="p">,</span> <span class="n">extension</span><span class="p">,</span> <span class="n">save</span> <span class="o">=</span> <span class="bp">False</span><span class="p">):</span>
+ <span class="n">inputs</span> <span class="o">=</span> <span class="p">{}</span>
+ <span class="k">for</span> <span class="n">i</span><span class="p">,</span><span class="nb">input</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="n">job</span><span class="p">[</span><span class="s">"inputs"</span><span class="p">]):</span>
+ <span class="n">ftype</span> <span class="o">=</span> <span class="n">conf</span><span class="o">.</span><span class="n">valid</span><span class="p">[</span><span class="n">job</span><span class="p">[</span><span class="s">"executable"</span><span class="p">]][</span><span class="s">"inputs"</span><span class="p">][</span><span class="n">i</span><span class="p">]</span>
+ <span class="k">if</span> <span class="nb">input</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">rawFiles</span><span class="p">[</span><span class="nb">type</span><span class="p">]:</span>
+ <span class="n">inputs</span><span class="p">[</span><span class="nb">input</span><span class="p">]</span> <span class="o">=</span> <span class="p">{</span><span class="s">"file"</span><span class="p">:</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">basename</span><span class="p">(</span><span class="nb">input</span><span class="p">),</span> <span class="s">"transfer"</span><span class="p">:</span> <span class="n">save</span><span class="p">}</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="n">ex</span> <span class="o">=</span> <span class="n">extension</span> <span class="k">if</span> <span class="n">job</span><span class="p">[</span><span class="s">"name"</span><span class="p">]</span> <span class="o">==</span> <span class="bp">self</span><span class="o">.</span><span class="n">workflow</span><span class="p">[</span><span class="s">"workflows"</span><span class="p">][</span><span class="nb">type</span><span class="p">][</span><span class="mi">0</span><span class="p">][</span><span class="s">"name"</span><span class="p">]</span> <span class="k">else</span> <span class="n">conf</span><span class="o">.</span><span class="n">fileExtensions</span><span class="p">[</span><span class="n">ftype</span><span class="p">]</span>
+ <span class="n">inputs</span><span class="p">[</span><span class="nb">input</span><span class="p">]</span> <span class="o">=</span> <span class="p">{</span><span class="s">"file"</span><span class="p">:</span> <span class="n">basename</span> <span class="o">+</span> <span class="s">"_"</span> <span class="o">+</span> <span class="nb">input</span> <span class="o">+</span> <span class="n">ex</span><span class="p">,</span> <span class="s">"transfer"</span><span class="p">:</span> <span class="n">save</span><span class="p">}</span>
+ <span class="k">return</span> <span class="n">inputs</span>
+
+ <span class="k">def</span> <span class="nf">_loadJobOutputs</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">job</span><span class="p">,</span> <span class="nb">type</span><span class="p">,</span> <span class="n">basename</span><span class="p">,</span> <span class="n">save</span><span class="p">):</span>
+ <span class="n">outputs</span> <span class="o">=</span> <span class="p">{}</span>
+ <span class="k">for</span> <span class="n">i</span><span class="p">,</span><span class="n">output</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="n">job</span><span class="p">[</span><span class="s">"outputs"</span><span class="p">]):</span>
+ <span class="k">if</span> <span class="n">output</span> <span class="o">!=</span> <span class="s">"none"</span><span class="p">:</span>
+ <span class="n">outputs</span><span class="p">[</span><span class="n">output</span><span class="p">]</span> <span class="o">=</span> <span class="p">{</span><span class="s">"file"</span><span class="p">:</span> <span class="n">basename</span> <span class="o">+</span> <span class="s">"_"</span> <span class="o">+</span> <span class="n">output</span> <span class="o">+</span> <span class="n">conf</span><span class="o">.</span><span class="n">fileExtensions</span><span class="p">[</span><span class="n">conf</span><span class="o">.</span><span class="n">valid</span><span class="p">[</span><span class="n">job</span><span class="p">[</span><span class="s">"executable"</span><span class="p">]][</span><span class="s">"outputs"</span><span class="p">][</span><span class="n">i</span><span class="p">]],</span> <span class="s">"transfer"</span><span class="p">:</span> <span class="n">save</span><span class="p">}</span>
+ <span class="k">return</span> <span class="n">outputs</span>
+
+ <span class="c">#def _loadJobOutputs(self, job, type, basename):</span>
+ <span class="c"># return dict((output, basename + "_" + output + conf.fileExtensions[conf.valid[job["executable"]]["outputs"][i]]) for i,output in enumerate(job["outputs"]) if output != "none")</span>
+
+ <span class="k">def</span> <span class="nf">_createDax</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">loc</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> Loads all jobs into the dax, and then writes the dax</span>
+<span class="sd"> to input/workflow.dax</span>
+<span class="sd"> """</span>
+ <span class="n">exDep</span> <span class="o">=</span> <span class="p">{}</span>
+ <span class="n">exInput</span> <span class="o">=</span> <span class="p">{}</span>
+ <span class="n">clusternum</span> <span class="o">=</span> <span class="p">{}</span>
+ <span class="n">meancluster</span> <span class="o">=</span> <span class="p">{}</span>
+
+ <span class="n">save</span> <span class="o">=</span> <span class="bp">True</span> <span class="k">if</span> <span class="s">"save-steps"</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">workflow</span><span class="p">[</span><span class="s">"options"</span><span class="p">]</span> <span class="k">else</span> <span class="bp">False</span>
+ <span class="k">for</span> <span class="nb">type</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">workflow</span><span class="p">[</span><span class="s">"workflows"</span><span class="p">]:</span>
+ <span class="n">exDep</span><span class="p">[</span><span class="nb">type</span><span class="p">]</span> <span class="o">=</span> <span class="p">[[]]</span>
+ <span class="n">exInput</span><span class="p">[</span><span class="nb">type</span><span class="p">]</span> <span class="o">=</span> <span class="p">[{}]</span>
+ <span class="n">jobnum</span> <span class="o">=</span> <span class="o">-</span><span class="mi">1</span>
+ <span class="n">clusternum</span><span class="p">[</span><span class="nb">type</span><span class="p">]</span> <span class="o">=</span> <span class="mi">0</span>
+ <span class="n">meancluster</span><span class="p">[</span><span class="nb">type</span><span class="p">]</span> <span class="o">=</span> <span class="mi">0</span>
+ <span class="n">exNames</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">workflow</span><span class="p">[</span><span class="s">"extract"</span><span class="p">][</span><span class="s">"workflows"</span><span class="p">][</span><span class="nb">type</span><span class="p">][</span><span class="s">"depends"</span><span class="p">]</span>
+ <span class="k">for</span> <span class="n">infile</span> <span class="ow">in</span> <span class="p">[</span><span class="n">x</span> <span class="k">for</span> <span class="n">x</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">files</span><span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">dax</span><span class="p">][</span><span class="nb">type</span><span class="p">][</span><span class="s">"input"</span><span class="p">]</span> <span class="k">if</span> <span class="s">"."</span> <span class="o">+</span> <span class="n">x</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s">"."</span><span class="p">)[</span><span class="mi">1</span><span class="p">]</span> <span class="ow">in</span> <span class="n">conf</span><span class="o">.</span><span class="n">imageExtensions</span><span class="p">]:</span>
+ <span class="k">if</span> <span class="s">"cluster"</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">config</span><span class="p">:</span>
+ <span class="n">jobnum</span> <span class="o">+=</span> <span class="mi">1</span>
+ <span class="k">if</span> <span class="n">jobnum</span> <span class="o">==</span> <span class="bp">self</span><span class="o">.</span><span class="n">config</span><span class="p">[</span><span class="s">"cluster"</span><span class="p">]:</span>
+ <span class="n">jobnum</span> <span class="o">=</span> <span class="mi">0</span>
+ <span class="n">clusternum</span><span class="p">[</span><span class="nb">type</span><span class="p">]</span> <span class="o">+=</span> <span class="mi">1</span>
+ <span class="n">exDep</span><span class="p">[</span><span class="nb">type</span><span class="p">]</span><span class="o">.</span><span class="n">append</span><span class="p">([])</span>
+ <span class="n">exInput</span><span class="p">[</span><span class="nb">type</span><span class="p">]</span><span class="o">.</span><span class="n">append</span><span class="p">({})</span>
+ <span class="k">elif</span> <span class="p">((</span><span class="n">clusternum</span><span class="p">[</span><span class="nb">type</span><span class="p">]</span> <span class="o">*</span> <span class="mi">100</span> <span class="o">+</span> <span class="n">jobnum</span><span class="p">)</span> <span class="o">%</span> <span class="nb">int</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">config</span><span class="p">[</span><span class="s">"cluster"</span><span class="p">]</span> <span class="o">*</span> <span class="mf">0.3</span><span class="p">))</span> <span class="o">==</span> <span class="mi">0</span><span class="p">:</span>
+ <span class="n">meancluster</span><span class="p">[</span><span class="nb">type</span><span class="p">]</span> <span class="o">+=</span> <span class="mi">1</span>
+ <span class="n">extension</span> <span class="o">=</span> <span class="s">"."</span> <span class="o">+</span> <span class="n">infile</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s">"."</span><span class="p">)[</span><span class="mi">1</span><span class="p">]</span>
+ <span class="n">derivedPath</span> <span class="o">=</span> <span class="n">infile</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s">"_"</span><span class="p">)[</span><span class="mi">0</span><span class="p">]</span>
+ <span class="n">realname</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">files</span><span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">dax</span><span class="p">][</span><span class="nb">type</span><span class="p">][</span><span class="s">"input"</span><span class="p">][</span><span class="n">infile</span><span class="p">][</span><span class="s">"path"</span><span class="p">]</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s">"/"</span><span class="p">)[</span><span class="o">-</span><span class="mi">1</span><span class="p">]</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s">"."</span><span class="p">)[</span><span class="mi">0</span><span class="p">]</span>
+ <span class="k">for</span> <span class="n">stepnum</span><span class="p">,</span><span class="n">job</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">workflow</span><span class="p">[</span><span class="s">"workflows"</span><span class="p">][</span><span class="nb">type</span><span class="p">]):</span>
+ <span class="n">jobname</span> <span class="o">=</span> <span class="n">derivedPath</span> <span class="o">+</span> <span class="s">"_"</span> <span class="o">+</span> <span class="n">job</span><span class="p">[</span><span class="s">"name"</span><span class="p">]</span>
+ <span class="n">inputs</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_loadJobInputs</span><span class="p">(</span><span class="n">job</span><span class="p">,</span> <span class="nb">type</span><span class="p">,</span> <span class="n">derivedPath</span><span class="p">,</span> <span class="n">extension</span><span class="p">)</span>
+ <span class="k">if</span> <span class="n">job</span><span class="p">[</span><span class="s">"name"</span><span class="p">]</span> <span class="ow">in</span> <span class="n">exNames</span><span class="p">:</span>
+ <span class="n">outputs</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_loadJobOutputs</span><span class="p">(</span><span class="n">job</span><span class="p">,</span> <span class="nb">type</span><span class="p">,</span> <span class="n">derivedPath</span><span class="p">,</span> <span class="bp">True</span><span class="p">)</span>
+ <span class="n">exDep</span><span class="p">[</span><span class="nb">type</span><span class="p">][</span><span class="n">clusternum</span><span class="p">[</span><span class="nb">type</span><span class="p">]]</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">jobname</span><span class="p">)</span>
+ <span class="n">reqFile</span> <span class="o">=</span> <span class="n">derivedPath</span> <span class="o">+</span> <span class="s">"_"</span> <span class="o">+</span> <span class="bp">self</span><span class="o">.</span><span class="n">workflow</span><span class="p">[</span><span class="s">"extract"</span><span class="p">][</span><span class="s">"workflows"</span><span class="p">][</span><span class="nb">type</span><span class="p">][</span><span class="s">"inputs"</span><span class="p">][</span><span class="mi">0</span><span class="p">]</span> <span class="o">+</span> <span class="s">".png"</span>
+ <span class="n">exInput</span><span class="p">[</span><span class="nb">type</span><span class="p">][</span><span class="n">clusternum</span><span class="p">[</span><span class="nb">type</span><span class="p">]][</span><span class="n">reqFile</span><span class="p">]</span> <span class="o">=</span> <span class="p">{</span><span class="s">"file"</span><span class="p">:</span> <span class="n">reqFile</span><span class="p">,</span> <span class="s">"transfer"</span><span class="p">:</span> <span class="n">save</span><span class="p">}</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="n">outputs</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_loadJobOutputs</span><span class="p">(</span><span class="n">job</span><span class="p">,</span> <span class="nb">type</span><span class="p">,</span> <span class="n">derivedPath</span><span class="p">,</span> <span class="n">save</span><span class="p">)</span>
+ <span class="n">depends</span> <span class="o">=</span> <span class="p">[</span><span class="n">derivedPath</span> <span class="o">+</span> <span class="s">"_"</span> <span class="o">+</span> <span class="n">depend</span> <span class="k">for</span> <span class="n">depend</span> <span class="ow">in</span> <span class="n">job</span><span class="p">[</span><span class="s">"depends"</span><span class="p">]]</span> <span class="k">if</span> <span class="s">"depends"</span> <span class="ow">in</span> <span class="n">job</span> <span class="k">else</span> <span class="p">[]</span>
+ <span class="k">if</span> <span class="n">job</span><span class="p">[</span><span class="s">"executable"</span><span class="p">]</span> <span class="o">==</span> <span class="s">"pcv-meanshift"</span><span class="p">:</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_addJob</span><span class="p">(</span><span class="n">jobname</span><span class="p">,</span> <span class="n">job</span><span class="p">[</span><span class="s">"executable"</span><span class="p">],</span> <span class="n">inputs</span><span class="p">,</span> <span class="n">outputs</span><span class="p">,</span> <span class="n">job</span><span class="p">[</span><span class="s">"arguments"</span><span class="p">],</span> <span class="n">depends</span><span class="p">,</span> <span class="n">label</span> <span class="o">=</span> <span class="nb">type</span> <span class="o">+</span> <span class="s">"_step"</span> <span class="o">+</span> <span class="nb">str</span><span class="p">(</span><span class="n">stepnum</span><span class="p">)</span> <span class="o">+</span> <span class="s">"_cluster"</span> <span class="o">+</span> <span class="nb">str</span><span class="p">(</span><span class="n">meancluster</span><span class="p">[</span><span class="nb">type</span><span class="p">])</span> <span class="k">if</span> <span class="s">"cluster"</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">config</span> <span class="k">else</span> <span class="bp">None</span><span class="p">)</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_addJob</span><span class="p">(</span><span class="n">jobname</span><span class="p">,</span> <span class="n">job</span><span class="p">[</span><span class="s">"executable"</span><span class="p">],</span> <span class="n">inputs</span><span class="p">,</span> <span class="n">outputs</span><span class="p">,</span> <span class="n">job</span><span class="p">[</span><span class="s">"arguments"</span><span class="p">],</span> <span class="n">depends</span><span class="p">,</span> <span class="n">label</span> <span class="o">=</span> <span class="nb">type</span> <span class="o">+</span> <span class="s">"_step"</span> <span class="o">+</span> <span class="nb">str</span><span class="p">(</span><span class="n">stepnum</span><span class="p">)</span> <span class="o">+</span> <span class="s">"_cluster"</span> <span class="o">+</span> <span class="nb">str</span><span class="p">(</span><span class="n">clusternum</span><span class="p">[</span><span class="nb">type</span><span class="p">])</span> <span class="k">if</span> <span class="s">"cluster"</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">config</span> <span class="k">else</span> <span class="bp">None</span><span class="p">)</span>
+
+
+ <span class="n">maprc</span> <span class="o">=</span> <span class="nb">open</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">basepath</span> <span class="o">+</span> <span class="s">"/"</span> <span class="o">+</span> <span class="n">loc</span> <span class="o">+</span> <span class="s">"/map.rc"</span><span class="p">,</span> <span class="s">"a"</span><span class="p">)</span>
+ <span class="n">binDep</span> <span class="o">=</span> <span class="p">[]</span>
+ <span class="n">aggIn</span> <span class="o">=</span> <span class="p">{}</span>
+ <span class="k">for</span> <span class="nb">type</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">workflow</span><span class="p">[</span><span class="s">"workflows"</span><span class="p">]:</span>
+ <span class="k">for</span> <span class="n">q</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="mi">0</span><span class="p">,</span> <span class="n">clusternum</span><span class="p">[</span><span class="nb">type</span><span class="p">]</span> <span class="o">+</span> <span class="mi">1</span><span class="p">):</span>
+ <span class="n">arguments</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">workflow</span><span class="p">[</span><span class="s">"extract"</span><span class="p">][</span><span class="s">"workflows"</span><span class="p">][</span><span class="nb">type</span><span class="p">][</span><span class="s">"arguments"</span><span class="p">]</span>
+ <span class="k">if</span> <span class="s">"--input"</span> <span class="ow">in</span> <span class="n">arguments</span><span class="p">:</span>
+ <span class="k">del</span> <span class="n">arguments</span><span class="p">[</span><span class="s">"--input"</span><span class="p">]</span>
+ <span class="k">if</span> <span class="s">"histogram-bin"</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">workflow</span><span class="p">[</span><span class="s">"extract"</span><span class="p">]:</span>
+ <span class="k">if</span> <span class="nb">type</span> <span class="ow">in</span> <span class="p">[</span><span class="n">imtype</span> <span class="k">for</span> <span class="n">key</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">workflow</span><span class="p">[</span><span class="s">"extract"</span><span class="p">][</span><span class="s">"histogram-bin"</span><span class="p">][</span><span class="s">"--group"</span><span class="p">]</span> <span class="k">for</span> <span class="n">imtype</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">workflow</span><span class="p">[</span><span class="s">"extract"</span><span class="p">][</span><span class="s">"histogram-bin"</span><span class="p">][</span><span class="s">"--group"</span><span class="p">][</span><span class="n">key</span><span class="p">]]:</span>
+ <span class="n">arguments</span><span class="p">[</span><span class="s">"--colors"</span><span class="p">]</span> <span class="o">=</span> <span class="s">""</span>
+ <span class="n">arguments</span><span class="p">[</span><span class="s">"--db"</span><span class="p">]</span> <span class="o">=</span> <span class="s">"db"</span>
+ <span class="n">arguments</span><span class="p">[</span><span class="s">"--createdb"</span><span class="p">]</span> <span class="o">=</span> <span class="s">""</span>
+ <span class="n">arguments</span><span class="p">[</span><span class="s">"--inputs"</span><span class="p">]</span> <span class="o">=</span> <span class="s">" "</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">exInput</span><span class="p">[</span><span class="nb">type</span><span class="p">][</span><span class="n">q</span><span class="p">]</span><span class="o">.</span><span class="n">keys</span><span class="p">())</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_addFile</span><span class="p">(</span><span class="nb">type</span> <span class="o">+</span> <span class="nb">str</span><span class="p">(</span><span class="n">q</span><span class="p">)</span> <span class="o">+</span> <span class="s">".db"</span><span class="p">,</span> <span class="nb">type</span><span class="p">,</span> <span class="s">"output"</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_addJob</span><span class="p">(</span><span class="nb">type</span> <span class="o">+</span> <span class="s">"_extract"</span> <span class="o">+</span> <span class="nb">str</span><span class="p">(</span><span class="n">q</span><span class="p">),</span> <span class="s">"pcv-extract-multi"</span><span class="p">,</span> <span class="n">exInput</span><span class="p">[</span><span class="nb">type</span><span class="p">][</span><span class="n">q</span><span class="p">],</span> <span class="p">{</span><span class="s">"db"</span><span class="p">:</span> <span class="p">{</span><span class="s">"file"</span><span class="p">:</span> <span class="nb">type</span> <span class="o">+</span> <span class="nb">str</span><span class="p">(</span><span class="n">q</span><span class="p">)</span> <span class="o">+</span> <span class="s">".db"</span><span class="p">,</span> <span class="s">"transfer"</span><span class="p">:</span> <span class="bp">False</span><span class="p">}},</span> <span class="n">arguments</span><span class="p">,</span> <span class="n">exDep</span><span class="p">[</span><span class="nb">type</span><span class="p">][</span><span class="n">q</span><span class="p">])</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_addJob</span><span class="p">(</span><span class="nb">type</span> <span class="o">+</span> <span class="s">"_extract"</span> <span class="o">+</span> <span class="nb">str</span><span class="p">(</span><span class="n">q</span><span class="p">),</span> <span class="s">"pcv-extract-multi"</span><span class="p">,</span> <span class="n">exInput</span><span class="p">[</span><span class="nb">type</span><span class="p">][</span><span class="n">q</span><span class="p">],</span> <span class="p">{</span><span class="s">"db"</span><span class="p">:</span> <span class="p">{</span><span class="s">"file"</span><span class="p">:</span> <span class="nb">type</span> <span class="o">+</span> <span class="nb">str</span><span class="p">(</span><span class="n">q</span><span class="p">)</span> <span class="o">+</span> <span class="s">".db"</span><span class="p">,</span> <span class="s">"transfer"</span><span class="p">:</span> <span class="bp">False</span><span class="p">}},</span> <span class="n">arguments</span><span class="p">,</span> <span class="p">[],</span> <span class="n">dax</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">exdax</span><span class="p">)</span>
+ <span class="n">maprc</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="nb">type</span> <span class="o">+</span> <span class="nb">str</span><span class="p">(</span><span class="n">q</span><span class="p">)</span> <span class="o">+</span> <span class="s">".db"</span> <span class="o">+</span> <span class="s">" file://"</span> <span class="o">+</span> <span class="bp">self</span><span class="o">.</span><span class="n">basepath</span> <span class="o">+</span> <span class="s">"/output/"</span> <span class="o">+</span> <span class="nb">type</span> <span class="o">+</span> <span class="nb">str</span><span class="p">(</span><span class="n">q</span><span class="p">)</span> <span class="o">+</span> <span class="s">".db"</span> <span class="o">+</span> <span class="s">" pool=</span><span class="se">\"</span><span class="s">local</span><span class="se">\"\n</span><span class="s">"</span><span class="p">)</span>
+ <span class="n">binDep</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="nb">type</span> <span class="o">+</span> <span class="s">"_extract"</span> <span class="o">+</span> <span class="nb">str</span><span class="p">(</span><span class="n">q</span><span class="p">))</span>
+ <span class="n">aggIn</span><span class="p">[</span><span class="nb">type</span> <span class="o">+</span> <span class="nb">str</span><span class="p">(</span><span class="n">q</span><span class="p">)</span> <span class="o">+</span> <span class="s">".db"</span><span class="p">]</span> <span class="o">=</span> <span class="p">{</span><span class="s">"file"</span><span class="p">:</span> <span class="nb">type</span> <span class="o">+</span> <span class="nb">str</span><span class="p">(</span><span class="n">q</span><span class="p">)</span> <span class="o">+</span> <span class="s">".db"</span><span class="p">,</span> <span class="s">"transfer"</span><span class="p">:</span> <span class="bp">False</span><span class="p">}</span>
+ <span class="n">aggIn</span><span class="p">[</span><span class="s">"db"</span><span class="p">]</span> <span class="o">=</span> <span class="p">{</span><span class="s">"file"</span><span class="p">:</span> <span class="s">"img.db"</span><span class="p">,</span> <span class="s">"transfer"</span><span class="p">:</span> <span class="bp">False</span><span class="p">}</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_addJob</span><span class="p">(</span><span class="s">"sql_aggregate1"</span><span class="p">,</span> <span class="s">"pcv-sql-aggregate"</span><span class="p">,</span> <span class="n">aggIn</span><span class="p">,</span> <span class="p">{},</span> <span class="p">{</span><span class="s">"--db"</span><span class="p">:</span> <span class="s">"db"</span><span class="p">,</span> <span class="s">"--inputs"</span><span class="p">:</span> <span class="s">" "</span><span class="o">.</span><span class="n">join</span><span class="p">([</span><span class="n">aggIn</span><span class="p">[</span><span class="n">x</span><span class="p">][</span><span class="s">"file"</span><span class="p">]</span> <span class="k">for</span> <span class="n">x</span> <span class="ow">in</span> <span class="n">aggIn</span> <span class="k">if</span> <span class="n">x</span> <span class="o">!=</span> <span class="s">"db"</span><span class="p">])},</span> <span class="n">binDep</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_addJob</span><span class="p">(</span><span class="s">"sql_aggregate1"</span><span class="p">,</span> <span class="s">"pcv-sql-aggregate"</span><span class="p">,</span> <span class="n">aggIn</span><span class="p">,</span> <span class="p">{},</span> <span class="p">{</span><span class="s">"--db"</span><span class="p">:</span> <span class="s">"db"</span><span class="p">,</span> <span class="s">"--inputs"</span><span class="p">:</span> <span class="s">" "</span><span class="o">.</span><span class="n">join</span><span class="p">([</span><span class="n">aggIn</span><span class="p">[</span><span class="n">x</span><span class="p">][</span><span class="s">"file"</span><span class="p">]</span> <span class="k">for</span> <span class="n">x</span> <span class="ow">in</span> <span class="n">aggIn</span> <span class="k">if</span> <span class="n">x</span> <span class="o">!=</span> <span class="s">"db"</span><span class="p">])},</span> <span class="n">binDep</span><span class="p">,</span> <span class="n">dax</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">exdax</span><span class="p">)</span>
+
+ <span class="k">if</span> <span class="s">"histogram-bin"</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">workflow</span><span class="p">[</span><span class="s">"extract"</span><span class="p">]:</span>
+ <span class="n">outputs</span> <span class="o">=</span> <span class="p">{}</span>
+ <span class="k">for</span> <span class="n">name</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">workflow</span><span class="p">[</span><span class="s">"extract"</span><span class="p">][</span><span class="s">"histogram-bin"</span><span class="p">][</span><span class="s">"--group"</span><span class="p">]:</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_addFile</span><span class="p">(</span><span class="n">name</span> <span class="o">+</span> <span class="s">"_hist_bins.json"</span><span class="p">,</span> <span class="s">"raw"</span><span class="p">,</span> <span class="s">"output"</span><span class="p">)</span>
+ <span class="n">maprc</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="n">name</span> <span class="o">+</span> <span class="s">"_hist_bins.json"</span> <span class="o">+</span> <span class="s">" file://"</span> <span class="o">+</span> <span class="bp">self</span><span class="o">.</span><span class="n">basepath</span> <span class="o">+</span> <span class="s">"/output/"</span> <span class="o">+</span> <span class="n">name</span> <span class="o">+</span> <span class="s">"_hist_bins.json"</span> <span class="o">+</span> <span class="s">" pool=</span><span class="se">\"</span><span class="s">local</span><span class="se">\"\n</span><span class="s">"</span><span class="p">)</span>
+ <span class="n">outputs</span><span class="p">[</span><span class="n">name</span> <span class="o">+</span> <span class="s">"_hist_bins.json"</span><span class="p">]</span> <span class="o">=</span> <span class="p">{</span><span class="s">"file"</span><span class="p">:</span> <span class="n">name</span> <span class="o">+</span> <span class="s">"_hist_bins.json"</span><span class="p">,</span> <span class="s">"transfer"</span><span class="p">:</span> <span class="bp">True</span><span class="p">}</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_addJob</span><span class="p">(</span><span class="s">"bin_creation"</span><span class="p">,</span> <span class="s">"pcv-stats-histogram-bin"</span><span class="p">,</span> <span class="p">{</span><span class="s">"db"</span><span class="p">:</span> <span class="p">{</span><span class="s">"file"</span><span class="p">:</span> <span class="s">"img.db"</span><span class="p">,</span> <span class="s">"transfer"</span><span class="p">:</span> <span class="bp">True</span><span class="p">},</span> <span class="s">"extract.json"</span><span class="p">:</span> <span class="p">{</span><span class="s">"file"</span><span class="p">:</span> <span class="s">"extract.json"</span><span class="p">,</span> <span class="s">"transfer"</span><span class="p">:</span> <span class="bp">False</span><span class="p">}},</span> <span class="n">outputs</span><span class="p">,</span> <span class="p">{</span><span class="s">"--db"</span><span class="p">:</span> <span class="s">"db"</span><span class="p">,</span> <span class="s">"--options"</span><span class="p">:</span> <span class="s">"extract.json"</span><span class="p">,</span> <span class="s">"--intable"</span><span class="p">:</span> <span class="s">"images"</span><span class="p">,</span> <span class="s">"--outtable"</span><span class="p">:</span> <span class="s">"histogramBins"</span><span class="p">,</span> <span class="s">"--jsonwrite"</span><span class="p">:</span> <span class="s">""</span><span class="p">},</span> <span class="p">[</span><span class="s">"sql_aggregate1"</span><span class="p">])</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_addJob</span><span class="p">(</span><span class="s">"bin_creation"</span><span class="p">,</span> <span class="s">"pcv-stats-histogram-bin"</span><span class="p">,</span> <span class="p">{</span><span class="s">"db"</span><span class="p">:</span> <span class="p">{</span><span class="s">"file"</span><span class="p">:</span> <span class="s">"img.db"</span><span class="p">,</span> <span class="s">"transfer"</span><span class="p">:</span> <span class="bp">True</span><span class="p">},</span> <span class="s">"extract.json"</span><span class="p">:</span> <span class="p">{</span><span class="s">"file"</span><span class="p">:</span> <span class="s">"extract.json"</span><span class="p">,</span> <span class="s">"transfer"</span><span class="p">:</span> <span class="bp">False</span><span class="p">}},</span> <span class="n">outputs</span><span class="p">,</span> <span class="p">{</span><span class="s">"--db"</span><span class="p">:</span> <span class="s">"db"</span><span class="p">,</span> <span class="s">"--options"</span><span class="p">:</span> <span class="s">"extract.json"</span><span class="p">,</span> <span class="s">"--intable"</span><span class="p">:</span> <span class="s">"images"</span><span class="p">,</span> <span class="s">"--outtable"</span><span class="p">:</span> <span class="s">"histogramBins"</span><span class="p">,</span> <span class="s">"--jsonwrite"</span><span class="p">:</span> <span class="s">""</span><span class="p">,</span> <span class="s">"--overwrite"</span><span class="p">:</span> <span class="s">""</span><span class="p">},</span> <span class="p">[</span><span class="s">"sql_aggregate1"</span><span class="p">],</span> <span class="n">dax</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">exdax</span><span class="p">)</span>
+
+ <span class="n">binDep</span> <span class="o">=</span> <span class="p">[]</span>
+ <span class="nb">map</span> <span class="o">=</span> <span class="p">{}</span>
+
+ <span class="k">for</span> <span class="n">group</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">workflow</span><span class="p">[</span><span class="s">"extract"</span><span class="p">][</span><span class="s">"histogram-bin"</span><span class="p">][</span><span class="s">"--group"</span><span class="p">]:</span>
+ <span class="k">for</span> <span class="nb">type</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">workflow</span><span class="p">[</span><span class="s">"extract"</span><span class="p">][</span><span class="s">"histogram-bin"</span><span class="p">][</span><span class="s">"--group"</span><span class="p">][</span><span class="n">group</span><span class="p">]:</span>
+ <span class="nb">map</span><span class="p">[</span><span class="nb">type</span><span class="p">]</span> <span class="o">=</span> <span class="n">group</span>
+
+ <span class="k">for</span> <span class="nb">type</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">workflow</span><span class="p">[</span><span class="s">"workflows"</span><span class="p">]:</span>
+ <span class="k">for</span> <span class="n">q</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="mi">0</span><span class="p">,</span> <span class="n">clusternum</span><span class="p">[</span><span class="nb">type</span><span class="p">]</span> <span class="o">+</span> <span class="mi">1</span><span class="p">):</span>
+ <span class="n">arguments</span> <span class="o">=</span> <span class="p">{}</span>
+ <span class="n">arguments</span><span class="p">[</span><span class="s">"--db"</span><span class="p">]</span> <span class="o">=</span> <span class="s">"db"</span>
+ <span class="n">arguments</span><span class="p">[</span><span class="s">"--inputs"</span><span class="p">]</span> <span class="o">=</span> <span class="s">" "</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">exInput</span><span class="p">[</span><span class="nb">type</span><span class="p">][</span><span class="n">q</span><span class="p">]</span><span class="o">.</span><span class="n">keys</span><span class="p">())</span>
+ <span class="n">exInput</span><span class="p">[</span><span class="nb">type</span><span class="p">][</span><span class="n">q</span><span class="p">][</span><span class="s">"db"</span><span class="p">]</span> <span class="o">=</span> <span class="p">{</span><span class="s">"file"</span><span class="p">:</span> <span class="nb">type</span> <span class="o">+</span> <span class="nb">str</span><span class="p">(</span><span class="n">q</span><span class="p">)</span> <span class="o">+</span> <span class="s">".db"</span><span class="p">,</span> <span class="s">"transfer"</span><span class="p">:</span> <span class="bp">False</span><span class="p">}</span>
+ <span class="n">exInput</span><span class="p">[</span><span class="nb">type</span><span class="p">][</span><span class="n">q</span><span class="p">][</span><span class="s">"binfile"</span><span class="p">]</span> <span class="o">=</span> <span class="p">{</span><span class="s">"file"</span><span class="p">:</span> <span class="nb">map</span><span class="p">[</span><span class="nb">type</span><span class="p">]</span> <span class="o">+</span> <span class="s">"_hist_bins.json"</span><span class="p">,</span> <span class="s">"transfer"</span><span class="p">:</span> <span class="bp">False</span><span class="p">}</span>
+ <span class="n">arguments</span><span class="p">[</span><span class="s">"--bins"</span><span class="p">]</span> <span class="o">=</span> <span class="s">"binfile"</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_addJob</span><span class="p">(</span><span class="nb">type</span> <span class="o">+</span> <span class="s">"_extractBins"</span> <span class="o">+</span> <span class="nb">str</span><span class="p">(</span><span class="n">q</span><span class="p">),</span> <span class="s">"pcv-extract-multi"</span><span class="p">,</span> <span class="n">exInput</span><span class="p">[</span><span class="nb">type</span><span class="p">][</span><span class="n">q</span><span class="p">],</span> <span class="p">{},</span> <span class="n">arguments</span><span class="p">,</span> <span class="p">[</span><span class="s">"bin_creation"</span><span class="p">])</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_addJob</span><span class="p">(</span><span class="nb">type</span> <span class="o">+</span> <span class="s">"_extractBins"</span> <span class="o">+</span> <span class="nb">str</span><span class="p">(</span><span class="n">q</span><span class="p">),</span> <span class="s">"pcv-extract-multi"</span><span class="p">,</span> <span class="n">exInput</span><span class="p">[</span><span class="nb">type</span><span class="p">][</span><span class="n">q</span><span class="p">],</span> <span class="p">{},</span> <span class="n">arguments</span><span class="p">,</span> <span class="p">[</span><span class="s">"bin_creation"</span><span class="p">],</span> <span class="n">dax</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">exdax</span><span class="p">)</span>
+ <span class="n">binDep</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="nb">type</span> <span class="o">+</span> <span class="s">"_extractBins"</span> <span class="o">+</span> <span class="nb">str</span><span class="p">(</span><span class="n">q</span><span class="p">))</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_addJob</span><span class="p">(</span><span class="s">"sql_aggregate2"</span><span class="p">,</span> <span class="s">"pcv-sql-aggregate"</span><span class="p">,</span> <span class="n">aggIn</span><span class="p">,</span> <span class="p">{},</span> <span class="p">{</span><span class="s">"--db"</span><span class="p">:</span> <span class="s">"db"</span><span class="p">,</span> <span class="s">"--inputs"</span><span class="p">:</span> <span class="s">" "</span><span class="o">.</span><span class="n">join</span><span class="p">([</span><span class="n">aggIn</span><span class="p">[</span><span class="n">x</span><span class="p">][</span><span class="s">"file"</span><span class="p">]</span> <span class="k">for</span> <span class="n">x</span> <span class="ow">in</span> <span class="n">aggIn</span> <span class="k">if</span> <span class="n">x</span> <span class="o">!=</span> <span class="s">"db"</span><span class="p">])},</span> <span class="n">binDep</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_addJob</span><span class="p">(</span><span class="s">"sql_aggregate2"</span><span class="p">,</span> <span class="s">"pcv-sql-aggregate"</span><span class="p">,</span> <span class="n">aggIn</span><span class="p">,</span> <span class="p">{},</span> <span class="p">{</span><span class="s">"--db"</span><span class="p">:</span> <span class="s">"db"</span><span class="p">,</span> <span class="s">"--inputs"</span><span class="p">:</span> <span class="s">" "</span><span class="o">.</span><span class="n">join</span><span class="p">([</span><span class="n">aggIn</span><span class="p">[</span><span class="n">x</span><span class="p">][</span><span class="s">"file"</span><span class="p">]</span> <span class="k">for</span> <span class="n">x</span> <span class="ow">in</span> <span class="n">aggIn</span> <span class="k">if</span> <span class="n">x</span> <span class="o">!=</span> <span class="s">"db"</span><span class="p">])},</span> <span class="n">binDep</span><span class="p">,</span> <span class="n">dax</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">exdax</span><span class="p">)</span>
+
+ <span class="n">z</span> <span class="o">=</span> <span class="mi">2</span> <span class="k">if</span> <span class="s">"histogram-bin"</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">workflow</span><span class="p">[</span><span class="s">"extract"</span><span class="p">]</span> <span class="k">else</span> <span class="mi">1</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_addJob</span><span class="p">(</span><span class="s">"error-log"</span><span class="p">,</span> <span class="s">"pcv-error-log"</span><span class="p">,</span> <span class="p">{</span><span class="s">"db"</span><span class="p">:</span> <span class="p">{</span><span class="s">"file"</span><span class="p">:</span> <span class="s">"img.db"</span><span class="p">,</span> <span class="s">"transfer"</span><span class="p">:</span> <span class="bp">False</span><span class="p">}},</span> <span class="p">{</span><span class="s">"output"</span><span class="p">:</span> <span class="p">{</span><span class="s">"file"</span><span class="p">:</span> <span class="s">"img.log"</span><span class="p">,</span> <span class="s">"transfer"</span><span class="p">:</span> <span class="bp">True</span><span class="p">}},</span> <span class="p">{</span><span class="s">"--db"</span><span class="p">:</span> <span class="s">"db"</span><span class="p">,</span> <span class="s">"--output"</span><span class="p">:</span> <span class="s">"output"</span><span class="p">},</span> <span class="p">[</span><span class="s">"sql_aggregate"</span> <span class="o">+</span> <span class="nb">str</span><span class="p">(</span><span class="n">z</span><span class="p">)])</span>
+ <span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">basepath</span> <span class="o">+</span> <span class="s">"/"</span> <span class="o">+</span> <span class="n">loc</span> <span class="o">+</span> <span class="s">"/workflow.dax"</span><span class="p">,</span> <span class="s">"w"</span><span class="p">)</span> <span class="k">as</span> <span class="n">wh</span><span class="p">:</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">dax</span><span class="o">.</span><span class="n">writeXML</span><span class="p">(</span><span class="n">wh</span><span class="p">)</span>
+ <span class="k">return</span>
+
+ <span class="k">def</span> <span class="nf">_createExtract</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">loc</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> Creates the extraction step only dax!</span>
+<span class="sd"> """</span>
+ <span class="c">#self._addJob("extractOnly", "pcv-extract-all", self.exInput, {}, {"--db": "db", "--options": "extract.json"}, dax = self.exdax)</span>
+ <span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">basepath</span> <span class="o">+</span> <span class="s">"/"</span> <span class="o">+</span> <span class="n">loc</span> <span class="o">+</span> <span class="s">"/extract.dax"</span><span class="p">,</span> <span class="s">"w"</span><span class="p">)</span> <span class="k">as</span> <span class="n">wh</span><span class="p">:</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">exdax</span><span class="o">.</span><span class="n">writeXML</span><span class="p">(</span><span class="n">wh</span><span class="p">)</span>
+ <span class="k">return</span>
+
+ <span class="k">def</span> <span class="nf">_createReplica</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">loc</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> Creates the pegasus configuration replica catalog. input/conf.rc</span>
+<span class="sd"> """</span>
+ <span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">basepath</span> <span class="o">+</span> <span class="s">"/"</span> <span class="o">+</span> <span class="n">loc</span> <span class="o">+</span> <span class="s">"/conf.rc"</span><span class="p">,</span> <span class="s">"w"</span><span class="p">)</span> <span class="k">as</span> <span class="n">wh</span><span class="p">:</span>
+ <span class="n">pegasusrc</span> <span class="o">=</span> <span class="n">textwrap</span><span class="o">.</span><span class="n">dedent</span><span class="p">(</span><span class="s">"""</span><span class="se">\</span>
+<span class="s"> pegasus.catalog.site = XML</span>
+<span class="s"> pegasus.catalog.site.file = </span><span class="si">%s</span><span class="s">/sites.xml</span>
+<span class="s"> </span>
+<span class="s"> pegasus.condor.logs.symlink = false</span>
+<span class="s"> </span>
+<span class="s"> pegasus.transfer.links = true</span>
+<span class="s"> </span>
+<span class="s"> pegasus.data.configuration = sharedfs</span>
+<span class="s"> </span>
+<span class="s"> pegasus.dir.storage.mapper = Replica</span>
+<span class="s"> pegasus.dir.storage.mapper.replica = File</span>
+<span class="s"> pegasus.dir.storage.mapper.replica.file = </span><span class="si">%s</span><span class="s">/map.rc</span>
+<span class="s"> """</span> <span class="o">%</span> <span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">basepath</span> <span class="o">+</span> <span class="s">"/"</span> <span class="o">+</span> <span class="n">loc</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">basepath</span> <span class="o">+</span> <span class="s">"/"</span> <span class="o">+</span> <span class="n">loc</span><span class="p">))</span>
+ <span class="n">wh</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="n">pegasusrc</span><span class="p">)</span>
+ <span class="k">return</span>
+
+ <span class="k">def</span> <span class="nf">_createSites</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">loc</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> Creates the pegasus site catalog. input/sites.xml</span>
+<span class="sd"> """</span>
+ <span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">basepath</span> <span class="o">+</span> <span class="s">"/"</span> <span class="o">+</span> <span class="n">loc</span> <span class="o">+</span> <span class="s">"/sites.xml"</span><span class="p">,</span> <span class="s">"w"</span><span class="p">)</span> <span class="k">as</span> <span class="n">wh</span><span class="p">:</span>
+ <span class="n">sites</span> <span class="o">=</span> <span class="s">"""</span><span class="se">\</span>
+<span class="s"> <sitecatalog xmlns="http://pegasus.isi.edu/schema/sitecatalog" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://pegasus.isi.edu/schema/sitecatalog http://pegasus.isi.edu/schema/sc-4.0.xsd" version="4.0"></span>
+<span class="s"> </span>
+<span class="s"> <site handle="local" arch="x86_64" os="LINUX"></span>
+<span class="s"> <directory type="shared-scratch" path="</span><span class="si">%s</span><span class="s">"></span>
+<span class="s"> <file-server operation="all" url="file://</span><span class="si">%s</span><span class="s">" /></span>
+<span class="s"> </directory></span>
+<span class="s"> <directory type="local-storage" path="</span><span class="si">%s</span><span class="s">"></span>
+<span class="s"> <file-server operation="all" url="file://</span><span class="si">%s</span><span class="s">" /></span>
+<span class="s"> </directory></span>
+<span class="s"> """</span> <span class="o">%</span> <span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">basepath</span> <span class="o">+</span> <span class="s">"/work/imgproc/"</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">basepath</span> <span class="o">+</span> <span class="s">"/work/imgproc/"</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">basepath</span> <span class="o">+</span> <span class="s">"/output/"</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">basepath</span> <span class="o">+</span> <span class="s">"/output/"</span><span class="p">)</span>
+ <span class="k">for</span> <span class="n">namespace</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">config</span><span class="p">[</span><span class="s">"profile"</span><span class="p">]:</span>
+ <span class="k">for</span> <span class="n">key</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">config</span><span class="p">[</span><span class="s">"profile"</span><span class="p">][</span><span class="n">namespace</span><span class="p">]:</span>
+ <span class="n">val</span> <span class="o">=</span> <span class="s">":"</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">config</span><span class="p">[</span><span class="s">"profile"</span><span class="p">][</span><span class="n">namespace</span><span class="p">][</span><span class="n">key</span><span class="p">])</span> <span class="k">if</span> <span class="s">"path"</span> <span class="ow">in</span> <span class="n">key</span><span class="o">.</span><span class="n">lower</span><span class="p">()</span> <span class="k">else</span> <span class="bp">self</span><span class="o">.</span><span class="n">config</span><span class="p">[</span><span class="s">"profile"</span><span class="p">][</span><span class="n">namespace</span><span class="p">][</span><span class="n">key</span><span class="p">]</span>
+ <span class="n">sites</span> <span class="o">+=</span> <span class="s">"""</span><span class="se">\n\t</span><span class="s"><profile namespace="</span><span class="si">%s</span><span class="s">" key="</span><span class="si">%s</span><span class="s">"></span><span class="si">%s</span><span class="s"></profile> """</span> <span class="o">%</span> <span class="p">(</span><span class="n">namespace</span><span class="p">,</span> <span class="n">key</span><span class="p">,</span> <span class="n">val</span><span class="p">)</span>
+ <span class="n">sites</span> <span class="o">+=</span> <span class="s">"</site></sitecatalog>"</span>
+ <span class="n">sites</span> <span class="o">=</span> <span class="n">sites</span><span class="o">.</span><span class="n">replace</span><span class="p">(</span><span class="s">"</span><span class="se">\n</span><span class="s">"</span><span class="p">,</span><span class="s">""</span><span class="p">)</span>
+ <span class="n">wh</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s">"</span><span class="se">\n</span><span class="s">"</span><span class="o">.</span><span class="n">join</span><span class="p">([</span><span class="n">line</span> <span class="k">for</span> <span class="n">line</span> <span class="ow">in</span> <span class="n">xml</span><span class="o">.</span><span class="n">dom</span><span class="o">.</span><span class="n">minidom</span><span class="o">.</span><span class="n">parseString</span><span class="p">(</span><span class="n">sites</span><span class="p">)</span><span class="o">.</span><span class="n">toprettyxml</span><span class="p">()</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s">'</span><span class="se">\n</span><span class="s">'</span><span class="p">)</span> <span class="k">if</span> <span class="n">line</span><span class="o">.</span><span class="n">strip</span><span class="p">()]))</span>
+ <span class="k">return</span>
+
+ <span class="k">def</span> <span class="nf">_createSubmit</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">loc</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> Creates the pegasus submit script. submit.sh</span>
+<span class="sd"> """</span>
+ <span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">basepath</span> <span class="o">+</span> <span class="s">"/"</span> <span class="o">+</span> <span class="n">loc</span> <span class="o">+</span> <span class="s">"/submit.sh"</span><span class="p">,</span> <span class="s">"w"</span><span class="p">)</span> <span class="k">as</span> <span class="n">wh</span><span class="p">:</span>
+ <span class="n">submit</span> <span class="o">=</span> <span class="n">textwrap</span><span class="o">.</span><span class="n">dedent</span><span class="p">(</span><span class="s">"""</span><span class="se">\</span>
+<span class="s"> #!/bin/bash</span>
+<span class="s"> if [ "$1" = "--extract-only" ] || [ "$1" = "--extract" ] || [ "$1" = "-e" ]; then</span>
+<span class="s"> DAX="</span><span class="si">%s</span><span class="s">"</span>
+<span class="s"> else</span>
+<span class="s"> DAX="</span><span class="si">%s</span><span class="s">"</span>
+<span class="s"> fi</span>
+<span class="s"> plan=`pegasus-plan </span><span class="se">\\</span><span class="s"></span>
+<span class="s"> --conf "</span><span class="si">%s</span><span class="s">" </span><span class="se">\\</span><span class="s"></span>
+<span class="s"> --sites local </span><span class="se">\\</span><span class="s"></span>
+<span class="s"> --dir "</span><span class="si">%s</span><span class="s">" </span><span class="se">\\</span><span class="s"></span>
+<span class="s"> --output-site local </span><span class="se">\\</span><span class="s"></span>
+<span class="s"> --dax "$DAX" </span><span class="se">\\</span><span class="s"></span>
+<span class="s"> --randomdir </span><span class="se">\\</span><span class="s"></span>
+<span class="s"> """</span> <span class="o">%</span> <span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">basepath</span> <span class="o">+</span> <span class="s">"/"</span> <span class="o">+</span> <span class="n">loc</span> <span class="o">+</span> <span class="s">"/extract.dax"</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">basepath</span> <span class="o">+</span> <span class="s">"/"</span> <span class="o">+</span> <span class="n">loc</span> <span class="o">+</span> <span class="s">"/workflow.dax"</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">basepath</span> <span class="o">+</span> <span class="s">"/"</span> <span class="o">+</span> <span class="n">loc</span> <span class="o">+</span> <span class="s">"/conf.rc"</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">basepath</span> <span class="o">+</span> <span class="s">"/work/imgproc"</span><span class="p">))</span>
+ <span class="k">if</span> <span class="s">"cluster"</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">config</span><span class="p">:</span>
+ <span class="n">submit</span> <span class="o">+=</span> <span class="s">"""--cluster label </span><span class="se">\\\n</span><span class="s">"""</span>
+ <span class="n">submit</span> <span class="o">+=</span> <span class="n">textwrap</span><span class="o">.</span><span class="n">dedent</span><span class="p">(</span><span class="s">"""</span><span class="se">\</span>
+<span class="s"> --submit`</span>
+<span class="s"> </span>
+<span class="s"> status=`echo "$plan" | grep pegasus-status | tr -s ' '| cut -d ' ' -f 6`</span>
+<span class="s"> echo -e "#!/bin/bash</span>
+<span class="s"> pegasus-status -l $status" > status.sh</span>
+<span class="s"> chmod 744 status.sh</span>
+<span class="s"> </span>
+<span class="s"> remove=`echo "$plan" | grep pegasus-remove | tr -s ' '| cut -d ' ' -f 5`</span>
+<span class="s"> echo -e "#!/bin/bash</span>
+<span class="s"> pegasus-remove $remove" > remove.sh </span>
+<span class="s"> chmod 744 remove.sh</span>
+<span class="s"> </span>
+<span class="s"> echo "$plan"</span>
+<span class="s"> echo "Alternatively, you can use the status & remove scripts in the current directory!"</span>
+<span class="s"> </span>
+<span class="s"> """</span><span class="p">)</span>
+ <span class="n">wh</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="n">submit</span><span class="p">)</span>
+ <span class="n">os</span><span class="o">.</span><span class="n">chmod</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">basepath</span> <span class="o">+</span> <span class="s">"/"</span> <span class="o">+</span> <span class="n">loc</span> <span class="o">+</span> <span class="s">"/submit.sh"</span><span class="p">,</span> <span class="mo">0755</span><span class="p">)</span>
+ <span class="k">return</span>
+
+<div class="viewcode-block" id="ImageProcessor.create"><a class="viewcode-back" href="../../workflowimage.html#plantcv.workflow.ImageProcessor.create">[docs]</a> <span class="k">def</span> <span class="nf">create</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> Creates a new pegasus submission directory based on the current timestamp,</span>
+<span class="sd"> and populates it with all required information to submit a pegasus job.</span>
+<span class="sd"> """</span>
+ <span class="k">print</span> <span class="s">"Generating workflow. Please wait."</span>
+ <span class="n">loc</span> <span class="o">=</span> <span class="s">"/input/imgproc/"</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_createSetup</span><span class="p">()</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_copyFiles</span><span class="p">()</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_loadFiles</span><span class="p">(</span><span class="n">loc</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_loadExecutables</span><span class="p">()</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_loadNotify</span><span class="p">()</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_createDax</span><span class="p">(</span><span class="n">loc</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_createExtract</span><span class="p">(</span><span class="n">loc</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_createReplica</span><span class="p">(</span><span class="n">loc</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_createSites</span><span class="p">(</span><span class="n">loc</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_createSubmit</span><span class="p">(</span><span class="n">loc</span><span class="p">)</span>
+ <span class="k">return</span>
+
+</div></div>
+<div class="viewcode-block" id="ImageLoader"><a class="viewcode-back" href="../../indexing.html#plantcv.workflow.ImageLoader">[docs]</a><span class="k">class</span> <span class="nc">ImageLoader</span><span class="p">:</span>
+ <span class="sd">"""</span>
+<span class="sd"> This should handle all meta-data definitions</span>
+<span class="sd"> """</span>
+
+ <span class="k">def</span> <span class="nf">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">template</span><span class="p">,</span> <span class="n">output</span><span class="p">,</span> <span class="n">validOnly</span> <span class="o">=</span> <span class="bp">False</span><span class="p">,</span> <span class="n">overwrite</span> <span class="o">=</span> <span class="bp">False</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> :param template: Path to input template file, should be valid json.</span>
+<span class="sd"> :type template: str</span>
+<span class="sd"> """</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">templatePath</span> <span class="o">=</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">abspath</span><span class="p">(</span><span class="n">template</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">err</span> <span class="o">=</span> <span class="s">""</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">output</span> <span class="o">=</span> <span class="n">output</span> <span class="o">+</span> <span class="s">"/input/"</span>
+ <span class="k">try</span><span class="p">:</span>
+ <span class="nb">open</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">output</span> <span class="o">+</span> <span class="s">"/images.db"</span><span class="p">)</span>
+ <span class="k">except</span> <span class="ne">IOError</span><span class="p">:</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">err</span> <span class="o">+=</span> <span class="s">"Path Error: Cannot open output db file. </span><span class="se">\n</span><span class="s">"</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">validator</span> <span class="o">=</span> <span class="n">plantcv</span><span class="o">.</span><span class="n">validator</span><span class="o">.</span><span class="n">ImageLoader</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">templatePath</span><span class="p">)</span>
+ <span class="k">if</span> <span class="ow">not</span> <span class="bp">self</span><span class="o">.</span><span class="n">validator</span><span class="o">.</span><span class="n">isValid</span><span class="p">()</span> <span class="ow">or</span> <span class="n">validOnly</span><span class="p">:</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">validator</span><span class="o">.</span><span class="n">printErrors</span><span class="p">()</span>
+ <span class="n">sys</span><span class="o">.</span><span class="n">exit</span><span class="p">()</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">overwrite</span> <span class="o">=</span> <span class="n">overwrite</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">template</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">validator</span><span class="o">.</span><span class="n">data</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">template</span><span class="p">[</span><span class="s">"order"</span><span class="p">]</span><span class="o">.</span><span class="n">insert</span><span class="p">(</span><span class="mi">0</span><span class="p">,</span> <span class="s">"pegasusid"</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">count</span> <span class="o">=</span> <span class="p">{}</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">depth</span> <span class="o">=</span> <span class="nb">len</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">template</span><span class="p">[</span><span class="s">"path"</span><span class="p">]</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s">"/"</span><span class="p">))</span> <span class="o">-</span> <span class="mi">1</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">structure</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_dictTemplate</span><span class="p">()</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">data</span> <span class="o">=</span> <span class="p">[]</span>
+ <span class="k">return</span>
+
+ <span class="k">def</span> <span class="nf">_success</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+ <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">overwrite</span><span class="p">:</span>
+ <span class="k">print</span> <span class="s">"Directory re-crawled!"</span>
+ <span class="k">print</span> <span class="s">"Use pcv-run to submit your jobs."</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="k">print</span> <span class="s">"Directory setup successful!"</span>
+ <span class="k">print</span> <span class="s">"Define the required templates in "</span> <span class="o">+</span> <span class="bp">self</span><span class="o">.</span><span class="n">output</span> <span class="o">+</span> <span class="s">"."</span>
+ <span class="k">print</span> <span class="s">"Then use pcv-run to submit your jobs."</span>
+ <span class="k">return</span>
+
+ <span class="k">def</span> <span class="nf">_dictTemplate</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> Creates the first of two intermediary dictionaries for crawling. This relates</span>
+<span class="sd"> identifiers in the path, to a specified depth, as well as operators to split</span>
+<span class="sd"> the value at that depth.</span>
+<span class="sd"> """</span>
+ <span class="n">m</span> <span class="o">=</span> <span class="p">[</span><span class="n">x</span> <span class="k">for</span> <span class="n">x</span> <span class="ow">in</span> <span class="n">re</span><span class="o">.</span><span class="n">findall</span><span class="p">(</span><span class="s">r"%(\w+)%"</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">template</span><span class="p">[</span><span class="s">"path"</span><span class="p">])</span> <span class="k">if</span> <span class="n">x</span> <span class="o">!=</span> <span class="s">"null"</span><span class="p">]</span>
+ <span class="n">sp</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">template</span><span class="p">[</span><span class="s">"path"</span><span class="p">]</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s">"/"</span><span class="p">)</span>
+ <span class="n">d</span> <span class="o">=</span> <span class="p">{}</span>
+ <span class="k">for</span> <span class="n">key</span> <span class="ow">in</span> <span class="n">m</span><span class="p">:</span>
+ <span class="n">d</span><span class="p">[</span><span class="n">key</span><span class="p">]</span> <span class="o">=</span> <span class="p">{}</span>
+ <span class="n">d</span><span class="p">[</span><span class="n">key</span><span class="p">][</span><span class="s">"depth"</span><span class="p">]</span> <span class="o">=</span> <span class="p">[</span><span class="n">n</span> <span class="k">for</span> <span class="n">n</span><span class="p">,</span><span class="n">x</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="n">sp</span><span class="p">)</span> <span class="k">if</span> <span class="n">key</span> <span class="ow">in</span> <span class="n">x</span><span class="p">][</span><span class="mi">0</span><span class="p">]</span>
+ <span class="n">d</span><span class="p">[</span><span class="n">key</span><span class="p">][</span><span class="s">"split"</span><span class="p">]</span> <span class="o">=</span> <span class="p">[]</span>
+ <span class="n">val</span> <span class="o">=</span> <span class="n">sp</span><span class="p">[</span><span class="n">d</span><span class="p">[</span><span class="n">key</span><span class="p">][</span><span class="s">"depth"</span><span class="p">]]</span>
+ <span class="k">for</span> <span class="n">operator</span> <span class="ow">in</span> <span class="p">[</span><span class="s">" "</span><span class="p">,</span> <span class="s">"_"</span><span class="p">,</span> <span class="s">"-"</span><span class="p">]:</span>
+ <span class="k">if</span> <span class="n">operator</span> <span class="ow">in</span> <span class="n">val</span><span class="p">:</span>
+ <span class="n">b</span> <span class="o">=</span> <span class="n">val</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="n">operator</span><span class="p">)</span>
+ <span class="n">x</span> <span class="o">=</span> <span class="p">[</span><span class="n">n</span> <span class="k">for</span> <span class="n">n</span><span class="p">,</span><span class="n">x</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="n">b</span><span class="p">)</span> <span class="k">if</span> <span class="n">key</span> <span class="ow">in</span> <span class="n">x</span><span class="p">][</span><span class="mi">0</span><span class="p">]</span>
+ <span class="n">d</span><span class="p">[</span><span class="n">key</span><span class="p">][</span><span class="s">"split"</span><span class="p">]</span><span class="o">.</span><span class="n">append</span><span class="p">({</span><span class="s">"operator"</span><span class="p">:</span> <span class="n">operator</span><span class="p">,</span> <span class="s">"index"</span><span class="p">:</span> <span class="n">x</span><span class="p">})</span>
+ <span class="n">val</span> <span class="o">=</span> <span class="n">b</span><span class="p">[</span><span class="n">x</span><span class="p">]</span>
+ <span class="k">return</span> <span class="n">d</span>
+
+ <span class="k">def</span> <span class="nf">_loadStructure</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">splitPath</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> Creates the second of two intermediary dictionaries for crawling.</span>
+<span class="sd"> This utilizes the template created in _dictTemplate, and creates</span>
+<span class="sd"> a dictionary with actual values instead of structure.</span>
+<span class="sd"> """</span>
+ <span class="n">d</span> <span class="o">=</span><span class="p">{}</span>
+ <span class="k">for</span> <span class="n">key</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">structure</span><span class="p">:</span>
+ <span class="n">val</span> <span class="o">=</span> <span class="n">splitPath</span><span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">structure</span><span class="p">[</span><span class="n">key</span><span class="p">][</span><span class="s">"depth"</span><span class="p">]]</span>
+ <span class="k">for</span> <span class="n">operator</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">structure</span><span class="p">[</span><span class="n">key</span><span class="p">][</span><span class="s">"split"</span><span class="p">]:</span>
+ <span class="n">val</span> <span class="o">=</span> <span class="n">val</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="n">operator</span><span class="p">[</span><span class="s">"operator"</span><span class="p">])[</span><span class="n">operator</span><span class="p">[</span><span class="s">"index"</span><span class="p">]]</span>
+ <span class="n">d</span><span class="p">[</span><span class="n">key</span><span class="p">]</span> <span class="o">=</span> <span class="n">val</span>
+ <span class="k">return</span> <span class="n">d</span>
+
+ <span class="k">def</span> <span class="nf">_loadDataFile</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="nb">dict</span><span class="p">,</span> <span class="n">structure</span><span class="p">,</span> <span class="n">key</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> Loads data from a data file. If the specified key isn't in the file,</span>
+<span class="sd"> write 'UNKNOWN' instead.</span>
+<span class="sd"> """</span>
+ <span class="n">keyVal</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_convertReferences</span><span class="p">(</span><span class="n">structure</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">template</span><span class="p">[</span><span class="s">"data"</span><span class="p">][</span><span class="n">key</span><span class="p">][</span><span class="s">"key"</span><span class="p">])</span>
+ <span class="k">if</span> <span class="n">keyVal</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">filedata</span><span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">template</span><span class="p">[</span><span class="s">"data"</span><span class="p">][</span><span class="n">key</span><span class="p">][</span><span class="s">"value"</span><span class="p">]]:</span>
+ <span class="nb">dict</span><span class="p">[</span><span class="n">key</span><span class="p">]</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">filedata</span><span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">template</span><span class="p">[</span><span class="s">"data"</span><span class="p">][</span><span class="n">key</span><span class="p">][</span><span class="s">"value"</span><span class="p">]][</span><span class="n">keyVal</span><span class="p">]</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="nb">dict</span><span class="p">[</span><span class="n">key</span><span class="p">]</span> <span class="o">=</span> <span class="s">"UNKNOWN"</span>
+ <span class="k">return</span>
+
+ <span class="k">def</span> <span class="nf">_loadDataValue</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="nb">dict</span><span class="p">,</span> <span class="n">structure</span><span class="p">,</span> <span class="n">key</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> Loads a data value.</span>
+<span class="sd"> """</span>
+ <span class="n">val</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_convertReferences</span><span class="p">(</span><span class="n">structure</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">template</span><span class="p">[</span><span class="s">"data"</span><span class="p">][</span><span class="n">key</span><span class="p">][</span><span class="s">"value"</span><span class="p">])</span>
+ <span class="k">if</span> <span class="s">"translate"</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">template</span><span class="p">[</span><span class="s">"data"</span><span class="p">][</span><span class="n">key</span><span class="p">]:</span>
+ <span class="k">if</span> <span class="n">val</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">template</span><span class="p">[</span><span class="s">"translations"</span><span class="p">][</span><span class="n">key</span><span class="p">]:</span>
+ <span class="n">val</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">template</span><span class="p">[</span><span class="s">"translations"</span><span class="p">][</span><span class="n">key</span><span class="p">][</span><span class="n">val</span><span class="p">]</span>
+ <span class="nb">dict</span><span class="p">[</span><span class="n">key</span><span class="p">]</span> <span class="o">=</span> <span class="n">val</span>
+ <span class="k">return</span>
+
+ <span class="k">def</span> <span class="nf">_loadDataDate</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="nb">dict</span><span class="p">,</span> <span class="n">structure</span><span class="p">,</span> <span class="n">key</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> Loads a date.</span>
+<span class="sd"> """</span>
+ <span class="n">val</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_convertReferences</span><span class="p">(</span><span class="n">structure</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">template</span><span class="p">[</span><span class="s">"data"</span><span class="p">][</span><span class="n">key</span><span class="p">][</span><span class="s">"value"</span><span class="p">])</span>
+ <span class="n">format</span> <span class="o">=</span> <span class="s">""</span><span class="o">.</span><span class="n">join</span><span class="p">([</span><span class="n">x</span><span class="o">.</span><span class="n">replace</span><span class="p">(</span><span class="n">x</span><span class="p">,</span> <span class="s">"%"</span> <span class="o">+</span> <span class="n">x</span><span class="p">)</span> <span class="k">if</span> <span class="n">x</span> <span class="ow">in</span> <span class="n">conf</span><span class="o">.</span><span class="n">dateFormat</span> <span class="k">else</span> <span class="n">x</span> <span class="k">for</span> <span class="n">x</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">template</span><span class="p">[</span><span class="s">"data"</span><span class="p">][</span><span class="n">key</span><span class="p">][</span><span class="s">"format"</span><span class="p">]])</span>
+ <span class="n">val</span> <span class="o">=</span> <span class="n">datetime</span><span class="o">.</span><span class="n">datetime</span><span class="o">.</span><span class="n">strptime</span><span class="p">(</span><span class="n">val</span><span class="p">,</span> <span class="n">format</span><span class="p">)</span><span class="o">.</span><span class="n">strftime</span><span class="p">(</span><span class="s">"%Y-%m-</span><span class="si">%d</span><span class="s">"</span><span class="p">)</span>
+ <span class="nb">dict</span><span class="p">[</span><span class="n">key</span><span class="p">]</span> <span class="o">=</span> <span class="n">val</span>
+ <span class="k">return</span>
+
+ <span class="k">def</span> <span class="nf">_convertReferences</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">structure</span><span class="p">,</span> <span class="n">val</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> Replaces all references ('%%') to actual values.</span>
+<span class="sd"> """</span>
+ <span class="n">idList</span> <span class="o">=</span> <span class="p">[</span><span class="n">x</span> <span class="k">for</span> <span class="n">x</span> <span class="ow">in</span> <span class="n">re</span><span class="o">.</span><span class="n">findall</span><span class="p">(</span><span class="s">r"%(\w+)%"</span><span class="p">,</span> <span class="n">val</span><span class="p">)</span> <span class="k">if</span> <span class="n">x</span> <span class="o">!=</span> <span class="s">"null"</span><span class="p">]</span>
+ <span class="k">for</span> <span class="n">identifier</span> <span class="ow">in</span> <span class="n">idList</span><span class="p">:</span>
+ <span class="k">if</span> <span class="n">identifier</span> <span class="ow">in</span> <span class="n">structure</span><span class="p">:</span>
+ <span class="n">val</span> <span class="o">=</span> <span class="n">val</span><span class="o">.</span><span class="n">replace</span><span class="p">(</span><span class="s">"%"</span> <span class="o">+</span> <span class="n">identifier</span> <span class="o">+</span> <span class="s">"%"</span><span class="p">,</span> <span class="n">structure</span><span class="p">[</span><span class="n">identifier</span><span class="p">])</span>
+ <span class="k">return</span> <span class="n">val</span>
+
+ <span class="k">def</span> <span class="nf">_loadData</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">path</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> Loads all data for a particular path.</span>
+<span class="sd"> """</span>
+ <span class="n">temp</span> <span class="o">=</span> <span class="p">{}</span>
+ <span class="n">final</span> <span class="o">=</span> <span class="p">{}</span>
+ <span class="n">splitPath</span> <span class="o">=</span> <span class="n">path</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s">"/"</span><span class="p">)</span>
+ <span class="n">structure</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_loadStructure</span><span class="p">(</span><span class="n">splitPath</span><span class="p">)</span>
+ <span class="k">for</span> <span class="n">key</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">template</span><span class="p">[</span><span class="s">"data"</span><span class="p">]:</span>
+ <span class="n">d</span> <span class="o">=</span> <span class="p">{</span>
+ <span class="s">"value"</span><span class="p">:</span> <span class="bp">self</span><span class="o">.</span><span class="n">_loadDataValue</span><span class="p">,</span>
+ <span class="s">"file"</span><span class="p">:</span> <span class="bp">self</span><span class="o">.</span><span class="n">_loadDataFile</span><span class="p">,</span>
+ <span class="s">"date"</span><span class="p">:</span> <span class="bp">self</span><span class="o">.</span><span class="n">_loadDataDate</span>
+ <span class="p">}[</span><span class="bp">self</span><span class="o">.</span><span class="n">template</span><span class="p">[</span><span class="s">"data"</span><span class="p">][</span><span class="n">key</span><span class="p">][</span><span class="s">"type"</span><span class="p">]](</span><span class="n">final</span><span class="p">,</span> <span class="n">structure</span><span class="p">,</span> <span class="n">key</span><span class="p">)</span>
+ <span class="n">final</span><span class="p">[</span><span class="s">"path"</span><span class="p">]</span> <span class="o">=</span> <span class="n">path</span>
+ <span class="k">if</span> <span class="n">final</span><span class="p">[</span><span class="s">"imtype"</span><span class="p">]</span> <span class="ow">not</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">count</span><span class="p">:</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">count</span><span class="p">[</span><span class="n">final</span><span class="p">[</span><span class="s">"imtype"</span><span class="p">]]</span> <span class="o">=</span> <span class="mi">1</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">count</span><span class="p">[</span><span class="n">final</span><span class="p">[</span><span class="s">"imtype"</span><span class="p">]]</span> <span class="o">+=</span> <span class="mi">1</span>
+ <span class="n">final</span><span class="p">[</span><span class="s">"pegasusid"</span><span class="p">]</span> <span class="o">=</span> <span class="n">final</span><span class="p">[</span><span class="s">"imtype"</span><span class="p">]</span> <span class="o">+</span> <span class="nb">str</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">count</span><span class="p">[</span><span class="n">final</span><span class="p">[</span><span class="s">"imtype"</span><span class="p">]])</span>
+ <span class="k">return</span> <span class="n">final</span>
+
+ <span class="k">def</span> <span class="nf">_loadFiles</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> Reads all data from all specified files.</span>
+<span class="sd"> """</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">filedata</span> <span class="o">=</span> <span class="p">{}</span>
+ <span class="k">for</span> <span class="n">key</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">template</span><span class="p">[</span><span class="s">"data"</span><span class="p">]:</span>
+ <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">template</span><span class="p">[</span><span class="s">"data"</span><span class="p">][</span><span class="n">key</span><span class="p">][</span><span class="s">"type"</span><span class="p">]</span> <span class="o">==</span> <span class="s">"file"</span><span class="p">:</span>
+ <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">template</span><span class="p">[</span><span class="s">"data"</span><span class="p">][</span><span class="n">key</span><span class="p">][</span><span class="s">"value"</span><span class="p">]</span> <span class="ow">not</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">filedata</span><span class="p">:</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">filedata</span><span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">template</span><span class="p">[</span><span class="s">"data"</span><span class="p">][</span><span class="n">key</span><span class="p">][</span><span class="s">"value"</span><span class="p">]]</span> <span class="o">=</span> <span class="p">{}</span>
+ <span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">template</span><span class="p">[</span><span class="s">"data"</span><span class="p">][</span><span class="n">key</span><span class="p">][</span><span class="s">"value"</span><span class="p">],</span> <span class="s">"r"</span><span class="p">)</span> <span class="k">as</span> <span class="n">rh</span><span class="p">:</span>
+ <span class="k">for</span> <span class="n">line</span> <span class="ow">in</span> <span class="n">rh</span><span class="o">.</span><span class="n">readlines</span><span class="p">():</span>
+ <span class="n">info</span> <span class="o">=</span> <span class="n">line</span><span class="o">.</span><span class="n">strip</span><span class="p">()</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s">","</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">filedata</span><span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">template</span><span class="p">[</span><span class="s">"data"</span><span class="p">][</span><span class="n">key</span><span class="p">][</span><span class="s">"value"</span><span class="p">]][</span><span class="n">info</span><span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">template</span><span class="p">[</span><span class="s">"data"</span><span class="p">][</span><span class="n">key</span><span class="p">][</span><span class="s">"keyColumn"</span><span class="p">]]]</span> <span class="o">=</span> <span class="n">info</span><span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">template</span><span class="p">[</span><span class="s">"data"</span><span class="p">][</span><span class="n">key</span><span class="p">][</span><span class="s">"valueColumn"</span><span class="p">]]</span>
+ <span class="k">return</span>
+
+<div class="viewcode-block" id="ImageLoader.crawl"><a class="viewcode-back" href="../../indexing.html#plantcv.workflow.ImageLoader.crawl">[docs]</a> <span class="k">def</span> <span class="nf">crawl</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> Recursively walks through directories in base, and loads</span>
+<span class="sd"> the appropriate data.</span>
+<span class="sd"> """</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_loadFiles</span><span class="p">()</span>
+ <span class="k">for</span> <span class="n">root</span><span class="p">,</span> <span class="n">dirs</span><span class="p">,</span> <span class="n">files</span> <span class="ow">in</span> <span class="n">os</span><span class="o">.</span><span class="n">walk</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">template</span><span class="p">[</span><span class="s">"base"</span><span class="p">]):</span>
+ <span class="n">arr</span> <span class="o">=</span> <span class="n">root</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s">"/"</span><span class="p">)</span>
+ <span class="n">depth</span> <span class="o">=</span> <span class="nb">len</span><span class="p">(</span><span class="n">arr</span><span class="p">)</span>
+ <span class="k">if</span> <span class="p">(</span><span class="n">depth</span> <span class="o">==</span> <span class="bp">self</span><span class="o">.</span><span class="n">depth</span><span class="p">):</span>
+ <span class="k">for</span> <span class="nb">file</span> <span class="ow">in</span> <span class="n">files</span><span class="p">:</span>
+ <span class="k">if</span> <span class="nb">file</span><span class="p">[</span><span class="o">-</span><span class="nb">len</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">template</span><span class="p">[</span><span class="s">"filetype"</span><span class="p">]):]</span> <span class="o">==</span> <span class="bp">self</span><span class="o">.</span><span class="n">template</span><span class="p">[</span><span class="s">"filetype"</span><span class="p">]</span> <span class="ow">and</span> <span class="nb">file</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="o">!=</span> <span class="s">"."</span><span class="p">:</span>
+ <span class="n">d</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_loadData</span><span class="p">(</span><span class="n">root</span> <span class="o">+</span> <span class="s">"/"</span> <span class="o">+</span> <span class="nb">file</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">data</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">d</span><span class="p">)</span>
+ <span class="k">return</span>
+ </div>
+<div class="viewcode-block" id="ImageLoader.write"><a class="viewcode-back" href="../../indexing.html#plantcv.workflow.ImageLoader.write">[docs]</a> <span class="k">def</span> <span class="nf">write</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> Writes the data loaded from crawl into csv format based on 'order'</span>
+<span class="sd"> """</span>
+ <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">data</span><span class="p">:</span>
+ <span class="n">conn</span> <span class="o">=</span> <span class="n">sqlite3</span><span class="o">.</span><span class="n">connect</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">output</span> <span class="o">+</span> <span class="s">"/images.db"</span><span class="p">)</span>
+ <span class="n">tablestr</span> <span class="o">=</span> <span class="s">"(pegasusid PRIMARY KEY"</span>
+ <span class="k">for</span> <span class="n">x</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">template</span><span class="p">[</span><span class="s">"order"</span><span class="p">]:</span>
+ <span class="k">if</span> <span class="n">x</span> <span class="o">!=</span> <span class="s">"pegasusid"</span><span class="p">:</span>
+ <span class="n">tablestr</span> <span class="o">+=</span> <span class="s">","</span> <span class="o">+</span> <span class="nb">str</span><span class="p">(</span><span class="n">x</span><span class="p">)</span>
+ <span class="n">tablestr</span> <span class="o">+=</span> <span class="s">")"</span>
+ <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">overwrite</span><span class="p">:</span>
+ <span class="n">conn</span><span class="o">.</span><span class="n">execute</span><span class="p">(</span><span class="s">"DROP TABLE IF EXISTS images"</span><span class="p">)</span>
+ <span class="n">conn</span><span class="o">.</span><span class="n">commit</span><span class="p">()</span>
+ <span class="n">conn</span><span class="o">.</span><span class="n">execute</span><span class="p">(</span><span class="s">"CREATE TABLE images "</span> <span class="o">+</span> <span class="n">tablestr</span><span class="p">)</span>
+ <span class="n">writedata</span> <span class="o">=</span> <span class="p">[]</span>
+ <span class="k">for</span> <span class="n">row</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">data</span><span class="p">:</span>
+ <span class="n">writedata</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="nb">tuple</span><span class="p">([</span><span class="nb">str</span><span class="p">(</span><span class="n">row</span><span class="p">[</span><span class="n">x</span><span class="p">])</span> <span class="k">for</span> <span class="n">x</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">template</span><span class="p">[</span><span class="s">"order"</span><span class="p">]]))</span>
+ <span class="n">query</span> <span class="o">=</span> <span class="s">"insert into images "</span> <span class="o">+</span> <span class="nb">str</span><span class="p">(</span><span class="nb">tuple</span><span class="p">([</span><span class="nb">str</span><span class="p">(</span><span class="n">x</span><span class="p">)</span> <span class="k">for</span> <span class="n">x</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">template</span><span class="p">[</span><span class="s">"order"</span><span class="p">]]))</span> <span class="o">+</span> <span class="s">" values ("</span> <span class="o">+</span> <span class="p">(</span><span class="s">"?,"</span> <span class="o">*</span> <span class="nb">len</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">template</span><span class="p">[</span><span class="s">"order"</span><span class="p">]))[:</span><span class="o">-</span><span class="mi">1</span><span class="p">]</span> <span class="o">+</span> <span class="s">")"</span>
+ <span class="n">conn</span><span class="o">.</span><span class="n">executemany</span><span class="p">(</span><span class="n">query</span><span class="p">,</span> <span class="n">writedata</span><span class="p">)</span>
+ <span class="n">conn</span><span class="o">.</span><span class="n">commit</span><span class="p">()</span>
+ <span class="k">if</span> <span class="ow">not</span> <span class="bp">self</span><span class="o">.</span><span class="n">overwrite</span><span class="p">:</span>
+ <span class="n">shutil</span><span class="o">.</span><span class="n">copyfile</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">templatePath</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">output</span> <span class="o">+</span> <span class="s">"/crawl.json"</span><span class="p">)</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="k">print</span> <span class="s">"Call crawl first!"</span>
+ <span class="k">return</span>
+ </div></div>
+<span class="k">class</span> <span class="nc">DirectorySetup</span><span class="p">:</span>
+
+ <span class="k">def</span> <span class="nf">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">jobhome</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> :param jobhome: The base directory to setup a job.</span>
+<span class="sd"> :type jobhome: str</span>
+<span class="sd"> """</span>
+ <span class="k">if</span> <span class="ow">not</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">isdir</span><span class="p">(</span><span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">dirname</span><span class="p">(</span><span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">dirname</span><span class="p">(</span><span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">abspath</span><span class="p">(</span><span class="n">jobhome</span><span class="p">)</span> <span class="o">+</span> <span class="s">"/"</span><span class="p">))):</span>
+ <span class="k">print</span> <span class="s">"Can't create job folder, path doesn't exist!"</span>
+ <span class="n">sys</span><span class="o">.</span><span class="n">exit</span><span class="p">()</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">jobhome</span> <span class="o">=</span> <span class="n">jobhome</span>
+ <span class="k">return</span>
+
+ <span class="k">def</span> <span class="nf">_makeDir</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">dirpath</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> Makes a directory if it doesn't exist. Catches and</span>
+<span class="sd"> prints out common errors.</span>
+<span class="sd"> """</span>
+ <span class="k">try</span><span class="p">:</span>
+ <span class="n">os</span><span class="o">.</span><span class="n">makedirs</span><span class="p">(</span><span class="n">dirpath</span><span class="p">)</span>
+ <span class="k">except</span> <span class="ne">OSError</span> <span class="k">as</span> <span class="n">e</span><span class="p">:</span>
+ <span class="k">raise</span> <span class="ne">Exception</span><span class="p">({</span>
+ <span class="n">errno</span><span class="o">.</span><span class="n">EEXIST</span><span class="p">:</span> <span class="s">"Directory "</span> <span class="o">+</span> <span class="n">dirpath</span> <span class="o">+</span> <span class="s">" already exists!"</span><span class="p">,</span>
+ <span class="n">errno</span><span class="o">.</span><span class="n">EACCES</span><span class="p">:</span> <span class="s">"You don't have permission to create directory "</span> <span class="o">+</span> <span class="n">dirpath</span> <span class="o">+</span> <span class="s">"."</span><span class="p">,</span>
+ <span class="p">}</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="n">e</span><span class="o">.</span><span class="n">errno</span><span class="p">,</span> <span class="s">"Error for directory "</span> <span class="o">+</span> <span class="n">dirpath</span> <span class="o">+</span> <span class="s">" error:"</span> <span class="o">+</span> <span class="nb">str</span><span class="p">(</span><span class="n">e</span><span class="p">)))</span>
+ <span class="k">return</span>
+
+ <span class="k">def</span> <span class="nf">_makeFile</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">filepath</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> Opens a file to create it, uses append mode</span>
+<span class="sd"> so it doesn't overwrite any existing files.</span>
+<span class="sd"> """</span>
+ <span class="k">try</span><span class="p">:</span>
+ <span class="nb">open</span><span class="p">(</span><span class="n">filepath</span><span class="p">,</span> <span class="s">"a"</span><span class="p">)</span>
+ <span class="k">except</span> <span class="ne">OSError</span> <span class="k">as</span> <span class="n">e</span><span class="p">:</span>
+ <span class="k">raise</span> <span class="ne">Exception</span><span class="p">({</span>
+
+ <span class="p">}</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="n">e</span><span class="p">,</span> <span class="s">"Unsepcified error for file "</span> <span class="o">+</span> <span class="n">filepath</span><span class="p">))</span>
+ <span class="k">return</span>
+
+ <span class="k">def</span> <span class="nf">setup</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> Creates the directory structure needed to submit jobs,</span>
+<span class="sd"> and creates empty template files needed for job submission.</span>
+<span class="sd"> """</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_makeDir</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">jobhome</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_makeDir</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">jobhome</span> <span class="o">+</span> <span class="s">"/input/"</span><span class="p">)</span>
+ <span class="k">for</span> <span class="n">fname</span> <span class="ow">in</span> <span class="n">conf</span><span class="o">.</span><span class="n">jobFiles</span><span class="p">:</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_makeFile</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">jobhome</span> <span class="o">+</span> <span class="s">"/input/"</span> <span class="o">+</span> <span class="n">fname</span><span class="p">)</span>
+ <span class="k">return</span>
+
+
+
+</pre></div>
+
+ </div>
+
+ </div>
+</div>
+<footer class="footer">
+ <div class="container">
+ <p class="pull-right">
+ <a href="#">Back to top</a>
+
+ </p>
+ <p>
+ © Copyright 2015, Avi Knecht.<br/>
+ Created using <a href="http://sphinx.pocoo.org/">Sphinx</a> 1.3a0.<br/>
+ </p>
+ </div>
+</footer>
+ </body>
+</html>
\ No newline at end of file
diff --git a/docs/build/html/_sources/ex_script_color1.txt b/docs/build/html/_sources/ex_script_color1.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2cf85511e23f4b2a38ce290a013f613962577acd
--- /dev/null
+++ b/docs/build/html/_sources/ex_script_color1.txt
@@ -0,0 +1,333 @@
+.. |br| raw:: html
+
+ <br />
+
+Color Filter In Depth #1
+========================
+
+The :py:meth:`~ih.imgproc.Image.colorFilter` function is a very powerful and versatile function, that removes pixels
+from an image based on arbitrarily inputted logic. This example
+focuses solely on the uses and syntax of the :py:meth:`~ih.imgproc.Image.colorFilter` function. This function takes
+2 arguments. The first is the actual logic to solve, and this first argument will be the main focus of all
+color filter examples. The second argument is simply a region of interest -- namely where you want
+to apply your specified logic. If left blank, it simply applies it to the entire image. Let's talk
+about what we can do with logic. As stated under the function specific documentation, the supported
+characters for logic are: '+', '-', '*', '/', '>', '>=','==', '<', '<=', 'and', 'or', 'max', 'min', '(', ')', 'r', 'g', 'b', as well
+as any number.
+Excluding parenthesis, these can be broken down into 2 categories, operators and values. The operators
+are all the symbols before the parenthesis: '+', '-', '*', '/', '>', '>=','==', '<', '<=', 'and', 'or', 'max', and 'min'.
+The values are all the symbols after the parenthesis: 'r', 'g', 'b', and again, any number.
+Parenthesis are used to make sure your logic is well formed and easy to parse. Well formed logic means that each operator only acts
+on 2 values, and logic is surrounded by parenthesis. Thus ((r + g) + b) is well formed, but (r + g + b) is not. The logic argument for this function
+**must be well formed**. This is important to remember as we continue forward. Since we have fewer values than
+operators, let's talk about values first.
+
+
+Values are simply numbers. Numbers that are input as raw text are interpreted literally -- this is a dense way
+of saying that if a given number, say '15', occurs in your logic string, it is translated to the number 15. However,
+the other values hold special meaning relating to the colors of the image in question. 'r' is the value of the
+red channel, 'g' is the value of the green channel, 'b' is the value of the blue channel. If we are considering a particular pixel
+of an image, and let's say it has the following values for its channels in BGR order: [20, 30, 40]. For this pixel, 'r'
+equates to 40, 'g' equates to 30, and 'b' equates to 20. We apply operators
+to these values to remove pixels.
+
+
+By applying operators, we look to convert our values into a true or false output. The arithmetic operators
+('+', '-', '*', '/') do exactly what you'd expect to numbers. Thus, by themselves they do not return a true or false value.
+The comparison operators ('>', '>=', '==', '<', '<=') however, return true or false depending on what their comparison
+returns. 'max' and 'min' are used to select the maximum or minimum respectively of values. Thus (b max g) selects the
+maximum value between the blue and green channels. ((b min g) min r) selects the minimum of all three channels.
+Finally, 'and' and 'or' can be used to join together multiple pieces of logic. That's a lot of text to absorb -- let's look at some examples.
+
+Python Script
+-------------
+
+:download:`Download Script <../../examples/scripts/color1/color1.py>`
+
+:download:`Download Image <../images/sample/rgbtv1.png>`
+
+
+.. code-block:: python
+
+ import ih.imgproc
+
+ plant = ih.imgproc.Image("/path/to/your/image")
+ plant.save("base")
+
+ logicList = [
+ "(((r + g) + b) > 350)",
+ "(r >= 250)",
+ "((b > 150) and (b < 220))",
+ "((((b max g) max r) - ((b min g) min r)) > 20)",
+ "((((r + g) + b) > 700) or (((r + g) + b) < 100))",
+ "((r - g) > 50)",
+ "(((g - r) > 15) and (b < g))"
+ ]
+
+ for logic in logicList:
+ plant.restore("base")
+ plant.show("base")
+ plant.colorFilter(logic)
+ plant.show(logic)
+ plant.wait()
+
+This script applies different logic to the same image, while displaying both the base image
+and the filtered image at the same time. Let's talk about each individual piece of logic. First is "(((r + g) + b) > 350)". This
+will sum up the value of each channel (the intensity of the pixel) and compare this sum to 350. If the value is greater
+than 350, it will keep the pixel, otherwise it writes it as black. Here's the result:
+
+.. image:: ../images/sample/rgbtv1_small.png
+ :align: left
+
+.. image:: ../../examples/scripts/color1/logic0.png
+ :align: right
+
+
+|
+|
+|
+|
+|
+|
+|
+|
+|
+|
+|
+|
+|
+|
+|
+|
+|
+|
+|
+|
+|
+|
+|
+
+Next is "(r >= 250)". This simply keeps any pixel who has a red value greater than or equal
+to 250. Color channels range from 0 to 255, so 250 is very large. Here's the result:
+
+.. image:: ../images/sample/rgbtv1_small.png
+ :align: left
+
+.. image:: ../../examples/scripts/color1/logic1.png
+ :align: right
+
+
+|
+|
+|
+|
+|
+|
+|
+|
+|
+|
+|
+|
+|
+|
+|
+|
+|
+|
+|
+|
+|
+|
+|
+
+Next is "((b > 150) and (b < 220))". This will keep any pixel that has a blue value
+that is greater than 150 and less than 220. Here's the result:
+
+.. image:: ../images/sample/rgbtv1_small.png
+ :align: left
+
+.. image:: ../../examples/scripts/color1/logic2.png
+ :align: right
+
+|
+|
+|
+|
+|
+|
+|
+|
+|
+|
+|
+|
+|
+|
+|
+|
+|
+|
+|
+|
+|
+|
+|
+
+Next is ""((((b max g) max r) - ((b min g) min r)) > 20)",". This will keep any pixel
+whose maximum channel value is at least 20 greater than its minimum channel value. Here's the result:
+
+.. image:: ../images/sample/rgbtv1_small.png
+ :align: left
+
+.. image:: ../../examples/scripts/color1/logic3.png
+ :align: right
+
+|
+|
+|
+|
+|
+|
+|
+|
+|
+|
+|
+|
+|
+|
+|
+|
+|
+|
+|
+|
+|
+|
+|
+
+Next is "((((r + g) + b) > 700) or (((r + g) + b) < 100))". This will keep any pixel whose
+intensity is larger than 700 OR smaller than 100. Here's the result:
+
+.. image:: ../images/sample/rgbtv1_small.png
+ :align: left
+
+.. image:: ../../examples/scripts/color1/logic4.png
+ :align: right
+
+
+|
+|
+|
+|
+|
+|
+|
+|
+|
+|
+|
+|
+|
+|
+|
+|
+|
+|
+|
+|
+|
+|
+|
+
+Next is "((r - g) > 50)". This will keep any pixel that has a red channel value
+that is at least 50 greater than its green channel value. Here's the result:
+
+.. image:: ../images/sample/rgbtv1_small.png
+ :align: left
+
+.. image:: ../../examples/scripts/color1/logic5.png
+ :align: right
+
+|
+|
+|
+|
+|
+|
+|
+|
+|
+|
+|
+|
+|
+|
+|
+|
+|
+|
+|
+|
+|
+|
+|
+
+Finally, is "(((g - r) > 15) and (b < g))". This will keep any pixel that has a green channel value at least 15
+greater than the red channel value AND a blue channel value less than its green channel value. Here's the result:
+
+.. image:: ../images/sample/rgbtv1_small.png
+ :align: left
+
+.. image:: ../../examples/scripts/color1/logic6.png
+ :align: right
+
+|
+|
+|
+|
+|
+|
+|
+|
+|
+|
+|
+|
+|
+|
+|
+|
+|
+|
+|
+|
+|
+|
+|
+
+Command Line Script
+-------------------
+:download:`Download Script <../../examples/scripts/color1/color1.sh>`
+
+:download:`Download Image <../images/sample/rgbtv1.png>` (The image is identical to the one above)
+
+.. code-block:: bash
+
+ #!/bin/bash
+
+ ih-color-filter --input "/path/to/your/image" --output "logic0.png" --logic "(((r + g) + b) > 350)"
+ ih-color-filter --input "/path/to/your/image" --output "logic1.png" --logic "(r >= 250)"
+ ih-color-filter --input "/path/to/your/image" --output "logic2.png" --logic "((b > 150) and (b < 220))"
+ ih-color-filter --input "/path/to/your/image" --output "logic3.png" --logic "((((b max g) max r) - ((b min g) min r)) > 20)"
+ ih-color-filter --input "/path/to/your/image" --output "logic4.png" --logic "((((r + g) + b) > 700) or (((r + g) + b) < 100))"
+ ih-color-filter --input "/path/to/your/image" --output "logic5.png" --logic "((r - g) > 50)"
+ ih-color-filter --input "/path/to/your/image" --output "logic6.png" --logic "(((g - r) > 15) and (b < g))"
+
+This bash script performs the exact same color filtering as the above python script. Each color filter call
+must be done separately. Each takes in the same input file, and writes a separate output file.
+
+
+
+
diff --git a/docs/build/html/_sources/ex_script_core1.txt b/docs/build/html/_sources/ex_script_core1.txt
new file mode 100644
index 0000000000000000000000000000000000000000..60553c9e79da7fd07d7944ec8a12c73f781b68e8
--- /dev/null
+++ b/docs/build/html/_sources/ex_script_core1.txt
@@ -0,0 +1,198 @@
+Core Processing Example #1
+===========================
+This section will detail a shorter script that provides details on how to get started with
+script form image processing. The script will detail how to use several core functions
+to load, save, and show images.
+
+Python Script
+-----------------------
+:download:`Download Script <../../examples/scripts/core1/core1.py>`
+
+:download:`Download Image <../../examples/scripts/core1/base.png>`
+
+.. code-block:: python
+
+ import ih.imgproc
+
+ plant = ih.imgproc.Image("/path/to/your/image")
+
+ plant.save("base")
+ plant.show("base")
+ plant.write("base.png")
+
+ plant.convertColor("bgr", "gray")
+ plant.save("gray")
+ plant.show("gray")
+ plant.write("gray.png")
+
+ plant.threshold(50)
+ plant.save("thresh50")
+ plant.show("thresh50")
+ plant.restore("gray")
+
+ plant.threshold(75)
+ plant.save("thresh75")
+ plant.show("thresh75")
+ plant.restore("gray")
+
+ plant.threshold(100)
+ plant.save("thresh100")
+ plant.show("thresh100")
+ plant.restore("gray")
+
+ plant.wait()
+ plant.restore("thresh50")
+ plant.write("thresh50.png")
+
+This script shows how to get started with ih. Let's talk about it block by block:
+
+.. code-block:: python
+
+ import ih.imgproc
+ plant = ih.imgproc.Image("/path/to/your/image")
+
+These two lines setup your image. The first line imports a module, which is simply
+a grouping of related in code. In this case, we import the 'imgproc' module, which
+is a grouping of functions related to image processing. This module contains
+all of ih's image processing functionality, and as a result, is the code we want to import
+to process images. The second line creates an Image object named 'plant'.
+Object Oriented Programming (OOP) can be a hard concept to understand at first.
+In a simplistic form, objects are like nouns, and the methods we perform on the objects
+are like verbs. Our Image object has certain properties that make it that type of object,
+just like plants have properties that define them. This line accomplishes translating
+the actual image into a form understandable by the code. The 'plant' object now has
+properties that define it, and actions (methods) we can perform on it. The rest of the script
+deals specifically with the methods we can perform on our image objects.
+
+.. code-block:: python
+
+ plant.save("base")
+ plant.show("base")
+ plant.write("base.png")
+
+These three lines use three separate methods on our plant object, :py:meth:`~ih.imgproc.Image.save`,
+:py:meth:`~ih.imgproc.Image.show`, and :py:meth:`~ih.imgproc.Image.write`. Each of these
+methods performs exactly what its named -- the save method saves the image for future use, the show method
+displays the image, and the write method writes the image to a file. Each method has an argument
+passed into it, determining the name to be used in each case. Calling plant.save("base") saves the image
+with the name base, plant.show("base") shows the image with the window title base, and plant.write("base.png")
+writes the image to a file named base.png. Here's what our base image looks like:
+
+.. image:: ../../examples/scripts/core1/base.png
+ :align: center
+
+|
+
+.. code-block:: python
+
+ plant.convertColor("bgr", "gray")
+ plant.save("gray")
+ plant.show("gray")
+ plant.write("gray.png")
+
+The :py:meth:`~ih.imgproc.Image.convertColor` method performs a color spectrum shift, changing our image from a color image i.e. "bgr"
+to a gray scale image i.e. "gray". It should be noted, that all methods overwrite the current image -- which is way the save / restore
+functionality is so important. Additionally, converting an image to gray scale from color is an important non-linear shift.
+A color image is called "bgr" because of the three colors in the image, blue, green, and red. Each pixel has a value for
+each of these colors, or channels. Converting to gray condenses the image to a single channel -- intensity.
+This means that you **cannot** use :py:meth:`~ih.imgproc.Image.convertColor` to restore color to a gray scale image.
+Although we do not use it in this example, the reason for saving the base image is to restore color in a future step.
+The last three lines of this block of code perform the exact same function as the previous block, only using
+different names for saving, showing, and writing. Here's what our gray scale image looks like:
+
+.. image:: ../../examples/scripts/core1/gray.png
+ :align: center
+
+|
+
+.. code-block:: python
+
+ plant.threshold(50)
+ plant.save("thresh50")
+ plant.show("thresh50")
+ plant.restore("gray")
+
+Now that we have a gray scale image, we perform a :py:meth:`~ih.imgproc.Image.threshold` on it. This simply
+checks the value of each pixels intensity, and checks to see if it beats the cutoff we specify. In this case,
+if the pixel has an intensity greater than 50, we keep it. Intensity values range from 0 to 255. The
+:py:meth:`~ih.imgproc.Image.save` and :py:meth:`~ih.imgproc.Image.show` methods should be familiar,
+but the fourth line contains a new method, :py:meth:`~ih.imgproc.Image.restore`. This method restores
+the image to a previously saved image. In the previous block we saved our gray scale image under the name 'gray'.
+Here, we simply restore that image after thresholding. The purpose of this is to compare multiple threshold values.
+We restore the gray image at the end of each thresholding block to use the same image for thresholding. Here's the
+result of thresholding by 50:
+
+.. image:: ../../examples/scripts/core1/thresh50.png
+ :align: center
+
+|
+
+.. code-block:: python
+
+ plant.threshold(75)
+ plant.save("thresh75")
+ plant.show("thresh75")
+ plant.restore("gray")
+
+This block is identical to the previous one, except we use a threshold value of 75 instead of 50,
+and we rename our saved image and displayed image accordingly. Here's the result of thresholding
+by 75:
+
+.. image:: ../../examples/scripts/core1/thresh75.png
+ :align: center
+
+|
+
+.. code-block:: python
+
+ plant.threshold(100)
+ plant.save("thresh100")
+ plant.show("thresh100")
+ plant.restore("gray")
+
+This block is identical to the previous one, except we use a threshold value of 100 instead of 75,
+and we rename our saved image and displayed image accordingly. Here's the result of thresholding
+by 100:
+
+.. image:: ../../examples/scripts/core1/thresh100.png
+ :align: center
+
+|
+
+.. code-block:: python
+
+ plant.wait()
+ plant.restore("thresh50")
+ plant.write("thresh50.png")
+
+The final block introduces a new method, :py:meth:`~ih.imgproc.Image.wait`. This method
+simply halts execution until a key is pressed, then destroys all displayed windows. This
+means that once this point in the script is hit, there should be 5 open windows, the base image,
+the gray image, and one for each of the three thresholds. After execution is resumed,
+we restore the threshold by 50, and write it to a file.
+
+Command Line Script
+-------------------
+:download:`Download Script <../../examples/scripts/core1/core1.sh>`
+
+:download:`Download Image <../../examples/scripts/core1/base.png>` (The image is identical to the one above)
+
+.. code-block:: bash
+
+ #!/bin/bash
+
+ ih-convert-color --input "/path/to/your/image" --output "gray.png" --intype "bgr" --outtype "gray"
+ ih-threshold --input "gray.png" --output "thresh50.png" --thresh 50
+ ih-threshold --input "gray.png" --output "thresh75.png" --thresh 75
+ ih-threshold --input "gray.png" --output "thresh100.png" --thresh 100
+
+This bash script performs the exact same workflow as the one above. Although not major, it is important to note the
+differences between library and command line access. Command line access loads and writes an image at each step,
+whereas library access loads once, and only writes when you tell it to. Additionally, script names are close to that
+of the method, and all follow lower case format, with words seperated by dashes, and ih prependening all commands.
+The most notable difference, is that a restore method is unnecessary with command-line input. We simply reuse the gray.png
+file we wrote once. Additionally, there is no initial setup, you simply begin processing. The arguments pased into the
+command line arguments match identically with the method arguments above.
+
+
+
diff --git a/docs/build/html/_sources/ex_script_core2.txt b/docs/build/html/_sources/ex_script_core2.txt
new file mode 100644
index 0000000000000000000000000000000000000000..aa561789d99fe2375017ef428c56d9dcfad22598
--- /dev/null
+++ b/docs/build/html/_sources/ex_script_core2.txt
@@ -0,0 +1,314 @@
+Core Processing Example #2
+===========================
+This section will go over a longer script that provides details on many different image processing
+functions including blurring, thresholding, morphologies, color filtering, and contour cutting, as
+well as many core functions, such as save, restore, show, and write.
+
+Python Script
+-----------------------
+:download:`Download Script <../../examples/scripts/core2/core2.py>`
+
+:download:`Download Image <../../examples/scripts/core2/base.png>`
+
+.. code-block:: python
+
+ import ih.imgproc
+ plant = ih.imgproc.Image("/path/to/your/image")
+
+ plant.save("base")
+ plant.show("base")
+
+ plant.convertColor("bgr", "gray")
+ plant.show("grayscale")
+
+ plant.gaussianBlur((5, 5))
+ plant.show("blur")
+
+ plant.adaptiveThreshold(255, "mean", "binary", 15, 3)
+ plant.show("adaptive threshold")
+
+ plant.bitwise_not()
+ plant.show("invert")
+
+ plant.convertColor("gray", "bgr")
+ plant.bitwise_and("base")
+ plant.show("recolor")
+
+ plant.morphology("open", "rect", (3, 3))
+ plant.show("morph")
+
+ plant.colorFilter("(((max - min) > 40) and ((b - g) < 30))", [plant.y - 350, -1, -1, -1])
+ plant.show("filter")
+ plant.save("filter")
+
+ plant.convertColor("bgr", "gray")
+ plant.threshold(0)
+ plant.save("binary")
+ plant.restore("filter")
+
+ plant.contourCut("binary", basemin = 500, resize = True)
+ plant.show("final")
+ plant.write("final.png")
+
+ print "total plant pixels = ",plant.extractPixels()
+ print "[plant height, plant width] = ",plant.extractDimensions()
+ print "Nonzero color data -- [ [bmean, bmed], [gmean, gmed], [rmean, rmed] ] = ",plant.extractColorData()
+ print "With zero color data -- [ [bmean, bmed], [gmean, gmed], [rmean, rmed] ] = ",plant.extractColorData(nonzero = False)
+
+ plant.wait()
+
+This script show cases several features of ih, is fairly simple and fairly accurate. Let's talk about it block by block:
+
+.. code-block:: python
+
+ import ih.imgproc
+ plant = ih.imgproc.Image("/path/to/your/image")
+
+These two lines setup your image. The first line imports the actual library to be used, and in this case we
+want the imgproc module from ih. The second line creates an object of your image, named 'plant'. Our image
+has been loaded in, so we are ready for processing.
+
+.. code-block:: python
+
+ plant.save("base")
+ plant.show("base")
+
+These two lines don't do any actual processing yet. The :py:meth:`~ih.imgproc.Image.save` method saves what our image currently looks like
+for future use. This will be used in a later step to re-constitute the color of the image. We fed in the name
+'base', and that's how we will refer to this saved image in the future. The 'show' method simply opens a window
+of the current image. Show automatically resizes an image down if it is too large (which it will be). We also
+fed in the name base which means our window will have the title 'base'. If a name is not fed in, the titles
+will simply be numbered. Here's what our base image looks like:
+
+.. image:: ../../examples/scripts/core2/base_small.png
+ :align: center
+
+For viewing purposes all images have been greatly reduced in size. On to the next block:
+
+.. code-block:: python
+
+ plant.convertColor("bgr", "gray")
+ plant.show("grayscale")
+
+Now we do some actual processing! The :py:meth:`~ih.imgproc.Image.convertColor` method does exactly that -- changes the spectrum of the image.
+Currently, supported spectrums are "bgr", "hsv", "lab", "ycrcb", and "gray". It is important to remember that
+many spectrum changes are one-directional. In this case, we convert "bgr" to "gray", giving us a grayscale image.
+If we then called the same function in reverse i.e. plant.convertColor("gray", "bgr"), our image would look exactly the same.
+You can find more information on this in the :py:meth:`~ih.imgproc.Image.convertColor` method. Again, we use
+'show' to view the result of our step. Here's what our gray scale image looks like:
+
+.. image:: ../../examples/scripts/core2/gray_small.png
+ :align: center
+
+|
+
+.. code-block:: python
+
+ plant.gaussianBlur((5, 5))
+ plant.show("blur")
+
+Here we blur the image slightly, using :py:meth:`~ih.imgproc.Image.gaussianBlur` with a kernel of size 5 x 5.
+The first number specifies the height of the kernel, and the second the width of the kernel. Blurring an image
+before thresholding will help smooth the result, and remove more noise from the image. Here's our result:
+
+.. image:: ../../examples/scripts/core2/blur_small.png
+ :align: center
+
+|
+
+.. code-block:: python
+
+ plant.adaptiveThreshold(255, "mean", "binary", 15, 3)
+ plant.show("adaptive threshold")
+
+Next, we threshold our gray image. Normal thresholding (see the :py:meth:`~ih.imgproc.Image.threshold` method) simply
+checks to see if each pixel in the image is greater than the specified threshold. The :py:meth:`~ih.imgproc.Image.adaptiveThreshold` method
+breaks up the image into windows, and considers each window separately. '255' represents the value we assign to a pixel if it beats the
+threshold. "mean" is the adaptive method we use -- we take the average of the pixels in a window to determine the threshold.
+"binary" is the threshold type. 15 is the window size -- which means we consider 15 x 15 blocks of pixels as each window. 3
+is a constant that is subtracted from the calculated threshold for each window. Again, we use 'show' to view the result of our step.
+Here's what our image looks like after adaptive thresholding:
+
+.. image:: ../../examples/scripts/core2/thresh_small.png
+ :align: center
+
+|
+
+.. code-block:: python
+
+ plant.bitwise_not()
+ plant.show("inverted")
+
+The :py:meth:`~ih.imgproc.Image.bitwise_not` method inverts an image. If the image is a color image it processes each channel separately.
+Inverting the image is going to be important for our next step. Here's the inverted image:
+
+.. image:: ../../examples/scripts/core2/invert_small.png
+ :align: center
+
+|
+
+.. code-block:: python
+
+ plant.convertColor("gray", "bgr")
+ plant.bitwise_and("base")
+ plant.show("recolor")
+
+This step recolors the image to the original colors which we saved under the name 'base'. :py:meth:`~ih.imgproc.Image.bitwise_and`
+computes the logical and of two images. This function can only be used on two images of the same shape. In this case, our base
+image has 3 channels, an r, g, and b channel, but our gray image only has 1 channel, intensity. Even though :py:meth:`~ih.imgproc.Image.convertColor`
+won't change what the image looks like, we need to ensure that both images have the same number of channels before computing the bitwise_and.
+This extra convertColor step doesn't need to happen when using command-line scripts for processing, because images are saved and loaded as
+3 channel images. Here's the recolored image:
+
+.. image:: ../../examples/scripts/core2/recolor_small.png
+ :align: center
+
+We've stripped a lot of the background out of image with pretty good accuracy.
+We need to clean up the noise around the bottom, and clean up the pot still.
+
+.. code-block:: python
+
+ plant.morphology("open", "rect", (3, 3))
+ plant.show("morph")
+
+:py:meth:`~ih.imgproc.Image.morphology` uses one of several different methods to adjust the structure of your image.
+In this case, we use morphological opening -- this erodes all borders in the image, and then adds borders back on to
+the shapes still in the image. In this case, it removes a lot of the noise around the bottom without hurting the
+plant very much:
+
+.. image:: ../../examples/scripts/core2/morph_small.png
+ :align: center
+
+Now we need to filter out the carrier, as well as the track from the bottom of the image.
+
+.. code-block:: python
+
+ plant.colorFilter("(((max - min) > 40) and ((b - g) < 30))", [plant.y - 350, -1, -1, -1])
+ plant.show("filter")
+ plant.save("filter")
+
+:py:meth:`~ih.imgproc.Image.colorFilter` is a powerful method that takes 2 arguments, the first is logic, the second is a region of interest.
+The logic argument to colorFilter must be well formed based on symbolic logic rules. This means that operators can only act on two operands,
+which means that your logic string may have more parenthesis than if it were in a standard language. You can find more information under the
+:py:meth:`~ih.imgproc.Image.colorFilter` docs. Based on our logic, we only keep a pixel if it meets both of the following conditions:
+the maximum value of the pixel (max([r, g, b])) minus the minimum value of the pixel (min([r, g, b])) is greater than 40, and the blue value
+of the pixel minus the green value of the pixel is less than 30. The first condition removes all gray pixels. Gray colors have lower variance between
+the three channels and we target them likewise. This piece will filter out the track and the bright colors of the pot. The second condition will remove
+the blue part of the part. The next argument is our region of interest. All roi's have the following form [ystart, yend, xstart, xend], due to the order
+which opencv uses. Additionally, -1 can be used as a placeholder for any value in an roi, and represents the far edge for that value. For start values
+-1 is equivalent to 0, for end values -1 is equivalent to the maximal width or height of the image. Finally,
+the plant object internally maintains a width as 'x' and a height as 'y'. plant.x will return the plant's width, and plant.y will return the
+plant's height. So, in this case our region of interest targets only the bottom 350 pixels of the image. ystart is at plant.y - 350, and we use the maximal
+height of the image for yend. We also target the entire width of the plant -- we use -1 for both xstart and xend. Here's the image after filtration:
+
+.. image:: ../../examples/scripts/core2/filter_small.png
+ :align: center
+
+At this point we will call our image processing good, and crop the image down to just the plant, so we can get an accurate height and width.
+To do this, we will use the :py:meth:`~ih.imgproc.Image.contourCut` function. This function requires a color image, and a binary image.
+We have saved our current image under the name 'filter', so we need to prepare a binary image:
+
+.. code-block:: python
+
+ plant.convertColor("bgr", "gray")
+ plant.threshold(0)
+ plant.save("binary")
+ plant.restore("filter")
+
+We can't threshold color images, so we begin by using :py:meth:`~ih.imgproc.Image.convertColor` to convert our image to gray scale. Next, we
+use :py:meth:`~ih.imgproc.Image.threshold` with a thresh value of 0 to threshold our image. With a threshold of 0, as long as any pixel is
+non-zero, it will be kept. This means that we will create a binary image that is an exact structural replica of our current image. We save
+this image for later use under the name 'binary'. Final, we :py:meth:`~ih.imgproc.Image.restore~ our color image we previously saved.
+The restore method changes the current image to a previously saved one. Here's what our binary image looks like:
+
+.. image:: ../../examples/scripts/core2/binary_small.png
+ :align: center
+
+|
+
+.. code-block:: python
+
+ plant.contourCut("binary", basemin = 500, resize = True)
+ plant.show("final")
+ plant.write("final.png")
+
+Finally, we use :py:meth:`~ih.imgproc.Image.contourCut` to crop our image. contourCut removes pieces of an
+image based on the size of contours, which are clusters of pixels in the image. Noise in the image is spread
+out in small clusters, but the plant is connected. Specifying a sufficiently large threshold value will cause
+the noise to get excluded from the image. The final roi of the image is determined by the contours that are
+larger than the threshold value, and the image is cropped such that all the contours remain in the image. The
+image calculates contours from the binary image, but returns a final image based on the colors of the current image.
+We feed in 'binary' as our binary image, specify a threshold area of 500 pixels, and specify resize = True. If resize
+is false, the image won't be resized, and instead, all pixels outside the roi will be set off. We :py:meth:`~ih.imgproc.Image.write`
+our final image to "final.png". By default, images are written to the current directory, unless you specify an outputdir when
+you create the plant object. Here's the final, un-scaled image:
+
+.. image:: ../../examples/scripts/core2/final.png
+ :align: center
+
+Now that our image is processed, we extract data from it:
+
+.. code-block:: python
+
+ print "total plant pixels = ",plant.extractPixels()
+ print "[plant height, plant width] = ",plant.extractDimensions()
+ print "Nonzero color data -- [ [bmean, bmed], [gmean, gmed], [rmean, rmed] ] = ",plant.extractColorData()
+ print "With zero color data -- [ [bmean, bmed], [gmean, gmed], [rmean, rmed] ] = ",plant.extractColorData(nonzero = False)
+
+Each of these lines print out information about our final image. :py:meth:`~ih.imgproc.Image.extractPixels` returns the
+total number of non-zero pixels in the image. :py:meth:`~ih.imgproc.Image.extractDimensions` returns the height and
+width of the plant. :py:meth:`~ih.imgproc.Image.extractColorData` calculates histograms for each individual color channel
+of the image, and returns the median and mean for each histogram. By default, it only uses non-zero values in its calculations,
+but you can specify nonzero = False to use all values. Your output should look something like this:
+
+.. code-block:: python
+
+ total plant pixels = 21964
+ [plant height, plant width] = [637, 668]
+ Nonzero color data -- [ [bmean, bmed], [gmean, gmed], [rmean, rmed] ] = [[56.514124293785308, 11.0], [71.787162162162161, 34.5], [67.78235294117647, 25.0]]
+ With zero color data -- [ [bmean, bmed], [gmean, gmed], [rmean, rmed] ] = [[35.67578125, 10.0], [53.78515625, 9.0], [44.4140625, 9.0]]
+
+Finally, hiding at the end is the following line:
+
+.. code-block:: python
+
+ plant.wait()
+
+The :py:meth:`~ih.imgproc.Image.wait` does exactly that, and is a wrapper to 2 opencv functions. First, the function
+will pause execution, and all of the images you displayed will stay open in the named windows you specified. Second,
+while focused on one of your displayed windows, if you press any key, it will remove all the windows, and continue execution
+of the program -- which in this case means the program will stop.
+
+Command Line Script
+-------------------
+:download:`Download Script <../../examples/scripts/core2/core2.sh>`
+
+:download:`Download Image <../../examples/scripts/core2/base.png>` (The image is identical to the one above)
+
+.. code-block:: bash
+
+ #!/bin/bash
+
+ ih-convert-color --input "/path/to/your/image" --output "gray.png" --intype "bgr" --outtype "gray"
+ ih-gaussian-blur --input "gray.png" --output "blur.png" --kwidth 5 --kheight 5
+ ih-adaptive-threshold --input "blur.png" --output "thresh.png" --value 255 --adaptiveType "mean" --thresholdType "binary" --blockSize 15 --C 3
+ ih-bitwise-not --input "thresh.png" --output "invert.png"
+ ih-bitwise-and --input1 "base.png" --input2 "invert.png" --output "recolor.png"
+ ih-morphology --input "recolor.png" --output "morph.png" --morphType "open" --ktype "rect" --kwidth 3 --kheight 3
+ ih-color-filter --input "morph.png" --output "filter.png" --logic "(((max - min) > 40) and ((b - g) < 30))" --ystart "y - 350"
+ ih-threshold --input "filter.png" --output "binary.png" --thresh 0
+ ih-contour-cut --input "filter.png" --binary "binary.png" --output "final.png" --basemin 500 --resize
+
+This bash script should perform the exact same workflow as the one above. Although not major, it is important to note the
+differences between library and command line access. Command line access loads and writes an image at each step,
+whereas library access loads once, and only writes when you tell it to. Additionally, script names are close to that
+of the method, and all follow lower case format, with words seperated by dashes, and ih prependening all commands.
+Most arguments are the same, but because we can't specify tuples or lists from the command line, arguments like kernels and
+regions of interest have to change. Individual arguments are defined, as you can see in gaussian-blur, morphology, and
+color-fitler. kwidth and kheight have to specified individual, and ystart, yend, xstart, xend have to be specified individual.
+-1 is assumed as the default value for roi, so any value you don't specify will be the edge for that position as specified
+above. For the contour-cut 'resize' argument, you don't have to specify true, as simply adding --resize will imply
+you want to resize.
+
+
+
diff --git a/docs/build/html/_sources/ex_workflow_1.txt b/docs/build/html/_sources/ex_workflow_1.txt
new file mode 100644
index 0000000000000000000000000000000000000000..5e754eb48e5ac8422779ab6c84b82705fd64d53c
--- /dev/null
+++ b/docs/build/html/_sources/ex_workflow_1.txt
@@ -0,0 +1,906 @@
+.. raw:: html
+
+ <style> .red {color:red} .blue {color:blue} .green {color:green} .orange {color:orange} </style>
+
+.. role:: red
+
+.. role:: blue
+
+.. role:: green
+
+.. role:: orange
+
+Workflow Example #1
+===========================
+This section will detail the steps involved with creating a super-computer
+workflow. It assumes that you have the proper environment setup
+already on a grid computer with Condor and Pegasus installed.
+Workflow generation is designed specifically for high throughput
+data sets -- this example uses a data set of ~80,000 images. Additionally,
+this tutorial serves to show how to setup and run a workflow, not
+explaining the analysis choices made when designing a workflow. This workflow
+was created using experiment '0184 Uni Nebraska Rice 1' data, on
+Tusker at the Holland Computing Center.
+
+Final Templates
+----------------
+:download:`Image Loading <../../examples/workflows/current/crawl.json>`
+
+:download:`Image Processing <../../examples/workflows/current/imgproc.json>`
+
+:download:`Configuration <../../examples/workflows/current/config.json>`
+
+:download:`Genotype Key File <../../examples/workflows/current/GenKey.csv>`
+
+:download:`ROI files <../../examples/workflows/current/roi.tar.gz>`
+
+Image Loading
+-------------
+In this workflow example, we will use data acquired from LemnaTec's
+imaging system, for experiment 0184. The input data structure has been
+altered slightly from the raw LemnaTec data. Although none of the data
+changed, an extra directory was added to help break up the data set.
+Here are several examples of paths to images:
+
+| /work/walia/common/ih/rawdata/0184 Uni Nebraska Rice 1/strain3/0184 Uni Nebraska Rice 1_023542-C_2013-09-05_05-18-33_455640/RGB SV1/0_0.png
+| /work/walia/common/ih/rawdata/0184 Uni Nebraska Rice 1/strain5/0184 Uni Nebraska Rice 1_023546-C_2013-08-21_05-22-52_432942/FLUO SV1/0_0.png
+| /work/walia/common/ih/rawdata/0184 Uni Nebraska Rice 1/strain93/0184 Uni Nebraska Rice 1_023722-S_2013-09-09_10-56-45_462980/RGB TV/0_0.png
+
+There are a total of 436 strain folders, 36 sub folders in each strain folder, and 12 additional image-type folders. For
+this experiment, we will be processing RGB SV1, RGB SV2, FLUO SV1, FLUO SV2, and RGB TV images for a total of 436 * 36 * 5 ~= 80,000 images.
+The image loading step takes care of two key problems posed by having large data sets (assuming correctly written template files). First,
+it tracks all images, and loads them into a single database, making it very easy to find and process files in the future. Second,
+all meta-data definitions are done as a result of the crawling -- no manual definitions are required. Consider our directory structure.
+There is a lot of information about each image in the names of the directories -- id numbers, whether or not the plant was stressed, the date, and the image
+type. With this motivation in mind, lets look at the loading template, crawl.json.
+
+.. code-block:: javascript
+
+ {
+ "path": "/work/walia/common/ih/rawdata/0184 Uni Nebraska Rice 1/%null%/%null%_%idnum%-%idchar%_%date%/%imgname%/0_0.png",
+ "base": "/work/walia/common/ih/rawdata/0184 Uni Nebraska Rice 1/",
+ "filetype": ".png",
+ "order": ["experiment", "id", "genotype", "date", "treatment", "imgname", "imtype", "path"],
+ "data": {
+ "experiment": {
+ "type": "value",
+ "value": "0184"
+ },
+ "id": {
+ "type": "value",
+ "value": "%idnum%-%idchar%"
+ },
+ "genotype": {
+ "type": "file",
+ "value": "/Users/aknecht/git/ih/old_scripts/2014-09-03/GenKey.csv",
+ "key": "%idnum%-%idchar%",
+ "keyColumn": 0,
+ "valueColumn": 1
+ },
+ "date": {
+ "type": "date",
+ "value": "%date%",
+ "format": "Y-m-d"
+ },
+ "treatment": {
+ "type": "value",
+ "translate": "true",
+ "value": "%idchar%"
+ },
+ "imgname": {
+ "type": "value",
+ "value": "%imgname%"
+ },
+ "imtype": {
+ "type": "value",
+ "translate": "true",
+ "value": "%imgname%"
+ }
+ },
+ "translations": {
+ "treatment": {
+ "S": "Stress",
+ "s": "Stress",
+ "C": "Control",
+ "c": "Control"
+ },
+ "imtype": {
+ "RGB SV1": "rgbsv",
+ "RGB SV2": "rgbsv",
+ "RGB TV": "rgbtv",
+ "FLUO SV1": "fluosv",
+ "FLUO SV2": "fluosv",
+ "FLUO TV": "fluotv",
+ "NIR SV1": "nirsv",
+ "NIR SV2": "nirsv",
+ "NIR TV": "nirtv",
+ "IR SV1": "irsv",
+ "IR SV2": "irsv",
+ "IR TV": "irtv"
+ }
+ }
+ }
+
+This template is fairly complex, so we will break it down into logical subunits. It should be noted,
+that the order of these definitions is not strict, the way they are written matches the thought process
+behind crawling.
+
+.. code-block:: javascript
+
+ "path": "/work/walia/common/ih/rawdata/0184 Uni Nebraska Rice 1/%null%/%null%_%idnum%-%idchar%_%date%/%imgname%/0_0.png",
+ "base": "/work/walia/common/ih/rawdata/0184 Uni Nebraska Rice 1/",
+
+The first two definitions map our way through the rest of the template. Above, we noted several important
+pieces of information in the name of the directories. We are doing exactly that here, except in a way that
+is more understandable to the computer. We mark important places in the directory structure by using % signs,
+along with names. The names themselves are not strictly checked, so use names that are easy to remember.
+Here we mark 4 places, with the identifiers 'idnum', 'idchar', 'date', and 'imgname'. The 'null' name is for a
+piece of information that isn't important, but still needs to be crawled. In this case, the 'strain' directories
+contain no information relevant to the images themselves. Also note the underscores and dashes in the definition.
+Path splitting to obtain information is possible by placing underscores (_), dashes (-), or spaces ( ) into your
+definition. To make it easier to see, look at our "path" definition side by side with an example path:
+
+| "path": "/work/walia/common/ih/rawdata/0184 Uni Nebraska Rice 1/**%null%**/%null%\_\ :red:`%idnum%`-\ :blue:`%idchar%`\_\ :green:`%date%`/\ :orange:`%imgname%`/0_0.png",
+| /work/walia/common/ih/rawdata/0184 Uni Nebraska Rice 1/**strain3**/0184 Uni Nebraska Rice 1\_\ :red:`023542`-\ :blue:`C`\_\ :green:`2013-09-05`\_05-18-33_455640/\ :orange:`RGB SV1`/0_0.png
+
+It becomes very apparent how each defined identifier lines up with the path. Creating this identifier string is
+a very key part of the template definition. It will likely take some time before you are completely comfortable
+writing identifier strings, and every workflow is different. The other workflow examples have different data paths
+for input files, so it is recommended you look at those as well. The identifiers will be used in further steps. The "base" definition
+is simply where crawling should start. It should be a subset of the "path" definition.
+
+.. code-block:: javascript
+
+ "filetype": ".png",
+ "order": ["experiment", "id", "genotype", "date", "treatment", "imgname", "imtype", "path"],
+
+The "filetype" definition is exactly that. It searches for all files in the final path that end in the specified filetype.
+The "order" definition is the order in which values are stored in to the database. It serves two purposes. Thematically,
+you can organize your columns the same way you would data. More importantly, it specifies which values are saved to the database.
+You can define any value in the "order" definition, however, there are **required** definitions as well. In addition,
+although there are some optional column names, many of the statistics function expect a given format for data.
+The names included above are the names that the statistics functions expect. They relate directly to information about each image.
+"experiment" is required, although we simply use it as additional information to help keep things organized. Data that comes
+from LemnaTec has id's assigned to them, in this case, "id" is the LemnaTec assigned value. "genotype" contains the identifier for
+which genotype the plant is. "date" is the date the plant was imaged. "treatment" is whether the plant is control or stressed.
+"imgname" is which type, shot, and number the plant is. Examples include RGB SV1, RGB SV2, RGB TV, FLUO SV1, FLUO SV2, FLUO TV e.t.c
+"imtype" is just which type and shot the plant is. Examples include rgbsv, rgbtv, fluosv, fluotv e.t.c. "imtype" is generally
+used more than it "imgname" counterpart. "path" is a required entry, and will be filed with the input path to the image.
+The final output path of the image is based on "experiment", "id", "date", "imtype", and "imgname", so defining
+these is very important.
+The next section we talk about is the data section. The purpose of the data section is to convert the identifiers from
+our "path" definition, to the names used in our "order" definition. Let's look at it one name at a time:
+
+.. code-block:: javascript
+
+ "data": {
+ "experiment": {
+ "type": "value",
+ "value": "0184"
+ },
+
+The first line simply shows how to start the data section. Specifying '"data": {' shows that all further entries
+are specifically related to data-mapping. Each value specified in the data section corresponds to a specific
+value in the "order" entry. The values defined in the data section are NOT order dependent, but we include
+them in the same order for ease of access. Finally, remember that each of these values is for *every* image.
+Our first example is defining a value for "experiment". It's important
+to note that "experiment" occurs in order. The names of entries in the data section must match the value
+in the "order" entry exactly. First we define the type of "experiment". Type's of data keys can be defined
+as "value", "file", or "date". Here, we define the type of experiment as a value. This means that the value of
+experiment will be saved as some combination of hard-coded characters, and identifiers, based on the "value" definition.
+In this case, we do not use identifiers in our "value" definition. We simply save the value for experiment for every image
+as 0184.
+
+.. code-block:: javascript
+
+ "id": {
+ "type": "value",
+ "value": "%idnum%-%idchar%"
+ },
+
+Here, we define the "id" for each plant. We also define it as type "value", but this time we use identifiers in
+the value. This will load the identifiers from the path directly into the value for id. Looking at our path definition and test path again:
+
+| "path": "/work/walia/common/ih/rawdata/0184 Uni Nebraska Rice 1/**%null%**/%null%\_\ :red:`%idnum%`-\ :blue:`%idchar%`\_\ :green:`%date%`/\ :orange:`%imgname%`/0_0.png",
+| /work/walia/common/ih/rawdata/0184 Uni Nebraska Rice 1/**strain3**/0184 Uni Nebraska Rice 1\_\ :red:`023542`-\ :blue:`C`\_\ :green:`2013-09-05`\_05-18-33_455640/\ :orange:`RGB SV1`/0_0.png
+
+For this example, the value of id would be loaded as "023542-C". It may seem unnecessary to break up 'idnum' and 'idchar', since we use them together here,
+however, we use 'idchar' by itself in a later step. It's important to make sure that the identifiers you use match exactly with those used in the path.
+Any value not surrounded by percent signs will be hard-coded into the output value. So the "-" between our "idnum" and "idchar" identifiers is hard-coded
+into the output value.
+
+.. code-block:: javascript
+
+ "genotype": {
+ "type": "file",
+ "value": "GenKey.csv",
+ "key": "%idnum%-%idchar%",
+ "keyColumn": 0,
+ "valueColumn": 1
+ },
+
+Here, we define the "genotype" for each plant. This time, the type is "file". This type of data key searches through the rows of a file,
+assuming that there is a mapping of key -> value in your row. If you look at the :download:`Genotype Key File <../../examples/workflows/current/GenKey.csv>`,
+you can see that it is a csv file with two columns. We can see that the first column contains values that look like our "id" value. The second column
+contains our genotype string -- our target value. The "file" type always assumes your input is some sort of value separated file. It doesn't necessarily have to be
+separated by commas, but that is the default functionality. If your file is separated by something other than commas, specify the "separator" option. There are three
+other required definitions for "file" type data keys. You need to define "key", "keyColumn", and "valueColumn". The columns themselves are 0-indexed. In this case, our "keyColumn" is 0, because
+our key is located in the 0th column. "valueColumn" is 1, because our key is located in the 1st column. Finally, our "key" value is the same as our "id". This
+will sift through our file until it finds the row who's 0th column is our "key" value. Then, it returns the value of 1st column. Looking at our path definition and test path again:
+
+| "path": "/work/walia/common/ih/rawdata/0184 Uni Nebraska Rice 1/**%null%**/%null%\_\ :red:`%idnum%`-\ :blue:`%idchar%`\_\ :green:`%date%`/\ :orange:`%imgname%`/0_0.png",
+| /work/walia/common/ih/rawdata/0184 Uni Nebraska Rice 1/**strain3**/0184 Uni Nebraska Rice 1\_\ :red:`023542`-\ :blue:`C`\_\ :green:`2013-09-05`\_05-18-33_455640/\ :orange:`RGB SV1`/0_0.png
+
+We will sift through our file looking for "023542-C" (which occurs in the 243rd line). It will then return the corresponding genotype string
+located in the same row, namely UNL032
+
+.. code-block:: javascript
+
+ "date": {
+ "type": "date",
+ "value": "%date%",
+ "format": "Y-m-d"
+ },
+
+Here, we define the "date" for each plant. We use our final type, "date". The only additional argument to the date type
+is "format", which specifies the input format of the date. The date type loads in values based on a combination of identifiers and hard-coded values again,
+but afterwards, it converts the date to Y-m-d format. In this case, because the input type is defined as "Y-m-d" using a date type
+isn't strictly required, we use it as an example though. The date input string can contain "Y", "y", "M", "m", "d", "B", "b" as format characters,
+and uses "-", "/", " ", and "_" as separators.
+
+ .. code-block:: javascript
+
+ "treatment": {
+ "type": "value",
+ "translate": "true",
+ "value": "%idchar%"
+ },
+ "imgname": {
+ "type": "value",
+ "value": "%imgname%"
+ },
+ "imtype": {
+ "type": "value",
+ "translate": "true",
+ "value": "%imgname%"
+ }
+
+We include the last three together, because they are all of type "value", and simply use one of the identifiers from the base path in their value.
+However, it is important to note that two of these values have an additional option, namely "translate": "true". This specifies that the input value
+should be mapped to a different output value. This functions very similar to a file mapping, except the mapping is defined inside the template.
+It should be noted, that if the "translate" option exists in the data key, then it will check for a translation. Even if you specify "translate": "false",
+it will still check for a translation. Let's look at the translation section:
+
+.. code-block:: javascript
+
+ "translations": {
+ "treatment": {
+ "S": "Stress",
+ "s": "Stress",
+ "C": "Control",
+ "c": "Control"
+ },
+ "imtype": {
+ "RGB SV1": "rgbsv",
+ "RGB SV2": "rgbsv",
+ "RGB TV": "rgbtv",
+ "FLUO SV1": "fluosv",
+ "FLUO SV2": "fluosv",
+ "FLUO TV": "fluotv",
+ "NIR SV1": "nirsv",
+ "NIR SV2": "nirsv",
+ "NIR TV": "nirtv",
+ "IR SV1": "irsv",
+ "IR SV2": "irsv",
+ "IR TV": "irtv"
+ }
+ }
+
+The translation keys line up exactly with the data keys that have "translate": "true" specified. The data-mapping to perform is simply defined in-line
+as key-value parings. This is effective for small sets, but is inefficient for large translation sets, such as the genotype file mapping.
+Here, the "treatment" translation takes a single character, and maps it to a word. We simply convert the 1 character idchar into the full word
+"Control" or "Stress". Looking at our path definition and test path again:
+
+| "path": "/work/walia/common/ih/rawdata/0184 Uni Nebraska Rice 1/**%null%**/%null%\_\ :red:`%idnum%`-\ :blue:`%idchar%`\_\ :green:`%date%`/\ :orange:`%imgname%`/0_0.png",
+| /work/walia/common/ih/rawdata/0184 Uni Nebraska Rice 1/**strain3**/0184 Uni Nebraska Rice 1\_\ :red:`023542`-\ :blue:`C`\_\ :green:`2013-09-05`\_05-18-33_455640/\ :orange:`RGB SV1`/0_0.png
+
+In this case, our idchar is 'C', this means that the "treatment" data key, will get mapped to "Control". We also have a translation defined for "imtype". Looking at our test path,
+our imgname is "RGB SV1". This means that the "imtype" data key will get mapped to "rgbsv". Remember, the key difference between defining translations, and using file mapping is size.
+
+With our template written, we can now load the images. We do this using the 'ih-setup' command as follows:
+
+.. code-block:: bash
+
+ ih-setup --dir "DIR_NAME" --template "crawl.json"
+
+This will setup a workflow submission directory with the name "DIR_NAME". It will create an input folder,
+and populate that input folder with the images database, the crawl.json template file, and empty template files required for job submission.
+Next we will look at defining the configuration file!
+
+Configuration
+-------------
+
+The config file contains information that shouldn't really change from run to run. It contains things like installation directories, environment
+variables, and job clustering. Let's take a look.
+
+.. code-block:: javascript
+
+ {
+ "installdir": "/work/walia/common/ih/pymodules/bin/",
+ "profile": {
+ "pegasus": {
+ "style": "glite"
+ },
+ "condor": {
+ "grid_resource": "pbs",
+ "universe": "vanilla"
+ },
+ "env": {
+ "PATH": "/work/walia/common/ih/pymodules/bin/",
+ "LD_LIBRARY_PATH": "/work/walia/common/ih/pymodules/opencv_lib/"
+ }
+ },
+ "cluster": 100,
+ "email": "avi@kurtknecht.com"
+ }
+
+The "installdir" definition is the location where all of ih's scripts are installed. It may seem
+unnecessary to include this as well as a path, but it is important for pegasus to know the exact location
+of executable files. The "profile" defintion supports inclusion of any-possible profile variable for
+the sites.xml. This is taken directly from the pegasus docs. To run the workflow on HCC & OSG,
+we specify "pegasus"->"style"->"glite", and "condor"->"grid_resource"->"pbs". The "env" definition
+passes environment variables through to the script. In this case, we pass in two different path variables.
+One is the location of other executable scripts, in this case our custom python install. The LD_LIBRARY_PATH
+is for the location of the required libraries for opencv. It should be noted, that multiple path variables can be included
+by specifying the value as a list i.e. If you specify "PATH": ["/test/path/1/", "/test/path/2/"], both paths will
+be loaded into the sites.xml. "cluster" specifies how many jobs you want to clump together. Most jobs take
+seconds to run, so running-the entire workflow unclustered is very-inefficient. A cluster size of 100 is used here,
+which means that jobs will be run in batches of 100. The "email" option defines which email to send the results to upon
+completion of the workflow.
+
+Processing
+----------
+
+The image processing template contains what image processing functions to use and in what order. Separate workflows
+are defined for each image type -- as a result the template is quite long. Here it is in full:
+
+.. code-block:: javascript
+
+ {
+ "workflows": {
+ "fluosv": [
+ {
+ "name": "pot_filter_1",
+ "executable": "ih-color-filter",
+ "inputs": ["base", "/work/walia/common/ih/workflows/0184/input/fluosv_pot1.json"],
+ "outputs": ["pot1"],
+ "arguments": {
+ "--logic": "(((((((r - g) < 30) and (((r + g) + b) < 110)) or ((((r + g) + b) > 110) and ((r - g) < 50))) or (((r - g) < 25) and ((g - r) < 25))) or (g > 60)) not 1)"
+ }
+ },
+ {
+ "name": "pot_filter_2",
+ "executable": "ih-color-filter",
+ "inputs": ["pot1", "/work/walia/common/ih/workflows/0184/input/fluosv_pot2.json"],
+ "outputs": ["pot2"],
+ "arguments": {
+ "--logic": "(((r + g) + b) > 120)"
+ },
+ "depends": ["pot_filter_1"]
+ },
+ {
+ "name": "main_filter",
+ "executable": "ih-color-filter",
+ "inputs": ["pot2"],
+ "outputs": ["filter"],
+ "arguments": {
+ "--logic": "((r - g) > 10)"
+ },
+ "depends": ["pot_filter_2"]
+ },
+ {
+ "name": "crop",
+ "executable": "ih-crop",
+ "inputs": ["filter", "/work/walia/common/ih/workflows/0184/input/fluosv_edge.json"],
+ "outputs": ["edged"],
+ "arguments": {},
+ "depends": ["main_filter"]
+ },
+ {
+ "name": "cut",
+ "executable": "ih-contour-cut",
+ "inputs": ["edged", "edged"],
+ "outputs": ["final"],
+ "arguments": {
+ "--resize": "",
+ "--basemin": 75
+ },
+ "depends": ["crop"]
+ }
+ ],
+ "rgbtv": [
+ {
+ "name": "normalize",
+ "executable": "ih-normalize-intensity",
+ "inputs": ["base"],
+ "outputs": ["normal"],
+ "arguments": {}
+ },
+ {
+ "name": "meanshift",
+ "executable": "ih-meanshift",
+ "inputs": ["normal"],
+ "outputs": ["shift"],
+ "arguments": {
+ "--spatial_radius": 4,
+ "--range_radius": 4,
+ "--min_density": 40
+ },
+ "depends": ["normalize"]
+ },
+ {
+ "name": "main_filter",
+ "executable": "ih-color-filter",
+ "inputs": ["shift"],
+ "outputs": ["filter"],
+ "arguments": {
+ "--logic": "(((g > r) and (g > b)) and ((((b max g) max r) - ((b min g) min r)) > 20))"
+ },
+ "depends": ["meanshift"]
+ },
+ {
+ "name": "closing",
+ "executable": "ih-morphology",
+ "inputs": ["filter"],
+ "outputs": ["morphed"],
+ "arguments": {
+ "--ktype": "ellipse",
+ "--kwidth": 5,
+ "--kheight": 5,
+ "--morphType": "close"
+ },
+ "depends": ["main_filter"]
+ },
+ {
+ "name": "crop",
+ "executable": "ih-crop",
+ "inputs": ["morphed", "/work/walia/common/ih/workflows/0184/input/rgbtv_edge.json"],
+ "outputs": ["edged"],
+ "arguments": {},
+ "depends": ["closing"]
+ },
+ {
+ "name": "reconstitute",
+ "executable": "ih-bitwise-and",
+ "inputs": ["edged", "base"],
+ "outputs": ["recolor"],
+ "arguments": {},
+ "depends": ["crop"]
+ },
+ {
+ "name": "cut",
+ "executable": "ih-contour-cut",
+ "inputs": ["recolor", "recolor"],
+ "outputs": ["final"],
+ "arguments": {
+ "--basemin": 200,
+ "--resize": ""
+ },
+ "depends": ["reconstitute"]
+ }
+ ],
+ "rgbsv": [
+ {
+ "name": "pot-detect",
+ "executable": "ih-color-filter",
+ "inputs": ["base"],
+ "outputs": ["pot"],
+ "arguments": {
+ "--logic": "((((r + g) + b) < 100) or (((b - r) > 40) and ((b - g) > 30)))"
+ }
+ },
+ {
+ "name": "pot-crop",
+ "executable": "ih-contour-cut",
+ "inputs": ["pot", "pot"],
+ "outputs": ["unused_1", "pot_roi"],
+ "arguments": {
+ "--basemin": 100,
+ "--padminy": 100,
+ "--padmaxy": 2000,
+ "--padminx": -25,
+ "--padmaxx": -25,
+ "--returnBound": ""
+ },
+ "depends": ["pot-detect"]
+ },
+ {
+ "name": "box-crop",
+ "executable": "ih-contour-cut",
+ "inputs": ["pot", "pot"],
+ "outputs": ["unused_2", "box_roi"],
+ "arguments": {
+ "--basemin": 100,
+ "--padminy": 35,
+ "--padmaxy": 2000,
+ "--padminx": 25,
+ "--padmaxx": 25,
+ "--returnBound": ""
+ },
+ "depends": ["pot-detect"]
+ },
+ {
+ "name": "gray",
+ "executable": "ih-convert-color",
+ "inputs": ["base"],
+ "outputs": ["grayscale"],
+ "arguments": {
+ "--intype": "bgr",
+ "--outtype": "gray"
+ }
+ },
+ {
+ "name": "blur",
+ "executable": "ih-gaussian-blur",
+ "inputs": ["grayscale"],
+ "outputs": ["blurred"],
+ "arguments": {
+ "--kwidth": 5,
+ "--kheight": 5
+ },
+ "depends": ["gray"]
+ },
+ {
+ "name": "thresh",
+ "executable": "ih-adaptive-threshold",
+ "inputs": ["blurred"],
+ "outputs": ["thresh"],
+ "arguments": {
+ "--value": 200,
+ "--thresholdType": "binary",
+ "--adaptiveType": "mean",
+ "--blockSize": 15,
+ "--C": 3
+ },
+ "depends": ["blur"]
+ },
+ {
+ "name": "reconstitute1",
+ "executable": "ih-bitwise-and",
+ "inputs": ["thresh", "base"],
+ "outputs": ["recolor1"],
+ "arguments": {},
+ "depends": ["thresh"]
+ },
+ {
+ "name": "meanshift",
+ "executable": "ih-meanshift",
+ "inputs": ["recolor1"],
+ "outputs": ["shift"],
+ "arguments": {
+ "--spatial_radius": 2,
+ "--range_radius": 2,
+ "--min_density": 50
+ },
+ "depends": ["reconstitute1"]
+ },
+ {
+ "name": "pot-filter",
+ "executable": "ih-color-filter",
+ "inputs": ["shift", "pot_roi"],
+ "outputs": ["pot_filtered"],
+ "arguments": {
+ "--logic": "((((((((((r > g) and (r > b)) and (((b max g) - (b min g)) < (((r + g) + b) / 20))) or ((((b max g) max r) - ((b min g) min r)) < 10)) or ((b > r) and ((b > g) or (g > r)))) or (((r + g) + b) < 220)) or ((((r + g) + b) < 350) and ((((b max g) max r) - ((b min g) min r)) < 25))) or ((b > g) and (r > g))) or (((((r - g) > 5) and ((g - b) > 5)) and ((r - g) < 25)) and ((g - b) < 25))) not 1)"
+ },
+ "depends": ["meanshift", "pot-crop"]
+ },
+ {
+ "name": "box-filter",
+ "executable": "ih-color-filter",
+ "inputs": ["pot_filtered", "box_roi"],
+ "outputs": ["box_filtered"],
+ "arguments": {
+ "--logic": "(((((r > g) and (r > b)) and (((b max g) - (b min g)) < (((r + g) + b) / 20))) or ((((b max g) max r) - ((b min g) min r)) < 10)) not 1)"
+ },
+ "depends": ["pot-filter", "box-crop"]
+ },
+ {
+ "name": "gfilter1",
+ "executable": "ih-color-filter",
+ "inputs": ["box_filtered", "/work/walia/common/ih/workflows/0184/input/rgbsv_gray1.json"],
+ "outputs": ["gray_filtered1"],
+ "arguments": {
+ "--logic": "((((b max g) max r) - ((b min g) min r)) > 50)"
+ },
+ "depends": ["box-filter", "box-crop"]
+ },
+ {
+ "name": "gfilter2",
+ "executable": "ih-color-filter",
+ "inputs": ["gray_filtered1", "/work/walia/common/ih/workflows/0184/input/rgbsv_gray2.json"],
+ "outputs": ["gray_filtered2"],
+ "arguments": {
+ "--logic": "((((b max g) max r) - ((b min g) min r)) > 100)"
+ },
+ "depends": ["gfilter1"]
+ },
+ {
+ "name": "crop",
+ "executable": "ih-crop",
+ "inputs": ["gray_filtered2", "/work/walia/common/ih/workflows/0184/input/rgbsv_edge.json"],
+ "outputs": ["edged"],
+ "arguments": {},
+ "depends": ["gfilter2"]
+ },
+ {
+ "name": "reconstitute2",
+ "executable": "ih-bitwise-and",
+ "inputs": ["edged", "base"],
+ "outputs": ["recolor2"],
+ "arguments": {},
+ "depends": ["crop"]
+ },
+ {
+ "name": "cut",
+ "executable": "ih-contour-cut",
+ "inputs": ["recolor2", "recolor2"],
+ "outputs": ["final"],
+ "arguments": {
+ "--basemin": 50,
+ "--resize": ""
+ },
+ "depends": ["reconstitute2"]
+ }
+ ]
+ },
+ "options": {
+
+ },
+ "extract": {
+ "histogram-bin": {
+ "--group": {"rgb": ["rgbsv", "rgbtv"], "fluo": ["fluosv"]},
+ "--chunks": {"rgb": 5, "fluo": 6},
+ "--channels": {"rgb": [0, 1, 2], "fluo": [1, 2]}
+ },
+ "workflows": {
+ "rgbsv": {
+ "inputs": ["final"],
+ "arguments": {
+ "--dimensions": "",
+ "--pixels": "",
+ "--moments": ""
+ },
+ "depends": ["cut"]
+ },
+ "rgbtv": {
+ "inputs": ["final"],
+ "arguments": {
+ "--dimensions": "",
+ "--pixels": "",
+ "--moments": ""
+ },
+ "depends": ["cut"]
+ },
+ "fluosv": {
+ "inputs": ["final"],
+ "arguments": {
+ "--dimensions": "",
+ "--pixels": "",
+ "--moments": ""
+ },
+ "depends": ["cut"]
+ }
+ }
+ }
+ }
+
+
+Let's break it down into more manageable chunks. We will look at a few jobs from the workflows.
+First, note that all workflow definitions must be under the "workflows" key. Secondly,
+note that the names of the workflows i.e. in this case "fluosv", must match the image types
+of images in your database. Each workflow is defined as a list of jobs. The jobs aren't
+necessarily executed in the order you specify them in the list, but you should structure
+your job definition such that it follows the list order as closely as possible for ease
+of reading. Each individual job has 5 required definitions, and 1 optional one. For each
+job you **must** define a name, an executable, the job inputs, the job outputs, and the job arguments.
+Note that you must include "arguments" even if it is left blank.
+For each job you may optionally define dependent jobs. Let's look at the first job we define for fluosv:
+
+.. code-block:: javascript
+
+ {
+ "name": "pot_filter_1",
+ "executable": "ih-color-filter",
+ "inputs": ["base", "/work/walia/common/ih/workflows/0184/input/fluosv_pot1.json"],
+ "outputs": ["pot1"],
+ "arguments": {
+ "--logic": "(((((((r - g) < 30) and (((r + g) + b) < 110)) or ((((r + g) + b) > 110) and ((r - g) < 50))) or (((r - g) < 25) and ((g - r) < 25))) or (g > 60)) not 1)"
+ }
+ },
+
+Here, we define the name as "pot_filter_1". Names are used to apply a more meaningful label
+to each job for the user, as well as used for dependencies in later processing steps.
+We define the executable we want to use as "ih-color-filter" -- This executable is used for
+processing user defined color logic, and will not be talked about in depth here. We define two inputs
+for our function. The first is "base" -- which serves as a placeholder for raw images. You can use
+this input in any step and it will load in the starting image. This is important for steps such
+as reconstiuting the color of the image. The second argument we feed is a path to a roi file.
+Here are the contents of the file:
+
+.. code-block:: javascript
+
+ {
+ "ystart": 1110,
+ "yend": "y",
+ "xstart": 369,
+ "xend": 669
+ }
+
+The roi file simply defines the region we want to apply our color-filter to.
+The roi file will automatically convert "y" to the maximum height, and "x" to the maximum
+width. Additionally it supports simply arithmetic, thus you could enter "y - 300" for
+"yend". If this input is left blank, it simply applies the color-filter to the entire image.
+We define the output as "pot1". This means that the intermediate file will be saved with
+a name of "pot1". Additionally, we can now use "pot1" as input in further steps. Finally
+we define the arguments of our processing functino -- in this case only one, our logic
+string. This job is the first job in our processing workflow, so we define no dependencies.
+We now look at the second job for fluosv:
+
+.. code-block:: javascript
+
+ {
+ "name": "pot_filter_2",
+ "executable": "ih-color-filter",
+ "inputs": ["pot1", "/work/walia/common/ih/workflows/0184/input/fluosv_pot2.json"],
+ "outputs": ["pot2"],
+ "arguments": {
+ "--logic": "(((r + g) + b) > 120)"
+ },
+ "depends": ["pot_filter_1"]
+ },
+
+Note that the input image is now "pot1" instead of "base". This chains the output
+of the previous step into the input of this step. To fully accomplish this, we must define
+dependency. Our first job was named "pot_filter_1", and we can see this name in our
+dependency list. A job can have multiple dependencies, you simply separate the names with
+commas i.e. "depends": ["job1", "job2", "job3"]. Whenever you use the output of a previous
+job, you must include it in the dependency list. Some functions output roi files instead of,
+or in addition to images. You can similarly use these roi files as input in future steps,
+provided that you include them in the proper location in your "inputs" definition. As a
+demonstration of this, we look at two jobs from the rgbsv workflow, "box-crop" and "box-filter".
+"box-crop" outputs "box_roi" which we use as a roi for "box-filter". There are two other definitions
+in the processing template. One is for "options" -- which is left blank in this case. Currently,
+the only supported option is "save-steps". If you specify:
+
+.. code-block:: javascript
+
+ "options": {
+ "save-step": "true"
+ },
+
+Each intermediary step (including roi files) will be saved to the final output folder. Otherwise,
+only the final processed image will be saved. Lastly, "extract" is required, and here you specify
+all the numeric information you want to extract from your final images. Let's take a look:
+
+.. code-block:: javascript
+
+ "extract": {
+ "histogram-bin": {
+ "--group": {"rgb": ["rgbsv", "rgbtv"], "fluo": ["fluosv"]},
+ "--chunks": {"rgb": 5, "fluo": 6},
+ "--channels": {"rgb": [0, 1, 2], "fluo": [1, 2]}
+ },
+ "workflows": {
+ "rgbsv": {
+ "inputs": ["final"],
+ "arguments": {
+ "--dimensions": "",
+ "--pixels": "",
+ "--moments": ""
+ },
+ "depends": ["cut"]
+ },
+ "rgbtv": {
+ "inputs": ["final"],
+ "arguments": {
+ "--dimensions": "",
+ "--pixels": "",
+ "--moments": ""
+ },
+ "depends": ["cut"]
+ },
+ "fluosv": {
+ "inputs": ["final"],
+ "arguments": {
+ "--dimensions": "",
+ "--pixels": "",
+ "--moments": ""
+ },
+ "depends": ["cut"]
+ }
+ }
+ }
+
+There is an optional special key you can define -- "histogram-bin" -- in the
+extract section. Specifying this key allows you to perform an experiment-wise histogram
+calculation of color-channel information to generate relevant bins. It performs the
+following steps: 1. Calculate color histogram for each processed image. 2. Sum
+the histograms to get a histogram for the entire data set. 3. Segment the histogram
+into equal area pieces as based on the inputs. 4. Generate complete permutation
+of bins based on the divided histogram. In the "histogram-bin" section we
+first define "--group". This allows us to group one or more imtypes from separate
+workflows together. In this case, we group "rgbsv" and "rgbtv" together. This
+allows us to consider color information from the RGB spectrum as a whole.
+We name this group "rgb" -- group names are important for future "histogram-bin"
+definitions. Next is "--chunks". For each group, you simply define how many
+pieces you want the total calculated histogram to be broken up into. Remember
+that color-space is 3 dimensional -- this means that specifying chunks = 5
+will generate :math:`5^{3} = 125` bins. Finally, we define what channels to
+process for each group. Channel 0 corresponds to blue, channel 1 corresponds
+to green, and channel 2 corresponds to red. In this case, we leave channel 0
+out of fluorescence processing -- this is because a majority of the blue values
+in the image are either 0 or 1. Any channel left out will simply be given a range of [0, 255]
+for every generated bin.
+
+The definitions in each individual "workflow" extract information from each individual
+image. You must define "inputs" and "depends" so that the extraction script
+can locate the image you want to extract data from (it does not necessarily have to be the
+final image, though it generally is). In the arguments section, you define a list of the
+numeric information you want to extract. For an example of all arguments you can specify,
+look at the ih-extract script. If you specify "histogram-bin" for a particular
+imtype, the "--colors" options is added automatically.
+
+Finally, to actually generate your workflow, use the ih-run command.
+You should have setup a directory from the crawling step when you executed
+
+.. code-block:: bash
+
+ ih-setup --dir "DIR_NAME" --template "crawl.json"
+
+The easiest way to run ih-run is to change directories to "DIR_NAME", then
+simply run:
+
+.. code-block:: bash
+
+ ih-run
+
+with no arguments! Run with the -h option to see options. Additionally, the validator
+for processing workflows is very powerful. Use --validate to run in validate only mode
+to help debug your workflow as you create it. Depending on how many input images,
+it may take a while to write the necessary submission files (sometimes 10-20 minutes).
+
+Submission
+-----------
+Upon sucessful completion of ih-run, a date and timestamped folder should be created
+with the following structure:
+
+.. code-block:: bash
+
+ date-timestamp/
+ input/
+ imgproc/
+ -sites.xml
+ -conf.rc
+ -map.rc
+ -extract.dax
+ -workflow.dax
+ -notify.sh
+ -submit.sh
+ rawfiles/
+ templates/
+ output/
+ -output.db
+ work/
+
+The work directory is where actual processing is done -- but initially starts empty. The output
+folder starts only with the output database, but contains no images to start with. The input folder
+contains a copy of your submitted templates in the templates folder, and a copy of all non-image raw-input files
+in the rawfiles folder. Finally, within the imgproc folder are the actual files required to submit
+a pegasus workflow. All you need to do to submit is execute the submit.sh script. This will launch your
+workflow, as well as creating a status.sh script for easy monitoring, and a remove.sh script if you
+want to remove your workflow.
+
+
+
+
+
diff --git a/docs/build/html/_sources/examples.txt b/docs/build/html/_sources/examples.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f33a32b58e2adfc04e2c317cfcf94afccc6088da
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+++ b/docs/build/html/_sources/examples.txt
@@ -0,0 +1,49 @@
+..
+ REMEMBER TO UPDATE THE HIDDEN TOC TREE
+ AS SCRIPTS ARE ADDED TO THE EXAMPLES PAGE!!!
+
+.. toctree::
+ :hidden:
+
+ ex_script_core1
+ ex_script_core2
+ ex_script_color1
+ ex_workflow_1.rst
+
+Examples
+========
+Working through examples is a much better way of learning how to use ih than
+reading implementation details. Additionally, creating workflows is a complicated
+multi-step process. As such, many examples are detailed below, falling into
+two broad categories. Script examples are those that deal with local computing.
+Each script example includes a test image to download, as well as scripts
+for library and command-line usage of ih. Workflow examples are those that
+deal with distributed computing. They include template files for download,
+but due to their nature, image sets are not available for download.
+However, data sets are available through the OSG (Open Science Grid). Workflow examples
+are very complex. Step by step instructions are provided, but it is **highly** recommended
+to work through script examples before jumping into workflow examples.
+
+
+Script Examples
+---------------
+There are many different script examples. Some are specific to functions,
+others cover a broad range of functions. If you are getting started,
+begin by working through the core processing examples. In particular,
+if you are unfamiliar with Python, the first core processing script attempts
+to explain some basic terms.
+
+Core Processing
+^^^^^^^^^^^^^^^
+:doc:`Core Processing #1 <ex_script_core1>`, difficulty = easy.
+
+:doc:`Core Processing #2 <ex_script_core2>`, difficulty = medium.
+
+Color Filter
+^^^^^^^^^^^^
+:doc:`Color Filter #1 <ex_script_color1>`, difficulty = medium.
+
+Workflow Examples
+-----------------
+
+:doc:`Workflow #1 <ex_workflow_1>`, difficulty = complex.
diff --git a/docs/build/html/_sources/index.txt b/docs/build/html/_sources/index.txt
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+++ b/docs/build/html/_sources/index.txt
@@ -0,0 +1,27 @@
+Welcome to Image Harvest documentation!
+==============================================================
+
+Link to GitHub: `ih <https://git.unl.edu/aknecht2/ih/>`_
+
+Contents:
+
+.. toctree::
+ :maxdepth: 2
+
+ introduction
+ installation
+ start
+ examples
+ processing
+ viewer
+ statistics
+ indexing
+ workflowimage
+ workflowstats
+
+Indices and tables
+==================
+
+* :ref:`genindex`
+* :ref:`modindex`
+* :ref:`search`
diff --git a/docs/build/html/_sources/indexing.txt b/docs/build/html/_sources/indexing.txt
new file mode 100644
index 0000000000000000000000000000000000000000..10810fc623ea8dae0ea84f5a013da3a9fe4e84ed
--- /dev/null
+++ b/docs/build/html/_sources/indexing.txt
@@ -0,0 +1,5 @@
+Image Loading
+==============
+
+.. autoclass:: ih.workflow.ImageLoader
+ :members:
diff --git a/docs/build/html/_sources/installation.txt b/docs/build/html/_sources/installation.txt
new file mode 100644
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@@ -0,0 +1,222 @@
+Installation
+=============
+
+It is recommended to use the latest stable version for each of the dependencies. Package
+manager software is sometimes behind, so for some dependencies you may have to download and
+install a more recent version. Many systems come with a development tools package which
+should be installed. Most of the requirements below requires a c and c++ compiler, and some
+require a fortran compiler.
+
+Dependencies
+------------
+* `Matplotlib <http://matplotlib.org/>`_ >= 1.3.1
+* `NumPy <http://www.numpy.org/>`_ >= 1.7
+* `OpenCV <http://opencv.org/>`_ == 2.4.x
+ * GTK2 (including headers) >= 2.24
+ * blas >= 3.2.1
+ * lapack >= 3.2.1
+ * libav >= 0.5.3
+ * cmake >= 2.8.12
+ * `ffmpeg <https://www.ffmpeg.org/>`_ >= 2.0.5
+* `Pandas <http://pandas.pydata.org/>`_ >= 0.13.1
+ * `Cython <http://cython.org/>`_ >= 0.21.1
+ * `python-dateutil <https://labix.org/python-dateutil>`_ >= 1.4.1
+* `PyMeanShift <https://code.google.com/p/pymeanshift/>`_ >= 0.2.0
+* `SciPy <http://www.scipy.org/>`_ >= 0.13.1
+* `Pegasus <http://pegasus.isi.edu/>`_ >= 4.4.0
+ * Java >= 1.8
+ * Perl >= 5.10
+* `HTCondor <http://research.cs.wisc.edu/htcondor/>`_ >= 8.3.0
+
+Pegasus and HTCondor are only required if you wish to use the super computer workflow generation functionality.
+Additionally, many super computing environments may already have Pegasus, HTCondor, and other
+dependencies installed. There are resources available for quickly installing the `SciPy Stack <http://www.scipy.org/install.html>`_,
+which includes the NumPy, SciPy, Pandas, and Matplotlib. The installation tutorials for Mac OSX, and Windows
+specifically leave out Pegasus and HTCondor, as they are expected to be machines for local testing, not for
+submitting grid jobs. Finally, Image Harvest can be installed by downloading a zip file from the repo
+(`link <https://git.unl.edu/aknecht2/ih>`_), and running 'python setup.py install'.
+
+
+
+Centos 6.5
+----------
+It is **highly** recommended that you use anaconda (or another python package manager such as pip) to install the python packages. The installation
+process becomes much simpler and faster.
+
+With Anaconda
+^^^^^^^^^^^^^
+
+.. code-block:: bash
+
+ # Update
+ sudo yum -y update
+
+ # Set up condor repo
+ cd /etc/yum.repos.d
+ sudo wget http://research.cs.wisc.edu/htcondor/yum/repo.d/htcondor-stable-rhel6.repo
+ sudo wget http://research.cs.wisc.edu/htcondor/yum/RPM-GPG-KEY-HTCondor
+ sudo rpm --import RPM-GPG-KEY-HTCondor
+
+ # Install packages
+ sudo yum -y install java-1.8.0-* perl condor.x86_64
+
+ # Download Pegasus
+ wget -O pegasus.tar.gz http://download.pegasus.isi.edu/pegasus/4.4.0/pegasus-worker-4.4.0-x86_64_rhel_6.tar.gz
+ tar -zxvf pegasus.tar.gz
+
+ # Download and install anaconda
+ wget -O anaconda.sh http://09c8d0b2229f813c1b93-c95ac804525aac4b6dba79b00b39d1d3.r79.cf1.rackcdn.com/Anaconda-2.1.0-Linux-x86_64.sh
+ bash anaconda.sh -b
+
+ # Install *almost* everything in one line
+ conda install numpy scipy pandas matplotlib opencv
+
+ # Download PyMeanShift and install, assuming directory is 'pymeanshift'
+ cd pymeanshift
+ sudo python setup.py install
+
+ # Install Image Harvest, assuming directory is 'ih.git'
+ cd ih.git
+ sudo python setup.py install
+
+ # Make sure to move the pegasus python files into the anaconda package folder
+ # Update the following command as necessary
+ cp -r pegasus-4.4.0/lib64/python2.6/site-packages/Pegasus ~/anaconda/lib/python2.7/site-packages/
+ # and to update your bash profile to include the pegasus commands,
+ # or cp the pegasus commands to /usr/bin or /usr/local/bin
+ cp pegasus-4.4.0/bin/* /usr/bin/
+
+
+Ubuntu 12.04
+------------
+
+It is **highly** recommended that you use anaconda (or another python package manager such as pip) to install the python packages. The installation
+process becomes much simpler and faster.
+
+With Anaconda
+^^^^^^^^^^^^^
+
+.. code-block:: bash
+
+ # Update
+ sudo apt-get -y update
+
+ # Install build-essential
+ sudo apt-get -y install build-essential
+
+ # Setup condor repository
+ sudo bash -c 'echo "deb http://research.cs.wisc.edu/htcondor/debian/stable/ wheezy contrib" >> /etc/apt/sources.list'
+ wget -qO - http://research.cs.wisc.edu/htcondor/debian/HTCondor-Release.gpg.key | sudo apt-key add -
+ sudo apt-get -y update
+ sudo apt-get install condor
+
+ # Install dependencies
+ sudo apt-get -y install software-properties-common python-software-properties perl
+ sudo add-apt-repository -y ppa:webupd8team/java
+ sudo apt-get update
+ sudo apt-get -y install oracle-java8-installer
+ # A license agrement will pop up here...
+
+
+ # Download pegasus
+ wget http://download.pegasus.isi.edu/pegasus/4.4.0/pegasus_4.4.0-1+deb7_amd64.deb
+ tar -zxvf pegasus.tar.gz
+
+ # Download and install anaconda
+ wget -O anaconda.sh http://09c8d0b2229f813c1b93-c95ac804525aac4b6dba79b00b39d1d3.r79.cf1.rackcdn.com/Anaconda-2.1.0-Linux-x86_64.sh
+ bash anaconda.sh -b
+
+ # Install *almost* everything in one line
+ conda install numpy scipy pandas matplotlib opencv
+
+ # Download PyMeanShift and install, assuming directory is 'pymeanshift'
+ cd pymeanshift
+ sudo python setup.py install
+
+ # Install Image Harvest, assuming directory is 'ih.git'
+ cd ih.git
+ sudo python setup.py install
+
+ # Make sure to move the pegasus python files into the anaconda package folder
+ # Update the following command as necessary
+ cp -r pegasus-4.4.0/lib64/python2.6/site-packages/Pegasus ~/anaconda/lib/python2.7/site-packages/
+ # and to update your bash profile to include the pegasus commands,
+ # or cp the pegasus commands to /usr/bin or /usr/local/bin
+ cp pegasus-4.4.0/bin/* /usr/bin/
+
+Mac OSX
+--------
+
+Installation for local testing is a breeze with `brew <http://brew.sh>`_. Installing
+brew simply requires copying a line into a terminal. The only two packages
+you need to manual download will be PyMeanShift and Image Harvest.
+NOTE: You will have to install XCode, and the XCode Command Line Tools if you have not already. It's a free download
+from the App Store.
+After you have downloaded the packages and installed brew, run the following:
+
+.. code-block:: bash
+
+ # Install *almost* everything in one line
+ brew tap homebrew/science
+ brew tap homebrew/python
+ brew update && brew upgrade
+ brew install numpy scipy matplotlib pandaseq opencv
+ # You need to make sure your PYTHONPATH
+ # points to the installed packages.
+ # We point to the brew installed packages first,
+ # to make sure there are no conflicts with system python.
+ export PYTHONPATH=`brew --prefix`/lib/python2.7/site-packages/:$PYTHONPATH
+
+ # Download PyMeanShift and install, assuming directory is 'pymeanshift'
+ cd pymeanshift
+ sudo python setup.py install
+
+ # Download Image Harvest and install, assuming directory is 'ih.git'
+ cd ih.git
+ sudo python setup.py install
+
+ # That's it!
+
+Windows
+--------
+
+Windows requires a little more work, and in fact, windows doesn't even come with python.
+Installing requires adjusting some system settings as well. You will need to manually
+install several packages before `pip <https://pypi.python.org/pypi/pip>`_ can put
+in work. First, install `python2.7 <https://www.python.org/downloads/>`_. Next,
+you have to add python to your PATH environment variable.
+
+* Windows 7: Right click on Computer > properties > Advanced system settings > Advanced Tab > Enviornment Variables
+* Windows 8: Control Panel > System > Advanced system settings > Advanced Tab > Environment Variables
+
+You should see two boxes. One that says "User variables for <user>", and the other that says
+"System variables". Scroll through the "System variables" box until you find the 'Path' variable.
+It should look like lots of paths separated by semicolons. Edit Path, and add two new paths,
+'C:\\Python2.7\\' and 'C:\\Python2.7\\Scripts\\'. Make sure to keep each path separated by a semicolon.
+Next, you need to install a `c++ compiler <http://www.microsoft.com/en-us/download/details.aspx?id=44266>`_ --
+simply download the installer and run it.
+Finally, download and install `pip <https://pypi.python.org/pypi/pip>`_. There should
+simply be a giant script you copy to a local file, and execute with python.
+
+
+Now, you can install all the dependent python packages by finding the correct version for your os,
+and downloading them from this `link <http://www.lfd.uci.edu/~gohlke/pythonlibs/>`_. You will need the same
+list as above that is, numpy, scipy, pandas, matplotlib, and opencv.
+
+.. code-block:: bash
+
+ # For each downloaded wheel file, you will
+ # need to run the following from a command prompt
+ pip install name.whl
+ # Then, download pymeanshift and install, run installer.
+ # Then, download Image Harvest and install, assuming directory is 'ih.git'
+ cd ih.git
+ python setup.py install
+
+One final note, when loading images, python expects forward slashes not back slashes,
+and does not expect the C: for absolute paths. If you have an image called "test.jpg"
+in your downloads folder, the correct path for python is "/Users/username/Downloads/test.jpg".
+
+
+
+
diff --git a/docs/build/html/_sources/introduction.txt b/docs/build/html/_sources/introduction.txt
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+Introduction
+============
+
+Image Harvest (ih) is an open-source `Python <https://www.python.org/>`_ library for processing and analyzing plant images.
+The software uses `OpenCV <http://opencv.org/>`_ for image processing, and `SciPy <http://www.scipy.org/>`_ for statistics.
+Besides inclusion of stand-alone scripts to access processing and statistics functions, ih is integrated with
+`Pegasus <pegasus.isi.edu>`_ to create and submit workflows to super computers.
+
+Many software tools already exist to perform image analysis. The ability to create distributed computing workflows
+is one of the features that makes ih distinct. Workflow generation is completely adaptable to any input, and can
+be customized using many different modular processing components.
+
+Image Harvest is a work in a progress. For any help, questions, or bugs, please contact: avi@kurtknecht.com
+
diff --git a/docs/build/html/_sources/processing.txt b/docs/build/html/_sources/processing.txt
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@@ -0,0 +1,10 @@
+Image Processing
+================
+
+This page contains specific implementation details of image processing functions.
+Additionally, the next page contains an interactive image processing function viewer.
+It allows for adjusting inputs and seeing results of many different functions
+on several different sample input images.
+
+.. autoclass:: ih.imgproc.Image
+ :members:
diff --git a/docs/build/html/_sources/start.txt b/docs/build/html/_sources/start.txt
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@@ -0,0 +1,70 @@
+Getting Started
+===============
+
+There are 3 main ways of accessing the software.
+
+1. Library Access
+ The image processing and statistics functions can be accessed by importing ih.
+ Within your script you create objects out of individual plant images and process them
+ directly. Ex:
+
+ .. code-block:: python
+
+ # import ih
+ import ih.imgproc
+ # load your image as an object
+ plant = ih.imgproc.Image("/home/user/image.png", outputdir = "/home/user/")
+ # execute processing functions, in this simple case,
+ # the image is converted to grayscale, then thresholded.
+ plant.convertColor("bgr", "gray")
+ plant.threshold(127)
+ # write the output
+ plant.write("threshold.png")
+
+ This method is good for testing and adjusting your image processing workflow,
+ but does not scale well for large sets of images.
+2. Command Line Access
+ ih comes with dozens of micro-scripts providing individual access to each
+ function. Each script takes an input image, and writes an output image. The
+ previous example would be done with two commands as follows:
+
+ .. code-block:: bash
+
+ #!/bin/bash
+ ih-convert-color --input "/home/user/image.png" --output "/home/user/gray.png" --intype "bgr" --outtype "gray"
+ ih-threshold --input "/home/user/gray.png" --output "/home/user/threshold.png" --thresh 127
+
+ This method is slightly different than the previous one in a few aspects. The names of the command line
+ scripts will not exactly match the names of the functions. Because each script takes an image and
+ writes an image, it is important to chain the output of one command into the input of the next command.
+ This method can also be used to test your workflow. Super computer workflows use this method for processing,
+ so familiarity with command-line arguments are helpful, and ensure your large-scale runs process correctly.
+
+3. Workflow Generation
+ Super computer workflow generation and submission is complicated enough that there isn't a simple
+ starter script, but it can be broken down into three major steps. Each step is handled by user defined
+ json template files.
+
+ i. Image Loading
+ Input images can range from automated systems such as LemnaTec, to pictures taken by hand.
+ Besides the images themselves being different, the format of the input also differs greatly
+ from source to source. This step sets up the base job submission directory, and loads
+ images into a database, to keep the format consistent for all inputs. Loading requires
+ a template that defines where and how to load images into the database, as well as metadata
+ to load for each image. Metadata for images is not defined for each individual image, but
+ rather, is loaded from the directory structure / names of the images.
+ ii. Image Processing
+ This step requires two inputs, a workflow template file, and a config file. The workflow template
+ file defines what image-processing scripts to use, and in what order. Additionally, which numeric
+ variables to extract are defined in the workflow template files. The config file is for several
+ pieces of system information, such as environment variables, and job cluster size.
+ iii. Statistics
+ This step also requires two inputs, a workflow template file, and a config file. The workflow template
+ file is identical to that of the previous step, except using statistic processing scripts. The
+ config file for this step is completely identical to that of the previous step. Statistics workflows
+ require that data has been processed, which means an image-processing workflow must be run first.
+ Additionally, statistics workflows are still a work in progress.
+
+The next session details several tutorials of how to use ih, for both local and distributed computing. It
+is recommended that you familiarize yourself with local computing examples before jumping into generating
+super computer workflows. Implementation details of specific functions can be found in further sections.
diff --git a/docs/build/html/_sources/statistics.txt b/docs/build/html/_sources/statistics.txt
new file mode 100644
index 0000000000000000000000000000000000000000..26ece9af671212dd2db39d51a8509c9c9e6fd111
--- /dev/null
+++ b/docs/build/html/_sources/statistics.txt
@@ -0,0 +1,8 @@
+Statistics
+==========
+
+Statistics analysis is currently being worked on!
+
+.. autoclass:: ih.statistics.Stats
+ :members:
+
diff --git a/docs/build/html/_sources/viewer.txt b/docs/build/html/_sources/viewer.txt
new file mode 100644
index 0000000000000000000000000000000000000000..48a696db71d433f6bfc08ad50bfab53de8390c3c
--- /dev/null
+++ b/docs/build/html/_sources/viewer.txt
@@ -0,0 +1,104 @@
+Image Processing Viewer
+========================
+
+.. raw:: html
+
+ <script type="text/javascript" src="/Users/aknecht/git/ih/docs/images/viewer.json"></script>
+ <script type="text/javascript">
+ base = "/Users/aknecht/git/ih/docs/images/"
+ // base = "/cropstressgenomics.org/data/viewerim/"
+ $(function() {
+ $("#function").on("change", function() {
+ optstr = ""
+ if ($("#function").val() == "bitwise_not" || $("#function").val() == "normalizeByIntensity") {
+ optstr += "<input type='hidden' class='imload' />";
+ }
+ for (var ordernum in data[$("#function").val()]["order"]) {
+ option = data[$("#function").val()]["order"][ordernum]
+ optstr += "<div class='form-group'>";
+ optstr += "<label for='" + option + "'>" + option + "</label>";
+ optstr += "<select class='form-control imload' name='" + option + "' id='load_" + ordernum + "'>";
+ for (var arg in data[$("#function").val()][option]) {
+ optstr += "<option value='" + data[$("#function").val()][option][arg] + "'>" + data[$("#function").val()][option][arg] + "</option>";
+ }
+ optstr += "</select>"
+ optstr += "</div>";
+ }
+ $("#options").html(optstr);
+ $("#options .imload").trigger("change");
+ });
+ $("#image").on("change", function() {
+ $("#inputImage").html("<img src='" + base + "sample/" + $("#image").val() + "' />");
+ $("#options .imload").trigger("change");
+ });
+ $("#options").on("change", ".imload", function() {
+ var l = $("#options > div").length;
+ var impath = base + "/" + $("#function").val() + "/"
+ for (var i = 0; i < l; i++) {
+ impath += $("#load_" + i).attr("name");
+ impath += $("#load_" + i).val()
+ }
+ impath += $("#image").val();
+ $("#outputImage").html("<img src='" + escape(impath) + "' />");
+ });
+ $("#function").trigger("change");
+ $("#image").trigger("change");
+ });
+ </script>
+ <div class="row">
+ <div style="height:613px;" class="col-md-2">
+ <form>
+ <div class="form-group">
+ <label for="function">Function</label>
+ <select class="form-control" id="function">
+ <option value="adaptiveThreshold">Adaptive Threshold</option>
+ <option value="bitwise_and">Bitwise And</option>
+ <option value="bitwise_not">Bitwise Not</option>
+ <option value="bitwise_or">Bitwise Or</option>
+ <option value="bitwise_xor">Bitwise XOr</option>
+ <option value="blur">Blur</option>
+ <option value="colorFilter">Color Filter</option>
+ <option value="convertColor">Convert Color</option>
+ <option value="crop">Crop</option>
+ <option value="edges">Edges</option>
+ <option value="gaussianBlur">Gaussian Blur</option>
+ <option value="kmeans">Kmeans</option>
+ <option value="meanshift">Mean Shift Segmentation</option>
+ <option value="morphology">Morphology</option>
+ <option value="normalizeByIntensity">Normalize By Intensity</option>
+ <option value="threshold">Threshold</option>
+ </select>
+ </div>
+ <div class="form-group">
+ <label for="image">Images</label>
+ <select class="form-control" id="image">
+ <option value="rgbsv1.png">rgbsv1</option>
+ <option value="rgbsv2.png">rgbsv2</option>
+ <option value="rgbsv3.png">rgbsv3</option>
+ <option value="rgbtv1.png">rgbtv1</option>
+ <option value="rgbtv2.png">rgbtv2</option>
+ <option value="rgbtv3.png">rgbtv3</option>
+ <option value="fluosv1.png">fluosv1</option>
+ <option value="fluosv2.png">fluosv2</option>
+ </select>
+ </div>
+ <div class="form-group">
+ <label for="options">Options</label>
+ <hr style="margin-top:0px;margin-bottom:5px;">
+ </div>
+ <div id="options">
+
+ </div>
+ </form>
+ </div>
+ <div id="inputImage" style="height:613px;" class="col-md-5">
+
+ </div>
+ <div id="outputImage" style="height:613px;" class="col-md-5">
+
+ </div>
+ </div>
+ <div class="row">
+ <br />
+ </div>
+
\ No newline at end of file
diff --git a/docs/build/html/_sources/workflowimage.txt b/docs/build/html/_sources/workflowimage.txt
new file mode 100644
index 0000000000000000000000000000000000000000..3c01f2e405cc09e7020cf0339f54d97b3a678896
--- /dev/null
+++ b/docs/build/html/_sources/workflowimage.txt
@@ -0,0 +1,4 @@
+Image Processing Workflows
+==========================
+.. autoclass:: ih.workflow.ImageProcessor
+ :members:
diff --git a/docs/build/html/_sources/workflowstats.txt b/docs/build/html/_sources/workflowstats.txt
new file mode 100644
index 0000000000000000000000000000000000000000..bcbfdba941da6e77aa62a375d8c0eda6eb626143
--- /dev/null
+++ b/docs/build/html/_sources/workflowstats.txt
@@ -0,0 +1,4 @@
+Statistics Workflows
+==========================
+.. autoclass:: ih.workflow.Statistics
+ :members:
diff --git a/docs/build/html/_static/ajax-loader.gif b/docs/build/html/_static/ajax-loader.gif
new file mode 100644
index 0000000000000000000000000000000000000000..61faf8cab23993bd3e1560bff0668bd628642330
Binary files /dev/null and b/docs/build/html/_static/ajax-loader.gif differ
diff --git a/docs/build/html/_static/basic.css b/docs/build/html/_static/basic.css
new file mode 100644
index 0000000000000000000000000000000000000000..50d4e4e8f84daf3217a07e95d54b29e77f983b7f
--- /dev/null
+++ b/docs/build/html/_static/basic.css
@@ -0,0 +1,555 @@
+/*
+ * basic.css
+ * ~~~~~~~~~
+ *
+ * Sphinx stylesheet -- basic theme.
+ *
+ * :copyright: Copyright 2007-2014 by the Sphinx team, see AUTHORS.
+ * :license: BSD, see LICENSE for details.
+ *
+ */
+
+/* -- main layout ----------------------------------------------------------- */
+
+div.clearer {
+ clear: both;
+}
+
+/* -- relbar ---------------------------------------------------------------- */
+
+div.related {
+ width: 100%;
+ font-size: 90%;
+}
+
+div.related h3 {
+ display: none;
+}
+
+div.related ul {
+ margin: 0;
+ padding: 0 0 0 10px;
+ list-style: none;
+}
+
+div.related li {
+ display: inline;
+}
+
+div.related li.right {
+ float: right;
+ margin-right: 5px;
+}
+
+/* -- sidebar --------------------------------------------------------------- */
+
+div.sphinxsidebarwrapper {
+ padding: 10px 5px 0 10px;
+}
+
+div.sphinxsidebar {
+ float: left;
+ width: 230px;
+ margin-left: -100%;
+ font-size: 90%;
+}
+
+div.sphinxsidebar ul {
+ list-style: none;
+}
+
+div.sphinxsidebar ul ul,
+div.sphinxsidebar ul.want-points {
+ margin-left: 20px;
+ list-style: square;
+}
+
+div.sphinxsidebar ul ul {
+ margin-top: 0;
+ margin-bottom: 0;
+}
+
+div.sphinxsidebar form {
+ margin-top: 10px;
+}
+
+div.sphinxsidebar input {
+ border: 1px solid #98dbcc;
+ font-family: sans-serif;
+ font-size: 1em;
+}
+
+div.sphinxsidebar #searchbox input[type="text"] {
+ width: 170px;
+}
+
+div.sphinxsidebar #searchbox input[type="submit"] {
+ width: 30px;
+}
+
+img {
+ border: 0;
+ max-width: 100%;
+}
+
+/* -- search page ----------------------------------------------------------- */
+
+ul.search {
+ margin: 10px 0 0 20px;
+ padding: 0;
+}
+
+ul.search li {
+ padding: 5px 0 5px 20px;
+ background-image: url(file.png);
+ background-repeat: no-repeat;
+ background-position: 0 7px;
+}
+
+ul.search li a {
+ font-weight: bold;
+}
+
+ul.search li div.context {
+ color: #888;
+ margin: 2px 0 0 30px;
+ text-align: left;
+}
+
+ul.keywordmatches li.goodmatch a {
+ font-weight: bold;
+}
+
+/* -- index page ------------------------------------------------------------ */
+
+table.contentstable {
+ width: 90%;
+}
+
+table.contentstable p.biglink {
+ line-height: 150%;
+}
+
+a.biglink {
+ font-size: 1.3em;
+}
+
+span.linkdescr {
+ font-style: italic;
+ padding-top: 5px;
+ font-size: 90%;
+}
+
+/* -- general index --------------------------------------------------------- */
+
+table.indextable {
+ width: 100%;
+}
+
+table.indextable td {
+ text-align: left;
+ vertical-align: top;
+}
+
+table.indextable dl, table.indextable dd {
+ margin-top: 0;
+ margin-bottom: 0;
+}
+
+table.indextable tr.pcap {
+ height: 10px;
+}
+
+table.indextable tr.cap {
+ margin-top: 10px;
+ background-color: #f2f2f2;
+}
+
+img.toggler {
+ margin-right: 3px;
+ margin-top: 3px;
+ cursor: pointer;
+}
+
+div.modindex-jumpbox {
+ border-top: 1px solid #ddd;
+ border-bottom: 1px solid #ddd;
+ margin: 1em 0 1em 0;
+ padding: 0.4em;
+}
+
+div.genindex-jumpbox {
+ border-top: 1px solid #ddd;
+ border-bottom: 1px solid #ddd;
+ margin: 1em 0 1em 0;
+ padding: 0.4em;
+}
+
+/* -- general body styles --------------------------------------------------- */
+
+a.headerlink {
+ visibility: hidden;
+}
+
+h1:hover > a.headerlink,
+h2:hover > a.headerlink,
+h3:hover > a.headerlink,
+h4:hover > a.headerlink,
+h5:hover > a.headerlink,
+h6:hover > a.headerlink,
+dt:hover > a.headerlink {
+ visibility: visible;
+}
+
+div.body p.caption {
+ text-align: inherit;
+}
+
+div.body td {
+ text-align: left;
+}
+
+.field-list ul {
+ padding-left: 1em;
+}
+
+.first {
+ margin-top: 0 !important;
+}
+
+p.rubric {
+ margin-top: 30px;
+ font-weight: bold;
+}
+
+img.align-left, .figure.align-left, object.align-left {
+ clear: left;
+ float: left;
+ margin-right: 1em;
+}
+
+img.align-right, .figure.align-right, object.align-right {
+ clear: right;
+ float: right;
+ margin-left: 1em;
+}
+
+img.align-center, .figure.align-center, object.align-center {
+ display: block;
+ margin-left: auto;
+ margin-right: auto;
+}
+
+.align-left {
+ text-align: left;
+}
+
+.align-center {
+ text-align: center;
+}
+
+.align-right {
+ text-align: right;
+}
+
+/* -- sidebars -------------------------------------------------------------- */
+
+div.sidebar {
+ margin: 0 0 0.5em 1em;
+ border: 1px solid #ddb;
+ padding: 7px 7px 0 7px;
+ background-color: #ffe;
+ width: 40%;
+ float: right;
+}
+
+p.sidebar-title {
+ font-weight: bold;
+}
+
+/* -- topics ---------------------------------------------------------------- */
+
+div.topic {
+ border: 1px solid #ccc;
+ padding: 7px 7px 0 7px;
+ margin: 10px 0 10px 0;
+}
+
+p.topic-title {
+ font-size: 1.1em;
+ font-weight: bold;
+ margin-top: 10px;
+}
+
+/* -- admonitions ----------------------------------------------------------- */
+
+div.admonition {
+ margin-top: 10px;
+ margin-bottom: 10px;
+ padding: 7px;
+}
+
+div.admonition dt {
+ font-weight: bold;
+}
+
+div.admonition dl {
+ margin-bottom: 0;
+}
+
+p.admonition-title {
+ margin: 0px 10px 5px 0px;
+ font-weight: bold;
+}
+
+div.body p.centered {
+ text-align: center;
+ margin-top: 25px;
+}
+
+/* -- tables ---------------------------------------------------------------- */
+
+table.docutils {
+ border: 0;
+ border-collapse: collapse;
+}
+
+table.docutils td, table.docutils th {
+ padding: 1px 8px 1px 5px;
+ border-top: 0;
+ border-left: 0;
+ border-right: 0;
+ border-bottom: 1px solid #aaa;
+}
+
+table.field-list td, table.field-list th {
+ border: 0 !important;
+}
+
+table.footnote td, table.footnote th {
+ border: 0 !important;
+}
+
+th {
+ text-align: left;
+ padding-right: 5px;
+}
+
+table.citation {
+ border-left: solid 1px gray;
+ margin-left: 1px;
+}
+
+table.citation td {
+ border-bottom: none;
+}
+
+/* -- other body styles ----------------------------------------------------- */
+
+ol.arabic {
+ list-style: decimal;
+}
+
+ol.loweralpha {
+ list-style: lower-alpha;
+}
+
+ol.upperalpha {
+ list-style: upper-alpha;
+}
+
+ol.lowerroman {
+ list-style: lower-roman;
+}
+
+ol.upperroman {
+ list-style: upper-roman;
+}
+
+dl {
+ margin-bottom: 15px;
+}
+
+dd p {
+ margin-top: 0px;
+}
+
+dd ul, dd table {
+ margin-bottom: 10px;
+}
+
+dd {
+ margin-top: 3px;
+ margin-bottom: 10px;
+ margin-left: 30px;
+}
+
+dt:target, .highlighted {
+ background-color: #fbe54e;
+}
+
+dl.glossary dt {
+ font-weight: bold;
+ font-size: 1.1em;
+}
+
+.field-list ul {
+ margin: 0;
+ padding-left: 1em;
+}
+
+.field-list p {
+ margin: 0;
+}
+
+.optional {
+ font-size: 1.3em;
+}
+
+.sig-paren {
+ font-size: larger;
+}
+
+.versionmodified {
+ font-style: italic;
+}
+
+.system-message {
+ background-color: #fda;
+ padding: 5px;
+ border: 3px solid red;
+}
+
+.footnote:target {
+ background-color: #ffa;
+}
+
+.line-block {
+ display: block;
+ margin-top: 1em;
+ margin-bottom: 1em;
+}
+
+.line-block .line-block {
+ margin-top: 0;
+ margin-bottom: 0;
+ margin-left: 1.5em;
+}
+
+.guilabel, .menuselection {
+ font-family: sans-serif;
+}
+
+.accelerator {
+ text-decoration: underline;
+}
+
+.classifier {
+ font-style: oblique;
+}
+
+abbr, acronym {
+ border-bottom: dotted 1px;
+ cursor: help;
+}
+
+/* -- code displays --------------------------------------------------------- */
+
+pre {
+ overflow: auto;
+ overflow-y: hidden; /* fixes display issues on Chrome browsers */
+}
+
+td.linenos pre {
+ padding: 5px 0px;
+ border: 0;
+ background-color: transparent;
+ color: #aaa;
+}
+
+table.highlighttable {
+ margin-left: 0.5em;
+}
+
+table.highlighttable td {
+ padding: 0 0.5em 0 0.5em;
+}
+
+div.code-block-caption {
+ padding: 2px 5px;
+ font-size: small;
+}
+
+div.code-block-filename code {
+ background-color: transparent;
+}
+
+div.code-block-caption + pre,
+div.code-block-caption + div.highlight > pre {
+ margin-top: 0;
+}
+
+code.descname {
+ background-color: transparent;
+ font-weight: bold;
+ font-size: 1.2em;
+}
+
+code.descclassname {
+ background-color: transparent;
+}
+
+code.xref, a code {
+ background-color: transparent;
+ font-weight: bold;
+}
+
+h1 code, h2 code, h3 code, h4 code, h5 code, h6 code {
+ background-color: transparent;
+}
+
+.viewcode-link {
+ float: right;
+}
+
+.viewcode-back {
+ float: right;
+ font-family: sans-serif;
+}
+
+div.viewcode-block:target {
+ margin: -1px -10px;
+ padding: 0 10px;
+}
+
+/* -- math display ---------------------------------------------------------- */
+
+img.math {
+ vertical-align: middle;
+}
+
+div.body div.math p {
+ text-align: center;
+}
+
+span.eqno {
+ float: right;
+}
+
+/* -- printout stylesheet --------------------------------------------------- */
+
+@media print {
+ div.document,
+ div.documentwrapper,
+ div.bodywrapper {
+ margin: 0 !important;
+ width: 100%;
+ }
+
+ div.sphinxsidebar,
+ div.related,
+ div.footer,
+ #top-link {
+ display: none;
+ }
+}
\ No newline at end of file
diff --git a/docs/build/html/_static/bootstrap-2.3.2/css/bootstrap-responsive.css b/docs/build/html/_static/bootstrap-2.3.2/css/bootstrap-responsive.css
new file mode 100644
index 0000000000000000000000000000000000000000..09e88ce3fecc2812ad729e156975e2e53f8aea22
--- /dev/null
+++ b/docs/build/html/_static/bootstrap-2.3.2/css/bootstrap-responsive.css
@@ -0,0 +1,1109 @@
+/*!
+ * Bootstrap Responsive v2.3.2
+ *
+ * Copyright 2012 Twitter, Inc
+ * Licensed under the Apache License v2.0
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Designed and built with all the love in the world @twitter by @mdo and @fat.
+ */
+
+.clearfix {
+ *zoom: 1;
+}
+
+.clearfix:before,
+.clearfix:after {
+ display: table;
+ line-height: 0;
+ content: "";
+}
+
+.clearfix:after {
+ clear: both;
+}
+
+.hide-text {
+ font: 0/0 a;
+ color: transparent;
+ text-shadow: none;
+ background-color: transparent;
+ border: 0;
+}
+
+.input-block-level {
+ display: block;
+ width: 100%;
+ min-height: 30px;
+ -webkit-box-sizing: border-box;
+ -moz-box-sizing: border-box;
+ box-sizing: border-box;
+}
+
+@-ms-viewport {
+ width: device-width;
+}
+
+.hidden {
+ display: none;
+ visibility: hidden;
+}
+
+.visible-phone {
+ display: none !important;
+}
+
+.visible-tablet {
+ display: none !important;
+}
+
+.hidden-desktop {
+ display: none !important;
+}
+
+.visible-desktop {
+ display: inherit !important;
+}
+
+@media (min-width: 768px) and (max-width: 979px) {
+ .hidden-desktop {
+ display: inherit !important;
+ }
+ .visible-desktop {
+ display: none !important ;
+ }
+ .visible-tablet {
+ display: inherit !important;
+ }
+ .hidden-tablet {
+ display: none !important;
+ }
+}
+
+@media (max-width: 767px) {
+ .hidden-desktop {
+ display: inherit !important;
+ }
+ .visible-desktop {
+ display: none !important;
+ }
+ .visible-phone {
+ display: inherit !important;
+ }
+ .hidden-phone {
+ display: none !important;
+ }
+}
+
+.visible-print {
+ display: none !important;
+}
+
+@media print {
+ .visible-print {
+ display: inherit !important;
+ }
+ .hidden-print {
+ display: none !important;
+ }
+}
+
+@media (min-width: 1200px) {
+ .row {
+ margin-left: -30px;
+ *zoom: 1;
+ }
+ .row:before,
+ .row:after {
+ display: table;
+ line-height: 0;
+ content: "";
+ }
+ .row:after {
+ clear: both;
+ }
+ [class*="span"] {
+ float: left;
+ min-height: 1px;
+ margin-left: 30px;
+ }
+ .container,
+ .navbar-static-top .container,
+ .navbar-fixed-top .container,
+ .navbar-fixed-bottom .container {
+ width: 1170px;
+ }
+ .span12 {
+ width: 1170px;
+ }
+ .span11 {
+ width: 1070px;
+ }
+ .span10 {
+ width: 970px;
+ }
+ .span9 {
+ width: 870px;
+ }
+ .span8 {
+ width: 770px;
+ }
+ .span7 {
+ width: 670px;
+ }
+ .span6 {
+ width: 570px;
+ }
+ .span5 {
+ width: 470px;
+ }
+ .span4 {
+ width: 370px;
+ }
+ .span3 {
+ width: 270px;
+ }
+ .span2 {
+ width: 170px;
+ }
+ .span1 {
+ width: 70px;
+ }
+ .offset12 {
+ margin-left: 1230px;
+ }
+ .offset11 {
+ margin-left: 1130px;
+ }
+ .offset10 {
+ margin-left: 1030px;
+ }
+ .offset9 {
+ margin-left: 930px;
+ }
+ .offset8 {
+ margin-left: 830px;
+ }
+ .offset7 {
+ margin-left: 730px;
+ }
+ .offset6 {
+ margin-left: 630px;
+ }
+ .offset5 {
+ margin-left: 530px;
+ }
+ .offset4 {
+ margin-left: 430px;
+ }
+ .offset3 {
+ margin-left: 330px;
+ }
+ .offset2 {
+ margin-left: 230px;
+ }
+ .offset1 {
+ margin-left: 130px;
+ }
+ .row-fluid {
+ width: 100%;
+ *zoom: 1;
+ }
+ .row-fluid:before,
+ .row-fluid:after {
+ display: table;
+ line-height: 0;
+ content: "";
+ }
+ .row-fluid:after {
+ clear: both;
+ }
+ .row-fluid [class*="span"] {
+ display: block;
+ float: left;
+ width: 100%;
+ min-height: 30px;
+ margin-left: 2.564102564102564%;
+ *margin-left: 2.5109110747408616%;
+ -webkit-box-sizing: border-box;
+ -moz-box-sizing: border-box;
+ box-sizing: border-box;
+ }
+ .row-fluid [class*="span"]:first-child {
+ margin-left: 0;
+ }
+ .row-fluid .controls-row [class*="span"] + [class*="span"] {
+ margin-left: 2.564102564102564%;
+ }
+ .row-fluid .span12 {
+ width: 100%;
+ *width: 99.94680851063829%;
+ }
+ .row-fluid .span11 {
+ width: 91.45299145299145%;
+ *width: 91.39979996362975%;
+ }
+ .row-fluid .span10 {
+ width: 82.90598290598291%;
+ *width: 82.8527914166212%;
+ }
+ .row-fluid .span9 {
+ width: 74.35897435897436%;
+ *width: 74.30578286961266%;
+ }
+ .row-fluid .span8 {
+ width: 65.81196581196582%;
+ *width: 65.75877432260411%;
+ }
+ .row-fluid .span7 {
+ width: 57.26495726495726%;
+ *width: 57.21176577559556%;
+ }
+ .row-fluid .span6 {
+ width: 48.717948717948715%;
+ *width: 48.664757228587014%;
+ }
+ .row-fluid .span5 {
+ width: 40.17094017094017%;
+ *width: 40.11774868157847%;
+ }
+ .row-fluid .span4 {
+ width: 31.623931623931625%;
+ *width: 31.570740134569924%;
+ }
+ .row-fluid .span3 {
+ width: 23.076923076923077%;
+ *width: 23.023731587561375%;
+ }
+ .row-fluid .span2 {
+ width: 14.52991452991453%;
+ *width: 14.476723040552828%;
+ }
+ .row-fluid .span1 {
+ width: 5.982905982905983%;
+ *width: 5.929714493544281%;
+ }
+ .row-fluid .offset12 {
+ margin-left: 105.12820512820512%;
+ *margin-left: 105.02182214948171%;
+ }
+ .row-fluid .offset12:first-child {
+ margin-left: 102.56410256410257%;
+ *margin-left: 102.45771958537915%;
+ }
+ .row-fluid .offset11 {
+ margin-left: 96.58119658119658%;
+ *margin-left: 96.47481360247316%;
+ }
+ .row-fluid .offset11:first-child {
+ margin-left: 94.01709401709402%;
+ *margin-left: 93.91071103837061%;
+ }
+ .row-fluid .offset10 {
+ margin-left: 88.03418803418803%;
+ *margin-left: 87.92780505546462%;
+ }
+ .row-fluid .offset10:first-child {
+ margin-left: 85.47008547008548%;
+ *margin-left: 85.36370249136206%;
+ }
+ .row-fluid .offset9 {
+ margin-left: 79.48717948717949%;
+ *margin-left: 79.38079650845607%;
+ }
+ .row-fluid .offset9:first-child {
+ margin-left: 76.92307692307693%;
+ *margin-left: 76.81669394435352%;
+ }
+ .row-fluid .offset8 {
+ margin-left: 70.94017094017094%;
+ *margin-left: 70.83378796144753%;
+ }
+ .row-fluid .offset8:first-child {
+ margin-left: 68.37606837606839%;
+ *margin-left: 68.26968539734497%;
+ }
+ .row-fluid .offset7 {
+ margin-left: 62.393162393162385%;
+ *margin-left: 62.28677941443899%;
+ }
+ .row-fluid .offset7:first-child {
+ margin-left: 59.82905982905982%;
+ *margin-left: 59.72267685033642%;
+ }
+ .row-fluid .offset6 {
+ margin-left: 53.84615384615384%;
+ *margin-left: 53.739770867430444%;
+ }
+ .row-fluid .offset6:first-child {
+ margin-left: 51.28205128205128%;
+ *margin-left: 51.175668303327875%;
+ }
+ .row-fluid .offset5 {
+ margin-left: 45.299145299145295%;
+ *margin-left: 45.1927623204219%;
+ }
+ .row-fluid .offset5:first-child {
+ margin-left: 42.73504273504273%;
+ *margin-left: 42.62865975631933%;
+ }
+ .row-fluid .offset4 {
+ margin-left: 36.75213675213675%;
+ *margin-left: 36.645753773413354%;
+ }
+ .row-fluid .offset4:first-child {
+ margin-left: 34.18803418803419%;
+ *margin-left: 34.081651209310785%;
+ }
+ .row-fluid .offset3 {
+ margin-left: 28.205128205128204%;
+ *margin-left: 28.0987452264048%;
+ }
+ .row-fluid .offset3:first-child {
+ margin-left: 25.641025641025642%;
+ *margin-left: 25.53464266230224%;
+ }
+ .row-fluid .offset2 {
+ margin-left: 19.65811965811966%;
+ *margin-left: 19.551736679396257%;
+ }
+ .row-fluid .offset2:first-child {
+ margin-left: 17.094017094017094%;
+ *margin-left: 16.98763411529369%;
+ }
+ .row-fluid .offset1 {
+ margin-left: 11.11111111111111%;
+ *margin-left: 11.004728132387708%;
+ }
+ .row-fluid .offset1:first-child {
+ margin-left: 8.547008547008547%;
+ *margin-left: 8.440625568285142%;
+ }
+ input,
+ textarea,
+ .uneditable-input {
+ margin-left: 0;
+ }
+ .controls-row [class*="span"] + [class*="span"] {
+ margin-left: 30px;
+ }
+ input.span12,
+ textarea.span12,
+ .uneditable-input.span12 {
+ width: 1156px;
+ }
+ input.span11,
+ textarea.span11,
+ .uneditable-input.span11 {
+ width: 1056px;
+ }
+ input.span10,
+ textarea.span10,
+ .uneditable-input.span10 {
+ width: 956px;
+ }
+ input.span9,
+ textarea.span9,
+ .uneditable-input.span9 {
+ width: 856px;
+ }
+ input.span8,
+ textarea.span8,
+ .uneditable-input.span8 {
+ width: 756px;
+ }
+ input.span7,
+ textarea.span7,
+ .uneditable-input.span7 {
+ width: 656px;
+ }
+ input.span6,
+ textarea.span6,
+ .uneditable-input.span6 {
+ width: 556px;
+ }
+ input.span5,
+ textarea.span5,
+ .uneditable-input.span5 {
+ width: 456px;
+ }
+ input.span4,
+ textarea.span4,
+ .uneditable-input.span4 {
+ width: 356px;
+ }
+ input.span3,
+ textarea.span3,
+ .uneditable-input.span3 {
+ width: 256px;
+ }
+ input.span2,
+ textarea.span2,
+ .uneditable-input.span2 {
+ width: 156px;
+ }
+ input.span1,
+ textarea.span1,
+ .uneditable-input.span1 {
+ width: 56px;
+ }
+ .thumbnails {
+ margin-left: -30px;
+ }
+ .thumbnails > li {
+ margin-left: 30px;
+ }
+ .row-fluid .thumbnails {
+ margin-left: 0;
+ }
+}
+
+@media (min-width: 768px) and (max-width: 979px) {
+ .row {
+ margin-left: -20px;
+ *zoom: 1;
+ }
+ .row:before,
+ .row:after {
+ display: table;
+ line-height: 0;
+ content: "";
+ }
+ .row:after {
+ clear: both;
+ }
+ [class*="span"] {
+ float: left;
+ min-height: 1px;
+ margin-left: 20px;
+ }
+ .container,
+ .navbar-static-top .container,
+ .navbar-fixed-top .container,
+ .navbar-fixed-bottom .container {
+ width: 724px;
+ }
+ .span12 {
+ width: 724px;
+ }
+ .span11 {
+ width: 662px;
+ }
+ .span10 {
+ width: 600px;
+ }
+ .span9 {
+ width: 538px;
+ }
+ .span8 {
+ width: 476px;
+ }
+ .span7 {
+ width: 414px;
+ }
+ .span6 {
+ width: 352px;
+ }
+ .span5 {
+ width: 290px;
+ }
+ .span4 {
+ width: 228px;
+ }
+ .span3 {
+ width: 166px;
+ }
+ .span2 {
+ width: 104px;
+ }
+ .span1 {
+ width: 42px;
+ }
+ .offset12 {
+ margin-left: 764px;
+ }
+ .offset11 {
+ margin-left: 702px;
+ }
+ .offset10 {
+ margin-left: 640px;
+ }
+ .offset9 {
+ margin-left: 578px;
+ }
+ .offset8 {
+ margin-left: 516px;
+ }
+ .offset7 {
+ margin-left: 454px;
+ }
+ .offset6 {
+ margin-left: 392px;
+ }
+ .offset5 {
+ margin-left: 330px;
+ }
+ .offset4 {
+ margin-left: 268px;
+ }
+ .offset3 {
+ margin-left: 206px;
+ }
+ .offset2 {
+ margin-left: 144px;
+ }
+ .offset1 {
+ margin-left: 82px;
+ }
+ .row-fluid {
+ width: 100%;
+ *zoom: 1;
+ }
+ .row-fluid:before,
+ .row-fluid:after {
+ display: table;
+ line-height: 0;
+ content: "";
+ }
+ .row-fluid:after {
+ clear: both;
+ }
+ .row-fluid [class*="span"] {
+ display: block;
+ float: left;
+ width: 100%;
+ min-height: 30px;
+ margin-left: 2.7624309392265194%;
+ *margin-left: 2.709239449864817%;
+ -webkit-box-sizing: border-box;
+ -moz-box-sizing: border-box;
+ box-sizing: border-box;
+ }
+ .row-fluid [class*="span"]:first-child {
+ margin-left: 0;
+ }
+ .row-fluid .controls-row [class*="span"] + [class*="span"] {
+ margin-left: 2.7624309392265194%;
+ }
+ .row-fluid .span12 {
+ width: 100%;
+ *width: 99.94680851063829%;
+ }
+ .row-fluid .span11 {
+ width: 91.43646408839778%;
+ *width: 91.38327259903608%;
+ }
+ .row-fluid .span10 {
+ width: 82.87292817679558%;
+ *width: 82.81973668743387%;
+ }
+ .row-fluid .span9 {
+ width: 74.30939226519337%;
+ *width: 74.25620077583166%;
+ }
+ .row-fluid .span8 {
+ width: 65.74585635359117%;
+ *width: 65.69266486422946%;
+ }
+ .row-fluid .span7 {
+ width: 57.18232044198895%;
+ *width: 57.12912895262725%;
+ }
+ .row-fluid .span6 {
+ width: 48.61878453038674%;
+ *width: 48.56559304102504%;
+ }
+ .row-fluid .span5 {
+ width: 40.05524861878453%;
+ *width: 40.00205712942283%;
+ }
+ .row-fluid .span4 {
+ width: 31.491712707182323%;
+ *width: 31.43852121782062%;
+ }
+ .row-fluid .span3 {
+ width: 22.92817679558011%;
+ *width: 22.87498530621841%;
+ }
+ .row-fluid .span2 {
+ width: 14.3646408839779%;
+ *width: 14.311449394616199%;
+ }
+ .row-fluid .span1 {
+ width: 5.801104972375691%;
+ *width: 5.747913483013988%;
+ }
+ .row-fluid .offset12 {
+ margin-left: 105.52486187845304%;
+ *margin-left: 105.41847889972962%;
+ }
+ .row-fluid .offset12:first-child {
+ margin-left: 102.76243093922652%;
+ *margin-left: 102.6560479605031%;
+ }
+ .row-fluid .offset11 {
+ margin-left: 96.96132596685082%;
+ *margin-left: 96.8549429881274%;
+ }
+ .row-fluid .offset11:first-child {
+ margin-left: 94.1988950276243%;
+ *margin-left: 94.09251204890089%;
+ }
+ .row-fluid .offset10 {
+ margin-left: 88.39779005524862%;
+ *margin-left: 88.2914070765252%;
+ }
+ .row-fluid .offset10:first-child {
+ margin-left: 85.6353591160221%;
+ *margin-left: 85.52897613729868%;
+ }
+ .row-fluid .offset9 {
+ margin-left: 79.8342541436464%;
+ *margin-left: 79.72787116492299%;
+ }
+ .row-fluid .offset9:first-child {
+ margin-left: 77.07182320441989%;
+ *margin-left: 76.96544022569647%;
+ }
+ .row-fluid .offset8 {
+ margin-left: 71.2707182320442%;
+ *margin-left: 71.16433525332079%;
+ }
+ .row-fluid .offset8:first-child {
+ margin-left: 68.50828729281768%;
+ *margin-left: 68.40190431409427%;
+ }
+ .row-fluid .offset7 {
+ margin-left: 62.70718232044199%;
+ *margin-left: 62.600799341718584%;
+ }
+ .row-fluid .offset7:first-child {
+ margin-left: 59.94475138121547%;
+ *margin-left: 59.838368402492065%;
+ }
+ .row-fluid .offset6 {
+ margin-left: 54.14364640883978%;
+ *margin-left: 54.037263430116376%;
+ }
+ .row-fluid .offset6:first-child {
+ margin-left: 51.38121546961326%;
+ *margin-left: 51.27483249088986%;
+ }
+ .row-fluid .offset5 {
+ margin-left: 45.58011049723757%;
+ *margin-left: 45.47372751851417%;
+ }
+ .row-fluid .offset5:first-child {
+ margin-left: 42.81767955801105%;
+ *margin-left: 42.71129657928765%;
+ }
+ .row-fluid .offset4 {
+ margin-left: 37.01657458563536%;
+ *margin-left: 36.91019160691196%;
+ }
+ .row-fluid .offset4:first-child {
+ margin-left: 34.25414364640884%;
+ *margin-left: 34.14776066768544%;
+ }
+ .row-fluid .offset3 {
+ margin-left: 28.45303867403315%;
+ *margin-left: 28.346655695309746%;
+ }
+ .row-fluid .offset3:first-child {
+ margin-left: 25.69060773480663%;
+ *margin-left: 25.584224756083227%;
+ }
+ .row-fluid .offset2 {
+ margin-left: 19.88950276243094%;
+ *margin-left: 19.783119783707537%;
+ }
+ .row-fluid .offset2:first-child {
+ margin-left: 17.12707182320442%;
+ *margin-left: 17.02068884448102%;
+ }
+ .row-fluid .offset1 {
+ margin-left: 11.32596685082873%;
+ *margin-left: 11.219583872105325%;
+ }
+ .row-fluid .offset1:first-child {
+ margin-left: 8.56353591160221%;
+ *margin-left: 8.457152932878806%;
+ }
+ input,
+ textarea,
+ .uneditable-input {
+ margin-left: 0;
+ }
+ .controls-row [class*="span"] + [class*="span"] {
+ margin-left: 20px;
+ }
+ input.span12,
+ textarea.span12,
+ .uneditable-input.span12 {
+ width: 710px;
+ }
+ input.span11,
+ textarea.span11,
+ .uneditable-input.span11 {
+ width: 648px;
+ }
+ input.span10,
+ textarea.span10,
+ .uneditable-input.span10 {
+ width: 586px;
+ }
+ input.span9,
+ textarea.span9,
+ .uneditable-input.span9 {
+ width: 524px;
+ }
+ input.span8,
+ textarea.span8,
+ .uneditable-input.span8 {
+ width: 462px;
+ }
+ input.span7,
+ textarea.span7,
+ .uneditable-input.span7 {
+ width: 400px;
+ }
+ input.span6,
+ textarea.span6,
+ .uneditable-input.span6 {
+ width: 338px;
+ }
+ input.span5,
+ textarea.span5,
+ .uneditable-input.span5 {
+ width: 276px;
+ }
+ input.span4,
+ textarea.span4,
+ .uneditable-input.span4 {
+ width: 214px;
+ }
+ input.span3,
+ textarea.span3,
+ .uneditable-input.span3 {
+ width: 152px;
+ }
+ input.span2,
+ textarea.span2,
+ .uneditable-input.span2 {
+ width: 90px;
+ }
+ input.span1,
+ textarea.span1,
+ .uneditable-input.span1 {
+ width: 28px;
+ }
+}
+
+@media (max-width: 767px) {
+ body {
+ padding-right: 20px;
+ padding-left: 20px;
+ }
+ .navbar-fixed-top,
+ .navbar-fixed-bottom,
+ .navbar-static-top {
+ margin-right: -20px;
+ margin-left: -20px;
+ }
+ .container-fluid {
+ padding: 0;
+ }
+ .dl-horizontal dt {
+ float: none;
+ width: auto;
+ clear: none;
+ text-align: left;
+ }
+ .dl-horizontal dd {
+ margin-left: 0;
+ }
+ .container {
+ width: auto;
+ }
+ .row-fluid {
+ width: 100%;
+ }
+ .row,
+ .thumbnails {
+ margin-left: 0;
+ }
+ .thumbnails > li {
+ float: none;
+ margin-left: 0;
+ }
+ [class*="span"],
+ .uneditable-input[class*="span"],
+ .row-fluid [class*="span"] {
+ display: block;
+ float: none;
+ width: 100%;
+ margin-left: 0;
+ -webkit-box-sizing: border-box;
+ -moz-box-sizing: border-box;
+ box-sizing: border-box;
+ }
+ .span12,
+ .row-fluid .span12 {
+ width: 100%;
+ -webkit-box-sizing: border-box;
+ -moz-box-sizing: border-box;
+ box-sizing: border-box;
+ }
+ .row-fluid [class*="offset"]:first-child {
+ margin-left: 0;
+ }
+ .input-large,
+ .input-xlarge,
+ .input-xxlarge,
+ input[class*="span"],
+ select[class*="span"],
+ textarea[class*="span"],
+ .uneditable-input {
+ display: block;
+ width: 100%;
+ min-height: 30px;
+ -webkit-box-sizing: border-box;
+ -moz-box-sizing: border-box;
+ box-sizing: border-box;
+ }
+ .input-prepend input,
+ .input-append input,
+ .input-prepend input[class*="span"],
+ .input-append input[class*="span"] {
+ display: inline-block;
+ width: auto;
+ }
+ .controls-row [class*="span"] + [class*="span"] {
+ margin-left: 0;
+ }
+ .modal {
+ position: fixed;
+ top: 20px;
+ right: 20px;
+ left: 20px;
+ width: auto;
+ margin: 0;
+ }
+ .modal.fade {
+ top: -100px;
+ }
+ .modal.fade.in {
+ top: 20px;
+ }
+}
+
+@media (max-width: 480px) {
+ .nav-collapse {
+ -webkit-transform: translate3d(0, 0, 0);
+ }
+ .page-header h1 small {
+ display: block;
+ line-height: 20px;
+ }
+ input[type="checkbox"],
+ input[type="radio"] {
+ border: 1px solid #ccc;
+ }
+ .form-horizontal .control-label {
+ float: none;
+ width: auto;
+ padding-top: 0;
+ text-align: left;
+ }
+ .form-horizontal .controls {
+ margin-left: 0;
+ }
+ .form-horizontal .control-list {
+ padding-top: 0;
+ }
+ .form-horizontal .form-actions {
+ padding-right: 10px;
+ padding-left: 10px;
+ }
+ .media .pull-left,
+ .media .pull-right {
+ display: block;
+ float: none;
+ margin-bottom: 10px;
+ }
+ .media-object {
+ margin-right: 0;
+ margin-left: 0;
+ }
+ .modal {
+ top: 10px;
+ right: 10px;
+ left: 10px;
+ }
+ .modal-header .close {
+ padding: 10px;
+ margin: -10px;
+ }
+ .carousel-caption {
+ position: static;
+ }
+}
+
+@media (max-width: 979px) {
+ body {
+ padding-top: 0;
+ }
+ .navbar-fixed-top,
+ .navbar-fixed-bottom {
+ position: static;
+ }
+ .navbar-fixed-top {
+ margin-bottom: 20px;
+ }
+ .navbar-fixed-bottom {
+ margin-top: 20px;
+ }
+ .navbar-fixed-top .navbar-inner,
+ .navbar-fixed-bottom .navbar-inner {
+ padding: 5px;
+ }
+ .navbar .container {
+ width: auto;
+ padding: 0;
+ }
+ .navbar .brand {
+ padding-right: 10px;
+ padding-left: 10px;
+ margin: 0 0 0 -5px;
+ }
+ .nav-collapse {
+ clear: both;
+ }
+ .nav-collapse .nav {
+ float: none;
+ margin: 0 0 10px;
+ }
+ .nav-collapse .nav > li {
+ float: none;
+ }
+ .nav-collapse .nav > li > a {
+ margin-bottom: 2px;
+ }
+ .nav-collapse .nav > .divider-vertical {
+ display: none;
+ }
+ .nav-collapse .nav .nav-header {
+ color: #777777;
+ text-shadow: none;
+ }
+ .nav-collapse .nav > li > a,
+ .nav-collapse .dropdown-menu a {
+ padding: 9px 15px;
+ font-weight: bold;
+ color: #777777;
+ -webkit-border-radius: 3px;
+ -moz-border-radius: 3px;
+ border-radius: 3px;
+ }
+ .nav-collapse .btn {
+ padding: 4px 10px 4px;
+ font-weight: normal;
+ -webkit-border-radius: 4px;
+ -moz-border-radius: 4px;
+ border-radius: 4px;
+ }
+ .nav-collapse .dropdown-menu li + li a {
+ margin-bottom: 2px;
+ }
+ .nav-collapse .nav > li > a:hover,
+ .nav-collapse .nav > li > a:focus,
+ .nav-collapse .dropdown-menu a:hover,
+ .nav-collapse .dropdown-menu a:focus {
+ background-color: #f2f2f2;
+ }
+ .navbar-inverse .nav-collapse .nav > li > a,
+ .navbar-inverse .nav-collapse .dropdown-menu a {
+ color: #999999;
+ }
+ .navbar-inverse .nav-collapse .nav > li > a:hover,
+ .navbar-inverse .nav-collapse .nav > li > a:focus,
+ .navbar-inverse .nav-collapse .dropdown-menu a:hover,
+ .navbar-inverse .nav-collapse .dropdown-menu a:focus {
+ background-color: #111111;
+ }
+ .nav-collapse.in .btn-group {
+ padding: 0;
+ margin-top: 5px;
+ }
+ .nav-collapse .dropdown-menu {
+ position: static;
+ top: auto;
+ left: auto;
+ display: none;
+ float: none;
+ max-width: none;
+ padding: 0;
+ margin: 0 15px;
+ background-color: transparent;
+ border: none;
+ -webkit-border-radius: 0;
+ -moz-border-radius: 0;
+ border-radius: 0;
+ -webkit-box-shadow: none;
+ -moz-box-shadow: none;
+ box-shadow: none;
+ }
+ .nav-collapse .open > .dropdown-menu {
+ display: block;
+ }
+ .nav-collapse .dropdown-menu:before,
+ .nav-collapse .dropdown-menu:after {
+ display: none;
+ }
+ .nav-collapse .dropdown-menu .divider {
+ display: none;
+ }
+ .nav-collapse .nav > li > .dropdown-menu:before,
+ .nav-collapse .nav > li > .dropdown-menu:after {
+ display: none;
+ }
+ .nav-collapse .navbar-form,
+ .nav-collapse .navbar-search {
+ float: none;
+ padding: 10px 15px;
+ margin: 10px 0;
+ border-top: 1px solid #f2f2f2;
+ border-bottom: 1px solid #f2f2f2;
+ -webkit-box-shadow: inset 0 1px 0 rgba(255, 255, 255, 0.1), 0 1px 0 rgba(255, 255, 255, 0.1);
+ -moz-box-shadow: inset 0 1px 0 rgba(255, 255, 255, 0.1), 0 1px 0 rgba(255, 255, 255, 0.1);
+ box-shadow: inset 0 1px 0 rgba(255, 255, 255, 0.1), 0 1px 0 rgba(255, 255, 255, 0.1);
+ }
+ .navbar-inverse .nav-collapse .navbar-form,
+ .navbar-inverse .nav-collapse .navbar-search {
+ border-top-color: #111111;
+ border-bottom-color: #111111;
+ }
+ .navbar .nav-collapse .nav.pull-right {
+ float: none;
+ margin-left: 0;
+ }
+ .nav-collapse,
+ .nav-collapse.collapse {
+ height: 0;
+ overflow: hidden;
+ }
+ .navbar .btn-navbar {
+ display: block;
+ }
+ .navbar-static .navbar-inner {
+ padding-right: 10px;
+ padding-left: 10px;
+ }
+}
+
+@media (min-width: 980px) {
+ .nav-collapse.collapse {
+ height: auto !important;
+ overflow: visible !important;
+ }
+}
diff --git a/docs/build/html/_static/bootstrap-2.3.2/css/bootstrap-responsive.min.css b/docs/build/html/_static/bootstrap-2.3.2/css/bootstrap-responsive.min.css
new file mode 100644
index 0000000000000000000000000000000000000000..f4ede63f32e2ec803876a38efac05dd49acc4684
--- /dev/null
+++ b/docs/build/html/_static/bootstrap-2.3.2/css/bootstrap-responsive.min.css
@@ -0,0 +1,9 @@
+/*!
+ * Bootstrap Responsive v2.3.2
+ *
+ * Copyright 2012 Twitter, Inc
+ * Licensed under the Apache License v2.0
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Designed and built with all the love in the world @twitter by @mdo and @fat.
+ */.clearfix{*zoom:1}.clearfix:before,.clearfix:after{display:table;line-height:0;content:""}.clearfix:after{clear:both}.hide-text{font:0/0 a;color:transparent;text-shadow:none;background-color:transparent;border:0}.input-block-level{display:block;width:100%;min-height:30px;-webkit-box-sizing:border-box;-moz-box-sizing:border-box;box-sizing:border-box}@-ms-viewport{width:device-width}.hidden{display:none;visibility:hidden}.visible-phone{display:none!important}.visible-tablet{display:none!important}.hidden-desktop{display:none!important}.visible-desktop{display:inherit!important}@media(min-width:768px) and 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diff --git a/docs/build/html/_static/bootstrap-2.3.2/css/bootstrap.css b/docs/build/html/_static/bootstrap-2.3.2/css/bootstrap.css
new file mode 100644
index 0000000000000000000000000000000000000000..b725064aab21e434d29209d259d3892478aa9536
--- /dev/null
+++ b/docs/build/html/_static/bootstrap-2.3.2/css/bootstrap.css
@@ -0,0 +1,6167 @@
+/*!
+ * Bootstrap v2.3.2
+ *
+ * Copyright 2012 Twitter, Inc
+ * Licensed under the Apache License v2.0
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Designed and built with all the love in the world @twitter by @mdo and @fat.
+ */
+
+.clearfix {
+ *zoom: 1;
+}
+
+.clearfix:before,
+.clearfix:after {
+ display: table;
+ line-height: 0;
+ content: "";
+}
+
+.clearfix:after {
+ clear: both;
+}
+
+.hide-text {
+ font: 0/0 a;
+ color: transparent;
+ text-shadow: none;
+ background-color: transparent;
+ border: 0;
+}
+
+.input-block-level {
+ display: block;
+ width: 100%;
+ min-height: 30px;
+ -webkit-box-sizing: border-box;
+ -moz-box-sizing: border-box;
+ box-sizing: border-box;
+}
+
+article,
+aside,
+details,
+figcaption,
+figure,
+footer,
+header,
+hgroup,
+nav,
+section {
+ display: block;
+}
+
+audio,
+canvas,
+video {
+ display: inline-block;
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+input[type="datetime-local"]:focus,
+input[type="date"]:focus,
+input[type="month"]:focus,
+input[type="time"]:focus,
+input[type="week"]:focus,
+input[type="number"]:focus,
+input[type="email"]:focus,
+input[type="url"]:focus,
+input[type="search"]:focus,
+input[type="tel"]:focus,
+input[type="color"]:focus,
+.uneditable-input:focus {
+ border-color: rgba(82, 168, 236, 0.8);
+ outline: 0;
+ outline: thin dotted \9;
+ /* IE6-9 */
+
+ -webkit-box-shadow: inset 0 1px 1px rgba(0, 0, 0, 0.075), 0 0 8px rgba(82, 168, 236, 0.6);
+ -moz-box-shadow: inset 0 1px 1px rgba(0, 0, 0, 0.075), 0 0 8px rgba(82, 168, 236, 0.6);
+ box-shadow: inset 0 1px 1px rgba(0, 0, 0, 0.075), 0 0 8px rgba(82, 168, 236, 0.6);
+}
+
+input[type="radio"],
+input[type="checkbox"] {
+ margin: 4px 0 0;
+ margin-top: 1px \9;
+ *margin-top: 0;
+ line-height: normal;
+}
+
+input[type="file"],
+input[type="image"],
+input[type="submit"],
+input[type="reset"],
+input[type="button"],
+input[type="radio"],
+input[type="checkbox"] {
+ width: auto;
+}
+
+select,
+input[type="file"] {
+ height: 30px;
+ /* In IE7, the height of the select element cannot be changed by height, only font-size */
+
+ *margin-top: 4px;
+ /* For IE7, add top margin to align select with labels */
+
+ line-height: 30px;
+}
+
+select {
+ width: 220px;
+ background-color: #ffffff;
+ border: 1px solid #cccccc;
+}
+
+select[multiple],
+select[size] {
+ height: auto;
+}
+
+select:focus,
+input[type="file"]:focus,
+input[type="radio"]:focus,
+input[type="checkbox"]:focus {
+ outline: thin dotted #333;
+ outline: 5px auto -webkit-focus-ring-color;
+ outline-offset: -2px;
+}
+
+.uneditable-input,
+.uneditable-textarea {
+ color: #999999;
+ cursor: not-allowed;
+ background-color: #fcfcfc;
+ border-color: #cccccc;
+ -webkit-box-shadow: inset 0 1px 2px rgba(0, 0, 0, 0.025);
+ -moz-box-shadow: inset 0 1px 2px rgba(0, 0, 0, 0.025);
+ box-shadow: inset 0 1px 2px rgba(0, 0, 0, 0.025);
+}
+
+.uneditable-input {
+ overflow: hidden;
+ white-space: nowrap;
+}
+
+.uneditable-textarea {
+ width: auto;
+ height: auto;
+}
+
+input:-moz-placeholder,
+textarea:-moz-placeholder {
+ color: #999999;
+}
+
+input:-ms-input-placeholder,
+textarea:-ms-input-placeholder {
+ color: #999999;
+}
+
+input::-webkit-input-placeholder,
+textarea::-webkit-input-placeholder {
+ color: #999999;
+}
+
+.radio,
+.checkbox {
+ min-height: 20px;
+ padding-left: 20px;
+}
+
+.radio input[type="radio"],
+.checkbox input[type="checkbox"] {
+ float: left;
+ margin-left: -20px;
+}
+
+.controls > .radio:first-child,
+.controls > .checkbox:first-child {
+ padding-top: 5px;
+}
+
+.radio.inline,
+.checkbox.inline {
+ display: inline-block;
+ padding-top: 5px;
+ margin-bottom: 0;
+ vertical-align: middle;
+}
+
+.radio.inline + .radio.inline,
+.checkbox.inline + .checkbox.inline {
+ margin-left: 10px;
+}
+
+.input-mini {
+ width: 60px;
+}
+
+.input-small {
+ width: 90px;
+}
+
+.input-medium {
+ width: 150px;
+}
+
+.input-large {
+ width: 210px;
+}
+
+.input-xlarge {
+ width: 270px;
+}
+
+.input-xxlarge {
+ width: 530px;
+}
+
+input[class*="span"],
+select[class*="span"],
+textarea[class*="span"],
+.uneditable-input[class*="span"],
+.row-fluid input[class*="span"],
+.row-fluid select[class*="span"],
+.row-fluid textarea[class*="span"],
+.row-fluid .uneditable-input[class*="span"] {
+ float: none;
+ margin-left: 0;
+}
+
+.input-append input[class*="span"],
+.input-append .uneditable-input[class*="span"],
+.input-prepend input[class*="span"],
+.input-prepend .uneditable-input[class*="span"],
+.row-fluid input[class*="span"],
+.row-fluid select[class*="span"],
+.row-fluid textarea[class*="span"],
+.row-fluid .uneditable-input[class*="span"],
+.row-fluid .input-prepend [class*="span"],
+.row-fluid .input-append [class*="span"] {
+ display: inline-block;
+}
+
+input,
+textarea,
+.uneditable-input {
+ margin-left: 0;
+}
+
+.controls-row [class*="span"] + [class*="span"] {
+ margin-left: 20px;
+}
+
+input.span12,
+textarea.span12,
+.uneditable-input.span12 {
+ width: 926px;
+}
+
+input.span11,
+textarea.span11,
+.uneditable-input.span11 {
+ width: 846px;
+}
+
+input.span10,
+textarea.span10,
+.uneditable-input.span10 {
+ width: 766px;
+}
+
+input.span9,
+textarea.span9,
+.uneditable-input.span9 {
+ width: 686px;
+}
+
+input.span8,
+textarea.span8,
+.uneditable-input.span8 {
+ width: 606px;
+}
+
+input.span7,
+textarea.span7,
+.uneditable-input.span7 {
+ width: 526px;
+}
+
+input.span6,
+textarea.span6,
+.uneditable-input.span6 {
+ width: 446px;
+}
+
+input.span5,
+textarea.span5,
+.uneditable-input.span5 {
+ width: 366px;
+}
+
+input.span4,
+textarea.span4,
+.uneditable-input.span4 {
+ width: 286px;
+}
+
+input.span3,
+textarea.span3,
+.uneditable-input.span3 {
+ width: 206px;
+}
+
+input.span2,
+textarea.span2,
+.uneditable-input.span2 {
+ width: 126px;
+}
+
+input.span1,
+textarea.span1,
+.uneditable-input.span1 {
+ width: 46px;
+}
+
+.controls-row {
+ *zoom: 1;
+}
+
+.controls-row:before,
+.controls-row:after {
+ display: table;
+ line-height: 0;
+ content: "";
+}
+
+.controls-row:after {
+ clear: both;
+}
+
+.controls-row [class*="span"],
+.row-fluid .controls-row [class*="span"] {
+ float: left;
+}
+
+.controls-row .checkbox[class*="span"],
+.controls-row .radio[class*="span"] {
+ padding-top: 5px;
+}
+
+input[disabled],
+select[disabled],
+textarea[disabled],
+input[readonly],
+select[readonly],
+textarea[readonly] {
+ cursor: not-allowed;
+ background-color: #eeeeee;
+}
+
+input[type="radio"][disabled],
+input[type="checkbox"][disabled],
+input[type="radio"][readonly],
+input[type="checkbox"][readonly] {
+ background-color: transparent;
+}
+
+.control-group.warning .control-label,
+.control-group.warning .help-block,
+.control-group.warning .help-inline {
+ color: #c09853;
+}
+
+.control-group.warning .checkbox,
+.control-group.warning .radio,
+.control-group.warning input,
+.control-group.warning select,
+.control-group.warning textarea {
+ color: #c09853;
+}
+
+.control-group.warning input,
+.control-group.warning select,
+.control-group.warning textarea {
+ border-color: #c09853;
+ -webkit-box-shadow: inset 0 1px 1px rgba(0, 0, 0, 0.075);
+ -moz-box-shadow: inset 0 1px 1px rgba(0, 0, 0, 0.075);
+ box-shadow: inset 0 1px 1px rgba(0, 0, 0, 0.075);
+}
+
+.control-group.warning input:focus,
+.control-group.warning select:focus,
+.control-group.warning textarea:focus {
+ border-color: #a47e3c;
+ -webkit-box-shadow: inset 0 1px 1px rgba(0, 0, 0, 0.075), 0 0 6px #dbc59e;
+ -moz-box-shadow: inset 0 1px 1px rgba(0, 0, 0, 0.075), 0 0 6px #dbc59e;
+ box-shadow: inset 0 1px 1px rgba(0, 0, 0, 0.075), 0 0 6px #dbc59e;
+}
+
+.control-group.warning .input-prepend .add-on,
+.control-group.warning .input-append .add-on {
+ color: #c09853;
+ background-color: #fcf8e3;
+ border-color: #c09853;
+}
+
+.control-group.error .control-label,
+.control-group.error .help-block,
+.control-group.error .help-inline {
+ color: #b94a48;
+}
+
+.control-group.error .checkbox,
+.control-group.error .radio,
+.control-group.error input,
+.control-group.error select,
+.control-group.error textarea {
+ color: #b94a48;
+}
+
+.control-group.error input,
+.control-group.error select,
+.control-group.error textarea {
+ border-color: #b94a48;
+ -webkit-box-shadow: inset 0 1px 1px rgba(0, 0, 0, 0.075);
+ -moz-box-shadow: inset 0 1px 1px rgba(0, 0, 0, 0.075);
+ box-shadow: inset 0 1px 1px rgba(0, 0, 0, 0.075);
+}
+
+.control-group.error input:focus,
+.control-group.error select:focus,
+.control-group.error textarea:focus {
+ border-color: #953b39;
+ -webkit-box-shadow: inset 0 1px 1px rgba(0, 0, 0, 0.075), 0 0 6px #d59392;
+ -moz-box-shadow: inset 0 1px 1px rgba(0, 0, 0, 0.075), 0 0 6px #d59392;
+ box-shadow: inset 0 1px 1px rgba(0, 0, 0, 0.075), 0 0 6px #d59392;
+}
+
+.control-group.error .input-prepend .add-on,
+.control-group.error .input-append .add-on {
+ color: #b94a48;
+ background-color: #f2dede;
+ border-color: #b94a48;
+}
+
+.control-group.success .control-label,
+.control-group.success .help-block,
+.control-group.success .help-inline {
+ color: #468847;
+}
+
+.control-group.success .checkbox,
+.control-group.success .radio,
+.control-group.success input,
+.control-group.success select,
+.control-group.success textarea {
+ color: #468847;
+}
+
+.control-group.success input,
+.control-group.success select,
+.control-group.success textarea {
+ border-color: #468847;
+ -webkit-box-shadow: inset 0 1px 1px rgba(0, 0, 0, 0.075);
+ -moz-box-shadow: inset 0 1px 1px rgba(0, 0, 0, 0.075);
+ box-shadow: inset 0 1px 1px rgba(0, 0, 0, 0.075);
+}
+
+.control-group.success input:focus,
+.control-group.success select:focus,
+.control-group.success textarea:focus {
+ border-color: #356635;
+ -webkit-box-shadow: inset 0 1px 1px rgba(0, 0, 0, 0.075), 0 0 6px #7aba7b;
+ -moz-box-shadow: inset 0 1px 1px rgba(0, 0, 0, 0.075), 0 0 6px #7aba7b;
+ box-shadow: inset 0 1px 1px rgba(0, 0, 0, 0.075), 0 0 6px #7aba7b;
+}
+
+.control-group.success .input-prepend .add-on,
+.control-group.success .input-append .add-on {
+ color: #468847;
+ background-color: #dff0d8;
+ border-color: #468847;
+}
+
+.control-group.info .control-label,
+.control-group.info .help-block,
+.control-group.info .help-inline {
+ color: #3a87ad;
+}
+
+.control-group.info .checkbox,
+.control-group.info .radio,
+.control-group.info input,
+.control-group.info select,
+.control-group.info textarea {
+ color: #3a87ad;
+}
+
+.control-group.info input,
+.control-group.info select,
+.control-group.info textarea {
+ border-color: #3a87ad;
+ -webkit-box-shadow: inset 0 1px 1px rgba(0, 0, 0, 0.075);
+ -moz-box-shadow: inset 0 1px 1px rgba(0, 0, 0, 0.075);
+ box-shadow: inset 0 1px 1px rgba(0, 0, 0, 0.075);
+}
+
+.control-group.info input:focus,
+.control-group.info select:focus,
+.control-group.info textarea:focus {
+ border-color: #2d6987;
+ -webkit-box-shadow: inset 0 1px 1px rgba(0, 0, 0, 0.075), 0 0 6px #7ab5d3;
+ -moz-box-shadow: inset 0 1px 1px rgba(0, 0, 0, 0.075), 0 0 6px #7ab5d3;
+ box-shadow: inset 0 1px 1px rgba(0, 0, 0, 0.075), 0 0 6px #7ab5d3;
+}
+
+.control-group.info .input-prepend .add-on,
+.control-group.info .input-append .add-on {
+ color: #3a87ad;
+ background-color: #d9edf7;
+ border-color: #3a87ad;
+}
+
+input:focus:invalid,
+textarea:focus:invalid,
+select:focus:invalid {
+ color: #b94a48;
+ border-color: #ee5f5b;
+}
+
+input:focus:invalid:focus,
+textarea:focus:invalid:focus,
+select:focus:invalid:focus {
+ border-color: #e9322d;
+ -webkit-box-shadow: 0 0 6px #f8b9b7;
+ -moz-box-shadow: 0 0 6px #f8b9b7;
+ box-shadow: 0 0 6px #f8b9b7;
+}
+
+.form-actions {
+ padding: 19px 20px 20px;
+ margin-top: 20px;
+ margin-bottom: 20px;
+ background-color: #f5f5f5;
+ border-top: 1px solid #e5e5e5;
+ *zoom: 1;
+}
+
+.form-actions:before,
+.form-actions:after {
+ display: table;
+ line-height: 0;
+ content: "";
+}
+
+.form-actions:after {
+ clear: both;
+}
+
+.help-block,
+.help-inline {
+ color: #595959;
+}
+
+.help-block {
+ display: block;
+ margin-bottom: 10px;
+}
+
+.help-inline {
+ display: inline-block;
+ *display: inline;
+ padding-left: 5px;
+ vertical-align: middle;
+ *zoom: 1;
+}
+
+.input-append,
+.input-prepend {
+ display: inline-block;
+ margin-bottom: 10px;
+ font-size: 0;
+ white-space: nowrap;
+ vertical-align: middle;
+}
+
+.input-append input,
+.input-prepend input,
+.input-append select,
+.input-prepend select,
+.input-append .uneditable-input,
+.input-prepend .uneditable-input,
+.input-append .dropdown-menu,
+.input-prepend .dropdown-menu,
+.input-append .popover,
+.input-prepend .popover {
+ font-size: 14px;
+}
+
+.input-append input,
+.input-prepend input,
+.input-append select,
+.input-prepend select,
+.input-append .uneditable-input,
+.input-prepend .uneditable-input {
+ position: relative;
+ margin-bottom: 0;
+ *margin-left: 0;
+ vertical-align: top;
+ -webkit-border-radius: 0 4px 4px 0;
+ -moz-border-radius: 0 4px 4px 0;
+ border-radius: 0 4px 4px 0;
+}
+
+.input-append input:focus,
+.input-prepend input:focus,
+.input-append select:focus,
+.input-prepend select:focus,
+.input-append .uneditable-input:focus,
+.input-prepend .uneditable-input:focus {
+ z-index: 2;
+}
+
+.input-append .add-on,
+.input-prepend .add-on {
+ display: inline-block;
+ width: auto;
+ height: 20px;
+ min-width: 16px;
+ padding: 4px 5px;
+ font-size: 14px;
+ font-weight: normal;
+ line-height: 20px;
+ text-align: center;
+ text-shadow: 0 1px 0 #ffffff;
+ background-color: #eeeeee;
+ border: 1px solid #ccc;
+}
+
+.input-append .add-on,
+.input-prepend .add-on,
+.input-append .btn,
+.input-prepend .btn,
+.input-append .btn-group > .dropdown-toggle,
+.input-prepend .btn-group > .dropdown-toggle {
+ vertical-align: top;
+ -webkit-border-radius: 0;
+ -moz-border-radius: 0;
+ border-radius: 0;
+}
+
+.input-append .active,
+.input-prepend .active {
+ background-color: #a9dba9;
+ border-color: #46a546;
+}
+
+.input-prepend .add-on,
+.input-prepend .btn {
+ margin-right: -1px;
+}
+
+.input-prepend .add-on:first-child,
+.input-prepend .btn:first-child {
+ -webkit-border-radius: 4px 0 0 4px;
+ -moz-border-radius: 4px 0 0 4px;
+ border-radius: 4px 0 0 4px;
+}
+
+.input-append input,
+.input-append select,
+.input-append .uneditable-input {
+ -webkit-border-radius: 4px 0 0 4px;
+ -moz-border-radius: 4px 0 0 4px;
+ border-radius: 4px 0 0 4px;
+}
+
+.input-append input + .btn-group .btn:last-child,
+.input-append select + .btn-group .btn:last-child,
+.input-append .uneditable-input + .btn-group .btn:last-child {
+ -webkit-border-radius: 0 4px 4px 0;
+ -moz-border-radius: 0 4px 4px 0;
+ border-radius: 0 4px 4px 0;
+}
+
+.input-append .add-on,
+.input-append .btn,
+.input-append .btn-group {
+ margin-left: -1px;
+}
+
+.input-append .add-on:last-child,
+.input-append .btn:last-child,
+.input-append .btn-group:last-child > .dropdown-toggle {
+ -webkit-border-radius: 0 4px 4px 0;
+ -moz-border-radius: 0 4px 4px 0;
+ border-radius: 0 4px 4px 0;
+}
+
+.input-prepend.input-append input,
+.input-prepend.input-append select,
+.input-prepend.input-append .uneditable-input {
+ -webkit-border-radius: 0;
+ -moz-border-radius: 0;
+ border-radius: 0;
+}
+
+.input-prepend.input-append input + .btn-group .btn,
+.input-prepend.input-append select + .btn-group .btn,
+.input-prepend.input-append .uneditable-input + .btn-group .btn {
+ -webkit-border-radius: 0 4px 4px 0;
+ -moz-border-radius: 0 4px 4px 0;
+ border-radius: 0 4px 4px 0;
+}
+
+.input-prepend.input-append .add-on:first-child,
+.input-prepend.input-append .btn:first-child {
+ margin-right: -1px;
+ -webkit-border-radius: 4px 0 0 4px;
+ -moz-border-radius: 4px 0 0 4px;
+ border-radius: 4px 0 0 4px;
+}
+
+.input-prepend.input-append .add-on:last-child,
+.input-prepend.input-append .btn:last-child {
+ margin-left: -1px;
+ -webkit-border-radius: 0 4px 4px 0;
+ -moz-border-radius: 0 4px 4px 0;
+ border-radius: 0 4px 4px 0;
+}
+
+.input-prepend.input-append .btn-group:first-child {
+ margin-left: 0;
+}
+
+input.search-query {
+ padding-right: 14px;
+ padding-right: 4px \9;
+ padding-left: 14px;
+ padding-left: 4px \9;
+ /* IE7-8 doesn't have border-radius, so don't indent the padding */
+
+ margin-bottom: 0;
+ -webkit-border-radius: 15px;
+ -moz-border-radius: 15px;
+ border-radius: 15px;
+}
+
+/* Allow for input prepend/append in search forms */
+
+.form-search .input-append .search-query,
+.form-search .input-prepend .search-query {
+ -webkit-border-radius: 0;
+ -moz-border-radius: 0;
+ border-radius: 0;
+}
+
+.form-search .input-append .search-query {
+ -webkit-border-radius: 14px 0 0 14px;
+ -moz-border-radius: 14px 0 0 14px;
+ border-radius: 14px 0 0 14px;
+}
+
+.form-search .input-append .btn {
+ -webkit-border-radius: 0 14px 14px 0;
+ -moz-border-radius: 0 14px 14px 0;
+ border-radius: 0 14px 14px 0;
+}
+
+.form-search .input-prepend .search-query {
+ -webkit-border-radius: 0 14px 14px 0;
+ -moz-border-radius: 0 14px 14px 0;
+ border-radius: 0 14px 14px 0;
+}
+
+.form-search .input-prepend .btn {
+ -webkit-border-radius: 14px 0 0 14px;
+ -moz-border-radius: 14px 0 0 14px;
+ border-radius: 14px 0 0 14px;
+}
+
+.form-search input,
+.form-inline input,
+.form-horizontal input,
+.form-search textarea,
+.form-inline textarea,
+.form-horizontal textarea,
+.form-search select,
+.form-inline select,
+.form-horizontal select,
+.form-search .help-inline,
+.form-inline .help-inline,
+.form-horizontal .help-inline,
+.form-search .uneditable-input,
+.form-inline .uneditable-input,
+.form-horizontal .uneditable-input,
+.form-search .input-prepend,
+.form-inline .input-prepend,
+.form-horizontal .input-prepend,
+.form-search .input-append,
+.form-inline .input-append,
+.form-horizontal .input-append {
+ display: inline-block;
+ *display: inline;
+ margin-bottom: 0;
+ vertical-align: middle;
+ *zoom: 1;
+}
+
+.form-search .hide,
+.form-inline .hide,
+.form-horizontal .hide {
+ display: none;
+}
+
+.form-search label,
+.form-inline label,
+.form-search .btn-group,
+.form-inline .btn-group {
+ display: inline-block;
+}
+
+.form-search .input-append,
+.form-inline .input-append,
+.form-search .input-prepend,
+.form-inline .input-prepend {
+ margin-bottom: 0;
+}
+
+.form-search .radio,
+.form-search .checkbox,
+.form-inline .radio,
+.form-inline .checkbox {
+ padding-left: 0;
+ margin-bottom: 0;
+ vertical-align: middle;
+}
+
+.form-search .radio input[type="radio"],
+.form-search .checkbox input[type="checkbox"],
+.form-inline .radio input[type="radio"],
+.form-inline .checkbox input[type="checkbox"] {
+ float: left;
+ margin-right: 3px;
+ margin-left: 0;
+}
+
+.control-group {
+ margin-bottom: 10px;
+}
+
+legend + .control-group {
+ margin-top: 20px;
+ -webkit-margin-top-collapse: separate;
+}
+
+.form-horizontal .control-group {
+ margin-bottom: 20px;
+ *zoom: 1;
+}
+
+.form-horizontal .control-group:before,
+.form-horizontal .control-group:after {
+ display: table;
+ line-height: 0;
+ content: "";
+}
+
+.form-horizontal .control-group:after {
+ clear: both;
+}
+
+.form-horizontal .control-label {
+ float: left;
+ width: 160px;
+ padding-top: 5px;
+ text-align: right;
+}
+
+.form-horizontal .controls {
+ *display: inline-block;
+ *padding-left: 20px;
+ margin-left: 180px;
+ *margin-left: 0;
+}
+
+.form-horizontal .controls:first-child {
+ *padding-left: 180px;
+}
+
+.form-horizontal .help-block {
+ margin-bottom: 0;
+}
+
+.form-horizontal input + .help-block,
+.form-horizontal select + .help-block,
+.form-horizontal textarea + .help-block,
+.form-horizontal .uneditable-input + .help-block,
+.form-horizontal .input-prepend + .help-block,
+.form-horizontal .input-append + .help-block {
+ margin-top: 10px;
+}
+
+.form-horizontal .form-actions {
+ padding-left: 180px;
+}
+
+table {
+ max-width: 100%;
+ background-color: transparent;
+ border-collapse: collapse;
+ border-spacing: 0;
+}
+
+.table {
+ width: 100%;
+ margin-bottom: 20px;
+}
+
+.table th,
+.table td {
+ padding: 8px;
+ line-height: 20px;
+ text-align: left;
+ vertical-align: top;
+ border-top: 1px solid #dddddd;
+}
+
+.table th {
+ font-weight: bold;
+}
+
+.table thead th {
+ vertical-align: bottom;
+}
+
+.table caption + thead tr:first-child th,
+.table caption + thead tr:first-child td,
+.table colgroup + thead tr:first-child th,
+.table colgroup + thead tr:first-child td,
+.table thead:first-child tr:first-child th,
+.table thead:first-child tr:first-child td {
+ border-top: 0;
+}
+
+.table tbody + tbody {
+ border-top: 2px solid #dddddd;
+}
+
+.table .table {
+ background-color: #ffffff;
+}
+
+.table-condensed th,
+.table-condensed td {
+ padding: 4px 5px;
+}
+
+.table-bordered {
+ border: 1px solid #dddddd;
+ border-collapse: separate;
+ *border-collapse: collapse;
+ border-left: 0;
+ -webkit-border-radius: 4px;
+ -moz-border-radius: 4px;
+ border-radius: 4px;
+}
+
+.table-bordered th,
+.table-bordered td {
+ border-left: 1px solid #dddddd;
+}
+
+.table-bordered caption + thead tr:first-child th,
+.table-bordered caption + tbody tr:first-child th,
+.table-bordered caption + tbody tr:first-child td,
+.table-bordered colgroup + thead tr:first-child th,
+.table-bordered colgroup + tbody tr:first-child th,
+.table-bordered colgroup + tbody tr:first-child td,
+.table-bordered thead:first-child tr:first-child th,
+.table-bordered tbody:first-child tr:first-child th,
+.table-bordered tbody:first-child tr:first-child td {
+ border-top: 0;
+}
+
+.table-bordered thead:first-child tr:first-child > th:first-child,
+.table-bordered tbody:first-child tr:first-child > td:first-child,
+.table-bordered tbody:first-child tr:first-child > th:first-child {
+ -webkit-border-top-left-radius: 4px;
+ border-top-left-radius: 4px;
+ -moz-border-radius-topleft: 4px;
+}
+
+.table-bordered thead:first-child tr:first-child > th:last-child,
+.table-bordered tbody:first-child tr:first-child > td:last-child,
+.table-bordered tbody:first-child tr:first-child > th:last-child {
+ -webkit-border-top-right-radius: 4px;
+ border-top-right-radius: 4px;
+ -moz-border-radius-topright: 4px;
+}
+
+.table-bordered thead:last-child tr:last-child > th:first-child,
+.table-bordered tbody:last-child tr:last-child > td:first-child,
+.table-bordered tbody:last-child tr:last-child > th:first-child,
+.table-bordered tfoot:last-child tr:last-child > td:first-child,
+.table-bordered tfoot:last-child tr:last-child > th:first-child {
+ -webkit-border-bottom-left-radius: 4px;
+ border-bottom-left-radius: 4px;
+ -moz-border-radius-bottomleft: 4px;
+}
+
+.table-bordered thead:last-child tr:last-child > th:last-child,
+.table-bordered tbody:last-child tr:last-child > td:last-child,
+.table-bordered tbody:last-child tr:last-child > th:last-child,
+.table-bordered tfoot:last-child tr:last-child > td:last-child,
+.table-bordered tfoot:last-child tr:last-child > th:last-child {
+ -webkit-border-bottom-right-radius: 4px;
+ border-bottom-right-radius: 4px;
+ -moz-border-radius-bottomright: 4px;
+}
+
+.table-bordered tfoot + tbody:last-child tr:last-child td:first-child {
+ -webkit-border-bottom-left-radius: 0;
+ border-bottom-left-radius: 0;
+ -moz-border-radius-bottomleft: 0;
+}
+
+.table-bordered tfoot + tbody:last-child tr:last-child td:last-child {
+ -webkit-border-bottom-right-radius: 0;
+ border-bottom-right-radius: 0;
+ -moz-border-radius-bottomright: 0;
+}
+
+.table-bordered caption + thead tr:first-child th:first-child,
+.table-bordered caption + tbody tr:first-child td:first-child,
+.table-bordered colgroup + thead tr:first-child th:first-child,
+.table-bordered colgroup + tbody tr:first-child td:first-child {
+ -webkit-border-top-left-radius: 4px;
+ border-top-left-radius: 4px;
+ -moz-border-radius-topleft: 4px;
+}
+
+.table-bordered caption + thead tr:first-child th:last-child,
+.table-bordered caption + tbody tr:first-child td:last-child,
+.table-bordered colgroup + thead tr:first-child th:last-child,
+.table-bordered colgroup + tbody tr:first-child td:last-child {
+ -webkit-border-top-right-radius: 4px;
+ border-top-right-radius: 4px;
+ -moz-border-radius-topright: 4px;
+}
+
+.table-striped tbody > tr:nth-child(odd) > td,
+.table-striped tbody > tr:nth-child(odd) > th {
+ background-color: #f9f9f9;
+}
+
+.table-hover tbody tr:hover > td,
+.table-hover tbody tr:hover > th {
+ background-color: #f5f5f5;
+}
+
+table td[class*="span"],
+table th[class*="span"],
+.row-fluid table td[class*="span"],
+.row-fluid table th[class*="span"] {
+ display: table-cell;
+ float: none;
+ margin-left: 0;
+}
+
+.table td.span1,
+.table th.span1 {
+ float: none;
+ width: 44px;
+ margin-left: 0;
+}
+
+.table td.span2,
+.table th.span2 {
+ float: none;
+ width: 124px;
+ margin-left: 0;
+}
+
+.table td.span3,
+.table th.span3 {
+ float: none;
+ width: 204px;
+ margin-left: 0;
+}
+
+.table td.span4,
+.table th.span4 {
+ float: none;
+ width: 284px;
+ margin-left: 0;
+}
+
+.table td.span5,
+.table th.span5 {
+ float: none;
+ width: 364px;
+ margin-left: 0;
+}
+
+.table td.span6,
+.table th.span6 {
+ float: none;
+ width: 444px;
+ margin-left: 0;
+}
+
+.table td.span7,
+.table th.span7 {
+ float: none;
+ width: 524px;
+ margin-left: 0;
+}
+
+.table td.span8,
+.table th.span8 {
+ float: none;
+ width: 604px;
+ margin-left: 0;
+}
+
+.table td.span9,
+.table th.span9 {
+ float: none;
+ width: 684px;
+ margin-left: 0;
+}
+
+.table td.span10,
+.table th.span10 {
+ float: none;
+ width: 764px;
+ margin-left: 0;
+}
+
+.table td.span11,
+.table th.span11 {
+ float: none;
+ width: 844px;
+ margin-left: 0;
+}
+
+.table td.span12,
+.table th.span12 {
+ float: none;
+ width: 924px;
+ margin-left: 0;
+}
+
+.table tbody tr.success > td {
+ background-color: #dff0d8;
+}
+
+.table tbody tr.error > td {
+ background-color: #f2dede;
+}
+
+.table tbody tr.warning > td {
+ background-color: #fcf8e3;
+}
+
+.table tbody tr.info > td {
+ background-color: #d9edf7;
+}
+
+.table-hover tbody tr.success:hover > td {
+ background-color: #d0e9c6;
+}
+
+.table-hover tbody tr.error:hover > td {
+ background-color: #ebcccc;
+}
+
+.table-hover tbody tr.warning:hover > td {
+ background-color: #faf2cc;
+}
+
+.table-hover tbody tr.info:hover > td {
+ background-color: #c4e3f3;
+}
+
+[class^="icon-"],
+[class*=" icon-"] {
+ display: inline-block;
+ width: 14px;
+ height: 14px;
+ margin-top: 1px;
+ *margin-right: .3em;
+ line-height: 14px;
+ vertical-align: text-top;
+ background-image: url("../img/glyphicons-halflings.png");
+ background-position: 14px 14px;
+ background-repeat: no-repeat;
+}
+
+/* White icons with optional class, or on hover/focus/active states of certain elements */
+
+.icon-white,
+.nav-pills > .active > a > [class^="icon-"],
+.nav-pills > .active > a > [class*=" icon-"],
+.nav-list > .active > a > [class^="icon-"],
+.nav-list > .active > a > [class*=" icon-"],
+.navbar-inverse .nav > .active > a > [class^="icon-"],
+.navbar-inverse .nav > .active > a > [class*=" icon-"],
+.dropdown-menu > li > a:hover > [class^="icon-"],
+.dropdown-menu > li > a:focus > [class^="icon-"],
+.dropdown-menu > li > a:hover > [class*=" icon-"],
+.dropdown-menu > li > a:focus > [class*=" icon-"],
+.dropdown-menu > .active > a > [class^="icon-"],
+.dropdown-menu > .active > a > [class*=" icon-"],
+.dropdown-submenu:hover > a > [class^="icon-"],
+.dropdown-submenu:focus > a > [class^="icon-"],
+.dropdown-submenu:hover > a > [class*=" icon-"],
+.dropdown-submenu:focus > a > [class*=" icon-"] {
+ background-image: url("../img/glyphicons-halflings-white.png");
+}
+
+.icon-glass {
+ background-position: 0 0;
+}
+
+.icon-music {
+ background-position: -24px 0;
+}
+
+.icon-search {
+ background-position: -48px 0;
+}
+
+.icon-envelope {
+ background-position: -72px 0;
+}
+
+.icon-heart {
+ background-position: -96px 0;
+}
+
+.icon-star {
+ background-position: -120px 0;
+}
+
+.icon-star-empty {
+ background-position: -144px 0;
+}
+
+.icon-user {
+ background-position: -168px 0;
+}
+
+.icon-film {
+ background-position: -192px 0;
+}
+
+.icon-th-large {
+ background-position: -216px 0;
+}
+
+.icon-th {
+ background-position: -240px 0;
+}
+
+.icon-th-list {
+ background-position: -264px 0;
+}
+
+.icon-ok {
+ background-position: -288px 0;
+}
+
+.icon-remove {
+ background-position: -312px 0;
+}
+
+.icon-zoom-in {
+ background-position: -336px 0;
+}
+
+.icon-zoom-out {
+ background-position: -360px 0;
+}
+
+.icon-off {
+ background-position: -384px 0;
+}
+
+.icon-signal {
+ background-position: -408px 0;
+}
+
+.icon-cog {
+ background-position: -432px 0;
+}
+
+.icon-trash {
+ background-position: -456px 0;
+}
+
+.icon-home {
+ background-position: 0 -24px;
+}
+
+.icon-file {
+ background-position: -24px -24px;
+}
+
+.icon-time {
+ background-position: -48px -24px;
+}
+
+.icon-road {
+ background-position: -72px -24px;
+}
+
+.icon-download-alt {
+ background-position: -96px -24px;
+}
+
+.icon-download {
+ background-position: -120px -24px;
+}
+
+.icon-upload {
+ background-position: -144px -24px;
+}
+
+.icon-inbox {
+ background-position: -168px -24px;
+}
+
+.icon-play-circle {
+ background-position: -192px -24px;
+}
+
+.icon-repeat {
+ background-position: -216px -24px;
+}
+
+.icon-refresh {
+ background-position: -240px -24px;
+}
+
+.icon-list-alt {
+ background-position: -264px -24px;
+}
+
+.icon-lock {
+ background-position: -287px -24px;
+}
+
+.icon-flag {
+ background-position: -312px -24px;
+}
+
+.icon-headphones {
+ background-position: -336px -24px;
+}
+
+.icon-volume-off {
+ background-position: -360px -24px;
+}
+
+.icon-volume-down {
+ background-position: -384px -24px;
+}
+
+.icon-volume-up {
+ background-position: -408px -24px;
+}
+
+.icon-qrcode {
+ background-position: -432px -24px;
+}
+
+.icon-barcode {
+ background-position: -456px -24px;
+}
+
+.icon-tag {
+ background-position: 0 -48px;
+}
+
+.icon-tags {
+ background-position: -25px -48px;
+}
+
+.icon-book {
+ background-position: -48px -48px;
+}
+
+.icon-bookmark {
+ background-position: -72px -48px;
+}
+
+.icon-print {
+ background-position: -96px -48px;
+}
+
+.icon-camera {
+ background-position: -120px -48px;
+}
+
+.icon-font {
+ background-position: -144px -48px;
+}
+
+.icon-bold {
+ background-position: -167px -48px;
+}
+
+.icon-italic {
+ background-position: -192px -48px;
+}
+
+.icon-text-height {
+ background-position: -216px -48px;
+}
+
+.icon-text-width {
+ background-position: -240px -48px;
+}
+
+.icon-align-left {
+ background-position: -264px -48px;
+}
+
+.icon-align-center {
+ background-position: -288px -48px;
+}
+
+.icon-align-right {
+ background-position: -312px -48px;
+}
+
+.icon-align-justify {
+ background-position: -336px -48px;
+}
+
+.icon-list {
+ background-position: -360px -48px;
+}
+
+.icon-indent-left {
+ background-position: -384px -48px;
+}
+
+.icon-indent-right {
+ background-position: -408px -48px;
+}
+
+.icon-facetime-video {
+ background-position: -432px -48px;
+}
+
+.icon-picture {
+ background-position: -456px -48px;
+}
+
+.icon-pencil {
+ background-position: 0 -72px;
+}
+
+.icon-map-marker {
+ background-position: -24px -72px;
+}
+
+.icon-adjust {
+ background-position: -48px -72px;
+}
+
+.icon-tint {
+ background-position: -72px -72px;
+}
+
+.icon-edit {
+ background-position: -96px -72px;
+}
+
+.icon-share {
+ background-position: -120px -72px;
+}
+
+.icon-check {
+ background-position: -144px -72px;
+}
+
+.icon-move {
+ background-position: -168px -72px;
+}
+
+.icon-step-backward {
+ background-position: -192px -72px;
+}
+
+.icon-fast-backward {
+ background-position: -216px -72px;
+}
+
+.icon-backward {
+ background-position: -240px -72px;
+}
+
+.icon-play {
+ background-position: -264px -72px;
+}
+
+.icon-pause {
+ background-position: -288px -72px;
+}
+
+.icon-stop {
+ background-position: -312px -72px;
+}
+
+.icon-forward {
+ background-position: -336px -72px;
+}
+
+.icon-fast-forward {
+ background-position: -360px -72px;
+}
+
+.icon-step-forward {
+ background-position: -384px -72px;
+}
+
+.icon-eject {
+ background-position: -408px -72px;
+}
+
+.icon-chevron-left {
+ background-position: -432px -72px;
+}
+
+.icon-chevron-right {
+ background-position: -456px -72px;
+}
+
+.icon-plus-sign {
+ background-position: 0 -96px;
+}
+
+.icon-minus-sign {
+ background-position: -24px -96px;
+}
+
+.icon-remove-sign {
+ background-position: -48px -96px;
+}
+
+.icon-ok-sign {
+ background-position: -72px -96px;
+}
+
+.icon-question-sign {
+ background-position: -96px -96px;
+}
+
+.icon-info-sign {
+ background-position: -120px -96px;
+}
+
+.icon-screenshot {
+ background-position: -144px -96px;
+}
+
+.icon-remove-circle {
+ background-position: -168px -96px;
+}
+
+.icon-ok-circle {
+ background-position: -192px -96px;
+}
+
+.icon-ban-circle {
+ background-position: -216px -96px;
+}
+
+.icon-arrow-left {
+ background-position: -240px -96px;
+}
+
+.icon-arrow-right {
+ background-position: -264px -96px;
+}
+
+.icon-arrow-up {
+ background-position: -289px -96px;
+}
+
+.icon-arrow-down {
+ background-position: -312px -96px;
+}
+
+.icon-share-alt {
+ background-position: -336px -96px;
+}
+
+.icon-resize-full {
+ background-position: -360px -96px;
+}
+
+.icon-resize-small {
+ background-position: -384px -96px;
+}
+
+.icon-plus {
+ background-position: -408px -96px;
+}
+
+.icon-minus {
+ background-position: -433px -96px;
+}
+
+.icon-asterisk {
+ background-position: -456px -96px;
+}
+
+.icon-exclamation-sign {
+ background-position: 0 -120px;
+}
+
+.icon-gift {
+ background-position: -24px -120px;
+}
+
+.icon-leaf {
+ background-position: -48px -120px;
+}
+
+.icon-fire {
+ background-position: -72px -120px;
+}
+
+.icon-eye-open {
+ background-position: -96px -120px;
+}
+
+.icon-eye-close {
+ background-position: -120px -120px;
+}
+
+.icon-warning-sign {
+ background-position: -144px -120px;
+}
+
+.icon-plane {
+ background-position: -168px -120px;
+}
+
+.icon-calendar {
+ background-position: -192px -120px;
+}
+
+.icon-random {
+ width: 16px;
+ background-position: -216px -120px;
+}
+
+.icon-comment {
+ background-position: -240px -120px;
+}
+
+.icon-magnet {
+ background-position: -264px -120px;
+}
+
+.icon-chevron-up {
+ background-position: -288px -120px;
+}
+
+.icon-chevron-down {
+ background-position: -313px -119px;
+}
+
+.icon-retweet {
+ background-position: -336px -120px;
+}
+
+.icon-shopping-cart {
+ background-position: -360px -120px;
+}
+
+.icon-folder-close {
+ width: 16px;
+ background-position: -384px -120px;
+}
+
+.icon-folder-open {
+ width: 16px;
+ background-position: -408px -120px;
+}
+
+.icon-resize-vertical {
+ background-position: -432px -119px;
+}
+
+.icon-resize-horizontal {
+ background-position: -456px -118px;
+}
+
+.icon-hdd {
+ background-position: 0 -144px;
+}
+
+.icon-bullhorn {
+ background-position: -24px -144px;
+}
+
+.icon-bell {
+ background-position: -48px -144px;
+}
+
+.icon-certificate {
+ background-position: -72px -144px;
+}
+
+.icon-thumbs-up {
+ background-position: -96px -144px;
+}
+
+.icon-thumbs-down {
+ background-position: -120px -144px;
+}
+
+.icon-hand-right {
+ background-position: -144px -144px;
+}
+
+.icon-hand-left {
+ background-position: -168px -144px;
+}
+
+.icon-hand-up {
+ background-position: -192px -144px;
+}
+
+.icon-hand-down {
+ background-position: -216px -144px;
+}
+
+.icon-circle-arrow-right {
+ background-position: -240px -144px;
+}
+
+.icon-circle-arrow-left {
+ background-position: -264px -144px;
+}
+
+.icon-circle-arrow-up {
+ background-position: -288px -144px;
+}
+
+.icon-circle-arrow-down {
+ background-position: -312px -144px;
+}
+
+.icon-globe {
+ background-position: -336px -144px;
+}
+
+.icon-wrench {
+ background-position: -360px -144px;
+}
+
+.icon-tasks {
+ background-position: -384px -144px;
+}
+
+.icon-filter {
+ background-position: -408px -144px;
+}
+
+.icon-briefcase {
+ background-position: -432px -144px;
+}
+
+.icon-fullscreen {
+ background-position: -456px -144px;
+}
+
+.dropup,
+.dropdown {
+ position: relative;
+}
+
+.dropdown-toggle {
+ *margin-bottom: -3px;
+}
+
+.dropdown-toggle:active,
+.open .dropdown-toggle {
+ outline: 0;
+}
+
+.caret {
+ display: inline-block;
+ width: 0;
+ height: 0;
+ vertical-align: top;
+ border-top: 4px solid #000000;
+ border-right: 4px solid transparent;
+ border-left: 4px solid transparent;
+ content: "";
+}
+
+.dropdown .caret {
+ margin-top: 8px;
+ margin-left: 2px;
+}
+
+.dropdown-menu {
+ position: absolute;
+ top: 100%;
+ left: 0;
+ z-index: 1000;
+ display: none;
+ float: left;
+ min-width: 160px;
+ padding: 5px 0;
+ margin: 2px 0 0;
+ list-style: none;
+ background-color: #ffffff;
+ border: 1px solid #ccc;
+ border: 1px solid rgba(0, 0, 0, 0.2);
+ *border-right-width: 2px;
+ *border-bottom-width: 2px;
+ -webkit-border-radius: 6px;
+ -moz-border-radius: 6px;
+ border-radius: 6px;
+ -webkit-box-shadow: 0 5px 10px rgba(0, 0, 0, 0.2);
+ -moz-box-shadow: 0 5px 10px rgba(0, 0, 0, 0.2);
+ box-shadow: 0 5px 10px rgba(0, 0, 0, 0.2);
+ -webkit-background-clip: padding-box;
+ -moz-background-clip: padding;
+ background-clip: padding-box;
+}
+
+.dropdown-menu.pull-right {
+ right: 0;
+ left: auto;
+}
+
+.dropdown-menu .divider {
+ *width: 100%;
+ height: 1px;
+ margin: 9px 1px;
+ *margin: -5px 0 5px;
+ overflow: hidden;
+ background-color: #e5e5e5;
+ border-bottom: 1px solid #ffffff;
+}
+
+.dropdown-menu > li > a {
+ display: block;
+ padding: 3px 20px;
+ clear: both;
+ font-weight: normal;
+ line-height: 20px;
+ color: #333333;
+ white-space: nowrap;
+}
+
+.dropdown-menu > li > a:hover,
+.dropdown-menu > li > a:focus,
+.dropdown-submenu:hover > a,
+.dropdown-submenu:focus > a {
+ color: #ffffff;
+ text-decoration: none;
+ background-color: #0081c2;
+ background-image: -moz-linear-gradient(top, #0088cc, #0077b3);
+ background-image: -webkit-gradient(linear, 0 0, 0 100%, from(#0088cc), to(#0077b3));
+ background-image: -webkit-linear-gradient(top, #0088cc, #0077b3);
+ background-image: -o-linear-gradient(top, #0088cc, #0077b3);
+ background-image: linear-gradient(to bottom, #0088cc, #0077b3);
+ background-repeat: repeat-x;
+ filter: progid:DXImageTransform.Microsoft.gradient(startColorstr='#ff0088cc', endColorstr='#ff0077b3', GradientType=0);
+}
+
+.dropdown-menu > .active > a,
+.dropdown-menu > .active > a:hover,
+.dropdown-menu > .active > a:focus {
+ color: #ffffff;
+ text-decoration: none;
+ background-color: #0081c2;
+ background-image: -moz-linear-gradient(top, #0088cc, #0077b3);
+ background-image: -webkit-gradient(linear, 0 0, 0 100%, from(#0088cc), to(#0077b3));
+ background-image: -webkit-linear-gradient(top, #0088cc, #0077b3);
+ background-image: -o-linear-gradient(top, #0088cc, #0077b3);
+ background-image: linear-gradient(to bottom, #0088cc, #0077b3);
+ background-repeat: repeat-x;
+ outline: 0;
+ filter: progid:DXImageTransform.Microsoft.gradient(startColorstr='#ff0088cc', endColorstr='#ff0077b3', GradientType=0);
+}
+
+.dropdown-menu > .disabled > a,
+.dropdown-menu > .disabled > a:hover,
+.dropdown-menu > .disabled > a:focus {
+ color: #999999;
+}
+
+.dropdown-menu > .disabled > a:hover,
+.dropdown-menu > .disabled > a:focus {
+ text-decoration: none;
+ cursor: default;
+ background-color: transparent;
+ background-image: none;
+ filter: progid:DXImageTransform.Microsoft.gradient(enabled=false);
+}
+
+.open {
+ *z-index: 1000;
+}
+
+.open > .dropdown-menu {
+ display: block;
+}
+
+.dropdown-backdrop {
+ position: fixed;
+ top: 0;
+ right: 0;
+ bottom: 0;
+ left: 0;
+ z-index: 990;
+}
+
+.pull-right > .dropdown-menu {
+ right: 0;
+ left: auto;
+}
+
+.dropup .caret,
+.navbar-fixed-bottom .dropdown .caret {
+ border-top: 0;
+ border-bottom: 4px solid #000000;
+ content: "";
+}
+
+.dropup .dropdown-menu,
+.navbar-fixed-bottom .dropdown .dropdown-menu {
+ top: auto;
+ bottom: 100%;
+ margin-bottom: 1px;
+}
+
+.dropdown-submenu {
+ position: relative;
+}
+
+.dropdown-submenu > .dropdown-menu {
+ top: 0;
+ left: 100%;
+ margin-top: -6px;
+ margin-left: -1px;
+ -webkit-border-radius: 0 6px 6px 6px;
+ -moz-border-radius: 0 6px 6px 6px;
+ border-radius: 0 6px 6px 6px;
+}
+
+.dropdown-submenu:hover > .dropdown-menu {
+ display: block;
+}
+
+.dropup .dropdown-submenu > .dropdown-menu {
+ top: auto;
+ bottom: 0;
+ margin-top: 0;
+ margin-bottom: -2px;
+ -webkit-border-radius: 5px 5px 5px 0;
+ -moz-border-radius: 5px 5px 5px 0;
+ border-radius: 5px 5px 5px 0;
+}
+
+.dropdown-submenu > a:after {
+ display: block;
+ float: right;
+ width: 0;
+ height: 0;
+ margin-top: 5px;
+ margin-right: -10px;
+ border-color: transparent;
+ border-left-color: #cccccc;
+ border-style: solid;
+ border-width: 5px 0 5px 5px;
+ content: " ";
+}
+
+.dropdown-submenu:hover > a:after {
+ border-left-color: #ffffff;
+}
+
+.dropdown-submenu.pull-left {
+ float: none;
+}
+
+.dropdown-submenu.pull-left > .dropdown-menu {
+ left: -100%;
+ margin-left: 10px;
+ -webkit-border-radius: 6px 0 6px 6px;
+ -moz-border-radius: 6px 0 6px 6px;
+ border-radius: 6px 0 6px 6px;
+}
+
+.dropdown .dropdown-menu .nav-header {
+ padding-right: 20px;
+ padding-left: 20px;
+}
+
+.typeahead {
+ z-index: 1051;
+ margin-top: 2px;
+ -webkit-border-radius: 4px;
+ -moz-border-radius: 4px;
+ border-radius: 4px;
+}
+
+.well {
+ min-height: 20px;
+ padding: 19px;
+ margin-bottom: 20px;
+ background-color: #f5f5f5;
+ border: 1px solid #e3e3e3;
+ -webkit-border-radius: 4px;
+ -moz-border-radius: 4px;
+ border-radius: 4px;
+ -webkit-box-shadow: inset 0 1px 1px rgba(0, 0, 0, 0.05);
+ -moz-box-shadow: inset 0 1px 1px rgba(0, 0, 0, 0.05);
+ box-shadow: inset 0 1px 1px rgba(0, 0, 0, 0.05);
+}
+
+.well blockquote {
+ border-color: #ddd;
+ border-color: rgba(0, 0, 0, 0.15);
+}
+
+.well-large {
+ padding: 24px;
+ -webkit-border-radius: 6px;
+ -moz-border-radius: 6px;
+ border-radius: 6px;
+}
+
+.well-small {
+ padding: 9px;
+ -webkit-border-radius: 3px;
+ -moz-border-radius: 3px;
+ border-radius: 3px;
+}
+
+.fade {
+ opacity: 0;
+ -webkit-transition: opacity 0.15s linear;
+ -moz-transition: opacity 0.15s linear;
+ -o-transition: opacity 0.15s linear;
+ transition: opacity 0.15s linear;
+}
+
+.fade.in {
+ opacity: 1;
+}
+
+.collapse {
+ position: relative;
+ height: 0;
+ overflow: hidden;
+ -webkit-transition: height 0.35s ease;
+ -moz-transition: height 0.35s ease;
+ -o-transition: height 0.35s ease;
+ transition: height 0.35s ease;
+}
+
+.collapse.in {
+ height: auto;
+}
+
+.close {
+ float: right;
+ font-size: 20px;
+ font-weight: bold;
+ line-height: 20px;
+ color: #000000;
+ text-shadow: 0 1px 0 #ffffff;
+ opacity: 0.2;
+ filter: alpha(opacity=20);
+}
+
+.close:hover,
+.close:focus {
+ color: #000000;
+ text-decoration: none;
+ cursor: pointer;
+ opacity: 0.4;
+ filter: alpha(opacity=40);
+}
+
+button.close {
+ padding: 0;
+ cursor: pointer;
+ background: transparent;
+ border: 0;
+ -webkit-appearance: none;
+}
+
+.btn {
+ display: inline-block;
+ *display: inline;
+ padding: 4px 12px;
+ margin-bottom: 0;
+ *margin-left: .3em;
+ font-size: 14px;
+ line-height: 20px;
+ color: #333333;
+ text-align: center;
+ text-shadow: 0 1px 1px rgba(255, 255, 255, 0.75);
+ vertical-align: middle;
+ cursor: pointer;
+ background-color: #f5f5f5;
+ *background-color: #e6e6e6;
+ background-image: -moz-linear-gradient(top, #ffffff, #e6e6e6);
+ background-image: -webkit-gradient(linear, 0 0, 0 100%, from(#ffffff), to(#e6e6e6));
+ background-image: -webkit-linear-gradient(top, #ffffff, #e6e6e6);
+ background-image: -o-linear-gradient(top, #ffffff, #e6e6e6);
+ background-image: linear-gradient(to bottom, #ffffff, #e6e6e6);
+ background-repeat: repeat-x;
+ border: 1px solid #cccccc;
+ *border: 0;
+ border-color: #e6e6e6 #e6e6e6 #bfbfbf;
+ border-color: rgba(0, 0, 0, 0.1) rgba(0, 0, 0, 0.1) rgba(0, 0, 0, 0.25);
+ border-bottom-color: #b3b3b3;
+ -webkit-border-radius: 4px;
+ -moz-border-radius: 4px;
+ border-radius: 4px;
+ filter: progid:DXImageTransform.Microsoft.gradient(startColorstr='#ffffffff', endColorstr='#ffe6e6e6', GradientType=0);
+ filter: progid:DXImageTransform.Microsoft.gradient(enabled=false);
+ *zoom: 1;
+ -webkit-box-shadow: inset 0 1px 0 rgba(255, 255, 255, 0.2), 0 1px 2px rgba(0, 0, 0, 0.05);
+ -moz-box-shadow: inset 0 1px 0 rgba(255, 255, 255, 0.2), 0 1px 2px rgba(0, 0, 0, 0.05);
+ box-shadow: inset 0 1px 0 rgba(255, 255, 255, 0.2), 0 1px 2px rgba(0, 0, 0, 0.05);
+}
+
+.btn:hover,
+.btn:focus,
+.btn:active,
+.btn.active,
+.btn.disabled,
+.btn[disabled] {
+ color: #333333;
+ background-color: #e6e6e6;
+ *background-color: #d9d9d9;
+}
+
+.btn:active,
+.btn.active {
+ background-color: #cccccc \9;
+}
+
+.btn:first-child {
+ *margin-left: 0;
+}
+
+.btn:hover,
+.btn:focus {
+ color: #333333;
+ text-decoration: none;
+ background-position: 0 -15px;
+ -webkit-transition: background-position 0.1s linear;
+ -moz-transition: background-position 0.1s linear;
+ -o-transition: background-position 0.1s linear;
+ transition: background-position 0.1s linear;
+}
+
+.btn:focus {
+ outline: thin dotted #333;
+ outline: 5px auto -webkit-focus-ring-color;
+ outline-offset: -2px;
+}
+
+.btn.active,
+.btn:active {
+ background-image: none;
+ outline: 0;
+ -webkit-box-shadow: inset 0 2px 4px rgba(0, 0, 0, 0.15), 0 1px 2px rgba(0, 0, 0, 0.05);
+ -moz-box-shadow: inset 0 2px 4px rgba(0, 0, 0, 0.15), 0 1px 2px rgba(0, 0, 0, 0.05);
+ box-shadow: inset 0 2px 4px rgba(0, 0, 0, 0.15), 0 1px 2px rgba(0, 0, 0, 0.05);
+}
+
+.btn.disabled,
+.btn[disabled] {
+ cursor: default;
+ background-image: none;
+ opacity: 0.65;
+ filter: alpha(opacity=65);
+ -webkit-box-shadow: none;
+ -moz-box-shadow: none;
+ box-shadow: none;
+}
+
+.btn-large {
+ padding: 11px 19px;
+ font-size: 17.5px;
+ -webkit-border-radius: 6px;
+ -moz-border-radius: 6px;
+ border-radius: 6px;
+}
+
+.btn-large [class^="icon-"],
+.btn-large [class*=" icon-"] {
+ margin-top: 4px;
+}
+
+.btn-small {
+ padding: 2px 10px;
+ font-size: 11.9px;
+ -webkit-border-radius: 3px;
+ -moz-border-radius: 3px;
+ border-radius: 3px;
+}
+
+.btn-small [class^="icon-"],
+.btn-small [class*=" icon-"] {
+ margin-top: 0;
+}
+
+.btn-mini [class^="icon-"],
+.btn-mini [class*=" icon-"] {
+ margin-top: -1px;
+}
+
+.btn-mini {
+ padding: 0 6px;
+ font-size: 10.5px;
+ -webkit-border-radius: 3px;
+ -moz-border-radius: 3px;
+ border-radius: 3px;
+}
+
+.btn-block {
+ display: block;
+ width: 100%;
+ padding-right: 0;
+ padding-left: 0;
+ -webkit-box-sizing: border-box;
+ -moz-box-sizing: border-box;
+ box-sizing: border-box;
+}
+
+.btn-block + .btn-block {
+ margin-top: 5px;
+}
+
+input[type="submit"].btn-block,
+input[type="reset"].btn-block,
+input[type="button"].btn-block {
+ width: 100%;
+}
+
+.btn-primary.active,
+.btn-warning.active,
+.btn-danger.active,
+.btn-success.active,
+.btn-info.active,
+.btn-inverse.active {
+ color: rgba(255, 255, 255, 0.75);
+}
+
+.btn-primary {
+ color: #ffffff;
+ text-shadow: 0 -1px 0 rgba(0, 0, 0, 0.25);
+ background-color: #006dcc;
+ *background-color: #0044cc;
+ background-image: -moz-linear-gradient(top, #0088cc, #0044cc);
+ background-image: -webkit-gradient(linear, 0 0, 0 100%, from(#0088cc), to(#0044cc));
+ background-image: -webkit-linear-gradient(top, #0088cc, #0044cc);
+ background-image: -o-linear-gradient(top, #0088cc, #0044cc);
+ background-image: linear-gradient(to bottom, #0088cc, #0044cc);
+ background-repeat: repeat-x;
+ border-color: #0044cc #0044cc #002a80;
+ border-color: rgba(0, 0, 0, 0.1) rgba(0, 0, 0, 0.1) rgba(0, 0, 0, 0.25);
+ filter: progid:DXImageTransform.Microsoft.gradient(startColorstr='#ff0088cc', endColorstr='#ff0044cc', GradientType=0);
+ filter: progid:DXImageTransform.Microsoft.gradient(enabled=false);
+}
+
+.btn-primary:hover,
+.btn-primary:focus,
+.btn-primary:active,
+.btn-primary.active,
+.btn-primary.disabled,
+.btn-primary[disabled] {
+ color: #ffffff;
+ background-color: #0044cc;
+ *background-color: #003bb3;
+}
+
+.btn-primary:active,
+.btn-primary.active {
+ background-color: #003399 \9;
+}
+
+.btn-warning {
+ color: #ffffff;
+ text-shadow: 0 -1px 0 rgba(0, 0, 0, 0.25);
+ background-color: #faa732;
+ *background-color: #f89406;
+ background-image: -moz-linear-gradient(top, #fbb450, #f89406);
+ background-image: -webkit-gradient(linear, 0 0, 0 100%, from(#fbb450), to(#f89406));
+ background-image: -webkit-linear-gradient(top, #fbb450, #f89406);
+ background-image: -o-linear-gradient(top, #fbb450, #f89406);
+ background-image: linear-gradient(to bottom, #fbb450, #f89406);
+ background-repeat: repeat-x;
+ border-color: #f89406 #f89406 #ad6704;
+ border-color: rgba(0, 0, 0, 0.1) rgba(0, 0, 0, 0.1) rgba(0, 0, 0, 0.25);
+ filter: progid:DXImageTransform.Microsoft.gradient(startColorstr='#fffbb450', endColorstr='#fff89406', GradientType=0);
+ filter: progid:DXImageTransform.Microsoft.gradient(enabled=false);
+}
+
+.btn-warning:hover,
+.btn-warning:focus,
+.btn-warning:active,
+.btn-warning.active,
+.btn-warning.disabled,
+.btn-warning[disabled] {
+ color: #ffffff;
+ background-color: #f89406;
+ *background-color: #df8505;
+}
+
+.btn-warning:active,
+.btn-warning.active {
+ background-color: #c67605 \9;
+}
+
+.btn-danger {
+ color: #ffffff;
+ text-shadow: 0 -1px 0 rgba(0, 0, 0, 0.25);
+ background-color: #da4f49;
+ *background-color: #bd362f;
+ background-image: -moz-linear-gradient(top, #ee5f5b, #bd362f);
+ background-image: -webkit-gradient(linear, 0 0, 0 100%, from(#ee5f5b), to(#bd362f));
+ background-image: -webkit-linear-gradient(top, #ee5f5b, #bd362f);
+ background-image: -o-linear-gradient(top, #ee5f5b, #bd362f);
+ background-image: linear-gradient(to bottom, #ee5f5b, #bd362f);
+ background-repeat: repeat-x;
+ border-color: #bd362f #bd362f #802420;
+ border-color: rgba(0, 0, 0, 0.1) rgba(0, 0, 0, 0.1) rgba(0, 0, 0, 0.25);
+ filter: progid:DXImageTransform.Microsoft.gradient(startColorstr='#ffee5f5b', endColorstr='#ffbd362f', GradientType=0);
+ filter: progid:DXImageTransform.Microsoft.gradient(enabled=false);
+}
+
+.btn-danger:hover,
+.btn-danger:focus,
+.btn-danger:active,
+.btn-danger.active,
+.btn-danger.disabled,
+.btn-danger[disabled] {
+ color: #ffffff;
+ background-color: #bd362f;
+ *background-color: #a9302a;
+}
+
+.btn-danger:active,
+.btn-danger.active {
+ background-color: #942a25 \9;
+}
+
+.btn-success {
+ color: #ffffff;
+ text-shadow: 0 -1px 0 rgba(0, 0, 0, 0.25);
+ background-color: #5bb75b;
+ *background-color: #51a351;
+ background-image: -moz-linear-gradient(top, #62c462, #51a351);
+ background-image: -webkit-gradient(linear, 0 0, 0 100%, from(#62c462), to(#51a351));
+ background-image: -webkit-linear-gradient(top, #62c462, #51a351);
+ background-image: -o-linear-gradient(top, #62c462, #51a351);
+ background-image: linear-gradient(to bottom, #62c462, #51a351);
+ background-repeat: repeat-x;
+ border-color: #51a351 #51a351 #387038;
+ border-color: rgba(0, 0, 0, 0.1) rgba(0, 0, 0, 0.1) rgba(0, 0, 0, 0.25);
+ filter: progid:DXImageTransform.Microsoft.gradient(startColorstr='#ff62c462', endColorstr='#ff51a351', GradientType=0);
+ filter: progid:DXImageTransform.Microsoft.gradient(enabled=false);
+}
+
+.btn-success:hover,
+.btn-success:focus,
+.btn-success:active,
+.btn-success.active,
+.btn-success.disabled,
+.btn-success[disabled] {
+ color: #ffffff;
+ background-color: #51a351;
+ *background-color: #499249;
+}
+
+.btn-success:active,
+.btn-success.active {
+ background-color: #408140 \9;
+}
+
+.btn-info {
+ color: #ffffff;
+ text-shadow: 0 -1px 0 rgba(0, 0, 0, 0.25);
+ background-color: #49afcd;
+ *background-color: #2f96b4;
+ background-image: -moz-linear-gradient(top, #5bc0de, #2f96b4);
+ background-image: -webkit-gradient(linear, 0 0, 0 100%, from(#5bc0de), to(#2f96b4));
+ background-image: -webkit-linear-gradient(top, #5bc0de, #2f96b4);
+ background-image: -o-linear-gradient(top, #5bc0de, #2f96b4);
+ background-image: linear-gradient(to bottom, #5bc0de, #2f96b4);
+ background-repeat: repeat-x;
+ border-color: #2f96b4 #2f96b4 #1f6377;
+ border-color: rgba(0, 0, 0, 0.1) rgba(0, 0, 0, 0.1) rgba(0, 0, 0, 0.25);
+ filter: progid:DXImageTransform.Microsoft.gradient(startColorstr='#ff5bc0de', endColorstr='#ff2f96b4', GradientType=0);
+ filter: progid:DXImageTransform.Microsoft.gradient(enabled=false);
+}
+
+.btn-info:hover,
+.btn-info:focus,
+.btn-info:active,
+.btn-info.active,
+.btn-info.disabled,
+.btn-info[disabled] {
+ color: #ffffff;
+ background-color: #2f96b4;
+ *background-color: #2a85a0;
+}
+
+.btn-info:active,
+.btn-info.active {
+ background-color: #24748c \9;
+}
+
+.btn-inverse {
+ color: #ffffff;
+ text-shadow: 0 -1px 0 rgba(0, 0, 0, 0.25);
+ background-color: #363636;
+ *background-color: #222222;
+ background-image: -moz-linear-gradient(top, #444444, #222222);
+ background-image: -webkit-gradient(linear, 0 0, 0 100%, from(#444444), to(#222222));
+ background-image: -webkit-linear-gradient(top, #444444, #222222);
+ background-image: -o-linear-gradient(top, #444444, #222222);
+ background-image: linear-gradient(to bottom, #444444, #222222);
+ background-repeat: repeat-x;
+ border-color: #222222 #222222 #000000;
+ border-color: rgba(0, 0, 0, 0.1) rgba(0, 0, 0, 0.1) rgba(0, 0, 0, 0.25);
+ filter: progid:DXImageTransform.Microsoft.gradient(startColorstr='#ff444444', endColorstr='#ff222222', GradientType=0);
+ filter: progid:DXImageTransform.Microsoft.gradient(enabled=false);
+}
+
+.btn-inverse:hover,
+.btn-inverse:focus,
+.btn-inverse:active,
+.btn-inverse.active,
+.btn-inverse.disabled,
+.btn-inverse[disabled] {
+ color: #ffffff;
+ background-color: #222222;
+ *background-color: #151515;
+}
+
+.btn-inverse:active,
+.btn-inverse.active {
+ background-color: #080808 \9;
+}
+
+button.btn,
+input[type="submit"].btn {
+ *padding-top: 3px;
+ *padding-bottom: 3px;
+}
+
+button.btn::-moz-focus-inner,
+input[type="submit"].btn::-moz-focus-inner {
+ padding: 0;
+ border: 0;
+}
+
+button.btn.btn-large,
+input[type="submit"].btn.btn-large {
+ *padding-top: 7px;
+ *padding-bottom: 7px;
+}
+
+button.btn.btn-small,
+input[type="submit"].btn.btn-small {
+ *padding-top: 3px;
+ *padding-bottom: 3px;
+}
+
+button.btn.btn-mini,
+input[type="submit"].btn.btn-mini {
+ *padding-top: 1px;
+ *padding-bottom: 1px;
+}
+
+.btn-link,
+.btn-link:active,
+.btn-link[disabled] {
+ background-color: transparent;
+ background-image: none;
+ -webkit-box-shadow: none;
+ -moz-box-shadow: none;
+ box-shadow: none;
+}
+
+.btn-link {
+ color: #0088cc;
+ cursor: pointer;
+ border-color: transparent;
+ -webkit-border-radius: 0;
+ -moz-border-radius: 0;
+ border-radius: 0;
+}
+
+.btn-link:hover,
+.btn-link:focus {
+ color: #005580;
+ text-decoration: underline;
+ background-color: transparent;
+}
+
+.btn-link[disabled]:hover,
+.btn-link[disabled]:focus {
+ color: #333333;
+ text-decoration: none;
+}
+
+.btn-group {
+ position: relative;
+ display: inline-block;
+ *display: inline;
+ *margin-left: .3em;
+ font-size: 0;
+ white-space: nowrap;
+ vertical-align: middle;
+ *zoom: 1;
+}
+
+.btn-group:first-child {
+ *margin-left: 0;
+}
+
+.btn-group + .btn-group {
+ margin-left: 5px;
+}
+
+.btn-toolbar {
+ margin-top: 10px;
+ margin-bottom: 10px;
+ font-size: 0;
+}
+
+.btn-toolbar > .btn + .btn,
+.btn-toolbar > .btn-group + .btn,
+.btn-toolbar > .btn + .btn-group {
+ margin-left: 5px;
+}
+
+.btn-group > .btn {
+ position: relative;
+ -webkit-border-radius: 0;
+ -moz-border-radius: 0;
+ border-radius: 0;
+}
+
+.btn-group > .btn + .btn {
+ margin-left: -1px;
+}
+
+.btn-group > .btn,
+.btn-group > .dropdown-menu,
+.btn-group > .popover {
+ font-size: 14px;
+}
+
+.btn-group > .btn-mini {
+ font-size: 10.5px;
+}
+
+.btn-group > .btn-small {
+ font-size: 11.9px;
+}
+
+.btn-group > .btn-large {
+ font-size: 17.5px;
+}
+
+.btn-group > .btn:first-child {
+ margin-left: 0;
+ -webkit-border-bottom-left-radius: 4px;
+ border-bottom-left-radius: 4px;
+ -webkit-border-top-left-radius: 4px;
+ border-top-left-radius: 4px;
+ -moz-border-radius-bottomleft: 4px;
+ -moz-border-radius-topleft: 4px;
+}
+
+.btn-group > .btn:last-child,
+.btn-group > .dropdown-toggle {
+ -webkit-border-top-right-radius: 4px;
+ border-top-right-radius: 4px;
+ -webkit-border-bottom-right-radius: 4px;
+ border-bottom-right-radius: 4px;
+ -moz-border-radius-topright: 4px;
+ -moz-border-radius-bottomright: 4px;
+}
+
+.btn-group > .btn.large:first-child {
+ margin-left: 0;
+ -webkit-border-bottom-left-radius: 6px;
+ border-bottom-left-radius: 6px;
+ -webkit-border-top-left-radius: 6px;
+ border-top-left-radius: 6px;
+ -moz-border-radius-bottomleft: 6px;
+ -moz-border-radius-topleft: 6px;
+}
+
+.btn-group > .btn.large:last-child,
+.btn-group > .large.dropdown-toggle {
+ -webkit-border-top-right-radius: 6px;
+ border-top-right-radius: 6px;
+ -webkit-border-bottom-right-radius: 6px;
+ border-bottom-right-radius: 6px;
+ -moz-border-radius-topright: 6px;
+ -moz-border-radius-bottomright: 6px;
+}
+
+.btn-group > .btn:hover,
+.btn-group > .btn:focus,
+.btn-group > .btn:active,
+.btn-group > .btn.active {
+ z-index: 2;
+}
+
+.btn-group .dropdown-toggle:active,
+.btn-group.open .dropdown-toggle {
+ outline: 0;
+}
+
+.btn-group > .btn + .dropdown-toggle {
+ *padding-top: 5px;
+ padding-right: 8px;
+ *padding-bottom: 5px;
+ padding-left: 8px;
+ -webkit-box-shadow: inset 1px 0 0 rgba(255, 255, 255, 0.125), inset 0 1px 0 rgba(255, 255, 255, 0.2), 0 1px 2px rgba(0, 0, 0, 0.05);
+ -moz-box-shadow: inset 1px 0 0 rgba(255, 255, 255, 0.125), inset 0 1px 0 rgba(255, 255, 255, 0.2), 0 1px 2px rgba(0, 0, 0, 0.05);
+ box-shadow: inset 1px 0 0 rgba(255, 255, 255, 0.125), inset 0 1px 0 rgba(255, 255, 255, 0.2), 0 1px 2px rgba(0, 0, 0, 0.05);
+}
+
+.btn-group > .btn-mini + .dropdown-toggle {
+ *padding-top: 2px;
+ padding-right: 5px;
+ *padding-bottom: 2px;
+ padding-left: 5px;
+}
+
+.btn-group > .btn-small + .dropdown-toggle {
+ *padding-top: 5px;
+ *padding-bottom: 4px;
+}
+
+.btn-group > .btn-large + .dropdown-toggle {
+ *padding-top: 7px;
+ padding-right: 12px;
+ *padding-bottom: 7px;
+ padding-left: 12px;
+}
+
+.btn-group.open .dropdown-toggle {
+ background-image: none;
+ -webkit-box-shadow: inset 0 2px 4px rgba(0, 0, 0, 0.15), 0 1px 2px rgba(0, 0, 0, 0.05);
+ -moz-box-shadow: inset 0 2px 4px rgba(0, 0, 0, 0.15), 0 1px 2px rgba(0, 0, 0, 0.05);
+ box-shadow: inset 0 2px 4px rgba(0, 0, 0, 0.15), 0 1px 2px rgba(0, 0, 0, 0.05);
+}
+
+.btn-group.open .btn.dropdown-toggle {
+ background-color: #e6e6e6;
+}
+
+.btn-group.open .btn-primary.dropdown-toggle {
+ background-color: #0044cc;
+}
+
+.btn-group.open .btn-warning.dropdown-toggle {
+ background-color: #f89406;
+}
+
+.btn-group.open .btn-danger.dropdown-toggle {
+ background-color: #bd362f;
+}
+
+.btn-group.open .btn-success.dropdown-toggle {
+ background-color: #51a351;
+}
+
+.btn-group.open .btn-info.dropdown-toggle {
+ background-color: #2f96b4;
+}
+
+.btn-group.open .btn-inverse.dropdown-toggle {
+ background-color: #222222;
+}
+
+.btn .caret {
+ margin-top: 8px;
+ margin-left: 0;
+}
+
+.btn-large .caret {
+ margin-top: 6px;
+}
+
+.btn-large .caret {
+ border-top-width: 5px;
+ border-right-width: 5px;
+ border-left-width: 5px;
+}
+
+.btn-mini .caret,
+.btn-small .caret {
+ margin-top: 8px;
+}
+
+.dropup .btn-large .caret {
+ border-bottom-width: 5px;
+}
+
+.btn-primary .caret,
+.btn-warning .caret,
+.btn-danger .caret,
+.btn-info .caret,
+.btn-success .caret,
+.btn-inverse .caret {
+ border-top-color: #ffffff;
+ border-bottom-color: #ffffff;
+}
+
+.btn-group-vertical {
+ display: inline-block;
+ *display: inline;
+ /* IE7 inline-block hack */
+
+ *zoom: 1;
+}
+
+.btn-group-vertical > .btn {
+ display: block;
+ float: none;
+ max-width: 100%;
+ -webkit-border-radius: 0;
+ -moz-border-radius: 0;
+ border-radius: 0;
+}
+
+.btn-group-vertical > .btn + .btn {
+ margin-top: -1px;
+ margin-left: 0;
+}
+
+.btn-group-vertical > .btn:first-child {
+ -webkit-border-radius: 4px 4px 0 0;
+ -moz-border-radius: 4px 4px 0 0;
+ border-radius: 4px 4px 0 0;
+}
+
+.btn-group-vertical > .btn:last-child {
+ -webkit-border-radius: 0 0 4px 4px;
+ -moz-border-radius: 0 0 4px 4px;
+ border-radius: 0 0 4px 4px;
+}
+
+.btn-group-vertical > .btn-large:first-child {
+ -webkit-border-radius: 6px 6px 0 0;
+ -moz-border-radius: 6px 6px 0 0;
+ border-radius: 6px 6px 0 0;
+}
+
+.btn-group-vertical > .btn-large:last-child {
+ -webkit-border-radius: 0 0 6px 6px;
+ -moz-border-radius: 0 0 6px 6px;
+ border-radius: 0 0 6px 6px;
+}
+
+.alert {
+ padding: 8px 35px 8px 14px;
+ margin-bottom: 20px;
+ text-shadow: 0 1px 0 rgba(255, 255, 255, 0.5);
+ background-color: #fcf8e3;
+ border: 1px solid #fbeed5;
+ -webkit-border-radius: 4px;
+ -moz-border-radius: 4px;
+ border-radius: 4px;
+}
+
+.alert,
+.alert h4 {
+ color: #c09853;
+}
+
+.alert h4 {
+ margin: 0;
+}
+
+.alert .close {
+ position: relative;
+ top: -2px;
+ right: -21px;
+ line-height: 20px;
+}
+
+.alert-success {
+ color: #468847;
+ background-color: #dff0d8;
+ border-color: #d6e9c6;
+}
+
+.alert-success h4 {
+ color: #468847;
+}
+
+.alert-danger,
+.alert-error {
+ color: #b94a48;
+ background-color: #f2dede;
+ border-color: #eed3d7;
+}
+
+.alert-danger h4,
+.alert-error h4 {
+ color: #b94a48;
+}
+
+.alert-info {
+ color: #3a87ad;
+ background-color: #d9edf7;
+ border-color: #bce8f1;
+}
+
+.alert-info h4 {
+ color: #3a87ad;
+}
+
+.alert-block {
+ padding-top: 14px;
+ padding-bottom: 14px;
+}
+
+.alert-block > p,
+.alert-block > ul {
+ margin-bottom: 0;
+}
+
+.alert-block p + p {
+ margin-top: 5px;
+}
+
+.nav {
+ margin-bottom: 20px;
+ margin-left: 0;
+ list-style: none;
+}
+
+.nav > li > a {
+ display: block;
+}
+
+.nav > li > a:hover,
+.nav > li > a:focus {
+ text-decoration: none;
+ background-color: #eeeeee;
+}
+
+.nav > li > a > img {
+ max-width: none;
+}
+
+.nav > .pull-right {
+ float: right;
+}
+
+.nav-header {
+ display: block;
+ padding: 3px 15px;
+ font-size: 11px;
+ font-weight: bold;
+ line-height: 20px;
+ color: #999999;
+ text-shadow: 0 1px 0 rgba(255, 255, 255, 0.5);
+ text-transform: uppercase;
+}
+
+.nav li + .nav-header {
+ margin-top: 9px;
+}
+
+.nav-list {
+ padding-right: 15px;
+ padding-left: 15px;
+ margin-bottom: 0;
+}
+
+.nav-list > li > a,
+.nav-list .nav-header {
+ margin-right: -15px;
+ margin-left: -15px;
+ text-shadow: 0 1px 0 rgba(255, 255, 255, 0.5);
+}
+
+.nav-list > li > a {
+ padding: 3px 15px;
+}
+
+.nav-list > .active > a,
+.nav-list > .active > a:hover,
+.nav-list > .active > a:focus {
+ color: #ffffff;
+ text-shadow: 0 -1px 0 rgba(0, 0, 0, 0.2);
+ background-color: #0088cc;
+}
+
+.nav-list [class^="icon-"],
+.nav-list [class*=" icon-"] {
+ margin-right: 2px;
+}
+
+.nav-list .divider {
+ *width: 100%;
+ height: 1px;
+ margin: 9px 1px;
+ *margin: -5px 0 5px;
+ overflow: hidden;
+ background-color: #e5e5e5;
+ border-bottom: 1px solid #ffffff;
+}
+
+.nav-tabs,
+.nav-pills {
+ *zoom: 1;
+}
+
+.nav-tabs:before,
+.nav-pills:before,
+.nav-tabs:after,
+.nav-pills:after {
+ display: table;
+ line-height: 0;
+ content: "";
+}
+
+.nav-tabs:after,
+.nav-pills:after {
+ clear: both;
+}
+
+.nav-tabs > li,
+.nav-pills > li {
+ float: left;
+}
+
+.nav-tabs > li > a,
+.nav-pills > li > a {
+ padding-right: 12px;
+ padding-left: 12px;
+ margin-right: 2px;
+ line-height: 14px;
+}
+
+.nav-tabs {
+ border-bottom: 1px solid #ddd;
+}
+
+.nav-tabs > li {
+ margin-bottom: -1px;
+}
+
+.nav-tabs > li > a {
+ padding-top: 8px;
+ padding-bottom: 8px;
+ line-height: 20px;
+ border: 1px solid transparent;
+ -webkit-border-radius: 4px 4px 0 0;
+ -moz-border-radius: 4px 4px 0 0;
+ border-radius: 4px 4px 0 0;
+}
+
+.nav-tabs > li > a:hover,
+.nav-tabs > li > a:focus {
+ border-color: #eeeeee #eeeeee #dddddd;
+}
+
+.nav-tabs > .active > a,
+.nav-tabs > .active > a:hover,
+.nav-tabs > .active > a:focus {
+ color: #555555;
+ cursor: default;
+ background-color: #ffffff;
+ border: 1px solid #ddd;
+ border-bottom-color: transparent;
+}
+
+.nav-pills > li > a {
+ padding-top: 8px;
+ padding-bottom: 8px;
+ margin-top: 2px;
+ margin-bottom: 2px;
+ -webkit-border-radius: 5px;
+ -moz-border-radius: 5px;
+ border-radius: 5px;
+}
+
+.nav-pills > .active > a,
+.nav-pills > .active > a:hover,
+.nav-pills > .active > a:focus {
+ color: #ffffff;
+ background-color: #0088cc;
+}
+
+.nav-stacked > li {
+ float: none;
+}
+
+.nav-stacked > li > a {
+ margin-right: 0;
+}
+
+.nav-tabs.nav-stacked {
+ border-bottom: 0;
+}
+
+.nav-tabs.nav-stacked > li > a {
+ border: 1px solid #ddd;
+ -webkit-border-radius: 0;
+ -moz-border-radius: 0;
+ border-radius: 0;
+}
+
+.nav-tabs.nav-stacked > li:first-child > a {
+ -webkit-border-top-right-radius: 4px;
+ border-top-right-radius: 4px;
+ -webkit-border-top-left-radius: 4px;
+ border-top-left-radius: 4px;
+ -moz-border-radius-topright: 4px;
+ -moz-border-radius-topleft: 4px;
+}
+
+.nav-tabs.nav-stacked > li:last-child > a {
+ -webkit-border-bottom-right-radius: 4px;
+ border-bottom-right-radius: 4px;
+ -webkit-border-bottom-left-radius: 4px;
+ border-bottom-left-radius: 4px;
+ -moz-border-radius-bottomright: 4px;
+ -moz-border-radius-bottomleft: 4px;
+}
+
+.nav-tabs.nav-stacked > li > a:hover,
+.nav-tabs.nav-stacked > li > a:focus {
+ z-index: 2;
+ border-color: #ddd;
+}
+
+.nav-pills.nav-stacked > li > a {
+ margin-bottom: 3px;
+}
+
+.nav-pills.nav-stacked > li:last-child > a {
+ margin-bottom: 1px;
+}
+
+.nav-tabs .dropdown-menu {
+ -webkit-border-radius: 0 0 6px 6px;
+ -moz-border-radius: 0 0 6px 6px;
+ border-radius: 0 0 6px 6px;
+}
+
+.nav-pills .dropdown-menu {
+ -webkit-border-radius: 6px;
+ -moz-border-radius: 6px;
+ border-radius: 6px;
+}
+
+.nav .dropdown-toggle .caret {
+ margin-top: 6px;
+ border-top-color: #0088cc;
+ border-bottom-color: #0088cc;
+}
+
+.nav .dropdown-toggle:hover .caret,
+.nav .dropdown-toggle:focus .caret {
+ border-top-color: #005580;
+ border-bottom-color: #005580;
+}
+
+/* move down carets for tabs */
+
+.nav-tabs .dropdown-toggle .caret {
+ margin-top: 8px;
+}
+
+.nav .active .dropdown-toggle .caret {
+ border-top-color: #fff;
+ border-bottom-color: #fff;
+}
+
+.nav-tabs .active .dropdown-toggle .caret {
+ border-top-color: #555555;
+ border-bottom-color: #555555;
+}
+
+.nav > .dropdown.active > a:hover,
+.nav > .dropdown.active > a:focus {
+ cursor: pointer;
+}
+
+.nav-tabs .open .dropdown-toggle,
+.nav-pills .open .dropdown-toggle,
+.nav > li.dropdown.open.active > a:hover,
+.nav > li.dropdown.open.active > a:focus {
+ color: #ffffff;
+ background-color: #999999;
+ border-color: #999999;
+}
+
+.nav li.dropdown.open .caret,
+.nav li.dropdown.open.active .caret,
+.nav li.dropdown.open a:hover .caret,
+.nav li.dropdown.open a:focus .caret {
+ border-top-color: #ffffff;
+ border-bottom-color: #ffffff;
+ opacity: 1;
+ filter: alpha(opacity=100);
+}
+
+.tabs-stacked .open > a:hover,
+.tabs-stacked .open > a:focus {
+ border-color: #999999;
+}
+
+.tabbable {
+ *zoom: 1;
+}
+
+.tabbable:before,
+.tabbable:after {
+ display: table;
+ line-height: 0;
+ content: "";
+}
+
+.tabbable:after {
+ clear: both;
+}
+
+.tab-content {
+ overflow: auto;
+}
+
+.tabs-below > .nav-tabs,
+.tabs-right > .nav-tabs,
+.tabs-left > .nav-tabs {
+ border-bottom: 0;
+}
+
+.tab-content > .tab-pane,
+.pill-content > .pill-pane {
+ display: none;
+}
+
+.tab-content > .active,
+.pill-content > .active {
+ display: block;
+}
+
+.tabs-below > .nav-tabs {
+ border-top: 1px solid #ddd;
+}
+
+.tabs-below > .nav-tabs > li {
+ margin-top: -1px;
+ margin-bottom: 0;
+}
+
+.tabs-below > .nav-tabs > li > a {
+ -webkit-border-radius: 0 0 4px 4px;
+ -moz-border-radius: 0 0 4px 4px;
+ border-radius: 0 0 4px 4px;
+}
+
+.tabs-below > .nav-tabs > li > a:hover,
+.tabs-below > .nav-tabs > li > a:focus {
+ border-top-color: #ddd;
+ border-bottom-color: transparent;
+}
+
+.tabs-below > .nav-tabs > .active > a,
+.tabs-below > .nav-tabs > .active > a:hover,
+.tabs-below > .nav-tabs > .active > a:focus {
+ border-color: transparent #ddd #ddd #ddd;
+}
+
+.tabs-left > .nav-tabs > li,
+.tabs-right > .nav-tabs > li {
+ float: none;
+}
+
+.tabs-left > .nav-tabs > li > a,
+.tabs-right > .nav-tabs > li > a {
+ min-width: 74px;
+ margin-right: 0;
+ margin-bottom: 3px;
+}
+
+.tabs-left > .nav-tabs {
+ float: left;
+ margin-right: 19px;
+ border-right: 1px solid #ddd;
+}
+
+.tabs-left > .nav-tabs > li > a {
+ margin-right: -1px;
+ -webkit-border-radius: 4px 0 0 4px;
+ -moz-border-radius: 4px 0 0 4px;
+ border-radius: 4px 0 0 4px;
+}
+
+.tabs-left > .nav-tabs > li > a:hover,
+.tabs-left > .nav-tabs > li > a:focus {
+ border-color: #eeeeee #dddddd #eeeeee #eeeeee;
+}
+
+.tabs-left > .nav-tabs .active > a,
+.tabs-left > .nav-tabs .active > a:hover,
+.tabs-left > .nav-tabs .active > a:focus {
+ border-color: #ddd transparent #ddd #ddd;
+ *border-right-color: #ffffff;
+}
+
+.tabs-right > .nav-tabs {
+ float: right;
+ margin-left: 19px;
+ border-left: 1px solid #ddd;
+}
+
+.tabs-right > .nav-tabs > li > a {
+ margin-left: -1px;
+ -webkit-border-radius: 0 4px 4px 0;
+ -moz-border-radius: 0 4px 4px 0;
+ border-radius: 0 4px 4px 0;
+}
+
+.tabs-right > .nav-tabs > li > a:hover,
+.tabs-right > .nav-tabs > li > a:focus {
+ border-color: #eeeeee #eeeeee #eeeeee #dddddd;
+}
+
+.tabs-right > .nav-tabs .active > a,
+.tabs-right > .nav-tabs .active > a:hover,
+.tabs-right > .nav-tabs .active > a:focus {
+ border-color: #ddd #ddd #ddd transparent;
+ *border-left-color: #ffffff;
+}
+
+.nav > .disabled > a {
+ color: #999999;
+}
+
+.nav > .disabled > a:hover,
+.nav > .disabled > a:focus {
+ text-decoration: none;
+ cursor: default;
+ background-color: transparent;
+}
+
+.navbar {
+ *position: relative;
+ *z-index: 2;
+ margin-bottom: 20px;
+ overflow: visible;
+}
+
+.navbar-inner {
+ min-height: 40px;
+ padding-right: 20px;
+ padding-left: 20px;
+ background-color: #fafafa;
+ background-image: -moz-linear-gradient(top, #ffffff, #f2f2f2);
+ background-image: -webkit-gradient(linear, 0 0, 0 100%, from(#ffffff), to(#f2f2f2));
+ background-image: -webkit-linear-gradient(top, #ffffff, #f2f2f2);
+ background-image: -o-linear-gradient(top, #ffffff, #f2f2f2);
+ background-image: linear-gradient(to bottom, #ffffff, #f2f2f2);
+ background-repeat: repeat-x;
+ border: 1px solid #d4d4d4;
+ -webkit-border-radius: 4px;
+ -moz-border-radius: 4px;
+ border-radius: 4px;
+ filter: progid:DXImageTransform.Microsoft.gradient(startColorstr='#ffffffff', endColorstr='#fff2f2f2', GradientType=0);
+ *zoom: 1;
+ -webkit-box-shadow: 0 1px 4px rgba(0, 0, 0, 0.065);
+ -moz-box-shadow: 0 1px 4px rgba(0, 0, 0, 0.065);
+ box-shadow: 0 1px 4px rgba(0, 0, 0, 0.065);
+}
+
+.navbar-inner:before,
+.navbar-inner:after {
+ display: table;
+ line-height: 0;
+ content: "";
+}
+
+.navbar-inner:after {
+ clear: both;
+}
+
+.navbar .container {
+ width: auto;
+}
+
+.nav-collapse.collapse {
+ height: auto;
+ overflow: visible;
+}
+
+.navbar .brand {
+ display: block;
+ float: left;
+ padding: 10px 20px 10px;
+ margin-left: -20px;
+ font-size: 20px;
+ font-weight: 200;
+ color: #777777;
+ text-shadow: 0 1px 0 #ffffff;
+}
+
+.navbar .brand:hover,
+.navbar .brand:focus {
+ text-decoration: none;
+}
+
+.navbar-text {
+ margin-bottom: 0;
+ line-height: 40px;
+ color: #777777;
+}
+
+.navbar-link {
+ color: #777777;
+}
+
+.navbar-link:hover,
+.navbar-link:focus {
+ color: #333333;
+}
+
+.navbar .divider-vertical {
+ height: 40px;
+ margin: 0 9px;
+ border-right: 1px solid #ffffff;
+ border-left: 1px solid #f2f2f2;
+}
+
+.navbar .btn,
+.navbar .btn-group {
+ margin-top: 5px;
+}
+
+.navbar .btn-group .btn,
+.navbar .input-prepend .btn,
+.navbar .input-append .btn,
+.navbar .input-prepend .btn-group,
+.navbar .input-append .btn-group {
+ margin-top: 0;
+}
+
+.navbar-form {
+ margin-bottom: 0;
+ *zoom: 1;
+}
+
+.navbar-form:before,
+.navbar-form:after {
+ display: table;
+ line-height: 0;
+ content: "";
+}
+
+.navbar-form:after {
+ clear: both;
+}
+
+.navbar-form input,
+.navbar-form select,
+.navbar-form .radio,
+.navbar-form .checkbox {
+ margin-top: 5px;
+}
+
+.navbar-form input,
+.navbar-form select,
+.navbar-form .btn {
+ display: inline-block;
+ margin-bottom: 0;
+}
+
+.navbar-form input[type="image"],
+.navbar-form input[type="checkbox"],
+.navbar-form input[type="radio"] {
+ margin-top: 3px;
+}
+
+.navbar-form .input-append,
+.navbar-form .input-prepend {
+ margin-top: 5px;
+ white-space: nowrap;
+}
+
+.navbar-form .input-append input,
+.navbar-form .input-prepend input {
+ margin-top: 0;
+}
+
+.navbar-search {
+ position: relative;
+ float: left;
+ margin-top: 5px;
+ margin-bottom: 0;
+}
+
+.navbar-search .search-query {
+ padding: 4px 14px;
+ margin-bottom: 0;
+ font-family: "Helvetica Neue", Helvetica, Arial, sans-serif;
+ font-size: 13px;
+ font-weight: normal;
+ line-height: 1;
+ -webkit-border-radius: 15px;
+ -moz-border-radius: 15px;
+ border-radius: 15px;
+}
+
+.navbar-static-top {
+ position: static;
+ margin-bottom: 0;
+}
+
+.navbar-static-top .navbar-inner {
+ -webkit-border-radius: 0;
+ -moz-border-radius: 0;
+ border-radius: 0;
+}
+
+.navbar-fixed-top,
+.navbar-fixed-bottom {
+ position: fixed;
+ right: 0;
+ left: 0;
+ z-index: 1030;
+ margin-bottom: 0;
+}
+
+.navbar-fixed-top .navbar-inner,
+.navbar-static-top .navbar-inner {
+ border-width: 0 0 1px;
+}
+
+.navbar-fixed-bottom .navbar-inner {
+ border-width: 1px 0 0;
+}
+
+.navbar-fixed-top .navbar-inner,
+.navbar-fixed-bottom .navbar-inner {
+ padding-right: 0;
+ padding-left: 0;
+ -webkit-border-radius: 0;
+ -moz-border-radius: 0;
+ border-radius: 0;
+}
+
+.navbar-static-top .container,
+.navbar-fixed-top .container,
+.navbar-fixed-bottom .container {
+ width: 940px;
+}
+
+.navbar-fixed-top {
+ top: 0;
+}
+
+.navbar-fixed-top .navbar-inner,
+.navbar-static-top .navbar-inner {
+ -webkit-box-shadow: 0 1px 10px rgba(0, 0, 0, 0.1);
+ -moz-box-shadow: 0 1px 10px rgba(0, 0, 0, 0.1);
+ box-shadow: 0 1px 10px rgba(0, 0, 0, 0.1);
+}
+
+.navbar-fixed-bottom {
+ bottom: 0;
+}
+
+.navbar-fixed-bottom .navbar-inner {
+ -webkit-box-shadow: 0 -1px 10px rgba(0, 0, 0, 0.1);
+ -moz-box-shadow: 0 -1px 10px rgba(0, 0, 0, 0.1);
+ box-shadow: 0 -1px 10px rgba(0, 0, 0, 0.1);
+}
+
+.navbar .nav {
+ position: relative;
+ left: 0;
+ display: block;
+ float: left;
+ margin: 0 10px 0 0;
+}
+
+.navbar .nav.pull-right {
+ float: right;
+ margin-right: 0;
+}
+
+.navbar .nav > li {
+ float: left;
+}
+
+.navbar .nav > li > a {
+ float: none;
+ padding: 10px 15px 10px;
+ color: #777777;
+ text-decoration: none;
+ text-shadow: 0 1px 0 #ffffff;
+}
+
+.navbar .nav .dropdown-toggle .caret {
+ margin-top: 8px;
+}
+
+.navbar .nav > li > a:focus,
+.navbar .nav > li > a:hover {
+ color: #333333;
+ text-decoration: none;
+ background-color: transparent;
+}
+
+.navbar .nav > .active > a,
+.navbar .nav > .active > a:hover,
+.navbar .nav > .active > a:focus {
+ color: #555555;
+ text-decoration: none;
+ background-color: #e5e5e5;
+ -webkit-box-shadow: inset 0 3px 8px rgba(0, 0, 0, 0.125);
+ -moz-box-shadow: inset 0 3px 8px rgba(0, 0, 0, 0.125);
+ box-shadow: inset 0 3px 8px rgba(0, 0, 0, 0.125);
+}
+
+.navbar .btn-navbar {
+ display: none;
+ float: right;
+ padding: 7px 10px;
+ margin-right: 5px;
+ margin-left: 5px;
+ color: #ffffff;
+ text-shadow: 0 -1px 0 rgba(0, 0, 0, 0.25);
+ background-color: #ededed;
+ *background-color: #e5e5e5;
+ background-image: -moz-linear-gradient(top, #f2f2f2, #e5e5e5);
+ background-image: -webkit-gradient(linear, 0 0, 0 100%, from(#f2f2f2), to(#e5e5e5));
+ background-image: -webkit-linear-gradient(top, #f2f2f2, #e5e5e5);
+ background-image: -o-linear-gradient(top, #f2f2f2, #e5e5e5);
+ background-image: linear-gradient(to bottom, #f2f2f2, #e5e5e5);
+ background-repeat: repeat-x;
+ border-color: #e5e5e5 #e5e5e5 #bfbfbf;
+ border-color: rgba(0, 0, 0, 0.1) rgba(0, 0, 0, 0.1) rgba(0, 0, 0, 0.25);
+ filter: progid:DXImageTransform.Microsoft.gradient(startColorstr='#fff2f2f2', endColorstr='#ffe5e5e5', GradientType=0);
+ filter: progid:DXImageTransform.Microsoft.gradient(enabled=false);
+ -webkit-box-shadow: inset 0 1px 0 rgba(255, 255, 255, 0.1), 0 1px 0 rgba(255, 255, 255, 0.075);
+ -moz-box-shadow: inset 0 1px 0 rgba(255, 255, 255, 0.1), 0 1px 0 rgba(255, 255, 255, 0.075);
+ box-shadow: inset 0 1px 0 rgba(255, 255, 255, 0.1), 0 1px 0 rgba(255, 255, 255, 0.075);
+}
+
+.navbar .btn-navbar:hover,
+.navbar .btn-navbar:focus,
+.navbar .btn-navbar:active,
+.navbar .btn-navbar.active,
+.navbar .btn-navbar.disabled,
+.navbar .btn-navbar[disabled] {
+ color: #ffffff;
+ background-color: #e5e5e5;
+ *background-color: #d9d9d9;
+}
+
+.navbar .btn-navbar:active,
+.navbar .btn-navbar.active {
+ background-color: #cccccc \9;
+}
+
+.navbar .btn-navbar .icon-bar {
+ display: block;
+ width: 18px;
+ height: 2px;
+ background-color: #f5f5f5;
+ -webkit-border-radius: 1px;
+ -moz-border-radius: 1px;
+ border-radius: 1px;
+ -webkit-box-shadow: 0 1px 0 rgba(0, 0, 0, 0.25);
+ -moz-box-shadow: 0 1px 0 rgba(0, 0, 0, 0.25);
+ box-shadow: 0 1px 0 rgba(0, 0, 0, 0.25);
+}
+
+.btn-navbar .icon-bar + .icon-bar {
+ margin-top: 3px;
+}
+
+.navbar .nav > li > .dropdown-menu:before {
+ position: absolute;
+ top: -7px;
+ left: 9px;
+ display: inline-block;
+ border-right: 7px solid transparent;
+ border-bottom: 7px solid #ccc;
+ border-left: 7px solid transparent;
+ border-bottom-color: rgba(0, 0, 0, 0.2);
+ content: '';
+}
+
+.navbar .nav > li > .dropdown-menu:after {
+ position: absolute;
+ top: -6px;
+ left: 10px;
+ display: inline-block;
+ border-right: 6px solid transparent;
+ border-bottom: 6px solid #ffffff;
+ border-left: 6px solid transparent;
+ content: '';
+}
+
+.navbar-fixed-bottom .nav > li > .dropdown-menu:before {
+ top: auto;
+ bottom: -7px;
+ border-top: 7px solid #ccc;
+ border-bottom: 0;
+ border-top-color: rgba(0, 0, 0, 0.2);
+}
+
+.navbar-fixed-bottom .nav > li > .dropdown-menu:after {
+ top: auto;
+ bottom: -6px;
+ border-top: 6px solid #ffffff;
+ border-bottom: 0;
+}
+
+.navbar .nav li.dropdown > a:hover .caret,
+.navbar .nav li.dropdown > a:focus .caret {
+ border-top-color: #333333;
+ border-bottom-color: #333333;
+}
+
+.navbar .nav li.dropdown.open > .dropdown-toggle,
+.navbar .nav li.dropdown.active > .dropdown-toggle,
+.navbar .nav li.dropdown.open.active > .dropdown-toggle {
+ color: #555555;
+ background-color: #e5e5e5;
+}
+
+.navbar .nav li.dropdown > .dropdown-toggle .caret {
+ border-top-color: #777777;
+ border-bottom-color: #777777;
+}
+
+.navbar .nav li.dropdown.open > .dropdown-toggle .caret,
+.navbar .nav li.dropdown.active > .dropdown-toggle .caret,
+.navbar .nav li.dropdown.open.active > .dropdown-toggle .caret {
+ border-top-color: #555555;
+ border-bottom-color: #555555;
+}
+
+.navbar .pull-right > li > .dropdown-menu,
+.navbar .nav > li > .dropdown-menu.pull-right {
+ right: 0;
+ left: auto;
+}
+
+.navbar .pull-right > li > .dropdown-menu:before,
+.navbar .nav > li > .dropdown-menu.pull-right:before {
+ right: 12px;
+ left: auto;
+}
+
+.navbar .pull-right > li > .dropdown-menu:after,
+.navbar .nav > li > .dropdown-menu.pull-right:after {
+ right: 13px;
+ left: auto;
+}
+
+.navbar .pull-right > li > .dropdown-menu .dropdown-menu,
+.navbar .nav > li > .dropdown-menu.pull-right .dropdown-menu {
+ right: 100%;
+ left: auto;
+ margin-right: -1px;
+ margin-left: 0;
+ -webkit-border-radius: 6px 0 6px 6px;
+ -moz-border-radius: 6px 0 6px 6px;
+ border-radius: 6px 0 6px 6px;
+}
+
+.navbar-inverse .navbar-inner {
+ background-color: #1b1b1b;
+ background-image: -moz-linear-gradient(top, #222222, #111111);
+ background-image: -webkit-gradient(linear, 0 0, 0 100%, from(#222222), to(#111111));
+ background-image: -webkit-linear-gradient(top, #222222, #111111);
+ background-image: -o-linear-gradient(top, #222222, #111111);
+ background-image: linear-gradient(to bottom, #222222, #111111);
+ background-repeat: repeat-x;
+ border-color: #252525;
+ filter: progid:DXImageTransform.Microsoft.gradient(startColorstr='#ff222222', endColorstr='#ff111111', GradientType=0);
+}
+
+.navbar-inverse .brand,
+.navbar-inverse .nav > li > a {
+ color: #999999;
+ text-shadow: 0 -1px 0 rgba(0, 0, 0, 0.25);
+}
+
+.navbar-inverse .brand:hover,
+.navbar-inverse .nav > li > a:hover,
+.navbar-inverse .brand:focus,
+.navbar-inverse .nav > li > a:focus {
+ color: #ffffff;
+}
+
+.navbar-inverse .brand {
+ color: #999999;
+}
+
+.navbar-inverse .navbar-text {
+ color: #999999;
+}
+
+.navbar-inverse .nav > li > a:focus,
+.navbar-inverse .nav > li > a:hover {
+ color: #ffffff;
+ background-color: transparent;
+}
+
+.navbar-inverse .nav .active > a,
+.navbar-inverse .nav .active > a:hover,
+.navbar-inverse .nav .active > a:focus {
+ color: #ffffff;
+ background-color: #111111;
+}
+
+.navbar-inverse .navbar-link {
+ color: #999999;
+}
+
+.navbar-inverse .navbar-link:hover,
+.navbar-inverse .navbar-link:focus {
+ color: #ffffff;
+}
+
+.navbar-inverse .divider-vertical {
+ border-right-color: #222222;
+ border-left-color: #111111;
+}
+
+.navbar-inverse .nav li.dropdown.open > .dropdown-toggle,
+.navbar-inverse .nav li.dropdown.active > .dropdown-toggle,
+.navbar-inverse .nav li.dropdown.open.active > .dropdown-toggle {
+ color: #ffffff;
+ background-color: #111111;
+}
+
+.navbar-inverse .nav li.dropdown > a:hover .caret,
+.navbar-inverse .nav li.dropdown > a:focus .caret {
+ border-top-color: #ffffff;
+ border-bottom-color: #ffffff;
+}
+
+.navbar-inverse .nav li.dropdown > .dropdown-toggle .caret {
+ border-top-color: #999999;
+ border-bottom-color: #999999;
+}
+
+.navbar-inverse .nav li.dropdown.open > .dropdown-toggle .caret,
+.navbar-inverse .nav li.dropdown.active > .dropdown-toggle .caret,
+.navbar-inverse .nav li.dropdown.open.active > .dropdown-toggle .caret {
+ border-top-color: #ffffff;
+ border-bottom-color: #ffffff;
+}
+
+.navbar-inverse .navbar-search .search-query {
+ color: #ffffff;
+ background-color: #515151;
+ border-color: #111111;
+ -webkit-box-shadow: inset 0 1px 2px rgba(0, 0, 0, 0.1), 0 1px 0 rgba(255, 255, 255, 0.15);
+ -moz-box-shadow: inset 0 1px 2px rgba(0, 0, 0, 0.1), 0 1px 0 rgba(255, 255, 255, 0.15);
+ box-shadow: inset 0 1px 2px rgba(0, 0, 0, 0.1), 0 1px 0 rgba(255, 255, 255, 0.15);
+ -webkit-transition: none;
+ -moz-transition: none;
+ -o-transition: none;
+ transition: none;
+}
+
+.navbar-inverse .navbar-search .search-query:-moz-placeholder {
+ color: #cccccc;
+}
+
+.navbar-inverse .navbar-search .search-query:-ms-input-placeholder {
+ color: #cccccc;
+}
+
+.navbar-inverse .navbar-search .search-query::-webkit-input-placeholder {
+ color: #cccccc;
+}
+
+.navbar-inverse .navbar-search .search-query:focus,
+.navbar-inverse .navbar-search .search-query.focused {
+ padding: 5px 15px;
+ color: #333333;
+ text-shadow: 0 1px 0 #ffffff;
+ background-color: #ffffff;
+ border: 0;
+ outline: 0;
+ -webkit-box-shadow: 0 0 3px rgba(0, 0, 0, 0.15);
+ -moz-box-shadow: 0 0 3px rgba(0, 0, 0, 0.15);
+ box-shadow: 0 0 3px rgba(0, 0, 0, 0.15);
+}
+
+.navbar-inverse .btn-navbar {
+ color: #ffffff;
+ text-shadow: 0 -1px 0 rgba(0, 0, 0, 0.25);
+ background-color: #0e0e0e;
+ *background-color: #040404;
+ background-image: -moz-linear-gradient(top, #151515, #040404);
+ background-image: -webkit-gradient(linear, 0 0, 0 100%, from(#151515), to(#040404));
+ background-image: -webkit-linear-gradient(top, #151515, #040404);
+ background-image: -o-linear-gradient(top, #151515, #040404);
+ background-image: linear-gradient(to bottom, #151515, #040404);
+ background-repeat: repeat-x;
+ border-color: #040404 #040404 #000000;
+ border-color: rgba(0, 0, 0, 0.1) rgba(0, 0, 0, 0.1) rgba(0, 0, 0, 0.25);
+ filter: progid:DXImageTransform.Microsoft.gradient(startColorstr='#ff151515', endColorstr='#ff040404', GradientType=0);
+ filter: progid:DXImageTransform.Microsoft.gradient(enabled=false);
+}
+
+.navbar-inverse .btn-navbar:hover,
+.navbar-inverse .btn-navbar:focus,
+.navbar-inverse .btn-navbar:active,
+.navbar-inverse .btn-navbar.active,
+.navbar-inverse .btn-navbar.disabled,
+.navbar-inverse .btn-navbar[disabled] {
+ color: #ffffff;
+ background-color: #040404;
+ *background-color: #000000;
+}
+
+.navbar-inverse .btn-navbar:active,
+.navbar-inverse .btn-navbar.active {
+ background-color: #000000 \9;
+}
+
+.breadcrumb {
+ padding: 8px 15px;
+ margin: 0 0 20px;
+ list-style: none;
+ background-color: #f5f5f5;
+ -webkit-border-radius: 4px;
+ -moz-border-radius: 4px;
+ border-radius: 4px;
+}
+
+.breadcrumb > li {
+ display: inline-block;
+ *display: inline;
+ text-shadow: 0 1px 0 #ffffff;
+ *zoom: 1;
+}
+
+.breadcrumb > li > .divider {
+ padding: 0 5px;
+ color: #ccc;
+}
+
+.breadcrumb > .active {
+ color: #999999;
+}
+
+.pagination {
+ margin: 20px 0;
+}
+
+.pagination ul {
+ display: inline-block;
+ *display: inline;
+ margin-bottom: 0;
+ margin-left: 0;
+ -webkit-border-radius: 4px;
+ -moz-border-radius: 4px;
+ border-radius: 4px;
+ *zoom: 1;
+ -webkit-box-shadow: 0 1px 2px rgba(0, 0, 0, 0.05);
+ -moz-box-shadow: 0 1px 2px rgba(0, 0, 0, 0.05);
+ box-shadow: 0 1px 2px rgba(0, 0, 0, 0.05);
+}
+
+.pagination ul > li {
+ display: inline;
+}
+
+.pagination ul > li > a,
+.pagination ul > li > span {
+ float: left;
+ padding: 4px 12px;
+ line-height: 20px;
+ text-decoration: none;
+ background-color: #ffffff;
+ border: 1px solid #dddddd;
+ border-left-width: 0;
+}
+
+.pagination ul > li > a:hover,
+.pagination ul > li > a:focus,
+.pagination ul > .active > a,
+.pagination ul > .active > span {
+ background-color: #f5f5f5;
+}
+
+.pagination ul > .active > a,
+.pagination ul > .active > span {
+ color: #999999;
+ cursor: default;
+}
+
+.pagination ul > .disabled > span,
+.pagination ul > .disabled > a,
+.pagination ul > .disabled > a:hover,
+.pagination ul > .disabled > a:focus {
+ color: #999999;
+ cursor: default;
+ background-color: transparent;
+}
+
+.pagination ul > li:first-child > a,
+.pagination ul > li:first-child > span {
+ border-left-width: 1px;
+ -webkit-border-bottom-left-radius: 4px;
+ border-bottom-left-radius: 4px;
+ -webkit-border-top-left-radius: 4px;
+ border-top-left-radius: 4px;
+ -moz-border-radius-bottomleft: 4px;
+ -moz-border-radius-topleft: 4px;
+}
+
+.pagination ul > li:last-child > a,
+.pagination ul > li:last-child > span {
+ -webkit-border-top-right-radius: 4px;
+ border-top-right-radius: 4px;
+ -webkit-border-bottom-right-radius: 4px;
+ border-bottom-right-radius: 4px;
+ -moz-border-radius-topright: 4px;
+ -moz-border-radius-bottomright: 4px;
+}
+
+.pagination-centered {
+ text-align: center;
+}
+
+.pagination-right {
+ text-align: right;
+}
+
+.pagination-large ul > li > a,
+.pagination-large ul > li > span {
+ padding: 11px 19px;
+ font-size: 17.5px;
+}
+
+.pagination-large ul > li:first-child > a,
+.pagination-large ul > li:first-child > span {
+ -webkit-border-bottom-left-radius: 6px;
+ border-bottom-left-radius: 6px;
+ -webkit-border-top-left-radius: 6px;
+ border-top-left-radius: 6px;
+ -moz-border-radius-bottomleft: 6px;
+ -moz-border-radius-topleft: 6px;
+}
+
+.pagination-large ul > li:last-child > a,
+.pagination-large ul > li:last-child > span {
+ -webkit-border-top-right-radius: 6px;
+ border-top-right-radius: 6px;
+ -webkit-border-bottom-right-radius: 6px;
+ border-bottom-right-radius: 6px;
+ -moz-border-radius-topright: 6px;
+ -moz-border-radius-bottomright: 6px;
+}
+
+.pagination-mini ul > li:first-child > a,
+.pagination-small ul > li:first-child > a,
+.pagination-mini ul > li:first-child > span,
+.pagination-small ul > li:first-child > span {
+ -webkit-border-bottom-left-radius: 3px;
+ border-bottom-left-radius: 3px;
+ -webkit-border-top-left-radius: 3px;
+ border-top-left-radius: 3px;
+ -moz-border-radius-bottomleft: 3px;
+ -moz-border-radius-topleft: 3px;
+}
+
+.pagination-mini ul > li:last-child > a,
+.pagination-small ul > li:last-child > a,
+.pagination-mini ul > li:last-child > span,
+.pagination-small ul > li:last-child > span {
+ -webkit-border-top-right-radius: 3px;
+ border-top-right-radius: 3px;
+ -webkit-border-bottom-right-radius: 3px;
+ border-bottom-right-radius: 3px;
+ -moz-border-radius-topright: 3px;
+ -moz-border-radius-bottomright: 3px;
+}
+
+.pagination-small ul > li > a,
+.pagination-small ul > li > span {
+ padding: 2px 10px;
+ font-size: 11.9px;
+}
+
+.pagination-mini ul > li > a,
+.pagination-mini ul > li > span {
+ padding: 0 6px;
+ font-size: 10.5px;
+}
+
+.pager {
+ margin: 20px 0;
+ text-align: center;
+ list-style: none;
+ *zoom: 1;
+}
+
+.pager:before,
+.pager:after {
+ display: table;
+ line-height: 0;
+ content: "";
+}
+
+.pager:after {
+ clear: both;
+}
+
+.pager li {
+ display: inline;
+}
+
+.pager li > a,
+.pager li > span {
+ display: inline-block;
+ padding: 5px 14px;
+ background-color: #fff;
+ border: 1px solid #ddd;
+ -webkit-border-radius: 15px;
+ -moz-border-radius: 15px;
+ border-radius: 15px;
+}
+
+.pager li > a:hover,
+.pager li > a:focus {
+ text-decoration: none;
+ background-color: #f5f5f5;
+}
+
+.pager .next > a,
+.pager .next > span {
+ float: right;
+}
+
+.pager .previous > a,
+.pager .previous > span {
+ float: left;
+}
+
+.pager .disabled > a,
+.pager .disabled > a:hover,
+.pager .disabled > a:focus,
+.pager .disabled > span {
+ color: #999999;
+ cursor: default;
+ background-color: #fff;
+}
+
+.modal-backdrop {
+ position: fixed;
+ top: 0;
+ right: 0;
+ bottom: 0;
+ left: 0;
+ z-index: 1040;
+ background-color: #000000;
+}
+
+.modal-backdrop.fade {
+ opacity: 0;
+}
+
+.modal-backdrop,
+.modal-backdrop.fade.in {
+ opacity: 0.8;
+ filter: alpha(opacity=80);
+}
+
+.modal {
+ position: fixed;
+ top: 10%;
+ left: 50%;
+ z-index: 1050;
+ width: 560px;
+ margin-left: -280px;
+ background-color: #ffffff;
+ border: 1px solid #999;
+ border: 1px solid rgba(0, 0, 0, 0.3);
+ *border: 1px solid #999;
+ -webkit-border-radius: 6px;
+ -moz-border-radius: 6px;
+ border-radius: 6px;
+ outline: none;
+ -webkit-box-shadow: 0 3px 7px rgba(0, 0, 0, 0.3);
+ -moz-box-shadow: 0 3px 7px rgba(0, 0, 0, 0.3);
+ box-shadow: 0 3px 7px rgba(0, 0, 0, 0.3);
+ -webkit-background-clip: padding-box;
+ -moz-background-clip: padding-box;
+ background-clip: padding-box;
+}
+
+.modal.fade {
+ top: -25%;
+ -webkit-transition: opacity 0.3s linear, top 0.3s ease-out;
+ -moz-transition: opacity 0.3s linear, top 0.3s ease-out;
+ -o-transition: opacity 0.3s linear, top 0.3s ease-out;
+ transition: opacity 0.3s linear, top 0.3s ease-out;
+}
+
+.modal.fade.in {
+ top: 10%;
+}
+
+.modal-header {
+ padding: 9px 15px;
+ border-bottom: 1px solid #eee;
+}
+
+.modal-header .close {
+ margin-top: 2px;
+}
+
+.modal-header h3 {
+ margin: 0;
+ line-height: 30px;
+}
+
+.modal-body {
+ position: relative;
+ max-height: 400px;
+ padding: 15px;
+ overflow-y: auto;
+}
+
+.modal-form {
+ margin-bottom: 0;
+}
+
+.modal-footer {
+ padding: 14px 15px 15px;
+ margin-bottom: 0;
+ text-align: right;
+ background-color: #f5f5f5;
+ border-top: 1px solid #ddd;
+ -webkit-border-radius: 0 0 6px 6px;
+ -moz-border-radius: 0 0 6px 6px;
+ border-radius: 0 0 6px 6px;
+ *zoom: 1;
+ -webkit-box-shadow: inset 0 1px 0 #ffffff;
+ -moz-box-shadow: inset 0 1px 0 #ffffff;
+ box-shadow: inset 0 1px 0 #ffffff;
+}
+
+.modal-footer:before,
+.modal-footer:after {
+ display: table;
+ line-height: 0;
+ content: "";
+}
+
+.modal-footer:after {
+ clear: both;
+}
+
+.modal-footer .btn + .btn {
+ margin-bottom: 0;
+ margin-left: 5px;
+}
+
+.modal-footer .btn-group .btn + .btn {
+ margin-left: -1px;
+}
+
+.modal-footer .btn-block + .btn-block {
+ margin-left: 0;
+}
+
+.tooltip {
+ position: absolute;
+ z-index: 1030;
+ display: block;
+ font-size: 11px;
+ line-height: 1.4;
+ opacity: 0;
+ filter: alpha(opacity=0);
+ visibility: visible;
+}
+
+.tooltip.in {
+ opacity: 0.8;
+ filter: alpha(opacity=80);
+}
+
+.tooltip.top {
+ padding: 5px 0;
+ margin-top: -3px;
+}
+
+.tooltip.right {
+ padding: 0 5px;
+ margin-left: 3px;
+}
+
+.tooltip.bottom {
+ padding: 5px 0;
+ margin-top: 3px;
+}
+
+.tooltip.left {
+ padding: 0 5px;
+ margin-left: -3px;
+}
+
+.tooltip-inner {
+ max-width: 200px;
+ padding: 8px;
+ color: #ffffff;
+ text-align: center;
+ text-decoration: none;
+ background-color: #000000;
+ -webkit-border-radius: 4px;
+ -moz-border-radius: 4px;
+ border-radius: 4px;
+}
+
+.tooltip-arrow {
+ position: absolute;
+ width: 0;
+ height: 0;
+ border-color: transparent;
+ border-style: solid;
+}
+
+.tooltip.top .tooltip-arrow {
+ bottom: 0;
+ left: 50%;
+ margin-left: -5px;
+ border-top-color: #000000;
+ border-width: 5px 5px 0;
+}
+
+.tooltip.right .tooltip-arrow {
+ top: 50%;
+ left: 0;
+ margin-top: -5px;
+ border-right-color: #000000;
+ border-width: 5px 5px 5px 0;
+}
+
+.tooltip.left .tooltip-arrow {
+ top: 50%;
+ right: 0;
+ margin-top: -5px;
+ border-left-color: #000000;
+ border-width: 5px 0 5px 5px;
+}
+
+.tooltip.bottom .tooltip-arrow {
+ top: 0;
+ left: 50%;
+ margin-left: -5px;
+ border-bottom-color: #000000;
+ border-width: 0 5px 5px;
+}
+
+.popover {
+ position: absolute;
+ top: 0;
+ left: 0;
+ z-index: 1010;
+ display: none;
+ max-width: 276px;
+ padding: 1px;
+ text-align: left;
+ white-space: normal;
+ background-color: #ffffff;
+ border: 1px solid #ccc;
+ border: 1px solid rgba(0, 0, 0, 0.2);
+ -webkit-border-radius: 6px;
+ -moz-border-radius: 6px;
+ border-radius: 6px;
+ -webkit-box-shadow: 0 5px 10px rgba(0, 0, 0, 0.2);
+ -moz-box-shadow: 0 5px 10px rgba(0, 0, 0, 0.2);
+ box-shadow: 0 5px 10px rgba(0, 0, 0, 0.2);
+ -webkit-background-clip: padding-box;
+ -moz-background-clip: padding;
+ background-clip: padding-box;
+}
+
+.popover.top {
+ margin-top: -10px;
+}
+
+.popover.right {
+ margin-left: 10px;
+}
+
+.popover.bottom {
+ margin-top: 10px;
+}
+
+.popover.left {
+ margin-left: -10px;
+}
+
+.popover-title {
+ padding: 8px 14px;
+ margin: 0;
+ font-size: 14px;
+ font-weight: normal;
+ line-height: 18px;
+ background-color: #f7f7f7;
+ border-bottom: 1px solid #ebebeb;
+ -webkit-border-radius: 5px 5px 0 0;
+ -moz-border-radius: 5px 5px 0 0;
+ border-radius: 5px 5px 0 0;
+}
+
+.popover-title:empty {
+ display: none;
+}
+
+.popover-content {
+ padding: 9px 14px;
+}
+
+.popover .arrow,
+.popover .arrow:after {
+ position: absolute;
+ display: block;
+ width: 0;
+ height: 0;
+ border-color: transparent;
+ border-style: solid;
+}
+
+.popover .arrow {
+ border-width: 11px;
+}
+
+.popover .arrow:after {
+ border-width: 10px;
+ content: "";
+}
+
+.popover.top .arrow {
+ bottom: -11px;
+ left: 50%;
+ margin-left: -11px;
+ border-top-color: #999;
+ border-top-color: rgba(0, 0, 0, 0.25);
+ border-bottom-width: 0;
+}
+
+.popover.top .arrow:after {
+ bottom: 1px;
+ margin-left: -10px;
+ border-top-color: #ffffff;
+ border-bottom-width: 0;
+}
+
+.popover.right .arrow {
+ top: 50%;
+ left: -11px;
+ margin-top: -11px;
+ border-right-color: #999;
+ border-right-color: rgba(0, 0, 0, 0.25);
+ border-left-width: 0;
+}
+
+.popover.right .arrow:after {
+ bottom: -10px;
+ left: 1px;
+ border-right-color: #ffffff;
+ border-left-width: 0;
+}
+
+.popover.bottom .arrow {
+ top: -11px;
+ left: 50%;
+ margin-left: -11px;
+ border-bottom-color: #999;
+ border-bottom-color: rgba(0, 0, 0, 0.25);
+ border-top-width: 0;
+}
+
+.popover.bottom .arrow:after {
+ top: 1px;
+ margin-left: -10px;
+ border-bottom-color: #ffffff;
+ border-top-width: 0;
+}
+
+.popover.left .arrow {
+ top: 50%;
+ right: -11px;
+ margin-top: -11px;
+ border-left-color: #999;
+ border-left-color: rgba(0, 0, 0, 0.25);
+ border-right-width: 0;
+}
+
+.popover.left .arrow:after {
+ right: 1px;
+ bottom: -10px;
+ border-left-color: #ffffff;
+ border-right-width: 0;
+}
+
+.thumbnails {
+ margin-left: -20px;
+ list-style: none;
+ *zoom: 1;
+}
+
+.thumbnails:before,
+.thumbnails:after {
+ display: table;
+ line-height: 0;
+ content: "";
+}
+
+.thumbnails:after {
+ clear: both;
+}
+
+.row-fluid .thumbnails {
+ margin-left: 0;
+}
+
+.thumbnails > li {
+ float: left;
+ margin-bottom: 20px;
+ margin-left: 20px;
+}
+
+.thumbnail {
+ display: block;
+ padding: 4px;
+ line-height: 20px;
+ border: 1px solid #ddd;
+ -webkit-border-radius: 4px;
+ -moz-border-radius: 4px;
+ border-radius: 4px;
+ -webkit-box-shadow: 0 1px 3px rgba(0, 0, 0, 0.055);
+ -moz-box-shadow: 0 1px 3px rgba(0, 0, 0, 0.055);
+ box-shadow: 0 1px 3px rgba(0, 0, 0, 0.055);
+ -webkit-transition: all 0.2s ease-in-out;
+ -moz-transition: all 0.2s ease-in-out;
+ -o-transition: all 0.2s ease-in-out;
+ transition: all 0.2s ease-in-out;
+}
+
+a.thumbnail:hover,
+a.thumbnail:focus {
+ border-color: #0088cc;
+ -webkit-box-shadow: 0 1px 4px rgba(0, 105, 214, 0.25);
+ -moz-box-shadow: 0 1px 4px rgba(0, 105, 214, 0.25);
+ box-shadow: 0 1px 4px rgba(0, 105, 214, 0.25);
+}
+
+.thumbnail > img {
+ display: block;
+ max-width: 100%;
+ margin-right: auto;
+ margin-left: auto;
+}
+
+.thumbnail .caption {
+ padding: 9px;
+ color: #555555;
+}
+
+.media,
+.media-body {
+ overflow: hidden;
+ *overflow: visible;
+ zoom: 1;
+}
+
+.media,
+.media .media {
+ margin-top: 15px;
+}
+
+.media:first-child {
+ margin-top: 0;
+}
+
+.media-object {
+ display: block;
+}
+
+.media-heading {
+ margin: 0 0 5px;
+}
+
+.media > .pull-left {
+ margin-right: 10px;
+}
+
+.media > .pull-right {
+ margin-left: 10px;
+}
+
+.media-list {
+ margin-left: 0;
+ list-style: none;
+}
+
+.label,
+.badge {
+ display: inline-block;
+ padding: 2px 4px;
+ font-size: 11.844px;
+ font-weight: bold;
+ line-height: 14px;
+ color: #ffffff;
+ text-shadow: 0 -1px 0 rgba(0, 0, 0, 0.25);
+ white-space: nowrap;
+ vertical-align: baseline;
+ background-color: #999999;
+}
+
+.label {
+ -webkit-border-radius: 3px;
+ -moz-border-radius: 3px;
+ border-radius: 3px;
+}
+
+.badge {
+ padding-right: 9px;
+ padding-left: 9px;
+ -webkit-border-radius: 9px;
+ -moz-border-radius: 9px;
+ border-radius: 9px;
+}
+
+.label:empty,
+.badge:empty {
+ display: none;
+}
+
+a.label:hover,
+a.label:focus,
+a.badge:hover,
+a.badge:focus {
+ color: #ffffff;
+ text-decoration: none;
+ cursor: pointer;
+}
+
+.label-important,
+.badge-important {
+ background-color: #b94a48;
+}
+
+.label-important[href],
+.badge-important[href] {
+ background-color: #953b39;
+}
+
+.label-warning,
+.badge-warning {
+ background-color: #f89406;
+}
+
+.label-warning[href],
+.badge-warning[href] {
+ background-color: #c67605;
+}
+
+.label-success,
+.badge-success {
+ background-color: #468847;
+}
+
+.label-success[href],
+.badge-success[href] {
+ background-color: #356635;
+}
+
+.label-info,
+.badge-info {
+ background-color: #3a87ad;
+}
+
+.label-info[href],
+.badge-info[href] {
+ background-color: #2d6987;
+}
+
+.label-inverse,
+.badge-inverse {
+ background-color: #333333;
+}
+
+.label-inverse[href],
+.badge-inverse[href] {
+ background-color: #1a1a1a;
+}
+
+.btn .label,
+.btn .badge {
+ position: relative;
+ top: -1px;
+}
+
+.btn-mini .label,
+.btn-mini .badge {
+ top: 0;
+}
+
+@-webkit-keyframes progress-bar-stripes {
+ from {
+ background-position: 40px 0;
+ }
+ to {
+ background-position: 0 0;
+ }
+}
+
+@-moz-keyframes progress-bar-stripes {
+ from {
+ background-position: 40px 0;
+ }
+ to {
+ background-position: 0 0;
+ }
+}
+
+@-ms-keyframes progress-bar-stripes {
+ from {
+ background-position: 40px 0;
+ }
+ to {
+ background-position: 0 0;
+ }
+}
+
+@-o-keyframes progress-bar-stripes {
+ from {
+ background-position: 0 0;
+ }
+ to {
+ background-position: 40px 0;
+ }
+}
+
+@keyframes progress-bar-stripes {
+ from {
+ background-position: 40px 0;
+ }
+ to {
+ background-position: 0 0;
+ }
+}
+
+.progress {
+ height: 20px;
+ margin-bottom: 20px;
+ overflow: hidden;
+ background-color: #f7f7f7;
+ background-image: -moz-linear-gradient(top, #f5f5f5, #f9f9f9);
+ background-image: -webkit-gradient(linear, 0 0, 0 100%, from(#f5f5f5), to(#f9f9f9));
+ background-image: -webkit-linear-gradient(top, #f5f5f5, #f9f9f9);
+ background-image: -o-linear-gradient(top, #f5f5f5, #f9f9f9);
+ background-image: linear-gradient(to bottom, #f5f5f5, #f9f9f9);
+ background-repeat: repeat-x;
+ -webkit-border-radius: 4px;
+ -moz-border-radius: 4px;
+ border-radius: 4px;
+ filter: progid:DXImageTransform.Microsoft.gradient(startColorstr='#fff5f5f5', endColorstr='#fff9f9f9', GradientType=0);
+ -webkit-box-shadow: inset 0 1px 2px rgba(0, 0, 0, 0.1);
+ -moz-box-shadow: inset 0 1px 2px rgba(0, 0, 0, 0.1);
+ box-shadow: inset 0 1px 2px rgba(0, 0, 0, 0.1);
+}
+
+.progress .bar {
+ float: left;
+ width: 0;
+ height: 100%;
+ font-size: 12px;
+ color: #ffffff;
+ text-align: center;
+ text-shadow: 0 -1px 0 rgba(0, 0, 0, 0.25);
+ background-color: #0e90d2;
+ background-image: -moz-linear-gradient(top, #149bdf, #0480be);
+ background-image: -webkit-gradient(linear, 0 0, 0 100%, from(#149bdf), to(#0480be));
+ background-image: -webkit-linear-gradient(top, #149bdf, #0480be);
+ background-image: -o-linear-gradient(top, #149bdf, #0480be);
+ background-image: linear-gradient(to bottom, #149bdf, #0480be);
+ background-repeat: repeat-x;
+ filter: progid:DXImageTransform.Microsoft.gradient(startColorstr='#ff149bdf', endColorstr='#ff0480be', GradientType=0);
+ -webkit-box-shadow: inset 0 -1px 0 rgba(0, 0, 0, 0.15);
+ -moz-box-shadow: inset 0 -1px 0 rgba(0, 0, 0, 0.15);
+ box-shadow: inset 0 -1px 0 rgba(0, 0, 0, 0.15);
+ -webkit-box-sizing: border-box;
+ -moz-box-sizing: border-box;
+ box-sizing: border-box;
+ -webkit-transition: width 0.6s ease;
+ -moz-transition: width 0.6s ease;
+ -o-transition: width 0.6s ease;
+ transition: width 0.6s ease;
+}
+
+.progress .bar + .bar {
+ -webkit-box-shadow: inset 1px 0 0 rgba(0, 0, 0, 0.15), inset 0 -1px 0 rgba(0, 0, 0, 0.15);
+ -moz-box-shadow: inset 1px 0 0 rgba(0, 0, 0, 0.15), inset 0 -1px 0 rgba(0, 0, 0, 0.15);
+ box-shadow: inset 1px 0 0 rgba(0, 0, 0, 0.15), inset 0 -1px 0 rgba(0, 0, 0, 0.15);
+}
+
+.progress-striped .bar {
+ background-color: #149bdf;
+ background-image: -webkit-gradient(linear, 0 100%, 100% 0, color-stop(0.25, rgba(255, 255, 255, 0.15)), color-stop(0.25, transparent), color-stop(0.5, transparent), color-stop(0.5, rgba(255, 255, 255, 0.15)), color-stop(0.75, rgba(255, 255, 255, 0.15)), color-stop(0.75, transparent), to(transparent));
+ background-image: -webkit-linear-gradient(45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent);
+ background-image: -moz-linear-gradient(45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent);
+ background-image: -o-linear-gradient(45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent);
+ background-image: linear-gradient(45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent);
+ -webkit-background-size: 40px 40px;
+ -moz-background-size: 40px 40px;
+ -o-background-size: 40px 40px;
+ background-size: 40px 40px;
+}
+
+.progress.active .bar {
+ -webkit-animation: progress-bar-stripes 2s linear infinite;
+ -moz-animation: progress-bar-stripes 2s linear infinite;
+ -ms-animation: progress-bar-stripes 2s linear infinite;
+ -o-animation: progress-bar-stripes 2s linear infinite;
+ animation: progress-bar-stripes 2s linear infinite;
+}
+
+.progress-danger .bar,
+.progress .bar-danger {
+ background-color: #dd514c;
+ background-image: -moz-linear-gradient(top, #ee5f5b, #c43c35);
+ background-image: -webkit-gradient(linear, 0 0, 0 100%, from(#ee5f5b), to(#c43c35));
+ background-image: -webkit-linear-gradient(top, #ee5f5b, #c43c35);
+ background-image: -o-linear-gradient(top, #ee5f5b, #c43c35);
+ background-image: linear-gradient(to bottom, #ee5f5b, #c43c35);
+ background-repeat: repeat-x;
+ filter: progid:DXImageTransform.Microsoft.gradient(startColorstr='#ffee5f5b', endColorstr='#ffc43c35', GradientType=0);
+}
+
+.progress-danger.progress-striped .bar,
+.progress-striped .bar-danger {
+ background-color: #ee5f5b;
+ background-image: -webkit-gradient(linear, 0 100%, 100% 0, color-stop(0.25, rgba(255, 255, 255, 0.15)), color-stop(0.25, transparent), color-stop(0.5, transparent), color-stop(0.5, rgba(255, 255, 255, 0.15)), color-stop(0.75, rgba(255, 255, 255, 0.15)), color-stop(0.75, transparent), to(transparent));
+ background-image: -webkit-linear-gradient(45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent);
+ background-image: -moz-linear-gradient(45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent);
+ background-image: -o-linear-gradient(45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent);
+ background-image: linear-gradient(45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent);
+}
+
+.progress-success .bar,
+.progress .bar-success {
+ background-color: #5eb95e;
+ background-image: -moz-linear-gradient(top, #62c462, #57a957);
+ background-image: -webkit-gradient(linear, 0 0, 0 100%, from(#62c462), to(#57a957));
+ background-image: -webkit-linear-gradient(top, #62c462, #57a957);
+ background-image: -o-linear-gradient(top, #62c462, #57a957);
+ background-image: linear-gradient(to bottom, #62c462, #57a957);
+ background-repeat: repeat-x;
+ filter: progid:DXImageTransform.Microsoft.gradient(startColorstr='#ff62c462', endColorstr='#ff57a957', GradientType=0);
+}
+
+.progress-success.progress-striped .bar,
+.progress-striped .bar-success {
+ background-color: #62c462;
+ background-image: -webkit-gradient(linear, 0 100%, 100% 0, color-stop(0.25, rgba(255, 255, 255, 0.15)), color-stop(0.25, transparent), color-stop(0.5, transparent), color-stop(0.5, rgba(255, 255, 255, 0.15)), color-stop(0.75, rgba(255, 255, 255, 0.15)), color-stop(0.75, transparent), to(transparent));
+ background-image: -webkit-linear-gradient(45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent);
+ background-image: -moz-linear-gradient(45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent);
+ background-image: -o-linear-gradient(45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent);
+ background-image: linear-gradient(45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent);
+}
+
+.progress-info .bar,
+.progress .bar-info {
+ background-color: #4bb1cf;
+ background-image: -moz-linear-gradient(top, #5bc0de, #339bb9);
+ background-image: -webkit-gradient(linear, 0 0, 0 100%, from(#5bc0de), to(#339bb9));
+ background-image: -webkit-linear-gradient(top, #5bc0de, #339bb9);
+ background-image: -o-linear-gradient(top, #5bc0de, #339bb9);
+ background-image: linear-gradient(to bottom, #5bc0de, #339bb9);
+ background-repeat: repeat-x;
+ filter: progid:DXImageTransform.Microsoft.gradient(startColorstr='#ff5bc0de', endColorstr='#ff339bb9', GradientType=0);
+}
+
+.progress-info.progress-striped .bar,
+.progress-striped .bar-info {
+ background-color: #5bc0de;
+ background-image: -webkit-gradient(linear, 0 100%, 100% 0, color-stop(0.25, rgba(255, 255, 255, 0.15)), color-stop(0.25, transparent), color-stop(0.5, transparent), color-stop(0.5, rgba(255, 255, 255, 0.15)), color-stop(0.75, rgba(255, 255, 255, 0.15)), color-stop(0.75, transparent), to(transparent));
+ background-image: -webkit-linear-gradient(45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent);
+ background-image: -moz-linear-gradient(45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent);
+ background-image: -o-linear-gradient(45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent);
+ background-image: linear-gradient(45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent);
+}
+
+.progress-warning .bar,
+.progress .bar-warning {
+ background-color: #faa732;
+ background-image: -moz-linear-gradient(top, #fbb450, #f89406);
+ background-image: -webkit-gradient(linear, 0 0, 0 100%, from(#fbb450), to(#f89406));
+ background-image: -webkit-linear-gradient(top, #fbb450, #f89406);
+ background-image: -o-linear-gradient(top, #fbb450, #f89406);
+ background-image: linear-gradient(to bottom, #fbb450, #f89406);
+ background-repeat: repeat-x;
+ filter: progid:DXImageTransform.Microsoft.gradient(startColorstr='#fffbb450', endColorstr='#fff89406', GradientType=0);
+}
+
+.progress-warning.progress-striped .bar,
+.progress-striped .bar-warning {
+ background-color: #fbb450;
+ background-image: -webkit-gradient(linear, 0 100%, 100% 0, color-stop(0.25, rgba(255, 255, 255, 0.15)), color-stop(0.25, transparent), color-stop(0.5, transparent), color-stop(0.5, rgba(255, 255, 255, 0.15)), color-stop(0.75, rgba(255, 255, 255, 0.15)), color-stop(0.75, transparent), to(transparent));
+ background-image: -webkit-linear-gradient(45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent);
+ background-image: -moz-linear-gradient(45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent);
+ background-image: -o-linear-gradient(45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent);
+ background-image: linear-gradient(45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent);
+}
+
+.accordion {
+ margin-bottom: 20px;
+}
+
+.accordion-group {
+ margin-bottom: 2px;
+ border: 1px solid #e5e5e5;
+ -webkit-border-radius: 4px;
+ -moz-border-radius: 4px;
+ border-radius: 4px;
+}
+
+.accordion-heading {
+ border-bottom: 0;
+}
+
+.accordion-heading .accordion-toggle {
+ display: block;
+ padding: 8px 15px;
+}
+
+.accordion-toggle {
+ cursor: pointer;
+}
+
+.accordion-inner {
+ padding: 9px 15px;
+ border-top: 1px solid #e5e5e5;
+}
+
+.carousel {
+ position: relative;
+ margin-bottom: 20px;
+ line-height: 1;
+}
+
+.carousel-inner {
+ position: relative;
+ width: 100%;
+ overflow: hidden;
+}
+
+.carousel-inner > .item {
+ position: relative;
+ display: none;
+ -webkit-transition: 0.6s ease-in-out left;
+ -moz-transition: 0.6s ease-in-out left;
+ -o-transition: 0.6s ease-in-out left;
+ transition: 0.6s ease-in-out left;
+}
+
+.carousel-inner > .item > img,
+.carousel-inner > .item > a > img {
+ display: block;
+ line-height: 1;
+}
+
+.carousel-inner > .active,
+.carousel-inner > .next,
+.carousel-inner > .prev {
+ display: block;
+}
+
+.carousel-inner > .active {
+ left: 0;
+}
+
+.carousel-inner > .next,
+.carousel-inner > .prev {
+ position: absolute;
+ top: 0;
+ width: 100%;
+}
+
+.carousel-inner > .next {
+ left: 100%;
+}
+
+.carousel-inner > .prev {
+ left: -100%;
+}
+
+.carousel-inner > .next.left,
+.carousel-inner > .prev.right {
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diff --git a/docs/build/html/_static/bootstrap-2.3.2/css/bootstrap.min.css b/docs/build/html/_static/bootstrap-2.3.2/css/bootstrap.min.css
new file mode 100644
index 0000000000000000000000000000000000000000..b6428e695860151f82076e87810fe2d133339c2a
--- /dev/null
+++ b/docs/build/html/_static/bootstrap-2.3.2/css/bootstrap.min.css
@@ -0,0 +1,9 @@
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.bar-danger{background-color:#ee5f5b;background-image:-webkit-gradient(linear,0 100%,100% 0,color-stop(0.25,rgba(255,255,255,0.15)),color-stop(0.25,transparent),color-stop(0.5,transparent),color-stop(0.5,rgba(255,255,255,0.15)),color-stop(0.75,rgba(255,255,255,0.15)),color-stop(0.75,transparent),to(transparent));background-image:-webkit-linear-gradient(45deg,rgba(255,255,255,0.15) 25%,transparent 25%,transparent 50%,rgba(255,255,255,0.15) 50%,rgba(255,255,255,0.15) 75%,transparent 75%,transparent);background-image:-moz-linear-gradient(45deg,rgba(255,255,255,0.15) 25%,transparent 25%,transparent 50%,rgba(255,255,255,0.15) 50%,rgba(255,255,255,0.15) 75%,transparent 75%,transparent);background-image:-o-linear-gradient(45deg,rgba(255,255,255,0.15) 25%,transparent 25%,transparent 50%,rgba(255,255,255,0.15) 50%,rgba(255,255,255,0.15) 75%,transparent 75%,transparent);background-image:linear-gradient(45deg,rgba(255,255,255,0.15) 25%,transparent 25%,transparent 50%,rgba(255,255,255,0.15) 50%,rgba(255,255,255,0.15) 75%,transparent 75%,transparent)}.progress-success .bar,.progress .bar-success{background-color:#5eb95e;background-image:-moz-linear-gradient(top,#62c462,#57a957);background-image:-webkit-gradient(linear,0 0,0 100%,from(#62c462),to(#57a957));background-image:-webkit-linear-gradient(top,#62c462,#57a957);background-image:-o-linear-gradient(top,#62c462,#57a957);background-image:linear-gradient(to bottom,#62c462,#57a957);background-repeat:repeat-x;filter:progid:DXImageTransform.Microsoft.gradient(startColorstr='#ff62c462',endColorstr='#ff57a957',GradientType=0)}.progress-success.progress-striped .bar,.progress-striped .bar-success{background-color:#62c462;background-image:-webkit-gradient(linear,0 100%,100% 0,color-stop(0.25,rgba(255,255,255,0.15)),color-stop(0.25,transparent),color-stop(0.5,transparent),color-stop(0.5,rgba(255,255,255,0.15)),color-stop(0.75,rgba(255,255,255,0.15)),color-stop(0.75,transparent),to(transparent));background-image:-webkit-linear-gradient(45deg,rgba(255,255,255,0.15) 25%,transparent 25%,transparent 50%,rgba(255,255,255,0.15) 50%,rgba(255,255,255,0.15) 75%,transparent 75%,transparent);background-image:-moz-linear-gradient(45deg,rgba(255,255,255,0.15) 25%,transparent 25%,transparent 50%,rgba(255,255,255,0.15) 50%,rgba(255,255,255,0.15) 75%,transparent 75%,transparent);background-image:-o-linear-gradient(45deg,rgba(255,255,255,0.15) 25%,transparent 25%,transparent 50%,rgba(255,255,255,0.15) 50%,rgba(255,255,255,0.15) 75%,transparent 75%,transparent);background-image:linear-gradient(45deg,rgba(255,255,255,0.15) 25%,transparent 25%,transparent 50%,rgba(255,255,255,0.15) 50%,rgba(255,255,255,0.15) 75%,transparent 75%,transparent)}.progress-info .bar,.progress .bar-info{background-color:#4bb1cf;background-image:-moz-linear-gradient(top,#5bc0de,#339bb9);background-image:-webkit-gradient(linear,0 0,0 100%,from(#5bc0de),to(#339bb9));background-image:-webkit-linear-gradient(top,#5bc0de,#339bb9);background-image:-o-linear-gradient(top,#5bc0de,#339bb9);background-image:linear-gradient(to bottom,#5bc0de,#339bb9);background-repeat:repeat-x;filter:progid:DXImageTransform.Microsoft.gradient(startColorstr='#ff5bc0de',endColorstr='#ff339bb9',GradientType=0)}.progress-info.progress-striped .bar,.progress-striped .bar-info{background-color:#5bc0de;background-image:-webkit-gradient(linear,0 100%,100% 0,color-stop(0.25,rgba(255,255,255,0.15)),color-stop(0.25,transparent),color-stop(0.5,transparent),color-stop(0.5,rgba(255,255,255,0.15)),color-stop(0.75,rgba(255,255,255,0.15)),color-stop(0.75,transparent),to(transparent));background-image:-webkit-linear-gradient(45deg,rgba(255,255,255,0.15) 25%,transparent 25%,transparent 50%,rgba(255,255,255,0.15) 50%,rgba(255,255,255,0.15) 75%,transparent 75%,transparent);background-image:-moz-linear-gradient(45deg,rgba(255,255,255,0.15) 25%,transparent 25%,transparent 50%,rgba(255,255,255,0.15) 50%,rgba(255,255,255,0.15) 75%,transparent 75%,transparent);background-image:-o-linear-gradient(45deg,rgba(255,255,255,0.15) 25%,transparent 25%,transparent 50%,rgba(255,255,255,0.15) 50%,rgba(255,255,255,0.15) 75%,transparent 75%,transparent);background-image:linear-gradient(45deg,rgba(255,255,255,0.15) 25%,transparent 25%,transparent 50%,rgba(255,255,255,0.15) 50%,rgba(255,255,255,0.15) 75%,transparent 75%,transparent)}.progress-warning .bar,.progress .bar-warning{background-color:#faa732;background-image:-moz-linear-gradient(top,#fbb450,#f89406);background-image:-webkit-gradient(linear,0 0,0 100%,from(#fbb450),to(#f89406));background-image:-webkit-linear-gradient(top,#fbb450,#f89406);background-image:-o-linear-gradient(top,#fbb450,#f89406);background-image:linear-gradient(to bottom,#fbb450,#f89406);background-repeat:repeat-x;filter:progid:DXImageTransform.Microsoft.gradient(startColorstr='#fffbb450',endColorstr='#fff89406',GradientType=0)}.progress-warning.progress-striped .bar,.progress-striped .bar-warning{background-color:#fbb450;background-image:-webkit-gradient(linear,0 100%,100% 0,color-stop(0.25,rgba(255,255,255,0.15)),color-stop(0.25,transparent),color-stop(0.5,transparent),color-stop(0.5,rgba(255,255,255,0.15)),color-stop(0.75,rgba(255,255,255,0.15)),color-stop(0.75,transparent),to(transparent));background-image:-webkit-linear-gradient(45deg,rgba(255,255,255,0.15) 25%,transparent 25%,transparent 50%,rgba(255,255,255,0.15) 50%,rgba(255,255,255,0.15) 75%,transparent 75%,transparent);background-image:-moz-linear-gradient(45deg,rgba(255,255,255,0.15) 25%,transparent 25%,transparent 50%,rgba(255,255,255,0.15) 50%,rgba(255,255,255,0.15) 75%,transparent 75%,transparent);background-image:-o-linear-gradient(45deg,rgba(255,255,255,0.15) 25%,transparent 25%,transparent 50%,rgba(255,255,255,0.15) 50%,rgba(255,255,255,0.15) 75%,transparent 75%,transparent);background-image:linear-gradient(45deg,rgba(255,255,255,0.15) 25%,transparent 25%,transparent 50%,rgba(255,255,255,0.15) 50%,rgba(255,255,255,0.15) 75%,transparent 75%,transparent)}.accordion{margin-bottom:20px}.accordion-group{margin-bottom:2px;border:1px solid #e5e5e5;-webkit-border-radius:4px;-moz-border-radius:4px;border-radius:4px}.accordion-heading{border-bottom:0}.accordion-heading .accordion-toggle{display:block;padding:8px 15px}.accordion-toggle{cursor:pointer}.accordion-inner{padding:9px 15px;border-top:1px solid #e5e5e5}.carousel{position:relative;margin-bottom:20px;line-height:1}.carousel-inner{position:relative;width:100%;overflow:hidden}.carousel-inner>.item{position:relative;display:none;-webkit-transition:.6s ease-in-out left;-moz-transition:.6s ease-in-out left;-o-transition:.6s ease-in-out left;transition:.6s ease-in-out left}.carousel-inner>.item>img,.carousel-inner>.item>a>img{display:block;line-height:1}.carousel-inner>.active,.carousel-inner>.next,.carousel-inner>.prev{display:block}.carousel-inner>.active{left:0}.carousel-inner>.next,.carousel-inner>.prev{position:absolute;top:0;width:100%}.carousel-inner>.next{left:100%}.carousel-inner>.prev{left:-100%}.carousel-inner>.next.left,.carousel-inner>.prev.right{left:0}.carousel-inner>.active.left{left:-100%}.carousel-inner>.active.right{left:100%}.carousel-control{position:absolute;top:40%;left:15px;width:40px;height:40px;margin-top:-20px;font-size:60px;font-weight:100;line-height:30px;color:#fff;text-align:center;background:#222;border:3px solid #fff;-webkit-border-radius:23px;-moz-border-radius:23px;border-radius:23px;opacity:.5;filter:alpha(opacity=50)}.carousel-control.right{right:15px;left:auto}.carousel-control:hover,.carousel-control:focus{color:#fff;text-decoration:none;opacity:.9;filter:alpha(opacity=90)}.carousel-indicators{position:absolute;top:15px;right:15px;z-index:5;margin:0;list-style:none}.carousel-indicators li{display:block;float:left;width:10px;height:10px;margin-left:5px;text-indent:-999px;background-color:#ccc;background-color:rgba(255,255,255,0.25);border-radius:5px}.carousel-indicators .active{background-color:#fff}.carousel-caption{position:absolute;right:0;bottom:0;left:0;padding:15px;background:#333;background:rgba(0,0,0,0.75)}.carousel-caption h4,.carousel-caption p{line-height:20px;color:#fff}.carousel-caption h4{margin:0 0 5px}.carousel-caption p{margin-bottom:0}.hero-unit{padding:60px;margin-bottom:30px;font-size:18px;font-weight:200;line-height:30px;color:inherit;background-color:#eee;-webkit-border-radius:6px;-moz-border-radius:6px;border-radius:6px}.hero-unit h1{margin-bottom:0;font-size:60px;line-height:1;letter-spacing:-1px;color:inherit}.hero-unit li{line-height:30px}.pull-right{float:right}.pull-left{float:left}.hide{display:none}.show{display:block}.invisible{visibility:hidden}.affix{position:fixed}
diff --git a/docs/build/html/_static/bootstrap-2.3.2/img/glyphicons-halflings-white.png b/docs/build/html/_static/bootstrap-2.3.2/img/glyphicons-halflings-white.png
new file mode 100644
index 0000000000000000000000000000000000000000..3bf6484a29d8da269f9bc874b25493a45fae3bae
Binary files /dev/null and b/docs/build/html/_static/bootstrap-2.3.2/img/glyphicons-halflings-white.png differ
diff --git a/docs/build/html/_static/bootstrap-2.3.2/img/glyphicons-halflings.png b/docs/build/html/_static/bootstrap-2.3.2/img/glyphicons-halflings.png
new file mode 100644
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Binary files /dev/null and b/docs/build/html/_static/bootstrap-2.3.2/img/glyphicons-halflings.png differ
diff --git a/docs/build/html/_static/bootstrap-2.3.2/js/bootstrap.js b/docs/build/html/_static/bootstrap-2.3.2/js/bootstrap.js
new file mode 100644
index 0000000000000000000000000000000000000000..638bb18779550f8656f5f28e11f62bd37354940c
--- /dev/null
+++ b/docs/build/html/_static/bootstrap-2.3.2/js/bootstrap.js
@@ -0,0 +1,2287 @@
+/* ===================================================
+ * bootstrap-transition.js v2.3.2
+ * http://twitter.github.com/bootstrap/javascript.html#transitions
+ * ===================================================
+ * Copyright 2012 Twitter, Inc.
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ * ========================================================== */
+
+
+!function ($) {
+
+ "use strict"; // jshint ;_;
+
+
+ /* CSS TRANSITION SUPPORT (http://www.modernizr.com/)
+ * ======================================================= */
+
+ $(function () {
+
+ $.support.transition = (function () {
+
+ var transitionEnd = (function () {
+
+ var el = document.createElement('bootstrap')
+ , transEndEventNames = {
+ 'WebkitTransition' : 'webkitTransitionEnd'
+ , 'MozTransition' : 'transitionend'
+ , 'OTransition' : 'oTransitionEnd otransitionend'
+ , 'transition' : 'transitionend'
+ }
+ , name
+
+ for (name in transEndEventNames){
+ if (el.style[name] !== undefined) {
+ return transEndEventNames[name]
+ }
+ }
+
+ }())
+
+ return transitionEnd && {
+ end: transitionEnd
+ }
+
+ })()
+
+ })
+
+}(window.$jqTheme || window.jQuery);
+/* ==========================================================
+ * bootstrap-alert.js v2.3.2
+ * http://twitter.github.com/bootstrap/javascript.html#alerts
+ * ==========================================================
+ * Copyright 2012 Twitter, Inc.
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ * ========================================================== */
+
+
+!function ($) {
+
+ "use strict"; // jshint ;_;
+
+
+ /* ALERT CLASS DEFINITION
+ * ====================== */
+
+ var dismiss = '[data-dismiss="alert"]'
+ , Alert = function (el) {
+ $(el).on('click', dismiss, this.close)
+ }
+
+ Alert.prototype.close = function (e) {
+ var $this = $(this)
+ , selector = $this.attr('data-target')
+ , $parent
+
+ if (!selector) {
+ selector = $this.attr('href')
+ selector = selector && selector.replace(/.*(?=#[^\s]*$)/, '') //strip for ie7
+ }
+
+ $parent = $(selector)
+
+ e && e.preventDefault()
+
+ $parent.length || ($parent = $this.hasClass('alert') ? $this : $this.parent())
+
+ $parent.trigger(e = $.Event('close'))
+
+ if (e.isDefaultPrevented()) return
+
+ $parent.removeClass('in')
+
+ function removeElement() {
+ $parent
+ .trigger('closed')
+ .remove()
+ }
+
+ $.support.transition && $parent.hasClass('fade') ?
+ $parent.on($.support.transition.end, removeElement) :
+ removeElement()
+ }
+
+
+ /* ALERT PLUGIN DEFINITION
+ * ======================= */
+
+ var old = $.fn.alert
+
+ $.fn.alert = function (option) {
+ return this.each(function () {
+ var $this = $(this)
+ , data = $this.data('alert')
+ if (!data) $this.data('alert', (data = new Alert(this)))
+ if (typeof option == 'string') data[option].call($this)
+ })
+ }
+
+ $.fn.alert.Constructor = Alert
+
+
+ /* ALERT NO CONFLICT
+ * ================= */
+
+ $.fn.alert.noConflict = function () {
+ $.fn.alert = old
+ return this
+ }
+
+
+ /* ALERT DATA-API
+ * ============== */
+
+ $(document).on('click.alert.data-api', dismiss, Alert.prototype.close)
+
+}(window.$jqTheme || window.jQuery);
+/* ============================================================
+ * bootstrap-button.js v2.3.2
+ * http://twitter.github.com/bootstrap/javascript.html#buttons
+ * ============================================================
+ * Copyright 2012 Twitter, Inc.
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ * ============================================================ */
+
+
+!function ($) {
+
+ "use strict"; // jshint ;_;
+
+
+ /* BUTTON PUBLIC CLASS DEFINITION
+ * ============================== */
+
+ var Button = function (element, options) {
+ this.$element = $(element)
+ this.options = $.extend({}, $.fn.button.defaults, options)
+ }
+
+ Button.prototype.setState = function (state) {
+ var d = 'disabled'
+ , $el = this.$element
+ , data = $el.data()
+ , val = $el.is('input') ? 'val' : 'html'
+
+ state = state + 'Text'
+ data.resetText || $el.data('resetText', $el[val]())
+
+ $el[val](data[state] || this.options[state])
+
+ // push to event loop to allow forms to submit
+ setTimeout(function () {
+ state == 'loadingText' ?
+ $el.addClass(d).attr(d, d) :
+ $el.removeClass(d).removeAttr(d)
+ }, 0)
+ }
+
+ Button.prototype.toggle = function () {
+ var $parent = this.$element.closest('[data-toggle="buttons-radio"]')
+
+ $parent && $parent
+ .find('.active')
+ .removeClass('active')
+
+ this.$element.toggleClass('active')
+ }
+
+
+ /* BUTTON PLUGIN DEFINITION
+ * ======================== */
+
+ var old = $.fn.button
+
+ $.fn.button = function (option) {
+ return this.each(function () {
+ var $this = $(this)
+ , data = $this.data('button')
+ , options = typeof option == 'object' && option
+ if (!data) $this.data('button', (data = new Button(this, options)))
+ if (option == 'toggle') data.toggle()
+ else if (option) data.setState(option)
+ })
+ }
+
+ $.fn.button.defaults = {
+ loadingText: 'loading...'
+ }
+
+ $.fn.button.Constructor = Button
+
+
+ /* BUTTON NO CONFLICT
+ * ================== */
+
+ $.fn.button.noConflict = function () {
+ $.fn.button = old
+ return this
+ }
+
+
+ /* BUTTON DATA-API
+ * =============== */
+
+ $(document).on('click.button.data-api', '[data-toggle^=button]', function (e) {
+ var $btn = $(e.target)
+ if (!$btn.hasClass('btn')) $btn = $btn.closest('.btn')
+ $btn.button('toggle')
+ })
+
+}(window.$jqTheme || window.jQuery);
+/* ==========================================================
+ * bootstrap-carousel.js v2.3.2
+ * http://twitter.github.com/bootstrap/javascript.html#carousel
+ * ==========================================================
+ * Copyright 2012 Twitter, Inc.
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ * ========================================================== */
+
+
+!function ($) {
+
+ "use strict"; // jshint ;_;
+
+
+ /* CAROUSEL CLASS DEFINITION
+ * ========================= */
+
+ var Carousel = function (element, options) {
+ this.$element = $(element)
+ this.$indicators = this.$element.find('.carousel-indicators')
+ this.options = options
+ this.options.pause == 'hover' && this.$element
+ .on('mouseenter', $.proxy(this.pause, this))
+ .on('mouseleave', $.proxy(this.cycle, this))
+ }
+
+ Carousel.prototype = {
+
+ cycle: function (e) {
+ if (!e) this.paused = false
+ if (this.interval) clearInterval(this.interval);
+ this.options.interval
+ && !this.paused
+ && (this.interval = setInterval($.proxy(this.next, this), this.options.interval))
+ return this
+ }
+
+ , getActiveIndex: function () {
+ this.$active = this.$element.find('.item.active')
+ this.$items = this.$active.parent().children()
+ return this.$items.index(this.$active)
+ }
+
+ , to: function (pos) {
+ var activeIndex = this.getActiveIndex()
+ , that = this
+
+ if (pos > (this.$items.length - 1) || pos < 0) return
+
+ if (this.sliding) {
+ return this.$element.one('slid', function () {
+ that.to(pos)
+ })
+ }
+
+ if (activeIndex == pos) {
+ return this.pause().cycle()
+ }
+
+ return this.slide(pos > activeIndex ? 'next' : 'prev', $(this.$items[pos]))
+ }
+
+ , pause: function (e) {
+ if (!e) this.paused = true
+ if (this.$element.find('.next, .prev').length && $.support.transition.end) {
+ this.$element.trigger($.support.transition.end)
+ this.cycle(true)
+ }
+ clearInterval(this.interval)
+ this.interval = null
+ return this
+ }
+
+ , next: function () {
+ if (this.sliding) return
+ return this.slide('next')
+ }
+
+ , prev: function () {
+ if (this.sliding) return
+ return this.slide('prev')
+ }
+
+ , slide: function (type, next) {
+ var $active = this.$element.find('.item.active')
+ , $next = next || $active[type]()
+ , isCycling = this.interval
+ , direction = type == 'next' ? 'left' : 'right'
+ , fallback = type == 'next' ? 'first' : 'last'
+ , that = this
+ , e
+
+ this.sliding = true
+
+ isCycling && this.pause()
+
+ $next = $next.length ? $next : this.$element.find('.item')[fallback]()
+
+ e = $.Event('slide', {
+ relatedTarget: $next[0]
+ , direction: direction
+ })
+
+ if ($next.hasClass('active')) return
+
+ if (this.$indicators.length) {
+ this.$indicators.find('.active').removeClass('active')
+ this.$element.one('slid', function () {
+ var $nextIndicator = $(that.$indicators.children()[that.getActiveIndex()])
+ $nextIndicator && $nextIndicator.addClass('active')
+ })
+ }
+
+ if ($.support.transition && this.$element.hasClass('slide')) {
+ this.$element.trigger(e)
+ if (e.isDefaultPrevented()) return
+ $next.addClass(type)
+ $next[0].offsetWidth // force reflow
+ $active.addClass(direction)
+ $next.addClass(direction)
+ this.$element.one($.support.transition.end, function () {
+ $next.removeClass([type, direction].join(' ')).addClass('active')
+ $active.removeClass(['active', direction].join(' '))
+ that.sliding = false
+ setTimeout(function () { that.$element.trigger('slid') }, 0)
+ })
+ } else {
+ this.$element.trigger(e)
+ if (e.isDefaultPrevented()) return
+ $active.removeClass('active')
+ $next.addClass('active')
+ this.sliding = false
+ this.$element.trigger('slid')
+ }
+
+ isCycling && this.cycle()
+
+ return this
+ }
+
+ }
+
+
+ /* CAROUSEL PLUGIN DEFINITION
+ * ========================== */
+
+ var old = $.fn.carousel
+
+ $.fn.carousel = function (option) {
+ return this.each(function () {
+ var $this = $(this)
+ , data = $this.data('carousel')
+ , options = $.extend({}, $.fn.carousel.defaults, typeof option == 'object' && option)
+ , action = typeof option == 'string' ? option : options.slide
+ if (!data) $this.data('carousel', (data = new Carousel(this, options)))
+ if (typeof option == 'number') data.to(option)
+ else if (action) data[action]()
+ else if (options.interval) data.pause().cycle()
+ })
+ }
+
+ $.fn.carousel.defaults = {
+ interval: 5000
+ , pause: 'hover'
+ }
+
+ $.fn.carousel.Constructor = Carousel
+
+
+ /* CAROUSEL NO CONFLICT
+ * ==================== */
+
+ $.fn.carousel.noConflict = function () {
+ $.fn.carousel = old
+ return this
+ }
+
+ /* CAROUSEL DATA-API
+ * ================= */
+
+ $(document).on('click.carousel.data-api', '[data-slide], [data-slide-to]', function (e) {
+ var $this = $(this), href
+ , $target = $($this.attr('data-target') || (href = $this.attr('href')) && href.replace(/.*(?=#[^\s]+$)/, '')) //strip for ie7
+ , options = $.extend({}, $target.data(), $this.data())
+ , slideIndex
+
+ $target.carousel(options)
+
+ if (slideIndex = $this.attr('data-slide-to')) {
+ $target.data('carousel').pause().to(slideIndex).cycle()
+ }
+
+ e.preventDefault()
+ })
+
+}(window.$jqTheme || window.jQuery);
+/* =============================================================
+ * bootstrap-collapse.js v2.3.2
+ * http://twitter.github.com/bootstrap/javascript.html#collapse
+ * =============================================================
+ * Copyright 2012 Twitter, Inc.
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ * ============================================================ */
+
+
+!function ($) {
+
+ "use strict"; // jshint ;_;
+
+
+ /* COLLAPSE PUBLIC CLASS DEFINITION
+ * ================================ */
+
+ var Collapse = function (element, options) {
+ this.$element = $(element)
+ this.options = $.extend({}, $.fn.collapse.defaults, options)
+
+ if (this.options.parent) {
+ this.$parent = $(this.options.parent)
+ }
+
+ this.options.toggle && this.toggle()
+ }
+
+ Collapse.prototype = {
+
+ constructor: Collapse
+
+ , dimension: function () {
+ var hasWidth = this.$element.hasClass('width')
+ return hasWidth ? 'width' : 'height'
+ }
+
+ , show: function () {
+ var dimension
+ , scroll
+ , actives
+ , hasData
+
+ if (this.transitioning || this.$element.hasClass('in')) return
+
+ dimension = this.dimension()
+ scroll = $.camelCase(['scroll', dimension].join('-'))
+ actives = this.$parent && this.$parent.find('> .accordion-group > .in')
+
+ if (actives && actives.length) {
+ hasData = actives.data('collapse')
+ if (hasData && hasData.transitioning) return
+ actives.collapse('hide')
+ hasData || actives.data('collapse', null)
+ }
+
+ this.$element[dimension](0)
+ this.transition('addClass', $.Event('show'), 'shown')
+ $.support.transition && this.$element[dimension](this.$element[0][scroll])
+ }
+
+ , hide: function () {
+ var dimension
+ if (this.transitioning || !this.$element.hasClass('in')) return
+ dimension = this.dimension()
+ this.reset(this.$element[dimension]())
+ this.transition('removeClass', $.Event('hide'), 'hidden')
+ this.$element[dimension](0)
+ }
+
+ , reset: function (size) {
+ var dimension = this.dimension()
+
+ this.$element
+ .removeClass('collapse')
+ [dimension](size || 'auto')
+ [0].offsetWidth
+
+ this.$element[size !== null ? 'addClass' : 'removeClass']('collapse')
+
+ return this
+ }
+
+ , transition: function (method, startEvent, completeEvent) {
+ var that = this
+ , complete = function () {
+ if (startEvent.type == 'show') that.reset()
+ that.transitioning = 0
+ that.$element.trigger(completeEvent)
+ }
+
+ this.$element.trigger(startEvent)
+
+ if (startEvent.isDefaultPrevented()) return
+
+ this.transitioning = 1
+
+ this.$element[method]('in')
+
+ $.support.transition && this.$element.hasClass('collapse') ?
+ this.$element.one($.support.transition.end, complete) :
+ complete()
+ }
+
+ , toggle: function () {
+ this[this.$element.hasClass('in') ? 'hide' : 'show']()
+ }
+
+ }
+
+
+ /* COLLAPSE PLUGIN DEFINITION
+ * ========================== */
+
+ var old = $.fn.collapse
+
+ $.fn.collapse = function (option) {
+ return this.each(function () {
+ var $this = $(this)
+ , data = $this.data('collapse')
+ , options = $.extend({}, $.fn.collapse.defaults, $this.data(), typeof option == 'object' && option)
+ if (!data) $this.data('collapse', (data = new Collapse(this, options)))
+ if (typeof option == 'string') data[option]()
+ })
+ }
+
+ $.fn.collapse.defaults = {
+ toggle: true
+ }
+
+ $.fn.collapse.Constructor = Collapse
+
+
+ /* COLLAPSE NO CONFLICT
+ * ==================== */
+
+ $.fn.collapse.noConflict = function () {
+ $.fn.collapse = old
+ return this
+ }
+
+
+ /* COLLAPSE DATA-API
+ * ================= */
+
+ $(document).on('click.collapse.data-api', '[data-toggle=collapse]', function (e) {
+ var $this = $(this), href
+ , target = $this.attr('data-target')
+ || e.preventDefault()
+ || (href = $this.attr('href')) && href.replace(/.*(?=#[^\s]+$)/, '') //strip for ie7
+ , option = $(target).data('collapse') ? 'toggle' : $this.data()
+ $this[$(target).hasClass('in') ? 'addClass' : 'removeClass']('collapsed')
+ $(target).collapse(option)
+ })
+
+}(window.$jqTheme || window.jQuery);
+/* ============================================================
+ * bootstrap-dropdown.js v2.3.2
+ * http://twitter.github.com/bootstrap/javascript.html#dropdowns
+ * ============================================================
+ * Copyright 2012 Twitter, Inc.
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ * ============================================================ */
+
+
+!function ($) {
+
+ "use strict"; // jshint ;_;
+
+
+ /* DROPDOWN CLASS DEFINITION
+ * ========================= */
+
+ var toggle = '[data-toggle=dropdown]'
+ , Dropdown = function (element) {
+ var $el = $(element).on('click.dropdown.data-api', this.toggle)
+ $('html').on('click.dropdown.data-api', function () {
+ $el.parent().removeClass('open')
+ })
+ }
+
+ Dropdown.prototype = {
+
+ constructor: Dropdown
+
+ , toggle: function (e) {
+ var $this = $(this)
+ , $parent
+ , isActive
+
+ if ($this.is('.disabled, :disabled')) return
+
+ $parent = getParent($this)
+
+ isActive = $parent.hasClass('open')
+
+ clearMenus()
+
+ if (!isActive) {
+ if ('ontouchstart' in document.documentElement) {
+ // if mobile we we use a backdrop because click events don't delegate
+ $('<div class="dropdown-backdrop"/>').insertBefore($(this)).on('click', clearMenus)
+ }
+ $parent.toggleClass('open')
+ }
+
+ $this.focus()
+
+ return false
+ }
+
+ , keydown: function (e) {
+ var $this
+ , $items
+ , $active
+ , $parent
+ , isActive
+ , index
+
+ if (!/(38|40|27)/.test(e.keyCode)) return
+
+ $this = $(this)
+
+ e.preventDefault()
+ e.stopPropagation()
+
+ if ($this.is('.disabled, :disabled')) return
+
+ $parent = getParent($this)
+
+ isActive = $parent.hasClass('open')
+
+ if (!isActive || (isActive && e.keyCode == 27)) {
+ if (e.which == 27) $parent.find(toggle).focus()
+ return $this.click()
+ }
+
+ $items = $('[role=menu] li:not(.divider):visible a', $parent)
+
+ if (!$items.length) return
+
+ index = $items.index($items.filter(':focus'))
+
+ if (e.keyCode == 38 && index > 0) index-- // up
+ if (e.keyCode == 40 && index < $items.length - 1) index++ // down
+ if (!~index) index = 0
+
+ $items
+ .eq(index)
+ .focus()
+ }
+
+ }
+
+ function clearMenus() {
+ $('.dropdown-backdrop').remove()
+ $(toggle).each(function () {
+ getParent($(this)).removeClass('open')
+ })
+ }
+
+ function getParent($this) {
+ var selector = $this.attr('data-target')
+ , $parent
+
+ if (!selector) {
+ selector = $this.attr('href')
+ selector = selector && /#/.test(selector) && selector.replace(/.*(?=#[^\s]*$)/, '') //strip for ie7
+ }
+
+ $parent = selector && $(selector)
+
+ if (!$parent || !$parent.length) $parent = $this.parent()
+
+ return $parent
+ }
+
+
+ /* DROPDOWN PLUGIN DEFINITION
+ * ========================== */
+
+ var old = $.fn.dropdown
+
+ $.fn.dropdown = function (option) {
+ return this.each(function () {
+ var $this = $(this)
+ , data = $this.data('dropdown')
+ if (!data) $this.data('dropdown', (data = new Dropdown(this)))
+ if (typeof option == 'string') data[option].call($this)
+ })
+ }
+
+ $.fn.dropdown.Constructor = Dropdown
+
+
+ /* DROPDOWN NO CONFLICT
+ * ==================== */
+
+ $.fn.dropdown.noConflict = function () {
+ $.fn.dropdown = old
+ return this
+ }
+
+
+ /* APPLY TO STANDARD DROPDOWN ELEMENTS
+ * =================================== */
+
+ $(document)
+ .on('click.dropdown.data-api', clearMenus)
+ .on('click.dropdown.data-api', '.dropdown form', function (e) { e.stopPropagation() })
+ .on('click.dropdown.data-api' , toggle, Dropdown.prototype.toggle)
+ .on('keydown.dropdown.data-api', toggle + ', [role=menu]' , Dropdown.prototype.keydown)
+
+}(window.$jqTheme || window.jQuery);
+/* =========================================================
+ * bootstrap-modal.js v2.3.2
+ * http://twitter.github.com/bootstrap/javascript.html#modals
+ * =========================================================
+ * Copyright 2012 Twitter, Inc.
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ * ========================================================= */
+
+
+!function ($) {
+
+ "use strict"; // jshint ;_;
+
+
+ /* MODAL CLASS DEFINITION
+ * ====================== */
+
+ var Modal = function (element, options) {
+ this.options = options
+ this.$element = $(element)
+ .delegate('[data-dismiss="modal"]', 'click.dismiss.modal', $.proxy(this.hide, this))
+ this.options.remote && this.$element.find('.modal-body').load(this.options.remote)
+ }
+
+ Modal.prototype = {
+
+ constructor: Modal
+
+ , toggle: function () {
+ return this[!this.isShown ? 'show' : 'hide']()
+ }
+
+ , show: function () {
+ var that = this
+ , e = $.Event('show')
+
+ this.$element.trigger(e)
+
+ if (this.isShown || e.isDefaultPrevented()) return
+
+ this.isShown = true
+
+ this.escape()
+
+ this.backdrop(function () {
+ var transition = $.support.transition && that.$element.hasClass('fade')
+
+ if (!that.$element.parent().length) {
+ that.$element.appendTo(document.body) //don't move modals dom position
+ }
+
+ that.$element.show()
+
+ if (transition) {
+ that.$element[0].offsetWidth // force reflow
+ }
+
+ that.$element
+ .addClass('in')
+ .attr('aria-hidden', false)
+
+ that.enforceFocus()
+
+ transition ?
+ that.$element.one($.support.transition.end, function () { that.$element.focus().trigger('shown') }) :
+ that.$element.focus().trigger('shown')
+
+ })
+ }
+
+ , hide: function (e) {
+ e && e.preventDefault()
+
+ var that = this
+
+ e = $.Event('hide')
+
+ this.$element.trigger(e)
+
+ if (!this.isShown || e.isDefaultPrevented()) return
+
+ this.isShown = false
+
+ this.escape()
+
+ $(document).off('focusin.modal')
+
+ this.$element
+ .removeClass('in')
+ .attr('aria-hidden', true)
+
+ $.support.transition && this.$element.hasClass('fade') ?
+ this.hideWithTransition() :
+ this.hideModal()
+ }
+
+ , enforceFocus: function () {
+ var that = this
+ $(document).on('focusin.modal', function (e) {
+ if (that.$element[0] !== e.target && !that.$element.has(e.target).length) {
+ that.$element.focus()
+ }
+ })
+ }
+
+ , escape: function () {
+ var that = this
+ if (this.isShown && this.options.keyboard) {
+ this.$element.on('keyup.dismiss.modal', function ( e ) {
+ e.which == 27 && that.hide()
+ })
+ } else if (!this.isShown) {
+ this.$element.off('keyup.dismiss.modal')
+ }
+ }
+
+ , hideWithTransition: function () {
+ var that = this
+ , timeout = setTimeout(function () {
+ that.$element.off($.support.transition.end)
+ that.hideModal()
+ }, 500)
+
+ this.$element.one($.support.transition.end, function () {
+ clearTimeout(timeout)
+ that.hideModal()
+ })
+ }
+
+ , hideModal: function () {
+ var that = this
+ this.$element.hide()
+ this.backdrop(function () {
+ that.removeBackdrop()
+ that.$element.trigger('hidden')
+ })
+ }
+
+ , removeBackdrop: function () {
+ this.$backdrop && this.$backdrop.remove()
+ this.$backdrop = null
+ }
+
+ , backdrop: function (callback) {
+ var that = this
+ , animate = this.$element.hasClass('fade') ? 'fade' : ''
+
+ if (this.isShown && this.options.backdrop) {
+ var doAnimate = $.support.transition && animate
+
+ this.$backdrop = $('<div class="modal-backdrop ' + animate + '" />')
+ .appendTo(document.body)
+
+ this.$backdrop.click(
+ this.options.backdrop == 'static' ?
+ $.proxy(this.$element[0].focus, this.$element[0])
+ : $.proxy(this.hide, this)
+ )
+
+ if (doAnimate) this.$backdrop[0].offsetWidth // force reflow
+
+ this.$backdrop.addClass('in')
+
+ if (!callback) return
+
+ doAnimate ?
+ this.$backdrop.one($.support.transition.end, callback) :
+ callback()
+
+ } else if (!this.isShown && this.$backdrop) {
+ this.$backdrop.removeClass('in')
+
+ $.support.transition && this.$element.hasClass('fade')?
+ this.$backdrop.one($.support.transition.end, callback) :
+ callback()
+
+ } else if (callback) {
+ callback()
+ }
+ }
+ }
+
+
+ /* MODAL PLUGIN DEFINITION
+ * ======================= */
+
+ var old = $.fn.modal
+
+ $.fn.modal = function (option) {
+ return this.each(function () {
+ var $this = $(this)
+ , data = $this.data('modal')
+ , options = $.extend({}, $.fn.modal.defaults, $this.data(), typeof option == 'object' && option)
+ if (!data) $this.data('modal', (data = new Modal(this, options)))
+ if (typeof option == 'string') data[option]()
+ else if (options.show) data.show()
+ })
+ }
+
+ $.fn.modal.defaults = {
+ backdrop: true
+ , keyboard: true
+ , show: true
+ }
+
+ $.fn.modal.Constructor = Modal
+
+
+ /* MODAL NO CONFLICT
+ * ================= */
+
+ $.fn.modal.noConflict = function () {
+ $.fn.modal = old
+ return this
+ }
+
+
+ /* MODAL DATA-API
+ * ============== */
+
+ $(document).on('click.modal.data-api', '[data-toggle="modal"]', function (e) {
+ var $this = $(this)
+ , href = $this.attr('href')
+ , $target = $($this.attr('data-target') || (href && href.replace(/.*(?=#[^\s]+$)/, ''))) //strip for ie7
+ , option = $target.data('modal') ? 'toggle' : $.extend({ remote:!/#/.test(href) && href }, $target.data(), $this.data())
+
+ e.preventDefault()
+
+ $target
+ .modal(option)
+ .one('hide', function () {
+ $this.focus()
+ })
+ })
+
+}(window.$jqTheme || window.jQuery);
+/* ===========================================================
+ * bootstrap-tooltip.js v2.3.2
+ * http://twitter.github.com/bootstrap/javascript.html#tooltips
+ * Inspired by the original jQuery.tipsy by Jason Frame
+ * ===========================================================
+ * Copyright 2012 Twitter, Inc.
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ * ========================================================== */
+
+
+!function ($) {
+
+ "use strict"; // jshint ;_;
+
+
+ /* TOOLTIP PUBLIC CLASS DEFINITION
+ * =============================== */
+
+ var Tooltip = function (element, options) {
+ this.init('tooltip', element, options)
+ }
+
+ Tooltip.prototype = {
+
+ constructor: Tooltip
+
+ , init: function (type, element, options) {
+ var eventIn
+ , eventOut
+ , triggers
+ , trigger
+ , i
+
+ this.type = type
+ this.$element = $(element)
+ this.options = this.getOptions(options)
+ this.enabled = true
+
+ triggers = this.options.trigger.split(' ')
+
+ for (i = triggers.length; i--;) {
+ trigger = triggers[i]
+ if (trigger == 'click') {
+ this.$element.on('click.' + this.type, this.options.selector, $.proxy(this.toggle, this))
+ } else if (trigger != 'manual') {
+ eventIn = trigger == 'hover' ? 'mouseenter' : 'focus'
+ eventOut = trigger == 'hover' ? 'mouseleave' : 'blur'
+ this.$element.on(eventIn + '.' + this.type, this.options.selector, $.proxy(this.enter, this))
+ this.$element.on(eventOut + '.' + this.type, this.options.selector, $.proxy(this.leave, this))
+ }
+ }
+
+ this.options.selector ?
+ (this._options = $.extend({}, this.options, { trigger: 'manual', selector: '' })) :
+ this.fixTitle()
+ }
+
+ , getOptions: function (options) {
+ options = $.extend({}, $.fn[this.type].defaults, this.$element.data(), options)
+
+ if (options.delay && typeof options.delay == 'number') {
+ options.delay = {
+ show: options.delay
+ , hide: options.delay
+ }
+ }
+
+ return options
+ }
+
+ , enter: function (e) {
+ var defaults = $.fn[this.type].defaults
+ , options = {}
+ , self
+
+ this._options && $.each(this._options, function (key, value) {
+ if (defaults[key] != value) options[key] = value
+ }, this)
+
+ self = $(e.currentTarget)[this.type](options).data(this.type)
+
+ if (!self.options.delay || !self.options.delay.show) return self.show()
+
+ clearTimeout(this.timeout)
+ self.hoverState = 'in'
+ this.timeout = setTimeout(function() {
+ if (self.hoverState == 'in') self.show()
+ }, self.options.delay.show)
+ }
+
+ , leave: function (e) {
+ var self = $(e.currentTarget)[this.type](this._options).data(this.type)
+
+ if (this.timeout) clearTimeout(this.timeout)
+ if (!self.options.delay || !self.options.delay.hide) return self.hide()
+
+ self.hoverState = 'out'
+ this.timeout = setTimeout(function() {
+ if (self.hoverState == 'out') self.hide()
+ }, self.options.delay.hide)
+ }
+
+ , show: function () {
+ var $tip
+ , pos
+ , actualWidth
+ , actualHeight
+ , placement
+ , tp
+ , e = $.Event('show')
+
+ if (this.hasContent() && this.enabled) {
+ this.$element.trigger(e)
+ if (e.isDefaultPrevented()) return
+ $tip = this.tip()
+ this.setContent()
+
+ if (this.options.animation) {
+ $tip.addClass('fade')
+ }
+
+ placement = typeof this.options.placement == 'function' ?
+ this.options.placement.call(this, $tip[0], this.$element[0]) :
+ this.options.placement
+
+ $tip
+ .detach()
+ .css({ top: 0, left: 0, display: 'block' })
+
+ this.options.container ? $tip.appendTo(this.options.container) : $tip.insertAfter(this.$element)
+
+ pos = this.getPosition()
+
+ actualWidth = $tip[0].offsetWidth
+ actualHeight = $tip[0].offsetHeight
+
+ switch (placement) {
+ case 'bottom':
+ tp = {top: pos.top + pos.height, left: pos.left + pos.width / 2 - actualWidth / 2}
+ break
+ case 'top':
+ tp = {top: pos.top - actualHeight, left: pos.left + pos.width / 2 - actualWidth / 2}
+ break
+ case 'left':
+ tp = {top: pos.top + pos.height / 2 - actualHeight / 2, left: pos.left - actualWidth}
+ break
+ case 'right':
+ tp = {top: pos.top + pos.height / 2 - actualHeight / 2, left: pos.left + pos.width}
+ break
+ }
+
+ this.applyPlacement(tp, placement)
+ this.$element.trigger('shown')
+ }
+ }
+
+ , applyPlacement: function(offset, placement){
+ var $tip = this.tip()
+ , width = $tip[0].offsetWidth
+ , height = $tip[0].offsetHeight
+ , actualWidth
+ , actualHeight
+ , delta
+ , replace
+
+ $tip
+ .offset(offset)
+ .addClass(placement)
+ .addClass('in')
+
+ actualWidth = $tip[0].offsetWidth
+ actualHeight = $tip[0].offsetHeight
+
+ if (placement == 'top' && actualHeight != height) {
+ offset.top = offset.top + height - actualHeight
+ replace = true
+ }
+
+ if (placement == 'bottom' || placement == 'top') {
+ delta = 0
+
+ if (offset.left < 0){
+ delta = offset.left * -2
+ offset.left = 0
+ $tip.offset(offset)
+ actualWidth = $tip[0].offsetWidth
+ actualHeight = $tip[0].offsetHeight
+ }
+
+ this.replaceArrow(delta - width + actualWidth, actualWidth, 'left')
+ } else {
+ this.replaceArrow(actualHeight - height, actualHeight, 'top')
+ }
+
+ if (replace) $tip.offset(offset)
+ }
+
+ , replaceArrow: function(delta, dimension, position){
+ this
+ .arrow()
+ .css(position, delta ? (50 * (1 - delta / dimension) + "%") : '')
+ }
+
+ , setContent: function () {
+ var $tip = this.tip()
+ , title = this.getTitle()
+
+ $tip.find('.tooltip-inner')[this.options.html ? 'html' : 'text'](title)
+ $tip.removeClass('fade in top bottom left right')
+ }
+
+ , hide: function () {
+ var that = this
+ , $tip = this.tip()
+ , e = $.Event('hide')
+
+ this.$element.trigger(e)
+ if (e.isDefaultPrevented()) return
+
+ $tip.removeClass('in')
+
+ function removeWithAnimation() {
+ var timeout = setTimeout(function () {
+ $tip.off($.support.transition.end).detach()
+ }, 500)
+
+ $tip.one($.support.transition.end, function () {
+ clearTimeout(timeout)
+ $tip.detach()
+ })
+ }
+
+ $.support.transition && this.$tip.hasClass('fade') ?
+ removeWithAnimation() :
+ $tip.detach()
+
+ this.$element.trigger('hidden')
+
+ return this
+ }
+
+ , fixTitle: function () {
+ var $e = this.$element
+ if ($e.attr('title') || typeof($e.attr('data-original-title')) != 'string') {
+ $e.attr('data-original-title', $e.attr('title') || '').attr('title', '')
+ }
+ }
+
+ , hasContent: function () {
+ return this.getTitle()
+ }
+
+ , getPosition: function () {
+ var el = this.$element[0]
+ return $.extend({}, (typeof el.getBoundingClientRect == 'function') ? el.getBoundingClientRect() : {
+ width: el.offsetWidth
+ , height: el.offsetHeight
+ }, this.$element.offset())
+ }
+
+ , getTitle: function () {
+ var title
+ , $e = this.$element
+ , o = this.options
+
+ title = $e.attr('data-original-title')
+ || (typeof o.title == 'function' ? o.title.call($e[0]) : o.title)
+
+ return title
+ }
+
+ , tip: function () {
+ return this.$tip = this.$tip || $(this.options.template)
+ }
+
+ , arrow: function(){
+ return this.$arrow = this.$arrow || this.tip().find(".tooltip-arrow")
+ }
+
+ , validate: function () {
+ if (!this.$element[0].parentNode) {
+ this.hide()
+ this.$element = null
+ this.options = null
+ }
+ }
+
+ , enable: function () {
+ this.enabled = true
+ }
+
+ , disable: function () {
+ this.enabled = false
+ }
+
+ , toggleEnabled: function () {
+ this.enabled = !this.enabled
+ }
+
+ , toggle: function (e) {
+ var self = e ? $(e.currentTarget)[this.type](this._options).data(this.type) : this
+ self.tip().hasClass('in') ? self.hide() : self.show()
+ }
+
+ , destroy: function () {
+ this.hide().$element.off('.' + this.type).removeData(this.type)
+ }
+
+ }
+
+
+ /* TOOLTIP PLUGIN DEFINITION
+ * ========================= */
+
+ var old = $.fn.tooltip
+
+ $.fn.tooltip = function ( option ) {
+ return this.each(function () {
+ var $this = $(this)
+ , data = $this.data('tooltip')
+ , options = typeof option == 'object' && option
+ if (!data) $this.data('tooltip', (data = new Tooltip(this, options)))
+ if (typeof option == 'string') data[option]()
+ })
+ }
+
+ $.fn.tooltip.Constructor = Tooltip
+
+ $.fn.tooltip.defaults = {
+ animation: true
+ , placement: 'top'
+ , selector: false
+ , template: '<div class="tooltip"><div class="tooltip-arrow"></div><div class="tooltip-inner"></div></div>'
+ , trigger: 'hover focus'
+ , title: ''
+ , delay: 0
+ , html: false
+ , container: false
+ }
+
+
+ /* TOOLTIP NO CONFLICT
+ * =================== */
+
+ $.fn.tooltip.noConflict = function () {
+ $.fn.tooltip = old
+ return this
+ }
+
+}(window.$jqTheme || window.jQuery);
+/* ===========================================================
+ * bootstrap-popover.js v2.3.2
+ * http://twitter.github.com/bootstrap/javascript.html#popovers
+ * ===========================================================
+ * Copyright 2012 Twitter, Inc.
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ * =========================================================== */
+
+
+!function ($) {
+
+ "use strict"; // jshint ;_;
+
+
+ /* POPOVER PUBLIC CLASS DEFINITION
+ * =============================== */
+
+ var Popover = function (element, options) {
+ this.init('popover', element, options)
+ }
+
+
+ /* NOTE: POPOVER EXTENDS BOOTSTRAP-TOOLTIP.js
+ ========================================== */
+
+ Popover.prototype = $.extend({}, $.fn.tooltip.Constructor.prototype, {
+
+ constructor: Popover
+
+ , setContent: function () {
+ var $tip = this.tip()
+ , title = this.getTitle()
+ , content = this.getContent()
+
+ $tip.find('.popover-title')[this.options.html ? 'html' : 'text'](title)
+ $tip.find('.popover-content')[this.options.html ? 'html' : 'text'](content)
+
+ $tip.removeClass('fade top bottom left right in')
+ }
+
+ , hasContent: function () {
+ return this.getTitle() || this.getContent()
+ }
+
+ , getContent: function () {
+ var content
+ , $e = this.$element
+ , o = this.options
+
+ content = (typeof o.content == 'function' ? o.content.call($e[0]) : o.content)
+ || $e.attr('data-content')
+
+ return content
+ }
+
+ , tip: function () {
+ if (!this.$tip) {
+ this.$tip = $(this.options.template)
+ }
+ return this.$tip
+ }
+
+ , destroy: function () {
+ this.hide().$element.off('.' + this.type).removeData(this.type)
+ }
+
+ })
+
+
+ /* POPOVER PLUGIN DEFINITION
+ * ======================= */
+
+ var old = $.fn.popover
+
+ $.fn.popover = function (option) {
+ return this.each(function () {
+ var $this = $(this)
+ , data = $this.data('popover')
+ , options = typeof option == 'object' && option
+ if (!data) $this.data('popover', (data = new Popover(this, options)))
+ if (typeof option == 'string') data[option]()
+ })
+ }
+
+ $.fn.popover.Constructor = Popover
+
+ $.fn.popover.defaults = $.extend({} , $.fn.tooltip.defaults, {
+ placement: 'right'
+ , trigger: 'click'
+ , content: ''
+ , template: '<div class="popover"><div class="arrow"></div><h3 class="popover-title"></h3><div class="popover-content"></div></div>'
+ })
+
+
+ /* POPOVER NO CONFLICT
+ * =================== */
+
+ $.fn.popover.noConflict = function () {
+ $.fn.popover = old
+ return this
+ }
+
+}(window.$jqTheme || window.jQuery);
+/* =============================================================
+ * bootstrap-scrollspy.js v2.3.2
+ * http://twitter.github.com/bootstrap/javascript.html#scrollspy
+ * =============================================================
+ * Copyright 2012 Twitter, Inc.
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ * ============================================================== */
+
+
+!function ($) {
+
+ "use strict"; // jshint ;_;
+
+
+ /* SCROLLSPY CLASS DEFINITION
+ * ========================== */
+
+ function ScrollSpy(element, options) {
+ var process = $.proxy(this.process, this)
+ , $element = $(element).is('body') ? $(window) : $(element)
+ , href
+ this.options = $.extend({}, $.fn.scrollspy.defaults, options)
+ this.$scrollElement = $element.on('scroll.scroll-spy.data-api', process)
+ this.selector = (this.options.target
+ || ((href = $(element).attr('href')) && href.replace(/.*(?=#[^\s]+$)/, '')) //strip for ie7
+ || '') + ' .nav li > a'
+ this.$body = $('body')
+ this.refresh()
+ this.process()
+ }
+
+ ScrollSpy.prototype = {
+
+ constructor: ScrollSpy
+
+ , refresh: function () {
+ var self = this
+ , $targets
+
+ this.offsets = $([])
+ this.targets = $([])
+
+ $targets = this.$body
+ .find(this.selector)
+ .map(function () {
+ var $el = $(this)
+ , href = $el.data('target') || $el.attr('href')
+ , $href = /^#\w/.test(href) && $(href)
+ return ( $href
+ && $href.length
+ && [[ $href.position().top + (!$.isWindow(self.$scrollElement.get(0)) && self.$scrollElement.scrollTop()), href ]] ) || null
+ })
+ .sort(function (a, b) { return a[0] - b[0] })
+ .each(function () {
+ self.offsets.push(this[0])
+ self.targets.push(this[1])
+ })
+ }
+
+ , process: function () {
+ var scrollTop = this.$scrollElement.scrollTop() + this.options.offset
+ , scrollHeight = this.$scrollElement[0].scrollHeight || this.$body[0].scrollHeight
+ , maxScroll = scrollHeight - this.$scrollElement.height()
+ , offsets = this.offsets
+ , targets = this.targets
+ , activeTarget = this.activeTarget
+ , i
+
+ if (scrollTop >= maxScroll) {
+ return activeTarget != (i = targets.last()[0])
+ && this.activate ( i )
+ }
+
+ for (i = offsets.length; i--;) {
+ activeTarget != targets[i]
+ && scrollTop >= offsets[i]
+ && (!offsets[i + 1] || scrollTop <= offsets[i + 1])
+ && this.activate( targets[i] )
+ }
+ }
+
+ , activate: function (target) {
+ var active
+ , selector
+
+ this.activeTarget = target
+
+ $(this.selector)
+ .parent('.active')
+ .removeClass('active')
+
+ selector = this.selector
+ + '[data-target="' + target + '"],'
+ + this.selector + '[href="' + target + '"]'
+
+ active = $(selector)
+ .parent('li')
+ .addClass('active')
+
+ if (active.parent('.dropdown-menu').length) {
+ active = active.closest('li.dropdown').addClass('active')
+ }
+
+ active.trigger('activate')
+ }
+
+ }
+
+
+ /* SCROLLSPY PLUGIN DEFINITION
+ * =========================== */
+
+ var old = $.fn.scrollspy
+
+ $.fn.scrollspy = function (option) {
+ return this.each(function () {
+ var $this = $(this)
+ , data = $this.data('scrollspy')
+ , options = typeof option == 'object' && option
+ if (!data) $this.data('scrollspy', (data = new ScrollSpy(this, options)))
+ if (typeof option == 'string') data[option]()
+ })
+ }
+
+ $.fn.scrollspy.Constructor = ScrollSpy
+
+ $.fn.scrollspy.defaults = {
+ offset: 10
+ }
+
+
+ /* SCROLLSPY NO CONFLICT
+ * ===================== */
+
+ $.fn.scrollspy.noConflict = function () {
+ $.fn.scrollspy = old
+ return this
+ }
+
+
+ /* SCROLLSPY DATA-API
+ * ================== */
+
+ $(window).on('load', function () {
+ $('[data-spy="scroll"]').each(function () {
+ var $spy = $(this)
+ $spy.scrollspy($spy.data())
+ })
+ })
+
+}(window.$jqTheme || window.jQuery);
+/* ========================================================
+ * bootstrap-tab.js v2.3.2
+ * http://twitter.github.com/bootstrap/javascript.html#tabs
+ * ========================================================
+ * Copyright 2012 Twitter, Inc.
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ * ======================================================== */
+
+
+!function ($) {
+
+ "use strict"; // jshint ;_;
+
+
+ /* TAB CLASS DEFINITION
+ * ==================== */
+
+ var Tab = function (element) {
+ this.element = $(element)
+ }
+
+ Tab.prototype = {
+
+ constructor: Tab
+
+ , show: function () {
+ var $this = this.element
+ , $ul = $this.closest('ul:not(.dropdown-menu)')
+ , selector = $this.attr('data-target')
+ , previous
+ , $target
+ , e
+
+ if (!selector) {
+ selector = $this.attr('href')
+ selector = selector && selector.replace(/.*(?=#[^\s]*$)/, '') //strip for ie7
+ }
+
+ if ( $this.parent('li').hasClass('active') ) return
+
+ previous = $ul.find('.active:last a')[0]
+
+ e = $.Event('show', {
+ relatedTarget: previous
+ })
+
+ $this.trigger(e)
+
+ if (e.isDefaultPrevented()) return
+
+ $target = $(selector)
+
+ this.activate($this.parent('li'), $ul)
+ this.activate($target, $target.parent(), function () {
+ $this.trigger({
+ type: 'shown'
+ , relatedTarget: previous
+ })
+ })
+ }
+
+ , activate: function ( element, container, callback) {
+ var $active = container.find('> .active')
+ , transition = callback
+ && $.support.transition
+ && $active.hasClass('fade')
+
+ function next() {
+ $active
+ .removeClass('active')
+ .find('> .dropdown-menu > .active')
+ .removeClass('active')
+
+ element.addClass('active')
+
+ if (transition) {
+ element[0].offsetWidth // reflow for transition
+ element.addClass('in')
+ } else {
+ element.removeClass('fade')
+ }
+
+ if ( element.parent('.dropdown-menu') ) {
+ element.closest('li.dropdown').addClass('active')
+ }
+
+ callback && callback()
+ }
+
+ transition ?
+ $active.one($.support.transition.end, next) :
+ next()
+
+ $active.removeClass('in')
+ }
+ }
+
+
+ /* TAB PLUGIN DEFINITION
+ * ===================== */
+
+ var old = $.fn.tab
+
+ $.fn.tab = function ( option ) {
+ return this.each(function () {
+ var $this = $(this)
+ , data = $this.data('tab')
+ if (!data) $this.data('tab', (data = new Tab(this)))
+ if (typeof option == 'string') data[option]()
+ })
+ }
+
+ $.fn.tab.Constructor = Tab
+
+
+ /* TAB NO CONFLICT
+ * =============== */
+
+ $.fn.tab.noConflict = function () {
+ $.fn.tab = old
+ return this
+ }
+
+
+ /* TAB DATA-API
+ * ============ */
+
+ $(document).on('click.tab.data-api', '[data-toggle="tab"], [data-toggle="pill"]', function (e) {
+ e.preventDefault()
+ $(this).tab('show')
+ })
+
+}(window.$jqTheme || window.jQuery);
+/* =============================================================
+ * bootstrap-typeahead.js v2.3.2
+ * http://twitter.github.com/bootstrap/javascript.html#typeahead
+ * =============================================================
+ * Copyright 2012 Twitter, Inc.
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ * ============================================================ */
+
+
+!function($){
+
+ "use strict"; // jshint ;_;
+
+
+ /* TYPEAHEAD PUBLIC CLASS DEFINITION
+ * ================================= */
+
+ var Typeahead = function (element, options) {
+ this.$element = $(element)
+ this.options = $.extend({}, $.fn.typeahead.defaults, options)
+ this.matcher = this.options.matcher || this.matcher
+ this.sorter = this.options.sorter || this.sorter
+ this.highlighter = this.options.highlighter || this.highlighter
+ this.updater = this.options.updater || this.updater
+ this.source = this.options.source
+ this.$menu = $(this.options.menu)
+ this.shown = false
+ this.listen()
+ }
+
+ Typeahead.prototype = {
+
+ constructor: Typeahead
+
+ , select: function () {
+ var val = this.$menu.find('.active').attr('data-value')
+ this.$element
+ .val(this.updater(val))
+ .change()
+ return this.hide()
+ }
+
+ , updater: function (item) {
+ return item
+ }
+
+ , show: function () {
+ var pos = $.extend({}, this.$element.position(), {
+ height: this.$element[0].offsetHeight
+ })
+
+ this.$menu
+ .insertAfter(this.$element)
+ .css({
+ top: pos.top + pos.height
+ , left: pos.left
+ })
+ .show()
+
+ this.shown = true
+ return this
+ }
+
+ , hide: function () {
+ this.$menu.hide()
+ this.shown = false
+ return this
+ }
+
+ , lookup: function (event) {
+ var items
+
+ this.query = this.$element.val()
+
+ if (!this.query || this.query.length < this.options.minLength) {
+ return this.shown ? this.hide() : this
+ }
+
+ items = $.isFunction(this.source) ? this.source(this.query, $.proxy(this.process, this)) : this.source
+
+ return items ? this.process(items) : this
+ }
+
+ , process: function (items) {
+ var that = this
+
+ items = $.grep(items, function (item) {
+ return that.matcher(item)
+ })
+
+ items = this.sorter(items)
+
+ if (!items.length) {
+ return this.shown ? this.hide() : this
+ }
+
+ return this.render(items.slice(0, this.options.items)).show()
+ }
+
+ , matcher: function (item) {
+ return ~item.toLowerCase().indexOf(this.query.toLowerCase())
+ }
+
+ , sorter: function (items) {
+ var beginswith = []
+ , caseSensitive = []
+ , caseInsensitive = []
+ , item
+
+ while (item = items.shift()) {
+ if (!item.toLowerCase().indexOf(this.query.toLowerCase())) beginswith.push(item)
+ else if (~item.indexOf(this.query)) caseSensitive.push(item)
+ else caseInsensitive.push(item)
+ }
+
+ return beginswith.concat(caseSensitive, caseInsensitive)
+ }
+
+ , highlighter: function (item) {
+ var query = this.query.replace(/[\-\[\]{}()*+?.,\\\^$|#\s]/g, '\\$&')
+ return item.replace(new RegExp('(' + query + ')', 'ig'), function ($1, match) {
+ return '<strong>' + match + '</strong>'
+ })
+ }
+
+ , render: function (items) {
+ var that = this
+
+ items = $(items).map(function (i, item) {
+ i = $(that.options.item).attr('data-value', item)
+ i.find('a').html(that.highlighter(item))
+ return i[0]
+ })
+
+ items.first().addClass('active')
+ this.$menu.html(items)
+ return this
+ }
+
+ , next: function (event) {
+ var active = this.$menu.find('.active').removeClass('active')
+ , next = active.next()
+
+ if (!next.length) {
+ next = $(this.$menu.find('li')[0])
+ }
+
+ next.addClass('active')
+ }
+
+ , prev: function (event) {
+ var active = this.$menu.find('.active').removeClass('active')
+ , prev = active.prev()
+
+ if (!prev.length) {
+ prev = this.$menu.find('li').last()
+ }
+
+ prev.addClass('active')
+ }
+
+ , listen: function () {
+ this.$element
+ .on('focus', $.proxy(this.focus, this))
+ .on('blur', $.proxy(this.blur, this))
+ .on('keypress', $.proxy(this.keypress, this))
+ .on('keyup', $.proxy(this.keyup, this))
+
+ if (this.eventSupported('keydown')) {
+ this.$element.on('keydown', $.proxy(this.keydown, this))
+ }
+
+ this.$menu
+ .on('click', $.proxy(this.click, this))
+ .on('mouseenter', 'li', $.proxy(this.mouseenter, this))
+ .on('mouseleave', 'li', $.proxy(this.mouseleave, this))
+ }
+
+ , eventSupported: function(eventName) {
+ var isSupported = eventName in this.$element
+ if (!isSupported) {
+ this.$element.setAttribute(eventName, 'return;')
+ isSupported = typeof this.$element[eventName] === 'function'
+ }
+ return isSupported
+ }
+
+ , move: function (e) {
+ if (!this.shown) return
+
+ switch(e.keyCode) {
+ case 9: // tab
+ case 13: // enter
+ case 27: // escape
+ e.preventDefault()
+ break
+
+ case 38: // up arrow
+ e.preventDefault()
+ this.prev()
+ break
+
+ case 40: // down arrow
+ e.preventDefault()
+ this.next()
+ break
+ }
+
+ e.stopPropagation()
+ }
+
+ , keydown: function (e) {
+ this.suppressKeyPressRepeat = ~$.inArray(e.keyCode, [40,38,9,13,27])
+ this.move(e)
+ }
+
+ , keypress: function (e) {
+ if (this.suppressKeyPressRepeat) return
+ this.move(e)
+ }
+
+ , keyup: function (e) {
+ switch(e.keyCode) {
+ case 40: // down arrow
+ case 38: // up arrow
+ case 16: // shift
+ case 17: // ctrl
+ case 18: // alt
+ break
+
+ case 9: // tab
+ case 13: // enter
+ if (!this.shown) return
+ this.select()
+ break
+
+ case 27: // escape
+ if (!this.shown) return
+ this.hide()
+ break
+
+ default:
+ this.lookup()
+ }
+
+ e.stopPropagation()
+ e.preventDefault()
+ }
+
+ , focus: function (e) {
+ this.focused = true
+ }
+
+ , blur: function (e) {
+ this.focused = false
+ if (!this.mousedover && this.shown) this.hide()
+ }
+
+ , click: function (e) {
+ e.stopPropagation()
+ e.preventDefault()
+ this.select()
+ this.$element.focus()
+ }
+
+ , mouseenter: function (e) {
+ this.mousedover = true
+ this.$menu.find('.active').removeClass('active')
+ $(e.currentTarget).addClass('active')
+ }
+
+ , mouseleave: function (e) {
+ this.mousedover = false
+ if (!this.focused && this.shown) this.hide()
+ }
+
+ }
+
+
+ /* TYPEAHEAD PLUGIN DEFINITION
+ * =========================== */
+
+ var old = $.fn.typeahead
+
+ $.fn.typeahead = function (option) {
+ return this.each(function () {
+ var $this = $(this)
+ , data = $this.data('typeahead')
+ , options = typeof option == 'object' && option
+ if (!data) $this.data('typeahead', (data = new Typeahead(this, options)))
+ if (typeof option == 'string') data[option]()
+ })
+ }
+
+ $.fn.typeahead.defaults = {
+ source: []
+ , items: 8
+ , menu: '<ul class="typeahead dropdown-menu"></ul>'
+ , item: '<li><a href="#"></a></li>'
+ , minLength: 1
+ }
+
+ $.fn.typeahead.Constructor = Typeahead
+
+
+ /* TYPEAHEAD NO CONFLICT
+ * =================== */
+
+ $.fn.typeahead.noConflict = function () {
+ $.fn.typeahead = old
+ return this
+ }
+
+
+ /* TYPEAHEAD DATA-API
+ * ================== */
+
+ $(document).on('focus.typeahead.data-api', '[data-provide="typeahead"]', function (e) {
+ var $this = $(this)
+ if ($this.data('typeahead')) return
+ $this.typeahead($this.data())
+ })
+
+}(window.$jqTheme || window.jQuery);
+/* ==========================================================
+ * bootstrap-affix.js v2.3.2
+ * http://twitter.github.com/bootstrap/javascript.html#affix
+ * ==========================================================
+ * Copyright 2012 Twitter, Inc.
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ * ========================================================== */
+
+
+!function ($) {
+
+ "use strict"; // jshint ;_;
+
+
+ /* AFFIX CLASS DEFINITION
+ * ====================== */
+
+ var Affix = function (element, options) {
+ this.options = $.extend({}, $.fn.affix.defaults, options)
+ this.$window = $(window)
+ .on('scroll.affix.data-api', $.proxy(this.checkPosition, this))
+ .on('click.affix.data-api', $.proxy(function () { setTimeout($.proxy(this.checkPosition, this), 1) }, this))
+ this.$element = $(element)
+ this.checkPosition()
+ }
+
+ Affix.prototype.checkPosition = function () {
+ if (!this.$element.is(':visible')) return
+
+ var scrollHeight = $(document).height()
+ , scrollTop = this.$window.scrollTop()
+ , position = this.$element.offset()
+ , offset = this.options.offset
+ , offsetBottom = offset.bottom
+ , offsetTop = offset.top
+ , reset = 'affix affix-top affix-bottom'
+ , affix
+
+ if (typeof offset != 'object') offsetBottom = offsetTop = offset
+ if (typeof offsetTop == 'function') offsetTop = offset.top()
+ if (typeof offsetBottom == 'function') offsetBottom = offset.bottom()
+
+ affix = this.unpin != null && (scrollTop + this.unpin <= position.top) ?
+ false : offsetBottom != null && (position.top + this.$element.height() >= scrollHeight - offsetBottom) ?
+ 'bottom' : offsetTop != null && scrollTop <= offsetTop ?
+ 'top' : false
+
+ if (this.affixed === affix) return
+
+ this.affixed = affix
+ this.unpin = affix == 'bottom' ? position.top - scrollTop : null
+
+ this.$element.removeClass(reset).addClass('affix' + (affix ? '-' + affix : ''))
+ }
+
+
+ /* AFFIX PLUGIN DEFINITION
+ * ======================= */
+
+ var old = $.fn.affix
+
+ $.fn.affix = function (option) {
+ return this.each(function () {
+ var $this = $(this)
+ , data = $this.data('affix')
+ , options = typeof option == 'object' && option
+ if (!data) $this.data('affix', (data = new Affix(this, options)))
+ if (typeof option == 'string') data[option]()
+ })
+ }
+
+ $.fn.affix.Constructor = Affix
+
+ $.fn.affix.defaults = {
+ offset: 0
+ }
+
+
+ /* AFFIX NO CONFLICT
+ * ================= */
+
+ $.fn.affix.noConflict = function () {
+ $.fn.affix = old
+ return this
+ }
+
+
+ /* AFFIX DATA-API
+ * ============== */
+
+ $(window).on('load', function () {
+ $('[data-spy="affix"]').each(function () {
+ var $spy = $(this)
+ , data = $spy.data()
+
+ data.offset = data.offset || {}
+
+ data.offsetBottom && (data.offset.bottom = data.offsetBottom)
+ data.offsetTop && (data.offset.top = data.offsetTop)
+
+ $spy.affix(data)
+ })
+ })
+
+
+}(window.$jqTheme || window.jQuery);
diff --git a/docs/build/html/_static/bootstrap-2.3.2/js/bootstrap.min.js b/docs/build/html/_static/bootstrap-2.3.2/js/bootstrap.min.js
new file mode 100644
index 0000000000000000000000000000000000000000..3a3394bd45b74c92cd1925c9f8da42642314e055
--- /dev/null
+++ b/docs/build/html/_static/bootstrap-2.3.2/js/bootstrap.min.js
@@ -0,0 +1,6 @@
+/**
+* Bootstrap.js v2.3.2 by @fat & @mdo
+* Copyright 2012 Twitter, Inc.
+* http://www.apache.org/licenses/LICENSE-2.0.txt
+*/
+!function(e){"use strict";e(function(){e.support.transition=function(){var e=function(){var e=document.createElement("bootstrap"),t={WebkitTransition:"webkitTransitionEnd",MozTransition:"transitionend",OTransition:"oTransitionEnd otransitionend",transition:"transitionend"},n;for(n in t)if(e.style[n]!==undefined)return t[n]}();return e&&{end:e}}()})}(window.$jqTheme||window.jQuery),!function(e){"use strict";var t='[data-dismiss="alert"]',n=function(n){e(n).on("click",t,this.close)};n.prototype.close=function(t){function s(){i.trigger("closed").remove()}var n=e(this),r=n.attr("data-target"),i;r||(r=n.attr("href"),r=r&&r.replace(/.*(?=#[^\s]*$)/,"")),i=e(r),t&&t.preventDefault(),i.length||(i=n.hasClass("alert")?n:n.parent()),i.trigger(t=e.Event("close"));if(t.isDefaultPrevented())return;i.removeClass("in"),e.support.transition&&i.hasClass("fade")?i.on(e.support.transition.end,s):s()};var r=e.fn.alert;e.fn.alert=function(t){return this.each(function(){var 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n=e(this),r,i=e(n.attr("data-target")||(r=n.attr("href"))&&r.replace(/.*(?=#[^\s]+$)/,"")),s=e.extend({},i.data(),n.data()),o;i.carousel(s),(o=n.attr("data-slide-to"))&&i.data("carousel").pause().to(o).cycle(),t.preventDefault()})}(window.$jqTheme||window.jQuery),!function(e){"use strict";var t=function(t,n){this.$element=e(t),this.options=e.extend({},e.fn.collapse.defaults,n),this.options.parent&&(this.$parent=e(this.options.parent)),this.options.toggle&&this.toggle()};t.prototype={constructor:t,dimension:function(){var e=this.$element.hasClass("width");return e?"width":"height"},show:function(){var t,n,r,i;if(this.transitioning||this.$element.hasClass("in"))return;t=this.dimension(),n=e.camelCase(["scroll",t].join("-")),r=this.$parent&&this.$parent.find("> .accordion-group > 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this.$arrow=this.$arrow||this.tip().find(".tooltip-arrow")},validate:function(){this.$element[0].parentNode||(this.hide(),this.$element=null,this.options=null)},enable:function(){this.enabled=!0},disable:function(){this.enabled=!1},toggleEnabled:function(){this.enabled=!this.enabled},toggle:function(t){var n=t?e(t.currentTarget)[this.type](this._options).data(this.type):this;n.tip().hasClass("in")?n.hide():n.show()},destroy:function(){this.hide().$element.off("."+this.type).removeData(this.type)}};var n=e.fn.tooltip;e.fn.tooltip=function(n){return this.each(function(){var r=e(this),i=r.data("tooltip"),s=typeof n=="object"&&n;i||r.data("tooltip",i=new t(this,s)),typeof n=="string"&&i[n]()})},e.fn.tooltip.Constructor=t,e.fn.tooltip.defaults={animation:!0,placement:"top",selector:!1,template:'<div class="tooltip"><div class="tooltip-arrow"></div><div class="tooltip-inner"></div></div>',trigger:"hover focus",title:"",delay:0,html:!1,container:!1},e.fn.tooltip.noConflict=function(){return e.fn.tooltip=n,this}}(window.$jqTheme||window.jQuery),!function(e){"use strict";var t=function(e,t){this.init("popover",e,t)};t.prototype=e.extend({},e.fn.tooltip.Constructor.prototype,{constructor:t,setContent:function(){var e=this.tip(),t=this.getTitle(),n=this.getContent();e.find(".popover-title")[this.options.html?"html":"text"](t),e.find(".popover-content")[this.options.html?"html":"text"](n),e.removeClass("fade top bottom left right in")},hasContent:function(){return this.getTitle()||this.getContent()},getContent:function(){var e,t=this.$element,n=this.options;return e=(typeof n.content=="function"?n.content.call(t[0]):n.content)||t.attr("data-content"),e},tip:function(){return this.$tip||(this.$tip=e(this.options.template)),this.$tip},destroy:function(){this.hide().$element.off("."+this.type).removeData(this.type)}});var n=e.fn.popover;e.fn.popover=function(n){return this.each(function(){var r=e(this),i=r.data("popover"),s=typeof n=="object"&&n;i||r.data("popover",i=new 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n=e.fn.scrollspy;e.fn.scrollspy=function(n){return this.each(function(){var r=e(this),i=r.data("scrollspy"),s=typeof n=="object"&&n;i||r.data("scrollspy",i=new t(this,s)),typeof n=="string"&&i[n]()})},e.fn.scrollspy.Constructor=t,e.fn.scrollspy.defaults={offset:10},e.fn.scrollspy.noConflict=function(){return e.fn.scrollspy=n,this},e(window).on("load",function(){e('[data-spy="scroll"]').each(function(){var t=e(this);t.scrollspy(t.data())})})}(window.$jqTheme||window.jQuery),!function(e){"use strict";var t=function(t){this.element=e(t)};t.prototype={constructor:t,show:function(){var t=this.element,n=t.closest("ul:not(.dropdown-menu)"),r=t.attr("data-target"),i,s,o;r||(r=t.attr("href"),r=r&&r.replace(/.*(?=#[^\s]*$)/,""));if(t.parent("li").hasClass("active"))return;i=n.find(".active:last 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\ No newline at end of file
diff --git a/docs/build/html/_static/bootstrap-3.2.0/css/bootstrap-theme.css b/docs/build/html/_static/bootstrap-3.2.0/css/bootstrap-theme.css
new file mode 100644
index 0000000000000000000000000000000000000000..f860bbc069d8c3fb2b1432ec1b0ff35bf5ae027b
--- /dev/null
+++ b/docs/build/html/_static/bootstrap-3.2.0/css/bootstrap-theme.css
@@ -0,0 +1,442 @@
+/*!
+ * Bootstrap v3.2.0 (http://getbootstrap.com)
+ * Copyright 2011-2014 Twitter, Inc.
+ * Licensed under MIT (https://github.com/twbs/bootstrap/blob/master/LICENSE)
+ */
+
+.btn-default,
+.btn-primary,
+.btn-success,
+.btn-info,
+.btn-warning,
+.btn-danger {
+ text-shadow: 0 -1px 0 rgba(0, 0, 0, .2);
+ -webkit-box-shadow: inset 0 1px 0 rgba(255, 255, 255, .15), 0 1px 1px rgba(0, 0, 0, .075);
+ box-shadow: inset 0 1px 0 rgba(255, 255, 255, .15), 0 1px 1px rgba(0, 0, 0, .075);
+}
+.btn-default:active,
+.btn-primary:active,
+.btn-success:active,
+.btn-info:active,
+.btn-warning:active,
+.btn-danger:active,
+.btn-default.active,
+.btn-primary.active,
+.btn-success.active,
+.btn-info.active,
+.btn-warning.active,
+.btn-danger.active {
+ -webkit-box-shadow: inset 0 3px 5px rgba(0, 0, 0, .125);
+ box-shadow: inset 0 3px 5px rgba(0, 0, 0, .125);
+}
+.btn:active,
+.btn.active {
+ background-image: none;
+}
+.btn-default {
+ text-shadow: 0 1px 0 #fff;
+ background-image: -webkit-linear-gradient(top, #fff 0%, #e0e0e0 100%);
+ background-image: -o-linear-gradient(top, #fff 0%, #e0e0e0 100%);
+ background-image: -webkit-gradient(linear, left top, left bottom, from(#fff), to(#e0e0e0));
+ background-image: linear-gradient(to bottom, #fff 0%, #e0e0e0 100%);
+ filter: progid:DXImageTransform.Microsoft.gradient(startColorstr='#ffffffff', endColorstr='#ffe0e0e0', GradientType=0);
+ filter: progid:DXImageTransform.Microsoft.gradient(enabled = false);
+ background-repeat: repeat-x;
+ border-color: #dbdbdb;
+ border-color: #ccc;
+}
+.btn-default:hover,
+.btn-default:focus {
+ background-color: #e0e0e0;
+ background-position: 0 -15px;
+}
+.btn-default:active,
+.btn-default.active {
+ background-color: #e0e0e0;
+ border-color: #dbdbdb;
+}
+.btn-default:disabled,
+.btn-default[disabled] {
+ background-color: #e0e0e0;
+ background-image: none;
+}
+.btn-primary {
+ background-image: -webkit-linear-gradient(top, #428bca 0%, #2d6ca2 100%);
+ background-image: -o-linear-gradient(top, #428bca 0%, #2d6ca2 100%);
+ background-image: -webkit-gradient(linear, left top, left bottom, from(#428bca), to(#2d6ca2));
+ background-image: linear-gradient(to bottom, #428bca 0%, #2d6ca2 100%);
+ filter: progid:DXImageTransform.Microsoft.gradient(startColorstr='#ff428bca', endColorstr='#ff2d6ca2', GradientType=0);
+ filter: progid:DXImageTransform.Microsoft.gradient(enabled = false);
+ background-repeat: repeat-x;
+ border-color: #2b669a;
+}
+.btn-primary:hover,
+.btn-primary:focus {
+ background-color: #2d6ca2;
+ background-position: 0 -15px;
+}
+.btn-primary:active,
+.btn-primary.active {
+ background-color: #2d6ca2;
+ border-color: #2b669a;
+}
+.btn-primary:disabled,
+.btn-primary[disabled] {
+ background-color: #2d6ca2;
+ background-image: none;
+}
+.btn-success {
+ background-image: -webkit-linear-gradient(top, #5cb85c 0%, #419641 100%);
+ background-image: -o-linear-gradient(top, #5cb85c 0%, #419641 100%);
+ background-image: -webkit-gradient(linear, left top, left bottom, from(#5cb85c), to(#419641));
+ background-image: linear-gradient(to bottom, #5cb85c 0%, #419641 100%);
+ filter: progid:DXImageTransform.Microsoft.gradient(startColorstr='#ff5cb85c', endColorstr='#ff419641', GradientType=0);
+ filter: progid:DXImageTransform.Microsoft.gradient(enabled = false);
+ background-repeat: repeat-x;
+ border-color: #3e8f3e;
+}
+.btn-success:hover,
+.btn-success:focus {
+ background-color: #419641;
+ background-position: 0 -15px;
+}
+.btn-success:active,
+.btn-success.active {
+ background-color: #419641;
+ border-color: #3e8f3e;
+}
+.btn-success:disabled,
+.btn-success[disabled] {
+ background-color: #419641;
+ background-image: none;
+}
+.btn-info {
+ background-image: -webkit-linear-gradient(top, #5bc0de 0%, #2aabd2 100%);
+ background-image: -o-linear-gradient(top, #5bc0de 0%, #2aabd2 100%);
+ background-image: -webkit-gradient(linear, left top, left bottom, from(#5bc0de), to(#2aabd2));
+ background-image: linear-gradient(to bottom, #5bc0de 0%, #2aabd2 100%);
+ filter: progid:DXImageTransform.Microsoft.gradient(startColorstr='#ff5bc0de', endColorstr='#ff2aabd2', GradientType=0);
+ filter: progid:DXImageTransform.Microsoft.gradient(enabled = false);
+ background-repeat: repeat-x;
+ border-color: #28a4c9;
+}
+.btn-info:hover,
+.btn-info:focus {
+ background-color: #2aabd2;
+ background-position: 0 -15px;
+}
+.btn-info:active,
+.btn-info.active {
+ background-color: #2aabd2;
+ border-color: #28a4c9;
+}
+.btn-info:disabled,
+.btn-info[disabled] {
+ background-color: #2aabd2;
+ background-image: none;
+}
+.btn-warning {
+ background-image: -webkit-linear-gradient(top, #f0ad4e 0%, #eb9316 100%);
+ background-image: -o-linear-gradient(top, #f0ad4e 0%, #eb9316 100%);
+ background-image: -webkit-gradient(linear, left top, left bottom, from(#f0ad4e), to(#eb9316));
+ background-image: linear-gradient(to bottom, #f0ad4e 0%, #eb9316 100%);
+ filter: progid:DXImageTransform.Microsoft.gradient(startColorstr='#fff0ad4e', endColorstr='#ffeb9316', GradientType=0);
+ filter: progid:DXImageTransform.Microsoft.gradient(enabled = false);
+ background-repeat: repeat-x;
+ border-color: #e38d13;
+}
+.btn-warning:hover,
+.btn-warning:focus {
+ background-color: #eb9316;
+ background-position: 0 -15px;
+}
+.btn-warning:active,
+.btn-warning.active {
+ background-color: #eb9316;
+ border-color: #e38d13;
+}
+.btn-warning:disabled,
+.btn-warning[disabled] {
+ background-color: #eb9316;
+ background-image: none;
+}
+.btn-danger {
+ background-image: -webkit-linear-gradient(top, #d9534f 0%, #c12e2a 100%);
+ background-image: -o-linear-gradient(top, #d9534f 0%, #c12e2a 100%);
+ background-image: -webkit-gradient(linear, left top, left bottom, from(#d9534f), to(#c12e2a));
+ background-image: linear-gradient(to bottom, #d9534f 0%, #c12e2a 100%);
+ filter: progid:DXImageTransform.Microsoft.gradient(startColorstr='#ffd9534f', endColorstr='#ffc12e2a', GradientType=0);
+ filter: progid:DXImageTransform.Microsoft.gradient(enabled = false);
+ background-repeat: repeat-x;
+ border-color: #b92c28;
+}
+.btn-danger:hover,
+.btn-danger:focus {
+ background-color: #c12e2a;
+ background-position: 0 -15px;
+}
+.btn-danger:active,
+.btn-danger.active {
+ background-color: #c12e2a;
+ border-color: #b92c28;
+}
+.btn-danger:disabled,
+.btn-danger[disabled] {
+ background-color: #c12e2a;
+ background-image: none;
+}
+.thumbnail,
+.img-thumbnail {
+ -webkit-box-shadow: 0 1px 2px rgba(0, 0, 0, .075);
+ box-shadow: 0 1px 2px rgba(0, 0, 0, .075);
+}
+.dropdown-menu > li > a:hover,
+.dropdown-menu > li > a:focus {
+ background-color: #e8e8e8;
+ background-image: -webkit-linear-gradient(top, #f5f5f5 0%, #e8e8e8 100%);
+ background-image: -o-linear-gradient(top, #f5f5f5 0%, #e8e8e8 100%);
+ background-image: -webkit-gradient(linear, left top, left bottom, from(#f5f5f5), to(#e8e8e8));
+ background-image: linear-gradient(to bottom, #f5f5f5 0%, #e8e8e8 100%);
+ filter: progid:DXImageTransform.Microsoft.gradient(startColorstr='#fff5f5f5', endColorstr='#ffe8e8e8', GradientType=0);
+ background-repeat: repeat-x;
+}
+.dropdown-menu > .active > a,
+.dropdown-menu > .active > a:hover,
+.dropdown-menu > .active > a:focus {
+ background-color: #357ebd;
+ background-image: -webkit-linear-gradient(top, #428bca 0%, #357ebd 100%);
+ background-image: -o-linear-gradient(top, #428bca 0%, #357ebd 100%);
+ background-image: -webkit-gradient(linear, left top, left bottom, from(#428bca), to(#357ebd));
+ background-image: linear-gradient(to bottom, #428bca 0%, #357ebd 100%);
+ filter: progid:DXImageTransform.Microsoft.gradient(startColorstr='#ff428bca', endColorstr='#ff357ebd', GradientType=0);
+ background-repeat: repeat-x;
+}
+.navbar-default {
+ background-image: -webkit-linear-gradient(top, #fff 0%, #f8f8f8 100%);
+ background-image: -o-linear-gradient(top, #fff 0%, #f8f8f8 100%);
+ background-image: -webkit-gradient(linear, left top, left bottom, from(#fff), to(#f8f8f8));
+ background-image: linear-gradient(to bottom, #fff 0%, #f8f8f8 100%);
+ filter: progid:DXImageTransform.Microsoft.gradient(startColorstr='#ffffffff', endColorstr='#fff8f8f8', GradientType=0);
+ filter: progid:DXImageTransform.Microsoft.gradient(enabled = false);
+ background-repeat: repeat-x;
+ border-radius: 4px;
+ -webkit-box-shadow: inset 0 1px 0 rgba(255, 255, 255, .15), 0 1px 5px rgba(0, 0, 0, .075);
+ box-shadow: inset 0 1px 0 rgba(255, 255, 255, .15), 0 1px 5px rgba(0, 0, 0, .075);
+}
+.navbar-default .navbar-nav > .active > a {
+ background-image: -webkit-linear-gradient(top, #ebebeb 0%, #f3f3f3 100%);
+ background-image: -o-linear-gradient(top, #ebebeb 0%, #f3f3f3 100%);
+ background-image: -webkit-gradient(linear, left top, left bottom, from(#ebebeb), to(#f3f3f3));
+ background-image: linear-gradient(to bottom, #ebebeb 0%, #f3f3f3 100%);
+ filter: progid:DXImageTransform.Microsoft.gradient(startColorstr='#ffebebeb', endColorstr='#fff3f3f3', GradientType=0);
+ background-repeat: repeat-x;
+ -webkit-box-shadow: inset 0 3px 9px rgba(0, 0, 0, .075);
+ box-shadow: inset 0 3px 9px rgba(0, 0, 0, .075);
+}
+.navbar-brand,
+.navbar-nav > li > a {
+ text-shadow: 0 1px 0 rgba(255, 255, 255, .25);
+}
+.navbar-inverse {
+ background-image: -webkit-linear-gradient(top, #3c3c3c 0%, #222 100%);
+ background-image: -o-linear-gradient(top, #3c3c3c 0%, #222 100%);
+ background-image: -webkit-gradient(linear, left top, left bottom, from(#3c3c3c), to(#222));
+ background-image: linear-gradient(to bottom, #3c3c3c 0%, #222 100%);
+ filter: progid:DXImageTransform.Microsoft.gradient(startColorstr='#ff3c3c3c', endColorstr='#ff222222', GradientType=0);
+ filter: progid:DXImageTransform.Microsoft.gradient(enabled = false);
+ background-repeat: repeat-x;
+}
+.navbar-inverse .navbar-nav > .active > a {
+ background-image: -webkit-linear-gradient(top, #222 0%, #282828 100%);
+ background-image: -o-linear-gradient(top, #222 0%, #282828 100%);
+ background-image: -webkit-gradient(linear, left top, left bottom, from(#222), to(#282828));
+ background-image: linear-gradient(to bottom, #222 0%, #282828 100%);
+ filter: progid:DXImageTransform.Microsoft.gradient(startColorstr='#ff222222', endColorstr='#ff282828', GradientType=0);
+ background-repeat: repeat-x;
+ -webkit-box-shadow: inset 0 3px 9px rgba(0, 0, 0, .25);
+ box-shadow: inset 0 3px 9px rgba(0, 0, 0, .25);
+}
+.navbar-inverse .navbar-brand,
+.navbar-inverse .navbar-nav > li > a {
+ text-shadow: 0 -1px 0 rgba(0, 0, 0, .25);
+}
+.navbar-static-top,
+.navbar-fixed-top,
+.navbar-fixed-bottom {
+ border-radius: 0;
+}
+.alert {
+ text-shadow: 0 1px 0 rgba(255, 255, 255, .2);
+ -webkit-box-shadow: inset 0 1px 0 rgba(255, 255, 255, .25), 0 1px 2px rgba(0, 0, 0, .05);
+ box-shadow: inset 0 1px 0 rgba(255, 255, 255, .25), 0 1px 2px rgba(0, 0, 0, .05);
+}
+.alert-success {
+ background-image: -webkit-linear-gradient(top, #dff0d8 0%, #c8e5bc 100%);
+ background-image: -o-linear-gradient(top, #dff0d8 0%, #c8e5bc 100%);
+ background-image: -webkit-gradient(linear, left top, left bottom, from(#dff0d8), to(#c8e5bc));
+ background-image: linear-gradient(to bottom, #dff0d8 0%, #c8e5bc 100%);
+ filter: progid:DXImageTransform.Microsoft.gradient(startColorstr='#ffdff0d8', endColorstr='#ffc8e5bc', GradientType=0);
+ background-repeat: repeat-x;
+ border-color: #b2dba1;
+}
+.alert-info {
+ background-image: -webkit-linear-gradient(top, #d9edf7 0%, #b9def0 100%);
+ background-image: -o-linear-gradient(top, #d9edf7 0%, #b9def0 100%);
+ background-image: -webkit-gradient(linear, left top, left bottom, from(#d9edf7), to(#b9def0));
+ background-image: linear-gradient(to bottom, #d9edf7 0%, #b9def0 100%);
+ filter: progid:DXImageTransform.Microsoft.gradient(startColorstr='#ffd9edf7', endColorstr='#ffb9def0', GradientType=0);
+ background-repeat: repeat-x;
+ border-color: #9acfea;
+}
+.alert-warning {
+ background-image: -webkit-linear-gradient(top, #fcf8e3 0%, #f8efc0 100%);
+ background-image: -o-linear-gradient(top, #fcf8e3 0%, #f8efc0 100%);
+ background-image: -webkit-gradient(linear, left top, left bottom, from(#fcf8e3), to(#f8efc0));
+ background-image: linear-gradient(to bottom, #fcf8e3 0%, #f8efc0 100%);
+ filter: progid:DXImageTransform.Microsoft.gradient(startColorstr='#fffcf8e3', endColorstr='#fff8efc0', GradientType=0);
+ background-repeat: repeat-x;
+ border-color: #f5e79e;
+}
+.alert-danger {
+ background-image: -webkit-linear-gradient(top, #f2dede 0%, #e7c3c3 100%);
+ background-image: -o-linear-gradient(top, #f2dede 0%, #e7c3c3 100%);
+ background-image: -webkit-gradient(linear, left top, left bottom, from(#f2dede), to(#e7c3c3));
+ background-image: linear-gradient(to bottom, #f2dede 0%, #e7c3c3 100%);
+ filter: progid:DXImageTransform.Microsoft.gradient(startColorstr='#fff2dede', endColorstr='#ffe7c3c3', GradientType=0);
+ background-repeat: repeat-x;
+ border-color: #dca7a7;
+}
+.progress {
+ background-image: -webkit-linear-gradient(top, #ebebeb 0%, #f5f5f5 100%);
+ background-image: -o-linear-gradient(top, #ebebeb 0%, #f5f5f5 100%);
+ background-image: -webkit-gradient(linear, left top, left bottom, from(#ebebeb), to(#f5f5f5));
+ background-image: linear-gradient(to bottom, #ebebeb 0%, #f5f5f5 100%);
+ filter: progid:DXImageTransform.Microsoft.gradient(startColorstr='#ffebebeb', endColorstr='#fff5f5f5', GradientType=0);
+ background-repeat: repeat-x;
+}
+.progress-bar {
+ background-image: -webkit-linear-gradient(top, #428bca 0%, #3071a9 100%);
+ background-image: -o-linear-gradient(top, #428bca 0%, #3071a9 100%);
+ background-image: -webkit-gradient(linear, left top, left bottom, from(#428bca), to(#3071a9));
+ background-image: linear-gradient(to bottom, #428bca 0%, #3071a9 100%);
+ filter: progid:DXImageTransform.Microsoft.gradient(startColorstr='#ff428bca', endColorstr='#ff3071a9', GradientType=0);
+ background-repeat: repeat-x;
+}
+.progress-bar-success {
+ background-image: -webkit-linear-gradient(top, #5cb85c 0%, #449d44 100%);
+ background-image: -o-linear-gradient(top, #5cb85c 0%, #449d44 100%);
+ background-image: -webkit-gradient(linear, left top, left bottom, from(#5cb85c), to(#449d44));
+ background-image: linear-gradient(to bottom, #5cb85c 0%, #449d44 100%);
+ filter: progid:DXImageTransform.Microsoft.gradient(startColorstr='#ff5cb85c', endColorstr='#ff449d44', GradientType=0);
+ background-repeat: repeat-x;
+}
+.progress-bar-info {
+ background-image: -webkit-linear-gradient(top, #5bc0de 0%, #31b0d5 100%);
+ background-image: -o-linear-gradient(top, #5bc0de 0%, #31b0d5 100%);
+ background-image: -webkit-gradient(linear, left top, left bottom, from(#5bc0de), to(#31b0d5));
+ background-image: linear-gradient(to bottom, #5bc0de 0%, #31b0d5 100%);
+ filter: progid:DXImageTransform.Microsoft.gradient(startColorstr='#ff5bc0de', endColorstr='#ff31b0d5', GradientType=0);
+ background-repeat: repeat-x;
+}
+.progress-bar-warning {
+ background-image: -webkit-linear-gradient(top, #f0ad4e 0%, #ec971f 100%);
+ background-image: -o-linear-gradient(top, #f0ad4e 0%, #ec971f 100%);
+ background-image: -webkit-gradient(linear, left top, left bottom, from(#f0ad4e), to(#ec971f));
+ background-image: linear-gradient(to bottom, #f0ad4e 0%, #ec971f 100%);
+ filter: progid:DXImageTransform.Microsoft.gradient(startColorstr='#fff0ad4e', endColorstr='#ffec971f', GradientType=0);
+ background-repeat: repeat-x;
+}
+.progress-bar-danger {
+ background-image: -webkit-linear-gradient(top, #d9534f 0%, #c9302c 100%);
+ background-image: -o-linear-gradient(top, #d9534f 0%, #c9302c 100%);
+ background-image: -webkit-gradient(linear, left top, left bottom, from(#d9534f), to(#c9302c));
+ background-image: linear-gradient(to bottom, #d9534f 0%, #c9302c 100%);
+ filter: progid:DXImageTransform.Microsoft.gradient(startColorstr='#ffd9534f', endColorstr='#ffc9302c', GradientType=0);
+ background-repeat: repeat-x;
+}
+.progress-bar-striped {
+ background-image: -webkit-linear-gradient(45deg, rgba(255, 255, 255, .15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, .15) 50%, rgba(255, 255, 255, .15) 75%, transparent 75%, transparent);
+ background-image: -o-linear-gradient(45deg, rgba(255, 255, 255, .15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, .15) 50%, rgba(255, 255, 255, .15) 75%, transparent 75%, transparent);
+ background-image: linear-gradient(45deg, rgba(255, 255, 255, .15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, .15) 50%, rgba(255, 255, 255, .15) 75%, transparent 75%, transparent);
+}
+.list-group {
+ border-radius: 4px;
+ -webkit-box-shadow: 0 1px 2px rgba(0, 0, 0, .075);
+ box-shadow: 0 1px 2px rgba(0, 0, 0, .075);
+}
+.list-group-item.active,
+.list-group-item.active:hover,
+.list-group-item.active:focus {
+ text-shadow: 0 -1px 0 #3071a9;
+ background-image: -webkit-linear-gradient(top, #428bca 0%, #3278b3 100%);
+ background-image: -o-linear-gradient(top, #428bca 0%, #3278b3 100%);
+ background-image: -webkit-gradient(linear, left top, left bottom, from(#428bca), to(#3278b3));
+ background-image: linear-gradient(to bottom, #428bca 0%, #3278b3 100%);
+ filter: progid:DXImageTransform.Microsoft.gradient(startColorstr='#ff428bca', endColorstr='#ff3278b3', GradientType=0);
+ background-repeat: repeat-x;
+ border-color: #3278b3;
+}
+.panel {
+ -webkit-box-shadow: 0 1px 2px rgba(0, 0, 0, .05);
+ box-shadow: 0 1px 2px rgba(0, 0, 0, .05);
+}
+.panel-default > .panel-heading {
+ background-image: -webkit-linear-gradient(top, #f5f5f5 0%, #e8e8e8 100%);
+ background-image: -o-linear-gradient(top, #f5f5f5 0%, #e8e8e8 100%);
+ background-image: -webkit-gradient(linear, left top, left bottom, from(#f5f5f5), to(#e8e8e8));
+ background-image: linear-gradient(to bottom, #f5f5f5 0%, #e8e8e8 100%);
+ filter: progid:DXImageTransform.Microsoft.gradient(startColorstr='#fff5f5f5', endColorstr='#ffe8e8e8', GradientType=0);
+ background-repeat: repeat-x;
+}
+.panel-primary > .panel-heading {
+ background-image: -webkit-linear-gradient(top, #428bca 0%, #357ebd 100%);
+ background-image: -o-linear-gradient(top, #428bca 0%, #357ebd 100%);
+ background-image: -webkit-gradient(linear, left top, left bottom, from(#428bca), to(#357ebd));
+ background-image: linear-gradient(to bottom, #428bca 0%, #357ebd 100%);
+ filter: progid:DXImageTransform.Microsoft.gradient(startColorstr='#ff428bca', endColorstr='#ff357ebd', GradientType=0);
+ background-repeat: repeat-x;
+}
+.panel-success > .panel-heading {
+ background-image: -webkit-linear-gradient(top, #dff0d8 0%, #d0e9c6 100%);
+ background-image: -o-linear-gradient(top, #dff0d8 0%, #d0e9c6 100%);
+ background-image: -webkit-gradient(linear, left top, left bottom, from(#dff0d8), to(#d0e9c6));
+ background-image: linear-gradient(to bottom, #dff0d8 0%, #d0e9c6 100%);
+ filter: progid:DXImageTransform.Microsoft.gradient(startColorstr='#ffdff0d8', endColorstr='#ffd0e9c6', GradientType=0);
+ background-repeat: repeat-x;
+}
+.panel-info > .panel-heading {
+ background-image: -webkit-linear-gradient(top, #d9edf7 0%, #c4e3f3 100%);
+ background-image: -o-linear-gradient(top, #d9edf7 0%, #c4e3f3 100%);
+ background-image: -webkit-gradient(linear, left top, left bottom, from(#d9edf7), to(#c4e3f3));
+ background-image: linear-gradient(to bottom, #d9edf7 0%, #c4e3f3 100%);
+ filter: progid:DXImageTransform.Microsoft.gradient(startColorstr='#ffd9edf7', endColorstr='#ffc4e3f3', GradientType=0);
+ background-repeat: repeat-x;
+}
+.panel-warning > .panel-heading {
+ background-image: -webkit-linear-gradient(top, #fcf8e3 0%, #faf2cc 100%);
+ background-image: -o-linear-gradient(top, #fcf8e3 0%, #faf2cc 100%);
+ background-image: -webkit-gradient(linear, left top, left bottom, from(#fcf8e3), to(#faf2cc));
+ background-image: linear-gradient(to bottom, #fcf8e3 0%, #faf2cc 100%);
+ filter: progid:DXImageTransform.Microsoft.gradient(startColorstr='#fffcf8e3', endColorstr='#fffaf2cc', GradientType=0);
+ background-repeat: repeat-x;
+}
+.panel-danger > .panel-heading {
+ background-image: -webkit-linear-gradient(top, #f2dede 0%, #ebcccc 100%);
+ background-image: -o-linear-gradient(top, #f2dede 0%, #ebcccc 100%);
+ background-image: -webkit-gradient(linear, left top, left bottom, from(#f2dede), to(#ebcccc));
+ background-image: linear-gradient(to bottom, #f2dede 0%, #ebcccc 100%);
+ filter: progid:DXImageTransform.Microsoft.gradient(startColorstr='#fff2dede', endColorstr='#ffebcccc', GradientType=0);
+ background-repeat: repeat-x;
+}
+.well {
+ background-image: -webkit-linear-gradient(top, #e8e8e8 0%, #f5f5f5 100%);
+ background-image: -o-linear-gradient(top, #e8e8e8 0%, #f5f5f5 100%);
+ background-image: -webkit-gradient(linear, left top, left bottom, from(#e8e8e8), to(#f5f5f5));
+ background-image: linear-gradient(to bottom, #e8e8e8 0%, #f5f5f5 100%);
+ filter: progid:DXImageTransform.Microsoft.gradient(startColorstr='#ffe8e8e8', endColorstr='#fff5f5f5', GradientType=0);
+ background-repeat: repeat-x;
+ border-color: #dcdcdc;
+ -webkit-box-shadow: inset 0 1px 3px rgba(0, 0, 0, .05), 0 1px 0 rgba(255, 255, 255, .1);
+ box-shadow: inset 0 1px 3px rgba(0, 0, 0, .05), 0 1px 0 rgba(255, 255, 255, .1);
+}
+/*# sourceMappingURL=bootstrap-theme.css.map */
diff --git a/docs/build/html/_static/bootstrap-3.2.0/css/bootstrap-theme.css.map b/docs/build/html/_static/bootstrap-3.2.0/css/bootstrap-theme.css.map
new file mode 100644
index 0000000000000000000000000000000000000000..4cc41ab001ac92f916f6e0f112c8bfd2a352cb42
--- /dev/null
+++ b/docs/build/html/_static/bootstrap-3.2.0/css/bootstrap-theme.css.map
@@ -0,0 +1 @@
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@end-color: darken(@btn-color, 12%));\n .reset-filter(); // Disable gradients for IE9 because filter bleeds through rounded corners\n background-repeat: repeat-x;\n border-color: darken(@btn-color, 14%);\n\n &:hover,\n &:focus {\n background-color: darken(@btn-color, 12%);\n background-position: 0 -15px;\n }\n\n &:active,\n &.active {\n background-color: darken(@btn-color, 12%);\n border-color: darken(@btn-color, 14%);\n }\n\n &:disabled,\n &[disabled] {\n background-color: darken(@btn-color, 12%);\n background-image: none;\n }\n}\n\n// Common styles\n.btn {\n // Remove the gradient for the pressed/active state\n &:active,\n &.active {\n background-image: none;\n }\n}\n\n// Apply the mixin to the buttons\n.btn-default { .btn-styles(@btn-default-bg); text-shadow: 0 1px 0 #fff; border-color: #ccc; }\n.btn-primary { .btn-styles(@btn-primary-bg); }\n.btn-success { .btn-styles(@btn-success-bg); }\n.btn-info { .btn-styles(@btn-info-bg); }\n.btn-warning { .btn-styles(@btn-warning-bg); }\n.btn-danger { .btn-styles(@btn-danger-bg); }\n\n\n\n//\n// Images\n// --------------------------------------------------\n\n.thumbnail,\n.img-thumbnail {\n .box-shadow(0 1px 2px rgba(0,0,0,.075));\n}\n\n\n\n//\n// Dropdowns\n// --------------------------------------------------\n\n.dropdown-menu > li > a:hover,\n.dropdown-menu > li > a:focus {\n #gradient > .vertical(@start-color: @dropdown-link-hover-bg; @end-color: darken(@dropdown-link-hover-bg, 5%));\n background-color: darken(@dropdown-link-hover-bg, 5%);\n}\n.dropdown-menu > .active > a,\n.dropdown-menu > .active > a:hover,\n.dropdown-menu > .active > a:focus {\n #gradient > .vertical(@start-color: @dropdown-link-active-bg; @end-color: darken(@dropdown-link-active-bg, 5%));\n background-color: darken(@dropdown-link-active-bg, 5%);\n}\n\n\n\n//\n// Navbar\n// --------------------------------------------------\n\n// Default navbar\n.navbar-default {\n #gradient > .vertical(@start-color: lighten(@navbar-default-bg, 10%); @end-color: @navbar-default-bg);\n .reset-filter(); // Remove gradient in IE<10 to fix bug where dropdowns don't get triggered\n border-radius: @navbar-border-radius;\n @shadow: inset 0 1px 0 rgba(255,255,255,.15), 0 1px 5px rgba(0,0,0,.075);\n .box-shadow(@shadow);\n\n .navbar-nav > .active > a {\n #gradient > .vertical(@start-color: darken(@navbar-default-bg, 5%); @end-color: darken(@navbar-default-bg, 2%));\n .box-shadow(inset 0 3px 9px rgba(0,0,0,.075));\n }\n}\n.navbar-brand,\n.navbar-nav > li > a {\n text-shadow: 0 1px 0 rgba(255,255,255,.25);\n}\n\n// Inverted navbar\n.navbar-inverse {\n #gradient > .vertical(@start-color: lighten(@navbar-inverse-bg, 10%); @end-color: @navbar-inverse-bg);\n .reset-filter(); // Remove gradient in IE<10 to fix bug where dropdowns don't get triggered\n\n .navbar-nav > .active > a {\n #gradient > .vertical(@start-color: @navbar-inverse-bg; @end-color: lighten(@navbar-inverse-bg, 2.5%));\n .box-shadow(inset 0 3px 9px rgba(0,0,0,.25));\n }\n\n .navbar-brand,\n .navbar-nav > li > a {\n text-shadow: 0 -1px 0 rgba(0,0,0,.25);\n }\n}\n\n// Undo rounded corners in static and fixed navbars\n.navbar-static-top,\n.navbar-fixed-top,\n.navbar-fixed-bottom {\n border-radius: 0;\n}\n\n\n\n//\n// Alerts\n// --------------------------------------------------\n\n// Common styles\n.alert {\n text-shadow: 0 1px 0 rgba(255,255,255,.2);\n @shadow: inset 0 1px 0 rgba(255,255,255,.25), 0 1px 2px rgba(0,0,0,.05);\n .box-shadow(@shadow);\n}\n\n// Mixin for generating new styles\n.alert-styles(@color) {\n #gradient > .vertical(@start-color: @color; @end-color: darken(@color, 7.5%));\n border-color: darken(@color, 15%);\n}\n\n// Apply the mixin to the alerts\n.alert-success { .alert-styles(@alert-success-bg); }\n.alert-info { .alert-styles(@alert-info-bg); }\n.alert-warning { .alert-styles(@alert-warning-bg); }\n.alert-danger { .alert-styles(@alert-danger-bg); }\n\n\n\n//\n// Progress bars\n// --------------------------------------------------\n\n// Give the progress background some depth\n.progress {\n #gradient > .vertical(@start-color: darken(@progress-bg, 4%); @end-color: @progress-bg)\n}\n\n// Mixin for generating new styles\n.progress-bar-styles(@color) {\n #gradient > .vertical(@start-color: @color; @end-color: darken(@color, 10%));\n}\n\n// Apply the mixin to the progress bars\n.progress-bar { .progress-bar-styles(@progress-bar-bg); }\n.progress-bar-success { .progress-bar-styles(@progress-bar-success-bg); }\n.progress-bar-info { .progress-bar-styles(@progress-bar-info-bg); }\n.progress-bar-warning { .progress-bar-styles(@progress-bar-warning-bg); }\n.progress-bar-danger { .progress-bar-styles(@progress-bar-danger-bg); }\n\n// Reset the striped class because our mixins don't do multiple gradients and\n// the above custom styles override the new `.progress-bar-striped` in v3.2.0.\n.progress-bar-striped {\n #gradient > .striped();\n}\n\n\n//\n// List groups\n// --------------------------------------------------\n\n.list-group {\n border-radius: @border-radius-base;\n .box-shadow(0 1px 2px rgba(0,0,0,.075));\n}\n.list-group-item.active,\n.list-group-item.active:hover,\n.list-group-item.active:focus {\n text-shadow: 0 -1px 0 darken(@list-group-active-bg, 10%);\n #gradient > .vertical(@start-color: @list-group-active-bg; @end-color: darken(@list-group-active-bg, 7.5%));\n border-color: darken(@list-group-active-border, 7.5%);\n}\n\n\n\n//\n// Panels\n// --------------------------------------------------\n\n// Common styles\n.panel {\n .box-shadow(0 1px 2px rgba(0,0,0,.05));\n}\n\n// Mixin for generating new styles\n.panel-heading-styles(@color) {\n #gradient > .vertical(@start-color: @color; @end-color: darken(@color, 5%));\n}\n\n// Apply the mixin to the panel headings only\n.panel-default > .panel-heading { .panel-heading-styles(@panel-default-heading-bg); }\n.panel-primary > .panel-heading { .panel-heading-styles(@panel-primary-heading-bg); }\n.panel-success > .panel-heading { .panel-heading-styles(@panel-success-heading-bg); }\n.panel-info > .panel-heading { .panel-heading-styles(@panel-info-heading-bg); }\n.panel-warning > .panel-heading { .panel-heading-styles(@panel-warning-heading-bg); }\n.panel-danger > .panel-heading { .panel-heading-styles(@panel-danger-heading-bg); }\n\n\n\n//\n// Wells\n// --------------------------------------------------\n\n.well {\n #gradient > .vertical(@start-color: darken(@well-bg, 5%); @end-color: @well-bg);\n border-color: darken(@well-bg, 10%);\n @shadow: inset 0 1px 3px rgba(0,0,0,.05), 0 1px 0 rgba(255,255,255,.1);\n .box-shadow(@shadow);\n}\n","// Vendor Prefixes\n//\n// All vendor mixins are deprecated as of v3.2.0 due to the introduction of\n// Autoprefixer in our Gruntfile. They will be removed in v4.\n\n// - Animations\n// - Backface visibility\n// - Box shadow\n// - Box sizing\n// - Content columns\n// - Hyphens\n// - Placeholder text\n// - Transformations\n// - Transitions\n// - User Select\n\n\n// Animations\n.animation(@animation) {\n -webkit-animation: @animation;\n -o-animation: @animation;\n animation: @animation;\n}\n.animation-name(@name) {\n -webkit-animation-name: @name;\n animation-name: @name;\n}\n.animation-duration(@duration) {\n -webkit-animation-duration: @duration;\n animation-duration: @duration;\n}\n.animation-timing-function(@timing-function) {\n -webkit-animation-timing-function: @timing-function;\n animation-timing-function: @timing-function;\n}\n.animation-delay(@delay) {\n -webkit-animation-delay: @delay;\n animation-delay: @delay;\n}\n.animation-iteration-count(@iteration-count) {\n -webkit-animation-iteration-count: @iteration-count;\n animation-iteration-count: @iteration-count;\n}\n.animation-direction(@direction) {\n -webkit-animation-direction: @direction;\n animation-direction: @direction;\n}\n.animation-fill-mode(@fill-mode) {\n -webkit-animation-fill-mode: @fill-mode;\n animation-fill-mode: @fill-mode;\n}\n\n// Backface visibility\n// Prevent browsers from flickering when using CSS 3D transforms.\n// Default value is `visible`, but can be changed to `hidden`\n\n.backface-visibility(@visibility){\n -webkit-backface-visibility: @visibility;\n -moz-backface-visibility: @visibility;\n backface-visibility: @visibility;\n}\n\n// Drop shadows\n//\n// Note: Deprecated `.box-shadow()` as of v3.1.0 since all of Bootstrap's\n// supported browsers that have box shadow capabilities now support it.\n\n.box-shadow(@shadow) {\n -webkit-box-shadow: @shadow; // iOS <4.3 & Android <4.1\n box-shadow: @shadow;\n}\n\n// Box sizing\n.box-sizing(@boxmodel) {\n -webkit-box-sizing: @boxmodel;\n -moz-box-sizing: @boxmodel;\n box-sizing: @boxmodel;\n}\n\n// CSS3 Content Columns\n.content-columns(@column-count; @column-gap: @grid-gutter-width) {\n -webkit-column-count: @column-count;\n -moz-column-count: @column-count;\n column-count: @column-count;\n -webkit-column-gap: @column-gap;\n -moz-column-gap: @column-gap;\n column-gap: @column-gap;\n}\n\n// Optional hyphenation\n.hyphens(@mode: auto) {\n word-wrap: break-word;\n -webkit-hyphens: @mode;\n -moz-hyphens: @mode;\n -ms-hyphens: @mode; // IE10+\n -o-hyphens: @mode;\n hyphens: @mode;\n}\n\n// Placeholder text\n.placeholder(@color: @input-color-placeholder) {\n &::-moz-placeholder { color: @color; // Firefox\n opacity: 1; } // See https://github.com/twbs/bootstrap/pull/11526\n &:-ms-input-placeholder { color: @color; } // Internet Explorer 10+\n &::-webkit-input-placeholder { color: @color; } // Safari and Chrome\n}\n\n// Transformations\n.scale(@ratio) {\n -webkit-transform: scale(@ratio);\n -ms-transform: scale(@ratio); // IE9 only\n -o-transform: scale(@ratio);\n transform: scale(@ratio);\n}\n.scale(@ratioX; @ratioY) {\n -webkit-transform: scale(@ratioX, @ratioY);\n -ms-transform: scale(@ratioX, @ratioY); // IE9 only\n -o-transform: scale(@ratioX, @ratioY);\n transform: scale(@ratioX, @ratioY);\n}\n.scaleX(@ratio) {\n -webkit-transform: scaleX(@ratio);\n -ms-transform: scaleX(@ratio); // IE9 only\n -o-transform: scaleX(@ratio);\n transform: scaleX(@ratio);\n}\n.scaleY(@ratio) {\n -webkit-transform: scaleY(@ratio);\n -ms-transform: scaleY(@ratio); // IE9 only\n -o-transform: scaleY(@ratio);\n transform: scaleY(@ratio);\n}\n.skew(@x; @y) {\n -webkit-transform: skewX(@x) skewY(@y);\n -ms-transform: skewX(@x) skewY(@y); // See https://github.com/twbs/bootstrap/issues/4885; IE9+\n -o-transform: skewX(@x) skewY(@y);\n transform: skewX(@x) skewY(@y);\n}\n.translate(@x; @y) {\n -webkit-transform: translate(@x, @y);\n -ms-transform: translate(@x, @y); // IE9 only\n -o-transform: translate(@x, @y);\n transform: translate(@x, @y);\n}\n.translate3d(@x; @y; @z) {\n -webkit-transform: translate3d(@x, @y, @z);\n transform: translate3d(@x, @y, @z);\n}\n.rotate(@degrees) {\n -webkit-transform: rotate(@degrees);\n -ms-transform: rotate(@degrees); // IE9 only\n -o-transform: rotate(@degrees);\n transform: rotate(@degrees);\n}\n.rotateX(@degrees) {\n -webkit-transform: rotateX(@degrees);\n -ms-transform: rotateX(@degrees); // IE9 only\n -o-transform: rotateX(@degrees);\n transform: rotateX(@degrees);\n}\n.rotateY(@degrees) {\n -webkit-transform: rotateY(@degrees);\n -ms-transform: rotateY(@degrees); // IE9 only\n -o-transform: rotateY(@degrees);\n transform: rotateY(@degrees);\n}\n.perspective(@perspective) {\n -webkit-perspective: @perspective;\n -moz-perspective: @perspective;\n perspective: @perspective;\n}\n.perspective-origin(@perspective) {\n -webkit-perspective-origin: @perspective;\n -moz-perspective-origin: @perspective;\n perspective-origin: @perspective;\n}\n.transform-origin(@origin) {\n -webkit-transform-origin: @origin;\n -moz-transform-origin: @origin;\n -ms-transform-origin: @origin; // IE9 only\n transform-origin: @origin;\n}\n\n\n// Transitions\n\n.transition(@transition) {\n -webkit-transition: @transition;\n -o-transition: @transition;\n transition: @transition;\n}\n.transition-property(@transition-property) {\n -webkit-transition-property: @transition-property;\n transition-property: @transition-property;\n}\n.transition-delay(@transition-delay) {\n -webkit-transition-delay: @transition-delay;\n transition-delay: @transition-delay;\n}\n.transition-duration(@transition-duration) {\n -webkit-transition-duration: @transition-duration;\n transition-duration: @transition-duration;\n}\n.transition-timing-function(@timing-function) {\n -webkit-transition-timing-function: @timing-function;\n transition-timing-function: @timing-function;\n}\n.transition-transform(@transition) {\n -webkit-transition: -webkit-transform @transition;\n -moz-transition: -moz-transform @transition;\n -o-transition: -o-transform @transition;\n transition: transform @transition;\n}\n\n\n// User select\n// For selecting text on the page\n\n.user-select(@select) {\n -webkit-user-select: @select;\n -moz-user-select: @select;\n -ms-user-select: @select; // IE10+\n user-select: @select;\n}\n",null,"// Gradients\n\n#gradient {\n\n // Horizontal gradient, from left to right\n //\n // Creates two color stops, start and end, by specifying a color and position for each color stop.\n // Color stops are not available in IE9 and below.\n .horizontal(@start-color: #555; @end-color: #333; @start-percent: 0%; @end-percent: 100%) {\n background-image: -webkit-linear-gradient(left, @start-color @start-percent, @end-color @end-percent); // Safari 5.1-6, Chrome 10+\n background-image: -o-linear-gradient(left, @start-color @start-percent, @end-color @end-percent); // Opera 12\n background-image: linear-gradient(to right, @start-color @start-percent, @end-color @end-percent); // Standard, IE10, Firefox 16+, Opera 12.10+, Safari 7+, Chrome 26+\n background-repeat: repeat-x;\n filter: e(%(\"progid:DXImageTransform.Microsoft.gradient(startColorstr='%d', endColorstr='%d', GradientType=1)\",argb(@start-color),argb(@end-color))); // IE9 and down\n }\n\n // Vertical gradient, from top to bottom\n //\n // Creates two color stops, start and end, by specifying a color and position for each color stop.\n // Color stops are not available in IE9 and below.\n .vertical(@start-color: #555; @end-color: #333; @start-percent: 0%; @end-percent: 100%) {\n background-image: -webkit-linear-gradient(top, @start-color @start-percent, @end-color @end-percent); // Safari 5.1-6, Chrome 10+\n background-image: -o-linear-gradient(top, @start-color @start-percent, @end-color @end-percent); // Opera 12\n background-image: linear-gradient(to bottom, @start-color @start-percent, @end-color @end-percent); // Standard, IE10, Firefox 16+, Opera 12.10+, Safari 7+, Chrome 26+\n background-repeat: repeat-x;\n filter: e(%(\"progid:DXImageTransform.Microsoft.gradient(startColorstr='%d', endColorstr='%d', GradientType=0)\",argb(@start-color),argb(@end-color))); // IE9 and down\n }\n\n .directional(@start-color: #555; @end-color: #333; @deg: 45deg) {\n background-repeat: repeat-x;\n background-image: -webkit-linear-gradient(@deg, @start-color, @end-color); // Safari 5.1-6, Chrome 10+\n background-image: -o-linear-gradient(@deg, @start-color, @end-color); // Opera 12\n background-image: linear-gradient(@deg, @start-color, @end-color); // Standard, IE10, Firefox 16+, Opera 12.10+, Safari 7+, Chrome 26+\n }\n .horizontal-three-colors(@start-color: #00b3ee; @mid-color: #7a43b6; @color-stop: 50%; @end-color: #c3325f) {\n background-image: -webkit-linear-gradient(left, @start-color, @mid-color @color-stop, @end-color);\n background-image: -o-linear-gradient(left, @start-color, @mid-color @color-stop, @end-color);\n background-image: linear-gradient(to right, @start-color, @mid-color @color-stop, @end-color);\n background-repeat: no-repeat;\n filter: e(%(\"progid:DXImageTransform.Microsoft.gradient(startColorstr='%d', endColorstr='%d', GradientType=1)\",argb(@start-color),argb(@end-color))); // IE9 and down, gets no color-stop at all for proper fallback\n }\n .vertical-three-colors(@start-color: #00b3ee; @mid-color: #7a43b6; @color-stop: 50%; @end-color: #c3325f) {\n background-image: -webkit-linear-gradient(@start-color, @mid-color @color-stop, @end-color);\n background-image: -o-linear-gradient(@start-color, @mid-color @color-stop, @end-color);\n background-image: linear-gradient(@start-color, @mid-color @color-stop, @end-color);\n background-repeat: no-repeat;\n filter: e(%(\"progid:DXImageTransform.Microsoft.gradient(startColorstr='%d', endColorstr='%d', GradientType=0)\",argb(@start-color),argb(@end-color))); // IE9 and down, gets no color-stop at all for proper fallback\n }\n .radial(@inner-color: #555; @outer-color: #333) {\n background-image: -webkit-radial-gradient(circle, @inner-color, @outer-color);\n background-image: radial-gradient(circle, @inner-color, @outer-color);\n background-repeat: no-repeat;\n }\n .striped(@color: rgba(255,255,255,.15); @angle: 45deg) {\n background-image: -webkit-linear-gradient(@angle, @color 25%, transparent 25%, transparent 50%, @color 50%, @color 75%, transparent 75%, transparent);\n background-image: -o-linear-gradient(@angle, @color 25%, transparent 25%, transparent 50%, @color 50%, @color 75%, transparent 75%, transparent);\n background-image: linear-gradient(@angle, @color 25%, transparent 25%, transparent 50%, @color 50%, @color 75%, transparent 75%, transparent);\n }\n}\n","// Reset filters for IE\n//\n// When you need to remove a gradient background, do not forget to use this to reset\n// the IE filter for IE9 and below.\n\n.reset-filter() {\n filter: e(%(\"progid:DXImageTransform.Microsoft.gradient(enabled = false)\"));\n}\n"]}
\ No newline at end of file
diff --git a/docs/build/html/_static/bootstrap-3.2.0/css/bootstrap-theme.min.css b/docs/build/html/_static/bootstrap-3.2.0/css/bootstrap-theme.min.css
new file mode 100644
index 0000000000000000000000000000000000000000..2e97597c876ddd2c5d081dd27db3a90e61d925e9
--- /dev/null
+++ b/docs/build/html/_static/bootstrap-3.2.0/css/bootstrap-theme.min.css
@@ -0,0 +1,5 @@
+/*!
+ * Bootstrap v3.2.0 (http://getbootstrap.com)
+ * Copyright 2011-2014 Twitter, Inc.
+ * Licensed under MIT (https://github.com/twbs/bootstrap/blob/master/LICENSE)
+ */.btn-default,.btn-primary,.btn-success,.btn-info,.btn-warning,.btn-danger{text-shadow:0 -1px 0 rgba(0,0,0,.2);-webkit-box-shadow:inset 0 1px 0 rgba(255,255,255,.15),0 1px 1px rgba(0,0,0,.075);box-shadow:inset 0 1px 0 rgba(255,255,255,.15),0 1px 1px rgba(0,0,0,.075)}.btn-default:active,.btn-primary:active,.btn-success:active,.btn-info:active,.btn-warning:active,.btn-danger:active,.btn-default.active,.btn-primary.active,.btn-success.active,.btn-info.active,.btn-warning.active,.btn-danger.active{-webkit-box-shadow:inset 0 3px 5px rgba(0,0,0,.125);box-shadow:inset 0 3px 5px rgba(0,0,0,.125)}.btn:active,.btn.active{background-image:none}.btn-default{text-shadow:0 1px 0 #fff;background-image:-webkit-linear-gradient(top,#fff 0,#e0e0e0 100%);background-image:-o-linear-gradient(top,#fff 0,#e0e0e0 100%);background-image:-webkit-gradient(linear,left top,left bottom,from(#fff),to(#e0e0e0));background-image:linear-gradient(to bottom,#fff 0,#e0e0e0 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\ No newline at end of file
diff --git a/docs/build/html/_static/bootstrap-3.2.0/css/bootstrap.css b/docs/build/html/_static/bootstrap-3.2.0/css/bootstrap.css
new file mode 100644
index 0000000000000000000000000000000000000000..037dd0561510db605878e08bc9b513d79ffc9782
--- /dev/null
+++ b/docs/build/html/_static/bootstrap-3.2.0/css/bootstrap.css
@@ -0,0 +1,6203 @@
+/*!
+ * Bootstrap v3.2.0 (http://getbootstrap.com)
+ * Copyright 2011-2014 Twitter, Inc.
+ * Licensed under MIT (https://github.com/twbs/bootstrap/blob/master/LICENSE)
+ */
+
+/*! normalize.css v3.0.1 | MIT License | git.io/normalize */
+html {
+ font-family: sans-serif;
+ -webkit-text-size-adjust: 100%;
+ -ms-text-size-adjust: 100%;
+}
+body {
+ margin: 0;
+}
+article,
+aside,
+details,
+figcaption,
+figure,
+footer,
+header,
+hgroup,
+main,
+nav,
+section,
+summary {
+ display: block;
+}
+audio,
+canvas,
+progress,
+video {
+ display: inline-block;
+ vertical-align: baseline;
+}
+audio:not([controls]) {
+ display: none;
+ height: 0;
+}
+[hidden],
+template {
+ display: none;
+}
+a {
+ background: transparent;
+}
+a:active,
+a:hover {
+ outline: 0;
+}
+abbr[title] {
+ border-bottom: 1px dotted;
+}
+b,
+strong {
+ font-weight: bold;
+}
+dfn {
+ font-style: italic;
+}
+h1 {
+ margin: .67em 0;
+ font-size: 2em;
+}
+mark {
+ color: #000;
+ background: #ff0;
+}
+small {
+ font-size: 80%;
+}
+sub,
+sup {
+ position: relative;
+ font-size: 75%;
+ line-height: 0;
+ vertical-align: baseline;
+}
+sup {
+ top: -.5em;
+}
+sub {
+ bottom: -.25em;
+}
+img {
+ border: 0;
+}
+svg:not(:root) {
+ overflow: hidden;
+}
+figure {
+ margin: 1em 40px;
+}
+hr {
+ height: 0;
+ -webkit-box-sizing: content-box;
+ -moz-box-sizing: content-box;
+ box-sizing: content-box;
+}
+pre {
+ overflow: auto;
+}
+code,
+kbd,
+pre,
+samp {
+ font-family: monospace, monospace;
+ font-size: 1em;
+}
+button,
+input,
+optgroup,
+select,
+textarea {
+ margin: 0;
+ font: inherit;
+ color: inherit;
+}
+button {
+ overflow: visible;
+}
+button,
+select {
+ text-transform: none;
+}
+button,
+html input[type="button"],
+input[type="reset"],
+input[type="submit"] {
+ -webkit-appearance: button;
+ cursor: pointer;
+}
+button[disabled],
+html input[disabled] {
+ cursor: default;
+}
+button::-moz-focus-inner,
+input::-moz-focus-inner {
+ padding: 0;
+ border: 0;
+}
+input {
+ line-height: normal;
+}
+input[type="checkbox"],
+input[type="radio"] {
+ -webkit-box-sizing: border-box;
+ -moz-box-sizing: border-box;
+ box-sizing: border-box;
+ padding: 0;
+}
+input[type="number"]::-webkit-inner-spin-button,
+input[type="number"]::-webkit-outer-spin-button {
+ height: auto;
+}
+input[type="search"] {
+ -webkit-box-sizing: content-box;
+ -moz-box-sizing: content-box;
+ box-sizing: content-box;
+ -webkit-appearance: textfield;
+}
+input[type="search"]::-webkit-search-cancel-button,
+input[type="search"]::-webkit-search-decoration {
+ -webkit-appearance: none;
+}
+fieldset {
+ padding: .35em .625em .75em;
+ margin: 0 2px;
+ border: 1px solid #c0c0c0;
+}
+legend {
+ padding: 0;
+ border: 0;
+}
+textarea {
+ overflow: auto;
+}
+optgroup {
+ font-weight: bold;
+}
+table {
+ border-spacing: 0;
+ border-collapse: collapse;
+}
+td,
+th {
+ padding: 0;
+}
+@media print {
+ * {
+ color: #000 !important;
+ text-shadow: none !important;
+ background: transparent !important;
+ -webkit-box-shadow: none !important;
+ box-shadow: none !important;
+ }
+ a,
+ a:visited {
+ text-decoration: underline;
+ }
+ a[href]:after {
+ content: " (" attr(href) ")";
+ }
+ abbr[title]:after {
+ content: " (" attr(title) ")";
+ }
+ a[href^="javascript:"]:after,
+ a[href^="#"]:after {
+ content: "";
+ }
+ pre,
+ blockquote {
+ border: 1px solid #999;
+
+ page-break-inside: avoid;
+ }
+ thead {
+ display: table-header-group;
+ }
+ tr,
+ img {
+ page-break-inside: avoid;
+ }
+ img {
+ max-width: 100% !important;
+ }
+ p,
+ h2,
+ h3 {
+ orphans: 3;
+ widows: 3;
+ }
+ h2,
+ h3 {
+ page-break-after: avoid;
+ }
+ select {
+ background: #fff !important;
+ }
+ .navbar {
+ display: none;
+ }
+ .table td,
+ .table th {
+ background-color: #fff !important;
+ }
+ .btn > .caret,
+ .dropup > .btn > .caret {
+ border-top-color: #000 !important;
+ }
+ .label {
+ border: 1px solid #000;
+ }
+ .table {
+ border-collapse: collapse !important;
+ }
+ .table-bordered th,
+ .table-bordered td {
+ border: 1px solid #ddd !important;
+ }
+}
+@font-face {
+ font-family: 'Glyphicons Halflings';
+
+ src: url('../fonts/glyphicons-halflings-regular.eot');
+ src: url('../fonts/glyphicons-halflings-regular.eot?#iefix') format('embedded-opentype'), url('../fonts/glyphicons-halflings-regular.woff') format('woff'), url('../fonts/glyphicons-halflings-regular.ttf') format('truetype'), url('../fonts/glyphicons-halflings-regular.svg#glyphicons_halflingsregular') format('svg');
+}
+.glyphicon {
+ position: relative;
+ top: 1px;
+ display: inline-block;
+ font-family: 'Glyphicons Halflings';
+ font-style: normal;
+ font-weight: normal;
+ line-height: 1;
+
+ -webkit-font-smoothing: antialiased;
+ -moz-osx-font-smoothing: grayscale;
+}
+.glyphicon-asterisk:before {
+ content: "\2a";
+}
+.glyphicon-plus:before {
+ content: "\2b";
+}
+.glyphicon-euro:before {
+ content: "\20ac";
+}
+.glyphicon-minus:before {
+ content: "\2212";
+}
+.glyphicon-cloud:before {
+ content: "\2601";
+}
+.glyphicon-envelope:before {
+ content: "\2709";
+}
+.glyphicon-pencil:before {
+ content: "\270f";
+}
+.glyphicon-glass:before {
+ content: "\e001";
+}
+.glyphicon-music:before {
+ content: "\e002";
+}
+.glyphicon-search:before {
+ content: "\e003";
+}
+.glyphicon-heart:before {
+ content: "\e005";
+}
+.glyphicon-star:before {
+ content: "\e006";
+}
+.glyphicon-star-empty:before {
+ content: "\e007";
+}
+.glyphicon-user:before {
+ content: "\e008";
+}
+.glyphicon-film:before {
+ content: "\e009";
+}
+.glyphicon-th-large:before {
+ content: "\e010";
+}
+.glyphicon-th:before {
+ content: "\e011";
+}
+.glyphicon-th-list:before {
+ content: "\e012";
+}
+.glyphicon-ok:before {
+ content: "\e013";
+}
+.glyphicon-remove:before {
+ content: "\e014";
+}
+.glyphicon-zoom-in:before {
+ content: "\e015";
+}
+.glyphicon-zoom-out:before {
+ content: "\e016";
+}
+.glyphicon-off:before {
+ content: "\e017";
+}
+.glyphicon-signal:before {
+ content: "\e018";
+}
+.glyphicon-cog:before {
+ content: "\e019";
+}
+.glyphicon-trash:before {
+ content: "\e020";
+}
+.glyphicon-home:before {
+ content: "\e021";
+}
+.glyphicon-file:before {
+ content: "\e022";
+}
+.glyphicon-time:before {
+ content: "\e023";
+}
+.glyphicon-road:before {
+ content: "\e024";
+}
+.glyphicon-download-alt:before {
+ content: "\e025";
+}
+.glyphicon-download:before {
+ content: "\e026";
+}
+.glyphicon-upload:before {
+ content: "\e027";
+}
+.glyphicon-inbox:before {
+ content: "\e028";
+}
+.glyphicon-play-circle:before {
+ content: "\e029";
+}
+.glyphicon-repeat:before {
+ content: "\e030";
+}
+.glyphicon-refresh:before {
+ content: "\e031";
+}
+.glyphicon-list-alt:before {
+ content: "\e032";
+}
+.glyphicon-lock:before {
+ content: "\e033";
+}
+.glyphicon-flag:before {
+ content: "\e034";
+}
+.glyphicon-headphones:before {
+ content: "\e035";
+}
+.glyphicon-volume-off:before {
+ content: "\e036";
+}
+.glyphicon-volume-down:before {
+ content: "\e037";
+}
+.glyphicon-volume-up:before {
+ content: "\e038";
+}
+.glyphicon-qrcode:before {
+ content: "\e039";
+}
+.glyphicon-barcode:before {
+ content: "\e040";
+}
+.glyphicon-tag:before {
+ content: "\e041";
+}
+.glyphicon-tags:before {
+ content: "\e042";
+}
+.glyphicon-book:before {
+ content: "\e043";
+}
+.glyphicon-bookmark:before {
+ content: "\e044";
+}
+.glyphicon-print:before {
+ content: "\e045";
+}
+.glyphicon-camera:before {
+ content: "\e046";
+}
+.glyphicon-font:before {
+ content: "\e047";
+}
+.glyphicon-bold:before {
+ content: "\e048";
+}
+.glyphicon-italic:before {
+ content: "\e049";
+}
+.glyphicon-text-height:before {
+ content: "\e050";
+}
+.glyphicon-text-width:before {
+ content: "\e051";
+}
+.glyphicon-align-left:before {
+ content: "\e052";
+}
+.glyphicon-align-center:before {
+ content: "\e053";
+}
+.glyphicon-align-right:before {
+ content: "\e054";
+}
+.glyphicon-align-justify:before {
+ content: "\e055";
+}
+.glyphicon-list:before {
+ content: "\e056";
+}
+.glyphicon-indent-left:before {
+ content: "\e057";
+}
+.glyphicon-indent-right:before {
+ content: "\e058";
+}
+.glyphicon-facetime-video:before {
+ content: "\e059";
+}
+.glyphicon-picture:before {
+ content: "\e060";
+}
+.glyphicon-map-marker:before {
+ content: "\e062";
+}
+.glyphicon-adjust:before {
+ content: "\e063";
+}
+.glyphicon-tint:before {
+ content: "\e064";
+}
+.glyphicon-edit:before {
+ content: "\e065";
+}
+.glyphicon-share:before {
+ content: "\e066";
+}
+.glyphicon-check:before {
+ content: "\e067";
+}
+.glyphicon-move:before {
+ content: "\e068";
+}
+.glyphicon-step-backward:before {
+ content: "\e069";
+}
+.glyphicon-fast-backward:before {
+ content: "\e070";
+}
+.glyphicon-backward:before {
+ content: "\e071";
+}
+.glyphicon-play:before {
+ content: "\e072";
+}
+.glyphicon-pause:before {
+ content: "\e073";
+}
+.glyphicon-stop:before {
+ content: "\e074";
+}
+.glyphicon-forward:before {
+ content: "\e075";
+}
+.glyphicon-fast-forward:before {
+ content: "\e076";
+}
+.glyphicon-step-forward:before {
+ content: "\e077";
+}
+.glyphicon-eject:before {
+ content: "\e078";
+}
+.glyphicon-chevron-left:before {
+ content: "\e079";
+}
+.glyphicon-chevron-right:before {
+ content: "\e080";
+}
+.glyphicon-plus-sign:before {
+ content: "\e081";
+}
+.glyphicon-minus-sign:before {
+ content: "\e082";
+}
+.glyphicon-remove-sign:before {
+ content: "\e083";
+}
+.glyphicon-ok-sign:before {
+ content: "\e084";
+}
+.glyphicon-question-sign:before {
+ content: "\e085";
+}
+.glyphicon-info-sign:before {
+ content: "\e086";
+}
+.glyphicon-screenshot:before {
+ content: "\e087";
+}
+.glyphicon-remove-circle:before {
+ content: "\e088";
+}
+.glyphicon-ok-circle:before {
+ content: "\e089";
+}
+.glyphicon-ban-circle:before {
+ content: "\e090";
+}
+.glyphicon-arrow-left:before {
+ content: "\e091";
+}
+.glyphicon-arrow-right:before {
+ content: "\e092";
+}
+.glyphicon-arrow-up:before {
+ content: "\e093";
+}
+.glyphicon-arrow-down:before {
+ content: "\e094";
+}
+.glyphicon-share-alt:before {
+ content: "\e095";
+}
+.glyphicon-resize-full:before {
+ content: "\e096";
+}
+.glyphicon-resize-small:before {
+ content: "\e097";
+}
+.glyphicon-exclamation-sign:before {
+ content: "\e101";
+}
+.glyphicon-gift:before {
+ content: "\e102";
+}
+.glyphicon-leaf:before {
+ content: "\e103";
+}
+.glyphicon-fire:before {
+ content: "\e104";
+}
+.glyphicon-eye-open:before {
+ content: "\e105";
+}
+.glyphicon-eye-close:before {
+ content: "\e106";
+}
+.glyphicon-warning-sign:before {
+ content: "\e107";
+}
+.glyphicon-plane:before {
+ content: "\e108";
+}
+.glyphicon-calendar:before {
+ content: "\e109";
+}
+.glyphicon-random:before {
+ content: "\e110";
+}
+.glyphicon-comment:before {
+ content: "\e111";
+}
+.glyphicon-magnet:before {
+ content: "\e112";
+}
+.glyphicon-chevron-up:before {
+ content: "\e113";
+}
+.glyphicon-chevron-down:before {
+ content: "\e114";
+}
+.glyphicon-retweet:before {
+ content: "\e115";
+}
+.glyphicon-shopping-cart:before {
+ content: "\e116";
+}
+.glyphicon-folder-close:before {
+ content: "\e117";
+}
+.glyphicon-folder-open:before {
+ content: "\e118";
+}
+.glyphicon-resize-vertical:before {
+ content: "\e119";
+}
+.glyphicon-resize-horizontal:before {
+ content: "\e120";
+}
+.glyphicon-hdd:before {
+ content: "\e121";
+}
+.glyphicon-bullhorn:before {
+ content: "\e122";
+}
+.glyphicon-bell:before {
+ content: "\e123";
+}
+.glyphicon-certificate:before {
+ content: "\e124";
+}
+.glyphicon-thumbs-up:before {
+ content: "\e125";
+}
+.glyphicon-thumbs-down:before {
+ content: "\e126";
+}
+.glyphicon-hand-right:before {
+ content: "\e127";
+}
+.glyphicon-hand-left:before {
+ content: "\e128";
+}
+.glyphicon-hand-up:before {
+ content: "\e129";
+}
+.glyphicon-hand-down:before {
+ content: "\e130";
+}
+.glyphicon-circle-arrow-right:before {
+ content: "\e131";
+}
+.glyphicon-circle-arrow-left:before {
+ content: "\e132";
+}
+.glyphicon-circle-arrow-up:before {
+ content: "\e133";
+}
+.glyphicon-circle-arrow-down:before {
+ content: "\e134";
+}
+.glyphicon-globe:before {
+ content: "\e135";
+}
+.glyphicon-wrench:before {
+ content: "\e136";
+}
+.glyphicon-tasks:before {
+ content: "\e137";
+}
+.glyphicon-filter:before {
+ content: "\e138";
+}
+.glyphicon-briefcase:before {
+ content: "\e139";
+}
+.glyphicon-fullscreen:before {
+ content: "\e140";
+}
+.glyphicon-dashboard:before {
+ content: "\e141";
+}
+.glyphicon-paperclip:before {
+ content: "\e142";
+}
+.glyphicon-heart-empty:before {
+ content: "\e143";
+}
+.glyphicon-link:before {
+ content: "\e144";
+}
+.glyphicon-phone:before {
+ content: "\e145";
+}
+.glyphicon-pushpin:before {
+ content: "\e146";
+}
+.glyphicon-usd:before {
+ content: "\e148";
+}
+.glyphicon-gbp:before {
+ content: "\e149";
+}
+.glyphicon-sort:before {
+ content: "\e150";
+}
+.glyphicon-sort-by-alphabet:before {
+ content: "\e151";
+}
+.glyphicon-sort-by-alphabet-alt:before {
+ content: "\e152";
+}
+.glyphicon-sort-by-order:before {
+ content: "\e153";
+}
+.glyphicon-sort-by-order-alt:before {
+ content: "\e154";
+}
+.glyphicon-sort-by-attributes:before {
+ content: "\e155";
+}
+.glyphicon-sort-by-attributes-alt:before {
+ content: "\e156";
+}
+.glyphicon-unchecked:before {
+ content: "\e157";
+}
+.glyphicon-expand:before {
+ content: "\e158";
+}
+.glyphicon-collapse-down:before {
+ content: "\e159";
+}
+.glyphicon-collapse-up:before {
+ content: "\e160";
+}
+.glyphicon-log-in:before {
+ content: "\e161";
+}
+.glyphicon-flash:before {
+ content: "\e162";
+}
+.glyphicon-log-out:before {
+ content: "\e163";
+}
+.glyphicon-new-window:before {
+ content: "\e164";
+}
+.glyphicon-record:before {
+ content: "\e165";
+}
+.glyphicon-save:before {
+ content: "\e166";
+}
+.glyphicon-open:before {
+ content: "\e167";
+}
+.glyphicon-saved:before {
+ content: "\e168";
+}
+.glyphicon-import:before {
+ content: "\e169";
+}
+.glyphicon-export:before {
+ content: "\e170";
+}
+.glyphicon-send:before {
+ content: "\e171";
+}
+.glyphicon-floppy-disk:before {
+ content: "\e172";
+}
+.glyphicon-floppy-saved:before {
+ content: "\e173";
+}
+.glyphicon-floppy-remove:before {
+ content: "\e174";
+}
+.glyphicon-floppy-save:before {
+ content: "\e175";
+}
+.glyphicon-floppy-open:before {
+ content: "\e176";
+}
+.glyphicon-credit-card:before {
+ content: "\e177";
+}
+.glyphicon-transfer:before {
+ content: "\e178";
+}
+.glyphicon-cutlery:before {
+ content: "\e179";
+}
+.glyphicon-header:before {
+ content: "\e180";
+}
+.glyphicon-compressed:before {
+ content: "\e181";
+}
+.glyphicon-earphone:before {
+ content: "\e182";
+}
+.glyphicon-phone-alt:before {
+ content: "\e183";
+}
+.glyphicon-tower:before {
+ content: "\e184";
+}
+.glyphicon-stats:before {
+ content: "\e185";
+}
+.glyphicon-sd-video:before {
+ content: "\e186";
+}
+.glyphicon-hd-video:before {
+ content: "\e187";
+}
+.glyphicon-subtitles:before {
+ content: "\e188";
+}
+.glyphicon-sound-stereo:before {
+ content: "\e189";
+}
+.glyphicon-sound-dolby:before {
+ content: "\e190";
+}
+.glyphicon-sound-5-1:before {
+ content: "\e191";
+}
+.glyphicon-sound-6-1:before {
+ content: "\e192";
+}
+.glyphicon-sound-7-1:before {
+ content: "\e193";
+}
+.glyphicon-copyright-mark:before {
+ content: "\e194";
+}
+.glyphicon-registration-mark:before {
+ content: "\e195";
+}
+.glyphicon-cloud-download:before {
+ content: "\e197";
+}
+.glyphicon-cloud-upload:before {
+ content: "\e198";
+}
+.glyphicon-tree-conifer:before {
+ content: "\e199";
+}
+.glyphicon-tree-deciduous:before {
+ content: "\e200";
+}
+* {
+ -webkit-box-sizing: border-box;
+ -moz-box-sizing: border-box;
+ box-sizing: border-box;
+}
+*:before,
+*:after {
+ -webkit-box-sizing: border-box;
+ -moz-box-sizing: border-box;
+ box-sizing: border-box;
+}
+html {
+ font-size: 10px;
+
+ -webkit-tap-highlight-color: rgba(0, 0, 0, 0);
+}
+body {
+ font-family: "Helvetica Neue", Helvetica, Arial, sans-serif;
+ font-size: 14px;
+ line-height: 1.42857143;
+ color: #333;
+ background-color: #fff;
+}
+input,
+button,
+select,
+textarea {
+ font-family: inherit;
+ font-size: inherit;
+ line-height: inherit;
+}
+a {
+ color: #428bca;
+ text-decoration: none;
+}
+a:hover,
+a:focus {
+ color: #2a6496;
+ text-decoration: underline;
+}
+a:focus {
+ outline: thin dotted;
+ outline: 5px auto -webkit-focus-ring-color;
+ outline-offset: -2px;
+}
+figure {
+ margin: 0;
+}
+img {
+ vertical-align: middle;
+}
+.img-responsive,
+.thumbnail > img,
+.thumbnail a > img,
+.carousel-inner > .item > img,
+.carousel-inner > .item > a > img {
+ display: block;
+ width: 100% \9;
+ max-width: 100%;
+ height: auto;
+}
+.img-rounded {
+ border-radius: 6px;
+}
+.img-thumbnail {
+ display: inline-block;
+ width: 100% \9;
+ max-width: 100%;
+ height: auto;
+ padding: 4px;
+ line-height: 1.42857143;
+ background-color: #fff;
+ border: 1px solid #ddd;
+ border-radius: 4px;
+ -webkit-transition: all .2s ease-in-out;
+ -o-transition: all .2s ease-in-out;
+ transition: all .2s ease-in-out;
+}
+.img-circle {
+ border-radius: 50%;
+}
+hr {
+ margin-top: 20px;
+ margin-bottom: 20px;
+ border: 0;
+ border-top: 1px solid #eee;
+}
+.sr-only {
+ position: absolute;
+ width: 1px;
+ height: 1px;
+ padding: 0;
+ margin: -1px;
+ overflow: hidden;
+ clip: rect(0, 0, 0, 0);
+ border: 0;
+}
+.sr-only-focusable:active,
+.sr-only-focusable:focus {
+ position: static;
+ width: auto;
+ height: auto;
+ margin: 0;
+ overflow: visible;
+ clip: auto;
+}
+h1,
+h2,
+h3,
+h4,
+h5,
+h6,
+.h1,
+.h2,
+.h3,
+.h4,
+.h5,
+.h6 {
+ font-family: inherit;
+ font-weight: 500;
+ line-height: 1.1;
+ color: inherit;
+}
+h1 small,
+h2 small,
+h3 small,
+h4 small,
+h5 small,
+h6 small,
+.h1 small,
+.h2 small,
+.h3 small,
+.h4 small,
+.h5 small,
+.h6 small,
+h1 .small,
+h2 .small,
+h3 .small,
+h4 .small,
+h5 .small,
+h6 .small,
+.h1 .small,
+.h2 .small,
+.h3 .small,
+.h4 .small,
+.h5 .small,
+.h6 .small {
+ font-weight: normal;
+ line-height: 1;
+ color: #777;
+}
+h1,
+.h1,
+h2,
+.h2,
+h3,
+.h3 {
+ margin-top: 20px;
+ margin-bottom: 10px;
+}
+h1 small,
+.h1 small,
+h2 small,
+.h2 small,
+h3 small,
+.h3 small,
+h1 .small,
+.h1 .small,
+h2 .small,
+.h2 .small,
+h3 .small,
+.h3 .small {
+ font-size: 65%;
+}
+h4,
+.h4,
+h5,
+.h5,
+h6,
+.h6 {
+ margin-top: 10px;
+ margin-bottom: 10px;
+}
+h4 small,
+.h4 small,
+h5 small,
+.h5 small,
+h6 small,
+.h6 small,
+h4 .small,
+.h4 .small,
+h5 .small,
+.h5 .small,
+h6 .small,
+.h6 .small {
+ font-size: 75%;
+}
+h1,
+.h1 {
+ font-size: 36px;
+}
+h2,
+.h2 {
+ font-size: 30px;
+}
+h3,
+.h3 {
+ font-size: 24px;
+}
+h4,
+.h4 {
+ font-size: 18px;
+}
+h5,
+.h5 {
+ font-size: 14px;
+}
+h6,
+.h6 {
+ font-size: 12px;
+}
+p {
+ margin: 0 0 10px;
+}
+.lead {
+ margin-bottom: 20px;
+ font-size: 16px;
+ font-weight: 300;
+ line-height: 1.4;
+}
+@media (min-width: 768px) {
+ .lead {
+ font-size: 21px;
+ }
+}
+small,
+.small {
+ font-size: 85%;
+}
+cite {
+ font-style: normal;
+}
+mark,
+.mark {
+ padding: .2em;
+ background-color: #fcf8e3;
+}
+.text-left {
+ text-align: left;
+}
+.text-right {
+ text-align: right;
+}
+.text-center {
+ text-align: center;
+}
+.text-justify {
+ text-align: justify;
+}
+.text-nowrap {
+ white-space: nowrap;
+}
+.text-lowercase {
+ text-transform: lowercase;
+}
+.text-uppercase {
+ text-transform: uppercase;
+}
+.text-capitalize {
+ text-transform: capitalize;
+}
+.text-muted {
+ color: #777;
+}
+.text-primary {
+ color: #428bca;
+}
+a.text-primary:hover {
+ color: #3071a9;
+}
+.text-success {
+ color: #3c763d;
+}
+a.text-success:hover {
+ color: #2b542c;
+}
+.text-info {
+ color: #31708f;
+}
+a.text-info:hover {
+ color: #245269;
+}
+.text-warning {
+ color: #8a6d3b;
+}
+a.text-warning:hover {
+ color: #66512c;
+}
+.text-danger {
+ color: #a94442;
+}
+a.text-danger:hover {
+ color: #843534;
+}
+.bg-primary {
+ color: #fff;
+ background-color: #428bca;
+}
+a.bg-primary:hover {
+ background-color: #3071a9;
+}
+.bg-success {
+ background-color: #dff0d8;
+}
+a.bg-success:hover {
+ background-color: #c1e2b3;
+}
+.bg-info {
+ background-color: #d9edf7;
+}
+a.bg-info:hover {
+ background-color: #afd9ee;
+}
+.bg-warning {
+ background-color: #fcf8e3;
+}
+a.bg-warning:hover {
+ background-color: #f7ecb5;
+}
+.bg-danger {
+ background-color: #f2dede;
+}
+a.bg-danger:hover {
+ background-color: #e4b9b9;
+}
+.page-header {
+ padding-bottom: 9px;
+ margin: 40px 0 20px;
+ border-bottom: 1px solid #eee;
+}
+ul,
+ol {
+ margin-top: 0;
+ margin-bottom: 10px;
+}
+ul ul,
+ol ul,
+ul ol,
+ol ol {
+ margin-bottom: 0;
+}
+.list-unstyled {
+ padding-left: 0;
+ list-style: none;
+}
+.list-inline {
+ padding-left: 0;
+ margin-left: -5px;
+ list-style: none;
+}
+.list-inline > li {
+ display: inline-block;
+ padding-right: 5px;
+ padding-left: 5px;
+}
+dl {
+ margin-top: 0;
+ margin-bottom: 20px;
+}
+dt,
+dd {
+ line-height: 1.42857143;
+}
+dt {
+ font-weight: bold;
+}
+dd {
+ margin-left: 0;
+}
+@media (min-width: 768px) {
+ .dl-horizontal dt {
+ float: left;
+ width: 160px;
+ overflow: hidden;
+ clear: left;
+ text-align: right;
+ text-overflow: ellipsis;
+ white-space: nowrap;
+ }
+ .dl-horizontal dd {
+ margin-left: 180px;
+ }
+}
+abbr[title],
+abbr[data-original-title] {
+ cursor: help;
+ border-bottom: 1px dotted #777;
+}
+.initialism {
+ font-size: 90%;
+ text-transform: uppercase;
+}
+blockquote {
+ padding: 10px 20px;
+ margin: 0 0 20px;
+ font-size: 17.5px;
+ border-left: 5px solid #eee;
+}
+blockquote p:last-child,
+blockquote ul:last-child,
+blockquote ol:last-child {
+ margin-bottom: 0;
+}
+blockquote footer,
+blockquote small,
+blockquote .small {
+ display: block;
+ font-size: 80%;
+ line-height: 1.42857143;
+ color: #777;
+}
+blockquote footer:before,
+blockquote small:before,
+blockquote .small:before {
+ content: '\2014 \00A0';
+}
+.blockquote-reverse,
+blockquote.pull-right {
+ padding-right: 15px;
+ padding-left: 0;
+ text-align: right;
+ border-right: 5px solid #eee;
+ border-left: 0;
+}
+.blockquote-reverse footer:before,
+blockquote.pull-right footer:before,
+.blockquote-reverse small:before,
+blockquote.pull-right small:before,
+.blockquote-reverse .small:before,
+blockquote.pull-right .small:before {
+ content: '';
+}
+.blockquote-reverse footer:after,
+blockquote.pull-right footer:after,
+.blockquote-reverse small:after,
+blockquote.pull-right small:after,
+.blockquote-reverse .small:after,
+blockquote.pull-right .small:after {
+ content: '\00A0 \2014';
+}
+blockquote:before,
+blockquote:after {
+ content: "";
+}
+address {
+ margin-bottom: 20px;
+ font-style: normal;
+ line-height: 1.42857143;
+}
+code,
+kbd,
+pre,
+samp {
+ font-family: Menlo, Monaco, Consolas, "Courier New", monospace;
+}
+code {
+ padding: 2px 4px;
+ font-size: 90%;
+ color: #c7254e;
+ background-color: #f9f2f4;
+ border-radius: 4px;
+}
+kbd {
+ padding: 2px 4px;
+ font-size: 90%;
+ color: #fff;
+ background-color: #333;
+ border-radius: 3px;
+ -webkit-box-shadow: inset 0 -1px 0 rgba(0, 0, 0, .25);
+ box-shadow: inset 0 -1px 0 rgba(0, 0, 0, .25);
+}
+kbd kbd {
+ padding: 0;
+ font-size: 100%;
+ -webkit-box-shadow: none;
+ box-shadow: none;
+}
+pre {
+ display: block;
+ padding: 9.5px;
+ margin: 0 0 10px;
+ font-size: 13px;
+ line-height: 1.42857143;
+ color: #333;
+ word-break: break-all;
+ word-wrap: break-word;
+ background-color: #f5f5f5;
+ border: 1px solid #ccc;
+ border-radius: 4px;
+}
+pre code {
+ padding: 0;
+ font-size: inherit;
+ color: inherit;
+ white-space: pre-wrap;
+ background-color: transparent;
+ border-radius: 0;
+}
+.pre-scrollable {
+ max-height: 340px;
+ overflow-y: scroll;
+}
+.container {
+ padding-right: 15px;
+ padding-left: 15px;
+ margin-right: auto;
+ margin-left: auto;
+}
+@media (min-width: 768px) {
+ .container {
+ width: 750px;
+ }
+}
+@media (min-width: 992px) {
+ .container {
+ width: 970px;
+ }
+}
+@media (min-width: 1200px) {
+ .container {
+ width: 1170px;
+ }
+}
+.container-fluid {
+ padding-right: 15px;
+ padding-left: 15px;
+ margin-right: auto;
+ margin-left: auto;
+}
+.row {
+ margin-right: -15px;
+ margin-left: -15px;
+}
+.col-xs-1, .col-sm-1, .col-md-1, .col-lg-1, .col-xs-2, .col-sm-2, .col-md-2, .col-lg-2, .col-xs-3, .col-sm-3, .col-md-3, .col-lg-3, .col-xs-4, .col-sm-4, .col-md-4, .col-lg-4, .col-xs-5, .col-sm-5, .col-md-5, .col-lg-5, .col-xs-6, .col-sm-6, .col-md-6, .col-lg-6, .col-xs-7, .col-sm-7, .col-md-7, .col-lg-7, .col-xs-8, .col-sm-8, .col-md-8, .col-lg-8, .col-xs-9, .col-sm-9, .col-md-9, .col-lg-9, .col-xs-10, .col-sm-10, .col-md-10, .col-lg-10, .col-xs-11, .col-sm-11, .col-md-11, .col-lg-11, .col-xs-12, .col-sm-12, .col-md-12, .col-lg-12 {
+ position: relative;
+ min-height: 1px;
+ padding-right: 15px;
+ padding-left: 15px;
+}
+.col-xs-1, .col-xs-2, .col-xs-3, .col-xs-4, .col-xs-5, .col-xs-6, .col-xs-7, .col-xs-8, .col-xs-9, .col-xs-10, .col-xs-11, .col-xs-12 {
+ float: left;
+}
+.col-xs-12 {
+ width: 100%;
+}
+.col-xs-11 {
+ width: 91.66666667%;
+}
+.col-xs-10 {
+ width: 83.33333333%;
+}
+.col-xs-9 {
+ width: 75%;
+}
+.col-xs-8 {
+ width: 66.66666667%;
+}
+.col-xs-7 {
+ width: 58.33333333%;
+}
+.col-xs-6 {
+ width: 50%;
+}
+.col-xs-5 {
+ width: 41.66666667%;
+}
+.col-xs-4 {
+ width: 33.33333333%;
+}
+.col-xs-3 {
+ width: 25%;
+}
+.col-xs-2 {
+ width: 16.66666667%;
+}
+.col-xs-1 {
+ width: 8.33333333%;
+}
+.col-xs-pull-12 {
+ right: 100%;
+}
+.col-xs-pull-11 {
+ right: 91.66666667%;
+}
+.col-xs-pull-10 {
+ right: 83.33333333%;
+}
+.col-xs-pull-9 {
+ right: 75%;
+}
+.col-xs-pull-8 {
+ right: 66.66666667%;
+}
+.col-xs-pull-7 {
+ right: 58.33333333%;
+}
+.col-xs-pull-6 {
+ right: 50%;
+}
+.col-xs-pull-5 {
+ right: 41.66666667%;
+}
+.col-xs-pull-4 {
+ right: 33.33333333%;
+}
+.col-xs-pull-3 {
+ right: 25%;
+}
+.col-xs-pull-2 {
+ right: 16.66666667%;
+}
+.col-xs-pull-1 {
+ right: 8.33333333%;
+}
+.col-xs-pull-0 {
+ right: auto;
+}
+.col-xs-push-12 {
+ left: 100%;
+}
+.col-xs-push-11 {
+ left: 91.66666667%;
+}
+.col-xs-push-10 {
+ left: 83.33333333%;
+}
+.col-xs-push-9 {
+ left: 75%;
+}
+.col-xs-push-8 {
+ left: 66.66666667%;
+}
+.col-xs-push-7 {
+ left: 58.33333333%;
+}
+.col-xs-push-6 {
+ left: 50%;
+}
+.col-xs-push-5 {
+ left: 41.66666667%;
+}
+.col-xs-push-4 {
+ left: 33.33333333%;
+}
+.col-xs-push-3 {
+ left: 25%;
+}
+.col-xs-push-2 {
+ left: 16.66666667%;
+}
+.col-xs-push-1 {
+ left: 8.33333333%;
+}
+.col-xs-push-0 {
+ left: auto;
+}
+.col-xs-offset-12 {
+ margin-left: 100%;
+}
+.col-xs-offset-11 {
+ margin-left: 91.66666667%;
+}
+.col-xs-offset-10 {
+ margin-left: 83.33333333%;
+}
+.col-xs-offset-9 {
+ margin-left: 75%;
+}
+.col-xs-offset-8 {
+ margin-left: 66.66666667%;
+}
+.col-xs-offset-7 {
+ margin-left: 58.33333333%;
+}
+.col-xs-offset-6 {
+ margin-left: 50%;
+}
+.col-xs-offset-5 {
+ margin-left: 41.66666667%;
+}
+.col-xs-offset-4 {
+ margin-left: 33.33333333%;
+}
+.col-xs-offset-3 {
+ margin-left: 25%;
+}
+.col-xs-offset-2 {
+ margin-left: 16.66666667%;
+}
+.col-xs-offset-1 {
+ margin-left: 8.33333333%;
+}
+.col-xs-offset-0 {
+ margin-left: 0;
+}
+@media (min-width: 768px) {
+ .col-sm-1, .col-sm-2, .col-sm-3, .col-sm-4, .col-sm-5, .col-sm-6, .col-sm-7, .col-sm-8, .col-sm-9, .col-sm-10, .col-sm-11, .col-sm-12 {
+ float: left;
+ }
+ .col-sm-12 {
+ width: 100%;
+ }
+ .col-sm-11 {
+ width: 91.66666667%;
+ }
+ .col-sm-10 {
+ width: 83.33333333%;
+ }
+ .col-sm-9 {
+ width: 75%;
+ }
+ .col-sm-8 {
+ width: 66.66666667%;
+ }
+ .col-sm-7 {
+ width: 58.33333333%;
+ }
+ .col-sm-6 {
+ width: 50%;
+ }
+ .col-sm-5 {
+ width: 41.66666667%;
+ }
+ .col-sm-4 {
+ width: 33.33333333%;
+ }
+ .col-sm-3 {
+ width: 25%;
+ }
+ .col-sm-2 {
+ width: 16.66666667%;
+ }
+ .col-sm-1 {
+ width: 8.33333333%;
+ }
+ .col-sm-pull-12 {
+ right: 100%;
+ }
+ .col-sm-pull-11 {
+ right: 91.66666667%;
+ }
+ .col-sm-pull-10 {
+ right: 83.33333333%;
+ }
+ .col-sm-pull-9 {
+ right: 75%;
+ }
+ .col-sm-pull-8 {
+ right: 66.66666667%;
+ }
+ .col-sm-pull-7 {
+ right: 58.33333333%;
+ }
+ .col-sm-pull-6 {
+ right: 50%;
+ }
+ .col-sm-pull-5 {
+ right: 41.66666667%;
+ }
+ .col-sm-pull-4 {
+ right: 33.33333333%;
+ }
+ .col-sm-pull-3 {
+ right: 25%;
+ }
+ .col-sm-pull-2 {
+ right: 16.66666667%;
+ }
+ .col-sm-pull-1 {
+ right: 8.33333333%;
+ }
+ .col-sm-pull-0 {
+ right: auto;
+ }
+ .col-sm-push-12 {
+ left: 100%;
+ }
+ .col-sm-push-11 {
+ left: 91.66666667%;
+ }
+ .col-sm-push-10 {
+ left: 83.33333333%;
+ }
+ .col-sm-push-9 {
+ left: 75%;
+ }
+ .col-sm-push-8 {
+ left: 66.66666667%;
+ }
+ .col-sm-push-7 {
+ left: 58.33333333%;
+ }
+ .col-sm-push-6 {
+ left: 50%;
+ }
+ .col-sm-push-5 {
+ left: 41.66666667%;
+ }
+ .col-sm-push-4 {
+ left: 33.33333333%;
+ }
+ .col-sm-push-3 {
+ left: 25%;
+ }
+ .col-sm-push-2 {
+ left: 16.66666667%;
+ }
+ .col-sm-push-1 {
+ left: 8.33333333%;
+ }
+ .col-sm-push-0 {
+ left: auto;
+ }
+ .col-sm-offset-12 {
+ margin-left: 100%;
+ }
+ .col-sm-offset-11 {
+ margin-left: 91.66666667%;
+ }
+ .col-sm-offset-10 {
+ margin-left: 83.33333333%;
+ }
+ .col-sm-offset-9 {
+ margin-left: 75%;
+ }
+ .col-sm-offset-8 {
+ margin-left: 66.66666667%;
+ }
+ .col-sm-offset-7 {
+ margin-left: 58.33333333%;
+ }
+ .col-sm-offset-6 {
+ margin-left: 50%;
+ }
+ .col-sm-offset-5 {
+ margin-left: 41.66666667%;
+ }
+ .col-sm-offset-4 {
+ margin-left: 33.33333333%;
+ }
+ .col-sm-offset-3 {
+ margin-left: 25%;
+ }
+ .col-sm-offset-2 {
+ margin-left: 16.66666667%;
+ }
+ .col-sm-offset-1 {
+ margin-left: 8.33333333%;
+ }
+ .col-sm-offset-0 {
+ margin-left: 0;
+ }
+}
+@media (min-width: 992px) {
+ .col-md-1, .col-md-2, .col-md-3, .col-md-4, .col-md-5, .col-md-6, .col-md-7, .col-md-8, .col-md-9, .col-md-10, .col-md-11, .col-md-12 {
+ float: left;
+ }
+ .col-md-12 {
+ width: 100%;
+ }
+ .col-md-11 {
+ width: 91.66666667%;
+ }
+ .col-md-10 {
+ width: 83.33333333%;
+ }
+ .col-md-9 {
+ width: 75%;
+ }
+ .col-md-8 {
+ width: 66.66666667%;
+ }
+ .col-md-7 {
+ width: 58.33333333%;
+ }
+ .col-md-6 {
+ width: 50%;
+ }
+ .col-md-5 {
+ width: 41.66666667%;
+ }
+ .col-md-4 {
+ width: 33.33333333%;
+ }
+ .col-md-3 {
+ width: 25%;
+ }
+ .col-md-2 {
+ width: 16.66666667%;
+ }
+ .col-md-1 {
+ width: 8.33333333%;
+ }
+ .col-md-pull-12 {
+ right: 100%;
+ }
+ .col-md-pull-11 {
+ right: 91.66666667%;
+ }
+ .col-md-pull-10 {
+ right: 83.33333333%;
+ }
+ .col-md-pull-9 {
+ right: 75%;
+ }
+ .col-md-pull-8 {
+ right: 66.66666667%;
+ }
+ .col-md-pull-7 {
+ right: 58.33333333%;
+ }
+ .col-md-pull-6 {
+ right: 50%;
+ }
+ .col-md-pull-5 {
+ right: 41.66666667%;
+ }
+ .col-md-pull-4 {
+ right: 33.33333333%;
+ }
+ .col-md-pull-3 {
+ right: 25%;
+ }
+ .col-md-pull-2 {
+ right: 16.66666667%;
+ }
+ .col-md-pull-1 {
+ right: 8.33333333%;
+ }
+ .col-md-pull-0 {
+ right: auto;
+ }
+ .col-md-push-12 {
+ left: 100%;
+ }
+ .col-md-push-11 {
+ left: 91.66666667%;
+ }
+ .col-md-push-10 {
+ left: 83.33333333%;
+ }
+ .col-md-push-9 {
+ left: 75%;
+ }
+ .col-md-push-8 {
+ left: 66.66666667%;
+ }
+ .col-md-push-7 {
+ left: 58.33333333%;
+ }
+ .col-md-push-6 {
+ left: 50%;
+ }
+ .col-md-push-5 {
+ left: 41.66666667%;
+ }
+ .col-md-push-4 {
+ left: 33.33333333%;
+ }
+ .col-md-push-3 {
+ left: 25%;
+ }
+ .col-md-push-2 {
+ left: 16.66666667%;
+ }
+ .col-md-push-1 {
+ left: 8.33333333%;
+ }
+ .col-md-push-0 {
+ left: auto;
+ }
+ .col-md-offset-12 {
+ margin-left: 100%;
+ }
+ .col-md-offset-11 {
+ margin-left: 91.66666667%;
+ }
+ .col-md-offset-10 {
+ margin-left: 83.33333333%;
+ }
+ .col-md-offset-9 {
+ margin-left: 75%;
+ }
+ .col-md-offset-8 {
+ margin-left: 66.66666667%;
+ }
+ .col-md-offset-7 {
+ margin-left: 58.33333333%;
+ }
+ .col-md-offset-6 {
+ margin-left: 50%;
+ }
+ .col-md-offset-5 {
+ margin-left: 41.66666667%;
+ }
+ .col-md-offset-4 {
+ margin-left: 33.33333333%;
+ }
+ .col-md-offset-3 {
+ margin-left: 25%;
+ }
+ .col-md-offset-2 {
+ margin-left: 16.66666667%;
+ }
+ .col-md-offset-1 {
+ margin-left: 8.33333333%;
+ }
+ .col-md-offset-0 {
+ margin-left: 0;
+ }
+}
+@media (min-width: 1200px) {
+ .col-lg-1, .col-lg-2, .col-lg-3, .col-lg-4, .col-lg-5, .col-lg-6, .col-lg-7, .col-lg-8, .col-lg-9, .col-lg-10, .col-lg-11, .col-lg-12 {
+ float: left;
+ }
+ .col-lg-12 {
+ width: 100%;
+ }
+ .col-lg-11 {
+ width: 91.66666667%;
+ }
+ .col-lg-10 {
+ width: 83.33333333%;
+ }
+ .col-lg-9 {
+ width: 75%;
+ }
+ .col-lg-8 {
+ width: 66.66666667%;
+ }
+ .col-lg-7 {
+ width: 58.33333333%;
+ }
+ .col-lg-6 {
+ width: 50%;
+ }
+ .col-lg-5 {
+ width: 41.66666667%;
+ }
+ .col-lg-4 {
+ width: 33.33333333%;
+ }
+ .col-lg-3 {
+ width: 25%;
+ }
+ .col-lg-2 {
+ width: 16.66666667%;
+ }
+ .col-lg-1 {
+ width: 8.33333333%;
+ }
+ .col-lg-pull-12 {
+ right: 100%;
+ }
+ .col-lg-pull-11 {
+ right: 91.66666667%;
+ }
+ .col-lg-pull-10 {
+ right: 83.33333333%;
+ }
+ .col-lg-pull-9 {
+ right: 75%;
+ }
+ .col-lg-pull-8 {
+ right: 66.66666667%;
+ }
+ .col-lg-pull-7 {
+ right: 58.33333333%;
+ }
+ .col-lg-pull-6 {
+ right: 50%;
+ }
+ .col-lg-pull-5 {
+ right: 41.66666667%;
+ }
+ .col-lg-pull-4 {
+ right: 33.33333333%;
+ }
+ .col-lg-pull-3 {
+ right: 25%;
+ }
+ .col-lg-pull-2 {
+ right: 16.66666667%;
+ }
+ .col-lg-pull-1 {
+ right: 8.33333333%;
+ }
+ .col-lg-pull-0 {
+ right: auto;
+ }
+ .col-lg-push-12 {
+ left: 100%;
+ }
+ .col-lg-push-11 {
+ left: 91.66666667%;
+ }
+ .col-lg-push-10 {
+ left: 83.33333333%;
+ }
+ .col-lg-push-9 {
+ left: 75%;
+ }
+ .col-lg-push-8 {
+ left: 66.66666667%;
+ }
+ .col-lg-push-7 {
+ left: 58.33333333%;
+ }
+ .col-lg-push-6 {
+ left: 50%;
+ }
+ .col-lg-push-5 {
+ left: 41.66666667%;
+ }
+ .col-lg-push-4 {
+ left: 33.33333333%;
+ }
+ .col-lg-push-3 {
+ left: 25%;
+ }
+ .col-lg-push-2 {
+ left: 16.66666667%;
+ }
+ .col-lg-push-1 {
+ left: 8.33333333%;
+ }
+ .col-lg-push-0 {
+ left: auto;
+ }
+ .col-lg-offset-12 {
+ margin-left: 100%;
+ }
+ .col-lg-offset-11 {
+ margin-left: 91.66666667%;
+ }
+ .col-lg-offset-10 {
+ margin-left: 83.33333333%;
+ }
+ .col-lg-offset-9 {
+ margin-left: 75%;
+ }
+ .col-lg-offset-8 {
+ margin-left: 66.66666667%;
+ }
+ .col-lg-offset-7 {
+ margin-left: 58.33333333%;
+ }
+ .col-lg-offset-6 {
+ margin-left: 50%;
+ }
+ .col-lg-offset-5 {
+ margin-left: 41.66666667%;
+ }
+ .col-lg-offset-4 {
+ margin-left: 33.33333333%;
+ }
+ .col-lg-offset-3 {
+ margin-left: 25%;
+ }
+ .col-lg-offset-2 {
+ margin-left: 16.66666667%;
+ }
+ .col-lg-offset-1 {
+ margin-left: 8.33333333%;
+ }
+ .col-lg-offset-0 {
+ margin-left: 0;
+ }
+}
+table {
+ background-color: transparent;
+}
+th {
+ text-align: left;
+}
+.table {
+ width: 100%;
+ max-width: 100%;
+ margin-bottom: 20px;
+}
+.table > thead > tr > th,
+.table > tbody > tr > th,
+.table > tfoot > tr > th,
+.table > thead > tr > td,
+.table > tbody > tr > td,
+.table > tfoot > tr > td {
+ padding: 8px;
+ line-height: 1.42857143;
+ vertical-align: top;
+ border-top: 1px solid #ddd;
+}
+.table > thead > tr > th {
+ vertical-align: bottom;
+ border-bottom: 2px solid #ddd;
+}
+.table > caption + thead > tr:first-child > th,
+.table > colgroup + thead > tr:first-child > th,
+.table > thead:first-child > tr:first-child > th,
+.table > caption + thead > tr:first-child > td,
+.table > colgroup + thead > tr:first-child > td,
+.table > thead:first-child > tr:first-child > td {
+ border-top: 0;
+}
+.table > tbody + tbody {
+ border-top: 2px solid #ddd;
+}
+.table .table {
+ background-color: #fff;
+}
+.table-condensed > thead > tr > th,
+.table-condensed > tbody > tr > th,
+.table-condensed > tfoot > tr > th,
+.table-condensed > thead > tr > td,
+.table-condensed > tbody > tr > td,
+.table-condensed > tfoot > tr > td {
+ padding: 5px;
+}
+.table-bordered {
+ border: 1px solid #ddd;
+}
+.table-bordered > thead > tr > th,
+.table-bordered > tbody > tr > th,
+.table-bordered > tfoot > tr > th,
+.table-bordered > thead > tr > td,
+.table-bordered > tbody > tr > td,
+.table-bordered > tfoot > tr > td {
+ border: 1px solid #ddd;
+}
+.table-bordered > thead > tr > th,
+.table-bordered > thead > tr > td {
+ border-bottom-width: 2px;
+}
+.table-striped > tbody > tr:nth-child(odd) > td,
+.table-striped > tbody > tr:nth-child(odd) > th {
+ background-color: #f9f9f9;
+}
+.table-hover > tbody > tr:hover > td,
+.table-hover > tbody > tr:hover > th {
+ background-color: #f5f5f5;
+}
+table col[class*="col-"] {
+ position: static;
+ display: table-column;
+ float: none;
+}
+table td[class*="col-"],
+table th[class*="col-"] {
+ position: static;
+ display: table-cell;
+ float: none;
+}
+.table > thead > tr > td.active,
+.table > tbody > tr > td.active,
+.table > tfoot > tr > td.active,
+.table > thead > tr > th.active,
+.table > tbody > tr > th.active,
+.table > tfoot > tr > th.active,
+.table > thead > tr.active > td,
+.table > tbody > tr.active > td,
+.table > tfoot > tr.active > td,
+.table > thead > tr.active > th,
+.table > tbody > tr.active > th,
+.table > tfoot > tr.active > th {
+ background-color: #f5f5f5;
+}
+.table-hover > tbody > tr > td.active:hover,
+.table-hover > tbody > tr > th.active:hover,
+.table-hover > tbody > tr.active:hover > td,
+.table-hover > tbody > tr:hover > .active,
+.table-hover > tbody > tr.active:hover > th {
+ background-color: #e8e8e8;
+}
+.table > thead > tr > td.success,
+.table > tbody > tr > td.success,
+.table > tfoot > tr > td.success,
+.table > thead > tr > th.success,
+.table > tbody > tr > th.success,
+.table > tfoot > tr > th.success,
+.table > thead > tr.success > td,
+.table > tbody > tr.success > td,
+.table > tfoot > tr.success > td,
+.table > thead > tr.success > th,
+.table > tbody > tr.success > th,
+.table > tfoot > tr.success > th {
+ background-color: #dff0d8;
+}
+.table-hover > tbody > tr > td.success:hover,
+.table-hover > tbody > tr > th.success:hover,
+.table-hover > tbody > tr.success:hover > td,
+.table-hover > tbody > tr:hover > .success,
+.table-hover > tbody > tr.success:hover > th {
+ background-color: #d0e9c6;
+}
+.table > thead > tr > td.info,
+.table > tbody > tr > td.info,
+.table > tfoot > tr > td.info,
+.table > thead > tr > th.info,
+.table > tbody > tr > th.info,
+.table > tfoot > tr > th.info,
+.table > thead > tr.info > td,
+.table > tbody > tr.info > td,
+.table > tfoot > tr.info > td,
+.table > thead > tr.info > th,
+.table > tbody > tr.info > th,
+.table > tfoot > tr.info > th {
+ background-color: #d9edf7;
+}
+.table-hover > tbody > tr > td.info:hover,
+.table-hover > tbody > tr > th.info:hover,
+.table-hover > tbody > tr.info:hover > td,
+.table-hover > tbody > tr:hover > .info,
+.table-hover > tbody > tr.info:hover > th {
+ background-color: #c4e3f3;
+}
+.table > thead > tr > td.warning,
+.table > tbody > tr > td.warning,
+.table > tfoot > tr > td.warning,
+.table > thead > tr > th.warning,
+.table > tbody > tr > th.warning,
+.table > tfoot > tr > th.warning,
+.table > thead > tr.warning > td,
+.table > tbody > tr.warning > td,
+.table > tfoot > tr.warning > td,
+.table > thead > tr.warning > th,
+.table > tbody > tr.warning > th,
+.table > tfoot > tr.warning > th {
+ background-color: #fcf8e3;
+}
+.table-hover > tbody > tr > td.warning:hover,
+.table-hover > tbody > tr > th.warning:hover,
+.table-hover > tbody > tr.warning:hover > td,
+.table-hover > tbody > tr:hover > .warning,
+.table-hover > tbody > tr.warning:hover > th {
+ background-color: #faf2cc;
+}
+.table > thead > tr > td.danger,
+.table > tbody > tr > td.danger,
+.table > tfoot > tr > td.danger,
+.table > thead > tr > th.danger,
+.table > tbody > tr > th.danger,
+.table > tfoot > tr > th.danger,
+.table > thead > tr.danger > td,
+.table > tbody > tr.danger > td,
+.table > tfoot > tr.danger > td,
+.table > thead > tr.danger > th,
+.table > tbody > tr.danger > th,
+.table > tfoot > tr.danger > th {
+ background-color: #f2dede;
+}
+.table-hover > tbody > tr > td.danger:hover,
+.table-hover > tbody > tr > th.danger:hover,
+.table-hover > tbody > tr.danger:hover > td,
+.table-hover > tbody > tr:hover > .danger,
+.table-hover > tbody > tr.danger:hover > th {
+ background-color: #ebcccc;
+}
+@media screen and (max-width: 767px) {
+ .table-responsive {
+ width: 100%;
+ margin-bottom: 15px;
+ overflow-x: auto;
+ overflow-y: hidden;
+ -webkit-overflow-scrolling: touch;
+ -ms-overflow-style: -ms-autohiding-scrollbar;
+ border: 1px solid #ddd;
+ }
+ .table-responsive > .table {
+ margin-bottom: 0;
+ }
+ .table-responsive > .table > thead > tr > th,
+ .table-responsive > .table > tbody > tr > th,
+ .table-responsive > .table > tfoot > tr > th,
+ .table-responsive > .table > thead > tr > td,
+ .table-responsive > .table > tbody > tr > td,
+ .table-responsive > .table > tfoot > tr > td {
+ white-space: nowrap;
+ }
+ .table-responsive > .table-bordered {
+ border: 0;
+ }
+ .table-responsive > .table-bordered > thead > tr > th:first-child,
+ .table-responsive > .table-bordered > tbody > tr > th:first-child,
+ .table-responsive > .table-bordered > tfoot > tr > th:first-child,
+ .table-responsive > .table-bordered > thead > tr > td:first-child,
+ .table-responsive > .table-bordered > tbody > tr > td:first-child,
+ .table-responsive > .table-bordered > tfoot > tr > td:first-child {
+ border-left: 0;
+ }
+ .table-responsive > .table-bordered > thead > tr > th:last-child,
+ .table-responsive > .table-bordered > tbody > tr > th:last-child,
+ .table-responsive > .table-bordered > tfoot > tr > th:last-child,
+ .table-responsive > .table-bordered > thead > tr > td:last-child,
+ .table-responsive > .table-bordered > tbody > tr > td:last-child,
+ .table-responsive > .table-bordered > tfoot > tr > td:last-child {
+ border-right: 0;
+ }
+ .table-responsive > .table-bordered > tbody > tr:last-child > th,
+ .table-responsive > .table-bordered > tfoot > tr:last-child > th,
+ .table-responsive > .table-bordered > tbody > tr:last-child > td,
+ .table-responsive > .table-bordered > tfoot > tr:last-child > td {
+ border-bottom: 0;
+ }
+}
+fieldset {
+ min-width: 0;
+ padding: 0;
+ margin: 0;
+ border: 0;
+}
+legend {
+ display: block;
+ width: 100%;
+ padding: 0;
+ margin-bottom: 20px;
+ font-size: 21px;
+ line-height: inherit;
+ color: #333;
+ border: 0;
+ border-bottom: 1px solid #e5e5e5;
+}
+label {
+ display: inline-block;
+ max-width: 100%;
+ margin-bottom: 5px;
+ font-weight: bold;
+}
+input[type="search"] {
+ -webkit-box-sizing: border-box;
+ -moz-box-sizing: border-box;
+ box-sizing: border-box;
+}
+input[type="radio"],
+input[type="checkbox"] {
+ margin: 4px 0 0;
+ margin-top: 1px \9;
+ line-height: normal;
+}
+input[type="file"] {
+ display: block;
+}
+input[type="range"] {
+ display: block;
+ width: 100%;
+}
+select[multiple],
+select[size] {
+ height: auto;
+}
+input[type="file"]:focus,
+input[type="radio"]:focus,
+input[type="checkbox"]:focus {
+ outline: thin dotted;
+ outline: 5px auto -webkit-focus-ring-color;
+ outline-offset: -2px;
+}
+output {
+ display: block;
+ padding-top: 7px;
+ font-size: 14px;
+ line-height: 1.42857143;
+ color: #555;
+}
+.form-control {
+ display: block;
+ width: 100%;
+ height: 34px;
+ padding: 6px 12px;
+ font-size: 14px;
+ line-height: 1.42857143;
+ color: #555;
+ background-color: #fff;
+ background-image: none;
+ border: 1px solid #ccc;
+ border-radius: 4px;
+ -webkit-box-shadow: inset 0 1px 1px rgba(0, 0, 0, .075);
+ box-shadow: inset 0 1px 1px rgba(0, 0, 0, .075);
+ -webkit-transition: border-color ease-in-out .15s, -webkit-box-shadow ease-in-out .15s;
+ -o-transition: border-color ease-in-out .15s, box-shadow ease-in-out .15s;
+ transition: border-color ease-in-out .15s, box-shadow ease-in-out .15s;
+}
+.form-control:focus {
+ border-color: #66afe9;
+ outline: 0;
+ -webkit-box-shadow: inset 0 1px 1px rgba(0,0,0,.075), 0 0 8px rgba(102, 175, 233, .6);
+ box-shadow: inset 0 1px 1px rgba(0,0,0,.075), 0 0 8px rgba(102, 175, 233, .6);
+}
+.form-control::-moz-placeholder {
+ color: #777;
+ opacity: 1;
+}
+.form-control:-ms-input-placeholder {
+ color: #777;
+}
+.form-control::-webkit-input-placeholder {
+ color: #777;
+}
+.form-control[disabled],
+.form-control[readonly],
+fieldset[disabled] .form-control {
+ cursor: not-allowed;
+ background-color: #eee;
+ opacity: 1;
+}
+textarea.form-control {
+ height: auto;
+}
+input[type="search"] {
+ -webkit-appearance: none;
+}
+input[type="date"],
+input[type="time"],
+input[type="datetime-local"],
+input[type="month"] {
+ line-height: 34px;
+ line-height: 1.42857143 \0;
+}
+input[type="date"].input-sm,
+input[type="time"].input-sm,
+input[type="datetime-local"].input-sm,
+input[type="month"].input-sm {
+ line-height: 30px;
+}
+input[type="date"].input-lg,
+input[type="time"].input-lg,
+input[type="datetime-local"].input-lg,
+input[type="month"].input-lg {
+ line-height: 46px;
+}
+.form-group {
+ margin-bottom: 15px;
+}
+.radio,
+.checkbox {
+ position: relative;
+ display: block;
+ min-height: 20px;
+ margin-top: 10px;
+ margin-bottom: 10px;
+}
+.radio label,
+.checkbox label {
+ padding-left: 20px;
+ margin-bottom: 0;
+ font-weight: normal;
+ cursor: pointer;
+}
+.radio input[type="radio"],
+.radio-inline input[type="radio"],
+.checkbox input[type="checkbox"],
+.checkbox-inline input[type="checkbox"] {
+ position: absolute;
+ margin-top: 4px \9;
+ margin-left: -20px;
+}
+.radio + .radio,
+.checkbox + .checkbox {
+ margin-top: -5px;
+}
+.radio-inline,
+.checkbox-inline {
+ display: inline-block;
+ padding-left: 20px;
+ margin-bottom: 0;
+ font-weight: normal;
+ vertical-align: middle;
+ cursor: pointer;
+}
+.radio-inline + .radio-inline,
+.checkbox-inline + .checkbox-inline {
+ margin-top: 0;
+ margin-left: 10px;
+}
+input[type="radio"][disabled],
+input[type="checkbox"][disabled],
+input[type="radio"].disabled,
+input[type="checkbox"].disabled,
+fieldset[disabled] input[type="radio"],
+fieldset[disabled] input[type="checkbox"] {
+ cursor: not-allowed;
+}
+.radio-inline.disabled,
+.checkbox-inline.disabled,
+fieldset[disabled] .radio-inline,
+fieldset[disabled] .checkbox-inline {
+ cursor: not-allowed;
+}
+.radio.disabled label,
+.checkbox.disabled label,
+fieldset[disabled] .radio label,
+fieldset[disabled] .checkbox label {
+ cursor: not-allowed;
+}
+.form-control-static {
+ padding-top: 7px;
+ padding-bottom: 7px;
+ margin-bottom: 0;
+}
+.form-control-static.input-lg,
+.form-control-static.input-sm {
+ padding-right: 0;
+ padding-left: 0;
+}
+.input-sm,
+.form-horizontal .form-group-sm .form-control {
+ height: 30px;
+ padding: 5px 10px;
+ font-size: 12px;
+ line-height: 1.5;
+ border-radius: 3px;
+}
+select.input-sm {
+ height: 30px;
+ line-height: 30px;
+}
+textarea.input-sm,
+select[multiple].input-sm {
+ height: auto;
+}
+.input-lg,
+.form-horizontal .form-group-lg .form-control {
+ height: 46px;
+ padding: 10px 16px;
+ font-size: 18px;
+ line-height: 1.33;
+ border-radius: 6px;
+}
+select.input-lg {
+ height: 46px;
+ line-height: 46px;
+}
+textarea.input-lg,
+select[multiple].input-lg {
+ height: auto;
+}
+.has-feedback {
+ position: relative;
+}
+.has-feedback .form-control {
+ padding-right: 42.5px;
+}
+.form-control-feedback {
+ position: absolute;
+ top: 25px;
+ right: 0;
+ z-index: 2;
+ display: block;
+ width: 34px;
+ height: 34px;
+ line-height: 34px;
+ text-align: center;
+}
+.input-lg + .form-control-feedback {
+ width: 46px;
+ height: 46px;
+ line-height: 46px;
+}
+.input-sm + .form-control-feedback {
+ width: 30px;
+ height: 30px;
+ line-height: 30px;
+}
+.has-success .help-block,
+.has-success .control-label,
+.has-success .radio,
+.has-success .checkbox,
+.has-success .radio-inline,
+.has-success .checkbox-inline {
+ color: #3c763d;
+}
+.has-success .form-control {
+ border-color: #3c763d;
+ -webkit-box-shadow: inset 0 1px 1px rgba(0, 0, 0, .075);
+ box-shadow: inset 0 1px 1px rgba(0, 0, 0, .075);
+}
+.has-success .form-control:focus {
+ border-color: #2b542c;
+ -webkit-box-shadow: inset 0 1px 1px rgba(0, 0, 0, .075), 0 0 6px #67b168;
+ box-shadow: inset 0 1px 1px rgba(0, 0, 0, .075), 0 0 6px #67b168;
+}
+.has-success .input-group-addon {
+ color: #3c763d;
+ background-color: #dff0d8;
+ border-color: #3c763d;
+}
+.has-success .form-control-feedback {
+ color: #3c763d;
+}
+.has-warning .help-block,
+.has-warning .control-label,
+.has-warning .radio,
+.has-warning .checkbox,
+.has-warning .radio-inline,
+.has-warning .checkbox-inline {
+ color: #8a6d3b;
+}
+.has-warning .form-control {
+ border-color: #8a6d3b;
+ -webkit-box-shadow: inset 0 1px 1px rgba(0, 0, 0, .075);
+ box-shadow: inset 0 1px 1px rgba(0, 0, 0, .075);
+}
+.has-warning .form-control:focus {
+ border-color: #66512c;
+ -webkit-box-shadow: inset 0 1px 1px rgba(0, 0, 0, .075), 0 0 6px #c0a16b;
+ box-shadow: inset 0 1px 1px rgba(0, 0, 0, .075), 0 0 6px #c0a16b;
+}
+.has-warning .input-group-addon {
+ color: #8a6d3b;
+ background-color: #fcf8e3;
+ border-color: #8a6d3b;
+}
+.has-warning .form-control-feedback {
+ color: #8a6d3b;
+}
+.has-error .help-block,
+.has-error .control-label,
+.has-error .radio,
+.has-error .checkbox,
+.has-error .radio-inline,
+.has-error .checkbox-inline {
+ color: #a94442;
+}
+.has-error .form-control {
+ border-color: #a94442;
+ -webkit-box-shadow: inset 0 1px 1px rgba(0, 0, 0, .075);
+ box-shadow: inset 0 1px 1px rgba(0, 0, 0, .075);
+}
+.has-error .form-control:focus {
+ border-color: #843534;
+ -webkit-box-shadow: inset 0 1px 1px rgba(0, 0, 0, .075), 0 0 6px #ce8483;
+ box-shadow: inset 0 1px 1px rgba(0, 0, 0, .075), 0 0 6px #ce8483;
+}
+.has-error .input-group-addon {
+ color: #a94442;
+ background-color: #f2dede;
+ border-color: #a94442;
+}
+.has-error .form-control-feedback {
+ color: #a94442;
+}
+.has-feedback label.sr-only ~ .form-control-feedback {
+ top: 0;
+}
+.help-block {
+ display: block;
+ margin-top: 5px;
+ margin-bottom: 10px;
+ color: #737373;
+}
+@media (min-width: 768px) {
+ .form-inline .form-group {
+ display: inline-block;
+ margin-bottom: 0;
+ vertical-align: middle;
+ }
+ .form-inline .form-control {
+ display: inline-block;
+ width: auto;
+ vertical-align: middle;
+ }
+ .form-inline .input-group {
+ display: inline-table;
+ vertical-align: middle;
+ }
+ .form-inline .input-group .input-group-addon,
+ .form-inline .input-group .input-group-btn,
+ .form-inline .input-group .form-control {
+ width: auto;
+ }
+ .form-inline .input-group > .form-control {
+ width: 100%;
+ }
+ .form-inline .control-label {
+ margin-bottom: 0;
+ vertical-align: middle;
+ }
+ .form-inline .radio,
+ .form-inline .checkbox {
+ display: inline-block;
+ margin-top: 0;
+ margin-bottom: 0;
+ vertical-align: middle;
+ }
+ .form-inline .radio label,
+ .form-inline .checkbox label {
+ padding-left: 0;
+ }
+ .form-inline .radio input[type="radio"],
+ .form-inline .checkbox input[type="checkbox"] {
+ position: relative;
+ margin-left: 0;
+ }
+ .form-inline .has-feedback .form-control-feedback {
+ top: 0;
+ }
+}
+.form-horizontal .radio,
+.form-horizontal .checkbox,
+.form-horizontal .radio-inline,
+.form-horizontal .checkbox-inline {
+ padding-top: 7px;
+ margin-top: 0;
+ margin-bottom: 0;
+}
+.form-horizontal .radio,
+.form-horizontal .checkbox {
+ min-height: 27px;
+}
+.form-horizontal .form-group {
+ margin-right: -15px;
+ margin-left: -15px;
+}
+@media (min-width: 768px) {
+ .form-horizontal .control-label {
+ padding-top: 7px;
+ margin-bottom: 0;
+ text-align: right;
+ }
+}
+.form-horizontal .has-feedback .form-control-feedback {
+ top: 0;
+ right: 15px;
+}
+@media (min-width: 768px) {
+ .form-horizontal .form-group-lg .control-label {
+ padding-top: 14.3px;
+ }
+}
+@media (min-width: 768px) {
+ .form-horizontal .form-group-sm .control-label {
+ padding-top: 6px;
+ }
+}
+.btn {
+ display: inline-block;
+ padding: 6px 12px;
+ margin-bottom: 0;
+ font-size: 14px;
+ font-weight: normal;
+ line-height: 1.42857143;
+ text-align: center;
+ white-space: nowrap;
+ vertical-align: middle;
+ cursor: pointer;
+ -webkit-user-select: none;
+ -moz-user-select: none;
+ -ms-user-select: none;
+ user-select: none;
+ background-image: none;
+ border: 1px solid transparent;
+ border-radius: 4px;
+}
+.btn:focus,
+.btn:active:focus,
+.btn.active:focus {
+ outline: thin dotted;
+ outline: 5px auto -webkit-focus-ring-color;
+ outline-offset: -2px;
+}
+.btn:hover,
+.btn:focus {
+ color: #333;
+ text-decoration: none;
+}
+.btn:active,
+.btn.active {
+ background-image: none;
+ outline: 0;
+ -webkit-box-shadow: inset 0 3px 5px rgba(0, 0, 0, .125);
+ box-shadow: inset 0 3px 5px rgba(0, 0, 0, .125);
+}
+.btn.disabled,
+.btn[disabled],
+fieldset[disabled] .btn {
+ pointer-events: none;
+ cursor: not-allowed;
+ filter: alpha(opacity=65);
+ -webkit-box-shadow: none;
+ box-shadow: none;
+ opacity: .65;
+}
+.btn-default {
+ color: #333;
+ background-color: #fff;
+ border-color: #ccc;
+}
+.btn-default:hover,
+.btn-default:focus,
+.btn-default:active,
+.btn-default.active,
+.open > .dropdown-toggle.btn-default {
+ color: #333;
+ background-color: #e6e6e6;
+ border-color: #adadad;
+}
+.btn-default:active,
+.btn-default.active,
+.open > .dropdown-toggle.btn-default {
+ background-image: none;
+}
+.btn-default.disabled,
+.btn-default[disabled],
+fieldset[disabled] .btn-default,
+.btn-default.disabled:hover,
+.btn-default[disabled]:hover,
+fieldset[disabled] .btn-default:hover,
+.btn-default.disabled:focus,
+.btn-default[disabled]:focus,
+fieldset[disabled] .btn-default:focus,
+.btn-default.disabled:active,
+.btn-default[disabled]:active,
+fieldset[disabled] .btn-default:active,
+.btn-default.disabled.active,
+.btn-default[disabled].active,
+fieldset[disabled] .btn-default.active {
+ background-color: #fff;
+ border-color: #ccc;
+}
+.btn-default .badge {
+ color: #fff;
+ background-color: #333;
+}
+.btn-primary {
+ color: #fff;
+ background-color: #428bca;
+ border-color: #357ebd;
+}
+.btn-primary:hover,
+.btn-primary:focus,
+.btn-primary:active,
+.btn-primary.active,
+.open > .dropdown-toggle.btn-primary {
+ color: #fff;
+ background-color: #3071a9;
+ border-color: #285e8e;
+}
+.btn-primary:active,
+.btn-primary.active,
+.open > .dropdown-toggle.btn-primary {
+ background-image: none;
+}
+.btn-primary.disabled,
+.btn-primary[disabled],
+fieldset[disabled] .btn-primary,
+.btn-primary.disabled:hover,
+.btn-primary[disabled]:hover,
+fieldset[disabled] .btn-primary:hover,
+.btn-primary.disabled:focus,
+.btn-primary[disabled]:focus,
+fieldset[disabled] .btn-primary:focus,
+.btn-primary.disabled:active,
+.btn-primary[disabled]:active,
+fieldset[disabled] .btn-primary:active,
+.btn-primary.disabled.active,
+.btn-primary[disabled].active,
+fieldset[disabled] .btn-primary.active {
+ background-color: #428bca;
+ border-color: #357ebd;
+}
+.btn-primary .badge {
+ color: #428bca;
+ background-color: #fff;
+}
+.btn-success {
+ color: #fff;
+ background-color: #5cb85c;
+ border-color: #4cae4c;
+}
+.btn-success:hover,
+.btn-success:focus,
+.btn-success:active,
+.btn-success.active,
+.open > .dropdown-toggle.btn-success {
+ color: #fff;
+ background-color: #449d44;
+ border-color: #398439;
+}
+.btn-success:active,
+.btn-success.active,
+.open > .dropdown-toggle.btn-success {
+ background-image: none;
+}
+.btn-success.disabled,
+.btn-success[disabled],
+fieldset[disabled] .btn-success,
+.btn-success.disabled:hover,
+.btn-success[disabled]:hover,
+fieldset[disabled] .btn-success:hover,
+.btn-success.disabled:focus,
+.btn-success[disabled]:focus,
+fieldset[disabled] .btn-success:focus,
+.btn-success.disabled:active,
+.btn-success[disabled]:active,
+fieldset[disabled] .btn-success:active,
+.btn-success.disabled.active,
+.btn-success[disabled].active,
+fieldset[disabled] .btn-success.active {
+ background-color: #5cb85c;
+ border-color: #4cae4c;
+}
+.btn-success .badge {
+ color: #5cb85c;
+ background-color: #fff;
+}
+.btn-info {
+ color: #fff;
+ background-color: #5bc0de;
+ border-color: #46b8da;
+}
+.btn-info:hover,
+.btn-info:focus,
+.btn-info:active,
+.btn-info.active,
+.open > .dropdown-toggle.btn-info {
+ color: #fff;
+ background-color: #31b0d5;
+ border-color: #269abc;
+}
+.btn-info:active,
+.btn-info.active,
+.open > .dropdown-toggle.btn-info {
+ background-image: none;
+}
+.btn-info.disabled,
+.btn-info[disabled],
+fieldset[disabled] .btn-info,
+.btn-info.disabled:hover,
+.btn-info[disabled]:hover,
+fieldset[disabled] .btn-info:hover,
+.btn-info.disabled:focus,
+.btn-info[disabled]:focus,
+fieldset[disabled] .btn-info:focus,
+.btn-info.disabled:active,
+.btn-info[disabled]:active,
+fieldset[disabled] .btn-info:active,
+.btn-info.disabled.active,
+.btn-info[disabled].active,
+fieldset[disabled] .btn-info.active {
+ background-color: #5bc0de;
+ border-color: #46b8da;
+}
+.btn-info .badge {
+ color: #5bc0de;
+ background-color: #fff;
+}
+.btn-warning {
+ color: #fff;
+ background-color: #f0ad4e;
+ border-color: #eea236;
+}
+.btn-warning:hover,
+.btn-warning:focus,
+.btn-warning:active,
+.btn-warning.active,
+.open > .dropdown-toggle.btn-warning {
+ color: #fff;
+ background-color: #ec971f;
+ border-color: #d58512;
+}
+.btn-warning:active,
+.btn-warning.active,
+.open > .dropdown-toggle.btn-warning {
+ background-image: none;
+}
+.btn-warning.disabled,
+.btn-warning[disabled],
+fieldset[disabled] .btn-warning,
+.btn-warning.disabled:hover,
+.btn-warning[disabled]:hover,
+fieldset[disabled] .btn-warning:hover,
+.btn-warning.disabled:focus,
+.btn-warning[disabled]:focus,
+fieldset[disabled] .btn-warning:focus,
+.btn-warning.disabled:active,
+.btn-warning[disabled]:active,
+fieldset[disabled] .btn-warning:active,
+.btn-warning.disabled.active,
+.btn-warning[disabled].active,
+fieldset[disabled] .btn-warning.active {
+ background-color: #f0ad4e;
+ border-color: #eea236;
+}
+.btn-warning .badge {
+ color: #f0ad4e;
+ background-color: #fff;
+}
+.btn-danger {
+ color: #fff;
+ background-color: #d9534f;
+ border-color: #d43f3a;
+}
+.btn-danger:hover,
+.btn-danger:focus,
+.btn-danger:active,
+.btn-danger.active,
+.open > .dropdown-toggle.btn-danger {
+ color: #fff;
+ background-color: #c9302c;
+ border-color: #ac2925;
+}
+.btn-danger:active,
+.btn-danger.active,
+.open > .dropdown-toggle.btn-danger {
+ background-image: none;
+}
+.btn-danger.disabled,
+.btn-danger[disabled],
+fieldset[disabled] .btn-danger,
+.btn-danger.disabled:hover,
+.btn-danger[disabled]:hover,
+fieldset[disabled] .btn-danger:hover,
+.btn-danger.disabled:focus,
+.btn-danger[disabled]:focus,
+fieldset[disabled] .btn-danger:focus,
+.btn-danger.disabled:active,
+.btn-danger[disabled]:active,
+fieldset[disabled] .btn-danger:active,
+.btn-danger.disabled.active,
+.btn-danger[disabled].active,
+fieldset[disabled] .btn-danger.active {
+ background-color: #d9534f;
+ border-color: #d43f3a;
+}
+.btn-danger .badge {
+ color: #d9534f;
+ background-color: #fff;
+}
+.btn-link {
+ font-weight: normal;
+ color: #428bca;
+ cursor: pointer;
+ border-radius: 0;
+}
+.btn-link,
+.btn-link:active,
+.btn-link[disabled],
+fieldset[disabled] .btn-link {
+ background-color: transparent;
+ -webkit-box-shadow: none;
+ box-shadow: none;
+}
+.btn-link,
+.btn-link:hover,
+.btn-link:focus,
+.btn-link:active {
+ border-color: transparent;
+}
+.btn-link:hover,
+.btn-link:focus {
+ color: #2a6496;
+ text-decoration: underline;
+ background-color: transparent;
+}
+.btn-link[disabled]:hover,
+fieldset[disabled] .btn-link:hover,
+.btn-link[disabled]:focus,
+fieldset[disabled] .btn-link:focus {
+ color: #777;
+ text-decoration: none;
+}
+.btn-lg,
+.btn-group-lg > .btn {
+ padding: 10px 16px;
+ font-size: 18px;
+ line-height: 1.33;
+ border-radius: 6px;
+}
+.btn-sm,
+.btn-group-sm > .btn {
+ padding: 5px 10px;
+ font-size: 12px;
+ line-height: 1.5;
+ border-radius: 3px;
+}
+.btn-xs,
+.btn-group-xs > .btn {
+ padding: 1px 5px;
+ font-size: 12px;
+ line-height: 1.5;
+ border-radius: 3px;
+}
+.btn-block {
+ display: block;
+ width: 100%;
+}
+.btn-block + .btn-block {
+ margin-top: 5px;
+}
+input[type="submit"].btn-block,
+input[type="reset"].btn-block,
+input[type="button"].btn-block {
+ width: 100%;
+}
+.fade {
+ opacity: 0;
+ -webkit-transition: opacity .15s linear;
+ -o-transition: opacity .15s linear;
+ transition: opacity .15s linear;
+}
+.fade.in {
+ opacity: 1;
+}
+.collapse {
+ display: none;
+}
+.collapse.in {
+ display: block;
+}
+tr.collapse.in {
+ display: table-row;
+}
+tbody.collapse.in {
+ display: table-row-group;
+}
+.collapsing {
+ position: relative;
+ height: 0;
+ overflow: hidden;
+ -webkit-transition: height .35s ease;
+ -o-transition: height .35s ease;
+ transition: height .35s ease;
+}
+.caret {
+ display: inline-block;
+ width: 0;
+ height: 0;
+ margin-left: 2px;
+ vertical-align: middle;
+ border-top: 4px solid;
+ border-right: 4px solid transparent;
+ border-left: 4px solid transparent;
+}
+.dropdown {
+ position: relative;
+}
+.dropdown-toggle:focus {
+ outline: 0;
+}
+.dropdown-menu {
+ position: absolute;
+ top: 100%;
+ left: 0;
+ z-index: 1000;
+ display: none;
+ float: left;
+ min-width: 160px;
+ padding: 5px 0;
+ margin: 2px 0 0;
+ font-size: 14px;
+ text-align: left;
+ list-style: none;
+ background-color: #fff;
+ -webkit-background-clip: padding-box;
+ background-clip: padding-box;
+ border: 1px solid #ccc;
+ border: 1px solid rgba(0, 0, 0, .15);
+ border-radius: 4px;
+ -webkit-box-shadow: 0 6px 12px rgba(0, 0, 0, .175);
+ box-shadow: 0 6px 12px rgba(0, 0, 0, .175);
+}
+.dropdown-menu.pull-right {
+ right: 0;
+ left: auto;
+}
+.dropdown-menu .divider {
+ height: 1px;
+ margin: 9px 0;
+ overflow: hidden;
+ background-color: #e5e5e5;
+}
+.dropdown-menu > li > a {
+ display: block;
+ padding: 3px 20px;
+ clear: both;
+ font-weight: normal;
+ line-height: 1.42857143;
+ color: #333;
+ white-space: nowrap;
+}
+.dropdown-menu > li > a:hover,
+.dropdown-menu > li > a:focus {
+ color: #262626;
+ text-decoration: none;
+ background-color: #f5f5f5;
+}
+.dropdown-menu > .active > a,
+.dropdown-menu > .active > a:hover,
+.dropdown-menu > .active > a:focus {
+ color: #fff;
+ text-decoration: none;
+ background-color: #428bca;
+ outline: 0;
+}
+.dropdown-menu > .disabled > a,
+.dropdown-menu > .disabled > a:hover,
+.dropdown-menu > .disabled > a:focus {
+ color: #777;
+}
+.dropdown-menu > .disabled > a:hover,
+.dropdown-menu > .disabled > a:focus {
+ text-decoration: none;
+ cursor: not-allowed;
+ background-color: transparent;
+ background-image: none;
+ filter: progid:DXImageTransform.Microsoft.gradient(enabled = false);
+}
+.open > .dropdown-menu {
+ display: block;
+}
+.open > a {
+ outline: 0;
+}
+.dropdown-menu-right {
+ right: 0;
+ left: auto;
+}
+.dropdown-menu-left {
+ right: auto;
+ left: 0;
+}
+.dropdown-header {
+ display: block;
+ padding: 3px 20px;
+ font-size: 12px;
+ line-height: 1.42857143;
+ color: #777;
+ white-space: nowrap;
+}
+.dropdown-backdrop {
+ position: fixed;
+ top: 0;
+ right: 0;
+ bottom: 0;
+ left: 0;
+ z-index: 990;
+}
+.pull-right > .dropdown-menu {
+ right: 0;
+ left: auto;
+}
+.dropup .caret,
+.navbar-fixed-bottom .dropdown .caret {
+ content: "";
+ border-top: 0;
+ border-bottom: 4px solid;
+}
+.dropup .dropdown-menu,
+.navbar-fixed-bottom .dropdown .dropdown-menu {
+ top: auto;
+ bottom: 100%;
+ margin-bottom: 1px;
+}
+@media (min-width: 768px) {
+ .navbar-right .dropdown-menu {
+ right: 0;
+ left: auto;
+ }
+ .navbar-right .dropdown-menu-left {
+ right: auto;
+ left: 0;
+ }
+}
+.btn-group,
+.btn-group-vertical {
+ position: relative;
+ display: inline-block;
+ vertical-align: middle;
+}
+.btn-group > .btn,
+.btn-group-vertical > .btn {
+ position: relative;
+ float: left;
+}
+.btn-group > .btn:hover,
+.btn-group-vertical > .btn:hover,
+.btn-group > .btn:focus,
+.btn-group-vertical > .btn:focus,
+.btn-group > .btn:active,
+.btn-group-vertical > .btn:active,
+.btn-group > .btn.active,
+.btn-group-vertical > .btn.active {
+ z-index: 2;
+}
+.btn-group > .btn:focus,
+.btn-group-vertical > .btn:focus {
+ outline: 0;
+}
+.btn-group .btn + .btn,
+.btn-group .btn + .btn-group,
+.btn-group .btn-group + .btn,
+.btn-group .btn-group + .btn-group {
+ margin-left: -1px;
+}
+.btn-toolbar {
+ margin-left: -5px;
+}
+.btn-toolbar .btn-group,
+.btn-toolbar .input-group {
+ float: left;
+}
+.btn-toolbar > .btn,
+.btn-toolbar > .btn-group,
+.btn-toolbar > .input-group {
+ margin-left: 5px;
+}
+.btn-group > .btn:not(:first-child):not(:last-child):not(.dropdown-toggle) {
+ border-radius: 0;
+}
+.btn-group > .btn:first-child {
+ margin-left: 0;
+}
+.btn-group > .btn:first-child:not(:last-child):not(.dropdown-toggle) {
+ border-top-right-radius: 0;
+ border-bottom-right-radius: 0;
+}
+.btn-group > .btn:last-child:not(:first-child),
+.btn-group > .dropdown-toggle:not(:first-child) {
+ border-top-left-radius: 0;
+ border-bottom-left-radius: 0;
+}
+.btn-group > .btn-group {
+ float: left;
+}
+.btn-group > .btn-group:not(:first-child):not(:last-child) > .btn {
+ border-radius: 0;
+}
+.btn-group > .btn-group:first-child > .btn:last-child,
+.btn-group > .btn-group:first-child > .dropdown-toggle {
+ border-top-right-radius: 0;
+ border-bottom-right-radius: 0;
+}
+.btn-group > .btn-group:last-child > .btn:first-child {
+ border-top-left-radius: 0;
+ border-bottom-left-radius: 0;
+}
+.btn-group .dropdown-toggle:active,
+.btn-group.open .dropdown-toggle {
+ outline: 0;
+}
+.btn-group > .btn + .dropdown-toggle {
+ padding-right: 8px;
+ padding-left: 8px;
+}
+.btn-group > .btn-lg + .dropdown-toggle {
+ padding-right: 12px;
+ padding-left: 12px;
+}
+.btn-group.open .dropdown-toggle {
+ -webkit-box-shadow: inset 0 3px 5px rgba(0, 0, 0, .125);
+ box-shadow: inset 0 3px 5px rgba(0, 0, 0, .125);
+}
+.btn-group.open .dropdown-toggle.btn-link {
+ -webkit-box-shadow: none;
+ box-shadow: none;
+}
+.btn .caret {
+ margin-left: 0;
+}
+.btn-lg .caret {
+ border-width: 5px 5px 0;
+ border-bottom-width: 0;
+}
+.dropup .btn-lg .caret {
+ border-width: 0 5px 5px;
+}
+.btn-group-vertical > .btn,
+.btn-group-vertical > .btn-group,
+.btn-group-vertical > .btn-group > .btn {
+ display: block;
+ float: none;
+ width: 100%;
+ max-width: 100%;
+}
+.btn-group-vertical > .btn-group > .btn {
+ float: none;
+}
+.btn-group-vertical > .btn + .btn,
+.btn-group-vertical > .btn + .btn-group,
+.btn-group-vertical > .btn-group + .btn,
+.btn-group-vertical > .btn-group + .btn-group {
+ margin-top: -1px;
+ margin-left: 0;
+}
+.btn-group-vertical > .btn:not(:first-child):not(:last-child) {
+ border-radius: 0;
+}
+.btn-group-vertical > .btn:first-child:not(:last-child) {
+ border-top-right-radius: 4px;
+ border-bottom-right-radius: 0;
+ border-bottom-left-radius: 0;
+}
+.btn-group-vertical > .btn:last-child:not(:first-child) {
+ border-top-left-radius: 0;
+ border-top-right-radius: 0;
+ border-bottom-left-radius: 4px;
+}
+.btn-group-vertical > .btn-group:not(:first-child):not(:last-child) > .btn {
+ border-radius: 0;
+}
+.btn-group-vertical > .btn-group:first-child:not(:last-child) > .btn:last-child,
+.btn-group-vertical > .btn-group:first-child:not(:last-child) > .dropdown-toggle {
+ border-bottom-right-radius: 0;
+ border-bottom-left-radius: 0;
+}
+.btn-group-vertical > .btn-group:last-child:not(:first-child) > .btn:first-child {
+ border-top-left-radius: 0;
+ border-top-right-radius: 0;
+}
+.btn-group-justified {
+ display: table;
+ width: 100%;
+ table-layout: fixed;
+ border-collapse: separate;
+}
+.btn-group-justified > .btn,
+.btn-group-justified > .btn-group {
+ display: table-cell;
+ float: none;
+ width: 1%;
+}
+.btn-group-justified > .btn-group .btn {
+ width: 100%;
+}
+.btn-group-justified > .btn-group .dropdown-menu {
+ left: auto;
+}
+[data-toggle="buttons"] > .btn > input[type="radio"],
+[data-toggle="buttons"] > .btn > input[type="checkbox"] {
+ position: absolute;
+ z-index: -1;
+ filter: alpha(opacity=0);
+ opacity: 0;
+}
+.input-group {
+ position: relative;
+ display: table;
+ border-collapse: separate;
+}
+.input-group[class*="col-"] {
+ float: none;
+ padding-right: 0;
+ padding-left: 0;
+}
+.input-group .form-control {
+ position: relative;
+ z-index: 2;
+ float: left;
+ width: 100%;
+ margin-bottom: 0;
+}
+.input-group-lg > .form-control,
+.input-group-lg > .input-group-addon,
+.input-group-lg > .input-group-btn > .btn {
+ height: 46px;
+ padding: 10px 16px;
+ font-size: 18px;
+ line-height: 1.33;
+ border-radius: 6px;
+}
+select.input-group-lg > .form-control,
+select.input-group-lg > .input-group-addon,
+select.input-group-lg > .input-group-btn > .btn {
+ height: 46px;
+ line-height: 46px;
+}
+textarea.input-group-lg > .form-control,
+textarea.input-group-lg > .input-group-addon,
+textarea.input-group-lg > .input-group-btn > .btn,
+select[multiple].input-group-lg > .form-control,
+select[multiple].input-group-lg > .input-group-addon,
+select[multiple].input-group-lg > .input-group-btn > .btn {
+ height: auto;
+}
+.input-group-sm > .form-control,
+.input-group-sm > .input-group-addon,
+.input-group-sm > .input-group-btn > .btn {
+ height: 30px;
+ padding: 5px 10px;
+ font-size: 12px;
+ line-height: 1.5;
+ border-radius: 3px;
+}
+select.input-group-sm > .form-control,
+select.input-group-sm > .input-group-addon,
+select.input-group-sm > .input-group-btn > .btn {
+ height: 30px;
+ line-height: 30px;
+}
+textarea.input-group-sm > .form-control,
+textarea.input-group-sm > .input-group-addon,
+textarea.input-group-sm > .input-group-btn > .btn,
+select[multiple].input-group-sm > .form-control,
+select[multiple].input-group-sm > .input-group-addon,
+select[multiple].input-group-sm > .input-group-btn > .btn {
+ height: auto;
+}
+.input-group-addon,
+.input-group-btn,
+.input-group .form-control {
+ display: table-cell;
+}
+.input-group-addon:not(:first-child):not(:last-child),
+.input-group-btn:not(:first-child):not(:last-child),
+.input-group .form-control:not(:first-child):not(:last-child) {
+ border-radius: 0;
+}
+.input-group-addon,
+.input-group-btn {
+ width: 1%;
+ white-space: nowrap;
+ vertical-align: middle;
+}
+.input-group-addon {
+ padding: 6px 12px;
+ font-size: 14px;
+ font-weight: normal;
+ line-height: 1;
+ color: #555;
+ text-align: center;
+ background-color: #eee;
+ border: 1px solid #ccc;
+ border-radius: 4px;
+}
+.input-group-addon.input-sm {
+ padding: 5px 10px;
+ font-size: 12px;
+ border-radius: 3px;
+}
+.input-group-addon.input-lg {
+ padding: 10px 16px;
+ font-size: 18px;
+ border-radius: 6px;
+}
+.input-group-addon input[type="radio"],
+.input-group-addon input[type="checkbox"] {
+ margin-top: 0;
+}
+.input-group .form-control:first-child,
+.input-group-addon:first-child,
+.input-group-btn:first-child > .btn,
+.input-group-btn:first-child > .btn-group > .btn,
+.input-group-btn:first-child > .dropdown-toggle,
+.input-group-btn:last-child > .btn:not(:last-child):not(.dropdown-toggle),
+.input-group-btn:last-child > .btn-group:not(:last-child) > .btn {
+ border-top-right-radius: 0;
+ border-bottom-right-radius: 0;
+}
+.input-group-addon:first-child {
+ border-right: 0;
+}
+.input-group .form-control:last-child,
+.input-group-addon:last-child,
+.input-group-btn:last-child > .btn,
+.input-group-btn:last-child > .btn-group > .btn,
+.input-group-btn:last-child > .dropdown-toggle,
+.input-group-btn:first-child > .btn:not(:first-child),
+.input-group-btn:first-child > .btn-group:not(:first-child) > .btn {
+ border-top-left-radius: 0;
+ border-bottom-left-radius: 0;
+}
+.input-group-addon:last-child {
+ border-left: 0;
+}
+.input-group-btn {
+ position: relative;
+ font-size: 0;
+ white-space: nowrap;
+}
+.input-group-btn > .btn {
+ position: relative;
+}
+.input-group-btn > .btn + .btn {
+ margin-left: -1px;
+}
+.input-group-btn > .btn:hover,
+.input-group-btn > .btn:focus,
+.input-group-btn > .btn:active {
+ z-index: 2;
+}
+.input-group-btn:first-child > .btn,
+.input-group-btn:first-child > .btn-group {
+ margin-right: -1px;
+}
+.input-group-btn:last-child > .btn,
+.input-group-btn:last-child > .btn-group {
+ margin-left: -1px;
+}
+.nav {
+ padding-left: 0;
+ margin-bottom: 0;
+ list-style: none;
+}
+.nav > li {
+ position: relative;
+ display: block;
+}
+.nav > li > a {
+ position: relative;
+ display: block;
+ padding: 10px 15px;
+}
+.nav > li > a:hover,
+.nav > li > a:focus {
+ text-decoration: none;
+ background-color: #eee;
+}
+.nav > li.disabled > a {
+ color: #777;
+}
+.nav > li.disabled > a:hover,
+.nav > li.disabled > a:focus {
+ color: #777;
+ text-decoration: none;
+ cursor: not-allowed;
+ background-color: transparent;
+}
+.nav .open > a,
+.nav .open > a:hover,
+.nav .open > a:focus {
+ background-color: #eee;
+ border-color: #428bca;
+}
+.nav .nav-divider {
+ height: 1px;
+ margin: 9px 0;
+ overflow: hidden;
+ background-color: #e5e5e5;
+}
+.nav > li > a > img {
+ max-width: none;
+}
+.nav-tabs {
+ border-bottom: 1px solid #ddd;
+}
+.nav-tabs > li {
+ float: left;
+ margin-bottom: -1px;
+}
+.nav-tabs > li > a {
+ margin-right: 2px;
+ line-height: 1.42857143;
+ border: 1px solid transparent;
+ border-radius: 4px 4px 0 0;
+}
+.nav-tabs > li > a:hover {
+ border-color: #eee #eee #ddd;
+}
+.nav-tabs > li.active > a,
+.nav-tabs > li.active > a:hover,
+.nav-tabs > li.active > a:focus {
+ color: #555;
+ cursor: default;
+ background-color: #fff;
+ border: 1px solid #ddd;
+ border-bottom-color: transparent;
+}
+.nav-tabs.nav-justified {
+ width: 100%;
+ border-bottom: 0;
+}
+.nav-tabs.nav-justified > li {
+ float: none;
+}
+.nav-tabs.nav-justified > li > a {
+ margin-bottom: 5px;
+ text-align: center;
+}
+.nav-tabs.nav-justified > .dropdown .dropdown-menu {
+ top: auto;
+ left: auto;
+}
+@media (min-width: 768px) {
+ .nav-tabs.nav-justified > li {
+ display: table-cell;
+ width: 1%;
+ }
+ .nav-tabs.nav-justified > li > a {
+ margin-bottom: 0;
+ }
+}
+.nav-tabs.nav-justified > li > a {
+ margin-right: 0;
+ border-radius: 4px;
+}
+.nav-tabs.nav-justified > .active > a,
+.nav-tabs.nav-justified > .active > a:hover,
+.nav-tabs.nav-justified > .active > a:focus {
+ border: 1px solid #ddd;
+}
+@media (min-width: 768px) {
+ .nav-tabs.nav-justified > li > a {
+ border-bottom: 1px solid #ddd;
+ border-radius: 4px 4px 0 0;
+ }
+ .nav-tabs.nav-justified > .active > a,
+ .nav-tabs.nav-justified > .active > a:hover,
+ .nav-tabs.nav-justified > .active > a:focus {
+ border-bottom-color: #fff;
+ }
+}
+.nav-pills > li {
+ float: left;
+}
+.nav-pills > li > a {
+ border-radius: 4px;
+}
+.nav-pills > li + li {
+ margin-left: 2px;
+}
+.nav-pills > li.active > a,
+.nav-pills > li.active > a:hover,
+.nav-pills > li.active > a:focus {
+ color: #fff;
+ background-color: #428bca;
+}
+.nav-stacked > li {
+ float: none;
+}
+.nav-stacked > li + li {
+ margin-top: 2px;
+ margin-left: 0;
+}
+.nav-justified {
+ width: 100%;
+}
+.nav-justified > li {
+ float: none;
+}
+.nav-justified > li > a {
+ margin-bottom: 5px;
+ text-align: center;
+}
+.nav-justified > .dropdown .dropdown-menu {
+ top: auto;
+ left: auto;
+}
+@media (min-width: 768px) {
+ .nav-justified > li {
+ display: table-cell;
+ width: 1%;
+ }
+ .nav-justified > li > a {
+ margin-bottom: 0;
+ }
+}
+.nav-tabs-justified {
+ border-bottom: 0;
+}
+.nav-tabs-justified > li > a {
+ margin-right: 0;
+ border-radius: 4px;
+}
+.nav-tabs-justified > .active > a,
+.nav-tabs-justified > .active > a:hover,
+.nav-tabs-justified > .active > a:focus {
+ border: 1px solid #ddd;
+}
+@media (min-width: 768px) {
+ .nav-tabs-justified > li > a {
+ border-bottom: 1px solid #ddd;
+ border-radius: 4px 4px 0 0;
+ }
+ .nav-tabs-justified > .active > a,
+ .nav-tabs-justified > .active > a:hover,
+ .nav-tabs-justified > .active > a:focus {
+ border-bottom-color: #fff;
+ }
+}
+.tab-content > .tab-pane {
+ display: none;
+}
+.tab-content > .active {
+ display: block;
+}
+.nav-tabs .dropdown-menu {
+ margin-top: -1px;
+ border-top-left-radius: 0;
+ border-top-right-radius: 0;
+}
+.navbar {
+ position: relative;
+ min-height: 50px;
+ margin-bottom: 20px;
+ border: 1px solid transparent;
+}
+@media (min-width: 768px) {
+ .navbar {
+ border-radius: 4px;
+ }
+}
+@media (min-width: 768px) {
+ .navbar-header {
+ float: left;
+ }
+}
+.navbar-collapse {
+ padding-right: 15px;
+ padding-left: 15px;
+ overflow-x: visible;
+ -webkit-overflow-scrolling: touch;
+ border-top: 1px solid transparent;
+ -webkit-box-shadow: inset 0 1px 0 rgba(255, 255, 255, .1);
+ box-shadow: inset 0 1px 0 rgba(255, 255, 255, .1);
+}
+.navbar-collapse.in {
+ overflow-y: auto;
+}
+@media (min-width: 768px) {
+ .navbar-collapse {
+ width: auto;
+ border-top: 0;
+ -webkit-box-shadow: none;
+ box-shadow: none;
+ }
+ .navbar-collapse.collapse {
+ display: block !important;
+ height: auto !important;
+ padding-bottom: 0;
+ overflow: visible !important;
+ }
+ .navbar-collapse.in {
+ overflow-y: visible;
+ }
+ .navbar-fixed-top .navbar-collapse,
+ .navbar-static-top .navbar-collapse,
+ .navbar-fixed-bottom .navbar-collapse {
+ padding-right: 0;
+ padding-left: 0;
+ }
+}
+.navbar-fixed-top .navbar-collapse,
+.navbar-fixed-bottom .navbar-collapse {
+ max-height: 340px;
+}
+@media (max-width: 480px) and (orientation: landscape) {
+ .navbar-fixed-top .navbar-collapse,
+ .navbar-fixed-bottom .navbar-collapse {
+ max-height: 200px;
+ }
+}
+.container > .navbar-header,
+.container-fluid > .navbar-header,
+.container > .navbar-collapse,
+.container-fluid > .navbar-collapse {
+ margin-right: -15px;
+ margin-left: -15px;
+}
+@media (min-width: 768px) {
+ .container > .navbar-header,
+ .container-fluid > .navbar-header,
+ .container > .navbar-collapse,
+ .container-fluid > .navbar-collapse {
+ margin-right: 0;
+ margin-left: 0;
+ }
+}
+.navbar-static-top {
+ z-index: 1000;
+ border-width: 0 0 1px;
+}
+@media (min-width: 768px) {
+ .navbar-static-top {
+ border-radius: 0;
+ }
+}
+.navbar-fixed-top,
+.navbar-fixed-bottom {
+ position: fixed;
+ right: 0;
+ left: 0;
+ z-index: 1030;
+ -webkit-transform: translate3d(0, 0, 0);
+ -o-transform: translate3d(0, 0, 0);
+ transform: translate3d(0, 0, 0);
+}
+@media (min-width: 768px) {
+ .navbar-fixed-top,
+ .navbar-fixed-bottom {
+ border-radius: 0;
+ }
+}
+.navbar-fixed-top {
+ top: 0;
+ border-width: 0 0 1px;
+}
+.navbar-fixed-bottom {
+ bottom: 0;
+ margin-bottom: 0;
+ border-width: 1px 0 0;
+}
+.navbar-brand {
+ float: left;
+ height: 50px;
+ padding: 15px 15px;
+ font-size: 18px;
+ line-height: 20px;
+}
+.navbar-brand:hover,
+.navbar-brand:focus {
+ text-decoration: none;
+}
+@media (min-width: 768px) {
+ .navbar > .container .navbar-brand,
+ .navbar > .container-fluid .navbar-brand {
+ margin-left: -15px;
+ }
+}
+.navbar-toggle {
+ position: relative;
+ float: right;
+ padding: 9px 10px;
+ margin-top: 8px;
+ margin-right: 15px;
+ margin-bottom: 8px;
+ background-color: transparent;
+ background-image: none;
+ border: 1px solid transparent;
+ border-radius: 4px;
+}
+.navbar-toggle:focus {
+ outline: 0;
+}
+.navbar-toggle .icon-bar {
+ display: block;
+ width: 22px;
+ height: 2px;
+ border-radius: 1px;
+}
+.navbar-toggle .icon-bar + .icon-bar {
+ margin-top: 4px;
+}
+@media (min-width: 768px) {
+ .navbar-toggle {
+ display: none;
+ }
+}
+.navbar-nav {
+ margin: 7.5px -15px;
+}
+.navbar-nav > li > a {
+ padding-top: 10px;
+ padding-bottom: 10px;
+ line-height: 20px;
+}
+@media (max-width: 767px) {
+ .navbar-nav .open .dropdown-menu {
+ position: static;
+ float: none;
+ width: auto;
+ margin-top: 0;
+ background-color: transparent;
+ border: 0;
+ -webkit-box-shadow: none;
+ box-shadow: none;
+ }
+ .navbar-nav .open .dropdown-menu > li > a,
+ .navbar-nav .open .dropdown-menu .dropdown-header {
+ padding: 5px 15px 5px 25px;
+ }
+ .navbar-nav .open .dropdown-menu > li > a {
+ line-height: 20px;
+ }
+ .navbar-nav .open .dropdown-menu > li > a:hover,
+ .navbar-nav .open .dropdown-menu > li > a:focus {
+ background-image: none;
+ }
+}
+@media (min-width: 768px) {
+ .navbar-nav {
+ float: left;
+ margin: 0;
+ }
+ .navbar-nav > li {
+ float: left;
+ }
+ .navbar-nav > li > a {
+ padding-top: 15px;
+ padding-bottom: 15px;
+ }
+ .navbar-nav.navbar-right:last-child {
+ margin-right: -15px;
+ }
+}
+@media (min-width: 768px) {
+ .navbar-left {
+ float: left !important;
+ }
+ .navbar-right {
+ float: right !important;
+ }
+}
+.navbar-form {
+ padding: 10px 15px;
+ margin-top: 8px;
+ margin-right: -15px;
+ margin-bottom: 8px;
+ margin-left: -15px;
+ border-top: 1px solid transparent;
+ border-bottom: 1px solid transparent;
+ -webkit-box-shadow: inset 0 1px 0 rgba(255, 255, 255, .1), 0 1px 0 rgba(255, 255, 255, .1);
+ box-shadow: inset 0 1px 0 rgba(255, 255, 255, .1), 0 1px 0 rgba(255, 255, 255, .1);
+}
+@media (min-width: 768px) {
+ .navbar-form .form-group {
+ display: inline-block;
+ margin-bottom: 0;
+ vertical-align: middle;
+ }
+ .navbar-form .form-control {
+ display: inline-block;
+ width: auto;
+ vertical-align: middle;
+ }
+ .navbar-form .input-group {
+ display: inline-table;
+ vertical-align: middle;
+ }
+ .navbar-form .input-group .input-group-addon,
+ .navbar-form .input-group .input-group-btn,
+ .navbar-form .input-group .form-control {
+ width: auto;
+ }
+ .navbar-form .input-group > .form-control {
+ width: 100%;
+ }
+ .navbar-form .control-label {
+ margin-bottom: 0;
+ vertical-align: middle;
+ }
+ .navbar-form .radio,
+ .navbar-form .checkbox {
+ display: inline-block;
+ margin-top: 0;
+ margin-bottom: 0;
+ vertical-align: middle;
+ }
+ .navbar-form .radio label,
+ .navbar-form .checkbox label {
+ padding-left: 0;
+ }
+ .navbar-form .radio input[type="radio"],
+ .navbar-form .checkbox input[type="checkbox"] {
+ position: relative;
+ margin-left: 0;
+ }
+ .navbar-form .has-feedback .form-control-feedback {
+ top: 0;
+ }
+}
+@media (max-width: 767px) {
+ .navbar-form .form-group {
+ margin-bottom: 5px;
+ }
+}
+@media (min-width: 768px) {
+ .navbar-form {
+ width: auto;
+ padding-top: 0;
+ padding-bottom: 0;
+ margin-right: 0;
+ margin-left: 0;
+ border: 0;
+ -webkit-box-shadow: none;
+ box-shadow: none;
+ }
+ .navbar-form.navbar-right:last-child {
+ margin-right: -15px;
+ }
+}
+.navbar-nav > li > .dropdown-menu {
+ margin-top: 0;
+ border-top-left-radius: 0;
+ border-top-right-radius: 0;
+}
+.navbar-fixed-bottom .navbar-nav > li > .dropdown-menu {
+ border-bottom-right-radius: 0;
+ border-bottom-left-radius: 0;
+}
+.navbar-btn {
+ margin-top: 8px;
+ margin-bottom: 8px;
+}
+.navbar-btn.btn-sm {
+ margin-top: 10px;
+ margin-bottom: 10px;
+}
+.navbar-btn.btn-xs {
+ margin-top: 14px;
+ margin-bottom: 14px;
+}
+.navbar-text {
+ margin-top: 15px;
+ margin-bottom: 15px;
+}
+@media (min-width: 768px) {
+ .navbar-text {
+ float: left;
+ margin-right: 15px;
+ margin-left: 15px;
+ }
+ .navbar-text.navbar-right:last-child {
+ margin-right: 0;
+ }
+}
+.navbar-default {
+ background-color: #f8f8f8;
+ border-color: #e7e7e7;
+}
+.navbar-default .navbar-brand {
+ color: #777;
+}
+.navbar-default .navbar-brand:hover,
+.navbar-default .navbar-brand:focus {
+ color: #5e5e5e;
+ background-color: transparent;
+}
+.navbar-default .navbar-text {
+ color: #777;
+}
+.navbar-default .navbar-nav > li > a {
+ color: #777;
+}
+.navbar-default .navbar-nav > li > a:hover,
+.navbar-default .navbar-nav > li > a:focus {
+ color: #333;
+ background-color: transparent;
+}
+.navbar-default .navbar-nav > .active > a,
+.navbar-default .navbar-nav > .active > a:hover,
+.navbar-default .navbar-nav > .active > a:focus {
+ color: #555;
+ background-color: #e7e7e7;
+}
+.navbar-default .navbar-nav > .disabled > a,
+.navbar-default .navbar-nav > .disabled > a:hover,
+.navbar-default .navbar-nav > .disabled > a:focus {
+ color: #ccc;
+ background-color: transparent;
+}
+.navbar-default .navbar-toggle {
+ border-color: #ddd;
+}
+.navbar-default .navbar-toggle:hover,
+.navbar-default .navbar-toggle:focus {
+ background-color: #ddd;
+}
+.navbar-default .navbar-toggle .icon-bar {
+ background-color: #888;
+}
+.navbar-default .navbar-collapse,
+.navbar-default .navbar-form {
+ border-color: #e7e7e7;
+}
+.navbar-default .navbar-nav > .open > a,
+.navbar-default .navbar-nav > .open > a:hover,
+.navbar-default .navbar-nav > .open > a:focus {
+ color: #555;
+ background-color: #e7e7e7;
+}
+@media (max-width: 767px) {
+ .navbar-default .navbar-nav .open .dropdown-menu > li > a {
+ color: #777;
+ }
+ .navbar-default .navbar-nav .open .dropdown-menu > li > a:hover,
+ .navbar-default .navbar-nav .open .dropdown-menu > li > a:focus {
+ color: #333;
+ background-color: transparent;
+ }
+ .navbar-default .navbar-nav .open .dropdown-menu > .active > a,
+ .navbar-default .navbar-nav .open .dropdown-menu > .active > a:hover,
+ .navbar-default .navbar-nav .open .dropdown-menu > .active > a:focus {
+ color: #555;
+ background-color: #e7e7e7;
+ }
+ .navbar-default .navbar-nav .open .dropdown-menu > .disabled > a,
+ .navbar-default .navbar-nav .open .dropdown-menu > .disabled > a:hover,
+ .navbar-default .navbar-nav .open .dropdown-menu > .disabled > a:focus {
+ color: #ccc;
+ background-color: transparent;
+ }
+}
+.navbar-default .navbar-link {
+ color: #777;
+}
+.navbar-default .navbar-link:hover {
+ color: #333;
+}
+.navbar-default .btn-link {
+ color: #777;
+}
+.navbar-default .btn-link:hover,
+.navbar-default .btn-link:focus {
+ color: #333;
+}
+.navbar-default .btn-link[disabled]:hover,
+fieldset[disabled] .navbar-default .btn-link:hover,
+.navbar-default .btn-link[disabled]:focus,
+fieldset[disabled] .navbar-default .btn-link:focus {
+ color: #ccc;
+}
+.navbar-inverse {
+ background-color: #222;
+ border-color: #080808;
+}
+.navbar-inverse .navbar-brand {
+ color: #777;
+}
+.navbar-inverse .navbar-brand:hover,
+.navbar-inverse .navbar-brand:focus {
+ color: #fff;
+ background-color: transparent;
+}
+.navbar-inverse .navbar-text {
+ color: #777;
+}
+.navbar-inverse .navbar-nav > li > a {
+ color: #777;
+}
+.navbar-inverse .navbar-nav > li > a:hover,
+.navbar-inverse .navbar-nav > li > a:focus {
+ color: #fff;
+ background-color: transparent;
+}
+.navbar-inverse .navbar-nav > .active > a,
+.navbar-inverse .navbar-nav > .active > a:hover,
+.navbar-inverse .navbar-nav > .active > a:focus {
+ color: #fff;
+ background-color: #080808;
+}
+.navbar-inverse .navbar-nav > .disabled > a,
+.navbar-inverse .navbar-nav > .disabled > a:hover,
+.navbar-inverse .navbar-nav > .disabled > a:focus {
+ color: #444;
+ background-color: transparent;
+}
+.navbar-inverse .navbar-toggle {
+ border-color: #333;
+}
+.navbar-inverse .navbar-toggle:hover,
+.navbar-inverse .navbar-toggle:focus {
+ background-color: #333;
+}
+.navbar-inverse .navbar-toggle .icon-bar {
+ background-color: #fff;
+}
+.navbar-inverse .navbar-collapse,
+.navbar-inverse .navbar-form {
+ border-color: #101010;
+}
+.navbar-inverse .navbar-nav > .open > a,
+.navbar-inverse .navbar-nav > .open > a:hover,
+.navbar-inverse .navbar-nav > .open > a:focus {
+ color: #fff;
+ background-color: #080808;
+}
+@media (max-width: 767px) {
+ .navbar-inverse .navbar-nav .open .dropdown-menu > .dropdown-header {
+ border-color: #080808;
+ }
+ .navbar-inverse .navbar-nav .open .dropdown-menu .divider {
+ background-color: #080808;
+ }
+ .navbar-inverse .navbar-nav .open .dropdown-menu > li > a {
+ color: #777;
+ }
+ .navbar-inverse .navbar-nav .open .dropdown-menu > li > a:hover,
+ .navbar-inverse .navbar-nav .open .dropdown-menu > li > a:focus {
+ color: #fff;
+ background-color: transparent;
+ }
+ .navbar-inverse .navbar-nav .open .dropdown-menu > .active > a,
+ .navbar-inverse .navbar-nav .open .dropdown-menu > .active > a:hover,
+ .navbar-inverse .navbar-nav .open .dropdown-menu > .active > a:focus {
+ color: #fff;
+ background-color: #080808;
+ }
+ .navbar-inverse .navbar-nav .open .dropdown-menu > .disabled > a,
+ .navbar-inverse .navbar-nav .open .dropdown-menu > .disabled > a:hover,
+ .navbar-inverse .navbar-nav .open .dropdown-menu > .disabled > a:focus {
+ color: #444;
+ background-color: transparent;
+ }
+}
+.navbar-inverse .navbar-link {
+ color: #777;
+}
+.navbar-inverse .navbar-link:hover {
+ color: #fff;
+}
+.navbar-inverse .btn-link {
+ color: #777;
+}
+.navbar-inverse .btn-link:hover,
+.navbar-inverse .btn-link:focus {
+ color: #fff;
+}
+.navbar-inverse .btn-link[disabled]:hover,
+fieldset[disabled] .navbar-inverse .btn-link:hover,
+.navbar-inverse .btn-link[disabled]:focus,
+fieldset[disabled] .navbar-inverse .btn-link:focus {
+ color: #444;
+}
+.breadcrumb {
+ padding: 8px 15px;
+ margin-bottom: 20px;
+ list-style: none;
+ background-color: #f5f5f5;
+ border-radius: 4px;
+}
+.breadcrumb > li {
+ display: inline-block;
+}
+.breadcrumb > li + li:before {
+ padding: 0 5px;
+ color: #ccc;
+ content: "/\00a0";
+}
+.breadcrumb > .active {
+ color: #777;
+}
+.pagination {
+ display: inline-block;
+ padding-left: 0;
+ margin: 20px 0;
+ border-radius: 4px;
+}
+.pagination > li {
+ display: inline;
+}
+.pagination > li > a,
+.pagination > li > span {
+ position: relative;
+ float: left;
+ padding: 6px 12px;
+ margin-left: -1px;
+ line-height: 1.42857143;
+ color: #428bca;
+ text-decoration: none;
+ background-color: #fff;
+ border: 1px solid #ddd;
+}
+.pagination > li:first-child > a,
+.pagination > li:first-child > span {
+ margin-left: 0;
+ border-top-left-radius: 4px;
+ border-bottom-left-radius: 4px;
+}
+.pagination > li:last-child > a,
+.pagination > li:last-child > span {
+ border-top-right-radius: 4px;
+ border-bottom-right-radius: 4px;
+}
+.pagination > li > a:hover,
+.pagination > li > span:hover,
+.pagination > li > a:focus,
+.pagination > li > span:focus {
+ color: #2a6496;
+ background-color: #eee;
+ border-color: #ddd;
+}
+.pagination > .active > a,
+.pagination > .active > span,
+.pagination > .active > a:hover,
+.pagination > .active > span:hover,
+.pagination > .active > a:focus,
+.pagination > .active > span:focus {
+ z-index: 2;
+ color: #fff;
+ cursor: default;
+ background-color: #428bca;
+ border-color: #428bca;
+}
+.pagination > .disabled > span,
+.pagination > .disabled > span:hover,
+.pagination > .disabled > span:focus,
+.pagination > .disabled > a,
+.pagination > .disabled > a:hover,
+.pagination > .disabled > a:focus {
+ color: #777;
+ cursor: not-allowed;
+ background-color: #fff;
+ border-color: #ddd;
+}
+.pagination-lg > li > a,
+.pagination-lg > li > span {
+ padding: 10px 16px;
+ font-size: 18px;
+}
+.pagination-lg > li:first-child > a,
+.pagination-lg > li:first-child > span {
+ border-top-left-radius: 6px;
+ border-bottom-left-radius: 6px;
+}
+.pagination-lg > li:last-child > a,
+.pagination-lg > li:last-child > span {
+ border-top-right-radius: 6px;
+ border-bottom-right-radius: 6px;
+}
+.pagination-sm > li > a,
+.pagination-sm > li > span {
+ padding: 5px 10px;
+ font-size: 12px;
+}
+.pagination-sm > li:first-child > a,
+.pagination-sm > li:first-child > span {
+ border-top-left-radius: 3px;
+ border-bottom-left-radius: 3px;
+}
+.pagination-sm > li:last-child > a,
+.pagination-sm > li:last-child > span {
+ border-top-right-radius: 3px;
+ border-bottom-right-radius: 3px;
+}
+.pager {
+ padding-left: 0;
+ margin: 20px 0;
+ text-align: center;
+ list-style: none;
+}
+.pager li {
+ display: inline;
+}
+.pager li > a,
+.pager li > span {
+ display: inline-block;
+ padding: 5px 14px;
+ background-color: #fff;
+ border: 1px solid #ddd;
+ border-radius: 15px;
+}
+.pager li > a:hover,
+.pager li > a:focus {
+ text-decoration: none;
+ background-color: #eee;
+}
+.pager .next > a,
+.pager .next > span {
+ float: right;
+}
+.pager .previous > a,
+.pager .previous > span {
+ float: left;
+}
+.pager .disabled > a,
+.pager .disabled > a:hover,
+.pager .disabled > a:focus,
+.pager .disabled > span {
+ color: #777;
+ cursor: not-allowed;
+ background-color: #fff;
+}
+.label {
+ display: inline;
+ padding: .2em .6em .3em;
+ font-size: 75%;
+ font-weight: bold;
+ line-height: 1;
+ color: #fff;
+ text-align: center;
+ white-space: nowrap;
+ vertical-align: baseline;
+ border-radius: .25em;
+}
+a.label:hover,
+a.label:focus {
+ color: #fff;
+ text-decoration: none;
+ cursor: pointer;
+}
+.label:empty {
+ display: none;
+}
+.btn .label {
+ position: relative;
+ top: -1px;
+}
+.label-default {
+ background-color: #777;
+}
+.label-default[href]:hover,
+.label-default[href]:focus {
+ background-color: #5e5e5e;
+}
+.label-primary {
+ background-color: #428bca;
+}
+.label-primary[href]:hover,
+.label-primary[href]:focus {
+ background-color: #3071a9;
+}
+.label-success {
+ background-color: #5cb85c;
+}
+.label-success[href]:hover,
+.label-success[href]:focus {
+ background-color: #449d44;
+}
+.label-info {
+ background-color: #5bc0de;
+}
+.label-info[href]:hover,
+.label-info[href]:focus {
+ background-color: #31b0d5;
+}
+.label-warning {
+ background-color: #f0ad4e;
+}
+.label-warning[href]:hover,
+.label-warning[href]:focus {
+ background-color: #ec971f;
+}
+.label-danger {
+ background-color: #d9534f;
+}
+.label-danger[href]:hover,
+.label-danger[href]:focus {
+ background-color: #c9302c;
+}
+.badge {
+ display: inline-block;
+ min-width: 10px;
+ padding: 3px 7px;
+ font-size: 12px;
+ font-weight: bold;
+ line-height: 1;
+ color: #fff;
+ text-align: center;
+ white-space: nowrap;
+ vertical-align: baseline;
+ background-color: #777;
+ border-radius: 10px;
+}
+.badge:empty {
+ display: none;
+}
+.btn .badge {
+ position: relative;
+ top: -1px;
+}
+.btn-xs .badge {
+ top: 0;
+ padding: 1px 5px;
+}
+a.badge:hover,
+a.badge:focus {
+ color: #fff;
+ text-decoration: none;
+ cursor: pointer;
+}
+a.list-group-item.active > .badge,
+.nav-pills > .active > a > .badge {
+ color: #428bca;
+ background-color: #fff;
+}
+.nav-pills > li > a > .badge {
+ margin-left: 3px;
+}
+.jumbotron {
+ padding: 30px;
+ margin-bottom: 30px;
+ color: inherit;
+ background-color: #eee;
+}
+.jumbotron h1,
+.jumbotron .h1 {
+ color: inherit;
+}
+.jumbotron p {
+ margin-bottom: 15px;
+ font-size: 21px;
+ font-weight: 200;
+}
+.jumbotron > hr {
+ border-top-color: #d5d5d5;
+}
+.container .jumbotron {
+ border-radius: 6px;
+}
+.jumbotron .container {
+ max-width: 100%;
+}
+@media screen and (min-width: 768px) {
+ .jumbotron {
+ padding-top: 48px;
+ padding-bottom: 48px;
+ }
+ .container .jumbotron {
+ padding-right: 60px;
+ padding-left: 60px;
+ }
+ .jumbotron h1,
+ .jumbotron .h1 {
+ font-size: 63px;
+ }
+}
+.thumbnail {
+ display: block;
+ padding: 4px;
+ margin-bottom: 20px;
+ line-height: 1.42857143;
+ background-color: #fff;
+ border: 1px solid #ddd;
+ border-radius: 4px;
+ -webkit-transition: all .2s ease-in-out;
+ -o-transition: all .2s ease-in-out;
+ transition: all .2s ease-in-out;
+}
+.thumbnail > img,
+.thumbnail a > img {
+ margin-right: auto;
+ margin-left: auto;
+}
+a.thumbnail:hover,
+a.thumbnail:focus,
+a.thumbnail.active {
+ border-color: #428bca;
+}
+.thumbnail .caption {
+ padding: 9px;
+ color: #333;
+}
+.alert {
+ padding: 15px;
+ margin-bottom: 20px;
+ border: 1px solid transparent;
+ border-radius: 4px;
+}
+.alert h4 {
+ margin-top: 0;
+ color: inherit;
+}
+.alert .alert-link {
+ font-weight: bold;
+}
+.alert > p,
+.alert > ul {
+ margin-bottom: 0;
+}
+.alert > p + p {
+ margin-top: 5px;
+}
+.alert-dismissable,
+.alert-dismissible {
+ padding-right: 35px;
+}
+.alert-dismissable .close,
+.alert-dismissible .close {
+ position: relative;
+ top: -2px;
+ right: -21px;
+ color: inherit;
+}
+.alert-success {
+ color: #3c763d;
+ background-color: #dff0d8;
+ border-color: #d6e9c6;
+}
+.alert-success hr {
+ border-top-color: #c9e2b3;
+}
+.alert-success .alert-link {
+ color: #2b542c;
+}
+.alert-info {
+ color: #31708f;
+ background-color: #d9edf7;
+ border-color: #bce8f1;
+}
+.alert-info hr {
+ border-top-color: #a6e1ec;
+}
+.alert-info .alert-link {
+ color: #245269;
+}
+.alert-warning {
+ color: #8a6d3b;
+ background-color: #fcf8e3;
+ border-color: #faebcc;
+}
+.alert-warning hr {
+ border-top-color: #f7e1b5;
+}
+.alert-warning .alert-link {
+ color: #66512c;
+}
+.alert-danger {
+ color: #a94442;
+ background-color: #f2dede;
+ border-color: #ebccd1;
+}
+.alert-danger hr {
+ border-top-color: #e4b9c0;
+}
+.alert-danger .alert-link {
+ color: #843534;
+}
+@-webkit-keyframes progress-bar-stripes {
+ from {
+ background-position: 40px 0;
+ }
+ to {
+ background-position: 0 0;
+ }
+}
+@-o-keyframes progress-bar-stripes {
+ from {
+ background-position: 40px 0;
+ }
+ to {
+ background-position: 0 0;
+ }
+}
+@keyframes progress-bar-stripes {
+ from {
+ background-position: 40px 0;
+ }
+ to {
+ background-position: 0 0;
+ }
+}
+.progress {
+ height: 20px;
+ margin-bottom: 20px;
+ overflow: hidden;
+ background-color: #f5f5f5;
+ border-radius: 4px;
+ -webkit-box-shadow: inset 0 1px 2px rgba(0, 0, 0, .1);
+ box-shadow: inset 0 1px 2px rgba(0, 0, 0, .1);
+}
+.progress-bar {
+ float: left;
+ width: 0;
+ height: 100%;
+ font-size: 12px;
+ line-height: 20px;
+ color: #fff;
+ text-align: center;
+ background-color: #428bca;
+ -webkit-box-shadow: inset 0 -1px 0 rgba(0, 0, 0, .15);
+ box-shadow: inset 0 -1px 0 rgba(0, 0, 0, .15);
+ -webkit-transition: width .6s ease;
+ -o-transition: width .6s ease;
+ transition: width .6s ease;
+}
+.progress-striped .progress-bar,
+.progress-bar-striped {
+ background-image: -webkit-linear-gradient(45deg, rgba(255, 255, 255, .15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, .15) 50%, rgba(255, 255, 255, .15) 75%, transparent 75%, transparent);
+ background-image: -o-linear-gradient(45deg, rgba(255, 255, 255, .15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, .15) 50%, rgba(255, 255, 255, .15) 75%, transparent 75%, transparent);
+ background-image: linear-gradient(45deg, rgba(255, 255, 255, .15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, .15) 50%, rgba(255, 255, 255, .15) 75%, transparent 75%, transparent);
+ -webkit-background-size: 40px 40px;
+ background-size: 40px 40px;
+}
+.progress.active .progress-bar,
+.progress-bar.active {
+ -webkit-animation: progress-bar-stripes 2s linear infinite;
+ -o-animation: progress-bar-stripes 2s linear infinite;
+ animation: progress-bar-stripes 2s linear infinite;
+}
+.progress-bar[aria-valuenow="1"],
+.progress-bar[aria-valuenow="2"] {
+ min-width: 30px;
+}
+.progress-bar[aria-valuenow="0"] {
+ min-width: 30px;
+ color: #777;
+ background-color: transparent;
+ background-image: none;
+ -webkit-box-shadow: none;
+ box-shadow: none;
+}
+.progress-bar-success {
+ background-color: #5cb85c;
+}
+.progress-striped .progress-bar-success {
+ background-image: -webkit-linear-gradient(45deg, rgba(255, 255, 255, .15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, .15) 50%, rgba(255, 255, 255, .15) 75%, transparent 75%, transparent);
+ background-image: -o-linear-gradient(45deg, rgba(255, 255, 255, .15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, .15) 50%, rgba(255, 255, 255, .15) 75%, transparent 75%, transparent);
+ background-image: linear-gradient(45deg, rgba(255, 255, 255, .15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, .15) 50%, rgba(255, 255, 255, .15) 75%, transparent 75%, transparent);
+}
+.progress-bar-info {
+ background-color: #5bc0de;
+}
+.progress-striped .progress-bar-info {
+ background-image: -webkit-linear-gradient(45deg, rgba(255, 255, 255, .15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, .15) 50%, rgba(255, 255, 255, .15) 75%, transparent 75%, transparent);
+ background-image: -o-linear-gradient(45deg, rgba(255, 255, 255, .15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, .15) 50%, rgba(255, 255, 255, .15) 75%, transparent 75%, transparent);
+ background-image: linear-gradient(45deg, rgba(255, 255, 255, .15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, .15) 50%, rgba(255, 255, 255, .15) 75%, transparent 75%, transparent);
+}
+.progress-bar-warning {
+ background-color: #f0ad4e;
+}
+.progress-striped .progress-bar-warning {
+ background-image: -webkit-linear-gradient(45deg, rgba(255, 255, 255, .15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, .15) 50%, rgba(255, 255, 255, .15) 75%, transparent 75%, transparent);
+ background-image: -o-linear-gradient(45deg, rgba(255, 255, 255, .15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, .15) 50%, rgba(255, 255, 255, .15) 75%, transparent 75%, transparent);
+ background-image: linear-gradient(45deg, rgba(255, 255, 255, .15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, .15) 50%, rgba(255, 255, 255, .15) 75%, transparent 75%, transparent);
+}
+.progress-bar-danger {
+ background-color: #d9534f;
+}
+.progress-striped .progress-bar-danger {
+ background-image: -webkit-linear-gradient(45deg, rgba(255, 255, 255, .15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, .15) 50%, rgba(255, 255, 255, .15) 75%, transparent 75%, transparent);
+ background-image: -o-linear-gradient(45deg, rgba(255, 255, 255, .15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, .15) 50%, rgba(255, 255, 255, .15) 75%, transparent 75%, transparent);
+ background-image: linear-gradient(45deg, rgba(255, 255, 255, .15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, .15) 50%, rgba(255, 255, 255, .15) 75%, transparent 75%, transparent);
+}
+.media,
+.media-body {
+ overflow: hidden;
+ zoom: 1;
+}
+.media,
+.media .media {
+ margin-top: 15px;
+}
+.media:first-child {
+ margin-top: 0;
+}
+.media-object {
+ display: block;
+}
+.media-heading {
+ margin: 0 0 5px;
+}
+.media > .pull-left {
+ margin-right: 10px;
+}
+.media > .pull-right {
+ margin-left: 10px;
+}
+.media-list {
+ padding-left: 0;
+ list-style: none;
+}
+.list-group {
+ padding-left: 0;
+ margin-bottom: 20px;
+}
+.list-group-item {
+ position: relative;
+ display: block;
+ padding: 10px 15px;
+ margin-bottom: -1px;
+ background-color: #fff;
+ border: 1px solid #ddd;
+}
+.list-group-item:first-child {
+ border-top-left-radius: 4px;
+ border-top-right-radius: 4px;
+}
+.list-group-item:last-child {
+ margin-bottom: 0;
+ border-bottom-right-radius: 4px;
+ border-bottom-left-radius: 4px;
+}
+.list-group-item > .badge {
+ float: right;
+}
+.list-group-item > .badge + .badge {
+ margin-right: 5px;
+}
+a.list-group-item {
+ color: #555;
+}
+a.list-group-item .list-group-item-heading {
+ color: #333;
+}
+a.list-group-item:hover,
+a.list-group-item:focus {
+ color: #555;
+ text-decoration: none;
+ background-color: #f5f5f5;
+}
+.list-group-item.disabled,
+.list-group-item.disabled:hover,
+.list-group-item.disabled:focus {
+ color: #777;
+ background-color: #eee;
+}
+.list-group-item.disabled .list-group-item-heading,
+.list-group-item.disabled:hover .list-group-item-heading,
+.list-group-item.disabled:focus .list-group-item-heading {
+ color: inherit;
+}
+.list-group-item.disabled .list-group-item-text,
+.list-group-item.disabled:hover .list-group-item-text,
+.list-group-item.disabled:focus .list-group-item-text {
+ color: #777;
+}
+.list-group-item.active,
+.list-group-item.active:hover,
+.list-group-item.active:focus {
+ z-index: 2;
+ color: #fff;
+ background-color: #428bca;
+ border-color: #428bca;
+}
+.list-group-item.active .list-group-item-heading,
+.list-group-item.active:hover .list-group-item-heading,
+.list-group-item.active:focus .list-group-item-heading,
+.list-group-item.active .list-group-item-heading > small,
+.list-group-item.active:hover .list-group-item-heading > small,
+.list-group-item.active:focus .list-group-item-heading > small,
+.list-group-item.active .list-group-item-heading > .small,
+.list-group-item.active:hover .list-group-item-heading > .small,
+.list-group-item.active:focus .list-group-item-heading > .small {
+ color: inherit;
+}
+.list-group-item.active .list-group-item-text,
+.list-group-item.active:hover .list-group-item-text,
+.list-group-item.active:focus .list-group-item-text {
+ color: #e1edf7;
+}
+.list-group-item-success {
+ color: #3c763d;
+ background-color: #dff0d8;
+}
+a.list-group-item-success {
+ color: #3c763d;
+}
+a.list-group-item-success .list-group-item-heading {
+ color: inherit;
+}
+a.list-group-item-success:hover,
+a.list-group-item-success:focus {
+ color: #3c763d;
+ background-color: #d0e9c6;
+}
+a.list-group-item-success.active,
+a.list-group-item-success.active:hover,
+a.list-group-item-success.active:focus {
+ color: #fff;
+ background-color: #3c763d;
+ border-color: #3c763d;
+}
+.list-group-item-info {
+ color: #31708f;
+ background-color: #d9edf7;
+}
+a.list-group-item-info {
+ color: #31708f;
+}
+a.list-group-item-info .list-group-item-heading {
+ color: inherit;
+}
+a.list-group-item-info:hover,
+a.list-group-item-info:focus {
+ color: #31708f;
+ background-color: #c4e3f3;
+}
+a.list-group-item-info.active,
+a.list-group-item-info.active:hover,
+a.list-group-item-info.active:focus {
+ color: #fff;
+ background-color: #31708f;
+ border-color: #31708f;
+}
+.list-group-item-warning {
+ color: #8a6d3b;
+ background-color: #fcf8e3;
+}
+a.list-group-item-warning {
+ color: #8a6d3b;
+}
+a.list-group-item-warning .list-group-item-heading {
+ color: inherit;
+}
+a.list-group-item-warning:hover,
+a.list-group-item-warning:focus {
+ color: #8a6d3b;
+ background-color: #faf2cc;
+}
+a.list-group-item-warning.active,
+a.list-group-item-warning.active:hover,
+a.list-group-item-warning.active:focus {
+ color: #fff;
+ background-color: #8a6d3b;
+ border-color: #8a6d3b;
+}
+.list-group-item-danger {
+ color: #a94442;
+ background-color: #f2dede;
+}
+a.list-group-item-danger {
+ color: #a94442;
+}
+a.list-group-item-danger .list-group-item-heading {
+ color: inherit;
+}
+a.list-group-item-danger:hover,
+a.list-group-item-danger:focus {
+ color: #a94442;
+ background-color: #ebcccc;
+}
+a.list-group-item-danger.active,
+a.list-group-item-danger.active:hover,
+a.list-group-item-danger.active:focus {
+ color: #fff;
+ background-color: #a94442;
+ border-color: #a94442;
+}
+.list-group-item-heading {
+ margin-top: 0;
+ margin-bottom: 5px;
+}
+.list-group-item-text {
+ margin-bottom: 0;
+ line-height: 1.3;
+}
+.panel {
+ margin-bottom: 20px;
+ background-color: #fff;
+ border: 1px solid transparent;
+ border-radius: 4px;
+ -webkit-box-shadow: 0 1px 1px rgba(0, 0, 0, .05);
+ box-shadow: 0 1px 1px rgba(0, 0, 0, .05);
+}
+.panel-body {
+ padding: 15px;
+}
+.panel-heading {
+ padding: 10px 15px;
+ border-bottom: 1px solid transparent;
+ border-top-left-radius: 3px;
+ border-top-right-radius: 3px;
+}
+.panel-heading > .dropdown .dropdown-toggle {
+ color: inherit;
+}
+.panel-title {
+ margin-top: 0;
+ margin-bottom: 0;
+ font-size: 16px;
+ color: inherit;
+}
+.panel-title > a {
+ color: inherit;
+}
+.panel-footer {
+ padding: 10px 15px;
+ background-color: #f5f5f5;
+ border-top: 1px solid #ddd;
+ border-bottom-right-radius: 3px;
+ border-bottom-left-radius: 3px;
+}
+.panel > .list-group {
+ margin-bottom: 0;
+}
+.panel > .list-group .list-group-item {
+ border-width: 1px 0;
+ border-radius: 0;
+}
+.panel > .list-group:first-child .list-group-item:first-child {
+ border-top: 0;
+ border-top-left-radius: 3px;
+ border-top-right-radius: 3px;
+}
+.panel > .list-group:last-child .list-group-item:last-child {
+ border-bottom: 0;
+ border-bottom-right-radius: 3px;
+ border-bottom-left-radius: 3px;
+}
+.panel-heading + .list-group .list-group-item:first-child {
+ border-top-width: 0;
+}
+.list-group + .panel-footer {
+ border-top-width: 0;
+}
+.panel > .table,
+.panel > .table-responsive > .table,
+.panel > .panel-collapse > .table {
+ margin-bottom: 0;
+}
+.panel > .table:first-child,
+.panel > .table-responsive:first-child > .table:first-child {
+ border-top-left-radius: 3px;
+ border-top-right-radius: 3px;
+}
+.panel > .table:first-child > thead:first-child > tr:first-child td:first-child,
+.panel > .table-responsive:first-child > .table:first-child > thead:first-child > tr:first-child td:first-child,
+.panel > .table:first-child > tbody:first-child > tr:first-child td:first-child,
+.panel > .table-responsive:first-child > .table:first-child > tbody:first-child > tr:first-child td:first-child,
+.panel > .table:first-child > thead:first-child > tr:first-child th:first-child,
+.panel > .table-responsive:first-child > .table:first-child > thead:first-child > tr:first-child th:first-child,
+.panel > .table:first-child > tbody:first-child > tr:first-child th:first-child,
+.panel > .table-responsive:first-child > .table:first-child > tbody:first-child > tr:first-child th:first-child {
+ border-top-left-radius: 3px;
+}
+.panel > .table:first-child > thead:first-child > tr:first-child td:last-child,
+.panel > .table-responsive:first-child > .table:first-child > thead:first-child > tr:first-child td:last-child,
+.panel > .table:first-child > tbody:first-child > tr:first-child td:last-child,
+.panel > .table-responsive:first-child > .table:first-child > tbody:first-child > tr:first-child td:last-child,
+.panel > .table:first-child > thead:first-child > tr:first-child th:last-child,
+.panel > .table-responsive:first-child > .table:first-child > thead:first-child > tr:first-child th:last-child,
+.panel > .table:first-child > tbody:first-child > tr:first-child th:last-child,
+.panel > .table-responsive:first-child > .table:first-child > tbody:first-child > tr:first-child th:last-child {
+ border-top-right-radius: 3px;
+}
+.panel > .table:last-child,
+.panel > .table-responsive:last-child > .table:last-child {
+ border-bottom-right-radius: 3px;
+ border-bottom-left-radius: 3px;
+}
+.panel > .table:last-child > tbody:last-child > tr:last-child td:first-child,
+.panel > .table-responsive:last-child > .table:last-child > tbody:last-child > tr:last-child td:first-child,
+.panel > .table:last-child > tfoot:last-child > tr:last-child td:first-child,
+.panel > .table-responsive:last-child > .table:last-child > tfoot:last-child > tr:last-child td:first-child,
+.panel > .table:last-child > tbody:last-child > tr:last-child th:first-child,
+.panel > .table-responsive:last-child > .table:last-child > tbody:last-child > tr:last-child th:first-child,
+.panel > .table:last-child > tfoot:last-child > tr:last-child th:first-child,
+.panel > .table-responsive:last-child > .table:last-child > tfoot:last-child > tr:last-child th:first-child {
+ border-bottom-left-radius: 3px;
+}
+.panel > .table:last-child > tbody:last-child > tr:last-child td:last-child,
+.panel > .table-responsive:last-child > .table:last-child > tbody:last-child > tr:last-child td:last-child,
+.panel > .table:last-child > tfoot:last-child > tr:last-child td:last-child,
+.panel > .table-responsive:last-child > .table:last-child > tfoot:last-child > tr:last-child td:last-child,
+.panel > .table:last-child > tbody:last-child > tr:last-child th:last-child,
+.panel > .table-responsive:last-child > .table:last-child > tbody:last-child > tr:last-child th:last-child,
+.panel > .table:last-child > tfoot:last-child > tr:last-child th:last-child,
+.panel > .table-responsive:last-child > .table:last-child > tfoot:last-child > tr:last-child th:last-child {
+ border-bottom-right-radius: 3px;
+}
+.panel > .panel-body + .table,
+.panel > .panel-body + .table-responsive {
+ border-top: 1px solid #ddd;
+}
+.panel > .table > tbody:first-child > tr:first-child th,
+.panel > .table > tbody:first-child > tr:first-child td {
+ border-top: 0;
+}
+.panel > .table-bordered,
+.panel > .table-responsive > .table-bordered {
+ border: 0;
+}
+.panel > .table-bordered > thead > tr > th:first-child,
+.panel > .table-responsive > .table-bordered > thead > tr > th:first-child,
+.panel > .table-bordered > tbody > tr > th:first-child,
+.panel > .table-responsive > .table-bordered > tbody > tr > th:first-child,
+.panel > .table-bordered > tfoot > tr > th:first-child,
+.panel > .table-responsive > .table-bordered > tfoot > tr > th:first-child,
+.panel > .table-bordered > thead > tr > td:first-child,
+.panel > .table-responsive > .table-bordered > thead > tr > td:first-child,
+.panel > .table-bordered > tbody > tr > td:first-child,
+.panel > .table-responsive > .table-bordered > tbody > tr > td:first-child,
+.panel > .table-bordered > tfoot > tr > td:first-child,
+.panel > .table-responsive > .table-bordered > tfoot > tr > td:first-child {
+ border-left: 0;
+}
+.panel > .table-bordered > thead > tr > th:last-child,
+.panel > .table-responsive > .table-bordered > thead > tr > th:last-child,
+.panel > .table-bordered > tbody > tr > th:last-child,
+.panel > .table-responsive > .table-bordered > tbody > tr > th:last-child,
+.panel > .table-bordered > tfoot > tr > th:last-child,
+.panel > .table-responsive > .table-bordered > tfoot > tr > th:last-child,
+.panel > .table-bordered > thead > tr > td:last-child,
+.panel > .table-responsive > .table-bordered > thead > tr > td:last-child,
+.panel > .table-bordered > tbody > tr > td:last-child,
+.panel > .table-responsive > .table-bordered > tbody > tr > td:last-child,
+.panel > .table-bordered > tfoot > tr > td:last-child,
+.panel > .table-responsive > .table-bordered > tfoot > tr > td:last-child {
+ border-right: 0;
+}
+.panel > .table-bordered > thead > tr:first-child > td,
+.panel > .table-responsive > .table-bordered > thead > tr:first-child > td,
+.panel > .table-bordered > tbody > tr:first-child > td,
+.panel > .table-responsive > .table-bordered > tbody > tr:first-child > td,
+.panel > .table-bordered > thead > tr:first-child > th,
+.panel > .table-responsive > .table-bordered > thead > tr:first-child > th,
+.panel > .table-bordered > tbody > tr:first-child > th,
+.panel > .table-responsive > .table-bordered > tbody > tr:first-child > th {
+ border-bottom: 0;
+}
+.panel > .table-bordered > tbody > tr:last-child > td,
+.panel > .table-responsive > .table-bordered > tbody > tr:last-child > td,
+.panel > .table-bordered > tfoot > tr:last-child > td,
+.panel > .table-responsive > .table-bordered > tfoot > tr:last-child > td,
+.panel > .table-bordered > tbody > tr:last-child > th,
+.panel > .table-responsive > .table-bordered > tbody > tr:last-child > th,
+.panel > .table-bordered > tfoot > tr:last-child > th,
+.panel > .table-responsive > .table-bordered > tfoot > tr:last-child > th {
+ border-bottom: 0;
+}
+.panel > .table-responsive {
+ margin-bottom: 0;
+ border: 0;
+}
+.panel-group {
+ margin-bottom: 20px;
+}
+.panel-group .panel {
+ margin-bottom: 0;
+ border-radius: 4px;
+}
+.panel-group .panel + .panel {
+ margin-top: 5px;
+}
+.panel-group .panel-heading {
+ border-bottom: 0;
+}
+.panel-group .panel-heading + .panel-collapse > .panel-body {
+ border-top: 1px solid #ddd;
+}
+.panel-group .panel-footer {
+ border-top: 0;
+}
+.panel-group .panel-footer + .panel-collapse .panel-body {
+ border-bottom: 1px solid #ddd;
+}
+.panel-default {
+ border-color: #ddd;
+}
+.panel-default > .panel-heading {
+ color: #333;
+ background-color: #f5f5f5;
+ border-color: #ddd;
+}
+.panel-default > .panel-heading + .panel-collapse > .panel-body {
+ border-top-color: #ddd;
+}
+.panel-default > .panel-heading .badge {
+ color: #f5f5f5;
+ background-color: #333;
+}
+.panel-default > .panel-footer + .panel-collapse > .panel-body {
+ border-bottom-color: #ddd;
+}
+.panel-primary {
+ border-color: #428bca;
+}
+.panel-primary > .panel-heading {
+ color: #fff;
+ background-color: #428bca;
+ border-color: #428bca;
+}
+.panel-primary > .panel-heading + .panel-collapse > .panel-body {
+ border-top-color: #428bca;
+}
+.panel-primary > .panel-heading .badge {
+ color: #428bca;
+ background-color: #fff;
+}
+.panel-primary > .panel-footer + .panel-collapse > .panel-body {
+ border-bottom-color: #428bca;
+}
+.panel-success {
+ border-color: #d6e9c6;
+}
+.panel-success > .panel-heading {
+ color: #3c763d;
+ background-color: #dff0d8;
+ border-color: #d6e9c6;
+}
+.panel-success > .panel-heading + .panel-collapse > .panel-body {
+ border-top-color: #d6e9c6;
+}
+.panel-success > .panel-heading .badge {
+ color: #dff0d8;
+ background-color: #3c763d;
+}
+.panel-success > .panel-footer + .panel-collapse > .panel-body {
+ border-bottom-color: #d6e9c6;
+}
+.panel-info {
+ border-color: #bce8f1;
+}
+.panel-info > .panel-heading {
+ color: #31708f;
+ background-color: #d9edf7;
+ border-color: #bce8f1;
+}
+.panel-info > .panel-heading + .panel-collapse > .panel-body {
+ border-top-color: #bce8f1;
+}
+.panel-info > .panel-heading .badge {
+ color: #d9edf7;
+ background-color: #31708f;
+}
+.panel-info > .panel-footer + .panel-collapse > .panel-body {
+ border-bottom-color: #bce8f1;
+}
+.panel-warning {
+ border-color: #faebcc;
+}
+.panel-warning > .panel-heading {
+ color: #8a6d3b;
+ background-color: #fcf8e3;
+ border-color: #faebcc;
+}
+.panel-warning > .panel-heading + .panel-collapse > .panel-body {
+ border-top-color: #faebcc;
+}
+.panel-warning > .panel-heading .badge {
+ color: #fcf8e3;
+ background-color: #8a6d3b;
+}
+.panel-warning > .panel-footer + .panel-collapse > .panel-body {
+ border-bottom-color: #faebcc;
+}
+.panel-danger {
+ border-color: #ebccd1;
+}
+.panel-danger > .panel-heading {
+ color: #a94442;
+ background-color: #f2dede;
+ border-color: #ebccd1;
+}
+.panel-danger > .panel-heading + .panel-collapse > .panel-body {
+ border-top-color: #ebccd1;
+}
+.panel-danger > .panel-heading .badge {
+ color: #f2dede;
+ background-color: #a94442;
+}
+.panel-danger > .panel-footer + .panel-collapse > .panel-body {
+ border-bottom-color: #ebccd1;
+}
+.embed-responsive {
+ position: relative;
+ display: block;
+ height: 0;
+ padding: 0;
+ overflow: hidden;
+}
+.embed-responsive .embed-responsive-item,
+.embed-responsive iframe,
+.embed-responsive embed,
+.embed-responsive object {
+ position: absolute;
+ top: 0;
+ bottom: 0;
+ left: 0;
+ width: 100%;
+ height: 100%;
+ border: 0;
+}
+.embed-responsive.embed-responsive-16by9 {
+ padding-bottom: 56.25%;
+}
+.embed-responsive.embed-responsive-4by3 {
+ padding-bottom: 75%;
+}
+.well {
+ min-height: 20px;
+ padding: 19px;
+ margin-bottom: 20px;
+ background-color: #f5f5f5;
+ border: 1px solid #e3e3e3;
+ border-radius: 4px;
+ -webkit-box-shadow: inset 0 1px 1px rgba(0, 0, 0, .05);
+ box-shadow: inset 0 1px 1px rgba(0, 0, 0, .05);
+}
+.well blockquote {
+ border-color: #ddd;
+ border-color: rgba(0, 0, 0, .15);
+}
+.well-lg {
+ padding: 24px;
+ border-radius: 6px;
+}
+.well-sm {
+ padding: 9px;
+ border-radius: 3px;
+}
+.close {
+ float: right;
+ font-size: 21px;
+ font-weight: bold;
+ line-height: 1;
+ color: #000;
+ text-shadow: 0 1px 0 #fff;
+ filter: alpha(opacity=20);
+ opacity: .2;
+}
+.close:hover,
+.close:focus {
+ color: #000;
+ text-decoration: none;
+ cursor: pointer;
+ filter: alpha(opacity=50);
+ opacity: .5;
+}
+button.close {
+ -webkit-appearance: none;
+ padding: 0;
+ cursor: pointer;
+ background: transparent;
+ border: 0;
+}
+.modal-open {
+ overflow: hidden;
+}
+.modal {
+ position: fixed;
+ top: 0;
+ right: 0;
+ bottom: 0;
+ left: 0;
+ z-index: 1050;
+ display: none;
+ overflow: hidden;
+ -webkit-overflow-scrolling: touch;
+ outline: 0;
+}
+.modal.fade .modal-dialog {
+ -webkit-transition: -webkit-transform .3s ease-out;
+ -o-transition: -o-transform .3s ease-out;
+ transition: transform .3s ease-out;
+ -webkit-transform: translate3d(0, -25%, 0);
+ -o-transform: translate3d(0, -25%, 0);
+ transform: translate3d(0, -25%, 0);
+}
+.modal.in .modal-dialog {
+ -webkit-transform: translate3d(0, 0, 0);
+ -o-transform: translate3d(0, 0, 0);
+ transform: translate3d(0, 0, 0);
+}
+.modal-open .modal {
+ overflow-x: hidden;
+ overflow-y: auto;
+}
+.modal-dialog {
+ position: relative;
+ width: auto;
+ margin: 10px;
+}
+.modal-content {
+ position: relative;
+ background-color: #fff;
+ -webkit-background-clip: padding-box;
+ background-clip: padding-box;
+ border: 1px solid #999;
+ border: 1px solid rgba(0, 0, 0, .2);
+ border-radius: 6px;
+ outline: 0;
+ -webkit-box-shadow: 0 3px 9px rgba(0, 0, 0, .5);
+ box-shadow: 0 3px 9px rgba(0, 0, 0, .5);
+}
+.modal-backdrop {
+ position: fixed;
+ top: 0;
+ right: 0;
+ bottom: 0;
+ left: 0;
+ z-index: 1040;
+ background-color: #000;
+}
+.modal-backdrop.fade {
+ filter: alpha(opacity=0);
+ opacity: 0;
+}
+.modal-backdrop.in {
+ filter: alpha(opacity=50);
+ opacity: .5;
+}
+.modal-header {
+ min-height: 16.42857143px;
+ padding: 15px;
+ border-bottom: 1px solid #e5e5e5;
+}
+.modal-header .close {
+ margin-top: -2px;
+}
+.modal-title {
+ margin: 0;
+ line-height: 1.42857143;
+}
+.modal-body {
+ position: relative;
+ padding: 15px;
+}
+.modal-footer {
+ padding: 15px;
+ text-align: right;
+ border-top: 1px solid #e5e5e5;
+}
+.modal-footer .btn + .btn {
+ margin-bottom: 0;
+ margin-left: 5px;
+}
+.modal-footer .btn-group .btn + .btn {
+ margin-left: -1px;
+}
+.modal-footer .btn-block + .btn-block {
+ margin-left: 0;
+}
+.modal-scrollbar-measure {
+ position: absolute;
+ top: -9999px;
+ width: 50px;
+ height: 50px;
+ overflow: scroll;
+}
+@media (min-width: 768px) {
+ .modal-dialog {
+ width: 600px;
+ margin: 30px auto;
+ }
+ .modal-content {
+ -webkit-box-shadow: 0 5px 15px rgba(0, 0, 0, .5);
+ box-shadow: 0 5px 15px rgba(0, 0, 0, .5);
+ }
+ .modal-sm {
+ width: 300px;
+ }
+}
+@media (min-width: 992px) {
+ .modal-lg {
+ width: 900px;
+ }
+}
+.tooltip {
+ position: absolute;
+ z-index: 1070;
+ display: block;
+ font-size: 12px;
+ line-height: 1.4;
+ visibility: visible;
+ filter: alpha(opacity=0);
+ opacity: 0;
+}
+.tooltip.in {
+ filter: alpha(opacity=90);
+ opacity: .9;
+}
+.tooltip.top {
+ padding: 5px 0;
+ margin-top: -3px;
+}
+.tooltip.right {
+ padding: 0 5px;
+ margin-left: 3px;
+}
+.tooltip.bottom {
+ padding: 5px 0;
+ margin-top: 3px;
+}
+.tooltip.left {
+ padding: 0 5px;
+ margin-left: -3px;
+}
+.tooltip-inner {
+ max-width: 200px;
+ padding: 3px 8px;
+ color: #fff;
+ text-align: center;
+ text-decoration: none;
+ background-color: #000;
+ border-radius: 4px;
+}
+.tooltip-arrow {
+ position: absolute;
+ width: 0;
+ height: 0;
+ border-color: transparent;
+ border-style: solid;
+}
+.tooltip.top .tooltip-arrow {
+ bottom: 0;
+ left: 50%;
+ margin-left: -5px;
+ border-width: 5px 5px 0;
+ border-top-color: #000;
+}
+.tooltip.top-left .tooltip-arrow {
+ bottom: 0;
+ left: 5px;
+ border-width: 5px 5px 0;
+ border-top-color: #000;
+}
+.tooltip.top-right .tooltip-arrow {
+ right: 5px;
+ bottom: 0;
+ border-width: 5px 5px 0;
+ border-top-color: #000;
+}
+.tooltip.right .tooltip-arrow {
+ top: 50%;
+ left: 0;
+ margin-top: -5px;
+ border-width: 5px 5px 5px 0;
+ border-right-color: #000;
+}
+.tooltip.left .tooltip-arrow {
+ top: 50%;
+ right: 0;
+ margin-top: -5px;
+ border-width: 5px 0 5px 5px;
+ border-left-color: #000;
+}
+.tooltip.bottom .tooltip-arrow {
+ top: 0;
+ left: 50%;
+ margin-left: -5px;
+ border-width: 0 5px 5px;
+ border-bottom-color: #000;
+}
+.tooltip.bottom-left .tooltip-arrow {
+ top: 0;
+ left: 5px;
+ border-width: 0 5px 5px;
+ border-bottom-color: #000;
+}
+.tooltip.bottom-right .tooltip-arrow {
+ top: 0;
+ right: 5px;
+ border-width: 0 5px 5px;
+ border-bottom-color: #000;
+}
+.popover {
+ position: absolute;
+ top: 0;
+ left: 0;
+ z-index: 1060;
+ display: none;
+ max-width: 276px;
+ padding: 1px;
+ text-align: left;
+ white-space: normal;
+ background-color: #fff;
+ -webkit-background-clip: padding-box;
+ background-clip: padding-box;
+ border: 1px solid #ccc;
+ border: 1px solid rgba(0, 0, 0, .2);
+ border-radius: 6px;
+ -webkit-box-shadow: 0 5px 10px rgba(0, 0, 0, .2);
+ box-shadow: 0 5px 10px rgba(0, 0, 0, .2);
+}
+.popover.top {
+ margin-top: -10px;
+}
+.popover.right {
+ margin-left: 10px;
+}
+.popover.bottom {
+ margin-top: 10px;
+}
+.popover.left {
+ margin-left: -10px;
+}
+.popover-title {
+ padding: 8px 14px;
+ margin: 0;
+ font-size: 14px;
+ font-weight: normal;
+ line-height: 18px;
+ background-color: #f7f7f7;
+ border-bottom: 1px solid #ebebeb;
+ border-radius: 5px 5px 0 0;
+}
+.popover-content {
+ padding: 9px 14px;
+}
+.popover > .arrow,
+.popover > .arrow:after {
+ position: absolute;
+ display: block;
+ width: 0;
+ height: 0;
+ border-color: transparent;
+ border-style: solid;
+}
+.popover > .arrow {
+ border-width: 11px;
+}
+.popover > .arrow:after {
+ content: "";
+ border-width: 10px;
+}
+.popover.top > .arrow {
+ bottom: -11px;
+ left: 50%;
+ margin-left: -11px;
+ border-top-color: #999;
+ border-top-color: rgba(0, 0, 0, .25);
+ border-bottom-width: 0;
+}
+.popover.top > .arrow:after {
+ bottom: 1px;
+ margin-left: -10px;
+ content: " ";
+ border-top-color: #fff;
+ border-bottom-width: 0;
+}
+.popover.right > .arrow {
+ top: 50%;
+ left: -11px;
+ margin-top: -11px;
+ border-right-color: #999;
+ border-right-color: rgba(0, 0, 0, .25);
+ border-left-width: 0;
+}
+.popover.right > .arrow:after {
+ bottom: -10px;
+ left: 1px;
+ content: " ";
+ border-right-color: #fff;
+ border-left-width: 0;
+}
+.popover.bottom > .arrow {
+ top: -11px;
+ left: 50%;
+ margin-left: -11px;
+ border-top-width: 0;
+ border-bottom-color: #999;
+ border-bottom-color: rgba(0, 0, 0, .25);
+}
+.popover.bottom > .arrow:after {
+ top: 1px;
+ margin-left: -10px;
+ content: " ";
+ border-top-width: 0;
+ border-bottom-color: #fff;
+}
+.popover.left > .arrow {
+ top: 50%;
+ right: -11px;
+ margin-top: -11px;
+ border-right-width: 0;
+ border-left-color: #999;
+ border-left-color: rgba(0, 0, 0, .25);
+}
+.popover.left > .arrow:after {
+ right: 1px;
+ bottom: -10px;
+ content: " ";
+ border-right-width: 0;
+ border-left-color: #fff;
+}
+.carousel {
+ position: relative;
+}
+.carousel-inner {
+ position: relative;
+ width: 100%;
+ overflow: hidden;
+}
+.carousel-inner > .item {
+ position: relative;
+ display: none;
+ -webkit-transition: .6s ease-in-out left;
+ -o-transition: .6s ease-in-out left;
+ transition: .6s ease-in-out left;
+}
+.carousel-inner > .item > img,
+.carousel-inner > .item > a > img {
+ line-height: 1;
+}
+.carousel-inner > .active,
+.carousel-inner > .next,
+.carousel-inner > .prev {
+ display: block;
+}
+.carousel-inner > .active {
+ left: 0;
+}
+.carousel-inner > .next,
+.carousel-inner > .prev {
+ position: absolute;
+ top: 0;
+ width: 100%;
+}
+.carousel-inner > .next {
+ left: 100%;
+}
+.carousel-inner > .prev {
+ left: -100%;
+}
+.carousel-inner > .next.left,
+.carousel-inner > .prev.right {
+ left: 0;
+}
+.carousel-inner > .active.left {
+ left: -100%;
+}
+.carousel-inner > .active.right {
+ left: 100%;
+}
+.carousel-control {
+ position: absolute;
+ top: 0;
+ bottom: 0;
+ left: 0;
+ width: 15%;
+ font-size: 20px;
+ color: #fff;
+ text-align: center;
+ text-shadow: 0 1px 2px rgba(0, 0, 0, .6);
+ filter: alpha(opacity=50);
+ opacity: .5;
+}
+.carousel-control.left {
+ background-image: -webkit-linear-gradient(left, rgba(0, 0, 0, .5) 0%, rgba(0, 0, 0, .0001) 100%);
+ background-image: -o-linear-gradient(left, rgba(0, 0, 0, .5) 0%, rgba(0, 0, 0, .0001) 100%);
+ background-image: -webkit-gradient(linear, left top, right top, from(rgba(0, 0, 0, .5)), to(rgba(0, 0, 0, .0001)));
+ background-image: linear-gradient(to right, rgba(0, 0, 0, .5) 0%, rgba(0, 0, 0, .0001) 100%);
+ filter: progid:DXImageTransform.Microsoft.gradient(startColorstr='#80000000', endColorstr='#00000000', GradientType=1);
+ background-repeat: repeat-x;
+}
+.carousel-control.right {
+ right: 0;
+ left: auto;
+ background-image: -webkit-linear-gradient(left, rgba(0, 0, 0, .0001) 0%, rgba(0, 0, 0, .5) 100%);
+ background-image: -o-linear-gradient(left, rgba(0, 0, 0, .0001) 0%, rgba(0, 0, 0, .5) 100%);
+ background-image: -webkit-gradient(linear, left top, right top, from(rgba(0, 0, 0, .0001)), to(rgba(0, 0, 0, .5)));
+ background-image: linear-gradient(to right, rgba(0, 0, 0, .0001) 0%, rgba(0, 0, 0, .5) 100%);
+ filter: progid:DXImageTransform.Microsoft.gradient(startColorstr='#00000000', endColorstr='#80000000', GradientType=1);
+ background-repeat: repeat-x;
+}
+.carousel-control:hover,
+.carousel-control:focus {
+ color: #fff;
+ text-decoration: none;
+ filter: alpha(opacity=90);
+ outline: 0;
+ opacity: .9;
+}
+.carousel-control .icon-prev,
+.carousel-control .icon-next,
+.carousel-control .glyphicon-chevron-left,
+.carousel-control .glyphicon-chevron-right {
+ position: absolute;
+ top: 50%;
+ z-index: 5;
+ display: inline-block;
+}
+.carousel-control .icon-prev,
+.carousel-control .glyphicon-chevron-left {
+ left: 50%;
+ margin-left: -10px;
+}
+.carousel-control .icon-next,
+.carousel-control .glyphicon-chevron-right {
+ right: 50%;
+ margin-right: -10px;
+}
+.carousel-control .icon-prev,
+.carousel-control .icon-next {
+ width: 20px;
+ height: 20px;
+ margin-top: -10px;
+ font-family: serif;
+}
+.carousel-control .icon-prev:before {
+ content: '\2039';
+}
+.carousel-control .icon-next:before {
+ content: '\203a';
+}
+.carousel-indicators {
+ position: absolute;
+ bottom: 10px;
+ left: 50%;
+ z-index: 15;
+ width: 60%;
+ padding-left: 0;
+ margin-left: -30%;
+ text-align: center;
+ list-style: none;
+}
+.carousel-indicators li {
+ display: inline-block;
+ width: 10px;
+ height: 10px;
+ margin: 1px;
+ text-indent: -999px;
+ cursor: pointer;
+ background-color: #000 \9;
+ background-color: rgba(0, 0, 0, 0);
+ border: 1px solid #fff;
+ border-radius: 10px;
+}
+.carousel-indicators .active {
+ width: 12px;
+ height: 12px;
+ margin: 0;
+ background-color: #fff;
+}
+.carousel-caption {
+ position: absolute;
+ right: 15%;
+ bottom: 20px;
+ left: 15%;
+ z-index: 10;
+ padding-top: 20px;
+ padding-bottom: 20px;
+ color: #fff;
+ text-align: center;
+ text-shadow: 0 1px 2px rgba(0, 0, 0, .6);
+}
+.carousel-caption .btn {
+ text-shadow: none;
+}
+@media screen and (min-width: 768px) {
+ .carousel-control .glyphicon-chevron-left,
+ .carousel-control .glyphicon-chevron-right,
+ .carousel-control .icon-prev,
+ .carousel-control .icon-next {
+ width: 30px;
+ height: 30px;
+ margin-top: -15px;
+ font-size: 30px;
+ }
+ .carousel-control .glyphicon-chevron-left,
+ .carousel-control .icon-prev {
+ margin-left: -15px;
+ }
+ .carousel-control .glyphicon-chevron-right,
+ .carousel-control .icon-next {
+ margin-right: -15px;
+ }
+ .carousel-caption {
+ right: 20%;
+ left: 20%;
+ padding-bottom: 30px;
+ }
+ .carousel-indicators {
+ bottom: 20px;
+ }
+}
+.clearfix:before,
+.clearfix:after,
+.dl-horizontal dd:before,
+.dl-horizontal dd:after,
+.container:before,
+.container:after,
+.container-fluid:before,
+.container-fluid:after,
+.row:before,
+.row:after,
+.form-horizontal .form-group:before,
+.form-horizontal .form-group:after,
+.btn-toolbar:before,
+.btn-toolbar:after,
+.btn-group-vertical > .btn-group:before,
+.btn-group-vertical > .btn-group:after,
+.nav:before,
+.nav:after,
+.navbar:before,
+.navbar:after,
+.navbar-header:before,
+.navbar-header:after,
+.navbar-collapse:before,
+.navbar-collapse:after,
+.pager:before,
+.pager:after,
+.panel-body:before,
+.panel-body:after,
+.modal-footer:before,
+.modal-footer:after {
+ display: table;
+ content: " ";
+}
+.clearfix:after,
+.dl-horizontal dd:after,
+.container:after,
+.container-fluid:after,
+.row:after,
+.form-horizontal .form-group:after,
+.btn-toolbar:after,
+.btn-group-vertical > .btn-group:after,
+.nav:after,
+.navbar:after,
+.navbar-header:after,
+.navbar-collapse:after,
+.pager:after,
+.panel-body:after,
+.modal-footer:after {
+ clear: both;
+}
+.center-block {
+ display: block;
+ margin-right: auto;
+ margin-left: auto;
+}
+.pull-right {
+ float: right !important;
+}
+.pull-left {
+ float: left !important;
+}
+.hide {
+ display: none !important;
+}
+.show {
+ display: block !important;
+}
+.invisible {
+ visibility: hidden;
+}
+.text-hide {
+ font: 0/0 a;
+ color: transparent;
+ text-shadow: none;
+ background-color: transparent;
+ border: 0;
+}
+.hidden {
+ display: none !important;
+ visibility: hidden !important;
+}
+.affix {
+ position: fixed;
+ -webkit-transform: translate3d(0, 0, 0);
+ -o-transform: translate3d(0, 0, 0);
+ transform: translate3d(0, 0, 0);
+}
+@-ms-viewport {
+ width: device-width;
+}
+.visible-xs,
+.visible-sm,
+.visible-md,
+.visible-lg {
+ display: none !important;
+}
+.visible-xs-block,
+.visible-xs-inline,
+.visible-xs-inline-block,
+.visible-sm-block,
+.visible-sm-inline,
+.visible-sm-inline-block,
+.visible-md-block,
+.visible-md-inline,
+.visible-md-inline-block,
+.visible-lg-block,
+.visible-lg-inline,
+.visible-lg-inline-block {
+ display: none !important;
+}
+@media (max-width: 767px) {
+ .visible-xs {
+ display: block !important;
+ }
+ table.visible-xs {
+ display: table;
+ }
+ tr.visible-xs {
+ display: table-row !important;
+ }
+ th.visible-xs,
+ td.visible-xs {
+ display: table-cell !important;
+ }
+}
+@media (max-width: 767px) {
+ .visible-xs-block {
+ display: block !important;
+ }
+}
+@media (max-width: 767px) {
+ .visible-xs-inline {
+ display: inline !important;
+ }
+}
+@media (max-width: 767px) {
+ .visible-xs-inline-block {
+ display: inline-block !important;
+ }
+}
+@media (min-width: 768px) and (max-width: 991px) {
+ .visible-sm {
+ display: block !important;
+ }
+ table.visible-sm {
+ display: table;
+ }
+ tr.visible-sm {
+ display: table-row !important;
+ }
+ th.visible-sm,
+ td.visible-sm {
+ display: table-cell !important;
+ }
+}
+@media (min-width: 768px) and (max-width: 991px) {
+ .visible-sm-block {
+ display: block !important;
+ }
+}
+@media (min-width: 768px) and (max-width: 991px) {
+ .visible-sm-inline {
+ display: inline !important;
+ }
+}
+@media (min-width: 768px) and (max-width: 991px) {
+ .visible-sm-inline-block {
+ display: inline-block !important;
+ }
+}
+@media (min-width: 992px) and (max-width: 1199px) {
+ .visible-md {
+ display: block !important;
+ }
+ table.visible-md {
+ display: table;
+ }
+ tr.visible-md {
+ display: table-row !important;
+ }
+ th.visible-md,
+ td.visible-md {
+ display: table-cell !important;
+ }
+}
+@media (min-width: 992px) and (max-width: 1199px) {
+ .visible-md-block {
+ display: block !important;
+ }
+}
+@media (min-width: 992px) and (max-width: 1199px) {
+ .visible-md-inline {
+ display: inline !important;
+ }
+}
+@media (min-width: 992px) and (max-width: 1199px) {
+ .visible-md-inline-block {
+ display: inline-block !important;
+ }
+}
+@media (min-width: 1200px) {
+ .visible-lg {
+ display: block !important;
+ }
+ table.visible-lg {
+ display: table;
+ }
+ tr.visible-lg {
+ display: table-row !important;
+ }
+ th.visible-lg,
+ td.visible-lg {
+ display: table-cell !important;
+ }
+}
+@media (min-width: 1200px) {
+ .visible-lg-block {
+ display: block !important;
+ }
+}
+@media (min-width: 1200px) {
+ .visible-lg-inline {
+ display: inline !important;
+ }
+}
+@media (min-width: 1200px) {
+ .visible-lg-inline-block {
+ display: inline-block !important;
+ }
+}
+@media (max-width: 767px) {
+ .hidden-xs {
+ display: none !important;
+ }
+}
+@media (min-width: 768px) and (max-width: 991px) {
+ .hidden-sm {
+ display: none !important;
+ }
+}
+@media (min-width: 992px) and (max-width: 1199px) {
+ .hidden-md {
+ display: none !important;
+ }
+}
+@media (min-width: 1200px) {
+ .hidden-lg {
+ display: none !important;
+ }
+}
+.visible-print {
+ display: none !important;
+}
+@media print {
+ .visible-print {
+ display: block !important;
+ }
+ table.visible-print {
+ display: table;
+ }
+ tr.visible-print {
+ display: table-row !important;
+ }
+ th.visible-print,
+ td.visible-print {
+ display: table-cell !important;
+ }
+}
+.visible-print-block {
+ display: none !important;
+}
+@media print {
+ .visible-print-block {
+ display: block !important;
+ }
+}
+.visible-print-inline {
+ display: none !important;
+}
+@media print {
+ .visible-print-inline {
+ display: inline !important;
+ }
+}
+.visible-print-inline-block {
+ display: none !important;
+}
+@media print {
+ .visible-print-inline-block {
+ display: inline-block !important;
+ }
+}
+@media print {
+ .hidden-print {
+ display: none !important;
+ }
+}
+/*# sourceMappingURL=bootstrap.css.map */
diff --git a/docs/build/html/_static/bootstrap-3.2.0/css/bootstrap.css.map b/docs/build/html/_static/bootstrap-3.2.0/css/bootstrap.css.map
new file mode 100644
index 0000000000000000000000000000000000000000..bfb5616891b8d59dea9003d767fd30c9840a6437
--- /dev/null
+++ b/docs/build/html/_static/bootstrap-3.2.0/css/bootstrap.css.map
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normalize.css v3.0.1 | MIT License | git.io/normalize */\n\n//\n// 1. Set default font family to sans-serif.\n// 2. Prevent iOS text size adjust after orientation change, without disabling\n// user zoom.\n//\n\nhtml {\n font-family: sans-serif; // 1\n -ms-text-size-adjust: 100%; // 2\n -webkit-text-size-adjust: 100%; // 2\n}\n\n//\n// Remove default margin.\n//\n\nbody {\n margin: 0;\n}\n\n// HTML5 display definitions\n// ==========================================================================\n\n//\n// Correct `block` display not defined for any HTML5 element in IE 8/9.\n// Correct `block` display not defined for `details` or `summary` in IE 10/11 and Firefox.\n// Correct `block` display not defined for `main` in IE 11.\n//\n\narticle,\naside,\ndetails,\nfigcaption,\nfigure,\nfooter,\nheader,\nhgroup,\nmain,\nnav,\nsection,\nsummary {\n display: block;\n}\n\n//\n// 1. Correct `inline-block` display not defined in IE 8/9.\n// 2. Normalize vertical alignment of `progress` in Chrome, Firefox, and Opera.\n//\n\naudio,\ncanvas,\nprogress,\nvideo {\n display: inline-block; // 1\n vertical-align: baseline; // 2\n}\n\n//\n// Prevent modern browsers from displaying `audio` without controls.\n// Remove excess height in iOS 5 devices.\n//\n\naudio:not([controls]) {\n display: none;\n height: 0;\n}\n\n//\n// Address `[hidden]` styling not present in IE 8/9/10.\n// Hide the `template` element in IE 8/9/11, Safari, and Firefox < 22.\n//\n\n[hidden],\ntemplate {\n display: none;\n}\n\n// Links\n// ==========================================================================\n\n//\n// Remove the gray background color from active links in IE 10.\n//\n\na {\n background: transparent;\n}\n\n//\n// Improve readability when focused and also mouse hovered in all browsers.\n//\n\na:active,\na:hover {\n outline: 0;\n}\n\n// Text-level semantics\n// ==========================================================================\n\n//\n// Address styling not present in IE 8/9/10/11, Safari, and Chrome.\n//\n\nabbr[title] {\n border-bottom: 1px dotted;\n}\n\n//\n// Address style set to `bolder` in Firefox 4+, Safari, and Chrome.\n//\n\nb,\nstrong {\n font-weight: bold;\n}\n\n//\n// Address styling not present in Safari and Chrome.\n//\n\ndfn {\n font-style: italic;\n}\n\n//\n// Address variable `h1` font-size and margin within `section` and `article`\n// contexts in Firefox 4+, Safari, and Chrome.\n//\n\nh1 {\n font-size: 2em;\n margin: 0.67em 0;\n}\n\n//\n// Address styling not present in IE 8/9.\n//\n\nmark {\n background: #ff0;\n color: #000;\n}\n\n//\n// Address inconsistent and variable font size in all browsers.\n//\n\nsmall {\n font-size: 80%;\n}\n\n//\n// Prevent `sub` and `sup` affecting `line-height` in all browsers.\n//\n\nsub,\nsup {\n font-size: 75%;\n line-height: 0;\n position: relative;\n vertical-align: baseline;\n}\n\nsup {\n top: -0.5em;\n}\n\nsub {\n bottom: -0.25em;\n}\n\n// Embedded content\n// ==========================================================================\n\n//\n// Remove border when inside `a` element in IE 8/9/10.\n//\n\nimg {\n border: 0;\n}\n\n//\n// Correct overflow not hidden in IE 9/10/11.\n//\n\nsvg:not(:root) {\n overflow: hidden;\n}\n\n// Grouping content\n// ==========================================================================\n\n//\n// Address margin not present in IE 8/9 and Safari.\n//\n\nfigure {\n margin: 1em 40px;\n}\n\n//\n// Address differences between Firefox and other browsers.\n//\n\nhr {\n -moz-box-sizing: content-box;\n box-sizing: content-box;\n height: 0;\n}\n\n//\n// Contain overflow in all browsers.\n//\n\npre {\n overflow: auto;\n}\n\n//\n// Address odd `em`-unit font size rendering in all browsers.\n//\n\ncode,\nkbd,\npre,\nsamp {\n font-family: monospace, monospace;\n font-size: 1em;\n}\n\n// Forms\n// ==========================================================================\n\n//\n// Known limitation: by default, Chrome and Safari on OS X allow very limited\n// styling of `select`, unless a `border` property is set.\n//\n\n//\n// 1. Correct color not being inherited.\n// Known issue: affects color of disabled elements.\n// 2. Correct font properties not being inherited.\n// 3. Address margins set differently in Firefox 4+, Safari, and Chrome.\n//\n\nbutton,\ninput,\noptgroup,\nselect,\ntextarea {\n color: inherit; // 1\n font: inherit; // 2\n margin: 0; // 3\n}\n\n//\n// Address `overflow` set to `hidden` in IE 8/9/10/11.\n//\n\nbutton {\n overflow: visible;\n}\n\n//\n// Address inconsistent `text-transform` inheritance for `button` and `select`.\n// All other form control elements do not inherit `text-transform` values.\n// Correct `button` style inheritance in Firefox, IE 8/9/10/11, and Opera.\n// Correct `select` style inheritance in Firefox.\n//\n\nbutton,\nselect {\n text-transform: none;\n}\n\n//\n// 1. Avoid the WebKit bug in Android 4.0.* where (2) destroys native `audio`\n// and `video` controls.\n// 2. Correct inability to style clickable `input` types in iOS.\n// 3. Improve usability and consistency of cursor style between image-type\n// `input` and others.\n//\n\nbutton,\nhtml input[type=\"button\"], // 1\ninput[type=\"reset\"],\ninput[type=\"submit\"] {\n -webkit-appearance: button; // 2\n cursor: pointer; // 3\n}\n\n//\n// Re-set default cursor for disabled elements.\n//\n\nbutton[disabled],\nhtml input[disabled] {\n cursor: default;\n}\n\n//\n// Remove inner padding and border in Firefox 4+.\n//\n\nbutton::-moz-focus-inner,\ninput::-moz-focus-inner {\n border: 0;\n padding: 0;\n}\n\n//\n// Address Firefox 4+ setting `line-height` on `input` using `!important` in\n// the UA stylesheet.\n//\n\ninput {\n line-height: normal;\n}\n\n//\n// It's recommended that you don't attempt to style these elements.\n// Firefox's implementation doesn't respect box-sizing, padding, or width.\n//\n// 1. Address box sizing set to `content-box` in IE 8/9/10.\n// 2. Remove excess padding in IE 8/9/10.\n//\n\ninput[type=\"checkbox\"],\ninput[type=\"radio\"] {\n box-sizing: border-box; // 1\n padding: 0; // 2\n}\n\n//\n// Fix the cursor style for Chrome's increment/decrement buttons. For certain\n// `font-size` values of the `input`, it causes the cursor style of the\n// decrement button to change from `default` to `text`.\n//\n\ninput[type=\"number\"]::-webkit-inner-spin-button,\ninput[type=\"number\"]::-webkit-outer-spin-button {\n height: auto;\n}\n\n//\n// 1. Address `appearance` set to `searchfield` in Safari and Chrome.\n// 2. Address `box-sizing` set to `border-box` in Safari and Chrome\n// (include `-moz` to future-proof).\n//\n\ninput[type=\"search\"] {\n -webkit-appearance: textfield; // 1\n -moz-box-sizing: content-box;\n -webkit-box-sizing: content-box; // 2\n box-sizing: content-box;\n}\n\n//\n// Remove inner padding and search cancel button in Safari and Chrome on OS X.\n// Safari (but not Chrome) clips the cancel button when the search input has\n// padding (and `textfield` appearance).\n//\n\ninput[type=\"search\"]::-webkit-search-cancel-button,\ninput[type=\"search\"]::-webkit-search-decoration {\n -webkit-appearance: none;\n}\n\n//\n// Define consistent border, margin, and padding.\n//\n\nfieldset {\n border: 1px solid #c0c0c0;\n margin: 0 2px;\n padding: 0.35em 0.625em 0.75em;\n}\n\n//\n// 1. Correct `color` not being inherited in IE 8/9/10/11.\n// 2. Remove padding so people aren't caught out if they zero out fieldsets.\n//\n\nlegend {\n border: 0; // 1\n padding: 0; // 2\n}\n\n//\n// Remove default vertical scrollbar in IE 8/9/10/11.\n//\n\ntextarea {\n overflow: auto;\n}\n\n//\n// Don't inherit the `font-weight` (applied by a rule above).\n// NOTE: the default cannot safely be changed in Chrome and Safari on OS X.\n//\n\noptgroup {\n font-weight: bold;\n}\n\n// Tables\n// ==========================================================================\n\n//\n// Remove most spacing between table cells.\n//\n\ntable {\n border-collapse: collapse;\n border-spacing: 0;\n}\n\ntd,\nth {\n padding: 0;\n}\n","//\n// Basic print styles\n// --------------------------------------------------\n// Source: https://github.com/h5bp/html5-boilerplate/blob/master/css/main.css\n\n@media print {\n\n * {\n text-shadow: none !important;\n color: #000 !important; // Black prints faster: h5bp.com/s\n background: transparent !important;\n box-shadow: none !important;\n }\n\n a,\n a:visited {\n text-decoration: underline;\n }\n\n a[href]:after {\n content: \" (\" attr(href) \")\";\n }\n\n abbr[title]:after {\n content: \" (\" attr(title) \")\";\n }\n\n // Don't show links for images, or javascript/internal links\n a[href^=\"javascript:\"]:after,\n a[href^=\"#\"]:after {\n content: \"\";\n }\n\n pre,\n blockquote {\n border: 1px solid #999;\n page-break-inside: avoid;\n }\n\n thead {\n display: table-header-group; // h5bp.com/t\n }\n\n tr,\n img {\n page-break-inside: avoid;\n }\n\n img {\n max-width: 100% !important;\n }\n\n p,\n h2,\n h3 {\n orphans: 3;\n widows: 3;\n }\n\n h2,\n h3 {\n page-break-after: avoid;\n }\n\n // Chrome (OSX) fix for https://github.com/twbs/bootstrap/issues/11245\n // Once fixed, we can just straight up remove this.\n select {\n background: #fff !important;\n }\n\n // Bootstrap components\n .navbar {\n display: none;\n }\n .table {\n td,\n th {\n background-color: #fff !important;\n }\n }\n .btn,\n .dropup > .btn {\n > .caret {\n border-top-color: #000 !important;\n }\n }\n .label {\n border: 1px solid #000;\n }\n\n .table {\n border-collapse: collapse !important;\n }\n .table-bordered {\n th,\n td {\n border: 1px solid #ddd !important;\n }\n }\n\n}\n","//\n// Glyphicons for Bootstrap\n//\n// Since icons are fonts, they can be placed anywhere text is placed and are\n// thus automatically sized to match the surrounding child. To use, create an\n// inline element with the appropriate classes, like so:\n//\n// <a href=\"#\"><span class=\"glyphicon glyphicon-star\"></span> Star</a>\n\n// Import the fonts\n@font-face {\n font-family: 'Glyphicons Halflings';\n src: url('@{icon-font-path}@{icon-font-name}.eot');\n src: url('@{icon-font-path}@{icon-font-name}.eot?#iefix') format('embedded-opentype'),\n url('@{icon-font-path}@{icon-font-name}.woff') format('woff'),\n url('@{icon-font-path}@{icon-font-name}.ttf') format('truetype'),\n url('@{icon-font-path}@{icon-font-name}.svg#@{icon-font-svg-id}') format('svg');\n}\n\n// Catchall baseclass\n.glyphicon {\n position: relative;\n top: 1px;\n display: inline-block;\n font-family: 'Glyphicons Halflings';\n font-style: normal;\n font-weight: normal;\n line-height: 1;\n -webkit-font-smoothing: antialiased;\n -moz-osx-font-smoothing: grayscale;\n}\n\n// Individual icons\n.glyphicon-asterisk { &:before { content: \"\\2a\"; } }\n.glyphicon-plus { &:before { content: \"\\2b\"; } }\n.glyphicon-euro { &:before { content: \"\\20ac\"; } }\n.glyphicon-minus { &:before { content: \"\\2212\"; } }\n.glyphicon-cloud { &:before { content: \"\\2601\"; } }\n.glyphicon-envelope { &:before { content: \"\\2709\"; } }\n.glyphicon-pencil { &:before { content: \"\\270f\"; } }\n.glyphicon-glass { &:before { content: \"\\e001\"; } }\n.glyphicon-music { &:before { content: \"\\e002\"; } }\n.glyphicon-search { &:before { content: \"\\e003\"; } }\n.glyphicon-heart { &:before { content: \"\\e005\"; } }\n.glyphicon-star { &:before { content: \"\\e006\"; } }\n.glyphicon-star-empty { &:before { content: \"\\e007\"; } }\n.glyphicon-user { &:before { content: \"\\e008\"; } }\n.glyphicon-film { &:before { content: \"\\e009\"; } }\n.glyphicon-th-large { &:before { content: \"\\e010\"; } }\n.glyphicon-th { &:before { content: \"\\e011\"; } }\n.glyphicon-th-list { &:before { content: \"\\e012\"; } }\n.glyphicon-ok { &:before { content: \"\\e013\"; } }\n.glyphicon-remove { &:before { content: \"\\e014\"; } }\n.glyphicon-zoom-in { &:before { content: \"\\e015\"; } }\n.glyphicon-zoom-out { &:before { content: \"\\e016\"; } }\n.glyphicon-off { &:before { content: \"\\e017\"; } }\n.glyphicon-signal { &:before { content: \"\\e018\"; } }\n.glyphicon-cog { &:before { content: \"\\e019\"; } }\n.glyphicon-trash { &:before { content: \"\\e020\"; } }\n.glyphicon-home { &:before { content: \"\\e021\"; } }\n.glyphicon-file { &:before { content: \"\\e022\"; } }\n.glyphicon-time { &:before { content: \"\\e023\"; } }\n.glyphicon-road { &:before { content: \"\\e024\"; } }\n.glyphicon-download-alt { &:before { content: \"\\e025\"; } }\n.glyphicon-download { &:before { content: \"\\e026\"; } }\n.glyphicon-upload { &:before { content: \"\\e027\"; } }\n.glyphicon-inbox { &:before { content: \"\\e028\"; } }\n.glyphicon-play-circle { &:before { content: \"\\e029\"; } }\n.glyphicon-repeat { &:before { content: \"\\e030\"; } }\n.glyphicon-refresh { &:before { content: \"\\e031\"; } }\n.glyphicon-list-alt { &:before { content: \"\\e032\"; } }\n.glyphicon-lock { &:before { content: \"\\e033\"; } }\n.glyphicon-flag { &:before { content: \"\\e034\"; } }\n.glyphicon-headphones { &:before { content: \"\\e035\"; } }\n.glyphicon-volume-off { &:before { content: \"\\e036\"; } }\n.glyphicon-volume-down { &:before { content: \"\\e037\"; } }\n.glyphicon-volume-up { &:before { content: \"\\e038\"; } }\n.glyphicon-qrcode { &:before { content: \"\\e039\"; } }\n.glyphicon-barcode { &:before { content: \"\\e040\"; } }\n.glyphicon-tag { &:before { content: \"\\e041\"; } }\n.glyphicon-tags { &:before { content: \"\\e042\"; } }\n.glyphicon-book { &:before { content: \"\\e043\"; } }\n.glyphicon-bookmark { &:before { content: \"\\e044\"; } }\n.glyphicon-print { &:before { content: \"\\e045\"; } }\n.glyphicon-camera { &:before { content: \"\\e046\"; } }\n.glyphicon-font { &:before { content: \"\\e047\"; } }\n.glyphicon-bold { &:before { content: \"\\e048\"; } }\n.glyphicon-italic { &:before { content: \"\\e049\"; } }\n.glyphicon-text-height { &:before { content: \"\\e050\"; } }\n.glyphicon-text-width { &:before { content: \"\\e051\"; } }\n.glyphicon-align-left { &:before { content: \"\\e052\"; } }\n.glyphicon-align-center { &:before { content: \"\\e053\"; } }\n.glyphicon-align-right { &:before { content: \"\\e054\"; } }\n.glyphicon-align-justify { &:before { content: \"\\e055\"; } }\n.glyphicon-list { &:before { content: \"\\e056\"; } }\n.glyphicon-indent-left { &:before { content: \"\\e057\"; } }\n.glyphicon-indent-right { &:before { content: \"\\e058\"; } }\n.glyphicon-facetime-video { &:before { content: \"\\e059\"; } }\n.glyphicon-picture { &:before { content: \"\\e060\"; } }\n.glyphicon-map-marker { &:before { content: \"\\e062\"; } }\n.glyphicon-adjust { &:before { content: \"\\e063\"; } }\n.glyphicon-tint { &:before { content: \"\\e064\"; } }\n.glyphicon-edit { &:before { content: \"\\e065\"; } }\n.glyphicon-share { &:before { content: \"\\e066\"; } }\n.glyphicon-check { &:before { content: \"\\e067\"; } }\n.glyphicon-move { &:before { content: \"\\e068\"; } }\n.glyphicon-step-backward { &:before { content: \"\\e069\"; } }\n.glyphicon-fast-backward { &:before { content: \"\\e070\"; } }\n.glyphicon-backward { &:before { content: \"\\e071\"; } }\n.glyphicon-play { &:before { content: \"\\e072\"; } }\n.glyphicon-pause { &:before { content: \"\\e073\"; } }\n.glyphicon-stop { &:before { content: \"\\e074\"; } }\n.glyphicon-forward { &:before { content: \"\\e075\"; } }\n.glyphicon-fast-forward { &:before { content: \"\\e076\"; } }\n.glyphicon-step-forward { &:before { content: \"\\e077\"; } }\n.glyphicon-eject { &:before { content: \"\\e078\"; } }\n.glyphicon-chevron-left { &:before { content: \"\\e079\"; } }\n.glyphicon-chevron-right { &:before { content: \"\\e080\"; } }\n.glyphicon-plus-sign { &:before { content: \"\\e081\"; } }\n.glyphicon-minus-sign { &:before { content: \"\\e082\"; } }\n.glyphicon-remove-sign { &:before { content: \"\\e083\"; } }\n.glyphicon-ok-sign { &:before { content: \"\\e084\"; } }\n.glyphicon-question-sign { &:before { content: \"\\e085\"; } }\n.glyphicon-info-sign { &:before { content: \"\\e086\"; } }\n.glyphicon-screenshot { &:before { content: \"\\e087\"; } }\n.glyphicon-remove-circle { &:before { content: \"\\e088\"; } }\n.glyphicon-ok-circle { &:before { content: \"\\e089\"; } }\n.glyphicon-ban-circle { &:before { content: \"\\e090\"; } }\n.glyphicon-arrow-left { &:before { content: \"\\e091\"; } }\n.glyphicon-arrow-right { &:before { content: \"\\e092\"; } }\n.glyphicon-arrow-up { &:before { content: \"\\e093\"; } }\n.glyphicon-arrow-down { &:before { content: \"\\e094\"; } }\n.glyphicon-share-alt { &:before { content: \"\\e095\"; } }\n.glyphicon-resize-full { &:before { content: \"\\e096\"; } }\n.glyphicon-resize-small { &:before { content: \"\\e097\"; } }\n.glyphicon-exclamation-sign { &:before { content: \"\\e101\"; } }\n.glyphicon-gift { &:before { content: \"\\e102\"; } }\n.glyphicon-leaf { &:before { content: \"\\e103\"; } }\n.glyphicon-fire { &:before { content: \"\\e104\"; } }\n.glyphicon-eye-open { &:before { content: \"\\e105\"; } }\n.glyphicon-eye-close { &:before { content: \"\\e106\"; } }\n.glyphicon-warning-sign { &:before { content: \"\\e107\"; } }\n.glyphicon-plane { &:before { content: \"\\e108\"; } }\n.glyphicon-calendar { &:before { content: \"\\e109\"; } }\n.glyphicon-random { &:before { content: \"\\e110\"; } }\n.glyphicon-comment { &:before { content: \"\\e111\"; } }\n.glyphicon-magnet { &:before { content: \"\\e112\"; } }\n.glyphicon-chevron-up { &:before { content: \"\\e113\"; } }\n.glyphicon-chevron-down { &:before { content: \"\\e114\"; } }\n.glyphicon-retweet { &:before { content: \"\\e115\"; } }\n.glyphicon-shopping-cart { &:before { content: \"\\e116\"; } }\n.glyphicon-folder-close { &:before { content: \"\\e117\"; } }\n.glyphicon-folder-open { &:before { content: \"\\e118\"; } }\n.glyphicon-resize-vertical { &:before { content: \"\\e119\"; } }\n.glyphicon-resize-horizontal { &:before { content: \"\\e120\"; } }\n.glyphicon-hdd { &:before { content: \"\\e121\"; } }\n.glyphicon-bullhorn { &:before { content: \"\\e122\"; } }\n.glyphicon-bell { &:before { content: \"\\e123\"; } }\n.glyphicon-certificate { &:before { content: \"\\e124\"; } }\n.glyphicon-thumbs-up { &:before { content: \"\\e125\"; } }\n.glyphicon-thumbs-down { &:before { content: \"\\e126\"; } }\n.glyphicon-hand-right { &:before { content: \"\\e127\"; } }\n.glyphicon-hand-left { &:before { content: \"\\e128\"; } }\n.glyphicon-hand-up { &:before { content: \"\\e129\"; } }\n.glyphicon-hand-down { &:before { content: \"\\e130\"; } }\n.glyphicon-circle-arrow-right { &:before { content: \"\\e131\"; } }\n.glyphicon-circle-arrow-left { &:before { content: \"\\e132\"; } }\n.glyphicon-circle-arrow-up { &:before { content: \"\\e133\"; } }\n.glyphicon-circle-arrow-down { &:before { content: \"\\e134\"; } }\n.glyphicon-globe { &:before { content: \"\\e135\"; } }\n.glyphicon-wrench { &:before { content: \"\\e136\"; } }\n.glyphicon-tasks { &:before { content: \"\\e137\"; } }\n.glyphicon-filter { &:before { content: \"\\e138\"; } }\n.glyphicon-briefcase { &:before { content: \"\\e139\"; } }\n.glyphicon-fullscreen { &:before { content: \"\\e140\"; } }\n.glyphicon-dashboard { &:before { content: \"\\e141\"; } }\n.glyphicon-paperclip { &:before { content: \"\\e142\"; } }\n.glyphicon-heart-empty { &:before { content: \"\\e143\"; } }\n.glyphicon-link { &:before { content: \"\\e144\"; } }\n.glyphicon-phone { &:before { content: \"\\e145\"; } }\n.glyphicon-pushpin { &:before { content: \"\\e146\"; } }\n.glyphicon-usd { &:before { content: \"\\e148\"; } }\n.glyphicon-gbp { &:before { content: \"\\e149\"; } }\n.glyphicon-sort { &:before { content: \"\\e150\"; } }\n.glyphicon-sort-by-alphabet { &:before { content: \"\\e151\"; } }\n.glyphicon-sort-by-alphabet-alt { &:before { content: \"\\e152\"; } }\n.glyphicon-sort-by-order { &:before { content: \"\\e153\"; } }\n.glyphicon-sort-by-order-alt { &:before { content: \"\\e154\"; } }\n.glyphicon-sort-by-attributes { &:before { content: \"\\e155\"; } }\n.glyphicon-sort-by-attributes-alt { &:before { content: \"\\e156\"; } }\n.glyphicon-unchecked { &:before { content: \"\\e157\"; } }\n.glyphicon-expand { &:before { content: \"\\e158\"; } }\n.glyphicon-collapse-down { &:before { content: \"\\e159\"; } }\n.glyphicon-collapse-up { &:before { content: \"\\e160\"; } }\n.glyphicon-log-in { &:before { content: \"\\e161\"; } }\n.glyphicon-flash { &:before { content: \"\\e162\"; } }\n.glyphicon-log-out { &:before { content: \"\\e163\"; } }\n.glyphicon-new-window { &:before { content: \"\\e164\"; } }\n.glyphicon-record { &:before { content: \"\\e165\"; } }\n.glyphicon-save { &:before { content: \"\\e166\"; } }\n.glyphicon-open { &:before { content: \"\\e167\"; } }\n.glyphicon-saved { &:before { content: \"\\e168\"; } }\n.glyphicon-import { &:before { content: \"\\e169\"; } }\n.glyphicon-export { &:before { content: \"\\e170\"; } }\n.glyphicon-send { &:before { content: \"\\e171\"; } }\n.glyphicon-floppy-disk { &:before { content: \"\\e172\"; } }\n.glyphicon-floppy-saved { &:before { content: \"\\e173\"; } }\n.glyphicon-floppy-remove { &:before { content: \"\\e174\"; } }\n.glyphicon-floppy-save { &:before { content: \"\\e175\"; } }\n.glyphicon-floppy-open { &:before { content: \"\\e176\"; } }\n.glyphicon-credit-card { &:before { content: \"\\e177\"; } }\n.glyphicon-transfer { &:before { content: \"\\e178\"; } }\n.glyphicon-cutlery { &:before { content: \"\\e179\"; } }\n.glyphicon-header { &:before { content: \"\\e180\"; } }\n.glyphicon-compressed { &:before { content: \"\\e181\"; } }\n.glyphicon-earphone { &:before { content: \"\\e182\"; } }\n.glyphicon-phone-alt { &:before { content: \"\\e183\"; } }\n.glyphicon-tower { &:before { content: \"\\e184\"; } }\n.glyphicon-stats { &:before { content: \"\\e185\"; } }\n.glyphicon-sd-video { &:before { content: \"\\e186\"; } }\n.glyphicon-hd-video { &:before { content: \"\\e187\"; } }\n.glyphicon-subtitles { &:before { content: \"\\e188\"; } }\n.glyphicon-sound-stereo { &:before { content: \"\\e189\"; } }\n.glyphicon-sound-dolby { &:before { content: \"\\e190\"; } }\n.glyphicon-sound-5-1 { &:before { content: \"\\e191\"; } }\n.glyphicon-sound-6-1 { &:before { content: \"\\e192\"; } }\n.glyphicon-sound-7-1 { &:before { content: \"\\e193\"; } }\n.glyphicon-copyright-mark { &:before { content: \"\\e194\"; } }\n.glyphicon-registration-mark { &:before { content: \"\\e195\"; } }\n.glyphicon-cloud-download { &:before { content: \"\\e197\"; } }\n.glyphicon-cloud-upload { &:before { content: \"\\e198\"; } }\n.glyphicon-tree-conifer { &:before { content: \"\\e199\"; } }\n.glyphicon-tree-deciduous { &:before { content: \"\\e200\"; } }\n","//\n// Scaffolding\n// --------------------------------------------------\n\n\n// Reset the box-sizing\n//\n// Heads up! This reset may cause conflicts with some third-party widgets.\n// For recommendations on resolving such conflicts, see\n// http://getbootstrap.com/getting-started/#third-box-sizing\n* {\n .box-sizing(border-box);\n}\n*:before,\n*:after {\n .box-sizing(border-box);\n}\n\n\n// Body reset\n\nhtml {\n font-size: 10px;\n -webkit-tap-highlight-color: rgba(0,0,0,0);\n}\n\nbody {\n font-family: @font-family-base;\n font-size: @font-size-base;\n line-height: @line-height-base;\n color: @text-color;\n background-color: @body-bg;\n}\n\n// Reset fonts for relevant elements\ninput,\nbutton,\nselect,\ntextarea {\n font-family: inherit;\n font-size: inherit;\n line-height: inherit;\n}\n\n\n// Links\n\na {\n color: @link-color;\n text-decoration: none;\n\n &:hover,\n &:focus {\n color: @link-hover-color;\n text-decoration: underline;\n }\n\n &:focus {\n .tab-focus();\n }\n}\n\n\n// Figures\n//\n// We reset this here because previously Normalize had no `figure` margins. This\n// ensures we don't break anyone's use of the element.\n\nfigure {\n margin: 0;\n}\n\n\n// Images\n\nimg {\n vertical-align: middle;\n}\n\n// Responsive images (ensure images don't scale beyond their parents)\n.img-responsive {\n .img-responsive();\n}\n\n// Rounded corners\n.img-rounded {\n border-radius: @border-radius-large;\n}\n\n// Image thumbnails\n//\n// Heads up! This is mixin-ed into thumbnails.less for `.thumbnail`.\n.img-thumbnail {\n padding: @thumbnail-padding;\n line-height: @line-height-base;\n background-color: @thumbnail-bg;\n border: 1px solid @thumbnail-border;\n border-radius: @thumbnail-border-radius;\n .transition(all .2s ease-in-out);\n\n // Keep them at most 100% wide\n .img-responsive(inline-block);\n}\n\n// Perfect circle\n.img-circle {\n border-radius: 50%; // set radius in percents\n}\n\n\n// Horizontal rules\n\nhr {\n margin-top: @line-height-computed;\n margin-bottom: @line-height-computed;\n border: 0;\n border-top: 1px solid @hr-border;\n}\n\n\n// Only display content to screen readers\n//\n// See: http://a11yproject.com/posts/how-to-hide-content/\n\n.sr-only {\n position: absolute;\n width: 1px;\n height: 1px;\n margin: -1px;\n padding: 0;\n overflow: hidden;\n clip: rect(0,0,0,0);\n border: 0;\n}\n\n// Use in conjunction with .sr-only to only display content when it's focused.\n// Useful for \"Skip to main content\" links; see http://www.w3.org/TR/2013/NOTE-WCAG20-TECHS-20130905/G1\n// Credit: HTML5 Boilerplate\n\n.sr-only-focusable {\n &:active,\n &:focus {\n position: static;\n width: auto;\n height: auto;\n margin: 0;\n overflow: visible;\n clip: auto;\n }\n}\n","// Vendor Prefixes\n//\n// All vendor mixins are deprecated as of v3.2.0 due to the introduction of\n// Autoprefixer in our Gruntfile. They will be removed in v4.\n\n// - Animations\n// - Backface visibility\n// - Box shadow\n// - Box sizing\n// - Content columns\n// - Hyphens\n// - Placeholder text\n// - Transformations\n// - Transitions\n// - User Select\n\n\n// Animations\n.animation(@animation) {\n -webkit-animation: @animation;\n -o-animation: @animation;\n animation: @animation;\n}\n.animation-name(@name) {\n -webkit-animation-name: @name;\n animation-name: @name;\n}\n.animation-duration(@duration) {\n -webkit-animation-duration: @duration;\n animation-duration: @duration;\n}\n.animation-timing-function(@timing-function) {\n -webkit-animation-timing-function: @timing-function;\n animation-timing-function: @timing-function;\n}\n.animation-delay(@delay) {\n -webkit-animation-delay: @delay;\n animation-delay: @delay;\n}\n.animation-iteration-count(@iteration-count) {\n -webkit-animation-iteration-count: @iteration-count;\n animation-iteration-count: @iteration-count;\n}\n.animation-direction(@direction) {\n -webkit-animation-direction: @direction;\n animation-direction: @direction;\n}\n.animation-fill-mode(@fill-mode) {\n -webkit-animation-fill-mode: @fill-mode;\n animation-fill-mode: @fill-mode;\n}\n\n// Backface visibility\n// Prevent browsers from flickering when using CSS 3D transforms.\n// Default value is `visible`, but can be changed to `hidden`\n\n.backface-visibility(@visibility){\n -webkit-backface-visibility: @visibility;\n -moz-backface-visibility: @visibility;\n backface-visibility: @visibility;\n}\n\n// Drop shadows\n//\n// Note: Deprecated `.box-shadow()` as of v3.1.0 since all of Bootstrap's\n// supported browsers that have box shadow capabilities now support it.\n\n.box-shadow(@shadow) {\n -webkit-box-shadow: @shadow; // iOS <4.3 & Android <4.1\n box-shadow: @shadow;\n}\n\n// Box sizing\n.box-sizing(@boxmodel) {\n -webkit-box-sizing: @boxmodel;\n -moz-box-sizing: @boxmodel;\n box-sizing: @boxmodel;\n}\n\n// CSS3 Content Columns\n.content-columns(@column-count; @column-gap: @grid-gutter-width) {\n -webkit-column-count: @column-count;\n -moz-column-count: @column-count;\n column-count: @column-count;\n -webkit-column-gap: @column-gap;\n -moz-column-gap: @column-gap;\n column-gap: @column-gap;\n}\n\n// Optional hyphenation\n.hyphens(@mode: auto) {\n word-wrap: break-word;\n -webkit-hyphens: @mode;\n -moz-hyphens: @mode;\n -ms-hyphens: @mode; // IE10+\n -o-hyphens: @mode;\n hyphens: @mode;\n}\n\n// Placeholder text\n.placeholder(@color: @input-color-placeholder) {\n &::-moz-placeholder { color: @color; // Firefox\n opacity: 1; } // See https://github.com/twbs/bootstrap/pull/11526\n &:-ms-input-placeholder { color: @color; } // Internet Explorer 10+\n &::-webkit-input-placeholder { color: @color; } // Safari and Chrome\n}\n\n// Transformations\n.scale(@ratio) {\n -webkit-transform: scale(@ratio);\n -ms-transform: scale(@ratio); // IE9 only\n -o-transform: scale(@ratio);\n transform: scale(@ratio);\n}\n.scale(@ratioX; @ratioY) {\n -webkit-transform: scale(@ratioX, @ratioY);\n -ms-transform: scale(@ratioX, @ratioY); // IE9 only\n -o-transform: scale(@ratioX, @ratioY);\n transform: scale(@ratioX, @ratioY);\n}\n.scaleX(@ratio) {\n -webkit-transform: scaleX(@ratio);\n -ms-transform: scaleX(@ratio); // IE9 only\n -o-transform: scaleX(@ratio);\n transform: scaleX(@ratio);\n}\n.scaleY(@ratio) {\n -webkit-transform: scaleY(@ratio);\n -ms-transform: scaleY(@ratio); // IE9 only\n -o-transform: scaleY(@ratio);\n transform: scaleY(@ratio);\n}\n.skew(@x; @y) {\n -webkit-transform: skewX(@x) skewY(@y);\n -ms-transform: skewX(@x) skewY(@y); // See https://github.com/twbs/bootstrap/issues/4885; IE9+\n -o-transform: skewX(@x) skewY(@y);\n transform: skewX(@x) skewY(@y);\n}\n.translate(@x; @y) {\n -webkit-transform: translate(@x, @y);\n -ms-transform: translate(@x, @y); // IE9 only\n -o-transform: translate(@x, @y);\n transform: translate(@x, @y);\n}\n.translate3d(@x; @y; @z) {\n -webkit-transform: translate3d(@x, @y, @z);\n transform: translate3d(@x, @y, @z);\n}\n.rotate(@degrees) {\n -webkit-transform: rotate(@degrees);\n -ms-transform: rotate(@degrees); // IE9 only\n -o-transform: rotate(@degrees);\n transform: rotate(@degrees);\n}\n.rotateX(@degrees) {\n -webkit-transform: rotateX(@degrees);\n -ms-transform: rotateX(@degrees); // IE9 only\n -o-transform: rotateX(@degrees);\n transform: rotateX(@degrees);\n}\n.rotateY(@degrees) {\n -webkit-transform: rotateY(@degrees);\n -ms-transform: rotateY(@degrees); // IE9 only\n -o-transform: rotateY(@degrees);\n transform: rotateY(@degrees);\n}\n.perspective(@perspective) {\n -webkit-perspective: @perspective;\n -moz-perspective: @perspective;\n perspective: @perspective;\n}\n.perspective-origin(@perspective) {\n -webkit-perspective-origin: @perspective;\n -moz-perspective-origin: @perspective;\n perspective-origin: @perspective;\n}\n.transform-origin(@origin) {\n -webkit-transform-origin: @origin;\n -moz-transform-origin: @origin;\n -ms-transform-origin: @origin; // IE9 only\n transform-origin: @origin;\n}\n\n\n// Transitions\n\n.transition(@transition) {\n -webkit-transition: @transition;\n -o-transition: @transition;\n transition: @transition;\n}\n.transition-property(@transition-property) {\n -webkit-transition-property: @transition-property;\n transition-property: @transition-property;\n}\n.transition-delay(@transition-delay) {\n -webkit-transition-delay: @transition-delay;\n transition-delay: @transition-delay;\n}\n.transition-duration(@transition-duration) {\n -webkit-transition-duration: @transition-duration;\n transition-duration: @transition-duration;\n}\n.transition-timing-function(@timing-function) {\n -webkit-transition-timing-function: @timing-function;\n transition-timing-function: @timing-function;\n}\n.transition-transform(@transition) {\n -webkit-transition: -webkit-transform @transition;\n -moz-transition: -moz-transform @transition;\n -o-transition: -o-transform @transition;\n transition: transform @transition;\n}\n\n\n// User select\n// For selecting text on the page\n\n.user-select(@select) {\n -webkit-user-select: @select;\n -moz-user-select: @select;\n -ms-user-select: @select; // IE10+\n user-select: @select;\n}\n","// WebKit-style focus\n\n.tab-focus() {\n // Default\n outline: thin dotted;\n // WebKit\n outline: 5px auto -webkit-focus-ring-color;\n outline-offset: -2px;\n}\n","// Image Mixins\n// - Responsive image\n// - Retina image\n\n\n// Responsive image\n//\n// Keep images from scaling beyond the width of their parents.\n.img-responsive(@display: block) {\n display: @display;\n width: 100% \\9; // Force IE10 and below to size SVG images correctly\n max-width: 100%; // Part 1: Set a maximum relative to the parent\n height: auto; // Part 2: Scale the height according to the width, otherwise you get stretching\n}\n\n\n// Retina image\n//\n// Short retina mixin for setting background-image and -size. Note that the\n// spelling of `min--moz-device-pixel-ratio` is intentional.\n.img-retina(@file-1x; @file-2x; @width-1x; @height-1x) {\n background-image: url(\"@{file-1x}\");\n\n @media\n only screen and (-webkit-min-device-pixel-ratio: 2),\n only screen and ( min--moz-device-pixel-ratio: 2),\n only screen and ( -o-min-device-pixel-ratio: 2/1),\n only screen and ( min-device-pixel-ratio: 2),\n only screen and ( min-resolution: 192dpi),\n only screen and ( min-resolution: 2dppx) {\n background-image: url(\"@{file-2x}\");\n background-size: @width-1x @height-1x;\n }\n}\n","//\n// Typography\n// --------------------------------------------------\n\n\n// Headings\n// -------------------------\n\nh1, h2, h3, h4, h5, h6,\n.h1, .h2, .h3, .h4, .h5, .h6 {\n font-family: @headings-font-family;\n font-weight: @headings-font-weight;\n line-height: @headings-line-height;\n color: @headings-color;\n\n small,\n .small {\n font-weight: normal;\n line-height: 1;\n color: @headings-small-color;\n }\n}\n\nh1, .h1,\nh2, .h2,\nh3, .h3 {\n margin-top: @line-height-computed;\n margin-bottom: (@line-height-computed / 2);\n\n small,\n .small {\n font-size: 65%;\n }\n}\nh4, .h4,\nh5, .h5,\nh6, .h6 {\n margin-top: (@line-height-computed / 2);\n margin-bottom: (@line-height-computed / 2);\n\n small,\n .small {\n font-size: 75%;\n }\n}\n\nh1, .h1 { font-size: @font-size-h1; }\nh2, .h2 { font-size: @font-size-h2; }\nh3, .h3 { font-size: @font-size-h3; }\nh4, .h4 { font-size: @font-size-h4; }\nh5, .h5 { font-size: @font-size-h5; }\nh6, .h6 { font-size: @font-size-h6; }\n\n\n// Body text\n// -------------------------\n\np {\n margin: 0 0 (@line-height-computed / 2);\n}\n\n.lead {\n margin-bottom: @line-height-computed;\n font-size: floor((@font-size-base * 1.15));\n font-weight: 300;\n line-height: 1.4;\n\n @media (min-width: @screen-sm-min) {\n font-size: (@font-size-base * 1.5);\n }\n}\n\n\n// Emphasis & misc\n// -------------------------\n\n// Ex: (12px small font / 14px base font) * 100% = about 85%\nsmall,\n.small {\n font-size: floor((100% * @font-size-small / @font-size-base));\n}\n\n// Undo browser default styling\ncite {\n font-style: normal;\n}\n\nmark,\n.mark {\n background-color: @state-warning-bg;\n padding: .2em;\n}\n\n// Alignment\n.text-left { text-align: left; }\n.text-right { text-align: right; }\n.text-center { text-align: center; }\n.text-justify { text-align: justify; }\n.text-nowrap { white-space: nowrap; }\n\n// Transformation\n.text-lowercase { text-transform: lowercase; }\n.text-uppercase { text-transform: uppercase; }\n.text-capitalize { text-transform: capitalize; }\n\n// Contextual colors\n.text-muted {\n color: @text-muted;\n}\n.text-primary {\n .text-emphasis-variant(@brand-primary);\n}\n.text-success {\n .text-emphasis-variant(@state-success-text);\n}\n.text-info {\n .text-emphasis-variant(@state-info-text);\n}\n.text-warning {\n .text-emphasis-variant(@state-warning-text);\n}\n.text-danger {\n .text-emphasis-variant(@state-danger-text);\n}\n\n// Contextual backgrounds\n// For now we'll leave these alongside the text classes until v4 when we can\n// safely shift things around (per SemVer rules).\n.bg-primary {\n // Given the contrast here, this is the only class to have its color inverted\n // automatically.\n color: #fff;\n .bg-variant(@brand-primary);\n}\n.bg-success {\n .bg-variant(@state-success-bg);\n}\n.bg-info {\n .bg-variant(@state-info-bg);\n}\n.bg-warning {\n .bg-variant(@state-warning-bg);\n}\n.bg-danger {\n .bg-variant(@state-danger-bg);\n}\n\n\n// Page header\n// -------------------------\n\n.page-header {\n padding-bottom: ((@line-height-computed / 2) - 1);\n margin: (@line-height-computed * 2) 0 @line-height-computed;\n border-bottom: 1px solid @page-header-border-color;\n}\n\n\n// Lists\n// -------------------------\n\n// Unordered and Ordered lists\nul,\nol {\n margin-top: 0;\n margin-bottom: (@line-height-computed / 2);\n ul,\n ol {\n margin-bottom: 0;\n }\n}\n\n// List options\n\n// Unstyled keeps list items block level, just removes default browser padding and list-style\n.list-unstyled {\n padding-left: 0;\n list-style: none;\n}\n\n// Inline turns list items into inline-block\n.list-inline {\n .list-unstyled();\n margin-left: -5px;\n\n > li {\n display: inline-block;\n padding-left: 5px;\n padding-right: 5px;\n }\n}\n\n// Description Lists\ndl {\n margin-top: 0; // Remove browser default\n margin-bottom: @line-height-computed;\n}\ndt,\ndd {\n line-height: @line-height-base;\n}\ndt {\n font-weight: bold;\n}\ndd {\n margin-left: 0; // Undo browser default\n}\n\n// Horizontal description lists\n//\n// Defaults to being stacked without any of the below styles applied, until the\n// grid breakpoint is reached (default of ~768px).\n\n.dl-horizontal {\n dd {\n &:extend(.clearfix all); // Clear the floated `dt` if an empty `dd` is present\n }\n\n @media (min-width: @grid-float-breakpoint) {\n dt {\n float: left;\n width: (@dl-horizontal-offset - 20);\n clear: left;\n text-align: right;\n .text-overflow();\n }\n dd {\n margin-left: @dl-horizontal-offset;\n }\n }\n}\n\n\n// Misc\n// -------------------------\n\n// Abbreviations and acronyms\nabbr[title],\n// Add data-* attribute to help out our tooltip plugin, per https://github.com/twbs/bootstrap/issues/5257\nabbr[data-original-title] {\n cursor: help;\n border-bottom: 1px dotted @abbr-border-color;\n}\n.initialism {\n font-size: 90%;\n text-transform: uppercase;\n}\n\n// Blockquotes\nblockquote {\n padding: (@line-height-computed / 2) @line-height-computed;\n margin: 0 0 @line-height-computed;\n font-size: @blockquote-font-size;\n border-left: 5px solid @blockquote-border-color;\n\n p,\n ul,\n ol {\n &:last-child {\n margin-bottom: 0;\n }\n }\n\n // Note: Deprecated small and .small as of v3.1.0\n // Context: https://github.com/twbs/bootstrap/issues/11660\n footer,\n small,\n .small {\n display: block;\n font-size: 80%; // back to default font-size\n line-height: @line-height-base;\n color: @blockquote-small-color;\n\n &:before {\n content: '\\2014 \\00A0'; // em dash, nbsp\n }\n }\n}\n\n// Opposite alignment of blockquote\n//\n// Heads up: `blockquote.pull-right` has been deprecated as of v3.1.0.\n.blockquote-reverse,\nblockquote.pull-right {\n padding-right: 15px;\n padding-left: 0;\n border-right: 5px solid @blockquote-border-color;\n border-left: 0;\n text-align: right;\n\n // Account for citation\n footer,\n small,\n .small {\n &:before { content: ''; }\n &:after {\n content: '\\00A0 \\2014'; // nbsp, em dash\n }\n }\n}\n\n// Quotes\nblockquote:before,\nblockquote:after {\n content: \"\";\n}\n\n// Addresses\naddress {\n margin-bottom: @line-height-computed;\n font-style: normal;\n line-height: @line-height-base;\n}\n","// Typography\n\n.text-emphasis-variant(@color) {\n color: @color;\n a&:hover {\n color: darken(@color, 10%);\n }\n}\n","// Contextual backgrounds\n\n.bg-variant(@color) {\n background-color: @color;\n a&:hover {\n background-color: darken(@color, 10%);\n }\n}\n","// Text overflow\n// Requires inline-block or block for proper styling\n\n.text-overflow() {\n overflow: hidden;\n text-overflow: ellipsis;\n white-space: nowrap;\n}\n","//\n// Code (inline and block)\n// --------------------------------------------------\n\n\n// Inline and block code styles\ncode,\nkbd,\npre,\nsamp {\n font-family: @font-family-monospace;\n}\n\n// Inline code\ncode {\n padding: 2px 4px;\n font-size: 90%;\n color: @code-color;\n background-color: @code-bg;\n border-radius: @border-radius-base;\n}\n\n// User input typically entered via keyboard\nkbd {\n padding: 2px 4px;\n font-size: 90%;\n color: @kbd-color;\n background-color: @kbd-bg;\n border-radius: @border-radius-small;\n box-shadow: inset 0 -1px 0 rgba(0,0,0,.25);\n\n kbd {\n padding: 0;\n font-size: 100%;\n box-shadow: none;\n }\n}\n\n// Blocks of code\npre {\n display: block;\n padding: ((@line-height-computed - 1) / 2);\n margin: 0 0 (@line-height-computed / 2);\n font-size: (@font-size-base - 1); // 14px to 13px\n line-height: @line-height-base;\n word-break: break-all;\n word-wrap: break-word;\n color: @pre-color;\n background-color: @pre-bg;\n border: 1px solid @pre-border-color;\n border-radius: @border-radius-base;\n\n // Account for some code outputs that place code tags in pre tags\n code {\n padding: 0;\n font-size: inherit;\n color: inherit;\n white-space: pre-wrap;\n background-color: transparent;\n border-radius: 0;\n }\n}\n\n// Enable scrollable blocks of code\n.pre-scrollable {\n max-height: @pre-scrollable-max-height;\n overflow-y: scroll;\n}\n","//\n// Grid system\n// --------------------------------------------------\n\n\n// Container widths\n//\n// Set the container width, and override it for fixed navbars in media queries.\n\n.container {\n .container-fixed();\n\n @media (min-width: @screen-sm-min) {\n width: @container-sm;\n }\n @media (min-width: @screen-md-min) {\n width: @container-md;\n }\n @media (min-width: @screen-lg-min) {\n width: @container-lg;\n }\n}\n\n\n// Fluid container\n//\n// Utilizes the mixin meant for fixed width containers, but without any defined\n// width for fluid, full width layouts.\n\n.container-fluid {\n .container-fixed();\n}\n\n\n// Row\n//\n// Rows contain and clear the floats of your columns.\n\n.row {\n .make-row();\n}\n\n\n// Columns\n//\n// Common styles for small and large grid columns\n\n.make-grid-columns();\n\n\n// Extra small grid\n//\n// Columns, offsets, pushes, and pulls for extra small devices like\n// smartphones.\n\n.make-grid(xs);\n\n\n// Small grid\n//\n// Columns, offsets, pushes, and pulls for the small device range, from phones\n// to tablets.\n\n@media (min-width: @screen-sm-min) {\n .make-grid(sm);\n}\n\n\n// Medium grid\n//\n// Columns, offsets, pushes, and pulls for the desktop device range.\n\n@media (min-width: @screen-md-min) {\n .make-grid(md);\n}\n\n\n// Large grid\n//\n// Columns, offsets, pushes, and pulls for the large desktop device range.\n\n@media (min-width: @screen-lg-min) {\n .make-grid(lg);\n}\n","// Grid system\n//\n// Generate semantic grid columns with these mixins.\n\n// Centered container element\n.container-fixed(@gutter: @grid-gutter-width) {\n margin-right: auto;\n margin-left: auto;\n padding-left: (@gutter / 2);\n padding-right: (@gutter / 2);\n &:extend(.clearfix all);\n}\n\n// Creates a wrapper for a series of columns\n.make-row(@gutter: @grid-gutter-width) {\n margin-left: (@gutter / -2);\n margin-right: (@gutter / -2);\n &:extend(.clearfix all);\n}\n\n// Generate the extra small columns\n.make-xs-column(@columns; @gutter: @grid-gutter-width) {\n position: relative;\n float: left;\n width: percentage((@columns / @grid-columns));\n min-height: 1px;\n padding-left: (@gutter / 2);\n padding-right: (@gutter / 2);\n}\n.make-xs-column-offset(@columns) {\n margin-left: percentage((@columns / @grid-columns));\n}\n.make-xs-column-push(@columns) {\n left: percentage((@columns / @grid-columns));\n}\n.make-xs-column-pull(@columns) {\n right: percentage((@columns / @grid-columns));\n}\n\n// Generate the small columns\n.make-sm-column(@columns; @gutter: @grid-gutter-width) {\n position: relative;\n min-height: 1px;\n padding-left: (@gutter / 2);\n padding-right: (@gutter / 2);\n\n @media (min-width: @screen-sm-min) {\n float: left;\n width: percentage((@columns / @grid-columns));\n }\n}\n.make-sm-column-offset(@columns) {\n @media (min-width: @screen-sm-min) {\n margin-left: percentage((@columns / @grid-columns));\n }\n}\n.make-sm-column-push(@columns) {\n @media (min-width: @screen-sm-min) {\n left: percentage((@columns / @grid-columns));\n }\n}\n.make-sm-column-pull(@columns) {\n @media (min-width: @screen-sm-min) {\n right: percentage((@columns / @grid-columns));\n }\n}\n\n// Generate the medium columns\n.make-md-column(@columns; @gutter: @grid-gutter-width) {\n position: relative;\n min-height: 1px;\n padding-left: (@gutter / 2);\n padding-right: (@gutter / 2);\n\n @media (min-width: @screen-md-min) {\n float: left;\n width: percentage((@columns / @grid-columns));\n }\n}\n.make-md-column-offset(@columns) {\n @media (min-width: @screen-md-min) {\n margin-left: percentage((@columns / @grid-columns));\n }\n}\n.make-md-column-push(@columns) {\n @media (min-width: @screen-md-min) {\n left: percentage((@columns / @grid-columns));\n }\n}\n.make-md-column-pull(@columns) {\n @media (min-width: @screen-md-min) {\n right: percentage((@columns / @grid-columns));\n }\n}\n\n// Generate the large columns\n.make-lg-column(@columns; @gutter: @grid-gutter-width) {\n position: relative;\n min-height: 1px;\n padding-left: (@gutter / 2);\n padding-right: (@gutter / 2);\n\n @media (min-width: @screen-lg-min) {\n float: left;\n width: percentage((@columns / @grid-columns));\n }\n}\n.make-lg-column-offset(@columns) {\n @media (min-width: @screen-lg-min) {\n margin-left: percentage((@columns / @grid-columns));\n }\n}\n.make-lg-column-push(@columns) {\n @media (min-width: @screen-lg-min) {\n left: percentage((@columns / @grid-columns));\n }\n}\n.make-lg-column-pull(@columns) {\n @media (min-width: @screen-lg-min) {\n right: percentage((@columns / @grid-columns));\n }\n}\n","// Framework grid generation\n//\n// Used only by Bootstrap to generate the correct number of grid classes given\n// any value of `@grid-columns`.\n\n.make-grid-columns() {\n // Common styles for all sizes of grid columns, widths 1-12\n .col(@index) when (@index = 1) { // initial\n @item: ~\".col-xs-@{index}, .col-sm-@{index}, .col-md-@{index}, .col-lg-@{index}\";\n .col((@index + 1), @item);\n }\n .col(@index, @list) when (@index =< @grid-columns) { // general; \"=<\" isn't a typo\n @item: ~\".col-xs-@{index}, .col-sm-@{index}, .col-md-@{index}, .col-lg-@{index}\";\n .col((@index + 1), ~\"@{list}, @{item}\");\n }\n .col(@index, @list) when (@index > @grid-columns) { // terminal\n @{list} {\n position: relative;\n // Prevent columns from collapsing when empty\n min-height: 1px;\n // Inner gutter via padding\n padding-left: (@grid-gutter-width / 2);\n padding-right: (@grid-gutter-width / 2);\n }\n }\n .col(1); // kickstart it\n}\n\n.float-grid-columns(@class) {\n .col(@index) when (@index = 1) { // initial\n @item: ~\".col-@{class}-@{index}\";\n .col((@index + 1), @item);\n }\n .col(@index, @list) when (@index =< @grid-columns) { // general\n @item: ~\".col-@{class}-@{index}\";\n .col((@index + 1), ~\"@{list}, @{item}\");\n }\n .col(@index, @list) when (@index > @grid-columns) { // terminal\n @{list} {\n float: left;\n }\n }\n .col(1); // kickstart it\n}\n\n.calc-grid-column(@index, @class, @type) when (@type = width) and (@index > 0) {\n .col-@{class}-@{index} {\n width: percentage((@index / @grid-columns));\n }\n}\n.calc-grid-column(@index, @class, @type) when (@type = push) and (@index > 0) {\n .col-@{class}-push-@{index} {\n left: percentage((@index / @grid-columns));\n }\n}\n.calc-grid-column(@index, @class, @type) when (@type = push) and (@index = 0) {\n .col-@{class}-push-0 {\n left: auto;\n }\n}\n.calc-grid-column(@index, @class, @type) when (@type = pull) and (@index > 0) {\n .col-@{class}-pull-@{index} {\n right: percentage((@index / @grid-columns));\n }\n}\n.calc-grid-column(@index, @class, @type) when (@type = pull) and (@index = 0) {\n .col-@{class}-pull-0 {\n right: auto;\n }\n}\n.calc-grid-column(@index, @class, @type) when (@type = offset) {\n .col-@{class}-offset-@{index} {\n margin-left: percentage((@index / @grid-columns));\n }\n}\n\n// Basic looping in LESS\n.loop-grid-columns(@index, @class, @type) when (@index >= 0) {\n .calc-grid-column(@index, @class, @type);\n // next iteration\n .loop-grid-columns((@index - 1), @class, @type);\n}\n\n// Create grid for specific class\n.make-grid(@class) {\n .float-grid-columns(@class);\n .loop-grid-columns(@grid-columns, @class, width);\n .loop-grid-columns(@grid-columns, @class, pull);\n .loop-grid-columns(@grid-columns, @class, push);\n .loop-grid-columns(@grid-columns, @class, offset);\n}\n","//\n// Tables\n// --------------------------------------------------\n\n\ntable {\n background-color: @table-bg;\n}\nth {\n text-align: left;\n}\n\n\n// Baseline styles\n\n.table {\n width: 100%;\n max-width: 100%;\n margin-bottom: @line-height-computed;\n // Cells\n > thead,\n > tbody,\n > tfoot {\n > tr {\n > th,\n > td {\n padding: @table-cell-padding;\n line-height: @line-height-base;\n vertical-align: top;\n border-top: 1px solid @table-border-color;\n }\n }\n }\n // Bottom align for column headings\n > thead > tr > th {\n vertical-align: bottom;\n border-bottom: 2px solid @table-border-color;\n }\n // Remove top border from thead by default\n > caption + thead,\n > colgroup + thead,\n > thead:first-child {\n > tr:first-child {\n > th,\n > td {\n border-top: 0;\n }\n }\n }\n // Account for multiple tbody instances\n > tbody + tbody {\n border-top: 2px solid @table-border-color;\n }\n\n // Nesting\n .table {\n background-color: @body-bg;\n }\n}\n\n\n// Condensed table w/ half padding\n\n.table-condensed {\n > thead,\n > tbody,\n > tfoot {\n > tr {\n > th,\n > td {\n padding: @table-condensed-cell-padding;\n }\n }\n }\n}\n\n\n// Bordered version\n//\n// Add borders all around the table and between all the columns.\n\n.table-bordered {\n border: 1px solid @table-border-color;\n > thead,\n > tbody,\n > tfoot {\n > tr {\n > th,\n > td {\n border: 1px solid @table-border-color;\n }\n }\n }\n > thead > tr {\n > th,\n > td {\n border-bottom-width: 2px;\n }\n }\n}\n\n\n// Zebra-striping\n//\n// Default zebra-stripe styles (alternating gray and transparent backgrounds)\n\n.table-striped {\n > tbody > tr:nth-child(odd) {\n > td,\n > th {\n background-color: @table-bg-accent;\n }\n }\n}\n\n\n// Hover effect\n//\n// Placed here since it has to come after the potential zebra striping\n\n.table-hover {\n > tbody > tr:hover {\n > td,\n > th {\n background-color: @table-bg-hover;\n }\n }\n}\n\n\n// Table cell sizing\n//\n// Reset default table behavior\n\ntable col[class*=\"col-\"] {\n position: static; // Prevent border hiding in Firefox and IE9/10 (see https://github.com/twbs/bootstrap/issues/11623)\n float: none;\n display: table-column;\n}\ntable {\n td,\n th {\n &[class*=\"col-\"] {\n position: static; // Prevent border hiding in Firefox and IE9/10 (see https://github.com/twbs/bootstrap/issues/11623)\n float: none;\n display: table-cell;\n }\n }\n}\n\n\n// Table backgrounds\n//\n// Exact selectors below required to override `.table-striped` and prevent\n// inheritance to nested tables.\n\n// Generate the contextual variants\n.table-row-variant(active; @table-bg-active);\n.table-row-variant(success; @state-success-bg);\n.table-row-variant(info; @state-info-bg);\n.table-row-variant(warning; @state-warning-bg);\n.table-row-variant(danger; @state-danger-bg);\n\n\n// Responsive tables\n//\n// Wrap your tables in `.table-responsive` and we'll make them mobile friendly\n// by enabling horizontal scrolling. Only applies <768px. Everything above that\n// will display normally.\n\n.table-responsive {\n @media screen and (max-width: @screen-xs-max) {\n width: 100%;\n margin-bottom: (@line-height-computed * 0.75);\n overflow-y: hidden;\n overflow-x: auto;\n -ms-overflow-style: -ms-autohiding-scrollbar;\n border: 1px solid @table-border-color;\n -webkit-overflow-scrolling: touch;\n\n // Tighten up spacing\n > .table {\n margin-bottom: 0;\n\n // Ensure the content doesn't wrap\n > thead,\n > tbody,\n > tfoot {\n > tr {\n > th,\n > td {\n white-space: nowrap;\n }\n }\n }\n }\n\n // Special overrides for the bordered tables\n > .table-bordered {\n border: 0;\n\n // Nuke the appropriate borders so that the parent can handle them\n > thead,\n > tbody,\n > tfoot {\n > tr {\n > th:first-child,\n > td:first-child {\n border-left: 0;\n }\n > th:last-child,\n > td:last-child {\n border-right: 0;\n }\n }\n }\n\n // Only nuke the last row's bottom-border in `tbody` and `tfoot` since\n // chances are there will be only one `tr` in a `thead` and that would\n // remove the border altogether.\n > tbody,\n > tfoot {\n > tr:last-child {\n > th,\n > td {\n border-bottom: 0;\n }\n }\n }\n\n }\n }\n}\n","// Tables\n\n.table-row-variant(@state; @background) {\n // Exact selectors below required to override `.table-striped` and prevent\n // inheritance to nested tables.\n .table > thead > tr,\n .table > tbody > tr,\n .table > tfoot > tr {\n > td.@{state},\n > th.@{state},\n &.@{state} > td,\n &.@{state} > th {\n background-color: @background;\n }\n }\n\n // Hover states for `.table-hover`\n // Note: this is not available for cells or rows within `thead` or `tfoot`.\n .table-hover > tbody > tr {\n > td.@{state}:hover,\n > th.@{state}:hover,\n &.@{state}:hover > td,\n &:hover > .@{state},\n &.@{state}:hover > th {\n background-color: darken(@background, 5%);\n }\n }\n}\n","//\n// Forms\n// --------------------------------------------------\n\n\n// Normalize non-controls\n//\n// Restyle and baseline non-control form elements.\n\nfieldset {\n padding: 0;\n margin: 0;\n border: 0;\n // Chrome and Firefox set a `min-width: min-content;` on fieldsets,\n // so we reset that to ensure it behaves more like a standard block element.\n // See https://github.com/twbs/bootstrap/issues/12359.\n min-width: 0;\n}\n\nlegend {\n display: block;\n width: 100%;\n padding: 0;\n margin-bottom: @line-height-computed;\n font-size: (@font-size-base * 1.5);\n line-height: inherit;\n color: @legend-color;\n border: 0;\n border-bottom: 1px solid @legend-border-color;\n}\n\nlabel {\n display: inline-block;\n max-width: 100%; // Force IE8 to wrap long content (see https://github.com/twbs/bootstrap/issues/13141)\n margin-bottom: 5px;\n font-weight: bold;\n}\n\n\n// Normalize form controls\n//\n// While most of our form styles require extra classes, some basic normalization\n// is required to ensure optimum display with or without those classes to better\n// address browser inconsistencies.\n\n// Override content-box in Normalize (* isn't specific enough)\ninput[type=\"search\"] {\n .box-sizing(border-box);\n}\n\n// Position radios and checkboxes better\ninput[type=\"radio\"],\ninput[type=\"checkbox\"] {\n margin: 4px 0 0;\n margin-top: 1px \\9; // IE8-9\n line-height: normal;\n}\n\n// Set the height of file controls to match text inputs\ninput[type=\"file\"] {\n display: block;\n}\n\n// Make range inputs behave like textual form controls\ninput[type=\"range\"] {\n display: block;\n width: 100%;\n}\n\n// Make multiple select elements height not fixed\nselect[multiple],\nselect[size] {\n height: auto;\n}\n\n// Focus for file, radio, and checkbox\ninput[type=\"file\"]:focus,\ninput[type=\"radio\"]:focus,\ninput[type=\"checkbox\"]:focus {\n .tab-focus();\n}\n\n// Adjust output element\noutput {\n display: block;\n padding-top: (@padding-base-vertical + 1);\n font-size: @font-size-base;\n line-height: @line-height-base;\n color: @input-color;\n}\n\n\n// Common form controls\n//\n// Shared size and type resets for form controls. Apply `.form-control` to any\n// of the following form controls:\n//\n// select\n// textarea\n// input[type=\"text\"]\n// input[type=\"password\"]\n// input[type=\"datetime\"]\n// input[type=\"datetime-local\"]\n// input[type=\"date\"]\n// input[type=\"month\"]\n// input[type=\"time\"]\n// input[type=\"week\"]\n// input[type=\"number\"]\n// input[type=\"email\"]\n// input[type=\"url\"]\n// input[type=\"search\"]\n// input[type=\"tel\"]\n// input[type=\"color\"]\n\n.form-control {\n display: block;\n width: 100%;\n height: @input-height-base; // Make inputs at least the height of their button counterpart (base line-height + padding + border)\n padding: @padding-base-vertical @padding-base-horizontal;\n font-size: @font-size-base;\n line-height: @line-height-base;\n color: @input-color;\n background-color: @input-bg;\n background-image: none; // Reset unusual Firefox-on-Android default style; see https://github.com/necolas/normalize.css/issues/214\n border: 1px solid @input-border;\n border-radius: @input-border-radius;\n .box-shadow(inset 0 1px 1px rgba(0,0,0,.075));\n .transition(~\"border-color ease-in-out .15s, box-shadow ease-in-out .15s\");\n\n // Customize the `:focus` state to imitate native WebKit styles.\n .form-control-focus();\n\n // Placeholder\n .placeholder();\n\n // Disabled and read-only inputs\n //\n // HTML5 says that controls under a fieldset > legend:first-child won't be\n // disabled if the fieldset is disabled. Due to implementation difficulty, we\n // don't honor that edge case; we style them as disabled anyway.\n &[disabled],\n &[readonly],\n fieldset[disabled] & {\n cursor: not-allowed;\n background-color: @input-bg-disabled;\n opacity: 1; // iOS fix for unreadable disabled content\n }\n\n // Reset height for `textarea`s\n textarea& {\n height: auto;\n }\n}\n\n\n// Search inputs in iOS\n//\n// This overrides the extra rounded corners on search inputs in iOS so that our\n// `.form-control` class can properly style them. Note that this cannot simply\n// be added to `.form-control` as it's not specific enough. For details, see\n// https://github.com/twbs/bootstrap/issues/11586.\n\ninput[type=\"search\"] {\n -webkit-appearance: none;\n}\n\n\n// Special styles for iOS temporal inputs\n//\n// In Mobile Safari, setting `display: block` on temporal inputs causes the\n// text within the input to become vertically misaligned.\n// As a workaround, we set a pixel line-height that matches the\n// given height of the input. Since this fucks up everything else, we have to\n// appropriately reset it for Internet Explorer and the size variations.\n\ninput[type=\"date\"],\ninput[type=\"time\"],\ninput[type=\"datetime-local\"],\ninput[type=\"month\"] {\n line-height: @input-height-base;\n // IE8+ misaligns the text within date inputs, so we reset\n line-height: @line-height-base ~\"\\0\";\n\n &.input-sm {\n line-height: @input-height-small;\n }\n &.input-lg {\n line-height: @input-height-large;\n }\n}\n\n\n// Form groups\n//\n// Designed to help with the organization and spacing of vertical forms. For\n// horizontal forms, use the predefined grid classes.\n\n.form-group {\n margin-bottom: 15px;\n}\n\n\n// Checkboxes and radios\n//\n// Indent the labels to position radios/checkboxes as hanging controls.\n\n.radio,\n.checkbox {\n position: relative;\n display: block;\n min-height: @line-height-computed; // clear the floating input if there is no label text\n margin-top: 10px;\n margin-bottom: 10px;\n\n label {\n padding-left: 20px;\n margin-bottom: 0;\n font-weight: normal;\n cursor: pointer;\n }\n}\n.radio input[type=\"radio\"],\n.radio-inline input[type=\"radio\"],\n.checkbox input[type=\"checkbox\"],\n.checkbox-inline input[type=\"checkbox\"] {\n position: absolute;\n margin-left: -20px;\n margin-top: 4px \\9;\n}\n\n.radio + .radio,\n.checkbox + .checkbox {\n margin-top: -5px; // Move up sibling radios or checkboxes for tighter spacing\n}\n\n// Radios and checkboxes on same line\n.radio-inline,\n.checkbox-inline {\n display: inline-block;\n padding-left: 20px;\n margin-bottom: 0;\n vertical-align: middle;\n font-weight: normal;\n cursor: pointer;\n}\n.radio-inline + .radio-inline,\n.checkbox-inline + .checkbox-inline {\n margin-top: 0;\n margin-left: 10px; // space out consecutive inline controls\n}\n\n// Apply same disabled cursor tweak as for inputs\n// Some special care is needed because <label>s don't inherit their parent's `cursor`.\n//\n// Note: Neither radios nor checkboxes can be readonly.\ninput[type=\"radio\"],\ninput[type=\"checkbox\"] {\n &[disabled],\n &.disabled,\n fieldset[disabled] & {\n cursor: not-allowed;\n }\n}\n// These classes are used directly on <label>s\n.radio-inline,\n.checkbox-inline {\n &.disabled,\n fieldset[disabled] & {\n cursor: not-allowed;\n }\n}\n// These classes are used on elements with <label> descendants\n.radio,\n.checkbox {\n &.disabled,\n fieldset[disabled] & {\n label {\n cursor: not-allowed;\n }\n }\n}\n\n\n// Static form control text\n//\n// Apply class to a `p` element to make any string of text align with labels in\n// a horizontal form layout.\n\n.form-control-static {\n // Size it appropriately next to real form controls\n padding-top: (@padding-base-vertical + 1);\n padding-bottom: (@padding-base-vertical + 1);\n // Remove default margin from `p`\n margin-bottom: 0;\n\n &.input-lg,\n &.input-sm {\n padding-left: 0;\n padding-right: 0;\n }\n}\n\n\n// Form control sizing\n//\n// Build on `.form-control` with modifier classes to decrease or increase the\n// height and font-size of form controls.\n\n.input-sm {\n .input-size(@input-height-small; @padding-small-vertical; @padding-small-horizontal; @font-size-small; @line-height-small; @border-radius-small);\n}\n\n.input-lg {\n .input-size(@input-height-large; @padding-large-vertical; @padding-large-horizontal; @font-size-large; @line-height-large; @border-radius-large);\n}\n\n\n// Form control feedback states\n//\n// Apply contextual and semantic states to individual form controls.\n\n.has-feedback {\n // Enable absolute positioning\n position: relative;\n\n // Ensure icons don't overlap text\n .form-control {\n padding-right: (@input-height-base * 1.25);\n }\n}\n// Feedback icon (requires .glyphicon classes)\n.form-control-feedback {\n position: absolute;\n top: (@line-height-computed + 5); // Height of the `label` and its margin\n right: 0;\n z-index: 2; // Ensure icon is above input groups\n display: block;\n width: @input-height-base;\n height: @input-height-base;\n line-height: @input-height-base;\n text-align: center;\n}\n.input-lg + .form-control-feedback {\n width: @input-height-large;\n height: @input-height-large;\n line-height: @input-height-large;\n}\n.input-sm + .form-control-feedback {\n width: @input-height-small;\n height: @input-height-small;\n line-height: @input-height-small;\n}\n\n// Feedback states\n.has-success {\n .form-control-validation(@state-success-text; @state-success-text; @state-success-bg);\n}\n.has-warning {\n .form-control-validation(@state-warning-text; @state-warning-text; @state-warning-bg);\n}\n.has-error {\n .form-control-validation(@state-danger-text; @state-danger-text; @state-danger-bg);\n}\n\n\n// Reposition feedback icon if label is hidden with \"screenreader only\" state\n.has-feedback label.sr-only ~ .form-control-feedback {\n top: 0;\n}\n\n\n// Help text\n//\n// Apply to any element you wish to create light text for placement immediately\n// below a form control. Use for general help, formatting, or instructional text.\n\n.help-block {\n display: block; // account for any element using help-block\n margin-top: 5px;\n margin-bottom: 10px;\n color: lighten(@text-color, 25%); // lighten the text some for contrast\n}\n\n\n\n// Inline forms\n//\n// Make forms appear inline(-block) by adding the `.form-inline` class. Inline\n// forms begin stacked on extra small (mobile) devices and then go inline when\n// viewports reach <768px.\n//\n// Requires wrapping inputs and labels with `.form-group` for proper display of\n// default HTML form controls and our custom form controls (e.g., input groups).\n//\n// Heads up! This is mixin-ed into `.navbar-form` in navbars.less.\n\n.form-inline {\n\n // Kick in the inline\n @media (min-width: @screen-sm-min) {\n // Inline-block all the things for \"inline\"\n .form-group {\n display: inline-block;\n margin-bottom: 0;\n vertical-align: middle;\n }\n\n // In navbar-form, allow folks to *not* use `.form-group`\n .form-control {\n display: inline-block;\n width: auto; // Prevent labels from stacking above inputs in `.form-group`\n vertical-align: middle;\n }\n\n .input-group {\n display: inline-table;\n vertical-align: middle;\n\n .input-group-addon,\n .input-group-btn,\n .form-control {\n width: auto;\n }\n }\n\n // Input groups need that 100% width though\n .input-group > .form-control {\n width: 100%;\n }\n\n .control-label {\n margin-bottom: 0;\n vertical-align: middle;\n }\n\n // Remove default margin on radios/checkboxes that were used for stacking, and\n // then undo the floating of radios and checkboxes to match (which also avoids\n // a bug in WebKit: https://github.com/twbs/bootstrap/issues/1969).\n .radio,\n .checkbox {\n display: inline-block;\n margin-top: 0;\n margin-bottom: 0;\n vertical-align: middle;\n\n label {\n padding-left: 0;\n }\n }\n .radio input[type=\"radio\"],\n .checkbox input[type=\"checkbox\"] {\n position: relative;\n margin-left: 0;\n }\n\n // Validation states\n //\n // Reposition the icon because it's now within a grid column and columns have\n // `position: relative;` on them. Also accounts for the grid gutter padding.\n .has-feedback .form-control-feedback {\n top: 0;\n }\n }\n}\n\n\n// Horizontal forms\n//\n// Horizontal forms are built on grid classes and allow you to create forms with\n// labels on the left and inputs on the right.\n\n.form-horizontal {\n\n // Consistent vertical alignment of radios and checkboxes\n //\n // Labels also get some reset styles, but that is scoped to a media query below.\n .radio,\n .checkbox,\n .radio-inline,\n .checkbox-inline {\n margin-top: 0;\n margin-bottom: 0;\n padding-top: (@padding-base-vertical + 1); // Default padding plus a border\n }\n // Account for padding we're adding to ensure the alignment and of help text\n // and other content below items\n .radio,\n .checkbox {\n min-height: (@line-height-computed + (@padding-base-vertical + 1));\n }\n\n // Make form groups behave like rows\n .form-group {\n .make-row();\n }\n\n // Reset spacing and right align labels, but scope to media queries so that\n // labels on narrow viewports stack the same as a default form example.\n @media (min-width: @screen-sm-min) {\n .control-label {\n text-align: right;\n margin-bottom: 0;\n padding-top: (@padding-base-vertical + 1); // Default padding plus a border\n }\n }\n\n // Validation states\n //\n // Reposition the icon because it's now within a grid column and columns have\n // `position: relative;` on them. Also accounts for the grid gutter padding.\n .has-feedback .form-control-feedback {\n top: 0;\n right: (@grid-gutter-width / 2);\n }\n\n // Form group sizes\n //\n // Quick utility class for applying `.input-lg` and `.input-sm` styles to the\n // inputs and labels within a `.form-group`.\n .form-group-lg {\n @media (min-width: @screen-sm-min) {\n .control-label {\n padding-top: ((@padding-large-vertical * @line-height-large) + 1);\n }\n }\n .form-control {\n &:extend(.input-lg);\n }\n }\n .form-group-sm {\n @media (min-width: @screen-sm-min) {\n .control-label {\n padding-top: (@padding-small-vertical + 1);\n }\n }\n .form-control {\n &:extend(.input-sm);\n }\n }\n}\n","// Form validation states\n//\n// Used in forms.less to generate the form validation CSS for warnings, errors,\n// and successes.\n\n.form-control-validation(@text-color: #555; @border-color: #ccc; @background-color: #f5f5f5) {\n // Color the label and help text\n .help-block,\n .control-label,\n .radio,\n .checkbox,\n .radio-inline,\n .checkbox-inline {\n color: @text-color;\n }\n // Set the border and box shadow on specific inputs to match\n .form-control {\n border-color: @border-color;\n .box-shadow(inset 0 1px 1px rgba(0,0,0,.075)); // Redeclare so transitions work\n &:focus {\n border-color: darken(@border-color, 10%);\n @shadow: inset 0 1px 1px rgba(0,0,0,.075), 0 0 6px lighten(@border-color, 20%);\n .box-shadow(@shadow);\n }\n }\n // Set validation states also for addons\n .input-group-addon {\n color: @text-color;\n border-color: @border-color;\n background-color: @background-color;\n }\n // Optional feedback icon\n .form-control-feedback {\n color: @text-color;\n }\n}\n\n\n// Form control focus state\n//\n// Generate a customized focus state and for any input with the specified color,\n// which defaults to the `@input-border-focus` variable.\n//\n// We highly encourage you to not customize the default value, but instead use\n// this to tweak colors on an as-needed basis. This aesthetic change is based on\n// WebKit's default styles, but applicable to a wider range of browsers. Its\n// usability and accessibility should be taken into account with any change.\n//\n// Example usage: change the default blue border and shadow to white for better\n// contrast against a dark gray background.\n.form-control-focus(@color: @input-border-focus) {\n @color-rgba: rgba(red(@color), green(@color), blue(@color), .6);\n &:focus {\n border-color: @color;\n outline: 0;\n .box-shadow(~\"inset 0 1px 1px rgba(0,0,0,.075), 0 0 8px @{color-rgba}\");\n }\n}\n\n// Form control sizing\n//\n// Relative text size, padding, and border-radii changes for form controls. For\n// horizontal sizing, wrap controls in the predefined grid classes. `<select>`\n// element gets special love because it's special, and that's a fact!\n.input-size(@input-height; @padding-vertical; @padding-horizontal; @font-size; @line-height; @border-radius) {\n height: @input-height;\n padding: @padding-vertical @padding-horizontal;\n font-size: @font-size;\n line-height: @line-height;\n border-radius: @border-radius;\n\n select& {\n height: @input-height;\n line-height: @input-height;\n }\n\n textarea&,\n select[multiple]& {\n height: auto;\n }\n}\n","//\n// Buttons\n// --------------------------------------------------\n\n\n// Base styles\n// --------------------------------------------------\n\n.btn {\n display: inline-block;\n margin-bottom: 0; // For input.btn\n font-weight: @btn-font-weight;\n text-align: center;\n vertical-align: middle;\n cursor: pointer;\n background-image: none; // Reset unusual Firefox-on-Android default style; see https://github.com/necolas/normalize.css/issues/214\n border: 1px solid transparent;\n white-space: nowrap;\n .button-size(@padding-base-vertical; @padding-base-horizontal; @font-size-base; @line-height-base; @border-radius-base);\n .user-select(none);\n\n &,\n &:active,\n &.active {\n &:focus {\n .tab-focus();\n }\n }\n\n &:hover,\n &:focus {\n color: @btn-default-color;\n text-decoration: none;\n }\n\n &:active,\n &.active {\n outline: 0;\n background-image: none;\n .box-shadow(inset 0 3px 5px rgba(0,0,0,.125));\n }\n\n &.disabled,\n &[disabled],\n fieldset[disabled] & {\n cursor: not-allowed;\n pointer-events: none; // Future-proof disabling of clicks\n .opacity(.65);\n .box-shadow(none);\n }\n}\n\n\n// Alternate buttons\n// --------------------------------------------------\n\n.btn-default {\n .button-variant(@btn-default-color; @btn-default-bg; @btn-default-border);\n}\n.btn-primary {\n .button-variant(@btn-primary-color; @btn-primary-bg; @btn-primary-border);\n}\n// Success appears as green\n.btn-success {\n .button-variant(@btn-success-color; @btn-success-bg; @btn-success-border);\n}\n// Info appears as blue-green\n.btn-info {\n .button-variant(@btn-info-color; @btn-info-bg; @btn-info-border);\n}\n// Warning appears as orange\n.btn-warning {\n .button-variant(@btn-warning-color; @btn-warning-bg; @btn-warning-border);\n}\n// Danger and error appear as red\n.btn-danger {\n .button-variant(@btn-danger-color; @btn-danger-bg; @btn-danger-border);\n}\n\n\n// Link buttons\n// -------------------------\n\n// Make a button look and behave like a link\n.btn-link {\n color: @link-color;\n font-weight: normal;\n cursor: pointer;\n border-radius: 0;\n\n &,\n &:active,\n &[disabled],\n fieldset[disabled] & {\n background-color: transparent;\n .box-shadow(none);\n }\n &,\n &:hover,\n &:focus,\n &:active {\n border-color: transparent;\n }\n &:hover,\n &:focus {\n color: @link-hover-color;\n text-decoration: underline;\n background-color: transparent;\n }\n &[disabled],\n fieldset[disabled] & {\n &:hover,\n &:focus {\n color: @btn-link-disabled-color;\n text-decoration: none;\n }\n }\n}\n\n\n// Button Sizes\n// --------------------------------------------------\n\n.btn-lg {\n // line-height: ensure even-numbered height of button next to large input\n .button-size(@padding-large-vertical; @padding-large-horizontal; @font-size-large; @line-height-large; @border-radius-large);\n}\n.btn-sm {\n // line-height: ensure proper height of button next to small input\n .button-size(@padding-small-vertical; @padding-small-horizontal; @font-size-small; @line-height-small; @border-radius-small);\n}\n.btn-xs {\n .button-size(@padding-xs-vertical; @padding-xs-horizontal; @font-size-small; @line-height-small; @border-radius-small);\n}\n\n\n// Block button\n// --------------------------------------------------\n\n.btn-block {\n display: block;\n width: 100%;\n}\n\n// Vertically space out multiple block buttons\n.btn-block + .btn-block {\n margin-top: 5px;\n}\n\n// Specificity overrides\ninput[type=\"submit\"],\ninput[type=\"reset\"],\ninput[type=\"button\"] {\n &.btn-block {\n width: 100%;\n }\n}\n","// Button variants\n//\n// Easily pump out default styles, as well as :hover, :focus, :active,\n// and disabled options for all buttons\n\n.button-variant(@color; @background; @border) {\n color: @color;\n background-color: @background;\n border-color: @border;\n\n &:hover,\n &:focus,\n &:active,\n &.active,\n .open > .dropdown-toggle& {\n color: @color;\n background-color: darken(@background, 10%);\n border-color: darken(@border, 12%);\n }\n &:active,\n &.active,\n .open > .dropdown-toggle& {\n background-image: none;\n }\n &.disabled,\n &[disabled],\n fieldset[disabled] & {\n &,\n &:hover,\n &:focus,\n &:active,\n &.active {\n background-color: @background;\n border-color: @border;\n }\n }\n\n .badge {\n color: @background;\n background-color: @color;\n }\n}\n\n// Button sizes\n.button-size(@padding-vertical; @padding-horizontal; @font-size; @line-height; @border-radius) {\n padding: @padding-vertical @padding-horizontal;\n font-size: @font-size;\n line-height: @line-height;\n border-radius: @border-radius;\n}\n","// Opacity\n\n.opacity(@opacity) {\n opacity: @opacity;\n // IE8 filter\n @opacity-ie: (@opacity * 100);\n filter: ~\"alpha(opacity=@{opacity-ie})\";\n}\n","//\n// Component animations\n// --------------------------------------------------\n\n// Heads up!\n//\n// We don't use the `.opacity()` mixin here since it causes a bug with text\n// fields in IE7-8. Source: https://github.com/twbs/bootstrap/pull/3552.\n\n.fade {\n opacity: 0;\n .transition(opacity .15s linear);\n &.in {\n opacity: 1;\n }\n}\n\n.collapse {\n display: none;\n\n &.in { display: block; }\n tr&.in { display: table-row; }\n tbody&.in { display: table-row-group; }\n}\n\n.collapsing {\n position: relative;\n height: 0;\n overflow: hidden;\n .transition(height .35s ease);\n}\n","//\n// Dropdown menus\n// --------------------------------------------------\n\n\n// Dropdown arrow/caret\n.caret {\n display: inline-block;\n width: 0;\n height: 0;\n margin-left: 2px;\n vertical-align: middle;\n border-top: @caret-width-base solid;\n border-right: @caret-width-base solid transparent;\n border-left: @caret-width-base solid transparent;\n}\n\n// The dropdown wrapper (div)\n.dropdown {\n position: relative;\n}\n\n// Prevent the focus on the dropdown toggle when closing dropdowns\n.dropdown-toggle:focus {\n outline: 0;\n}\n\n// The dropdown menu (ul)\n.dropdown-menu {\n position: absolute;\n top: 100%;\n left: 0;\n z-index: @zindex-dropdown;\n display: none; // none by default, but block on \"open\" of the menu\n float: left;\n min-width: 160px;\n padding: 5px 0;\n margin: 2px 0 0; // override default ul\n list-style: none;\n font-size: @font-size-base;\n text-align: left; // Ensures proper alignment if parent has it changed (e.g., modal footer)\n background-color: @dropdown-bg;\n border: 1px solid @dropdown-fallback-border; // IE8 fallback\n border: 1px solid @dropdown-border;\n border-radius: @border-radius-base;\n .box-shadow(0 6px 12px rgba(0,0,0,.175));\n background-clip: padding-box;\n\n // Aligns the dropdown menu to right\n //\n // Deprecated as of 3.1.0 in favor of `.dropdown-menu-[dir]`\n &.pull-right {\n right: 0;\n left: auto;\n }\n\n // Dividers (basically an hr) within the dropdown\n .divider {\n .nav-divider(@dropdown-divider-bg);\n }\n\n // Links within the dropdown menu\n > li > a {\n display: block;\n padding: 3px 20px;\n clear: both;\n font-weight: normal;\n line-height: @line-height-base;\n color: @dropdown-link-color;\n white-space: nowrap; // prevent links from randomly breaking onto new lines\n }\n}\n\n// Hover/Focus state\n.dropdown-menu > li > a {\n &:hover,\n &:focus {\n text-decoration: none;\n color: @dropdown-link-hover-color;\n background-color: @dropdown-link-hover-bg;\n }\n}\n\n// Active state\n.dropdown-menu > .active > a {\n &,\n &:hover,\n &:focus {\n color: @dropdown-link-active-color;\n text-decoration: none;\n outline: 0;\n background-color: @dropdown-link-active-bg;\n }\n}\n\n// Disabled state\n//\n// Gray out text and ensure the hover/focus state remains gray\n\n.dropdown-menu > .disabled > a {\n &,\n &:hover,\n &:focus {\n color: @dropdown-link-disabled-color;\n }\n}\n// Nuke hover/focus effects\n.dropdown-menu > .disabled > a {\n &:hover,\n &:focus {\n text-decoration: none;\n background-color: transparent;\n background-image: none; // Remove CSS gradient\n .reset-filter();\n cursor: not-allowed;\n }\n}\n\n// Open state for the dropdown\n.open {\n // Show the menu\n > .dropdown-menu {\n display: block;\n }\n\n // Remove the outline when :focus is triggered\n > a {\n outline: 0;\n }\n}\n\n// Menu positioning\n//\n// Add extra class to `.dropdown-menu` to flip the alignment of the dropdown\n// menu with the parent.\n.dropdown-menu-right {\n left: auto; // Reset the default from `.dropdown-menu`\n right: 0;\n}\n// With v3, we enabled auto-flipping if you have a dropdown within a right\n// aligned nav component. To enable the undoing of that, we provide an override\n// to restore the default dropdown menu alignment.\n//\n// This is only for left-aligning a dropdown menu within a `.navbar-right` or\n// `.pull-right` nav component.\n.dropdown-menu-left {\n left: 0;\n right: auto;\n}\n\n// Dropdown section headers\n.dropdown-header {\n display: block;\n padding: 3px 20px;\n font-size: @font-size-small;\n line-height: @line-height-base;\n color: @dropdown-header-color;\n white-space: nowrap; // as with > li > a\n}\n\n// Backdrop to catch body clicks on mobile, etc.\n.dropdown-backdrop {\n position: fixed;\n left: 0;\n right: 0;\n bottom: 0;\n top: 0;\n z-index: (@zindex-dropdown - 10);\n}\n\n// Right aligned dropdowns\n.pull-right > .dropdown-menu {\n right: 0;\n left: auto;\n}\n\n// Allow for dropdowns to go bottom up (aka, dropup-menu)\n//\n// Just add .dropup after the standard .dropdown class and you're set, bro.\n// TODO: abstract this so that the navbar fixed styles are not placed here?\n\n.dropup,\n.navbar-fixed-bottom .dropdown {\n // Reverse the caret\n .caret {\n border-top: 0;\n border-bottom: @caret-width-base solid;\n content: \"\";\n }\n // Different positioning for bottom up menu\n .dropdown-menu {\n top: auto;\n bottom: 100%;\n margin-bottom: 1px;\n }\n}\n\n\n// Component alignment\n//\n// Reiterate per navbar.less and the modified component alignment there.\n\n@media (min-width: @grid-float-breakpoint) {\n .navbar-right {\n .dropdown-menu {\n .dropdown-menu-right();\n }\n // Necessary for overrides of the default right aligned menu.\n // Will remove come v4 in all likelihood.\n .dropdown-menu-left {\n .dropdown-menu-left();\n }\n }\n}\n\n","// Horizontal dividers\n//\n// Dividers (basically an hr) within dropdowns and nav lists\n\n.nav-divider(@color: #e5e5e5) {\n height: 1px;\n margin: ((@line-height-computed / 2) - 1) 0;\n overflow: hidden;\n background-color: @color;\n}\n","// Reset filters for IE\n//\n// When you need to remove a gradient background, do not forget to use this to reset\n// the IE filter for IE9 and below.\n\n.reset-filter() {\n filter: e(%(\"progid:DXImageTransform.Microsoft.gradient(enabled = false)\"));\n}\n","//\n// Button groups\n// --------------------------------------------------\n\n// Make the div behave like a button\n.btn-group,\n.btn-group-vertical {\n position: relative;\n display: inline-block;\n vertical-align: middle; // match .btn alignment given font-size hack above\n > .btn {\n position: relative;\n float: left;\n // Bring the \"active\" button to the front\n &:hover,\n &:focus,\n &:active,\n &.active {\n z-index: 2;\n }\n &:focus {\n // Remove focus outline when dropdown JS adds it after closing the menu\n outline: 0;\n }\n }\n}\n\n// Prevent double borders when buttons are next to each other\n.btn-group {\n .btn + .btn,\n .btn + .btn-group,\n .btn-group + .btn,\n .btn-group + .btn-group {\n margin-left: -1px;\n }\n}\n\n// Optional: Group multiple button groups together for a toolbar\n.btn-toolbar {\n margin-left: -5px; // Offset the first child's margin\n &:extend(.clearfix all);\n\n .btn-group,\n .input-group {\n float: left;\n }\n > .btn,\n > .btn-group,\n > .input-group {\n margin-left: 5px;\n }\n}\n\n.btn-group > .btn:not(:first-child):not(:last-child):not(.dropdown-toggle) {\n border-radius: 0;\n}\n\n// Set corners individual because sometimes a single button can be in a .btn-group and we need :first-child and :last-child to both match\n.btn-group > .btn:first-child {\n margin-left: 0;\n &:not(:last-child):not(.dropdown-toggle) {\n .border-right-radius(0);\n }\n}\n// Need .dropdown-toggle since :last-child doesn't apply given a .dropdown-menu immediately after it\n.btn-group > .btn:last-child:not(:first-child),\n.btn-group > .dropdown-toggle:not(:first-child) {\n .border-left-radius(0);\n}\n\n// Custom edits for including btn-groups within btn-groups (useful for including dropdown buttons within a btn-group)\n.btn-group > .btn-group {\n float: left;\n}\n.btn-group > .btn-group:not(:first-child):not(:last-child) > .btn {\n border-radius: 0;\n}\n.btn-group > .btn-group:first-child {\n > .btn:last-child,\n > .dropdown-toggle {\n .border-right-radius(0);\n }\n}\n.btn-group > .btn-group:last-child > .btn:first-child {\n .border-left-radius(0);\n}\n\n// On active and open, don't show outline\n.btn-group .dropdown-toggle:active,\n.btn-group.open .dropdown-toggle {\n outline: 0;\n}\n\n\n// Sizing\n//\n// Remix the default button sizing classes into new ones for easier manipulation.\n\n.btn-group-xs > .btn { &:extend(.btn-xs); }\n.btn-group-sm > .btn { &:extend(.btn-sm); }\n.btn-group-lg > .btn { &:extend(.btn-lg); }\n\n\n// Split button dropdowns\n// ----------------------\n\n// Give the line between buttons some depth\n.btn-group > .btn + .dropdown-toggle {\n padding-left: 8px;\n padding-right: 8px;\n}\n.btn-group > .btn-lg + .dropdown-toggle {\n padding-left: 12px;\n padding-right: 12px;\n}\n\n// The clickable button for toggling the menu\n// Remove the gradient and set the same inset shadow as the :active state\n.btn-group.open .dropdown-toggle {\n .box-shadow(inset 0 3px 5px rgba(0,0,0,.125));\n\n // Show no shadow for `.btn-link` since it has no other button styles.\n &.btn-link {\n .box-shadow(none);\n }\n}\n\n\n// Reposition the caret\n.btn .caret {\n margin-left: 0;\n}\n// Carets in other button sizes\n.btn-lg .caret {\n border-width: @caret-width-large @caret-width-large 0;\n border-bottom-width: 0;\n}\n// Upside down carets for .dropup\n.dropup .btn-lg .caret {\n border-width: 0 @caret-width-large @caret-width-large;\n}\n\n\n// Vertical button groups\n// ----------------------\n\n.btn-group-vertical {\n > .btn,\n > .btn-group,\n > .btn-group > .btn {\n display: block;\n float: none;\n width: 100%;\n max-width: 100%;\n }\n\n // Clear floats so dropdown menus can be properly placed\n > .btn-group {\n &:extend(.clearfix all);\n > .btn {\n float: none;\n }\n }\n\n > .btn + .btn,\n > .btn + .btn-group,\n > .btn-group + .btn,\n > .btn-group + .btn-group {\n margin-top: -1px;\n margin-left: 0;\n }\n}\n\n.btn-group-vertical > .btn {\n &:not(:first-child):not(:last-child) {\n border-radius: 0;\n }\n &:first-child:not(:last-child) {\n border-top-right-radius: @border-radius-base;\n .border-bottom-radius(0);\n }\n &:last-child:not(:first-child) {\n border-bottom-left-radius: @border-radius-base;\n .border-top-radius(0);\n }\n}\n.btn-group-vertical > .btn-group:not(:first-child):not(:last-child) > .btn {\n border-radius: 0;\n}\n.btn-group-vertical > .btn-group:first-child:not(:last-child) {\n > .btn:last-child,\n > .dropdown-toggle {\n .border-bottom-radius(0);\n }\n}\n.btn-group-vertical > .btn-group:last-child:not(:first-child) > .btn:first-child {\n .border-top-radius(0);\n}\n\n\n\n// Justified button groups\n// ----------------------\n\n.btn-group-justified {\n display: table;\n width: 100%;\n table-layout: fixed;\n border-collapse: separate;\n > .btn,\n > .btn-group {\n float: none;\n display: table-cell;\n width: 1%;\n }\n > .btn-group .btn {\n width: 100%;\n }\n\n > .btn-group .dropdown-menu {\n left: auto;\n }\n}\n\n\n// Checkbox and radio options\n//\n// In order to support the browser's form validation feedback, powered by the\n// `required` attribute, we have to \"hide\" the inputs via `opacity`. We cannot\n// use `display: none;` or `visibility: hidden;` as that also hides the popover.\n// This way, we ensure a DOM element is visible to position the popover from.\n//\n// See https://github.com/twbs/bootstrap/pull/12794 for more.\n\n[data-toggle=\"buttons\"] > .btn > input[type=\"radio\"],\n[data-toggle=\"buttons\"] > .btn > input[type=\"checkbox\"] {\n position: absolute;\n z-index: -1;\n .opacity(0);\n}\n","// Single side border-radius\n\n.border-top-radius(@radius) {\n border-top-right-radius: @radius;\n border-top-left-radius: @radius;\n}\n.border-right-radius(@radius) {\n border-bottom-right-radius: @radius;\n border-top-right-radius: @radius;\n}\n.border-bottom-radius(@radius) {\n border-bottom-right-radius: @radius;\n border-bottom-left-radius: @radius;\n}\n.border-left-radius(@radius) {\n border-bottom-left-radius: @radius;\n border-top-left-radius: @radius;\n}\n","//\n// Input groups\n// --------------------------------------------------\n\n// Base styles\n// -------------------------\n.input-group {\n position: relative; // For dropdowns\n display: table;\n border-collapse: separate; // prevent input groups from inheriting border styles from table cells when placed within a table\n\n // Undo padding and float of grid classes\n &[class*=\"col-\"] {\n float: none;\n padding-left: 0;\n padding-right: 0;\n }\n\n .form-control {\n // Ensure that the input is always above the *appended* addon button for\n // proper border colors.\n position: relative;\n z-index: 2;\n\n // IE9 fubars the placeholder attribute in text inputs and the arrows on\n // select elements in input groups. To fix it, we float the input. Details:\n // https://github.com/twbs/bootstrap/issues/11561#issuecomment-28936855\n float: left;\n\n width: 100%;\n margin-bottom: 0;\n }\n}\n\n// Sizing options\n//\n// Remix the default form control sizing classes into new ones for easier\n// manipulation.\n\n.input-group-lg > .form-control,\n.input-group-lg > .input-group-addon,\n.input-group-lg > .input-group-btn > .btn {\n .input-lg();\n}\n.input-group-sm > .form-control,\n.input-group-sm > .input-group-addon,\n.input-group-sm > .input-group-btn > .btn {\n .input-sm();\n}\n\n\n// Display as table-cell\n// -------------------------\n.input-group-addon,\n.input-group-btn,\n.input-group .form-control {\n display: table-cell;\n\n &:not(:first-child):not(:last-child) {\n border-radius: 0;\n }\n}\n// Addon and addon wrapper for buttons\n.input-group-addon,\n.input-group-btn {\n width: 1%;\n white-space: nowrap;\n vertical-align: middle; // Match the inputs\n}\n\n// Text input groups\n// -------------------------\n.input-group-addon {\n padding: @padding-base-vertical @padding-base-horizontal;\n font-size: @font-size-base;\n font-weight: normal;\n line-height: 1;\n color: @input-color;\n text-align: center;\n background-color: @input-group-addon-bg;\n border: 1px solid @input-group-addon-border-color;\n border-radius: @border-radius-base;\n\n // Sizing\n &.input-sm {\n padding: @padding-small-vertical @padding-small-horizontal;\n font-size: @font-size-small;\n border-radius: @border-radius-small;\n }\n &.input-lg {\n padding: @padding-large-vertical @padding-large-horizontal;\n font-size: @font-size-large;\n border-radius: @border-radius-large;\n }\n\n // Nuke default margins from checkboxes and radios to vertically center within.\n input[type=\"radio\"],\n input[type=\"checkbox\"] {\n margin-top: 0;\n }\n}\n\n// Reset rounded corners\n.input-group .form-control:first-child,\n.input-group-addon:first-child,\n.input-group-btn:first-child > .btn,\n.input-group-btn:first-child > .btn-group > .btn,\n.input-group-btn:first-child > .dropdown-toggle,\n.input-group-btn:last-child > .btn:not(:last-child):not(.dropdown-toggle),\n.input-group-btn:last-child > .btn-group:not(:last-child) > .btn {\n .border-right-radius(0);\n}\n.input-group-addon:first-child {\n border-right: 0;\n}\n.input-group .form-control:last-child,\n.input-group-addon:last-child,\n.input-group-btn:last-child > .btn,\n.input-group-btn:last-child > .btn-group > .btn,\n.input-group-btn:last-child > .dropdown-toggle,\n.input-group-btn:first-child > .btn:not(:first-child),\n.input-group-btn:first-child > .btn-group:not(:first-child) > .btn {\n .border-left-radius(0);\n}\n.input-group-addon:last-child {\n border-left: 0;\n}\n\n// Button input groups\n// -------------------------\n.input-group-btn {\n position: relative;\n // Jankily prevent input button groups from wrapping with `white-space` and\n // `font-size` in combination with `inline-block` on buttons.\n font-size: 0;\n white-space: nowrap;\n\n // Negative margin for spacing, position for bringing hovered/focused/actived\n // element above the siblings.\n > .btn {\n position: relative;\n + .btn {\n margin-left: -1px;\n }\n // Bring the \"active\" button to the front\n &:hover,\n &:focus,\n &:active {\n z-index: 2;\n }\n }\n\n // Negative margin to only have a 1px border between the two\n &:first-child {\n > .btn,\n > .btn-group {\n margin-right: -1px;\n }\n }\n &:last-child {\n > .btn,\n > .btn-group {\n margin-left: -1px;\n }\n }\n}\n","//\n// Navs\n// --------------------------------------------------\n\n\n// Base class\n// --------------------------------------------------\n\n.nav {\n margin-bottom: 0;\n padding-left: 0; // Override default ul/ol\n list-style: none;\n &:extend(.clearfix all);\n\n > li {\n position: relative;\n display: block;\n\n > a {\n position: relative;\n display: block;\n padding: @nav-link-padding;\n &:hover,\n &:focus {\n text-decoration: none;\n background-color: @nav-link-hover-bg;\n }\n }\n\n // Disabled state sets text to gray and nukes hover/tab effects\n &.disabled > a {\n color: @nav-disabled-link-color;\n\n &:hover,\n &:focus {\n color: @nav-disabled-link-hover-color;\n text-decoration: none;\n background-color: transparent;\n cursor: not-allowed;\n }\n }\n }\n\n // Open dropdowns\n .open > a {\n &,\n &:hover,\n &:focus {\n background-color: @nav-link-hover-bg;\n border-color: @link-color;\n }\n }\n\n // Nav dividers (deprecated with v3.0.1)\n //\n // This should have been removed in v3 with the dropping of `.nav-list`, but\n // we missed it. We don't currently support this anywhere, but in the interest\n // of maintaining backward compatibility in case you use it, it's deprecated.\n .nav-divider {\n .nav-divider();\n }\n\n // Prevent IE8 from misplacing imgs\n //\n // See https://github.com/h5bp/html5-boilerplate/issues/984#issuecomment-3985989\n > li > a > img {\n max-width: none;\n }\n}\n\n\n// Tabs\n// -------------------------\n\n// Give the tabs something to sit on\n.nav-tabs {\n border-bottom: 1px solid @nav-tabs-border-color;\n > li {\n float: left;\n // Make the list-items overlay the bottom border\n margin-bottom: -1px;\n\n // Actual tabs (as links)\n > a {\n margin-right: 2px;\n line-height: @line-height-base;\n border: 1px solid transparent;\n border-radius: @border-radius-base @border-radius-base 0 0;\n &:hover {\n border-color: @nav-tabs-link-hover-border-color @nav-tabs-link-hover-border-color @nav-tabs-border-color;\n }\n }\n\n // Active state, and its :hover to override normal :hover\n &.active > a {\n &,\n &:hover,\n &:focus {\n color: @nav-tabs-active-link-hover-color;\n background-color: @nav-tabs-active-link-hover-bg;\n border: 1px solid @nav-tabs-active-link-hover-border-color;\n border-bottom-color: transparent;\n cursor: default;\n }\n }\n }\n // pulling this in mainly for less shorthand\n &.nav-justified {\n .nav-justified();\n .nav-tabs-justified();\n }\n}\n\n\n// Pills\n// -------------------------\n.nav-pills {\n > li {\n float: left;\n\n // Links rendered as pills\n > a {\n border-radius: @nav-pills-border-radius;\n }\n + li {\n margin-left: 2px;\n }\n\n // Active state\n &.active > a {\n &,\n &:hover,\n &:focus {\n color: @nav-pills-active-link-hover-color;\n background-color: @nav-pills-active-link-hover-bg;\n }\n }\n }\n}\n\n\n// Stacked pills\n.nav-stacked {\n > li {\n float: none;\n + li {\n margin-top: 2px;\n margin-left: 0; // no need for this gap between nav items\n }\n }\n}\n\n\n// Nav variations\n// --------------------------------------------------\n\n// Justified nav links\n// -------------------------\n\n.nav-justified {\n width: 100%;\n\n > li {\n float: none;\n > a {\n text-align: center;\n margin-bottom: 5px;\n }\n }\n\n > .dropdown .dropdown-menu {\n top: auto;\n left: auto;\n }\n\n @media (min-width: @screen-sm-min) {\n > li {\n display: table-cell;\n width: 1%;\n > a {\n margin-bottom: 0;\n }\n }\n }\n}\n\n// Move borders to anchors instead of bottom of list\n//\n// Mixin for adding on top the shared `.nav-justified` styles for our tabs\n.nav-tabs-justified {\n border-bottom: 0;\n\n > li > a {\n // Override margin from .nav-tabs\n margin-right: 0;\n border-radius: @border-radius-base;\n }\n\n > .active > a,\n > .active > a:hover,\n > .active > a:focus {\n border: 1px solid @nav-tabs-justified-link-border-color;\n }\n\n @media (min-width: @screen-sm-min) {\n > li > a {\n border-bottom: 1px solid @nav-tabs-justified-link-border-color;\n border-radius: @border-radius-base @border-radius-base 0 0;\n }\n > .active > a,\n > .active > a:hover,\n > .active > a:focus {\n border-bottom-color: @nav-tabs-justified-active-link-border-color;\n }\n }\n}\n\n\n// Tabbable tabs\n// -------------------------\n\n// Hide tabbable panes to start, show them when `.active`\n.tab-content {\n > .tab-pane {\n display: none;\n }\n > .active {\n display: block;\n }\n}\n\n\n// Dropdowns\n// -------------------------\n\n// Specific dropdowns\n.nav-tabs .dropdown-menu {\n // make dropdown border overlap tab border\n margin-top: -1px;\n // Remove the top rounded corners here since there is a hard edge above the menu\n .border-top-radius(0);\n}\n","//\n// Navbars\n// --------------------------------------------------\n\n\n// Wrapper and base class\n//\n// Provide a static navbar from which we expand to create full-width, fixed, and\n// other navbar variations.\n\n.navbar {\n position: relative;\n min-height: @navbar-height; // Ensure a navbar always shows (e.g., without a .navbar-brand in collapsed mode)\n margin-bottom: @navbar-margin-bottom;\n border: 1px solid transparent;\n\n // Prevent floats from breaking the navbar\n &:extend(.clearfix all);\n\n @media (min-width: @grid-float-breakpoint) {\n border-radius: @navbar-border-radius;\n }\n}\n\n\n// Navbar heading\n//\n// Groups `.navbar-brand` and `.navbar-toggle` into a single component for easy\n// styling of responsive aspects.\n\n.navbar-header {\n &:extend(.clearfix all);\n\n @media (min-width: @grid-float-breakpoint) {\n float: left;\n }\n}\n\n\n// Navbar collapse (body)\n//\n// Group your navbar content into this for easy collapsing and expanding across\n// various device sizes. By default, this content is collapsed when <768px, but\n// will expand past that for a horizontal display.\n//\n// To start (on mobile devices) the navbar links, forms, and buttons are stacked\n// vertically and include a `max-height` to overflow in case you have too much\n// content for the user's viewport.\n\n.navbar-collapse {\n overflow-x: visible;\n padding-right: @navbar-padding-horizontal;\n padding-left: @navbar-padding-horizontal;\n border-top: 1px solid transparent;\n box-shadow: inset 0 1px 0 rgba(255,255,255,.1);\n &:extend(.clearfix all);\n -webkit-overflow-scrolling: touch;\n\n &.in {\n overflow-y: auto;\n }\n\n @media (min-width: @grid-float-breakpoint) {\n width: auto;\n border-top: 0;\n box-shadow: none;\n\n &.collapse {\n display: block !important;\n height: auto !important;\n padding-bottom: 0; // Override default setting\n overflow: visible !important;\n }\n\n &.in {\n overflow-y: visible;\n }\n\n // Undo the collapse side padding for navbars with containers to ensure\n // alignment of right-aligned contents.\n .navbar-fixed-top &,\n .navbar-static-top &,\n .navbar-fixed-bottom & {\n padding-left: 0;\n padding-right: 0;\n }\n }\n}\n\n.navbar-fixed-top,\n.navbar-fixed-bottom {\n .navbar-collapse {\n max-height: @navbar-collapse-max-height;\n\n @media (max-width: @screen-xs-min) and (orientation: landscape) {\n max-height: 200px;\n }\n }\n}\n\n\n// Both navbar header and collapse\n//\n// When a container is present, change the behavior of the header and collapse.\n\n.container,\n.container-fluid {\n > .navbar-header,\n > .navbar-collapse {\n margin-right: -@navbar-padding-horizontal;\n margin-left: -@navbar-padding-horizontal;\n\n @media (min-width: @grid-float-breakpoint) {\n margin-right: 0;\n margin-left: 0;\n }\n }\n}\n\n\n//\n// Navbar alignment options\n//\n// Display the navbar across the entirety of the page or fixed it to the top or\n// bottom of the page.\n\n// Static top (unfixed, but 100% wide) navbar\n.navbar-static-top {\n z-index: @zindex-navbar;\n border-width: 0 0 1px;\n\n @media (min-width: @grid-float-breakpoint) {\n border-radius: 0;\n }\n}\n\n// Fix the top/bottom navbars when screen real estate supports it\n.navbar-fixed-top,\n.navbar-fixed-bottom {\n position: fixed;\n right: 0;\n left: 0;\n z-index: @zindex-navbar-fixed;\n .translate3d(0, 0, 0);\n\n // Undo the rounded corners\n @media (min-width: @grid-float-breakpoint) {\n border-radius: 0;\n }\n}\n.navbar-fixed-top {\n top: 0;\n border-width: 0 0 1px;\n}\n.navbar-fixed-bottom {\n bottom: 0;\n margin-bottom: 0; // override .navbar defaults\n border-width: 1px 0 0;\n}\n\n\n// Brand/project name\n\n.navbar-brand {\n float: left;\n padding: @navbar-padding-vertical @navbar-padding-horizontal;\n font-size: @font-size-large;\n line-height: @line-height-computed;\n height: @navbar-height;\n\n &:hover,\n &:focus {\n text-decoration: none;\n }\n\n @media (min-width: @grid-float-breakpoint) {\n .navbar > .container &,\n .navbar > .container-fluid & {\n margin-left: -@navbar-padding-horizontal;\n }\n }\n}\n\n\n// Navbar toggle\n//\n// Custom button for toggling the `.navbar-collapse`, powered by the collapse\n// JavaScript plugin.\n\n.navbar-toggle {\n position: relative;\n float: right;\n margin-right: @navbar-padding-horizontal;\n padding: 9px 10px;\n .navbar-vertical-align(34px);\n background-color: transparent;\n background-image: none; // Reset unusual Firefox-on-Android default style; see https://github.com/necolas/normalize.css/issues/214\n border: 1px solid transparent;\n border-radius: @border-radius-base;\n\n // We remove the `outline` here, but later compensate by attaching `:hover`\n // styles to `:focus`.\n &:focus {\n outline: 0;\n }\n\n // Bars\n .icon-bar {\n display: block;\n width: 22px;\n height: 2px;\n border-radius: 1px;\n }\n .icon-bar + .icon-bar {\n margin-top: 4px;\n }\n\n @media (min-width: @grid-float-breakpoint) {\n display: none;\n }\n}\n\n\n// Navbar nav links\n//\n// Builds on top of the `.nav` components with its own modifier class to make\n// the nav the full height of the horizontal nav (above 768px).\n\n.navbar-nav {\n margin: (@navbar-padding-vertical / 2) -@navbar-padding-horizontal;\n\n > li > a {\n padding-top: 10px;\n padding-bottom: 10px;\n line-height: @line-height-computed;\n }\n\n @media (max-width: @grid-float-breakpoint-max) {\n // Dropdowns get custom display when collapsed\n .open .dropdown-menu {\n position: static;\n float: none;\n width: auto;\n margin-top: 0;\n background-color: transparent;\n border: 0;\n box-shadow: none;\n > li > a,\n .dropdown-header {\n padding: 5px 15px 5px 25px;\n }\n > li > a {\n line-height: @line-height-computed;\n &:hover,\n &:focus {\n background-image: none;\n }\n }\n }\n }\n\n // Uncollapse the nav\n @media (min-width: @grid-float-breakpoint) {\n float: left;\n margin: 0;\n\n > li {\n float: left;\n > a {\n padding-top: @navbar-padding-vertical;\n padding-bottom: @navbar-padding-vertical;\n }\n }\n\n &.navbar-right:last-child {\n margin-right: -@navbar-padding-horizontal;\n }\n }\n}\n\n\n// Component alignment\n//\n// Repurpose the pull utilities as their own navbar utilities to avoid specificity\n// issues with parents and chaining. Only do this when the navbar is uncollapsed\n// though so that navbar contents properly stack and align in mobile.\n\n@media (min-width: @grid-float-breakpoint) {\n .navbar-left { .pull-left(); }\n .navbar-right { .pull-right(); }\n}\n\n\n// Navbar form\n//\n// Extension of the `.form-inline` with some extra flavor for optimum display in\n// our navbars.\n\n.navbar-form {\n margin-left: -@navbar-padding-horizontal;\n margin-right: -@navbar-padding-horizontal;\n padding: 10px @navbar-padding-horizontal;\n border-top: 1px solid transparent;\n border-bottom: 1px solid transparent;\n @shadow: inset 0 1px 0 rgba(255,255,255,.1), 0 1px 0 rgba(255,255,255,.1);\n .box-shadow(@shadow);\n\n // Mixin behavior for optimum display\n .form-inline();\n\n .form-group {\n @media (max-width: @grid-float-breakpoint-max) {\n margin-bottom: 5px;\n }\n }\n\n // Vertically center in expanded, horizontal navbar\n .navbar-vertical-align(@input-height-base);\n\n // Undo 100% width for pull classes\n @media (min-width: @grid-float-breakpoint) {\n width: auto;\n border: 0;\n margin-left: 0;\n margin-right: 0;\n padding-top: 0;\n padding-bottom: 0;\n .box-shadow(none);\n\n // Outdent the form if last child to line up with content down the page\n &.navbar-right:last-child {\n margin-right: -@navbar-padding-horizontal;\n }\n }\n}\n\n\n// Dropdown menus\n\n// Menu position and menu carets\n.navbar-nav > li > .dropdown-menu {\n margin-top: 0;\n .border-top-radius(0);\n}\n// Menu position and menu caret support for dropups via extra dropup class\n.navbar-fixed-bottom .navbar-nav > li > .dropdown-menu {\n .border-bottom-radius(0);\n}\n\n\n// Buttons in navbars\n//\n// Vertically center a button within a navbar (when *not* in a form).\n\n.navbar-btn {\n .navbar-vertical-align(@input-height-base);\n\n &.btn-sm {\n .navbar-vertical-align(@input-height-small);\n }\n &.btn-xs {\n .navbar-vertical-align(22);\n }\n}\n\n\n// Text in navbars\n//\n// Add a class to make any element properly align itself vertically within the navbars.\n\n.navbar-text {\n .navbar-vertical-align(@line-height-computed);\n\n @media (min-width: @grid-float-breakpoint) {\n float: left;\n margin-left: @navbar-padding-horizontal;\n margin-right: @navbar-padding-horizontal;\n\n // Outdent the form if last child to line up with content down the page\n &.navbar-right:last-child {\n margin-right: 0;\n }\n }\n}\n\n// Alternate navbars\n// --------------------------------------------------\n\n// Default navbar\n.navbar-default {\n background-color: @navbar-default-bg;\n border-color: @navbar-default-border;\n\n .navbar-brand {\n color: @navbar-default-brand-color;\n &:hover,\n &:focus {\n color: @navbar-default-brand-hover-color;\n background-color: @navbar-default-brand-hover-bg;\n }\n }\n\n .navbar-text {\n color: @navbar-default-color;\n }\n\n .navbar-nav {\n > li > a {\n color: @navbar-default-link-color;\n\n &:hover,\n &:focus {\n color: @navbar-default-link-hover-color;\n background-color: @navbar-default-link-hover-bg;\n }\n }\n > .active > a {\n &,\n &:hover,\n &:focus {\n color: @navbar-default-link-active-color;\n background-color: @navbar-default-link-active-bg;\n }\n }\n > .disabled > a {\n &,\n &:hover,\n &:focus {\n color: @navbar-default-link-disabled-color;\n background-color: @navbar-default-link-disabled-bg;\n }\n }\n }\n\n .navbar-toggle {\n border-color: @navbar-default-toggle-border-color;\n &:hover,\n &:focus {\n background-color: @navbar-default-toggle-hover-bg;\n }\n .icon-bar {\n background-color: @navbar-default-toggle-icon-bar-bg;\n }\n }\n\n .navbar-collapse,\n .navbar-form {\n border-color: @navbar-default-border;\n }\n\n // Dropdown menu items\n .navbar-nav {\n // Remove background color from open dropdown\n > .open > a {\n &,\n &:hover,\n &:focus {\n background-color: @navbar-default-link-active-bg;\n color: @navbar-default-link-active-color;\n }\n }\n\n @media (max-width: @grid-float-breakpoint-max) {\n // Dropdowns get custom display when collapsed\n .open .dropdown-menu {\n > li > a {\n color: @navbar-default-link-color;\n &:hover,\n &:focus {\n color: @navbar-default-link-hover-color;\n background-color: @navbar-default-link-hover-bg;\n }\n }\n > .active > a {\n &,\n &:hover,\n &:focus {\n color: @navbar-default-link-active-color;\n background-color: @navbar-default-link-active-bg;\n }\n }\n > .disabled > a {\n &,\n &:hover,\n &:focus {\n color: @navbar-default-link-disabled-color;\n background-color: @navbar-default-link-disabled-bg;\n }\n }\n }\n }\n }\n\n\n // Links in navbars\n //\n // Add a class to ensure links outside the navbar nav are colored correctly.\n\n .navbar-link {\n color: @navbar-default-link-color;\n &:hover {\n color: @navbar-default-link-hover-color;\n }\n }\n\n .btn-link {\n color: @navbar-default-link-color;\n &:hover,\n &:focus {\n color: @navbar-default-link-hover-color;\n }\n &[disabled],\n fieldset[disabled] & {\n &:hover,\n &:focus {\n color: @navbar-default-link-disabled-color;\n }\n }\n }\n}\n\n// Inverse navbar\n\n.navbar-inverse {\n background-color: @navbar-inverse-bg;\n border-color: @navbar-inverse-border;\n\n .navbar-brand {\n color: @navbar-inverse-brand-color;\n &:hover,\n &:focus {\n color: @navbar-inverse-brand-hover-color;\n background-color: @navbar-inverse-brand-hover-bg;\n }\n }\n\n .navbar-text {\n color: @navbar-inverse-color;\n }\n\n .navbar-nav {\n > li > a {\n color: @navbar-inverse-link-color;\n\n &:hover,\n &:focus {\n color: @navbar-inverse-link-hover-color;\n background-color: @navbar-inverse-link-hover-bg;\n }\n }\n > .active > a {\n &,\n &:hover,\n &:focus {\n color: @navbar-inverse-link-active-color;\n background-color: @navbar-inverse-link-active-bg;\n }\n }\n > .disabled > a {\n &,\n &:hover,\n &:focus {\n color: @navbar-inverse-link-disabled-color;\n background-color: @navbar-inverse-link-disabled-bg;\n }\n }\n }\n\n // Darken the responsive nav toggle\n .navbar-toggle {\n border-color: @navbar-inverse-toggle-border-color;\n &:hover,\n &:focus {\n background-color: @navbar-inverse-toggle-hover-bg;\n }\n .icon-bar {\n background-color: @navbar-inverse-toggle-icon-bar-bg;\n }\n }\n\n .navbar-collapse,\n .navbar-form {\n border-color: darken(@navbar-inverse-bg, 7%);\n }\n\n // Dropdowns\n .navbar-nav {\n > .open > a {\n &,\n &:hover,\n &:focus {\n background-color: @navbar-inverse-link-active-bg;\n color: @navbar-inverse-link-active-color;\n }\n }\n\n @media (max-width: @grid-float-breakpoint-max) {\n // Dropdowns get custom display\n .open .dropdown-menu {\n > .dropdown-header {\n border-color: @navbar-inverse-border;\n }\n .divider {\n background-color: @navbar-inverse-border;\n }\n > li > a {\n color: @navbar-inverse-link-color;\n &:hover,\n &:focus {\n color: @navbar-inverse-link-hover-color;\n background-color: @navbar-inverse-link-hover-bg;\n }\n }\n > .active > a {\n &,\n &:hover,\n &:focus {\n color: @navbar-inverse-link-active-color;\n background-color: @navbar-inverse-link-active-bg;\n }\n }\n > .disabled > a {\n &,\n &:hover,\n &:focus {\n color: @navbar-inverse-link-disabled-color;\n background-color: @navbar-inverse-link-disabled-bg;\n }\n }\n }\n }\n }\n\n .navbar-link {\n color: @navbar-inverse-link-color;\n &:hover {\n color: @navbar-inverse-link-hover-color;\n }\n }\n\n .btn-link {\n color: @navbar-inverse-link-color;\n &:hover,\n &:focus {\n color: @navbar-inverse-link-hover-color;\n }\n &[disabled],\n fieldset[disabled] & {\n &:hover,\n &:focus {\n color: @navbar-inverse-link-disabled-color;\n }\n }\n }\n}\n","// Navbar vertical align\n//\n// Vertically center elements in the navbar.\n// Example: an element has a height of 30px, so write out `.navbar-vertical-align(30px);` to calculate the appropriate top margin.\n\n.navbar-vertical-align(@element-height) {\n margin-top: ((@navbar-height - @element-height) / 2);\n margin-bottom: ((@navbar-height - @element-height) / 2);\n}\n","//\n// Utility classes\n// --------------------------------------------------\n\n\n// Floats\n// -------------------------\n\n.clearfix {\n .clearfix();\n}\n.center-block {\n .center-block();\n}\n.pull-right {\n float: right !important;\n}\n.pull-left {\n float: left !important;\n}\n\n\n// Toggling content\n// -------------------------\n\n// Note: Deprecated .hide in favor of .hidden or .sr-only (as appropriate) in v3.0.1\n.hide {\n display: none !important;\n}\n.show {\n display: block !important;\n}\n.invisible {\n visibility: hidden;\n}\n.text-hide {\n .text-hide();\n}\n\n\n// Hide from screenreaders and browsers\n//\n// Credit: HTML5 Boilerplate\n\n.hidden {\n display: none !important;\n visibility: hidden !important;\n}\n\n\n// For Affix plugin\n// -------------------------\n\n.affix {\n position: fixed;\n .translate3d(0, 0, 0);\n}\n","//\n// Breadcrumbs\n// --------------------------------------------------\n\n\n.breadcrumb {\n padding: @breadcrumb-padding-vertical @breadcrumb-padding-horizontal;\n margin-bottom: @line-height-computed;\n list-style: none;\n background-color: @breadcrumb-bg;\n border-radius: @border-radius-base;\n\n > li {\n display: inline-block;\n\n + li:before {\n content: \"@{breadcrumb-separator}\\00a0\"; // Unicode space added since inline-block means non-collapsing white-space\n padding: 0 5px;\n color: @breadcrumb-color;\n }\n }\n\n > .active {\n color: @breadcrumb-active-color;\n }\n}\n","//\n// Pagination (multiple pages)\n// --------------------------------------------------\n.pagination {\n display: inline-block;\n padding-left: 0;\n margin: @line-height-computed 0;\n border-radius: @border-radius-base;\n\n > li {\n display: inline; // Remove list-style and block-level defaults\n > a,\n > span {\n position: relative;\n float: left; // Collapse white-space\n padding: @padding-base-vertical @padding-base-horizontal;\n line-height: @line-height-base;\n text-decoration: none;\n color: @pagination-color;\n background-color: @pagination-bg;\n border: 1px solid @pagination-border;\n margin-left: -1px;\n }\n &:first-child {\n > a,\n > span {\n margin-left: 0;\n .border-left-radius(@border-radius-base);\n }\n }\n &:last-child {\n > a,\n > span {\n .border-right-radius(@border-radius-base);\n }\n }\n }\n\n > li > a,\n > li > span {\n &:hover,\n &:focus {\n color: @pagination-hover-color;\n background-color: @pagination-hover-bg;\n border-color: @pagination-hover-border;\n }\n }\n\n > .active > a,\n > .active > span {\n &,\n &:hover,\n &:focus {\n z-index: 2;\n color: @pagination-active-color;\n background-color: @pagination-active-bg;\n border-color: @pagination-active-border;\n cursor: default;\n }\n }\n\n > .disabled {\n > span,\n > span:hover,\n > span:focus,\n > a,\n > a:hover,\n > a:focus {\n color: @pagination-disabled-color;\n background-color: @pagination-disabled-bg;\n border-color: @pagination-disabled-border;\n cursor: not-allowed;\n }\n }\n}\n\n// Sizing\n// --------------------------------------------------\n\n// Large\n.pagination-lg {\n .pagination-size(@padding-large-vertical; @padding-large-horizontal; @font-size-large; @border-radius-large);\n}\n\n// Small\n.pagination-sm {\n .pagination-size(@padding-small-vertical; @padding-small-horizontal; @font-size-small; @border-radius-small);\n}\n","// Pagination\n\n.pagination-size(@padding-vertical; @padding-horizontal; @font-size; @border-radius) {\n > li {\n > a,\n > span {\n padding: @padding-vertical @padding-horizontal;\n font-size: @font-size;\n }\n &:first-child {\n > a,\n > span {\n .border-left-radius(@border-radius);\n }\n }\n &:last-child {\n > a,\n > span {\n .border-right-radius(@border-radius);\n }\n }\n }\n}\n","//\n// Pager pagination\n// --------------------------------------------------\n\n\n.pager {\n padding-left: 0;\n margin: @line-height-computed 0;\n list-style: none;\n text-align: center;\n &:extend(.clearfix all);\n li {\n display: inline;\n > a,\n > span {\n display: inline-block;\n padding: 5px 14px;\n background-color: @pager-bg;\n border: 1px solid @pager-border;\n border-radius: @pager-border-radius;\n }\n\n > a:hover,\n > a:focus {\n text-decoration: none;\n background-color: @pager-hover-bg;\n }\n }\n\n .next {\n > a,\n > span {\n float: right;\n }\n }\n\n .previous {\n > a,\n > span {\n float: left;\n }\n }\n\n .disabled {\n > a,\n > a:hover,\n > a:focus,\n > span {\n color: @pager-disabled-color;\n background-color: @pager-bg;\n cursor: not-allowed;\n }\n }\n\n}\n","//\n// Labels\n// --------------------------------------------------\n\n.label {\n display: inline;\n padding: .2em .6em .3em;\n font-size: 75%;\n font-weight: bold;\n line-height: 1;\n color: @label-color;\n text-align: center;\n white-space: nowrap;\n vertical-align: baseline;\n border-radius: .25em;\n\n // Add hover effects, but only for links\n a& {\n &:hover,\n &:focus {\n color: @label-link-hover-color;\n text-decoration: none;\n cursor: pointer;\n }\n }\n\n // Empty labels collapse automatically (not available in IE8)\n &:empty {\n display: none;\n }\n\n // Quick fix for labels in buttons\n .btn & {\n position: relative;\n top: -1px;\n }\n}\n\n// Colors\n// Contextual variations (linked labels get darker on :hover)\n\n.label-default {\n .label-variant(@label-default-bg);\n}\n\n.label-primary {\n .label-variant(@label-primary-bg);\n}\n\n.label-success {\n .label-variant(@label-success-bg);\n}\n\n.label-info {\n .label-variant(@label-info-bg);\n}\n\n.label-warning {\n .label-variant(@label-warning-bg);\n}\n\n.label-danger {\n .label-variant(@label-danger-bg);\n}\n","// Labels\n\n.label-variant(@color) {\n background-color: @color;\n \n &[href] {\n &:hover,\n &:focus {\n background-color: darken(@color, 10%);\n }\n }\n}\n","//\n// Badges\n// --------------------------------------------------\n\n\n// Base class\n.badge {\n display: inline-block;\n min-width: 10px;\n padding: 3px 7px;\n font-size: @font-size-small;\n font-weight: @badge-font-weight;\n color: @badge-color;\n line-height: @badge-line-height;\n vertical-align: baseline;\n white-space: nowrap;\n text-align: center;\n background-color: @badge-bg;\n border-radius: @badge-border-radius;\n\n // Empty badges collapse automatically (not available in IE8)\n &:empty {\n display: none;\n }\n\n // Quick fix for badges in buttons\n .btn & {\n position: relative;\n top: -1px;\n }\n .btn-xs & {\n top: 0;\n padding: 1px 5px;\n }\n\n // Hover state, but only for links\n a& {\n &:hover,\n &:focus {\n color: @badge-link-hover-color;\n text-decoration: none;\n cursor: pointer;\n }\n }\n\n // Account for badges in navs\n a.list-group-item.active > &,\n .nav-pills > .active > a > & {\n color: @badge-active-color;\n background-color: @badge-active-bg;\n }\n .nav-pills > li > a > & {\n margin-left: 3px;\n }\n}\n","//\n// Jumbotron\n// --------------------------------------------------\n\n\n.jumbotron {\n padding: @jumbotron-padding;\n margin-bottom: @jumbotron-padding;\n color: @jumbotron-color;\n background-color: @jumbotron-bg;\n\n h1,\n .h1 {\n color: @jumbotron-heading-color;\n }\n p {\n margin-bottom: (@jumbotron-padding / 2);\n font-size: @jumbotron-font-size;\n font-weight: 200;\n }\n\n > hr {\n border-top-color: darken(@jumbotron-bg, 10%);\n }\n\n .container & {\n border-radius: @border-radius-large; // Only round corners at higher resolutions if contained in a container\n }\n\n .container {\n max-width: 100%;\n }\n\n @media screen and (min-width: @screen-sm-min) {\n padding-top: (@jumbotron-padding * 1.6);\n padding-bottom: (@jumbotron-padding * 1.6);\n\n .container & {\n padding-left: (@jumbotron-padding * 2);\n padding-right: (@jumbotron-padding * 2);\n }\n\n h1,\n .h1 {\n font-size: (@font-size-base * 4.5);\n }\n }\n}\n","//\n// Thumbnails\n// --------------------------------------------------\n\n\n// Mixin and adjust the regular image class\n.thumbnail {\n display: block;\n padding: @thumbnail-padding;\n margin-bottom: @line-height-computed;\n line-height: @line-height-base;\n background-color: @thumbnail-bg;\n border: 1px solid @thumbnail-border;\n border-radius: @thumbnail-border-radius;\n .transition(all .2s ease-in-out);\n\n > img,\n a > img {\n &:extend(.img-responsive);\n margin-left: auto;\n margin-right: auto;\n }\n\n // Add a hover state for linked versions only\n a&:hover,\n a&:focus,\n a&.active {\n border-color: @link-color;\n }\n\n // Image captions\n .caption {\n padding: @thumbnail-caption-padding;\n color: @thumbnail-caption-color;\n }\n}\n","//\n// Alerts\n// --------------------------------------------------\n\n\n// Base styles\n// -------------------------\n\n.alert {\n padding: @alert-padding;\n margin-bottom: @line-height-computed;\n border: 1px solid transparent;\n border-radius: @alert-border-radius;\n\n // Headings for larger alerts\n h4 {\n margin-top: 0;\n // Specified for the h4 to prevent conflicts of changing @headings-color\n color: inherit;\n }\n // Provide class for links that match alerts\n .alert-link {\n font-weight: @alert-link-font-weight;\n }\n\n // Improve alignment and spacing of inner content\n > p,\n > ul {\n margin-bottom: 0;\n }\n > p + p {\n margin-top: 5px;\n }\n}\n\n// Dismissible alerts\n//\n// Expand the right padding and account for the close button's positioning.\n\n.alert-dismissable, // The misspelled .alert-dismissable was deprecated in 3.2.0.\n.alert-dismissible {\n padding-right: (@alert-padding + 20);\n\n // Adjust close link position\n .close {\n position: relative;\n top: -2px;\n right: -21px;\n color: inherit;\n }\n}\n\n// Alternate styles\n//\n// Generate contextual modifier classes for colorizing the alert.\n\n.alert-success {\n .alert-variant(@alert-success-bg; @alert-success-border; @alert-success-text);\n}\n.alert-info {\n .alert-variant(@alert-info-bg; @alert-info-border; @alert-info-text);\n}\n.alert-warning {\n .alert-variant(@alert-warning-bg; @alert-warning-border; @alert-warning-text);\n}\n.alert-danger {\n .alert-variant(@alert-danger-bg; @alert-danger-border; @alert-danger-text);\n}\n","// Alerts\n\n.alert-variant(@background; @border; @text-color) {\n background-color: @background;\n border-color: @border;\n color: @text-color;\n\n hr {\n border-top-color: darken(@border, 5%);\n }\n .alert-link {\n color: darken(@text-color, 10%);\n }\n}\n","//\n// Progress bars\n// --------------------------------------------------\n\n\n// Bar animations\n// -------------------------\n\n// WebKit\n@-webkit-keyframes progress-bar-stripes {\n from { background-position: 40px 0; }\n to { background-position: 0 0; }\n}\n\n// Spec and IE10+\n@keyframes progress-bar-stripes {\n from { background-position: 40px 0; }\n to { background-position: 0 0; }\n}\n\n\n\n// Bar itself\n// -------------------------\n\n// Outer container\n.progress {\n overflow: hidden;\n height: @line-height-computed;\n margin-bottom: @line-height-computed;\n background-color: @progress-bg;\n border-radius: @border-radius-base;\n .box-shadow(inset 0 1px 2px rgba(0,0,0,.1));\n}\n\n// Bar of progress\n.progress-bar {\n float: left;\n width: 0%;\n height: 100%;\n font-size: @font-size-small;\n line-height: @line-height-computed;\n color: @progress-bar-color;\n text-align: center;\n background-color: @progress-bar-bg;\n .box-shadow(inset 0 -1px 0 rgba(0,0,0,.15));\n .transition(width .6s ease);\n}\n\n// Striped bars\n//\n// `.progress-striped .progress-bar` is deprecated as of v3.2.0 in favor of the\n// `.progress-bar-striped` class, which you just add to an existing\n// `.progress-bar`.\n.progress-striped .progress-bar,\n.progress-bar-striped {\n #gradient > .striped();\n background-size: 40px 40px;\n}\n\n// Call animation for the active one\n//\n// `.progress.active .progress-bar` is deprecated as of v3.2.0 in favor of the\n// `.progress-bar.active` approach.\n.progress.active .progress-bar,\n.progress-bar.active {\n .animation(progress-bar-stripes 2s linear infinite);\n}\n\n// Account for lower percentages\n.progress-bar {\n &[aria-valuenow=\"1\"],\n &[aria-valuenow=\"2\"] {\n min-width: 30px;\n }\n\n &[aria-valuenow=\"0\"] {\n color: @gray-light;\n min-width: 30px;\n background-color: transparent;\n background-image: none;\n box-shadow: none;\n }\n}\n\n\n\n// Variations\n// -------------------------\n\n.progress-bar-success {\n .progress-bar-variant(@progress-bar-success-bg);\n}\n\n.progress-bar-info {\n .progress-bar-variant(@progress-bar-info-bg);\n}\n\n.progress-bar-warning {\n .progress-bar-variant(@progress-bar-warning-bg);\n}\n\n.progress-bar-danger {\n .progress-bar-variant(@progress-bar-danger-bg);\n}\n","// Gradients\n\n#gradient {\n\n // Horizontal gradient, from left to right\n //\n // Creates two color stops, start and end, by specifying a color and position for each color stop.\n // Color stops are not available in IE9 and below.\n .horizontal(@start-color: #555; @end-color: #333; @start-percent: 0%; @end-percent: 100%) {\n background-image: -webkit-linear-gradient(left, @start-color @start-percent, @end-color @end-percent); // Safari 5.1-6, Chrome 10+\n background-image: -o-linear-gradient(left, @start-color @start-percent, @end-color @end-percent); // Opera 12\n background-image: linear-gradient(to right, @start-color @start-percent, @end-color @end-percent); // Standard, IE10, Firefox 16+, Opera 12.10+, Safari 7+, Chrome 26+\n background-repeat: repeat-x;\n filter: e(%(\"progid:DXImageTransform.Microsoft.gradient(startColorstr='%d', endColorstr='%d', GradientType=1)\",argb(@start-color),argb(@end-color))); // IE9 and down\n }\n\n // Vertical gradient, from top to bottom\n //\n // Creates two color stops, start and end, by specifying a color and position for each color stop.\n // Color stops are not available in IE9 and below.\n .vertical(@start-color: #555; @end-color: #333; @start-percent: 0%; @end-percent: 100%) {\n background-image: -webkit-linear-gradient(top, @start-color @start-percent, @end-color @end-percent); // Safari 5.1-6, Chrome 10+\n background-image: -o-linear-gradient(top, @start-color @start-percent, @end-color @end-percent); // Opera 12\n background-image: linear-gradient(to bottom, @start-color @start-percent, @end-color @end-percent); // Standard, IE10, Firefox 16+, Opera 12.10+, Safari 7+, Chrome 26+\n background-repeat: repeat-x;\n filter: e(%(\"progid:DXImageTransform.Microsoft.gradient(startColorstr='%d', endColorstr='%d', GradientType=0)\",argb(@start-color),argb(@end-color))); // IE9 and down\n }\n\n .directional(@start-color: #555; @end-color: #333; @deg: 45deg) {\n background-repeat: repeat-x;\n background-image: -webkit-linear-gradient(@deg, @start-color, @end-color); // Safari 5.1-6, Chrome 10+\n background-image: -o-linear-gradient(@deg, @start-color, @end-color); // Opera 12\n background-image: linear-gradient(@deg, @start-color, @end-color); // Standard, IE10, Firefox 16+, Opera 12.10+, Safari 7+, Chrome 26+\n }\n .horizontal-three-colors(@start-color: #00b3ee; @mid-color: #7a43b6; @color-stop: 50%; @end-color: #c3325f) {\n background-image: -webkit-linear-gradient(left, @start-color, @mid-color @color-stop, @end-color);\n background-image: -o-linear-gradient(left, @start-color, @mid-color @color-stop, @end-color);\n background-image: linear-gradient(to right, @start-color, @mid-color @color-stop, @end-color);\n background-repeat: no-repeat;\n filter: e(%(\"progid:DXImageTransform.Microsoft.gradient(startColorstr='%d', endColorstr='%d', GradientType=1)\",argb(@start-color),argb(@end-color))); // IE9 and down, gets no color-stop at all for proper fallback\n }\n .vertical-three-colors(@start-color: #00b3ee; @mid-color: #7a43b6; @color-stop: 50%; @end-color: #c3325f) {\n background-image: -webkit-linear-gradient(@start-color, @mid-color @color-stop, @end-color);\n background-image: -o-linear-gradient(@start-color, @mid-color @color-stop, @end-color);\n background-image: linear-gradient(@start-color, @mid-color @color-stop, @end-color);\n background-repeat: no-repeat;\n filter: e(%(\"progid:DXImageTransform.Microsoft.gradient(startColorstr='%d', endColorstr='%d', GradientType=0)\",argb(@start-color),argb(@end-color))); // IE9 and down, gets no color-stop at all for proper fallback\n }\n .radial(@inner-color: #555; @outer-color: #333) {\n background-image: -webkit-radial-gradient(circle, @inner-color, @outer-color);\n background-image: radial-gradient(circle, @inner-color, @outer-color);\n background-repeat: no-repeat;\n }\n .striped(@color: rgba(255,255,255,.15); @angle: 45deg) {\n background-image: -webkit-linear-gradient(@angle, @color 25%, transparent 25%, transparent 50%, @color 50%, @color 75%, transparent 75%, transparent);\n background-image: -o-linear-gradient(@angle, @color 25%, transparent 25%, transparent 50%, @color 50%, @color 75%, transparent 75%, transparent);\n background-image: linear-gradient(@angle, @color 25%, transparent 25%, transparent 50%, @color 50%, @color 75%, transparent 75%, transparent);\n }\n}\n","// Progress bars\n\n.progress-bar-variant(@color) {\n background-color: @color;\n\n // Deprecated parent class requirement as of v3.2.0\n .progress-striped & {\n #gradient > .striped();\n }\n}\n","// Media objects\n// Source: http://stubbornella.org/content/?p=497\n// --------------------------------------------------\n\n\n// Common styles\n// -------------------------\n\n// Clear the floats\n.media,\n.media-body {\n overflow: hidden;\n zoom: 1;\n}\n\n// Proper spacing between instances of .media\n.media,\n.media .media {\n margin-top: 15px;\n}\n.media:first-child {\n margin-top: 0;\n}\n\n// For images and videos, set to block\n.media-object {\n display: block;\n}\n\n// Reset margins on headings for tighter default spacing\n.media-heading {\n margin: 0 0 5px;\n}\n\n\n// Media image alignment\n// -------------------------\n\n.media {\n > .pull-left {\n margin-right: 10px;\n }\n > .pull-right {\n margin-left: 10px;\n }\n}\n\n\n// Media list variation\n// -------------------------\n\n// Undo default ul/ol styles\n.media-list {\n padding-left: 0;\n list-style: none;\n}\n","//\n// List groups\n// --------------------------------------------------\n\n\n// Base class\n//\n// Easily usable on <ul>, <ol>, or <div>.\n\n.list-group {\n // No need to set list-style: none; since .list-group-item is block level\n margin-bottom: 20px;\n padding-left: 0; // reset padding because ul and ol\n}\n\n\n// Individual list items\n//\n// Use on `li`s or `div`s within the `.list-group` parent.\n\n.list-group-item {\n position: relative;\n display: block;\n padding: 10px 15px;\n // Place the border on the list items and negative margin up for better styling\n margin-bottom: -1px;\n background-color: @list-group-bg;\n border: 1px solid @list-group-border;\n\n // Round the first and last items\n &:first-child {\n .border-top-radius(@list-group-border-radius);\n }\n &:last-child {\n margin-bottom: 0;\n .border-bottom-radius(@list-group-border-radius);\n }\n\n // Align badges within list items\n > .badge {\n float: right;\n }\n > .badge + .badge {\n margin-right: 5px;\n }\n}\n\n\n// Linked list items\n//\n// Use anchor elements instead of `li`s or `div`s to create linked list items.\n// Includes an extra `.active` modifier class for showing selected items.\n\na.list-group-item {\n color: @list-group-link-color;\n\n .list-group-item-heading {\n color: @list-group-link-heading-color;\n }\n\n // Hover state\n &:hover,\n &:focus {\n text-decoration: none;\n color: @list-group-link-hover-color;\n background-color: @list-group-hover-bg;\n }\n}\n\n.list-group-item {\n // Disabled state\n &.disabled,\n &.disabled:hover,\n &.disabled:focus {\n background-color: @list-group-disabled-bg;\n color: @list-group-disabled-color;\n\n // Force color to inherit for custom content\n .list-group-item-heading {\n color: inherit;\n }\n .list-group-item-text {\n color: @list-group-disabled-text-color;\n }\n }\n\n // Active class on item itself, not parent\n &.active,\n &.active:hover,\n &.active:focus {\n z-index: 2; // Place active items above their siblings for proper border styling\n color: @list-group-active-color;\n background-color: @list-group-active-bg;\n border-color: @list-group-active-border;\n\n // Force color to inherit for custom content\n .list-group-item-heading,\n .list-group-item-heading > small,\n .list-group-item-heading > .small {\n color: inherit;\n }\n .list-group-item-text {\n color: @list-group-active-text-color;\n }\n }\n}\n\n\n// Contextual variants\n//\n// Add modifier classes to change text and background color on individual items.\n// Organizationally, this must come after the `:hover` states.\n\n.list-group-item-variant(success; @state-success-bg; @state-success-text);\n.list-group-item-variant(info; @state-info-bg; @state-info-text);\n.list-group-item-variant(warning; @state-warning-bg; @state-warning-text);\n.list-group-item-variant(danger; @state-danger-bg; @state-danger-text);\n\n\n// Custom content options\n//\n// Extra classes for creating well-formatted content within `.list-group-item`s.\n\n.list-group-item-heading {\n margin-top: 0;\n margin-bottom: 5px;\n}\n.list-group-item-text {\n margin-bottom: 0;\n line-height: 1.3;\n}\n","// List Groups\n\n.list-group-item-variant(@state; @background; @color) {\n .list-group-item-@{state} {\n color: @color;\n background-color: @background;\n\n a& {\n color: @color;\n\n .list-group-item-heading {\n color: inherit;\n }\n\n &:hover,\n &:focus {\n color: @color;\n background-color: darken(@background, 5%);\n }\n &.active,\n &.active:hover,\n &.active:focus {\n color: #fff;\n background-color: @color;\n border-color: @color;\n }\n }\n }\n}\n","//\n// Panels\n// --------------------------------------------------\n\n\n// Base class\n.panel {\n margin-bottom: @line-height-computed;\n background-color: @panel-bg;\n border: 1px solid transparent;\n border-radius: @panel-border-radius;\n .box-shadow(0 1px 1px rgba(0,0,0,.05));\n}\n\n// Panel contents\n.panel-body {\n padding: @panel-body-padding;\n &:extend(.clearfix all);\n}\n\n// Optional heading\n.panel-heading {\n padding: @panel-heading-padding;\n border-bottom: 1px solid transparent;\n .border-top-radius((@panel-border-radius - 1));\n\n > .dropdown .dropdown-toggle {\n color: inherit;\n }\n}\n\n// Within heading, strip any `h*` tag of its default margins for spacing.\n.panel-title {\n margin-top: 0;\n margin-bottom: 0;\n font-size: ceil((@font-size-base * 1.125));\n color: inherit;\n\n > a {\n color: inherit;\n }\n}\n\n// Optional footer (stays gray in every modifier class)\n.panel-footer {\n padding: @panel-footer-padding;\n background-color: @panel-footer-bg;\n border-top: 1px solid @panel-inner-border;\n .border-bottom-radius((@panel-border-radius - 1));\n}\n\n\n// List groups in panels\n//\n// By default, space out list group content from panel headings to account for\n// any kind of custom content between the two.\n\n.panel {\n > .list-group {\n margin-bottom: 0;\n\n .list-group-item {\n border-width: 1px 0;\n border-radius: 0;\n }\n\n // Add border top radius for first one\n &:first-child {\n .list-group-item:first-child {\n border-top: 0;\n .border-top-radius((@panel-border-radius - 1));\n }\n }\n // Add border bottom radius for last one\n &:last-child {\n .list-group-item:last-child {\n border-bottom: 0;\n .border-bottom-radius((@panel-border-radius - 1));\n }\n }\n }\n}\n// Collapse space between when there's no additional content.\n.panel-heading + .list-group {\n .list-group-item:first-child {\n border-top-width: 0;\n }\n}\n.list-group + .panel-footer {\n border-top-width: 0;\n}\n\n// Tables in panels\n//\n// Place a non-bordered `.table` within a panel (not within a `.panel-body`) and\n// watch it go full width.\n\n.panel {\n > .table,\n > .table-responsive > .table,\n > .panel-collapse > .table {\n margin-bottom: 0;\n }\n // Add border top radius for first one\n > .table:first-child,\n > .table-responsive:first-child > .table:first-child {\n .border-top-radius((@panel-border-radius - 1));\n\n > thead:first-child,\n > tbody:first-child {\n > tr:first-child {\n td:first-child,\n th:first-child {\n border-top-left-radius: (@panel-border-radius - 1);\n }\n td:last-child,\n th:last-child {\n border-top-right-radius: (@panel-border-radius - 1);\n }\n }\n }\n }\n // Add border bottom radius for last one\n > .table:last-child,\n > .table-responsive:last-child > .table:last-child {\n .border-bottom-radius((@panel-border-radius - 1));\n\n > tbody:last-child,\n > tfoot:last-child {\n > tr:last-child {\n td:first-child,\n th:first-child {\n border-bottom-left-radius: (@panel-border-radius - 1);\n }\n td:last-child,\n th:last-child {\n border-bottom-right-radius: (@panel-border-radius - 1);\n }\n }\n }\n }\n > .panel-body + .table,\n > .panel-body + .table-responsive {\n border-top: 1px solid @table-border-color;\n }\n > .table > tbody:first-child > tr:first-child th,\n > .table > tbody:first-child > tr:first-child td {\n border-top: 0;\n }\n > .table-bordered,\n > .table-responsive > .table-bordered {\n border: 0;\n > thead,\n > tbody,\n > tfoot {\n > tr {\n > th:first-child,\n > td:first-child {\n border-left: 0;\n }\n > th:last-child,\n > td:last-child {\n border-right: 0;\n }\n }\n }\n > thead,\n > tbody {\n > tr:first-child {\n > td,\n > th {\n border-bottom: 0;\n }\n }\n }\n > tbody,\n > tfoot {\n > tr:last-child {\n > td,\n > th {\n border-bottom: 0;\n }\n }\n }\n }\n > .table-responsive {\n border: 0;\n margin-bottom: 0;\n }\n}\n\n\n// Collapsable panels (aka, accordion)\n//\n// Wrap a series of panels in `.panel-group` to turn them into an accordion with\n// the help of our collapse JavaScript plugin.\n\n.panel-group {\n margin-bottom: @line-height-computed;\n\n // Tighten up margin so it's only between panels\n .panel {\n margin-bottom: 0;\n border-radius: @panel-border-radius;\n + .panel {\n margin-top: 5px;\n }\n }\n\n .panel-heading {\n border-bottom: 0;\n + .panel-collapse > .panel-body {\n border-top: 1px solid @panel-inner-border;\n }\n }\n .panel-footer {\n border-top: 0;\n + .panel-collapse .panel-body {\n border-bottom: 1px solid @panel-inner-border;\n }\n }\n}\n\n\n// Contextual variations\n.panel-default {\n .panel-variant(@panel-default-border; @panel-default-text; @panel-default-heading-bg; @panel-default-border);\n}\n.panel-primary {\n .panel-variant(@panel-primary-border; @panel-primary-text; @panel-primary-heading-bg; @panel-primary-border);\n}\n.panel-success {\n .panel-variant(@panel-success-border; @panel-success-text; @panel-success-heading-bg; @panel-success-border);\n}\n.panel-info {\n .panel-variant(@panel-info-border; @panel-info-text; @panel-info-heading-bg; @panel-info-border);\n}\n.panel-warning {\n .panel-variant(@panel-warning-border; @panel-warning-text; @panel-warning-heading-bg; @panel-warning-border);\n}\n.panel-danger {\n .panel-variant(@panel-danger-border; @panel-danger-text; @panel-danger-heading-bg; @panel-danger-border);\n}\n","// Panels\n\n.panel-variant(@border; @heading-text-color; @heading-bg-color; @heading-border) {\n border-color: @border;\n\n & > .panel-heading {\n color: @heading-text-color;\n background-color: @heading-bg-color;\n border-color: @heading-border;\n\n + .panel-collapse > .panel-body {\n border-top-color: @border;\n }\n .badge {\n color: @heading-bg-color;\n background-color: @heading-text-color;\n }\n }\n & > .panel-footer {\n + .panel-collapse > .panel-body {\n border-bottom-color: @border;\n }\n }\n}\n","// Embeds responsive\n//\n// Credit: Nicolas Gallagher and SUIT CSS.\n\n.embed-responsive {\n position: relative;\n display: block;\n height: 0;\n padding: 0;\n overflow: hidden;\n\n .embed-responsive-item,\n iframe,\n embed,\n object {\n position: absolute;\n top: 0;\n left: 0;\n bottom: 0;\n height: 100%;\n width: 100%;\n border: 0;\n }\n\n // Modifier class for 16:9 aspect ratio\n &.embed-responsive-16by9 {\n padding-bottom: 56.25%;\n }\n\n // Modifier class for 4:3 aspect ratio\n &.embed-responsive-4by3 {\n padding-bottom: 75%;\n }\n}\n","//\n// Wells\n// --------------------------------------------------\n\n\n// Base class\n.well {\n min-height: 20px;\n padding: 19px;\n margin-bottom: 20px;\n background-color: @well-bg;\n border: 1px solid @well-border;\n border-radius: @border-radius-base;\n .box-shadow(inset 0 1px 1px rgba(0,0,0,.05));\n blockquote {\n border-color: #ddd;\n border-color: rgba(0,0,0,.15);\n }\n}\n\n// Sizes\n.well-lg {\n padding: 24px;\n border-radius: @border-radius-large;\n}\n.well-sm {\n padding: 9px;\n border-radius: @border-radius-small;\n}\n","//\n// Close icons\n// --------------------------------------------------\n\n\n.close {\n float: right;\n font-size: (@font-size-base * 1.5);\n font-weight: @close-font-weight;\n line-height: 1;\n color: @close-color;\n text-shadow: @close-text-shadow;\n .opacity(.2);\n\n &:hover,\n &:focus {\n color: @close-color;\n text-decoration: none;\n cursor: pointer;\n .opacity(.5);\n }\n\n // Additional properties for button version\n // iOS requires the button element instead of an anchor tag.\n // If you want the anchor version, it requires `href=\"#\"`.\n button& {\n padding: 0;\n cursor: pointer;\n background: transparent;\n border: 0;\n -webkit-appearance: none;\n }\n}\n","//\n// Modals\n// --------------------------------------------------\n\n// .modal-open - body class for killing the scroll\n// .modal - container to scroll within\n// .modal-dialog - positioning shell for the actual modal\n// .modal-content - actual modal w/ bg and corners and shit\n\n// Kill the scroll on the body\n.modal-open {\n overflow: hidden;\n}\n\n// Container that the modal scrolls within\n.modal {\n display: none;\n overflow: hidden;\n position: fixed;\n top: 0;\n right: 0;\n bottom: 0;\n left: 0;\n z-index: @zindex-modal;\n -webkit-overflow-scrolling: touch;\n\n // Prevent Chrome on Windows from adding a focus outline. For details, see\n // https://github.com/twbs/bootstrap/pull/10951.\n outline: 0;\n\n // When fading in the modal, animate it to slide down\n &.fade .modal-dialog {\n .translate3d(0, -25%, 0);\n .transition-transform(~\"0.3s ease-out\");\n }\n &.in .modal-dialog { .translate3d(0, 0, 0) }\n}\n.modal-open .modal {\n overflow-x: hidden;\n overflow-y: auto;\n}\n\n// Shell div to position the modal with bottom padding\n.modal-dialog {\n position: relative;\n width: auto;\n margin: 10px;\n}\n\n// Actual modal\n.modal-content {\n position: relative;\n background-color: @modal-content-bg;\n border: 1px solid @modal-content-fallback-border-color; //old browsers fallback (ie8 etc)\n border: 1px solid @modal-content-border-color;\n border-radius: @border-radius-large;\n .box-shadow(0 3px 9px rgba(0,0,0,.5));\n background-clip: padding-box;\n // Remove focus outline from opened modal\n outline: 0;\n}\n\n// Modal background\n.modal-backdrop {\n position: fixed;\n top: 0;\n right: 0;\n bottom: 0;\n left: 0;\n z-index: @zindex-modal-background;\n background-color: @modal-backdrop-bg;\n // Fade for backdrop\n &.fade { .opacity(0); }\n &.in { .opacity(@modal-backdrop-opacity); }\n}\n\n// Modal header\n// Top section of the modal w/ title and dismiss\n.modal-header {\n padding: @modal-title-padding;\n border-bottom: 1px solid @modal-header-border-color;\n min-height: (@modal-title-padding + @modal-title-line-height);\n}\n// Close icon\n.modal-header .close {\n margin-top: -2px;\n}\n\n// Title text within header\n.modal-title {\n margin: 0;\n line-height: @modal-title-line-height;\n}\n\n// Modal body\n// Where all modal content resides (sibling of .modal-header and .modal-footer)\n.modal-body {\n position: relative;\n padding: @modal-inner-padding;\n}\n\n// Footer (for actions)\n.modal-footer {\n padding: @modal-inner-padding;\n text-align: right; // right align buttons\n border-top: 1px solid @modal-footer-border-color;\n &:extend(.clearfix all); // clear it in case folks use .pull-* classes on buttons\n\n // Properly space out buttons\n .btn + .btn {\n margin-left: 5px;\n margin-bottom: 0; // account for input[type=\"submit\"] which gets the bottom margin like all other inputs\n }\n // but override that for button groups\n .btn-group .btn + .btn {\n margin-left: -1px;\n }\n // and override it for block buttons as well\n .btn-block + .btn-block {\n margin-left: 0;\n }\n}\n\n// Measure scrollbar width for padding body during modal show/hide\n.modal-scrollbar-measure {\n position: absolute;\n top: -9999px;\n width: 50px;\n height: 50px;\n overflow: scroll;\n}\n\n// Scale up the modal\n@media (min-width: @screen-sm-min) {\n // Automatically set modal's width for larger viewports\n .modal-dialog {\n width: @modal-md;\n margin: 30px auto;\n }\n .modal-content {\n .box-shadow(0 5px 15px rgba(0,0,0,.5));\n }\n\n // Modal sizes\n .modal-sm { width: @modal-sm; }\n}\n\n@media (min-width: @screen-md-min) {\n .modal-lg { width: @modal-lg; }\n}\n","//\n// Tooltips\n// --------------------------------------------------\n\n\n// Base class\n.tooltip {\n position: absolute;\n z-index: @zindex-tooltip;\n display: block;\n visibility: visible;\n font-size: @font-size-small;\n line-height: 1.4;\n .opacity(0);\n\n &.in { .opacity(@tooltip-opacity); }\n &.top { margin-top: -3px; padding: @tooltip-arrow-width 0; }\n &.right { margin-left: 3px; padding: 0 @tooltip-arrow-width; }\n &.bottom { margin-top: 3px; padding: @tooltip-arrow-width 0; }\n &.left { margin-left: -3px; padding: 0 @tooltip-arrow-width; }\n}\n\n// Wrapper for the tooltip content\n.tooltip-inner {\n max-width: @tooltip-max-width;\n padding: 3px 8px;\n color: @tooltip-color;\n text-align: center;\n text-decoration: none;\n background-color: @tooltip-bg;\n border-radius: @border-radius-base;\n}\n\n// Arrows\n.tooltip-arrow {\n position: absolute;\n width: 0;\n height: 0;\n border-color: transparent;\n border-style: solid;\n}\n.tooltip {\n &.top .tooltip-arrow {\n bottom: 0;\n left: 50%;\n margin-left: -@tooltip-arrow-width;\n border-width: @tooltip-arrow-width @tooltip-arrow-width 0;\n border-top-color: @tooltip-arrow-color;\n }\n &.top-left .tooltip-arrow {\n bottom: 0;\n left: @tooltip-arrow-width;\n border-width: @tooltip-arrow-width @tooltip-arrow-width 0;\n border-top-color: @tooltip-arrow-color;\n }\n &.top-right .tooltip-arrow {\n bottom: 0;\n right: @tooltip-arrow-width;\n border-width: @tooltip-arrow-width @tooltip-arrow-width 0;\n border-top-color: @tooltip-arrow-color;\n }\n &.right .tooltip-arrow {\n top: 50%;\n left: 0;\n margin-top: -@tooltip-arrow-width;\n border-width: @tooltip-arrow-width @tooltip-arrow-width @tooltip-arrow-width 0;\n border-right-color: @tooltip-arrow-color;\n }\n &.left .tooltip-arrow {\n top: 50%;\n right: 0;\n margin-top: -@tooltip-arrow-width;\n border-width: @tooltip-arrow-width 0 @tooltip-arrow-width @tooltip-arrow-width;\n border-left-color: @tooltip-arrow-color;\n }\n &.bottom .tooltip-arrow {\n top: 0;\n left: 50%;\n margin-left: -@tooltip-arrow-width;\n border-width: 0 @tooltip-arrow-width @tooltip-arrow-width;\n border-bottom-color: @tooltip-arrow-color;\n }\n &.bottom-left .tooltip-arrow {\n top: 0;\n left: @tooltip-arrow-width;\n border-width: 0 @tooltip-arrow-width @tooltip-arrow-width;\n border-bottom-color: @tooltip-arrow-color;\n }\n &.bottom-right .tooltip-arrow {\n top: 0;\n right: @tooltip-arrow-width;\n border-width: 0 @tooltip-arrow-width @tooltip-arrow-width;\n border-bottom-color: @tooltip-arrow-color;\n }\n}\n","//\n// Popovers\n// --------------------------------------------------\n\n\n.popover {\n position: absolute;\n top: 0;\n left: 0;\n z-index: @zindex-popover;\n display: none;\n max-width: @popover-max-width;\n padding: 1px;\n text-align: left; // Reset given new insertion method\n background-color: @popover-bg;\n background-clip: padding-box;\n border: 1px solid @popover-fallback-border-color;\n border: 1px solid @popover-border-color;\n border-radius: @border-radius-large;\n .box-shadow(0 5px 10px rgba(0,0,0,.2));\n\n // Overrides for proper insertion\n white-space: normal;\n\n // Offset the popover to account for the popover arrow\n &.top { margin-top: -@popover-arrow-width; }\n &.right { margin-left: @popover-arrow-width; }\n &.bottom { margin-top: @popover-arrow-width; }\n &.left { margin-left: -@popover-arrow-width; }\n}\n\n.popover-title {\n margin: 0; // reset heading margin\n padding: 8px 14px;\n font-size: @font-size-base;\n font-weight: normal;\n line-height: 18px;\n background-color: @popover-title-bg;\n border-bottom: 1px solid darken(@popover-title-bg, 5%);\n border-radius: (@border-radius-large - 1) (@border-radius-large - 1) 0 0;\n}\n\n.popover-content {\n padding: 9px 14px;\n}\n\n// Arrows\n//\n// .arrow is outer, .arrow:after is inner\n\n.popover > .arrow {\n &,\n &:after {\n position: absolute;\n display: block;\n width: 0;\n height: 0;\n border-color: transparent;\n border-style: solid;\n }\n}\n.popover > .arrow {\n border-width: @popover-arrow-outer-width;\n}\n.popover > .arrow:after {\n border-width: @popover-arrow-width;\n content: \"\";\n}\n\n.popover {\n &.top > .arrow {\n left: 50%;\n margin-left: -@popover-arrow-outer-width;\n border-bottom-width: 0;\n border-top-color: @popover-arrow-outer-fallback-color; // IE8 fallback\n border-top-color: @popover-arrow-outer-color;\n bottom: -@popover-arrow-outer-width;\n &:after {\n content: \" \";\n bottom: 1px;\n margin-left: -@popover-arrow-width;\n border-bottom-width: 0;\n border-top-color: @popover-arrow-color;\n }\n }\n &.right > .arrow {\n top: 50%;\n left: -@popover-arrow-outer-width;\n margin-top: -@popover-arrow-outer-width;\n border-left-width: 0;\n border-right-color: @popover-arrow-outer-fallback-color; // IE8 fallback\n border-right-color: @popover-arrow-outer-color;\n &:after {\n content: \" \";\n left: 1px;\n bottom: -@popover-arrow-width;\n border-left-width: 0;\n border-right-color: @popover-arrow-color;\n }\n }\n &.bottom > .arrow {\n left: 50%;\n margin-left: -@popover-arrow-outer-width;\n border-top-width: 0;\n border-bottom-color: @popover-arrow-outer-fallback-color; // IE8 fallback\n border-bottom-color: @popover-arrow-outer-color;\n top: -@popover-arrow-outer-width;\n &:after {\n content: \" \";\n top: 1px;\n margin-left: -@popover-arrow-width;\n border-top-width: 0;\n border-bottom-color: @popover-arrow-color;\n }\n }\n\n &.left > .arrow {\n top: 50%;\n right: -@popover-arrow-outer-width;\n margin-top: -@popover-arrow-outer-width;\n border-right-width: 0;\n border-left-color: @popover-arrow-outer-fallback-color; // IE8 fallback\n border-left-color: @popover-arrow-outer-color;\n &:after {\n content: \" \";\n right: 1px;\n border-right-width: 0;\n border-left-color: @popover-arrow-color;\n bottom: -@popover-arrow-width;\n }\n }\n\n}\n","//\n// Carousel\n// --------------------------------------------------\n\n\n// Wrapper for the slide container and indicators\n.carousel {\n position: relative;\n}\n\n.carousel-inner {\n position: relative;\n overflow: hidden;\n width: 100%;\n\n > .item {\n display: none;\n position: relative;\n .transition(.6s ease-in-out left);\n\n // Account for jankitude on images\n > img,\n > a > img {\n &:extend(.img-responsive);\n line-height: 1;\n }\n }\n\n > .active,\n > .next,\n > .prev {\n display: block;\n }\n\n > .active {\n left: 0;\n }\n\n > .next,\n > .prev {\n position: absolute;\n top: 0;\n width: 100%;\n }\n\n > .next {\n left: 100%;\n }\n > .prev {\n left: -100%;\n }\n > .next.left,\n > .prev.right {\n left: 0;\n }\n\n > .active.left {\n left: -100%;\n }\n > .active.right {\n left: 100%;\n }\n\n}\n\n// Left/right controls for nav\n// ---------------------------\n\n.carousel-control {\n position: absolute;\n top: 0;\n left: 0;\n bottom: 0;\n width: @carousel-control-width;\n .opacity(@carousel-control-opacity);\n font-size: @carousel-control-font-size;\n color: @carousel-control-color;\n text-align: center;\n text-shadow: @carousel-text-shadow;\n // We can't have this transition here because WebKit cancels the carousel\n // animation if you trip this while in the middle of another animation.\n\n // Set gradients for backgrounds\n &.left {\n #gradient > .horizontal(@start-color: rgba(0,0,0,.5); @end-color: rgba(0,0,0,.0001));\n }\n &.right {\n left: auto;\n right: 0;\n #gradient > .horizontal(@start-color: rgba(0,0,0,.0001); @end-color: rgba(0,0,0,.5));\n }\n\n // Hover/focus state\n &:hover,\n &:focus {\n outline: 0;\n color: @carousel-control-color;\n text-decoration: none;\n .opacity(.9);\n }\n\n // Toggles\n .icon-prev,\n .icon-next,\n .glyphicon-chevron-left,\n .glyphicon-chevron-right {\n position: absolute;\n top: 50%;\n z-index: 5;\n display: inline-block;\n }\n .icon-prev,\n .glyphicon-chevron-left {\n left: 50%;\n margin-left: -10px;\n }\n .icon-next,\n .glyphicon-chevron-right {\n right: 50%;\n margin-right: -10px;\n }\n .icon-prev,\n .icon-next {\n width: 20px;\n height: 20px;\n margin-top: -10px;\n font-family: serif;\n }\n\n\n .icon-prev {\n &:before {\n content: '\\2039';// SINGLE LEFT-POINTING ANGLE QUOTATION MARK (U+2039)\n }\n }\n .icon-next {\n &:before {\n content: '\\203a';// SINGLE RIGHT-POINTING ANGLE QUOTATION MARK (U+203A)\n }\n }\n}\n\n// Optional indicator pips\n//\n// Add an unordered list with the following class and add a list item for each\n// slide your carousel holds.\n\n.carousel-indicators {\n position: absolute;\n bottom: 10px;\n left: 50%;\n z-index: 15;\n width: 60%;\n margin-left: -30%;\n padding-left: 0;\n list-style: none;\n text-align: center;\n\n li {\n display: inline-block;\n width: 10px;\n height: 10px;\n margin: 1px;\n text-indent: -999px;\n border: 1px solid @carousel-indicator-border-color;\n border-radius: 10px;\n cursor: pointer;\n\n // IE8-9 hack for event handling\n //\n // Internet Explorer 8-9 does not support clicks on elements without a set\n // `background-color`. We cannot use `filter` since that's not viewed as a\n // background color by the browser. Thus, a hack is needed.\n //\n // For IE8, we set solid black as it doesn't support `rgba()`. For IE9, we\n // set alpha transparency for the best results possible.\n background-color: #000 \\9; // IE8\n background-color: rgba(0,0,0,0); // IE9\n }\n .active {\n margin: 0;\n width: 12px;\n height: 12px;\n background-color: @carousel-indicator-active-bg;\n }\n}\n\n// Optional captions\n// -----------------------------\n// Hidden by default for smaller viewports\n.carousel-caption {\n position: absolute;\n left: 15%;\n right: 15%;\n bottom: 20px;\n z-index: 10;\n padding-top: 20px;\n padding-bottom: 20px;\n color: @carousel-caption-color;\n text-align: center;\n text-shadow: @carousel-text-shadow;\n & .btn {\n text-shadow: none; // No shadow for button elements in carousel-caption\n }\n}\n\n\n// Scale up controls for tablets and up\n@media screen and (min-width: @screen-sm-min) {\n\n // Scale up the controls a smidge\n .carousel-control {\n .glyphicon-chevron-left,\n .glyphicon-chevron-right,\n .icon-prev,\n .icon-next {\n width: 30px;\n height: 30px;\n margin-top: -15px;\n font-size: 30px;\n }\n .glyphicon-chevron-left,\n .icon-prev {\n margin-left: -15px;\n }\n .glyphicon-chevron-right,\n .icon-next {\n margin-right: -15px;\n }\n }\n\n // Show and left align the captions\n .carousel-caption {\n left: 20%;\n right: 20%;\n padding-bottom: 30px;\n }\n\n // Move up the indicators\n .carousel-indicators {\n bottom: 20px;\n }\n}\n","// Clearfix\n//\n// For modern browsers\n// 1. The space content is one way to avoid an Opera bug when the\n// contenteditable attribute is included anywhere else in the document.\n// Otherwise it causes space to appear at the top and bottom of elements\n// that are clearfixed.\n// 2. The use of `table` rather than `block` is only necessary if using\n// `:before` to contain the top-margins of child elements.\n//\n// Source: http://nicolasgallagher.com/micro-clearfix-hack/\n\n.clearfix() {\n &:before,\n &:after {\n content: \" \"; // 1\n display: table; // 2\n }\n &:after {\n clear: both;\n }\n}\n","// Center-align a block level element\n\n.center-block() {\n display: block;\n margin-left: auto;\n margin-right: auto;\n}\n","// CSS image replacement\n//\n// Heads up! v3 launched with with only `.hide-text()`, but per our pattern for\n// mixins being reused as classes with the same name, this doesn't hold up. As\n// of v3.0.1 we have added `.text-hide()` and deprecated `.hide-text()`.\n//\n// Source: https://github.com/h5bp/html5-boilerplate/commit/aa0396eae757\n\n// Deprecated as of v3.0.1 (will be removed in v4)\n.hide-text() {\n font: ~\"0/0\" a;\n color: transparent;\n text-shadow: none;\n background-color: transparent;\n border: 0;\n}\n\n// New mixin to use as of v3.0.1\n.text-hide() {\n .hide-text();\n}\n","//\n// Responsive: Utility classes\n// --------------------------------------------------\n\n\n// IE10 in Windows (Phone) 8\n//\n// Support for responsive views via media queries is kind of borked in IE10, for\n// Surface/desktop in split view and for Windows Phone 8. This particular fix\n// must be accompanied by a snippet of JavaScript to sniff the user agent and\n// apply some conditional CSS to *only* the Surface/desktop Windows 8. Look at\n// our Getting Started page for more information on this bug.\n//\n// For more information, see the following:\n//\n// Issue: https://github.com/twbs/bootstrap/issues/10497\n// Docs: http://getbootstrap.com/getting-started/#support-ie10-width\n// Source: http://timkadlec.com/2013/01/windows-phone-8-and-device-width/\n// Source: http://timkadlec.com/2012/10/ie10-snap-mode-and-responsive-design/\n\n@-ms-viewport {\n width: device-width;\n}\n\n\n// Visibility utilities\n// Note: Deprecated .visible-xs, .visible-sm, .visible-md, and .visible-lg as of v3.2.0\n.visible-xs,\n.visible-sm,\n.visible-md,\n.visible-lg {\n .responsive-invisibility();\n}\n\n.visible-xs-block,\n.visible-xs-inline,\n.visible-xs-inline-block,\n.visible-sm-block,\n.visible-sm-inline,\n.visible-sm-inline-block,\n.visible-md-block,\n.visible-md-inline,\n.visible-md-inline-block,\n.visible-lg-block,\n.visible-lg-inline,\n.visible-lg-inline-block {\n display: none !important;\n}\n\n.visible-xs {\n @media (max-width: @screen-xs-max) {\n .responsive-visibility();\n }\n}\n.visible-xs-block {\n @media (max-width: @screen-xs-max) {\n display: block !important;\n }\n}\n.visible-xs-inline {\n @media (max-width: @screen-xs-max) {\n display: inline !important;\n }\n}\n.visible-xs-inline-block {\n @media (max-width: @screen-xs-max) {\n display: inline-block !important;\n }\n}\n\n.visible-sm {\n @media (min-width: @screen-sm-min) and (max-width: @screen-sm-max) {\n .responsive-visibility();\n }\n}\n.visible-sm-block {\n @media (min-width: @screen-sm-min) and (max-width: @screen-sm-max) {\n display: block !important;\n }\n}\n.visible-sm-inline {\n @media (min-width: @screen-sm-min) and (max-width: @screen-sm-max) {\n display: inline !important;\n }\n}\n.visible-sm-inline-block {\n @media (min-width: @screen-sm-min) and (max-width: @screen-sm-max) {\n display: inline-block !important;\n }\n}\n\n.visible-md {\n @media (min-width: @screen-md-min) and (max-width: @screen-md-max) {\n .responsive-visibility();\n }\n}\n.visible-md-block {\n @media (min-width: @screen-md-min) and (max-width: @screen-md-max) {\n display: block !important;\n }\n}\n.visible-md-inline {\n @media (min-width: @screen-md-min) and (max-width: @screen-md-max) {\n display: inline !important;\n }\n}\n.visible-md-inline-block {\n @media (min-width: @screen-md-min) and (max-width: @screen-md-max) {\n display: inline-block !important;\n }\n}\n\n.visible-lg {\n @media (min-width: @screen-lg-min) {\n .responsive-visibility();\n }\n}\n.visible-lg-block {\n @media (min-width: @screen-lg-min) {\n display: block !important;\n }\n}\n.visible-lg-inline {\n @media (min-width: @screen-lg-min) {\n display: inline !important;\n }\n}\n.visible-lg-inline-block {\n @media (min-width: @screen-lg-min) {\n display: inline-block !important;\n }\n}\n\n.hidden-xs {\n @media (max-width: @screen-xs-max) {\n .responsive-invisibility();\n }\n}\n.hidden-sm {\n @media (min-width: @screen-sm-min) and (max-width: @screen-sm-max) {\n .responsive-invisibility();\n }\n}\n.hidden-md {\n @media (min-width: @screen-md-min) and (max-width: @screen-md-max) {\n .responsive-invisibility();\n }\n}\n.hidden-lg {\n @media (min-width: @screen-lg-min) {\n .responsive-invisibility();\n }\n}\n\n\n// Print utilities\n//\n// Media queries are placed on the inside to be mixin-friendly.\n\n// Note: Deprecated .visible-print as of v3.2.0\n.visible-print {\n .responsive-invisibility();\n\n @media print {\n .responsive-visibility();\n }\n}\n.visible-print-block {\n display: none !important;\n\n @media print {\n display: block !important;\n }\n}\n.visible-print-inline {\n display: none !important;\n\n @media print {\n display: inline !important;\n }\n}\n.visible-print-inline-block {\n display: none !important;\n\n @media print {\n display: inline-block !important;\n }\n}\n\n.hidden-print {\n @media print {\n .responsive-invisibility();\n }\n}\n","// Responsive utilities\n\n//\n// More easily include all the states for responsive-utilities.less.\n.responsive-visibility() {\n display: block !important;\n table& { display: table; }\n tr& { display: table-row !important; }\n th&,\n td& { display: table-cell !important; }\n}\n\n.responsive-invisibility() {\n display: none !important;\n}\n"]}
\ No newline at end of file
diff --git a/docs/build/html/_static/bootstrap-3.2.0/css/bootstrap.min.css b/docs/build/html/_static/bootstrap-3.2.0/css/bootstrap.min.css
new file mode 100644
index 0000000000000000000000000000000000000000..a9f35ceedfac7fc0559b121bed105eaf80f10bf2
--- /dev/null
+++ b/docs/build/html/_static/bootstrap-3.2.0/css/bootstrap.min.css
@@ -0,0 +1,5 @@
+/*!
+ * Bootstrap v3.2.0 (http://getbootstrap.com)
+ * Copyright 2011-2014 Twitter, Inc.
+ * Licensed under MIT (https://github.com/twbs/bootstrap/blob/master/LICENSE)
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+<glyph unicode="" d="M-100 300v500q0 124 88 212t212 88h700q124 0 212 -88t88 -212v-500q0 -124 -88 -212t-212 -88h-700q-124 0 -212 88t-88 212zM100 200h900v700h-900v-700zM200 300h300v400h-200v100h-100v-500zM301 400v200h100v-200h-100zM601 300h100v100h-100v-100zM700 700h100 v-400h100v500h-200v-100z" />
+<glyph unicode="" d="M-100 300v500q0 124 88 212t212 88h700q124 0 212 -88t88 -212v-500q0 -124 -88 -212t-212 -88h-700q-124 0 -212 88t-88 212zM100 200h900v700h-900v-700zM200 700v100h300v-300h-99v-100h-100v100h99v200h-200zM201 300v100h100v-100h-100zM601 300v100h100v-100h-100z M700 700v100h200v-500h-100v400h-100z" />
+<glyph unicode="" d="M4 600q0 162 80 299t217 217t299 80t299 -80t217 -217t80 -299t-80 -299t-217 -217t-299 -80t-299 80t-217 217t-80 299zM186 600q0 -171 121.5 -292.5t292.5 -121.5t292.5 121.5t121.5 292.5t-121.5 292.5t-292.5 121.5t-292.5 -121.5t-121.5 -292.5zM400 500v200 l100 100h300v-100h-300v-200h300v-100h-300z" />
+<glyph unicode="" d="M0 600q0 162 80 299t217 217t299 80t299 -80t217 -217t80 -299t-80 -299t-217 -217t-299 -80t-299 80t-217 217t-80 299zM182 600q0 -171 121.5 -292.5t292.5 -121.5t292.5 121.5t121.5 292.5t-121.5 292.5t-292.5 121.5t-292.5 -121.5t-121.5 -292.5zM400 400v400h300 l100 -100v-100h-100v100h-200v-100h200v-100h-200v-100h-100zM700 400v100h100v-100h-100z" />
+<glyph unicode="" d="M-14 494q0 -80 56.5 -137t135.5 -57h222v300h400v-300h128q120 0 205 86.5t85 207.5t-85 207t-205 86q-46 0 -90 -14q-44 97 -134.5 156.5t-200.5 59.5q-152 0 -260 -107.5t-108 -260.5q0 -25 2 -37q-66 -14 -108.5 -67.5t-42.5 -122.5zM300 200h200v300h200v-300h200 l-300 -300z" />
+<glyph unicode="" d="M-14 494q0 -80 56.5 -137t135.5 -57h8l414 414l403 -403q94 26 154.5 104.5t60.5 178.5q0 120 -85 206.5t-205 86.5q-46 0 -90 -14q-44 97 -134.5 156.5t-200.5 59.5q-152 0 -260 -107.5t-108 -260.5q0 -25 2 -37q-66 -14 -108.5 -67.5t-42.5 -122.5zM300 200l300 300 l300 -300h-200v-300h-200v300h-200z" />
+<glyph unicode="" d="M100 200h400v-155l-75 -45h350l-75 45v155h400l-270 300h170l-270 300h170l-300 333l-300 -333h170l-270 -300h170z" />
+<glyph unicode="" d="M121 700q0 -53 28.5 -97t75.5 -65q-4 -16 -4 -38q0 -74 52.5 -126.5t126.5 -52.5q56 0 100 30v-306l-75 -45h350l-75 45v306q46 -30 100 -30q74 0 126.5 52.5t52.5 126.5q0 24 -9 55q50 32 79.5 83t29.5 112q0 90 -61.5 155.5t-150.5 71.5q-26 89 -99.5 145.5 t-167.5 56.5q-116 0 -197.5 -81.5t-81.5 -197.5q0 -4 1 -11.5t1 -11.5q-14 2 -23 2q-74 0 -126.5 -52.5t-52.5 -126.5z" />
+</font>
+</defs></svg>
\ No newline at end of file
diff --git a/docs/build/html/_static/bootstrap-3.2.0/fonts/glyphicons-halflings-regular.ttf b/docs/build/html/_static/bootstrap-3.2.0/fonts/glyphicons-halflings-regular.ttf
new file mode 100644
index 0000000000000000000000000000000000000000..67fa00bf83801d2fa568546b982c80d27f6ef74e
Binary files /dev/null and b/docs/build/html/_static/bootstrap-3.2.0/fonts/glyphicons-halflings-regular.ttf differ
diff --git a/docs/build/html/_static/bootstrap-3.2.0/fonts/glyphicons-halflings-regular.woff b/docs/build/html/_static/bootstrap-3.2.0/fonts/glyphicons-halflings-regular.woff
new file mode 100644
index 0000000000000000000000000000000000000000..8c54182aa5d4d1ab3c9171976b615c1dcb1dc187
Binary files /dev/null and b/docs/build/html/_static/bootstrap-3.2.0/fonts/glyphicons-halflings-regular.woff differ
diff --git a/docs/build/html/_static/bootstrap-3.2.0/js/bootstrap.js b/docs/build/html/_static/bootstrap-3.2.0/js/bootstrap.js
new file mode 100644
index 0000000000000000000000000000000000000000..7f5dbe57ba377936ec41f70ef7ce558a4aa8a498
--- /dev/null
+++ b/docs/build/html/_static/bootstrap-3.2.0/js/bootstrap.js
@@ -0,0 +1,2114 @@
+/*!
+ * Bootstrap v3.2.0 (http://getbootstrap.com)
+ * Copyright 2011-2014 Twitter, Inc.
+ * Licensed under MIT (https://github.com/twbs/bootstrap/blob/master/LICENSE)
+ */
+
+if (typeof (window.$jqTheme||window.jQuery) === 'undefined') { throw new Error('Bootstrap\'s JavaScript requires jQuery') }
+
+/* ========================================================================
+ * Bootstrap: transition.js v3.2.0
+ * http://getbootstrap.com/javascript/#transitions
+ * ========================================================================
+ * Copyright 2011-2014 Twitter, Inc.
+ * Licensed under MIT (https://github.com/twbs/bootstrap/blob/master/LICENSE)
+ * ======================================================================== */
+
+
++function ($) {
+ 'use strict';
+
+ // CSS TRANSITION SUPPORT (Shoutout: http://www.modernizr.com/)
+ // ============================================================
+
+ function transitionEnd() {
+ var el = document.createElement('bootstrap')
+
+ var transEndEventNames = {
+ WebkitTransition : 'webkitTransitionEnd',
+ MozTransition : 'transitionend',
+ OTransition : 'oTransitionEnd otransitionend',
+ transition : 'transitionend'
+ }
+
+ for (var name in transEndEventNames) {
+ if (el.style[name] !== undefined) {
+ return { end: transEndEventNames[name] }
+ }
+ }
+
+ return false // explicit for ie8 ( ._.)
+ }
+
+ // http://blog.alexmaccaw.com/css-transitions
+ $.fn.emulateTransitionEnd = function (duration) {
+ var called = false
+ var $el = this
+ $(this).one('bsTransitionEnd', function () { called = true })
+ var callback = function () { if (!called) $($el).trigger($.support.transition.end) }
+ setTimeout(callback, duration)
+ return this
+ }
+
+ $(function () {
+ $.support.transition = transitionEnd()
+
+ if (!$.support.transition) return
+
+ $.event.special.bsTransitionEnd = {
+ bindType: $.support.transition.end,
+ delegateType: $.support.transition.end,
+ handle: function (e) {
+ if ($(e.target).is(this)) return e.handleObj.handler.apply(this, arguments)
+ }
+ }
+ })
+
+}(window.$jqTheme||window.jQuery);
+
+/* ========================================================================
+ * Bootstrap: alert.js v3.2.0
+ * http://getbootstrap.com/javascript/#alerts
+ * ========================================================================
+ * Copyright 2011-2014 Twitter, Inc.
+ * Licensed under MIT (https://github.com/twbs/bootstrap/blob/master/LICENSE)
+ * ======================================================================== */
+
+
++function ($) {
+ 'use strict';
+
+ // ALERT CLASS DEFINITION
+ // ======================
+
+ var dismiss = '[data-dismiss="alert"]'
+ var Alert = function (el) {
+ $(el).on('click', dismiss, this.close)
+ }
+
+ Alert.VERSION = '3.2.0'
+
+ Alert.prototype.close = function (e) {
+ var $this = $(this)
+ var selector = $this.attr('data-target')
+
+ if (!selector) {
+ selector = $this.attr('href')
+ selector = selector && selector.replace(/.*(?=#[^\s]*$)/, '') // strip for ie7
+ }
+
+ var $parent = $(selector)
+
+ if (e) e.preventDefault()
+
+ if (!$parent.length) {
+ $parent = $this.hasClass('alert') ? $this : $this.parent()
+ }
+
+ $parent.trigger(e = $.Event('close.bs.alert'))
+
+ if (e.isDefaultPrevented()) return
+
+ $parent.removeClass('in')
+
+ function removeElement() {
+ // detach from parent, fire event then clean up data
+ $parent.detach().trigger('closed.bs.alert').remove()
+ }
+
+ $.support.transition && $parent.hasClass('fade') ?
+ $parent
+ .one('bsTransitionEnd', removeElement)
+ .emulateTransitionEnd(150) :
+ removeElement()
+ }
+
+
+ // ALERT PLUGIN DEFINITION
+ // =======================
+
+ function Plugin(option) {
+ return this.each(function () {
+ var $this = $(this)
+ var data = $this.data('bs.alert')
+
+ if (!data) $this.data('bs.alert', (data = new Alert(this)))
+ if (typeof option == 'string') data[option].call($this)
+ })
+ }
+
+ var old = $.fn.alert
+
+ $.fn.alert = Plugin
+ $.fn.alert.Constructor = Alert
+
+
+ // ALERT NO CONFLICT
+ // =================
+
+ $.fn.alert.noConflict = function () {
+ $.fn.alert = old
+ return this
+ }
+
+
+ // ALERT DATA-API
+ // ==============
+
+ $(document).on('click.bs.alert.data-api', dismiss, Alert.prototype.close)
+
+}(window.$jqTheme||window.jQuery);
+
+/* ========================================================================
+ * Bootstrap: button.js v3.2.0
+ * http://getbootstrap.com/javascript/#buttons
+ * ========================================================================
+ * Copyright 2011-2014 Twitter, Inc.
+ * Licensed under MIT (https://github.com/twbs/bootstrap/blob/master/LICENSE)
+ * ======================================================================== */
+
+
++function ($) {
+ 'use strict';
+
+ // BUTTON PUBLIC CLASS DEFINITION
+ // ==============================
+
+ var Button = function (element, options) {
+ this.$element = $(element)
+ this.options = $.extend({}, Button.DEFAULTS, options)
+ this.isLoading = false
+ }
+
+ Button.VERSION = '3.2.0'
+
+ Button.DEFAULTS = {
+ loadingText: 'loading...'
+ }
+
+ Button.prototype.setState = function (state) {
+ var d = 'disabled'
+ var $el = this.$element
+ var val = $el.is('input') ? 'val' : 'html'
+ var data = $el.data()
+
+ state = state + 'Text'
+
+ if (data.resetText == null) $el.data('resetText', $el[val]())
+
+ $el[val](data[state] == null ? this.options[state] : data[state])
+
+ // push to event loop to allow forms to submit
+ setTimeout($.proxy(function () {
+ if (state == 'loadingText') {
+ this.isLoading = true
+ $el.addClass(d).attr(d, d)
+ } else if (this.isLoading) {
+ this.isLoading = false
+ $el.removeClass(d).removeAttr(d)
+ }
+ }, this), 0)
+ }
+
+ Button.prototype.toggle = function () {
+ var changed = true
+ var $parent = this.$element.closest('[data-toggle="buttons"]')
+
+ if ($parent.length) {
+ var $input = this.$element.find('input')
+ if ($input.prop('type') == 'radio') {
+ if ($input.prop('checked') && this.$element.hasClass('active')) changed = false
+ else $parent.find('.active').removeClass('active')
+ }
+ if (changed) $input.prop('checked', !this.$element.hasClass('active')).trigger('change')
+ }
+
+ if (changed) this.$element.toggleClass('active')
+ }
+
+
+ // BUTTON PLUGIN DEFINITION
+ // ========================
+
+ function Plugin(option) {
+ return this.each(function () {
+ var $this = $(this)
+ var data = $this.data('bs.button')
+ var options = typeof option == 'object' && option
+
+ if (!data) $this.data('bs.button', (data = new Button(this, options)))
+
+ if (option == 'toggle') data.toggle()
+ else if (option) data.setState(option)
+ })
+ }
+
+ var old = $.fn.button
+
+ $.fn.button = Plugin
+ $.fn.button.Constructor = Button
+
+
+ // BUTTON NO CONFLICT
+ // ==================
+
+ $.fn.button.noConflict = function () {
+ $.fn.button = old
+ return this
+ }
+
+
+ // BUTTON DATA-API
+ // ===============
+
+ $(document).on('click.bs.button.data-api', '[data-toggle^="button"]', function (e) {
+ var $btn = $(e.target)
+ if (!$btn.hasClass('btn')) $btn = $btn.closest('.btn')
+ Plugin.call($btn, 'toggle')
+ e.preventDefault()
+ })
+
+}(window.$jqTheme||window.jQuery);
+
+/* ========================================================================
+ * Bootstrap: carousel.js v3.2.0
+ * http://getbootstrap.com/javascript/#carousel
+ * ========================================================================
+ * Copyright 2011-2014 Twitter, Inc.
+ * Licensed under MIT (https://github.com/twbs/bootstrap/blob/master/LICENSE)
+ * ======================================================================== */
+
+
++function ($) {
+ 'use strict';
+
+ // CAROUSEL CLASS DEFINITION
+ // =========================
+
+ var Carousel = function (element, options) {
+ this.$element = $(element).on('keydown.bs.carousel', $.proxy(this.keydown, this))
+ this.$indicators = this.$element.find('.carousel-indicators')
+ this.options = options
+ this.paused =
+ this.sliding =
+ this.interval =
+ this.$active =
+ this.$items = null
+
+ this.options.pause == 'hover' && this.$element
+ .on('mouseenter.bs.carousel', $.proxy(this.pause, this))
+ .on('mouseleave.bs.carousel', $.proxy(this.cycle, this))
+ }
+
+ Carousel.VERSION = '3.2.0'
+
+ Carousel.DEFAULTS = {
+ interval: 5000,
+ pause: 'hover',
+ wrap: true
+ }
+
+ Carousel.prototype.keydown = function (e) {
+ switch (e.which) {
+ case 37: this.prev(); break
+ case 39: this.next(); break
+ default: return
+ }
+
+ e.preventDefault()
+ }
+
+ Carousel.prototype.cycle = function (e) {
+ e || (this.paused = false)
+
+ this.interval && clearInterval(this.interval)
+
+ this.options.interval
+ && !this.paused
+ && (this.interval = setInterval($.proxy(this.next, this), this.options.interval))
+
+ return this
+ }
+
+ Carousel.prototype.getItemIndex = function (item) {
+ this.$items = item.parent().children('.item')
+ return this.$items.index(item || this.$active)
+ }
+
+ Carousel.prototype.to = function (pos) {
+ var that = this
+ var activeIndex = this.getItemIndex(this.$active = this.$element.find('.item.active'))
+
+ if (pos > (this.$items.length - 1) || pos < 0) return
+
+ if (this.sliding) return this.$element.one('slid.bs.carousel', function () { that.to(pos) }) // yes, "slid"
+ if (activeIndex == pos) return this.pause().cycle()
+
+ return this.slide(pos > activeIndex ? 'next' : 'prev', $(this.$items[pos]))
+ }
+
+ Carousel.prototype.pause = function (e) {
+ e || (this.paused = true)
+
+ if (this.$element.find('.next, .prev').length && $.support.transition) {
+ this.$element.trigger($.support.transition.end)
+ this.cycle(true)
+ }
+
+ this.interval = clearInterval(this.interval)
+
+ return this
+ }
+
+ Carousel.prototype.next = function () {
+ if (this.sliding) return
+ return this.slide('next')
+ }
+
+ Carousel.prototype.prev = function () {
+ if (this.sliding) return
+ return this.slide('prev')
+ }
+
+ Carousel.prototype.slide = function (type, next) {
+ var $active = this.$element.find('.item.active')
+ var $next = next || $active[type]()
+ var isCycling = this.interval
+ var direction = type == 'next' ? 'left' : 'right'
+ var fallback = type == 'next' ? 'first' : 'last'
+ var that = this
+
+ if (!$next.length) {
+ if (!this.options.wrap) return
+ $next = this.$element.find('.item')[fallback]()
+ }
+
+ if ($next.hasClass('active')) return (this.sliding = false)
+
+ var relatedTarget = $next[0]
+ var slideEvent = $.Event('slide.bs.carousel', {
+ relatedTarget: relatedTarget,
+ direction: direction
+ })
+ this.$element.trigger(slideEvent)
+ if (slideEvent.isDefaultPrevented()) return
+
+ this.sliding = true
+
+ isCycling && this.pause()
+
+ if (this.$indicators.length) {
+ this.$indicators.find('.active').removeClass('active')
+ var $nextIndicator = $(this.$indicators.children()[this.getItemIndex($next)])
+ $nextIndicator && $nextIndicator.addClass('active')
+ }
+
+ var slidEvent = $.Event('slid.bs.carousel', { relatedTarget: relatedTarget, direction: direction }) // yes, "slid"
+ if ($.support.transition && this.$element.hasClass('slide')) {
+ $next.addClass(type)
+ $next[0].offsetWidth // force reflow
+ $active.addClass(direction)
+ $next.addClass(direction)
+ $active
+ .one('bsTransitionEnd', function () {
+ $next.removeClass([type, direction].join(' ')).addClass('active')
+ $active.removeClass(['active', direction].join(' '))
+ that.sliding = false
+ setTimeout(function () {
+ that.$element.trigger(slidEvent)
+ }, 0)
+ })
+ .emulateTransitionEnd($active.css('transition-duration').slice(0, -1) * 1000)
+ } else {
+ $active.removeClass('active')
+ $next.addClass('active')
+ this.sliding = false
+ this.$element.trigger(slidEvent)
+ }
+
+ isCycling && this.cycle()
+
+ return this
+ }
+
+
+ // CAROUSEL PLUGIN DEFINITION
+ // ==========================
+
+ function Plugin(option) {
+ return this.each(function () {
+ var $this = $(this)
+ var data = $this.data('bs.carousel')
+ var options = $.extend({}, Carousel.DEFAULTS, $this.data(), typeof option == 'object' && option)
+ var action = typeof option == 'string' ? option : options.slide
+
+ if (!data) $this.data('bs.carousel', (data = new Carousel(this, options)))
+ if (typeof option == 'number') data.to(option)
+ else if (action) data[action]()
+ else if (options.interval) data.pause().cycle()
+ })
+ }
+
+ var old = $.fn.carousel
+
+ $.fn.carousel = Plugin
+ $.fn.carousel.Constructor = Carousel
+
+
+ // CAROUSEL NO CONFLICT
+ // ====================
+
+ $.fn.carousel.noConflict = function () {
+ $.fn.carousel = old
+ return this
+ }
+
+
+ // CAROUSEL DATA-API
+ // =================
+
+ $(document).on('click.bs.carousel.data-api', '[data-slide], [data-slide-to]', function (e) {
+ var href
+ var $this = $(this)
+ var $target = $($this.attr('data-target') || (href = $this.attr('href')) && href.replace(/.*(?=#[^\s]+$)/, '')) // strip for ie7
+ if (!$target.hasClass('carousel')) return
+ var options = $.extend({}, $target.data(), $this.data())
+ var slideIndex = $this.attr('data-slide-to')
+ if (slideIndex) options.interval = false
+
+ Plugin.call($target, options)
+
+ if (slideIndex) {
+ $target.data('bs.carousel').to(slideIndex)
+ }
+
+ e.preventDefault()
+ })
+
+ $(window).on('load', function () {
+ $('[data-ride="carousel"]').each(function () {
+ var $carousel = $(this)
+ Plugin.call($carousel, $carousel.data())
+ })
+ })
+
+}(window.$jqTheme||window.jQuery);
+
+/* ========================================================================
+ * Bootstrap: collapse.js v3.2.0
+ * http://getbootstrap.com/javascript/#collapse
+ * ========================================================================
+ * Copyright 2011-2014 Twitter, Inc.
+ * Licensed under MIT (https://github.com/twbs/bootstrap/blob/master/LICENSE)
+ * ======================================================================== */
+
+
++function ($) {
+ 'use strict';
+
+ // COLLAPSE PUBLIC CLASS DEFINITION
+ // ================================
+
+ var Collapse = function (element, options) {
+ this.$element = $(element)
+ this.options = $.extend({}, Collapse.DEFAULTS, options)
+ this.transitioning = null
+
+ if (this.options.parent) this.$parent = $(this.options.parent)
+ if (this.options.toggle) this.toggle()
+ }
+
+ Collapse.VERSION = '3.2.0'
+
+ Collapse.DEFAULTS = {
+ toggle: true
+ }
+
+ Collapse.prototype.dimension = function () {
+ var hasWidth = this.$element.hasClass('width')
+ return hasWidth ? 'width' : 'height'
+ }
+
+ Collapse.prototype.show = function () {
+ if (this.transitioning || this.$element.hasClass('in')) return
+
+ var startEvent = $.Event('show.bs.collapse')
+ this.$element.trigger(startEvent)
+ if (startEvent.isDefaultPrevented()) return
+
+ var actives = this.$parent && this.$parent.find('> .panel > .in')
+
+ if (actives && actives.length) {
+ var hasData = actives.data('bs.collapse')
+ if (hasData && hasData.transitioning) return
+ Plugin.call(actives, 'hide')
+ hasData || actives.data('bs.collapse', null)
+ }
+
+ var dimension = this.dimension()
+
+ this.$element
+ .removeClass('collapse')
+ .addClass('collapsing')[dimension](0)
+
+ this.transitioning = 1
+
+ var complete = function () {
+ this.$element
+ .removeClass('collapsing')
+ .addClass('collapse in')[dimension]('')
+ this.transitioning = 0
+ this.$element
+ .trigger('shown.bs.collapse')
+ }
+
+ if (!$.support.transition) return complete.call(this)
+
+ var scrollSize = $.camelCase(['scroll', dimension].join('-'))
+
+ this.$element
+ .one('bsTransitionEnd', $.proxy(complete, this))
+ .emulateTransitionEnd(350)[dimension](this.$element[0][scrollSize])
+ }
+
+ Collapse.prototype.hide = function () {
+ if (this.transitioning || !this.$element.hasClass('in')) return
+
+ var startEvent = $.Event('hide.bs.collapse')
+ this.$element.trigger(startEvent)
+ if (startEvent.isDefaultPrevented()) return
+
+ var dimension = this.dimension()
+
+ this.$element[dimension](this.$element[dimension]())[0].offsetHeight
+
+ this.$element
+ .addClass('collapsing')
+ .removeClass('collapse')
+ .removeClass('in')
+
+ this.transitioning = 1
+
+ var complete = function () {
+ this.transitioning = 0
+ this.$element
+ .trigger('hidden.bs.collapse')
+ .removeClass('collapsing')
+ .addClass('collapse')
+ }
+
+ if (!$.support.transition) return complete.call(this)
+
+ this.$element
+ [dimension](0)
+ .one('bsTransitionEnd', $.proxy(complete, this))
+ .emulateTransitionEnd(350)
+ }
+
+ Collapse.prototype.toggle = function () {
+ this[this.$element.hasClass('in') ? 'hide' : 'show']()
+ }
+
+
+ // COLLAPSE PLUGIN DEFINITION
+ // ==========================
+
+ function Plugin(option) {
+ return this.each(function () {
+ var $this = $(this)
+ var data = $this.data('bs.collapse')
+ var options = $.extend({}, Collapse.DEFAULTS, $this.data(), typeof option == 'object' && option)
+
+ if (!data && options.toggle && option == 'show') option = !option
+ if (!data) $this.data('bs.collapse', (data = new Collapse(this, options)))
+ if (typeof option == 'string') data[option]()
+ })
+ }
+
+ var old = $.fn.collapse
+
+ $.fn.collapse = Plugin
+ $.fn.collapse.Constructor = Collapse
+
+
+ // COLLAPSE NO CONFLICT
+ // ====================
+
+ $.fn.collapse.noConflict = function () {
+ $.fn.collapse = old
+ return this
+ }
+
+
+ // COLLAPSE DATA-API
+ // =================
+
+ $(document).on('click.bs.collapse.data-api', '[data-toggle="collapse"]', function (e) {
+ var href
+ var $this = $(this)
+ var target = $this.attr('data-target')
+ || e.preventDefault()
+ || (href = $this.attr('href')) && href.replace(/.*(?=#[^\s]+$)/, '') // strip for ie7
+ var $target = $(target)
+ var data = $target.data('bs.collapse')
+ var option = data ? 'toggle' : $this.data()
+ var parent = $this.attr('data-parent')
+ var $parent = parent && $(parent)
+
+ if (!data || !data.transitioning) {
+ if ($parent) $parent.find('[data-toggle="collapse"][data-parent="' + parent + '"]').not($this).addClass('collapsed')
+ $this[$target.hasClass('in') ? 'addClass' : 'removeClass']('collapsed')
+ }
+
+ Plugin.call($target, option)
+ })
+
+}(window.$jqTheme||window.jQuery);
+
+/* ========================================================================
+ * Bootstrap: dropdown.js v3.2.0
+ * http://getbootstrap.com/javascript/#dropdowns
+ * ========================================================================
+ * Copyright 2011-2014 Twitter, Inc.
+ * Licensed under MIT (https://github.com/twbs/bootstrap/blob/master/LICENSE)
+ * ======================================================================== */
+
+
++function ($) {
+ 'use strict';
+
+ // DROPDOWN CLASS DEFINITION
+ // =========================
+
+ var backdrop = '.dropdown-backdrop'
+ var toggle = '[data-toggle="dropdown"]'
+ var Dropdown = function (element) {
+ $(element).on('click.bs.dropdown', this.toggle)
+ }
+
+ Dropdown.VERSION = '3.2.0'
+
+ Dropdown.prototype.toggle = function (e) {
+ var $this = $(this)
+
+ if ($this.is('.disabled, :disabled')) return
+
+ var $parent = getParent($this)
+ var isActive = $parent.hasClass('open')
+
+ clearMenus()
+
+ if (!isActive) {
+ if ('ontouchstart' in document.documentElement && !$parent.closest('.navbar-nav').length) {
+ // if mobile we use a backdrop because click events don't delegate
+ $('<div class="dropdown-backdrop"/>').insertAfter($(this)).on('click', clearMenus)
+ }
+
+ var relatedTarget = { relatedTarget: this }
+ $parent.trigger(e = $.Event('show.bs.dropdown', relatedTarget))
+
+ if (e.isDefaultPrevented()) return
+
+ $this.trigger('focus')
+
+ $parent
+ .toggleClass('open')
+ .trigger('shown.bs.dropdown', relatedTarget)
+ }
+
+ return false
+ }
+
+ Dropdown.prototype.keydown = function (e) {
+ if (!/(38|40|27)/.test(e.keyCode)) return
+
+ var $this = $(this)
+
+ e.preventDefault()
+ e.stopPropagation()
+
+ if ($this.is('.disabled, :disabled')) return
+
+ var $parent = getParent($this)
+ var isActive = $parent.hasClass('open')
+
+ if (!isActive || (isActive && e.keyCode == 27)) {
+ if (e.which == 27) $parent.find(toggle).trigger('focus')
+ return $this.trigger('click')
+ }
+
+ var desc = ' li:not(.divider):visible a'
+ var $items = $parent.find('[role="menu"]' + desc + ', [role="listbox"]' + desc)
+
+ if (!$items.length) return
+
+ var index = $items.index($items.filter(':focus'))
+
+ if (e.keyCode == 38 && index > 0) index-- // up
+ if (e.keyCode == 40 && index < $items.length - 1) index++ // down
+ if (!~index) index = 0
+
+ $items.eq(index).trigger('focus')
+ }
+
+ function clearMenus(e) {
+ if (e && e.which === 3) return
+ $(backdrop).remove()
+ $(toggle).each(function () {
+ var $parent = getParent($(this))
+ var relatedTarget = { relatedTarget: this }
+ if (!$parent.hasClass('open')) return
+ $parent.trigger(e = $.Event('hide.bs.dropdown', relatedTarget))
+ if (e.isDefaultPrevented()) return
+ $parent.removeClass('open').trigger('hidden.bs.dropdown', relatedTarget)
+ })
+ }
+
+ function getParent($this) {
+ var selector = $this.attr('data-target')
+
+ if (!selector) {
+ selector = $this.attr('href')
+ selector = selector && /#[A-Za-z]/.test(selector) && selector.replace(/.*(?=#[^\s]*$)/, '') // strip for ie7
+ }
+
+ var $parent = selector && $(selector)
+
+ return $parent && $parent.length ? $parent : $this.parent()
+ }
+
+
+ // DROPDOWN PLUGIN DEFINITION
+ // ==========================
+
+ function Plugin(option) {
+ return this.each(function () {
+ var $this = $(this)
+ var data = $this.data('bs.dropdown')
+
+ if (!data) $this.data('bs.dropdown', (data = new Dropdown(this)))
+ if (typeof option == 'string') data[option].call($this)
+ })
+ }
+
+ var old = $.fn.dropdown
+
+ $.fn.dropdown = Plugin
+ $.fn.dropdown.Constructor = Dropdown
+
+
+ // DROPDOWN NO CONFLICT
+ // ====================
+
+ $.fn.dropdown.noConflict = function () {
+ $.fn.dropdown = old
+ return this
+ }
+
+
+ // APPLY TO STANDARD DROPDOWN ELEMENTS
+ // ===================================
+
+ $(document)
+ .on('click.bs.dropdown.data-api', clearMenus)
+ .on('click.bs.dropdown.data-api', '.dropdown form', function (e) { e.stopPropagation() })
+ .on('click.bs.dropdown.data-api', toggle, Dropdown.prototype.toggle)
+ .on('keydown.bs.dropdown.data-api', toggle + ', [role="menu"], [role="listbox"]', Dropdown.prototype.keydown)
+
+}(window.$jqTheme||window.jQuery);
+
+/* ========================================================================
+ * Bootstrap: modal.js v3.2.0
+ * http://getbootstrap.com/javascript/#modals
+ * ========================================================================
+ * Copyright 2011-2014 Twitter, Inc.
+ * Licensed under MIT (https://github.com/twbs/bootstrap/blob/master/LICENSE)
+ * ======================================================================== */
+
+
++function ($) {
+ 'use strict';
+
+ // MODAL CLASS DEFINITION
+ // ======================
+
+ var Modal = function (element, options) {
+ this.options = options
+ this.$body = $(document.body)
+ this.$element = $(element)
+ this.$backdrop =
+ this.isShown = null
+ this.scrollbarWidth = 0
+
+ if (this.options.remote) {
+ this.$element
+ .find('.modal-content')
+ .load(this.options.remote, $.proxy(function () {
+ this.$element.trigger('loaded.bs.modal')
+ }, this))
+ }
+ }
+
+ Modal.VERSION = '3.2.0'
+
+ Modal.DEFAULTS = {
+ backdrop: true,
+ keyboard: true,
+ show: true
+ }
+
+ Modal.prototype.toggle = function (_relatedTarget) {
+ return this.isShown ? this.hide() : this.show(_relatedTarget)
+ }
+
+ Modal.prototype.show = function (_relatedTarget) {
+ var that = this
+ var e = $.Event('show.bs.modal', { relatedTarget: _relatedTarget })
+
+ this.$element.trigger(e)
+
+ if (this.isShown || e.isDefaultPrevented()) return
+
+ this.isShown = true
+
+ this.checkScrollbar()
+ this.$body.addClass('modal-open')
+
+ this.setScrollbar()
+ this.escape()
+
+ this.$element.on('click.dismiss.bs.modal', '[data-dismiss="modal"]', $.proxy(this.hide, this))
+
+ this.backdrop(function () {
+ var transition = $.support.transition && that.$element.hasClass('fade')
+
+ if (!that.$element.parent().length) {
+ that.$element.appendTo(that.$body) // don't move modals dom position
+ }
+
+ that.$element
+ .show()
+ .scrollTop(0)
+
+ if (transition) {
+ that.$element[0].offsetWidth // force reflow
+ }
+
+ that.$element
+ .addClass('in')
+ .attr('aria-hidden', false)
+
+ that.enforceFocus()
+
+ var e = $.Event('shown.bs.modal', { relatedTarget: _relatedTarget })
+
+ transition ?
+ that.$element.find('.modal-dialog') // wait for modal to slide in
+ .one('bsTransitionEnd', function () {
+ that.$element.trigger('focus').trigger(e)
+ })
+ .emulateTransitionEnd(300) :
+ that.$element.trigger('focus').trigger(e)
+ })
+ }
+
+ Modal.prototype.hide = function (e) {
+ if (e) e.preventDefault()
+
+ e = $.Event('hide.bs.modal')
+
+ this.$element.trigger(e)
+
+ if (!this.isShown || e.isDefaultPrevented()) return
+
+ this.isShown = false
+
+ this.$body.removeClass('modal-open')
+
+ this.resetScrollbar()
+ this.escape()
+
+ $(document).off('focusin.bs.modal')
+
+ this.$element
+ .removeClass('in')
+ .attr('aria-hidden', true)
+ .off('click.dismiss.bs.modal')
+
+ $.support.transition && this.$element.hasClass('fade') ?
+ this.$element
+ .one('bsTransitionEnd', $.proxy(this.hideModal, this))
+ .emulateTransitionEnd(300) :
+ this.hideModal()
+ }
+
+ Modal.prototype.enforceFocus = function () {
+ $(document)
+ .off('focusin.bs.modal') // guard against infinite focus loop
+ .on('focusin.bs.modal', $.proxy(function (e) {
+ if (this.$element[0] !== e.target && !this.$element.has(e.target).length) {
+ this.$element.trigger('focus')
+ }
+ }, this))
+ }
+
+ Modal.prototype.escape = function () {
+ if (this.isShown && this.options.keyboard) {
+ this.$element.on('keyup.dismiss.bs.modal', $.proxy(function (e) {
+ e.which == 27 && this.hide()
+ }, this))
+ } else if (!this.isShown) {
+ this.$element.off('keyup.dismiss.bs.modal')
+ }
+ }
+
+ Modal.prototype.hideModal = function () {
+ var that = this
+ this.$element.hide()
+ this.backdrop(function () {
+ that.$element.trigger('hidden.bs.modal')
+ })
+ }
+
+ Modal.prototype.removeBackdrop = function () {
+ this.$backdrop && this.$backdrop.remove()
+ this.$backdrop = null
+ }
+
+ Modal.prototype.backdrop = function (callback) {
+ var that = this
+ var animate = this.$element.hasClass('fade') ? 'fade' : ''
+
+ if (this.isShown && this.options.backdrop) {
+ var doAnimate = $.support.transition && animate
+
+ this.$backdrop = $('<div class="modal-backdrop ' + animate + '" />')
+ .appendTo(this.$body)
+
+ this.$element.on('click.dismiss.bs.modal', $.proxy(function (e) {
+ if (e.target !== e.currentTarget) return
+ this.options.backdrop == 'static'
+ ? this.$element[0].focus.call(this.$element[0])
+ : this.hide.call(this)
+ }, this))
+
+ if (doAnimate) this.$backdrop[0].offsetWidth // force reflow
+
+ this.$backdrop.addClass('in')
+
+ if (!callback) return
+
+ doAnimate ?
+ this.$backdrop
+ .one('bsTransitionEnd', callback)
+ .emulateTransitionEnd(150) :
+ callback()
+
+ } else if (!this.isShown && this.$backdrop) {
+ this.$backdrop.removeClass('in')
+
+ var callbackRemove = function () {
+ that.removeBackdrop()
+ callback && callback()
+ }
+ $.support.transition && this.$element.hasClass('fade') ?
+ this.$backdrop
+ .one('bsTransitionEnd', callbackRemove)
+ .emulateTransitionEnd(150) :
+ callbackRemove()
+
+ } else if (callback) {
+ callback()
+ }
+ }
+
+ Modal.prototype.checkScrollbar = function () {
+ if (document.body.clientWidth >= window.innerWidth) return
+ this.scrollbarWidth = this.scrollbarWidth || this.measureScrollbar()
+ }
+
+ Modal.prototype.setScrollbar = function () {
+ var bodyPad = parseInt((this.$body.css('padding-right') || 0), 10)
+ if (this.scrollbarWidth) this.$body.css('padding-right', bodyPad + this.scrollbarWidth)
+ }
+
+ Modal.prototype.resetScrollbar = function () {
+ this.$body.css('padding-right', '')
+ }
+
+ Modal.prototype.measureScrollbar = function () { // thx walsh
+ var scrollDiv = document.createElement('div')
+ scrollDiv.className = 'modal-scrollbar-measure'
+ this.$body.append(scrollDiv)
+ var scrollbarWidth = scrollDiv.offsetWidth - scrollDiv.clientWidth
+ this.$body[0].removeChild(scrollDiv)
+ return scrollbarWidth
+ }
+
+
+ // MODAL PLUGIN DEFINITION
+ // =======================
+
+ function Plugin(option, _relatedTarget) {
+ return this.each(function () {
+ var $this = $(this)
+ var data = $this.data('bs.modal')
+ var options = $.extend({}, Modal.DEFAULTS, $this.data(), typeof option == 'object' && option)
+
+ if (!data) $this.data('bs.modal', (data = new Modal(this, options)))
+ if (typeof option == 'string') data[option](_relatedTarget)
+ else if (options.show) data.show(_relatedTarget)
+ })
+ }
+
+ var old = $.fn.modal
+
+ $.fn.modal = Plugin
+ $.fn.modal.Constructor = Modal
+
+
+ // MODAL NO CONFLICT
+ // =================
+
+ $.fn.modal.noConflict = function () {
+ $.fn.modal = old
+ return this
+ }
+
+
+ // MODAL DATA-API
+ // ==============
+
+ $(document).on('click.bs.modal.data-api', '[data-toggle="modal"]', function (e) {
+ var $this = $(this)
+ var href = $this.attr('href')
+ var $target = $($this.attr('data-target') || (href && href.replace(/.*(?=#[^\s]+$)/, ''))) // strip for ie7
+ var option = $target.data('bs.modal') ? 'toggle' : $.extend({ remote: !/#/.test(href) && href }, $target.data(), $this.data())
+
+ if ($this.is('a')) e.preventDefault()
+
+ $target.one('show.bs.modal', function (showEvent) {
+ if (showEvent.isDefaultPrevented()) return // only register focus restorer if modal will actually get shown
+ $target.one('hidden.bs.modal', function () {
+ $this.is(':visible') && $this.trigger('focus')
+ })
+ })
+ Plugin.call($target, option, this)
+ })
+
+}(window.$jqTheme||window.jQuery);
+
+/* ========================================================================
+ * Bootstrap: tooltip.js v3.2.0
+ * http://getbootstrap.com/javascript/#tooltip
+ * Inspired by the original jQuery.tipsy by Jason Frame
+ * ========================================================================
+ * Copyright 2011-2014 Twitter, Inc.
+ * Licensed under MIT (https://github.com/twbs/bootstrap/blob/master/LICENSE)
+ * ======================================================================== */
+
+
++function ($) {
+ 'use strict';
+
+ // TOOLTIP PUBLIC CLASS DEFINITION
+ // ===============================
+
+ var Tooltip = function (element, options) {
+ this.type =
+ this.options =
+ this.enabled =
+ this.timeout =
+ this.hoverState =
+ this.$element = null
+
+ this.init('tooltip', element, options)
+ }
+
+ Tooltip.VERSION = '3.2.0'
+
+ Tooltip.DEFAULTS = {
+ animation: true,
+ placement: 'top',
+ selector: false,
+ template: '<div class="tooltip" role="tooltip"><div class="tooltip-arrow"></div><div class="tooltip-inner"></div></div>',
+ trigger: 'hover focus',
+ title: '',
+ delay: 0,
+ html: false,
+ container: false,
+ viewport: {
+ selector: 'body',
+ padding: 0
+ }
+ }
+
+ Tooltip.prototype.init = function (type, element, options) {
+ this.enabled = true
+ this.type = type
+ this.$element = $(element)
+ this.options = this.getOptions(options)
+ this.$viewport = this.options.viewport && $(this.options.viewport.selector || this.options.viewport)
+
+ var triggers = this.options.trigger.split(' ')
+
+ for (var i = triggers.length; i--;) {
+ var trigger = triggers[i]
+
+ if (trigger == 'click') {
+ this.$element.on('click.' + this.type, this.options.selector, $.proxy(this.toggle, this))
+ } else if (trigger != 'manual') {
+ var eventIn = trigger == 'hover' ? 'mouseenter' : 'focusin'
+ var eventOut = trigger == 'hover' ? 'mouseleave' : 'focusout'
+
+ this.$element.on(eventIn + '.' + this.type, this.options.selector, $.proxy(this.enter, this))
+ this.$element.on(eventOut + '.' + this.type, this.options.selector, $.proxy(this.leave, this))
+ }
+ }
+
+ this.options.selector ?
+ (this._options = $.extend({}, this.options, { trigger: 'manual', selector: '' })) :
+ this.fixTitle()
+ }
+
+ Tooltip.prototype.getDefaults = function () {
+ return Tooltip.DEFAULTS
+ }
+
+ Tooltip.prototype.getOptions = function (options) {
+ options = $.extend({}, this.getDefaults(), this.$element.data(), options)
+
+ if (options.delay && typeof options.delay == 'number') {
+ options.delay = {
+ show: options.delay,
+ hide: options.delay
+ }
+ }
+
+ return options
+ }
+
+ Tooltip.prototype.getDelegateOptions = function () {
+ var options = {}
+ var defaults = this.getDefaults()
+
+ this._options && $.each(this._options, function (key, value) {
+ if (defaults[key] != value) options[key] = value
+ })
+
+ return options
+ }
+
+ Tooltip.prototype.enter = function (obj) {
+ var self = obj instanceof this.constructor ?
+ obj : $(obj.currentTarget).data('bs.' + this.type)
+
+ if (!self) {
+ self = new this.constructor(obj.currentTarget, this.getDelegateOptions())
+ $(obj.currentTarget).data('bs.' + this.type, self)
+ }
+
+ clearTimeout(self.timeout)
+
+ self.hoverState = 'in'
+
+ if (!self.options.delay || !self.options.delay.show) return self.show()
+
+ self.timeout = setTimeout(function () {
+ if (self.hoverState == 'in') self.show()
+ }, self.options.delay.show)
+ }
+
+ Tooltip.prototype.leave = function (obj) {
+ var self = obj instanceof this.constructor ?
+ obj : $(obj.currentTarget).data('bs.' + this.type)
+
+ if (!self) {
+ self = new this.constructor(obj.currentTarget, this.getDelegateOptions())
+ $(obj.currentTarget).data('bs.' + this.type, self)
+ }
+
+ clearTimeout(self.timeout)
+
+ self.hoverState = 'out'
+
+ if (!self.options.delay || !self.options.delay.hide) return self.hide()
+
+ self.timeout = setTimeout(function () {
+ if (self.hoverState == 'out') self.hide()
+ }, self.options.delay.hide)
+ }
+
+ Tooltip.prototype.show = function () {
+ var e = $.Event('show.bs.' + this.type)
+
+ if (this.hasContent() && this.enabled) {
+ this.$element.trigger(e)
+
+ var inDom = $.contains(document.documentElement, this.$element[0])
+ if (e.isDefaultPrevented() || !inDom) return
+ var that = this
+
+ var $tip = this.tip()
+
+ var tipId = this.getUID(this.type)
+
+ this.setContent()
+ $tip.attr('id', tipId)
+ this.$element.attr('aria-describedby', tipId)
+
+ if (this.options.animation) $tip.addClass('fade')
+
+ var placement = typeof this.options.placement == 'function' ?
+ this.options.placement.call(this, $tip[0], this.$element[0]) :
+ this.options.placement
+
+ var autoToken = /\s?auto?\s?/i
+ var autoPlace = autoToken.test(placement)
+ if (autoPlace) placement = placement.replace(autoToken, '') || 'top'
+
+ $tip
+ .detach()
+ .css({ top: 0, left: 0, display: 'block' })
+ .addClass(placement)
+ .data('bs.' + this.type, this)
+
+ this.options.container ? $tip.appendTo(this.options.container) : $tip.insertAfter(this.$element)
+
+ var pos = this.getPosition()
+ var actualWidth = $tip[0].offsetWidth
+ var actualHeight = $tip[0].offsetHeight
+
+ if (autoPlace) {
+ var orgPlacement = placement
+ var $parent = this.$element.parent()
+ var parentDim = this.getPosition($parent)
+
+ placement = placement == 'bottom' && pos.top + pos.height + actualHeight - parentDim.scroll > parentDim.height ? 'top' :
+ placement == 'top' && pos.top - parentDim.scroll - actualHeight < 0 ? 'bottom' :
+ placement == 'right' && pos.right + actualWidth > parentDim.width ? 'left' :
+ placement == 'left' && pos.left - actualWidth < parentDim.left ? 'right' :
+ placement
+
+ $tip
+ .removeClass(orgPlacement)
+ .addClass(placement)
+ }
+
+ var calculatedOffset = this.getCalculatedOffset(placement, pos, actualWidth, actualHeight)
+
+ this.applyPlacement(calculatedOffset, placement)
+
+ var complete = function () {
+ that.$element.trigger('shown.bs.' + that.type)
+ that.hoverState = null
+ }
+
+ $.support.transition && this.$tip.hasClass('fade') ?
+ $tip
+ .one('bsTransitionEnd', complete)
+ .emulateTransitionEnd(150) :
+ complete()
+ }
+ }
+
+ Tooltip.prototype.applyPlacement = function (offset, placement) {
+ var $tip = this.tip()
+ var width = $tip[0].offsetWidth
+ var height = $tip[0].offsetHeight
+
+ // manually read margins because getBoundingClientRect includes difference
+ var marginTop = parseInt($tip.css('margin-top'), 10)
+ var marginLeft = parseInt($tip.css('margin-left'), 10)
+
+ // we must check for NaN for ie 8/9
+ if (isNaN(marginTop)) marginTop = 0
+ if (isNaN(marginLeft)) marginLeft = 0
+
+ offset.top = offset.top + marginTop
+ offset.left = offset.left + marginLeft
+
+ // $.fn.offset doesn't round pixel values
+ // so we use setOffset directly with our own function B-0
+ $.offset.setOffset($tip[0], $.extend({
+ using: function (props) {
+ $tip.css({
+ top: Math.round(props.top),
+ left: Math.round(props.left)
+ })
+ }
+ }, offset), 0)
+
+ $tip.addClass('in')
+
+ // check to see if placing tip in new offset caused the tip to resize itself
+ var actualWidth = $tip[0].offsetWidth
+ var actualHeight = $tip[0].offsetHeight
+
+ if (placement == 'top' && actualHeight != height) {
+ offset.top = offset.top + height - actualHeight
+ }
+
+ var delta = this.getViewportAdjustedDelta(placement, offset, actualWidth, actualHeight)
+
+ if (delta.left) offset.left += delta.left
+ else offset.top += delta.top
+
+ var arrowDelta = delta.left ? delta.left * 2 - width + actualWidth : delta.top * 2 - height + actualHeight
+ var arrowPosition = delta.left ? 'left' : 'top'
+ var arrowOffsetPosition = delta.left ? 'offsetWidth' : 'offsetHeight'
+
+ $tip.offset(offset)
+ this.replaceArrow(arrowDelta, $tip[0][arrowOffsetPosition], arrowPosition)
+ }
+
+ Tooltip.prototype.replaceArrow = function (delta, dimension, position) {
+ this.arrow().css(position, delta ? (50 * (1 - delta / dimension) + '%') : '')
+ }
+
+ Tooltip.prototype.setContent = function () {
+ var $tip = this.tip()
+ var title = this.getTitle()
+
+ $tip.find('.tooltip-inner')[this.options.html ? 'html' : 'text'](title)
+ $tip.removeClass('fade in top bottom left right')
+ }
+
+ Tooltip.prototype.hide = function () {
+ var that = this
+ var $tip = this.tip()
+ var e = $.Event('hide.bs.' + this.type)
+
+ this.$element.removeAttr('aria-describedby')
+
+ function complete() {
+ if (that.hoverState != 'in') $tip.detach()
+ that.$element.trigger('hidden.bs.' + that.type)
+ }
+
+ this.$element.trigger(e)
+
+ if (e.isDefaultPrevented()) return
+
+ $tip.removeClass('in')
+
+ $.support.transition && this.$tip.hasClass('fade') ?
+ $tip
+ .one('bsTransitionEnd', complete)
+ .emulateTransitionEnd(150) :
+ complete()
+
+ this.hoverState = null
+
+ return this
+ }
+
+ Tooltip.prototype.fixTitle = function () {
+ var $e = this.$element
+ if ($e.attr('title') || typeof ($e.attr('data-original-title')) != 'string') {
+ $e.attr('data-original-title', $e.attr('title') || '').attr('title', '')
+ }
+ }
+
+ Tooltip.prototype.hasContent = function () {
+ return this.getTitle()
+ }
+
+ Tooltip.prototype.getPosition = function ($element) {
+ $element = $element || this.$element
+ var el = $element[0]
+ var isBody = el.tagName == 'BODY'
+ return $.extend({}, (typeof el.getBoundingClientRect == 'function') ? el.getBoundingClientRect() : null, {
+ scroll: isBody ? document.documentElement.scrollTop || document.body.scrollTop : $element.scrollTop(),
+ width: isBody ? $(window).width() : $element.outerWidth(),
+ height: isBody ? $(window).height() : $element.outerHeight()
+ }, isBody ? { top: 0, left: 0 } : $element.offset())
+ }
+
+ Tooltip.prototype.getCalculatedOffset = function (placement, pos, actualWidth, actualHeight) {
+ return placement == 'bottom' ? { top: pos.top + pos.height, left: pos.left + pos.width / 2 - actualWidth / 2 } :
+ placement == 'top' ? { top: pos.top - actualHeight, left: pos.left + pos.width / 2 - actualWidth / 2 } :
+ placement == 'left' ? { top: pos.top + pos.height / 2 - actualHeight / 2, left: pos.left - actualWidth } :
+ /* placement == 'right' */ { top: pos.top + pos.height / 2 - actualHeight / 2, left: pos.left + pos.width }
+
+ }
+
+ Tooltip.prototype.getViewportAdjustedDelta = function (placement, pos, actualWidth, actualHeight) {
+ var delta = { top: 0, left: 0 }
+ if (!this.$viewport) return delta
+
+ var viewportPadding = this.options.viewport && this.options.viewport.padding || 0
+ var viewportDimensions = this.getPosition(this.$viewport)
+
+ if (/right|left/.test(placement)) {
+ var topEdgeOffset = pos.top - viewportPadding - viewportDimensions.scroll
+ var bottomEdgeOffset = pos.top + viewportPadding - viewportDimensions.scroll + actualHeight
+ if (topEdgeOffset < viewportDimensions.top) { // top overflow
+ delta.top = viewportDimensions.top - topEdgeOffset
+ } else if (bottomEdgeOffset > viewportDimensions.top + viewportDimensions.height) { // bottom overflow
+ delta.top = viewportDimensions.top + viewportDimensions.height - bottomEdgeOffset
+ }
+ } else {
+ var leftEdgeOffset = pos.left - viewportPadding
+ var rightEdgeOffset = pos.left + viewportPadding + actualWidth
+ if (leftEdgeOffset < viewportDimensions.left) { // left overflow
+ delta.left = viewportDimensions.left - leftEdgeOffset
+ } else if (rightEdgeOffset > viewportDimensions.width) { // right overflow
+ delta.left = viewportDimensions.left + viewportDimensions.width - rightEdgeOffset
+ }
+ }
+
+ return delta
+ }
+
+ Tooltip.prototype.getTitle = function () {
+ var title
+ var $e = this.$element
+ var o = this.options
+
+ title = $e.attr('data-original-title')
+ || (typeof o.title == 'function' ? o.title.call($e[0]) : o.title)
+
+ return title
+ }
+
+ Tooltip.prototype.getUID = function (prefix) {
+ do prefix += ~~(Math.random() * 1000000)
+ while (document.getElementById(prefix))
+ return prefix
+ }
+
+ Tooltip.prototype.tip = function () {
+ return (this.$tip = this.$tip || $(this.options.template))
+ }
+
+ Tooltip.prototype.arrow = function () {
+ return (this.$arrow = this.$arrow || this.tip().find('.tooltip-arrow'))
+ }
+
+ Tooltip.prototype.validate = function () {
+ if (!this.$element[0].parentNode) {
+ this.hide()
+ this.$element = null
+ this.options = null
+ }
+ }
+
+ Tooltip.prototype.enable = function () {
+ this.enabled = true
+ }
+
+ Tooltip.prototype.disable = function () {
+ this.enabled = false
+ }
+
+ Tooltip.prototype.toggleEnabled = function () {
+ this.enabled = !this.enabled
+ }
+
+ Tooltip.prototype.toggle = function (e) {
+ var self = this
+ if (e) {
+ self = $(e.currentTarget).data('bs.' + this.type)
+ if (!self) {
+ self = new this.constructor(e.currentTarget, this.getDelegateOptions())
+ $(e.currentTarget).data('bs.' + this.type, self)
+ }
+ }
+
+ self.tip().hasClass('in') ? self.leave(self) : self.enter(self)
+ }
+
+ Tooltip.prototype.destroy = function () {
+ clearTimeout(this.timeout)
+ this.hide().$element.off('.' + this.type).removeData('bs.' + this.type)
+ }
+
+
+ // TOOLTIP PLUGIN DEFINITION
+ // =========================
+
+ function Plugin(option) {
+ return this.each(function () {
+ var $this = $(this)
+ var data = $this.data('bs.tooltip')
+ var options = typeof option == 'object' && option
+
+ if (!data && option == 'destroy') return
+ if (!data) $this.data('bs.tooltip', (data = new Tooltip(this, options)))
+ if (typeof option == 'string') data[option]()
+ })
+ }
+
+ var old = $.fn.tooltip
+
+ $.fn.tooltip = Plugin
+ $.fn.tooltip.Constructor = Tooltip
+
+
+ // TOOLTIP NO CONFLICT
+ // ===================
+
+ $.fn.tooltip.noConflict = function () {
+ $.fn.tooltip = old
+ return this
+ }
+
+}(window.$jqTheme||window.jQuery);
+
+/* ========================================================================
+ * Bootstrap: popover.js v3.2.0
+ * http://getbootstrap.com/javascript/#popovers
+ * ========================================================================
+ * Copyright 2011-2014 Twitter, Inc.
+ * Licensed under MIT (https://github.com/twbs/bootstrap/blob/master/LICENSE)
+ * ======================================================================== */
+
+
++function ($) {
+ 'use strict';
+
+ // POPOVER PUBLIC CLASS DEFINITION
+ // ===============================
+
+ var Popover = function (element, options) {
+ this.init('popover', element, options)
+ }
+
+ if (!$.fn.tooltip) throw new Error('Popover requires tooltip.js')
+
+ Popover.VERSION = '3.2.0'
+
+ Popover.DEFAULTS = $.extend({}, $.fn.tooltip.Constructor.DEFAULTS, {
+ placement: 'right',
+ trigger: 'click',
+ content: '',
+ template: '<div class="popover" role="tooltip"><div class="arrow"></div><h3 class="popover-title"></h3><div class="popover-content"></div></div>'
+ })
+
+
+ // NOTE: POPOVER EXTENDS tooltip.js
+ // ================================
+
+ Popover.prototype = $.extend({}, $.fn.tooltip.Constructor.prototype)
+
+ Popover.prototype.constructor = Popover
+
+ Popover.prototype.getDefaults = function () {
+ return Popover.DEFAULTS
+ }
+
+ Popover.prototype.setContent = function () {
+ var $tip = this.tip()
+ var title = this.getTitle()
+ var content = this.getContent()
+
+ $tip.find('.popover-title')[this.options.html ? 'html' : 'text'](title)
+ $tip.find('.popover-content').empty()[ // we use append for html objects to maintain js events
+ this.options.html ? (typeof content == 'string' ? 'html' : 'append') : 'text'
+ ](content)
+
+ $tip.removeClass('fade top bottom left right in')
+
+ // IE8 doesn't accept hiding via the `:empty` pseudo selector, we have to do
+ // this manually by checking the contents.
+ if (!$tip.find('.popover-title').html()) $tip.find('.popover-title').hide()
+ }
+
+ Popover.prototype.hasContent = function () {
+ return this.getTitle() || this.getContent()
+ }
+
+ Popover.prototype.getContent = function () {
+ var $e = this.$element
+ var o = this.options
+
+ return $e.attr('data-content')
+ || (typeof o.content == 'function' ?
+ o.content.call($e[0]) :
+ o.content)
+ }
+
+ Popover.prototype.arrow = function () {
+ return (this.$arrow = this.$arrow || this.tip().find('.arrow'))
+ }
+
+ Popover.prototype.tip = function () {
+ if (!this.$tip) this.$tip = $(this.options.template)
+ return this.$tip
+ }
+
+
+ // POPOVER PLUGIN DEFINITION
+ // =========================
+
+ function Plugin(option) {
+ return this.each(function () {
+ var $this = $(this)
+ var data = $this.data('bs.popover')
+ var options = typeof option == 'object' && option
+
+ if (!data && option == 'destroy') return
+ if (!data) $this.data('bs.popover', (data = new Popover(this, options)))
+ if (typeof option == 'string') data[option]()
+ })
+ }
+
+ var old = $.fn.popover
+
+ $.fn.popover = Plugin
+ $.fn.popover.Constructor = Popover
+
+
+ // POPOVER NO CONFLICT
+ // ===================
+
+ $.fn.popover.noConflict = function () {
+ $.fn.popover = old
+ return this
+ }
+
+}(window.$jqTheme||window.jQuery);
+
+/* ========================================================================
+ * Bootstrap: scrollspy.js v3.2.0
+ * http://getbootstrap.com/javascript/#scrollspy
+ * ========================================================================
+ * Copyright 2011-2014 Twitter, Inc.
+ * Licensed under MIT (https://github.com/twbs/bootstrap/blob/master/LICENSE)
+ * ======================================================================== */
+
+
++function ($) {
+ 'use strict';
+
+ // SCROLLSPY CLASS DEFINITION
+ // ==========================
+
+ function ScrollSpy(element, options) {
+ var process = $.proxy(this.process, this)
+
+ this.$body = $('body')
+ this.$scrollElement = $(element).is('body') ? $(window) : $(element)
+ this.options = $.extend({}, ScrollSpy.DEFAULTS, options)
+ this.selector = (this.options.target || '') + ' .nav li > a'
+ this.offsets = []
+ this.targets = []
+ this.activeTarget = null
+ this.scrollHeight = 0
+
+ this.$scrollElement.on('scroll.bs.scrollspy', process)
+ this.refresh()
+ this.process()
+ }
+
+ ScrollSpy.VERSION = '3.2.0'
+
+ ScrollSpy.DEFAULTS = {
+ offset: 10
+ }
+
+ ScrollSpy.prototype.getScrollHeight = function () {
+ return this.$scrollElement[0].scrollHeight || Math.max(this.$body[0].scrollHeight, document.documentElement.scrollHeight)
+ }
+
+ ScrollSpy.prototype.refresh = function () {
+ var offsetMethod = 'offset'
+ var offsetBase = 0
+
+ if (!$.isWindow(this.$scrollElement[0])) {
+ offsetMethod = 'position'
+ offsetBase = this.$scrollElement.scrollTop()
+ }
+
+ this.offsets = []
+ this.targets = []
+ this.scrollHeight = this.getScrollHeight()
+
+ var self = this
+
+ this.$body
+ .find(this.selector)
+ .map(function () {
+ var $el = $(this)
+ var href = $el.data('target') || $el.attr('href')
+ var $href = /^#./.test(href) && $(href)
+
+ return ($href
+ && $href.length
+ && $href.is(':visible')
+ && [[$href[offsetMethod]().top + offsetBase, href]]) || null
+ })
+ .sort(function (a, b) { return a[0] - b[0] })
+ .each(function () {
+ self.offsets.push(this[0])
+ self.targets.push(this[1])
+ })
+ }
+
+ ScrollSpy.prototype.process = function () {
+ var scrollTop = this.$scrollElement.scrollTop() + this.options.offset
+ var scrollHeight = this.getScrollHeight()
+ var maxScroll = this.options.offset + scrollHeight - this.$scrollElement.height()
+ var offsets = this.offsets
+ var targets = this.targets
+ var activeTarget = this.activeTarget
+ var i
+
+ if (this.scrollHeight != scrollHeight) {
+ this.refresh()
+ }
+
+ if (scrollTop >= maxScroll) {
+ return activeTarget != (i = targets[targets.length - 1]) && this.activate(i)
+ }
+
+ if (activeTarget && scrollTop <= offsets[0]) {
+ return activeTarget != (i = targets[0]) && this.activate(i)
+ }
+
+ for (i = offsets.length; i--;) {
+ activeTarget != targets[i]
+ && scrollTop >= offsets[i]
+ && (!offsets[i + 1] || scrollTop <= offsets[i + 1])
+ && this.activate(targets[i])
+ }
+ }
+
+ ScrollSpy.prototype.activate = function (target) {
+ this.activeTarget = target
+
+ $(this.selector)
+ .parentsUntil(this.options.target, '.active')
+ .removeClass('active')
+
+ var selector = this.selector +
+ '[data-target="' + target + '"],' +
+ this.selector + '[href="' + target + '"]'
+
+ var active = $(selector)
+ .parents('li')
+ .addClass('active')
+
+ if (active.parent('.dropdown-menu').length) {
+ active = active
+ .closest('li.dropdown')
+ .addClass('active')
+ }
+
+ active.trigger('activate.bs.scrollspy')
+ }
+
+
+ // SCROLLSPY PLUGIN DEFINITION
+ // ===========================
+
+ function Plugin(option) {
+ return this.each(function () {
+ var $this = $(this)
+ var data = $this.data('bs.scrollspy')
+ var options = typeof option == 'object' && option
+
+ if (!data) $this.data('bs.scrollspy', (data = new ScrollSpy(this, options)))
+ if (typeof option == 'string') data[option]()
+ })
+ }
+
+ var old = $.fn.scrollspy
+
+ $.fn.scrollspy = Plugin
+ $.fn.scrollspy.Constructor = ScrollSpy
+
+
+ // SCROLLSPY NO CONFLICT
+ // =====================
+
+ $.fn.scrollspy.noConflict = function () {
+ $.fn.scrollspy = old
+ return this
+ }
+
+
+ // SCROLLSPY DATA-API
+ // ==================
+
+ $(window).on('load.bs.scrollspy.data-api', function () {
+ $('[data-spy="scroll"]').each(function () {
+ var $spy = $(this)
+ Plugin.call($spy, $spy.data())
+ })
+ })
+
+}(window.$jqTheme||window.jQuery);
+
+/* ========================================================================
+ * Bootstrap: tab.js v3.2.0
+ * http://getbootstrap.com/javascript/#tabs
+ * ========================================================================
+ * Copyright 2011-2014 Twitter, Inc.
+ * Licensed under MIT (https://github.com/twbs/bootstrap/blob/master/LICENSE)
+ * ======================================================================== */
+
+
++function ($) {
+ 'use strict';
+
+ // TAB CLASS DEFINITION
+ // ====================
+
+ var Tab = function (element) {
+ this.element = $(element)
+ }
+
+ Tab.VERSION = '3.2.0'
+
+ Tab.prototype.show = function () {
+ var $this = this.element
+ var $ul = $this.closest('ul:not(.dropdown-menu)')
+ var selector = $this.data('target')
+
+ if (!selector) {
+ selector = $this.attr('href')
+ selector = selector && selector.replace(/.*(?=#[^\s]*$)/, '') // strip for ie7
+ }
+
+ if ($this.parent('li').hasClass('active')) return
+
+ var previous = $ul.find('.active:last a')[0]
+ var e = $.Event('show.bs.tab', {
+ relatedTarget: previous
+ })
+
+ $this.trigger(e)
+
+ if (e.isDefaultPrevented()) return
+
+ var $target = $(selector)
+
+ this.activate($this.closest('li'), $ul)
+ this.activate($target, $target.parent(), function () {
+ $this.trigger({
+ type: 'shown.bs.tab',
+ relatedTarget: previous
+ })
+ })
+ }
+
+ Tab.prototype.activate = function (element, container, callback) {
+ var $active = container.find('> .active')
+ var transition = callback
+ && $.support.transition
+ && $active.hasClass('fade')
+
+ function next() {
+ $active
+ .removeClass('active')
+ .find('> .dropdown-menu > .active')
+ .removeClass('active')
+
+ element.addClass('active')
+
+ if (transition) {
+ element[0].offsetWidth // reflow for transition
+ element.addClass('in')
+ } else {
+ element.removeClass('fade')
+ }
+
+ if (element.parent('.dropdown-menu')) {
+ element.closest('li.dropdown').addClass('active')
+ }
+
+ callback && callback()
+ }
+
+ transition ?
+ $active
+ .one('bsTransitionEnd', next)
+ .emulateTransitionEnd(150) :
+ next()
+
+ $active.removeClass('in')
+ }
+
+
+ // TAB PLUGIN DEFINITION
+ // =====================
+
+ function Plugin(option) {
+ return this.each(function () {
+ var $this = $(this)
+ var data = $this.data('bs.tab')
+
+ if (!data) $this.data('bs.tab', (data = new Tab(this)))
+ if (typeof option == 'string') data[option]()
+ })
+ }
+
+ var old = $.fn.tab
+
+ $.fn.tab = Plugin
+ $.fn.tab.Constructor = Tab
+
+
+ // TAB NO CONFLICT
+ // ===============
+
+ $.fn.tab.noConflict = function () {
+ $.fn.tab = old
+ return this
+ }
+
+
+ // TAB DATA-API
+ // ============
+
+ $(document).on('click.bs.tab.data-api', '[data-toggle="tab"], [data-toggle="pill"]', function (e) {
+ e.preventDefault()
+ Plugin.call($(this), 'show')
+ })
+
+}(window.$jqTheme||window.jQuery);
+
+/* ========================================================================
+ * Bootstrap: affix.js v3.2.0
+ * http://getbootstrap.com/javascript/#affix
+ * ========================================================================
+ * Copyright 2011-2014 Twitter, Inc.
+ * Licensed under MIT (https://github.com/twbs/bootstrap/blob/master/LICENSE)
+ * ======================================================================== */
+
+
++function ($) {
+ 'use strict';
+
+ // AFFIX CLASS DEFINITION
+ // ======================
+
+ var Affix = function (element, options) {
+ this.options = $.extend({}, Affix.DEFAULTS, options)
+
+ this.$target = $(this.options.target)
+ .on('scroll.bs.affix.data-api', $.proxy(this.checkPosition, this))
+ .on('click.bs.affix.data-api', $.proxy(this.checkPositionWithEventLoop, this))
+
+ this.$element = $(element)
+ this.affixed =
+ this.unpin =
+ this.pinnedOffset = null
+
+ this.checkPosition()
+ }
+
+ Affix.VERSION = '3.2.0'
+
+ Affix.RESET = 'affix affix-top affix-bottom'
+
+ Affix.DEFAULTS = {
+ offset: 0,
+ target: window
+ }
+
+ Affix.prototype.getPinnedOffset = function () {
+ if (this.pinnedOffset) return this.pinnedOffset
+ this.$element.removeClass(Affix.RESET).addClass('affix')
+ var scrollTop = this.$target.scrollTop()
+ var position = this.$element.offset()
+ return (this.pinnedOffset = position.top - scrollTop)
+ }
+
+ Affix.prototype.checkPositionWithEventLoop = function () {
+ setTimeout($.proxy(this.checkPosition, this), 1)
+ }
+
+ Affix.prototype.checkPosition = function () {
+ if (!this.$element.is(':visible')) return
+
+ var scrollHeight = $(document).height()
+ var scrollTop = this.$target.scrollTop()
+ var position = this.$element.offset()
+ var offset = this.options.offset
+ var offsetTop = offset.top
+ var offsetBottom = offset.bottom
+
+ if (typeof offset != 'object') offsetBottom = offsetTop = offset
+ if (typeof offsetTop == 'function') offsetTop = offset.top(this.$element)
+ if (typeof offsetBottom == 'function') offsetBottom = offset.bottom(this.$element)
+
+ var affix = this.unpin != null && (scrollTop + this.unpin <= position.top) ? false :
+ offsetBottom != null && (position.top + this.$element.height() >= scrollHeight - offsetBottom) ? 'bottom' :
+ offsetTop != null && (scrollTop <= offsetTop) ? 'top' : false
+
+ if (this.affixed === affix) return
+ if (this.unpin != null) this.$element.css('top', '')
+
+ var affixType = 'affix' + (affix ? '-' + affix : '')
+ var e = $.Event(affixType + '.bs.affix')
+
+ this.$element.trigger(e)
+
+ if (e.isDefaultPrevented()) return
+
+ this.affixed = affix
+ this.unpin = affix == 'bottom' ? this.getPinnedOffset() : null
+
+ this.$element
+ .removeClass(Affix.RESET)
+ .addClass(affixType)
+ .trigger($.Event(affixType.replace('affix', 'affixed')))
+
+ if (affix == 'bottom') {
+ this.$element.offset({
+ top: scrollHeight - this.$element.height() - offsetBottom
+ })
+ }
+ }
+
+
+ // AFFIX PLUGIN DEFINITION
+ // =======================
+
+ function Plugin(option) {
+ return this.each(function () {
+ var $this = $(this)
+ var data = $this.data('bs.affix')
+ var options = typeof option == 'object' && option
+
+ if (!data) $this.data('bs.affix', (data = new Affix(this, options)))
+ if (typeof option == 'string') data[option]()
+ })
+ }
+
+ var old = $.fn.affix
+
+ $.fn.affix = Plugin
+ $.fn.affix.Constructor = Affix
+
+
+ // AFFIX NO CONFLICT
+ // =================
+
+ $.fn.affix.noConflict = function () {
+ $.fn.affix = old
+ return this
+ }
+
+
+ // AFFIX DATA-API
+ // ==============
+
+ $(window).on('load', function () {
+ $('[data-spy="affix"]').each(function () {
+ var $spy = $(this)
+ var data = $spy.data()
+
+ data.offset = data.offset || {}
+
+ if (data.offsetBottom) data.offset.bottom = data.offsetBottom
+ if (data.offsetTop) data.offset.top = data.offsetTop
+
+ Plugin.call($spy, data)
+ })
+ })
+
+}(window.$jqTheme||window.jQuery);
diff --git a/docs/build/html/_static/bootstrap-3.2.0/js/bootstrap.min.js b/docs/build/html/_static/bootstrap-3.2.0/js/bootstrap.min.js
new file mode 100644
index 0000000000000000000000000000000000000000..b76d41c0f1a9d9f400a2baea6869a242e5ff318f
--- /dev/null
+++ b/docs/build/html/_static/bootstrap-3.2.0/js/bootstrap.min.js
@@ -0,0 +1,6 @@
+/*!
+ * Bootstrap v3.2.0 (http://getbootstrap.com)
+ * Copyright 2011-2014 Twitter, Inc.
+ * Licensed under MIT (https://github.com/twbs/bootstrap/blob/master/LICENSE)
+ */
+if("undefined"==typeof (window.$jqTheme||window.jQuery))throw new Error("Bootstrap's JavaScript requires jQuery");+function(a){"use strict";function b(){var a=document.createElement("bootstrap"),b={WebkitTransition:"webkitTransitionEnd",MozTransition:"transitionend",OTransition:"oTransitionEnd otransitionend",transition:"transitionend"};for(var c in b)if(void 0!==a.style[c])return{end:b[c]};return!1}a.fn.emulateTransitionEnd=function(b){var c=!1,d=this;a(this).one("bsTransitionEnd",function(){c=!0});var e=function(){c||a(d).trigger(a.support.transition.end)};return setTimeout(e,b),this},a(function(){a.support.transition=b(),a.support.transition&&(a.event.special.bsTransitionEnd={bindType:a.support.transition.end,delegateType:a.support.transition.end,handle:function(b){return a(b.target).is(this)?b.handleObj.handler.apply(this,arguments):void 0}})})}(window.$jqTheme||window.jQuery),+function(a){"use strict";function b(b){return this.each(function(){var c=a(this),e=c.data("bs.alert");e||c.data("bs.alert",e=new d(this)),"string"==typeof b&&e[b].call(c)})}var c='[data-dismiss="alert"]',d=function(b){a(b).on("click",c,this.close)};d.VERSION="3.2.0",d.prototype.close=function(b){function c(){f.detach().trigger("closed.bs.alert").remove()}var d=a(this),e=d.attr("data-target");e||(e=d.attr("href"),e=e&&e.replace(/.*(?=#[^\s]*$)/,""));var f=a(e);b&&b.preventDefault(),f.length||(f=d.hasClass("alert")?d:d.parent()),f.trigger(b=a.Event("close.bs.alert")),b.isDefaultPrevented()||(f.removeClass("in"),a.support.transition&&f.hasClass("fade")?f.one("bsTransitionEnd",c).emulateTransitionEnd(150):c())};var e=a.fn.alert;a.fn.alert=b,a.fn.alert.Constructor=d,a.fn.alert.noConflict=function(){return a.fn.alert=e,this},a(document).on("click.bs.alert.data-api",c,d.prototype.close)}(window.$jqTheme||window.jQuery),+function(a){"use strict";function b(b){return this.each(function(){var d=a(this),e=d.data("bs.button"),f="object"==typeof 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c.getBoundingClientRect?c.getBoundingClientRect():null,{scroll:d?document.documentElement.scrollTop||document.body.scrollTop:b.scrollTop(),width:d?a(window).width():b.outerWidth(),height:d?a(window).height():b.outerHeight()},d?{top:0,left:0}:b.offset())},c.prototype.getCalculatedOffset=function(a,b,c,d){return"bottom"==a?{top:b.top+b.height,left:b.left+b.width/2-c/2}:"top"==a?{top:b.top-d,left:b.left+b.width/2-c/2}:"left"==a?{top:b.top+b.height/2-d/2,left:b.left-c}:{top:b.top+b.height/2-d/2,left:b.left+b.width}},c.prototype.getViewportAdjustedDelta=function(a,b,c,d){var e={top:0,left:0};if(!this.$viewport)return e;var f=this.options.viewport&&this.options.viewport.padding||0,g=this.getPosition(this.$viewport);if(/right|left/.test(a)){var h=b.top-f-g.scroll,i=b.top+f-g.scroll+d;h<g.top?e.top=g.top-h:i>g.top+g.height&&(e.top=g.top+g.height-i)}else{var j=b.left-f,k=b.left+f+c;j<g.left?e.left=g.left-j:k>g.width&&(e.left=g.left+g.width-k)}return e},c.prototype.getTitle=function(){var a,b=this.$element,c=this.options;return a=b.attr("data-original-title")||("function"==typeof c.title?c.title.call(b[0]):c.title)},c.prototype.getUID=function(a){do a+=~~(1e6*Math.random());while(document.getElementById(a));return a},c.prototype.tip=function(){return this.$tip=this.$tip||a(this.options.template)},c.prototype.arrow=function(){return this.$arrow=this.$arrow||this.tip().find(".tooltip-arrow")},c.prototype.validate=function(){this.$element[0].parentNode||(this.hide(),this.$element=null,this.options=null)},c.prototype.enable=function(){this.enabled=!0},c.prototype.disable=function(){this.enabled=!1},c.prototype.toggleEnabled=function(){this.enabled=!this.enabled},c.prototype.toggle=function(b){var c=this;b&&(c=a(b.currentTarget).data("bs."+this.type),c||(c=new 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d=a.fn.popover;a.fn.popover=b,a.fn.popover.Constructor=c,a.fn.popover.noConflict=function(){return a.fn.popover=d,this}}(window.$jqTheme||window.jQuery),+function(a){"use strict";function b(c,d){var e=a.proxy(this.process,this);this.$body=a("body"),this.$scrollElement=a(a(c).is("body")?window:c),this.options=a.extend({},b.DEFAULTS,d),this.selector=(this.options.target||"")+" .nav li > a",this.offsets=[],this.targets=[],this.activeTarget=null,this.scrollHeight=0,this.$scrollElement.on("scroll.bs.scrollspy",e),this.refresh(),this.process()}function c(c){return this.each(function(){var d=a(this),e=d.data("bs.scrollspy"),f="object"==typeof c&&c;e||d.data("bs.scrollspy",e=new b(this,f)),"string"==typeof c&&e[c]()})}b.VERSION="3.2.0",b.DEFAULTS={offset:10},b.prototype.getScrollHeight=function(){return this.$scrollElement[0].scrollHeight||Math.max(this.$body[0].scrollHeight,document.documentElement.scrollHeight)},b.prototype.refresh=function(){var 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diff --git a/docs/build/html/_static/bootstrap-sphinx.css b/docs/build/html/_static/bootstrap-sphinx.css
new file mode 100644
index 0000000000000000000000000000000000000000..f38994e724c8fa50805bf3b01b135c44d0f6ae9f
--- /dev/null
+++ b/docs/build/html/_static/bootstrap-sphinx.css
@@ -0,0 +1,187 @@
+/*
+ * bootstrap-sphinx.css
+ * ~~~~~~~~~~~~~~~~~~~~
+ *
+ * Sphinx stylesheet -- Bootstrap theme.
+ */
+
+.navbar-inverse .brand {
+ color: #FFF;
+}
+
+/*
+ * Reset navbar styles from overrides in:
+ * https://bitbucket.org/birkenfeld/sphinx/commits/78d8ebf76b630ab4073a7328af9d91e8123b8d96
+ */
+.navbar .container {
+ padding-top: 0;
+}
+
+.page-top {
+ top: 0px;
+}
+
+
+
+
+
+ body {
+
+ padding-top: 40px;
+
+ }
+ .page-top {
+
+ top: 40px;
+
+ }
+
+
+
+.navbar-inner {
+ padding-left: 12px !important;
+ padding-right: 12px !important;
+}
+
+
+table {
+ border: 0;
+}
+
+.highlighttable .code pre {
+ font-size: 12px;
+}
+
+.highlighttable .linenos pre {
+ word-break: normal;
+ font-size: 12px;
+}
+
+div.highlight {
+ background: none;
+}
+
+a.footnote-reference {
+ vertical-align: super;
+ font-size: 75%;
+}
+
+table.footnote td.label {
+ font-size: 100%;
+ display: block;
+ line-height: normal;
+ background: inherit;
+}
+
+table.footnote {
+ width: auto;
+ margin-bottom: 0px;
+}
+
+table.field-list {
+ width: auto;
+}
+
+.footer {
+ width: 100%;
+ border-top: 1px solid #ccc;
+ padding-top: 10px;
+}
+
+.bs-sidenav form, .bs-sidenav #sourcelink {
+ padding: 5px 20px;
+}
+
+
+
+/* The code below is based on the bootstrap website sidebar */
+
+.bs-sidenav.affix {
+ position: static;
+}
+
+/* First level of nav */
+.bs-sidenav {
+ margin-top: 30px;
+ margin-bottom: 30px;
+ padding-top: 10px;
+ padding-bottom: 10px;
+ text-shadow: 0 1px 0 #fff;
+ background-color: #f7f5fa;
+ border-radius: 5px;
+}
+
+/* All levels of nav */
+.bs-sidenav .nav > li > a {
+ display: block;
+ color: #716b7a;
+ padding: 5px 20px;
+}
+.bs-sidenav .nav > li > a:hover,
+.bs-sidenav .nav > li > a:focus {
+ text-decoration: none;
+ background-color: #e5e3e9;
+ border-right: 1px solid #dbd8e0;
+}
+.bs-sidenav .nav > .active > a,
+.bs-sidenav .nav > .active:hover > a,
+.bs-sidenav .nav > .active:focus > a {
+ font-weight: bold;
+ color: #563d7c;
+ background-color: transparent;
+ border-right: 1px solid #563d7c;
+}
+
+.bs-sidenav .nav .nav > li > a {
+ padding-top: 3px;
+ padding-bottom: 3px;
+ padding-left: 30px;
+ font-size: 90%;
+}
+
+.bs-sidenav .nav .nav .nav > li > a {
+ padding-top: 3px;
+ padding-bottom: 3px;
+ padding-left: 40px;
+ font-size: 90%;
+}
+
+.bs-sidenav .nav .nav .nav .nav > li > a {
+ padding-top: 3px;
+ padding-bottom: 3px;
+ padding-left: 50px;
+ font-size: 90%;
+}
+
+/* Show and affix the side nav when space allows it */
+@media screen and (min-width: 992px) {
+ .bs-sidenav .nav > .active > ul {
+ display: block;
+ }
+ /* Widen the fixed sidenav */
+ .bs-sidenav.affix,
+ .bs-sidenav.affix-bottom {
+ width: 213px;
+ }
+ .bs-sidenav.affix {
+ position: fixed; /* Undo the static from mobile first approach */
+ top: 80px;
+ }
+ .bs-sidenav.affix-bottom {
+ position: absolute; /* Undo the static from mobile first approach */
+ }
+ .bs-sidenav.affix-bottom .bs-sidenav,
+ .bs-sidenav.affix .bs-sidenav {
+ margin-top: 0;
+ margin-bottom: 0;
+ }
+}
+@media screen and (min-width: 1200px) {
+ /* Widen the fixed sidenav again */
+ .bs-sidenav.affix-bottom,
+ .bs-sidenav.affix {
+ width: 263px;
+ }
+}
+
+
diff --git a/docs/build/html/_static/bootstrap-sphinx.js b/docs/build/html/_static/bootstrap-sphinx.js
new file mode 100644
index 0000000000000000000000000000000000000000..e5a0ccca05c04e4532fc2e97d2f94ffaa4b5261e
--- /dev/null
+++ b/docs/build/html/_static/bootstrap-sphinx.js
@@ -0,0 +1,173 @@
+(function ($) {
+ /**
+ * Patch TOC list.
+ *
+ * Will mutate the underlying span to have a correct ul for nav.
+ *
+ * @param $span: Span containing nested UL's to mutate.
+ * @param minLevel: Starting level for nested lists. (1: global, 2: local).
+ */
+ var patchToc = function ($ul, minLevel) {
+ var findA,
+ patchTables,
+ $localLi;
+
+ // Find all a "internal" tags, traversing recursively.
+ findA = function ($elem, level) {
+ level = level || 0;
+ var $items = $elem.find("> li > a.internal, > ul, > li > ul");
+
+ // Iterate everything in order.
+ $items.each(function (index, item) {
+ var $item = $(item),
+ tag = item.tagName.toLowerCase(),
+ $childrenLi = $item.children('li'),
+ $parentLi = $($item.parent('li'), $item.parent().parent('li'));
+
+ // Add dropdowns if more children and above minimum level.
+ if (tag === 'ul' && level >= minLevel && $childrenLi.length > 0) {
+ $parentLi
+ .addClass('dropdown-submenu')
+ .children('a').first().attr('tabindex', -1);
+
+ $item.addClass('dropdown-menu');
+ }
+
+ findA($item, level + 1);
+ });
+ };
+
+ findA($ul);
+ };
+
+ /**
+ * Patch all tables to remove ``docutils`` class and add Bootstrap base
+ * ``table`` class.
+ */
+ patchTables = function () {
+ $("table.docutils")
+ .removeClass("docutils")
+ .addClass("table")
+ .attr("border", 0);
+ };
+
+ $(window).load(function () {
+ /*
+ * Scroll the window to avoid the topnav bar
+ * https://github.com/twbs/bootstrap/issues/1768
+ */
+ if ($("#navbar.navbar-fixed-top").length > 0) {
+ var navHeight = $("#navbar").height(),
+ shiftWindow = function() { scrollBy(0, -navHeight - 10); };
+
+ if (location.hash) {
+ setTimeout(shiftWindow, 1);
+ }
+
+ window.addEventListener("hashchange", shiftWindow);
+ }
+ });
+
+ $(document).ready(function () {
+ // Add styling, structure to TOC's.
+ $(".dropdown-menu").each(function () {
+ $(this).find("ul").each(function (index, item){
+ var $item = $(item);
+ $item.addClass('unstyled');
+ });
+ });
+
+ // Global TOC.
+ if ($("ul.globaltoc li").length) {
+ patchToc($("ul.globaltoc"), 1);
+ } else {
+ // Remove Global TOC.
+ $(".globaltoc-container").remove();
+ }
+
+ // Local TOC.
+ $(".bs-sidenav ul").addClass("nav nav-list");
+ $(".bs-sidenav > ul > li > a").addClass("nav-header");
+
+
+ // back to top
+ setTimeout(function () {
+ var $sideBar = $('.bs-sidenav');
+
+ $sideBar.affix({
+ offset: {
+ top: function () {
+ var offsetTop = $sideBar.offset().top;
+ var sideBarMargin = parseInt($sideBar.children(0).css('margin-top'), 10);
+ var navOuterHeight = $('#navbar').height();
+
+ return (this.top = offsetTop - navOuterHeight - sideBarMargin);
+ }
+ , bottom: function () {
+ // add 25 because the footer height doesn't seem to be enough
+ return (this.bottom = $('.footer').outerHeight(true) + 25);
+ }
+ }
+ });
+ }, 100);
+
+
+ // Local TOC.
+ patchToc($("ul.localtoc"), 2);
+
+ // Mutate sub-lists (for bs-2.3.0).
+ $(".dropdown-menu ul").not(".dropdown-menu").each(function () {
+ var $ul = $(this),
+ $parent = $ul.parent(),
+ tag = $parent[0].tagName.toLowerCase(),
+ $kids = $ul.children().detach();
+
+ // Replace list with items if submenu header.
+ if (tag === "ul") {
+ $ul.replaceWith($kids);
+ } else if (tag === "li") {
+ // Insert into previous list.
+ $parent.after($kids);
+ $ul.remove();
+ }
+ });
+
+ // Add divider in page TOC.
+ $localLi = $("ul.localtoc li");
+ if ($localLi.length > 2) {
+ $localLi.first().after('<li class="divider"></li>');
+ }
+
+ // Manually add dropdown.
+ // Appears unnecessary as of:
+ // https://github.com/ryan-roemer/sphinx-bootstrap-theme/pull/90
+ // Remove next time around...
+ // a.dropdown-toggle class needed in globaltoc.html
+ //$('.dropdown-toggle').dropdown();
+
+ // Patch tables.
+ patchTables();
+
+ // Add Note, Warning styles. (BS v2,3 compatible).
+ $('.admonition').addClass('alert alert-info')
+ .filter('.warning, .caution')
+ .removeClass('alert-info')
+ .addClass('alert-warning').end()
+ .filter('.error, .danger')
+ .removeClass('alert-info')
+ .addClass('alert-danger alert-error').end();
+
+ // Inline code styles to Bootstrap style.
+ $('tt.docutils.literal').not(".xref").each(function (i, e) {
+ // ignore references
+ if (!$(e).parent().hasClass("reference")) {
+ $(e).replaceWith(function () {
+ return $("<code />").html($(this).html());
+ });
+ }});
+
+ // Update sourcelink to remove outerdiv (fixes appearance in navbar).
+ var $srcLink = $(".nav #sourcelink");
+ $srcLink.parent().html($srcLink.html());
+ });
+}(window.$jqTheme || window.jQuery));
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diff --git a/docs/build/html/_static/bootswatch-2.3.2/amelia/bootstrap.min.css b/docs/build/html/_static/bootswatch-2.3.2/amelia/bootstrap.min.css
new file mode 100644
index 0000000000000000000000000000000000000000..b8cea32837c975fcec3141fe64fd547f72b18216
--- /dev/null
+++ b/docs/build/html/_static/bootswatch-2.3.2/amelia/bootstrap.min.css
@@ -0,0 +1,9 @@
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new file mode 100644
index 0000000000000000000000000000000000000000..9740c15e57e804da526ec97e4a325e46b664f1cb
--- /dev/null
+++ b/docs/build/html/_static/bootswatch-2.3.2/cerulean/bootstrap.min.css
@@ -0,0 +1,9 @@
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diff --git a/docs/build/html/_static/bootswatch-2.3.2/cosmo/bootstrap.min.css b/docs/build/html/_static/bootswatch-2.3.2/cosmo/bootstrap.min.css
new file mode 100644
index 0000000000000000000000000000000000000000..cae7e4f8d29e4e2c2d8e048df0c04e5155394020
--- /dev/null
+++ b/docs/build/html/_static/bootswatch-2.3.2/cosmo/bootstrap.min.css
@@ -0,0 +1,9 @@
+@import url('//fonts.googleapis.com/css?family=Open+Sans:400italic,700italic,400,700');/*!
+ * Bootstrap v2.3.2
+ *
+ * Copyright 2012 Twitter, Inc
+ * Licensed under the Apache License v2.0
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Designed and built with all the love in the world @twitter by @mdo and @fat.
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diff --git a/docs/build/html/_static/bootswatch-2.3.2/cyborg/bootstrap.min.css b/docs/build/html/_static/bootswatch-2.3.2/cyborg/bootstrap.min.css
new file mode 100644
index 0000000000000000000000000000000000000000..894f3aacdd1257d71ef6c22e93835919162b3429
--- /dev/null
+++ b/docs/build/html/_static/bootswatch-2.3.2/cyborg/bootstrap.min.css
@@ -0,0 +1,9 @@
+@import url('//fonts.googleapis.com/css?family=Droid+Sans:400,700');/*!
+ * Bootstrap v2.3.2
+ *
+ * Copyright 2012 Twitter, Inc
+ * Licensed under the Apache License v2.0
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Designed and built with all the love in the world @twitter by @mdo and @fat.
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new file mode 100644
index 0000000000000000000000000000000000000000..a8ba38951343b7bbe39828d2c12aeb406b89bba5
--- /dev/null
+++ b/docs/build/html/_static/bootswatch-2.3.2/flatly/bootstrap.min.css
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diff --git a/docs/build/html/_static/bootswatch-2.3.2/readable/bootstrap.min.css b/docs/build/html/_static/bootswatch-2.3.2/readable/bootstrap.min.css
new file mode 100644
index 0000000000000000000000000000000000000000..0efc48fb63f2e724341cacabd7b099278a8c82a3
--- /dev/null
+++ b/docs/build/html/_static/bootswatch-2.3.2/readable/bootstrap.min.css
@@ -0,0 +1,9 @@
+@import url('//fonts.googleapis.com/css?family=Lora:400,700,400italic,700italic');/*!
+ * Bootstrap v2.3.2
+ *
+ * Copyright 2012 Twitter, Inc
+ * Licensed under the Apache License v2.0
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Designed and built with all the love in the world @twitter by @mdo and @fat.
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new file mode 100644
index 0000000000000000000000000000000000000000..a3e828f3c7265d17eebfc49127ea336db505d28d
--- /dev/null
+++ b/docs/build/html/_static/bootswatch-2.3.2/simplex/bootstrap.min.css
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diff --git a/docs/build/html/_static/bootswatch-2.3.2/slate/bootstrap.min.css b/docs/build/html/_static/bootswatch-2.3.2/slate/bootstrap.min.css
new file mode 100644
index 0000000000000000000000000000000000000000..40746a2af3650ed09f51c31caa755d2a1c36b5ff
--- /dev/null
+++ b/docs/build/html/_static/bootswatch-2.3.2/slate/bootstrap.min.css
@@ -0,0 +1,9 @@
+/*!
+ * Bootstrap v2.3.2
+ *
+ * Copyright 2012 Twitter, Inc
+ * Licensed under the Apache License v2.0
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Designed and built with all the love in the world @twitter by @mdo and @fat.
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diff --git a/docs/build/html/_static/bootswatch-2.3.2/spacelab/bootstrap.min.css b/docs/build/html/_static/bootswatch-2.3.2/spacelab/bootstrap.min.css
new file mode 100644
index 0000000000000000000000000000000000000000..7b7b4bb4a6b64ed89d939e519577478ba78ac602
--- /dev/null
+++ b/docs/build/html/_static/bootswatch-2.3.2/spacelab/bootstrap.min.css
@@ -0,0 +1,9 @@
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new file mode 100644
index 0000000000000000000000000000000000000000..6d5279cb6f92b5f87d11410c490aed92a75f14e8
--- /dev/null
+++ b/docs/build/html/_static/bootswatch-2.3.2/spruce/bootstrap.min.css
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new file mode 100644
index 0000000000000000000000000000000000000000..6635d7dba74a33447f2ecaa351c7a937d2dbc890
--- /dev/null
+++ b/docs/build/html/_static/bootswatch-2.3.2/superhero/bootstrap.min.css
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diff --git a/docs/build/html/_static/bootswatch-2.3.2/united/bootstrap.min.css b/docs/build/html/_static/bootswatch-2.3.2/united/bootstrap.min.css
new file mode 100644
index 0000000000000000000000000000000000000000..29cb6b617f2477379869e5f213e4b5913ac2c5a7
--- /dev/null
+++ b/docs/build/html/_static/bootswatch-2.3.2/united/bootstrap.min.css
@@ -0,0 +1,9 @@
+@import url(//fonts.googleapis.com/css?family=Ubuntu);/*!
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+ * Licensed under the Apache License v2.0
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
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diff --git a/docs/build/html/_static/bootswatch-3.2.0/amelia/bootstrap.min.css b/docs/build/html/_static/bootswatch-3.2.0/amelia/bootstrap.min.css
new file mode 100644
index 0000000000000000000000000000000000000000..91443344c7439c443f55e6d7c6002233a9111c00
--- /dev/null
+++ b/docs/build/html/_static/bootswatch-3.2.0/amelia/bootstrap.min.css
@@ -0,0 +1,7 @@
+@import url("//fonts.googleapis.com/css?family=Lobster|Cabin:400,700");/*!
+ * bootswatch v3.2.0
+ * Homepage: http://bootswatch.com
+ * Copyright 2012-2014 Thomas Park
+ * Licensed under MIT
+ * Based on Bootstrap
+*//*! normalize.css v3.0.1 | MIT License | git.io/normalize */html{font-family:sans-serif;-ms-text-size-adjust:100%;-webkit-text-size-adjust:100%}body{margin:0}article,aside,details,figcaption,figure,footer,header,hgroup,main,nav,section,summary{display:block}audio,canvas,progress,video{display:inline-block;vertical-align:baseline}audio:not([controls]){display:none;height:0}[hidden],template{display:none}a{background:transparent}a:active,a:hover{outline:0}abbr[title]{border-bottom:1px dotted}b,strong{font-weight:bold}dfn{font-style:italic}h1{font-size:2em;margin:0.67em 0}mark{background:#ff0;color:#000}small{font-size:80%}sub,sup{font-size:75%;line-height:0;position:relative;vertical-align:baseline}sup{top:-0.5em}sub{bottom:-0.25em}img{border:0}svg:not(:root){overflow:hidden}figure{margin:1em 40px}hr{-moz-box-sizing:content-box;box-sizing:content-box;height:0}pre{overflow:auto}code,kbd,pre,samp{font-family:monospace, 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diff --git a/docs/build/html/_static/bootswatch-3.2.0/cerulean/bootstrap.min.css b/docs/build/html/_static/bootswatch-3.2.0/cerulean/bootstrap.min.css
new file mode 100644
index 0000000000000000000000000000000000000000..769c9e9bcea1eca2ba2ed11f3dae095c3e78f207
--- /dev/null
+++ b/docs/build/html/_static/bootswatch-3.2.0/cerulean/bootstrap.min.css
@@ -0,0 +1,7 @@
+/*!
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diff --git a/docs/build/html/_static/bootswatch-3.2.0/cosmo/bootstrap.min.css b/docs/build/html/_static/bootswatch-3.2.0/cosmo/bootstrap.min.css
new file mode 100644
index 0000000000000000000000000000000000000000..caa18ae332781f6562751aa11561950904146751
--- /dev/null
+++ b/docs/build/html/_static/bootswatch-3.2.0/cosmo/bootstrap.min.css
@@ -0,0 +1,7 @@
+@import url("//fonts.googleapis.com/css?family=Source+Sans+Pro:300,400,700");/*!
+ * bootswatch v3.2.0
+ * Homepage: http://bootswatch.com
+ * Copyright 2012-2014 Thomas Park
+ * Licensed under MIT
+ * Based on Bootstrap
+*//*! normalize.css v3.0.1 | MIT License | git.io/normalize */html{font-family:sans-serif;-ms-text-size-adjust:100%;-webkit-text-size-adjust:100%}body{margin:0}article,aside,details,figcaption,figure,footer,header,hgroup,main,nav,section,summary{display:block}audio,canvas,progress,video{display:inline-block;vertical-align:baseline}audio:not([controls]){display:none;height:0}[hidden],template{display:none}a{background:transparent}a:active,a:hover{outline:0}abbr[title]{border-bottom:1px dotted}b,strong{font-weight:bold}dfn{font-style:italic}h1{font-size:2em;margin:0.67em 0}mark{background:#ff0;color:#000}small{font-size:80%}sub,sup{font-size:75%;line-height:0;position:relative;vertical-align:baseline}sup{top:-0.5em}sub{bottom:-0.25em}img{border:0}svg:not(:root){overflow:hidden}figure{margin:1em 40px}hr{-moz-box-sizing:content-box;box-sizing:content-box;height:0}pre{overflow:auto}code,kbd,pre,samp{font-family:monospace, 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diff --git a/docs/build/html/_static/bootswatch-3.2.0/custom/bootstrap.min.css b/docs/build/html/_static/bootswatch-3.2.0/custom/bootstrap.min.css
new file mode 100644
index 0000000000000000000000000000000000000000..5df7808858cd266ce27fd446ae53916553d2ee56
--- /dev/null
+++ b/docs/build/html/_static/bootswatch-3.2.0/custom/bootstrap.min.css
@@ -0,0 +1,7 @@
+/*!
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diff --git a/docs/build/html/_static/bootswatch-3.2.0/cyborg/bootstrap.min.css b/docs/build/html/_static/bootswatch-3.2.0/cyborg/bootstrap.min.css
new file mode 100644
index 0000000000000000000000000000000000000000..ce3f94908220d108be323d84c0b9aeedc3380cc9
--- /dev/null
+++ b/docs/build/html/_static/bootswatch-3.2.0/cyborg/bootstrap.min.css
@@ -0,0 +1,7 @@
+@import url("//fonts.googleapis.com/css?family=Roboto:400,700");/*!
+ * bootswatch v3.2.0
+ * Homepage: http://bootswatch.com
+ * Copyright 2012-2014 Thomas Park
+ * Licensed under MIT
+ * Based on Bootstrap
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diff --git a/docs/build/html/_static/bootswatch-3.2.0/darkly/bootstrap.min.css b/docs/build/html/_static/bootswatch-3.2.0/darkly/bootstrap.min.css
new file mode 100644
index 0000000000000000000000000000000000000000..1be8797a61f55fd1237d99dd42071ad52be951fd
--- /dev/null
+++ b/docs/build/html/_static/bootswatch-3.2.0/darkly/bootstrap.min.css
@@ -0,0 +1,7 @@
+@import url("//fonts.googleapis.com/css?family=Lato:400,700,400italic");/*!
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+ * Homepage: http://bootswatch.com
+ * Copyright 2012-2014 Thomas Park
+ * Licensed under MIT
+ * Based on Bootstrap
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diff --git a/docs/build/html/_static/bootswatch-3.2.0/flatly/bootstrap.min.css b/docs/build/html/_static/bootswatch-3.2.0/flatly/bootstrap.min.css
new file mode 100644
index 0000000000000000000000000000000000000000..32879dd4a094e02c90b48c43088a6a86c86d9ff2
--- /dev/null
+++ b/docs/build/html/_static/bootswatch-3.2.0/flatly/bootstrap.min.css
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+@import url("//fonts.googleapis.com/css?family=Lato:400,700,400italic");/*!
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+ * Copyright 2012-2014 Thomas Park
+ * Licensed under MIT
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diff --git a/docs/build/html/_static/bootswatch-3.2.0/lumen/bootstrap.min.css b/docs/build/html/_static/bootswatch-3.2.0/lumen/bootstrap.min.css
new file mode 100644
index 0000000000000000000000000000000000000000..89f692224163906a3497ff9d33b0dbeb3a419cbb
--- /dev/null
+++ b/docs/build/html/_static/bootswatch-3.2.0/lumen/bootstrap.min.css
@@ -0,0 +1,7 @@
+@import url("//fonts.googleapis.com/css?family=Source+Sans+Pro:300,400,700,400italic");/*!
+ * bootswatch v3.2.0
+ * Homepage: http://bootswatch.com
+ * Copyright 2012-2014 Thomas Park
+ * Licensed under MIT
+ * Based on Bootstrap
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new file mode 100644
index 0000000000000000000000000000000000000000..94f925331c4c21843620207ef7468378015feac6
--- /dev/null
+++ b/docs/build/html/_static/bootswatch-3.2.0/paper/bootstrap.min.css
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diff --git a/docs/build/html/_static/bootswatch-3.2.0/readable/bootstrap.min.css b/docs/build/html/_static/bootswatch-3.2.0/readable/bootstrap.min.css
new file mode 100644
index 0000000000000000000000000000000000000000..ecb54a0fff352c36fcd04c05e38e6a184a9aa379
--- /dev/null
+++ b/docs/build/html/_static/bootswatch-3.2.0/readable/bootstrap.min.css
@@ -0,0 +1,7 @@
+@import url("//fonts.googleapis.com/css?family=Raleway:400,700");/*!
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+ * Homepage: http://bootswatch.com
+ * Copyright 2012-2014 Thomas Park
+ * Licensed under MIT
+ * Based on Bootstrap
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diff --git a/docs/build/html/_static/bootswatch-3.2.0/sandstone/bootstrap.min.css b/docs/build/html/_static/bootswatch-3.2.0/sandstone/bootstrap.min.css
new file mode 100644
index 0000000000000000000000000000000000000000..137783ba2b75279b01e56b8e70294c8b0fa03fb5
--- /dev/null
+++ b/docs/build/html/_static/bootswatch-3.2.0/sandstone/bootstrap.min.css
@@ -0,0 +1,7 @@
+@import url("//fonts.googleapis.com/css?family=Roboto:400,500");/*!
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+ * Homepage: http://bootswatch.com
+ * Copyright 2012-2014 Thomas Park
+ * Licensed under MIT
+ * Based on Bootstrap
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diff --git a/docs/build/html/_static/bootswatch-3.2.0/simplex/bootstrap.min.css b/docs/build/html/_static/bootswatch-3.2.0/simplex/bootstrap.min.css
new file mode 100644
index 0000000000000000000000000000000000000000..a29a799a14ed70b1637aa6b6b8a3888b0772e239
--- /dev/null
+++ b/docs/build/html/_static/bootswatch-3.2.0/simplex/bootstrap.min.css
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+@import url("//fonts.googleapis.com/css?family=Open+Sans:400,700");/*!
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+ * Homepage: http://bootswatch.com
+ * Copyright 2012-2014 Thomas Park
+ * Licensed under MIT
+ * Based on Bootstrap
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diff --git a/docs/build/html/_static/bootswatch-3.2.0/slate/bootstrap.min.css b/docs/build/html/_static/bootswatch-3.2.0/slate/bootstrap.min.css
new file mode 100644
index 0000000000000000000000000000000000000000..f25e54da2badc974120155797d7408ede47a86e4
--- /dev/null
+++ b/docs/build/html/_static/bootswatch-3.2.0/slate/bootstrap.min.css
@@ -0,0 +1,7 @@
+/*!
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+ * Copyright 2012-2014 Thomas Park
+ * Licensed under MIT
+ * Based on Bootstrap
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diff --git a/docs/build/html/_static/bootswatch-3.2.0/spacelab/bootstrap.min.css b/docs/build/html/_static/bootswatch-3.2.0/spacelab/bootstrap.min.css
new file mode 100644
index 0000000000000000000000000000000000000000..55d0f170a8d5807f5054fa9245819cf6c5ce6b33
--- /dev/null
+++ b/docs/build/html/_static/bootswatch-3.2.0/spacelab/bootstrap.min.css
@@ -0,0 +1,7 @@
+@import url("//fonts.googleapis.com/css?family=Open+Sans:400italic,700italic,400,700");/*!
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+ * Homepage: http://bootswatch.com
+ * Copyright 2012-2014 Thomas Park
+ * Licensed under MIT
+ * Based on Bootstrap
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index 0000000000000000000000000000000000000000..b5829207cc0162583f6c9fb91ac46da1078fb02a
--- /dev/null
+++ b/docs/build/html/_static/bootswatch-3.2.0/superhero/bootstrap.min.css
@@ -0,0 +1,7 @@
+@import url("//fonts.googleapis.com/css?family=Lato:300,400,700");/*!
+ * bootswatch v3.2.0
+ * Homepage: http://bootswatch.com
+ * Copyright 2012-2014 Thomas Park
+ * Licensed under MIT
+ * Based on Bootstrap
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diff --git a/docs/build/html/_static/bootswatch-3.2.0/united/bootstrap.min.css b/docs/build/html/_static/bootswatch-3.2.0/united/bootstrap.min.css
new file mode 100644
index 0000000000000000000000000000000000000000..fa335b16857e6626c09c07fe7a000ca8e1ab079e
--- /dev/null
+++ b/docs/build/html/_static/bootswatch-3.2.0/united/bootstrap.min.css
@@ -0,0 +1,7 @@
+@import url("//fonts.googleapis.com/css?family=Ubuntu");/*!
+ * bootswatch v3.2.0
+ * Homepage: http://bootswatch.com
+ * Copyright 2012-2014 Thomas Park
+ * Licensed under MIT
+ * Based on Bootstrap
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diff --git a/docs/build/html/_static/bootswatch-3.2.0/yeti/bootstrap.min.css b/docs/build/html/_static/bootswatch-3.2.0/yeti/bootstrap.min.css
new file mode 100644
index 0000000000000000000000000000000000000000..32128a25feefbdfa7db66f3f4e4f0608c3ec918b
--- /dev/null
+++ b/docs/build/html/_static/bootswatch-3.2.0/yeti/bootstrap.min.css
@@ -0,0 +1,7 @@
+@import url("//fonts.googleapis.com/css?family=Open+Sans:300italic,400italic,700italic,400,300,700");/*!
+ * bootswatch v3.2.0
+ * Homepage: http://bootswatch.com
+ * Copyright 2012-2014 Thomas Park
+ * Licensed under MIT
+ * Based on Bootstrap
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+/*
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+ *
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+ *
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+
+@import url("basic.css");
+
+/* -- page layout ----------------------------------------------------------- */
+
+body {
+ font-family: sans-serif;
+ font-size: 100%;
+ background-color: #11303d;
+ color: #000;
+ margin: 0;
+ padding: 0;
+}
+
+div.document {
+ background-color: #1c4e63;
+}
+
+div.documentwrapper {
+ float: left;
+ width: 100%;
+}
+
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+ margin: 0 0 0 230px;
+}
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+ padding: 0 20px 30px 20px;
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+ padding: 9px 0 9px 0;
+ text-align: center;
+ font-size: 75%;
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+div.footer a {
+ color: #ffffff;
+ text-decoration: underline;
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+div.related {
+ background-color: #133f52;
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+ color: #ffffff;
+}
+
+div.related a {
+ color: #ffffff;
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+
+div.sphinxsidebar {
+ top: 30px;
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+ position: fixed;
+ overflow: auto;
+ height: auto;
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+/* this is nice, but it it leads to hidden headings when jumping
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+/* -- hyperlink styles ------------------------------------------------------ */
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+ line-height: 130%;
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+ border: 1px solid #ff6;
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+/*
+ * doctools.js
+ * ~~~~~~~~~~~
+ *
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+ * :license: BSD, see LICENSE for details.
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+/**
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+$u = _.noConflict();
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+/**
+ * make the code below compatible with browsers without
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+if (!window.console || !console.firebug) {
+ var names = ["log", "debug", "info", "warn", "error", "assert", "dir",
+ "dirxml", "group", "groupEnd", "time", "timeEnd", "count", "trace",
+ "profile", "profileEnd"];
+ window.console = {};
+ for (var i = 0; i < names.length; ++i)
+ window.console[names[i]] = function() {};
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+ */
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+/**
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+ */
+jQuery.urldecode = function(x) {
+ return decodeURIComponent(x).replace(/\+/g, ' ');
+};
+
+/**
+ * small helper function to urlencode strings
+ */
+jQuery.urlencode = encodeURIComponent;
+
+/**
+ * This function returns the parsed url parameters of the
+ * current request. Multiple values per key are supported,
+ * it will always return arrays of strings for the value parts.
+ */
+jQuery.getQueryParameters = function(s) {
+ if (typeof s == 'undefined')
+ s = document.location.search;
+ var parts = s.substr(s.indexOf('?') + 1).split('&');
+ var result = {};
+ for (var i = 0; i < parts.length; i++) {
+ var tmp = parts[i].split('=', 2);
+ var key = jQuery.urldecode(tmp[0]);
+ var value = jQuery.urldecode(tmp[1]);
+ if (key in result)
+ result[key].push(value);
+ else
+ result[key] = [value];
+ }
+ return result;
+};
+
+/**
+ * highlight a given string on a jquery object by wrapping it in
+ * span elements with the given class name.
+ */
+jQuery.fn.highlightText = function(text, className) {
+ function highlight(node) {
+ if (node.nodeType == 3) {
+ var val = node.nodeValue;
+ var pos = val.toLowerCase().indexOf(text);
+ if (pos >= 0 && !jQuery(node.parentNode).hasClass(className)) {
+ var span = document.createElement("span");
+ span.className = className;
+ span.appendChild(document.createTextNode(val.substr(pos, text.length)));
+ node.parentNode.insertBefore(span, node.parentNode.insertBefore(
+ document.createTextNode(val.substr(pos + text.length)),
+ node.nextSibling));
+ node.nodeValue = val.substr(0, pos);
+ }
+ }
+ else if (!jQuery(node).is("button, select, textarea")) {
+ jQuery.each(node.childNodes, function() {
+ highlight(this);
+ });
+ }
+ }
+ return this.each(function() {
+ highlight(this);
+ });
+};
+
+/**
+ * Small JavaScript module for the documentation.
+ */
+var Documentation = {
+
+ init : function() {
+ this.fixFirefoxAnchorBug();
+ this.highlightSearchWords();
+ this.initIndexTable();
+ },
+
+ /**
+ * i18n support
+ */
+ TRANSLATIONS : {},
+ PLURAL_EXPR : function(n) { return n == 1 ? 0 : 1; },
+ LOCALE : 'unknown',
+
+ // gettext and ngettext don't access this so that the functions
+ // can safely bound to a different name (_ = Documentation.gettext)
+ gettext : function(string) {
+ var translated = Documentation.TRANSLATIONS[string];
+ if (typeof translated == 'undefined')
+ return string;
+ return (typeof translated == 'string') ? translated : translated[0];
+ },
+
+ ngettext : function(singular, plural, n) {
+ var translated = Documentation.TRANSLATIONS[singular];
+ if (typeof translated == 'undefined')
+ return (n == 1) ? singular : plural;
+ return translated[Documentation.PLURALEXPR(n)];
+ },
+
+ addTranslations : function(catalog) {
+ for (var key in catalog.messages)
+ this.TRANSLATIONS[key] = catalog.messages[key];
+ this.PLURAL_EXPR = new Function('n', 'return +(' + catalog.plural_expr + ')');
+ this.LOCALE = catalog.locale;
+ },
+
+ /**
+ * add context elements like header anchor links
+ */
+ addContextElements : function() {
+ $('div[id] > :header:first').each(function() {
+ $('<a class="headerlink">\u00B6</a>').
+ attr('href', '#' + this.id).
+ attr('title', _('Permalink to this headline')).
+ appendTo(this);
+ });
+ $('dt[id]').each(function() {
+ $('<a class="headerlink">\u00B6</a>').
+ attr('href', '#' + this.id).
+ attr('title', _('Permalink to this definition')).
+ appendTo(this);
+ });
+ },
+
+ /**
+ * workaround a firefox stupidity
+ */
+ fixFirefoxAnchorBug : function() {
+ if (document.location.hash && $.browser.mozilla)
+ window.setTimeout(function() {
+ document.location.href += '';
+ }, 10);
+ },
+
+ /**
+ * highlight the search words provided in the url in the text
+ */
+ highlightSearchWords : function() {
+ var params = $.getQueryParameters();
+ var terms = (params.highlight) ? params.highlight[0].split(/\s+/) : [];
+ if (terms.length) {
+ var body = $('div.body');
+ if (!body.length) {
+ body = $('body');
+ }
+ window.setTimeout(function() {
+ $.each(terms, function() {
+ body.highlightText(this.toLowerCase(), 'highlighted');
+ });
+ }, 10);
+ $('<p class="highlight-link"><a href="javascript:Documentation.' +
+ 'hideSearchWords()">' + _('Hide Search Matches') + '</a></p>')
+ .appendTo($('#searchbox'));
+ }
+ },
+
+ /**
+ * init the domain index toggle buttons
+ */
+ initIndexTable : function() {
+ var togglers = $('img.toggler').click(function() {
+ var src = $(this).attr('src');
+ var idnum = $(this).attr('id').substr(7);
+ $('tr.cg-' + idnum).toggle();
+ if (src.substr(-9) == 'minus.png')
+ $(this).attr('src', src.substr(0, src.length-9) + 'plus.png');
+ else
+ $(this).attr('src', src.substr(0, src.length-8) + 'minus.png');
+ }).css('display', '');
+ if (DOCUMENTATION_OPTIONS.COLLAPSE_INDEX) {
+ togglers.click();
+ }
+ },
+
+ /**
+ * helper function to hide the search marks again
+ */
+ hideSearchWords : function() {
+ $('#searchbox .highlight-link').fadeOut(300);
+ $('span.highlighted').removeClass('highlighted');
+ },
+
+ /**
+ * make the url absolute
+ */
+ makeURL : function(relativeURL) {
+ return DOCUMENTATION_OPTIONS.URL_ROOT + '/' + relativeURL;
+ },
+
+ /**
+ * get the current relative url
+ */
+ getCurrentURL : function() {
+ var path = document.location.pathname;
+ var parts = path.split(/\//);
+ $.each(DOCUMENTATION_OPTIONS.URL_ROOT.split(/\//), function() {
+ if (this == '..')
+ parts.pop();
+ });
+ var url = parts.join('/');
+ return path.substring(url.lastIndexOf('/') + 1, path.length - 1);
+ }
+};
+
+// quick alias for translations
+_ = Documentation.gettext;
+
+$(document).ready(function() {
+ Documentation.init();
+});
diff --git a/docs/build/html/_static/down-pressed.png b/docs/build/html/_static/down-pressed.png
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diff --git a/docs/build/html/_static/jquery-1.8.3.js b/docs/build/html/_static/jquery-1.8.3.js
new file mode 100644
index 0000000000000000000000000000000000000000..8c24ffc610d6f5de6ffa9c992030800249612b9c
--- /dev/null
+++ b/docs/build/html/_static/jquery-1.8.3.js
@@ -0,0 +1,9472 @@
+/*!
+ * jQuery JavaScript Library v1.8.3
+ * http://jquery.com/
+ *
+ * Includes Sizzle.js
+ * http://sizzlejs.com/
+ *
+ * Copyright 2012 jQuery Foundation and other contributors
+ * Released under the MIT license
+ * http://jquery.org/license
+ *
+ * Date: Tue Nov 13 2012 08:20:33 GMT-0500 (Eastern Standard Time)
+ */
+(function( window, undefined ) {
+var
+ // A central reference to the root jQuery(document)
+ rootjQuery,
+
+ // The deferred used on DOM ready
+ readyList,
+
+ // Use the correct document accordingly with window argument (sandbox)
+ document = window.document,
+ location = window.location,
+ navigator = window.navigator,
+
+ // Map over jQuery in case of overwrite
+ _jQuery = window.jQuery,
+
+ // Map over the $ in case of overwrite
+ _$ = window.$,
+
+ // Save a reference to some core methods
+ core_push = Array.prototype.push,
+ core_slice = Array.prototype.slice,
+ core_indexOf = Array.prototype.indexOf,
+ core_toString = Object.prototype.toString,
+ core_hasOwn = Object.prototype.hasOwnProperty,
+ core_trim = String.prototype.trim,
+
+ // Define a local copy of jQuery
+ jQuery = function( selector, context ) {
+ // The jQuery object is actually just the init constructor 'enhanced'
+ return new jQuery.fn.init( selector, context, rootjQuery );
+ },
+
+ // Used for matching numbers
+ core_pnum = /[\-+]?(?:\d*\.|)\d+(?:[eE][\-+]?\d+|)/.source,
+
+ // Used for detecting and trimming whitespace
+ core_rnotwhite = /\S/,
+ core_rspace = /\s+/,
+
+ // Make sure we trim BOM and NBSP (here's looking at you, Safari 5.0 and IE)
+ rtrim = /^[\s\uFEFF\xA0]+|[\s\uFEFF\xA0]+$/g,
+
+ // A simple way to check for HTML strings
+ // Prioritize #id over <tag> to avoid XSS via location.hash (#9521)
+ rquickExpr = /^(?:[^#<]*(<[\w\W]+>)[^>]*$|#([\w\-]*)$)/,
+
+ // Match a standalone tag
+ rsingleTag = /^<(\w+)\s*\/?>(?:<\/\1>|)$/,
+
+ // JSON RegExp
+ rvalidchars = /^[\],:{}\s]*$/,
+ rvalidbraces = /(?:^|:|,)(?:\s*\[)+/g,
+ rvalidescape = /\\(?:["\\\/bfnrt]|u[\da-fA-F]{4})/g,
+ rvalidtokens = /"[^"\\\r\n]*"|true|false|null|-?(?:\d\d*\.|)\d+(?:[eE][\-+]?\d+|)/g,
+
+ // Matches dashed string for camelizing
+ rmsPrefix = /^-ms-/,
+ rdashAlpha = /-([\da-z])/gi,
+
+ // Used by jQuery.camelCase as callback to replace()
+ fcamelCase = function( all, letter ) {
+ return ( letter + "" ).toUpperCase();
+ },
+
+ // The ready event handler and self cleanup method
+ DOMContentLoaded = function() {
+ if ( document.addEventListener ) {
+ document.removeEventListener( "DOMContentLoaded", DOMContentLoaded, false );
+ jQuery.ready();
+ } else if ( document.readyState === "complete" ) {
+ // we're here because readyState === "complete" in oldIE
+ // which is good enough for us to call the dom ready!
+ document.detachEvent( "onreadystatechange", DOMContentLoaded );
+ jQuery.ready();
+ }
+ },
+
+ // [[Class]] -> type pairs
+ class2type = {};
+
+jQuery.fn = jQuery.prototype = {
+ constructor: jQuery,
+ init: function( selector, context, rootjQuery ) {
+ var match, elem, ret, doc;
+
+ // Handle $(""), $(null), $(undefined), $(false)
+ if ( !selector ) {
+ return this;
+ }
+
+ // Handle $(DOMElement)
+ if ( selector.nodeType ) {
+ this.context = this[0] = selector;
+ this.length = 1;
+ return this;
+ }
+
+ // Handle HTML strings
+ if ( typeof selector === "string" ) {
+ if ( selector.charAt(0) === "<" && selector.charAt( selector.length - 1 ) === ">" && selector.length >= 3 ) {
+ // Assume that strings that start and end with <> are HTML and skip the regex check
+ match = [ null, selector, null ];
+
+ } else {
+ match = rquickExpr.exec( selector );
+ }
+
+ // Match html or make sure no context is specified for #id
+ if ( match && (match[1] || !context) ) {
+
+ // HANDLE: $(html) -> $(array)
+ if ( match[1] ) {
+ context = context instanceof jQuery ? context[0] : context;
+ doc = ( context && context.nodeType ? context.ownerDocument || context : document );
+
+ // scripts is true for back-compat
+ selector = jQuery.parseHTML( match[1], doc, true );
+ if ( rsingleTag.test( match[1] ) && jQuery.isPlainObject( context ) ) {
+ this.attr.call( selector, context, true );
+ }
+
+ return jQuery.merge( this, selector );
+
+ // HANDLE: $(#id)
+ } else {
+ elem = document.getElementById( match[2] );
+
+ // Check parentNode to catch when Blackberry 4.6 returns
+ // nodes that are no longer in the document #6963
+ if ( elem && elem.parentNode ) {
+ // Handle the case where IE and Opera return items
+ // by name instead of ID
+ if ( elem.id !== match[2] ) {
+ return rootjQuery.find( selector );
+ }
+
+ // Otherwise, we inject the element directly into the jQuery object
+ this.length = 1;
+ this[0] = elem;
+ }
+
+ this.context = document;
+ this.selector = selector;
+ return this;
+ }
+
+ // HANDLE: $(expr, $(...))
+ } else if ( !context || context.jquery ) {
+ return ( context || rootjQuery ).find( selector );
+
+ // HANDLE: $(expr, context)
+ // (which is just equivalent to: $(context).find(expr)
+ } else {
+ return this.constructor( context ).find( selector );
+ }
+
+ // HANDLE: $(function)
+ // Shortcut for document ready
+ } else if ( jQuery.isFunction( selector ) ) {
+ return rootjQuery.ready( selector );
+ }
+
+ if ( selector.selector !== undefined ) {
+ this.selector = selector.selector;
+ this.context = selector.context;
+ }
+
+ return jQuery.makeArray( selector, this );
+ },
+
+ // Start with an empty selector
+ selector: "",
+
+ // The current version of jQuery being used
+ jquery: "1.8.3",
+
+ // The default length of a jQuery object is 0
+ length: 0,
+
+ // The number of elements contained in the matched element set
+ size: function() {
+ return this.length;
+ },
+
+ toArray: function() {
+ return core_slice.call( this );
+ },
+
+ // Get the Nth element in the matched element set OR
+ // Get the whole matched element set as a clean array
+ get: function( num ) {
+ return num == null ?
+
+ // Return a 'clean' array
+ this.toArray() :
+
+ // Return just the object
+ ( num < 0 ? this[ this.length + num ] : this[ num ] );
+ },
+
+ // Take an array of elements and push it onto the stack
+ // (returning the new matched element set)
+ pushStack: function( elems, name, selector ) {
+
+ // Build a new jQuery matched element set
+ var ret = jQuery.merge( this.constructor(), elems );
+
+ // Add the old object onto the stack (as a reference)
+ ret.prevObject = this;
+
+ ret.context = this.context;
+
+ if ( name === "find" ) {
+ ret.selector = this.selector + ( this.selector ? " " : "" ) + selector;
+ } else if ( name ) {
+ ret.selector = this.selector + "." + name + "(" + selector + ")";
+ }
+
+ // Return the newly-formed element set
+ return ret;
+ },
+
+ // Execute a callback for every element in the matched set.
+ // (You can seed the arguments with an array of args, but this is
+ // only used internally.)
+ each: function( callback, args ) {
+ return jQuery.each( this, callback, args );
+ },
+
+ ready: function( fn ) {
+ // Add the callback
+ jQuery.ready.promise().done( fn );
+
+ return this;
+ },
+
+ eq: function( i ) {
+ i = +i;
+ return i === -1 ?
+ this.slice( i ) :
+ this.slice( i, i + 1 );
+ },
+
+ first: function() {
+ return this.eq( 0 );
+ },
+
+ last: function() {
+ return this.eq( -1 );
+ },
+
+ slice: function() {
+ return this.pushStack( core_slice.apply( this, arguments ),
+ "slice", core_slice.call(arguments).join(",") );
+ },
+
+ map: function( callback ) {
+ return this.pushStack( jQuery.map(this, function( elem, i ) {
+ return callback.call( elem, i, elem );
+ }));
+ },
+
+ end: function() {
+ return this.prevObject || this.constructor(null);
+ },
+
+ // For internal use only.
+ // Behaves like an Array's method, not like a jQuery method.
+ push: core_push,
+ sort: [].sort,
+ splice: [].splice
+};
+
+// Give the init function the jQuery prototype for later instantiation
+jQuery.fn.init.prototype = jQuery.fn;
+
+jQuery.extend = jQuery.fn.extend = function() {
+ var options, name, src, copy, copyIsArray, clone,
+ target = arguments[0] || {},
+ i = 1,
+ length = arguments.length,
+ deep = false;
+
+ // Handle a deep copy situation
+ if ( typeof target === "boolean" ) {
+ deep = target;
+ target = arguments[1] || {};
+ // skip the boolean and the target
+ i = 2;
+ }
+
+ // Handle case when target is a string or something (possible in deep copy)
+ if ( typeof target !== "object" && !jQuery.isFunction(target) ) {
+ target = {};
+ }
+
+ // extend jQuery itself if only one argument is passed
+ if ( length === i ) {
+ target = this;
+ --i;
+ }
+
+ for ( ; i < length; i++ ) {
+ // Only deal with non-null/undefined values
+ if ( (options = arguments[ i ]) != null ) {
+ // Extend the base object
+ for ( name in options ) {
+ src = target[ name ];
+ copy = options[ name ];
+
+ // Prevent never-ending loop
+ if ( target === copy ) {
+ continue;
+ }
+
+ // Recurse if we're merging plain objects or arrays
+ if ( deep && copy && ( jQuery.isPlainObject(copy) || (copyIsArray = jQuery.isArray(copy)) ) ) {
+ if ( copyIsArray ) {
+ copyIsArray = false;
+ clone = src && jQuery.isArray(src) ? src : [];
+
+ } else {
+ clone = src && jQuery.isPlainObject(src) ? src : {};
+ }
+
+ // Never move original objects, clone them
+ target[ name ] = jQuery.extend( deep, clone, copy );
+
+ // Don't bring in undefined values
+ } else if ( copy !== undefined ) {
+ target[ name ] = copy;
+ }
+ }
+ }
+ }
+
+ // Return the modified object
+ return target;
+};
+
+jQuery.extend({
+ noConflict: function( deep ) {
+ if ( window.$ === jQuery ) {
+ window.$ = _$;
+ }
+
+ if ( deep && window.jQuery === jQuery ) {
+ window.jQuery = _jQuery;
+ }
+
+ return jQuery;
+ },
+
+ // Is the DOM ready to be used? Set to true once it occurs.
+ isReady: false,
+
+ // A counter to track how many items to wait for before
+ // the ready event fires. See #6781
+ readyWait: 1,
+
+ // Hold (or release) the ready event
+ holdReady: function( hold ) {
+ if ( hold ) {
+ jQuery.readyWait++;
+ } else {
+ jQuery.ready( true );
+ }
+ },
+
+ // Handle when the DOM is ready
+ ready: function( wait ) {
+
+ // Abort if there are pending holds or we're already ready
+ if ( wait === true ? --jQuery.readyWait : jQuery.isReady ) {
+ return;
+ }
+
+ // Make sure body exists, at least, in case IE gets a little overzealous (ticket #5443).
+ if ( !document.body ) {
+ return setTimeout( jQuery.ready, 1 );
+ }
+
+ // Remember that the DOM is ready
+ jQuery.isReady = true;
+
+ // If a normal DOM Ready event fired, decrement, and wait if need be
+ if ( wait !== true && --jQuery.readyWait > 0 ) {
+ return;
+ }
+
+ // If there are functions bound, to execute
+ readyList.resolveWith( document, [ jQuery ] );
+
+ // Trigger any bound ready events
+ if ( jQuery.fn.trigger ) {
+ jQuery( document ).trigger("ready").off("ready");
+ }
+ },
+
+ // See test/unit/core.js for details concerning isFunction.
+ // Since version 1.3, DOM methods and functions like alert
+ // aren't supported. They return false on IE (#2968).
+ isFunction: function( obj ) {
+ return jQuery.type(obj) === "function";
+ },
+
+ isArray: Array.isArray || function( obj ) {
+ return jQuery.type(obj) === "array";
+ },
+
+ isWindow: function( obj ) {
+ return obj != null && obj == obj.window;
+ },
+
+ isNumeric: function( obj ) {
+ return !isNaN( parseFloat(obj) ) && isFinite( obj );
+ },
+
+ type: function( obj ) {
+ return obj == null ?
+ String( obj ) :
+ class2type[ core_toString.call(obj) ] || "object";
+ },
+
+ isPlainObject: function( obj ) {
+ // Must be an Object.
+ // Because of IE, we also have to check the presence of the constructor property.
+ // Make sure that DOM nodes and window objects don't pass through, as well
+ if ( !obj || jQuery.type(obj) !== "object" || obj.nodeType || jQuery.isWindow( obj ) ) {
+ return false;
+ }
+
+ try {
+ // Not own constructor property must be Object
+ if ( obj.constructor &&
+ !core_hasOwn.call(obj, "constructor") &&
+ !core_hasOwn.call(obj.constructor.prototype, "isPrototypeOf") ) {
+ return false;
+ }
+ } catch ( e ) {
+ // IE8,9 Will throw exceptions on certain host objects #9897
+ return false;
+ }
+
+ // Own properties are enumerated firstly, so to speed up,
+ // if last one is own, then all properties are own.
+
+ var key;
+ for ( key in obj ) {}
+
+ return key === undefined || core_hasOwn.call( obj, key );
+ },
+
+ isEmptyObject: function( obj ) {
+ var name;
+ for ( name in obj ) {
+ return false;
+ }
+ return true;
+ },
+
+ error: function( msg ) {
+ throw new Error( msg );
+ },
+
+ // data: string of html
+ // context (optional): If specified, the fragment will be created in this context, defaults to document
+ // scripts (optional): If true, will include scripts passed in the html string
+ parseHTML: function( data, context, scripts ) {
+ var parsed;
+ if ( !data || typeof data !== "string" ) {
+ return null;
+ }
+ if ( typeof context === "boolean" ) {
+ scripts = context;
+ context = 0;
+ }
+ context = context || document;
+
+ // Single tag
+ if ( (parsed = rsingleTag.exec( data )) ) {
+ return [ context.createElement( parsed[1] ) ];
+ }
+
+ parsed = jQuery.buildFragment( [ data ], context, scripts ? null : [] );
+ return jQuery.merge( [],
+ (parsed.cacheable ? jQuery.clone( parsed.fragment ) : parsed.fragment).childNodes );
+ },
+
+ parseJSON: function( data ) {
+ if ( !data || typeof data !== "string") {
+ return null;
+ }
+
+ // Make sure leading/trailing whitespace is removed (IE can't handle it)
+ data = jQuery.trim( data );
+
+ // Attempt to parse using the native JSON parser first
+ if ( window.JSON && window.JSON.parse ) {
+ return window.JSON.parse( data );
+ }
+
+ // Make sure the incoming data is actual JSON
+ // Logic borrowed from http://json.org/json2.js
+ if ( rvalidchars.test( data.replace( rvalidescape, "@" )
+ .replace( rvalidtokens, "]" )
+ .replace( rvalidbraces, "")) ) {
+
+ return ( new Function( "return " + data ) )();
+
+ }
+ jQuery.error( "Invalid JSON: " + data );
+ },
+
+ // Cross-browser xml parsing
+ parseXML: function( data ) {
+ var xml, tmp;
+ if ( !data || typeof data !== "string" ) {
+ return null;
+ }
+ try {
+ if ( window.DOMParser ) { // Standard
+ tmp = new DOMParser();
+ xml = tmp.parseFromString( data , "text/xml" );
+ } else { // IE
+ xml = new ActiveXObject( "Microsoft.XMLDOM" );
+ xml.async = "false";
+ xml.loadXML( data );
+ }
+ } catch( e ) {
+ xml = undefined;
+ }
+ if ( !xml || !xml.documentElement || xml.getElementsByTagName( "parsererror" ).length ) {
+ jQuery.error( "Invalid XML: " + data );
+ }
+ return xml;
+ },
+
+ noop: function() {},
+
+ // Evaluates a script in a global context
+ // Workarounds based on findings by Jim Driscoll
+ // http://weblogs.java.net/blog/driscoll/archive/2009/09/08/eval-javascript-global-context
+ globalEval: function( data ) {
+ if ( data && core_rnotwhite.test( data ) ) {
+ // We use execScript on Internet Explorer
+ // We use an anonymous function so that context is window
+ // rather than jQuery in Firefox
+ ( window.execScript || function( data ) {
+ window[ "eval" ].call( window, data );
+ } )( data );
+ }
+ },
+
+ // Convert dashed to camelCase; used by the css and data modules
+ // Microsoft forgot to hump their vendor prefix (#9572)
+ camelCase: function( string ) {
+ return string.replace( rmsPrefix, "ms-" ).replace( rdashAlpha, fcamelCase );
+ },
+
+ nodeName: function( elem, name ) {
+ return elem.nodeName && elem.nodeName.toLowerCase() === name.toLowerCase();
+ },
+
+ // args is for internal usage only
+ each: function( obj, callback, args ) {
+ var name,
+ i = 0,
+ length = obj.length,
+ isObj = length === undefined || jQuery.isFunction( obj );
+
+ if ( args ) {
+ if ( isObj ) {
+ for ( name in obj ) {
+ if ( callback.apply( obj[ name ], args ) === false ) {
+ break;
+ }
+ }
+ } else {
+ for ( ; i < length; ) {
+ if ( callback.apply( obj[ i++ ], args ) === false ) {
+ break;
+ }
+ }
+ }
+
+ // A special, fast, case for the most common use of each
+ } else {
+ if ( isObj ) {
+ for ( name in obj ) {
+ if ( callback.call( obj[ name ], name, obj[ name ] ) === false ) {
+ break;
+ }
+ }
+ } else {
+ for ( ; i < length; ) {
+ if ( callback.call( obj[ i ], i, obj[ i++ ] ) === false ) {
+ break;
+ }
+ }
+ }
+ }
+
+ return obj;
+ },
+
+ // Use native String.trim function wherever possible
+ trim: core_trim && !core_trim.call("\uFEFF\xA0") ?
+ function( text ) {
+ return text == null ?
+ "" :
+ core_trim.call( text );
+ } :
+
+ // Otherwise use our own trimming functionality
+ function( text ) {
+ return text == null ?
+ "" :
+ ( text + "" ).replace( rtrim, "" );
+ },
+
+ // results is for internal usage only
+ makeArray: function( arr, results ) {
+ var type,
+ ret = results || [];
+
+ if ( arr != null ) {
+ // The window, strings (and functions) also have 'length'
+ // Tweaked logic slightly to handle Blackberry 4.7 RegExp issues #6930
+ type = jQuery.type( arr );
+
+ if ( arr.length == null || type === "string" || type === "function" || type === "regexp" || jQuery.isWindow( arr ) ) {
+ core_push.call( ret, arr );
+ } else {
+ jQuery.merge( ret, arr );
+ }
+ }
+
+ return ret;
+ },
+
+ inArray: function( elem, arr, i ) {
+ var len;
+
+ if ( arr ) {
+ if ( core_indexOf ) {
+ return core_indexOf.call( arr, elem, i );
+ }
+
+ len = arr.length;
+ i = i ? i < 0 ? Math.max( 0, len + i ) : i : 0;
+
+ for ( ; i < len; i++ ) {
+ // Skip accessing in sparse arrays
+ if ( i in arr && arr[ i ] === elem ) {
+ return i;
+ }
+ }
+ }
+
+ return -1;
+ },
+
+ merge: function( first, second ) {
+ var l = second.length,
+ i = first.length,
+ j = 0;
+
+ if ( typeof l === "number" ) {
+ for ( ; j < l; j++ ) {
+ first[ i++ ] = second[ j ];
+ }
+
+ } else {
+ while ( second[j] !== undefined ) {
+ first[ i++ ] = second[ j++ ];
+ }
+ }
+
+ first.length = i;
+
+ return first;
+ },
+
+ grep: function( elems, callback, inv ) {
+ var retVal,
+ ret = [],
+ i = 0,
+ length = elems.length;
+ inv = !!inv;
+
+ // Go through the array, only saving the items
+ // that pass the validator function
+ for ( ; i < length; i++ ) {
+ retVal = !!callback( elems[ i ], i );
+ if ( inv !== retVal ) {
+ ret.push( elems[ i ] );
+ }
+ }
+
+ return ret;
+ },
+
+ // arg is for internal usage only
+ map: function( elems, callback, arg ) {
+ var value, key,
+ ret = [],
+ i = 0,
+ length = elems.length,
+ // jquery objects are treated as arrays
+ isArray = elems instanceof jQuery || length !== undefined && typeof length === "number" && ( ( length > 0 && elems[ 0 ] && elems[ length -1 ] ) || length === 0 || jQuery.isArray( elems ) ) ;
+
+ // Go through the array, translating each of the items to their
+ if ( isArray ) {
+ for ( ; i < length; i++ ) {
+ value = callback( elems[ i ], i, arg );
+
+ if ( value != null ) {
+ ret[ ret.length ] = value;
+ }
+ }
+
+ // Go through every key on the object,
+ } else {
+ for ( key in elems ) {
+ value = callback( elems[ key ], key, arg );
+
+ if ( value != null ) {
+ ret[ ret.length ] = value;
+ }
+ }
+ }
+
+ // Flatten any nested arrays
+ return ret.concat.apply( [], ret );
+ },
+
+ // A global GUID counter for objects
+ guid: 1,
+
+ // Bind a function to a context, optionally partially applying any
+ // arguments.
+ proxy: function( fn, context ) {
+ var tmp, args, proxy;
+
+ if ( typeof context === "string" ) {
+ tmp = fn[ context ];
+ context = fn;
+ fn = tmp;
+ }
+
+ // Quick check to determine if target is callable, in the spec
+ // this throws a TypeError, but we will just return undefined.
+ if ( !jQuery.isFunction( fn ) ) {
+ return undefined;
+ }
+
+ // Simulated bind
+ args = core_slice.call( arguments, 2 );
+ proxy = function() {
+ return fn.apply( context, args.concat( core_slice.call( arguments ) ) );
+ };
+
+ // Set the guid of unique handler to the same of original handler, so it can be removed
+ proxy.guid = fn.guid = fn.guid || jQuery.guid++;
+
+ return proxy;
+ },
+
+ // Multifunctional method to get and set values of a collection
+ // The value/s can optionally be executed if it's a function
+ access: function( elems, fn, key, value, chainable, emptyGet, pass ) {
+ var exec,
+ bulk = key == null,
+ i = 0,
+ length = elems.length;
+
+ // Sets many values
+ if ( key && typeof key === "object" ) {
+ for ( i in key ) {
+ jQuery.access( elems, fn, i, key[i], 1, emptyGet, value );
+ }
+ chainable = 1;
+
+ // Sets one value
+ } else if ( value !== undefined ) {
+ // Optionally, function values get executed if exec is true
+ exec = pass === undefined && jQuery.isFunction( value );
+
+ if ( bulk ) {
+ // Bulk operations only iterate when executing function values
+ if ( exec ) {
+ exec = fn;
+ fn = function( elem, key, value ) {
+ return exec.call( jQuery( elem ), value );
+ };
+
+ // Otherwise they run against the entire set
+ } else {
+ fn.call( elems, value );
+ fn = null;
+ }
+ }
+
+ if ( fn ) {
+ for (; i < length; i++ ) {
+ fn( elems[i], key, exec ? value.call( elems[i], i, fn( elems[i], key ) ) : value, pass );
+ }
+ }
+
+ chainable = 1;
+ }
+
+ return chainable ?
+ elems :
+
+ // Gets
+ bulk ?
+ fn.call( elems ) :
+ length ? fn( elems[0], key ) : emptyGet;
+ },
+
+ now: function() {
+ return ( new Date() ).getTime();
+ }
+});
+
+jQuery.ready.promise = function( obj ) {
+ if ( !readyList ) {
+
+ readyList = jQuery.Deferred();
+
+ // Catch cases where $(document).ready() is called after the browser event has already occurred.
+ // we once tried to use readyState "interactive" here, but it caused issues like the one
+ // discovered by ChrisS here: http://bugs.jquery.com/ticket/12282#comment:15
+ if ( document.readyState === "complete" ) {
+ // Handle it asynchronously to allow scripts the opportunity to delay ready
+ setTimeout( jQuery.ready, 1 );
+
+ // Standards-based browsers support DOMContentLoaded
+ } else if ( document.addEventListener ) {
+ // Use the handy event callback
+ document.addEventListener( "DOMContentLoaded", DOMContentLoaded, false );
+
+ // A fallback to window.onload, that will always work
+ window.addEventListener( "load", jQuery.ready, false );
+
+ // If IE event model is used
+ } else {
+ // Ensure firing before onload, maybe late but safe also for iframes
+ document.attachEvent( "onreadystatechange", DOMContentLoaded );
+
+ // A fallback to window.onload, that will always work
+ window.attachEvent( "onload", jQuery.ready );
+
+ // If IE and not a frame
+ // continually check to see if the document is ready
+ var top = false;
+
+ try {
+ top = window.frameElement == null && document.documentElement;
+ } catch(e) {}
+
+ if ( top && top.doScroll ) {
+ (function doScrollCheck() {
+ if ( !jQuery.isReady ) {
+
+ try {
+ // Use the trick by Diego Perini
+ // http://javascript.nwbox.com/IEContentLoaded/
+ top.doScroll("left");
+ } catch(e) {
+ return setTimeout( doScrollCheck, 50 );
+ }
+
+ // and execute any waiting functions
+ jQuery.ready();
+ }
+ })();
+ }
+ }
+ }
+ return readyList.promise( obj );
+};
+
+// Populate the class2type map
+jQuery.each("Boolean Number String Function Array Date RegExp Object".split(" "), function(i, name) {
+ class2type[ "[object " + name + "]" ] = name.toLowerCase();
+});
+
+// All jQuery objects should point back to these
+rootjQuery = jQuery(document);
+// String to Object options format cache
+var optionsCache = {};
+
+// Convert String-formatted options into Object-formatted ones and store in cache
+function createOptions( options ) {
+ var object = optionsCache[ options ] = {};
+ jQuery.each( options.split( core_rspace ), function( _, flag ) {
+ object[ flag ] = true;
+ });
+ return object;
+}
+
+/*
+ * Create a callback list using the following parameters:
+ *
+ * options: an optional list of space-separated options that will change how
+ * the callback list behaves or a more traditional option object
+ *
+ * By default a callback list will act like an event callback list and can be
+ * "fired" multiple times.
+ *
+ * Possible options:
+ *
+ * once: will ensure the callback list can only be fired once (like a Deferred)
+ *
+ * memory: will keep track of previous values and will call any callback added
+ * after the list has been fired right away with the latest "memorized"
+ * values (like a Deferred)
+ *
+ * unique: will ensure a callback can only be added once (no duplicate in the list)
+ *
+ * stopOnFalse: interrupt callings when a callback returns false
+ *
+ */
+jQuery.Callbacks = function( options ) {
+
+ // Convert options from String-formatted to Object-formatted if needed
+ // (we check in cache first)
+ options = typeof options === "string" ?
+ ( optionsCache[ options ] || createOptions( options ) ) :
+ jQuery.extend( {}, options );
+
+ var // Last fire value (for non-forgettable lists)
+ memory,
+ // Flag to know if list was already fired
+ fired,
+ // Flag to know if list is currently firing
+ firing,
+ // First callback to fire (used internally by add and fireWith)
+ firingStart,
+ // End of the loop when firing
+ firingLength,
+ // Index of currently firing callback (modified by remove if needed)
+ firingIndex,
+ // Actual callback list
+ list = [],
+ // Stack of fire calls for repeatable lists
+ stack = !options.once && [],
+ // Fire callbacks
+ fire = function( data ) {
+ memory = options.memory && data;
+ fired = true;
+ firingIndex = firingStart || 0;
+ firingStart = 0;
+ firingLength = list.length;
+ firing = true;
+ for ( ; list && firingIndex < firingLength; firingIndex++ ) {
+ if ( list[ firingIndex ].apply( data[ 0 ], data[ 1 ] ) === false && options.stopOnFalse ) {
+ memory = false; // To prevent further calls using add
+ break;
+ }
+ }
+ firing = false;
+ if ( list ) {
+ if ( stack ) {
+ if ( stack.length ) {
+ fire( stack.shift() );
+ }
+ } else if ( memory ) {
+ list = [];
+ } else {
+ self.disable();
+ }
+ }
+ },
+ // Actual Callbacks object
+ self = {
+ // Add a callback or a collection of callbacks to the list
+ add: function() {
+ if ( list ) {
+ // First, we save the current length
+ var start = list.length;
+ (function add( args ) {
+ jQuery.each( args, function( _, arg ) {
+ var type = jQuery.type( arg );
+ if ( type === "function" ) {
+ if ( !options.unique || !self.has( arg ) ) {
+ list.push( arg );
+ }
+ } else if ( arg && arg.length && type !== "string" ) {
+ // Inspect recursively
+ add( arg );
+ }
+ });
+ })( arguments );
+ // Do we need to add the callbacks to the
+ // current firing batch?
+ if ( firing ) {
+ firingLength = list.length;
+ // With memory, if we're not firing then
+ // we should call right away
+ } else if ( memory ) {
+ firingStart = start;
+ fire( memory );
+ }
+ }
+ return this;
+ },
+ // Remove a callback from the list
+ remove: function() {
+ if ( list ) {
+ jQuery.each( arguments, function( _, arg ) {
+ var index;
+ while( ( index = jQuery.inArray( arg, list, index ) ) > -1 ) {
+ list.splice( index, 1 );
+ // Handle firing indexes
+ if ( firing ) {
+ if ( index <= firingLength ) {
+ firingLength--;
+ }
+ if ( index <= firingIndex ) {
+ firingIndex--;
+ }
+ }
+ }
+ });
+ }
+ return this;
+ },
+ // Control if a given callback is in the list
+ has: function( fn ) {
+ return jQuery.inArray( fn, list ) > -1;
+ },
+ // Remove all callbacks from the list
+ empty: function() {
+ list = [];
+ return this;
+ },
+ // Have the list do nothing anymore
+ disable: function() {
+ list = stack = memory = undefined;
+ return this;
+ },
+ // Is it disabled?
+ disabled: function() {
+ return !list;
+ },
+ // Lock the list in its current state
+ lock: function() {
+ stack = undefined;
+ if ( !memory ) {
+ self.disable();
+ }
+ return this;
+ },
+ // Is it locked?
+ locked: function() {
+ return !stack;
+ },
+ // Call all callbacks with the given context and arguments
+ fireWith: function( context, args ) {
+ args = args || [];
+ args = [ context, args.slice ? args.slice() : args ];
+ if ( list && ( !fired || stack ) ) {
+ if ( firing ) {
+ stack.push( args );
+ } else {
+ fire( args );
+ }
+ }
+ return this;
+ },
+ // Call all the callbacks with the given arguments
+ fire: function() {
+ self.fireWith( this, arguments );
+ return this;
+ },
+ // To know if the callbacks have already been called at least once
+ fired: function() {
+ return !!fired;
+ }
+ };
+
+ return self;
+};
+jQuery.extend({
+
+ Deferred: function( func ) {
+ var tuples = [
+ // action, add listener, listener list, final state
+ [ "resolve", "done", jQuery.Callbacks("once memory"), "resolved" ],
+ [ "reject", "fail", jQuery.Callbacks("once memory"), "rejected" ],
+ [ "notify", "progress", jQuery.Callbacks("memory") ]
+ ],
+ state = "pending",
+ promise = {
+ state: function() {
+ return state;
+ },
+ always: function() {
+ deferred.done( arguments ).fail( arguments );
+ return this;
+ },
+ then: function( /* fnDone, fnFail, fnProgress */ ) {
+ var fns = arguments;
+ return jQuery.Deferred(function( newDefer ) {
+ jQuery.each( tuples, function( i, tuple ) {
+ var action = tuple[ 0 ],
+ fn = fns[ i ];
+ // deferred[ done | fail | progress ] for forwarding actions to newDefer
+ deferred[ tuple[1] ]( jQuery.isFunction( fn ) ?
+ function() {
+ var returned = fn.apply( this, arguments );
+ if ( returned && jQuery.isFunction( returned.promise ) ) {
+ returned.promise()
+ .done( newDefer.resolve )
+ .fail( newDefer.reject )
+ .progress( newDefer.notify );
+ } else {
+ newDefer[ action + "With" ]( this === deferred ? newDefer : this, [ returned ] );
+ }
+ } :
+ newDefer[ action ]
+ );
+ });
+ fns = null;
+ }).promise();
+ },
+ // Get a promise for this deferred
+ // If obj is provided, the promise aspect is added to the object
+ promise: function( obj ) {
+ return obj != null ? jQuery.extend( obj, promise ) : promise;
+ }
+ },
+ deferred = {};
+
+ // Keep pipe for back-compat
+ promise.pipe = promise.then;
+
+ // Add list-specific methods
+ jQuery.each( tuples, function( i, tuple ) {
+ var list = tuple[ 2 ],
+ stateString = tuple[ 3 ];
+
+ // promise[ done | fail | progress ] = list.add
+ promise[ tuple[1] ] = list.add;
+
+ // Handle state
+ if ( stateString ) {
+ list.add(function() {
+ // state = [ resolved | rejected ]
+ state = stateString;
+
+ // [ reject_list | resolve_list ].disable; progress_list.lock
+ }, tuples[ i ^ 1 ][ 2 ].disable, tuples[ 2 ][ 2 ].lock );
+ }
+
+ // deferred[ resolve | reject | notify ] = list.fire
+ deferred[ tuple[0] ] = list.fire;
+ deferred[ tuple[0] + "With" ] = list.fireWith;
+ });
+
+ // Make the deferred a promise
+ promise.promise( deferred );
+
+ // Call given func if any
+ if ( func ) {
+ func.call( deferred, deferred );
+ }
+
+ // All done!
+ return deferred;
+ },
+
+ // Deferred helper
+ when: function( subordinate /* , ..., subordinateN */ ) {
+ var i = 0,
+ resolveValues = core_slice.call( arguments ),
+ length = resolveValues.length,
+
+ // the count of uncompleted subordinates
+ remaining = length !== 1 || ( subordinate && jQuery.isFunction( subordinate.promise ) ) ? length : 0,
+
+ // the master Deferred. If resolveValues consist of only a single Deferred, just use that.
+ deferred = remaining === 1 ? subordinate : jQuery.Deferred(),
+
+ // Update function for both resolve and progress values
+ updateFunc = function( i, contexts, values ) {
+ return function( value ) {
+ contexts[ i ] = this;
+ values[ i ] = arguments.length > 1 ? core_slice.call( arguments ) : value;
+ if( values === progressValues ) {
+ deferred.notifyWith( contexts, values );
+ } else if ( !( --remaining ) ) {
+ deferred.resolveWith( contexts, values );
+ }
+ };
+ },
+
+ progressValues, progressContexts, resolveContexts;
+
+ // add listeners to Deferred subordinates; treat others as resolved
+ if ( length > 1 ) {
+ progressValues = new Array( length );
+ progressContexts = new Array( length );
+ resolveContexts = new Array( length );
+ for ( ; i < length; i++ ) {
+ if ( resolveValues[ i ] && jQuery.isFunction( resolveValues[ i ].promise ) ) {
+ resolveValues[ i ].promise()
+ .done( updateFunc( i, resolveContexts, resolveValues ) )
+ .fail( deferred.reject )
+ .progress( updateFunc( i, progressContexts, progressValues ) );
+ } else {
+ --remaining;
+ }
+ }
+ }
+
+ // if we're not waiting on anything, resolve the master
+ if ( !remaining ) {
+ deferred.resolveWith( resolveContexts, resolveValues );
+ }
+
+ return deferred.promise();
+ }
+});
+jQuery.support = (function() {
+
+ var support,
+ all,
+ a,
+ select,
+ opt,
+ input,
+ fragment,
+ eventName,
+ i,
+ isSupported,
+ clickFn,
+ div = document.createElement("div");
+
+ // Setup
+ div.setAttribute( "className", "t" );
+ div.innerHTML = " <link/><table></table><a href='/a'>a</a><input type='checkbox'/>";
+
+ // Support tests won't run in some limited or non-browser environments
+ all = div.getElementsByTagName("*");
+ a = div.getElementsByTagName("a")[ 0 ];
+ if ( !all || !a || !all.length ) {
+ return {};
+ }
+
+ // First batch of tests
+ select = document.createElement("select");
+ opt = select.appendChild( document.createElement("option") );
+ input = div.getElementsByTagName("input")[ 0 ];
+
+ a.style.cssText = "top:1px;float:left;opacity:.5";
+ support = {
+ // IE strips leading whitespace when .innerHTML is used
+ leadingWhitespace: ( div.firstChild.nodeType === 3 ),
+
+ // Make sure that tbody elements aren't automatically inserted
+ // IE will insert them into empty tables
+ tbody: !div.getElementsByTagName("tbody").length,
+
+ // Make sure that link elements get serialized correctly by innerHTML
+ // This requires a wrapper element in IE
+ htmlSerialize: !!div.getElementsByTagName("link").length,
+
+ // Get the style information from getAttribute
+ // (IE uses .cssText instead)
+ style: /top/.test( a.getAttribute("style") ),
+
+ // Make sure that URLs aren't manipulated
+ // (IE normalizes it by default)
+ hrefNormalized: ( a.getAttribute("href") === "/a" ),
+
+ // Make sure that element opacity exists
+ // (IE uses filter instead)
+ // Use a regex to work around a WebKit issue. See #5145
+ opacity: /^0.5/.test( a.style.opacity ),
+
+ // Verify style float existence
+ // (IE uses styleFloat instead of cssFloat)
+ cssFloat: !!a.style.cssFloat,
+
+ // Make sure that if no value is specified for a checkbox
+ // that it defaults to "on".
+ // (WebKit defaults to "" instead)
+ checkOn: ( input.value === "on" ),
+
+ // Make sure that a selected-by-default option has a working selected property.
+ // (WebKit defaults to false instead of true, IE too, if it's in an optgroup)
+ optSelected: opt.selected,
+
+ // Test setAttribute on camelCase class. If it works, we need attrFixes when doing get/setAttribute (ie6/7)
+ getSetAttribute: div.className !== "t",
+
+ // Tests for enctype support on a form (#6743)
+ enctype: !!document.createElement("form").enctype,
+
+ // Makes sure cloning an html5 element does not cause problems
+ // Where outerHTML is undefined, this still works
+ html5Clone: document.createElement("nav").cloneNode( true ).outerHTML !== "<:nav></:nav>",
+
+ // jQuery.support.boxModel DEPRECATED in 1.8 since we don't support Quirks Mode
+ boxModel: ( document.compatMode === "CSS1Compat" ),
+
+ // Will be defined later
+ submitBubbles: true,
+ changeBubbles: true,
+ focusinBubbles: false,
+ deleteExpando: true,
+ noCloneEvent: true,
+ inlineBlockNeedsLayout: false,
+ shrinkWrapBlocks: false,
+ reliableMarginRight: true,
+ boxSizingReliable: true,
+ pixelPosition: false
+ };
+
+ // Make sure checked status is properly cloned
+ input.checked = true;
+ support.noCloneChecked = input.cloneNode( true ).checked;
+
+ // Make sure that the options inside disabled selects aren't marked as disabled
+ // (WebKit marks them as disabled)
+ select.disabled = true;
+ support.optDisabled = !opt.disabled;
+
+ // Test to see if it's possible to delete an expando from an element
+ // Fails in Internet Explorer
+ try {
+ delete div.test;
+ } catch( e ) {
+ support.deleteExpando = false;
+ }
+
+ if ( !div.addEventListener && div.attachEvent && div.fireEvent ) {
+ div.attachEvent( "onclick", clickFn = function() {
+ // Cloning a node shouldn't copy over any
+ // bound event handlers (IE does this)
+ support.noCloneEvent = false;
+ });
+ div.cloneNode( true ).fireEvent("onclick");
+ div.detachEvent( "onclick", clickFn );
+ }
+
+ // Check if a radio maintains its value
+ // after being appended to the DOM
+ input = document.createElement("input");
+ input.value = "t";
+ input.setAttribute( "type", "radio" );
+ support.radioValue = input.value === "t";
+
+ input.setAttribute( "checked", "checked" );
+
+ // #11217 - WebKit loses check when the name is after the checked attribute
+ input.setAttribute( "name", "t" );
+
+ div.appendChild( input );
+ fragment = document.createDocumentFragment();
+ fragment.appendChild( div.lastChild );
+
+ // WebKit doesn't clone checked state correctly in fragments
+ support.checkClone = fragment.cloneNode( true ).cloneNode( true ).lastChild.checked;
+
+ // Check if a disconnected checkbox will retain its checked
+ // value of true after appended to the DOM (IE6/7)
+ support.appendChecked = input.checked;
+
+ fragment.removeChild( input );
+ fragment.appendChild( div );
+
+ // Technique from Juriy Zaytsev
+ // http://perfectionkills.com/detecting-event-support-without-browser-sniffing/
+ // We only care about the case where non-standard event systems
+ // are used, namely in IE. Short-circuiting here helps us to
+ // avoid an eval call (in setAttribute) which can cause CSP
+ // to go haywire. See: https://developer.mozilla.org/en/Security/CSP
+ if ( div.attachEvent ) {
+ for ( i in {
+ submit: true,
+ change: true,
+ focusin: true
+ }) {
+ eventName = "on" + i;
+ isSupported = ( eventName in div );
+ if ( !isSupported ) {
+ div.setAttribute( eventName, "return;" );
+ isSupported = ( typeof div[ eventName ] === "function" );
+ }
+ support[ i + "Bubbles" ] = isSupported;
+ }
+ }
+
+ // Run tests that need a body at doc ready
+ jQuery(function() {
+ var container, div, tds, marginDiv,
+ divReset = "padding:0;margin:0;border:0;display:block;overflow:hidden;",
+ body = document.getElementsByTagName("body")[0];
+
+ if ( !body ) {
+ // Return for frameset docs that don't have a body
+ return;
+ }
+
+ container = document.createElement("div");
+ container.style.cssText = "visibility:hidden;border:0;width:0;height:0;position:static;top:0;margin-top:1px";
+ body.insertBefore( container, body.firstChild );
+
+ // Construct the test element
+ div = document.createElement("div");
+ container.appendChild( div );
+
+ // Check if table cells still have offsetWidth/Height when they are set
+ // to display:none and there are still other visible table cells in a
+ // table row; if so, offsetWidth/Height are not reliable for use when
+ // determining if an element has been hidden directly using
+ // display:none (it is still safe to use offsets if a parent element is
+ // hidden; don safety goggles and see bug #4512 for more information).
+ // (only IE 8 fails this test)
+ div.innerHTML = "<table><tr><td></td><td>t</td></tr></table>";
+ tds = div.getElementsByTagName("td");
+ tds[ 0 ].style.cssText = "padding:0;margin:0;border:0;display:none";
+ isSupported = ( tds[ 0 ].offsetHeight === 0 );
+
+ tds[ 0 ].style.display = "";
+ tds[ 1 ].style.display = "none";
+
+ // Check if empty table cells still have offsetWidth/Height
+ // (IE <= 8 fail this test)
+ support.reliableHiddenOffsets = isSupported && ( tds[ 0 ].offsetHeight === 0 );
+
+ // Check box-sizing and margin behavior
+ div.innerHTML = "";
+ div.style.cssText = "box-sizing:border-box;-moz-box-sizing:border-box;-webkit-box-sizing:border-box;padding:1px;border:1px;display:block;width:4px;margin-top:1%;position:absolute;top:1%;";
+ support.boxSizing = ( div.offsetWidth === 4 );
+ support.doesNotIncludeMarginInBodyOffset = ( body.offsetTop !== 1 );
+
+ // NOTE: To any future maintainer, we've window.getComputedStyle
+ // because jsdom on node.js will break without it.
+ if ( window.getComputedStyle ) {
+ support.pixelPosition = ( window.getComputedStyle( div, null ) || {} ).top !== "1%";
+ support.boxSizingReliable = ( window.getComputedStyle( div, null ) || { width: "4px" } ).width === "4px";
+
+ // Check if div with explicit width and no margin-right incorrectly
+ // gets computed margin-right based on width of container. For more
+ // info see bug #3333
+ // Fails in WebKit before Feb 2011 nightlies
+ // WebKit Bug 13343 - getComputedStyle returns wrong value for margin-right
+ marginDiv = document.createElement("div");
+ marginDiv.style.cssText = div.style.cssText = divReset;
+ marginDiv.style.marginRight = marginDiv.style.width = "0";
+ div.style.width = "1px";
+ div.appendChild( marginDiv );
+ support.reliableMarginRight =
+ !parseFloat( ( window.getComputedStyle( marginDiv, null ) || {} ).marginRight );
+ }
+
+ if ( typeof div.style.zoom !== "undefined" ) {
+ // Check if natively block-level elements act like inline-block
+ // elements when setting their display to 'inline' and giving
+ // them layout
+ // (IE < 8 does this)
+ div.innerHTML = "";
+ div.style.cssText = divReset + "width:1px;padding:1px;display:inline;zoom:1";
+ support.inlineBlockNeedsLayout = ( div.offsetWidth === 3 );
+
+ // Check if elements with layout shrink-wrap their children
+ // (IE 6 does this)
+ div.style.display = "block";
+ div.style.overflow = "visible";
+ div.innerHTML = "<div></div>";
+ div.firstChild.style.width = "5px";
+ support.shrinkWrapBlocks = ( div.offsetWidth !== 3 );
+
+ container.style.zoom = 1;
+ }
+
+ // Null elements to avoid leaks in IE
+ body.removeChild( container );
+ container = div = tds = marginDiv = null;
+ });
+
+ // Null elements to avoid leaks in IE
+ fragment.removeChild( div );
+ all = a = select = opt = input = fragment = div = null;
+
+ return support;
+})();
+var rbrace = /(?:\{[\s\S]*\}|\[[\s\S]*\])$/,
+ rmultiDash = /([A-Z])/g;
+
+jQuery.extend({
+ cache: {},
+
+ deletedIds: [],
+
+ // Remove at next major release (1.9/2.0)
+ uuid: 0,
+
+ // Unique for each copy of jQuery on the page
+ // Non-digits removed to match rinlinejQuery
+ expando: "jQuery" + ( jQuery.fn.jquery + Math.random() ).replace( /\D/g, "" ),
+
+ // The following elements throw uncatchable exceptions if you
+ // attempt to add expando properties to them.
+ noData: {
+ "embed": true,
+ // Ban all objects except for Flash (which handle expandos)
+ "object": "clsid:D27CDB6E-AE6D-11cf-96B8-444553540000",
+ "applet": true
+ },
+
+ hasData: function( elem ) {
+ elem = elem.nodeType ? jQuery.cache[ elem[jQuery.expando] ] : elem[ jQuery.expando ];
+ return !!elem && !isEmptyDataObject( elem );
+ },
+
+ data: function( elem, name, data, pvt /* Internal Use Only */ ) {
+ if ( !jQuery.acceptData( elem ) ) {
+ return;
+ }
+
+ var thisCache, ret,
+ internalKey = jQuery.expando,
+ getByName = typeof name === "string",
+
+ // We have to handle DOM nodes and JS objects differently because IE6-7
+ // can't GC object references properly across the DOM-JS boundary
+ isNode = elem.nodeType,
+
+ // Only DOM nodes need the global jQuery cache; JS object data is
+ // attached directly to the object so GC can occur automatically
+ cache = isNode ? jQuery.cache : elem,
+
+ // Only defining an ID for JS objects if its cache already exists allows
+ // the code to shortcut on the same path as a DOM node with no cache
+ id = isNode ? elem[ internalKey ] : elem[ internalKey ] && internalKey;
+
+ // Avoid doing any more work than we need to when trying to get data on an
+ // object that has no data at all
+ if ( (!id || !cache[id] || (!pvt && !cache[id].data)) && getByName && data === undefined ) {
+ return;
+ }
+
+ if ( !id ) {
+ // Only DOM nodes need a new unique ID for each element since their data
+ // ends up in the global cache
+ if ( isNode ) {
+ elem[ internalKey ] = id = jQuery.deletedIds.pop() || jQuery.guid++;
+ } else {
+ id = internalKey;
+ }
+ }
+
+ if ( !cache[ id ] ) {
+ cache[ id ] = {};
+
+ // Avoids exposing jQuery metadata on plain JS objects when the object
+ // is serialized using JSON.stringify
+ if ( !isNode ) {
+ cache[ id ].toJSON = jQuery.noop;
+ }
+ }
+
+ // An object can be passed to jQuery.data instead of a key/value pair; this gets
+ // shallow copied over onto the existing cache
+ if ( typeof name === "object" || typeof name === "function" ) {
+ if ( pvt ) {
+ cache[ id ] = jQuery.extend( cache[ id ], name );
+ } else {
+ cache[ id ].data = jQuery.extend( cache[ id ].data, name );
+ }
+ }
+
+ thisCache = cache[ id ];
+
+ // jQuery data() is stored in a separate object inside the object's internal data
+ // cache in order to avoid key collisions between internal data and user-defined
+ // data.
+ if ( !pvt ) {
+ if ( !thisCache.data ) {
+ thisCache.data = {};
+ }
+
+ thisCache = thisCache.data;
+ }
+
+ if ( data !== undefined ) {
+ thisCache[ jQuery.camelCase( name ) ] = data;
+ }
+
+ // Check for both converted-to-camel and non-converted data property names
+ // If a data property was specified
+ if ( getByName ) {
+
+ // First Try to find as-is property data
+ ret = thisCache[ name ];
+
+ // Test for null|undefined property data
+ if ( ret == null ) {
+
+ // Try to find the camelCased property
+ ret = thisCache[ jQuery.camelCase( name ) ];
+ }
+ } else {
+ ret = thisCache;
+ }
+
+ return ret;
+ },
+
+ removeData: function( elem, name, pvt /* Internal Use Only */ ) {
+ if ( !jQuery.acceptData( elem ) ) {
+ return;
+ }
+
+ var thisCache, i, l,
+
+ isNode = elem.nodeType,
+
+ // See jQuery.data for more information
+ cache = isNode ? jQuery.cache : elem,
+ id = isNode ? elem[ jQuery.expando ] : jQuery.expando;
+
+ // If there is already no cache entry for this object, there is no
+ // purpose in continuing
+ if ( !cache[ id ] ) {
+ return;
+ }
+
+ if ( name ) {
+
+ thisCache = pvt ? cache[ id ] : cache[ id ].data;
+
+ if ( thisCache ) {
+
+ // Support array or space separated string names for data keys
+ if ( !jQuery.isArray( name ) ) {
+
+ // try the string as a key before any manipulation
+ if ( name in thisCache ) {
+ name = [ name ];
+ } else {
+
+ // split the camel cased version by spaces unless a key with the spaces exists
+ name = jQuery.camelCase( name );
+ if ( name in thisCache ) {
+ name = [ name ];
+ } else {
+ name = name.split(" ");
+ }
+ }
+ }
+
+ for ( i = 0, l = name.length; i < l; i++ ) {
+ delete thisCache[ name[i] ];
+ }
+
+ // If there is no data left in the cache, we want to continue
+ // and let the cache object itself get destroyed
+ if ( !( pvt ? isEmptyDataObject : jQuery.isEmptyObject )( thisCache ) ) {
+ return;
+ }
+ }
+ }
+
+ // See jQuery.data for more information
+ if ( !pvt ) {
+ delete cache[ id ].data;
+
+ // Don't destroy the parent cache unless the internal data object
+ // had been the only thing left in it
+ if ( !isEmptyDataObject( cache[ id ] ) ) {
+ return;
+ }
+ }
+
+ // Destroy the cache
+ if ( isNode ) {
+ jQuery.cleanData( [ elem ], true );
+
+ // Use delete when supported for expandos or `cache` is not a window per isWindow (#10080)
+ } else if ( jQuery.support.deleteExpando || cache != cache.window ) {
+ delete cache[ id ];
+
+ // When all else fails, null
+ } else {
+ cache[ id ] = null;
+ }
+ },
+
+ // For internal use only.
+ _data: function( elem, name, data ) {
+ return jQuery.data( elem, name, data, true );
+ },
+
+ // A method for determining if a DOM node can handle the data expando
+ acceptData: function( elem ) {
+ var noData = elem.nodeName && jQuery.noData[ elem.nodeName.toLowerCase() ];
+
+ // nodes accept data unless otherwise specified; rejection can be conditional
+ return !noData || noData !== true && elem.getAttribute("classid") === noData;
+ }
+});
+
+jQuery.fn.extend({
+ data: function( key, value ) {
+ var parts, part, attr, name, l,
+ elem = this[0],
+ i = 0,
+ data = null;
+
+ // Gets all values
+ if ( key === undefined ) {
+ if ( this.length ) {
+ data = jQuery.data( elem );
+
+ if ( elem.nodeType === 1 && !jQuery._data( elem, "parsedAttrs" ) ) {
+ attr = elem.attributes;
+ for ( l = attr.length; i < l; i++ ) {
+ name = attr[i].name;
+
+ if ( !name.indexOf( "data-" ) ) {
+ name = jQuery.camelCase( name.substring(5) );
+
+ dataAttr( elem, name, data[ name ] );
+ }
+ }
+ jQuery._data( elem, "parsedAttrs", true );
+ }
+ }
+
+ return data;
+ }
+
+ // Sets multiple values
+ if ( typeof key === "object" ) {
+ return this.each(function() {
+ jQuery.data( this, key );
+ });
+ }
+
+ parts = key.split( ".", 2 );
+ parts[1] = parts[1] ? "." + parts[1] : "";
+ part = parts[1] + "!";
+
+ return jQuery.access( this, function( value ) {
+
+ if ( value === undefined ) {
+ data = this.triggerHandler( "getData" + part, [ parts[0] ] );
+
+ // Try to fetch any internally stored data first
+ if ( data === undefined && elem ) {
+ data = jQuery.data( elem, key );
+ data = dataAttr( elem, key, data );
+ }
+
+ return data === undefined && parts[1] ?
+ this.data( parts[0] ) :
+ data;
+ }
+
+ parts[1] = value;
+ this.each(function() {
+ var self = jQuery( this );
+
+ self.triggerHandler( "setData" + part, parts );
+ jQuery.data( this, key, value );
+ self.triggerHandler( "changeData" + part, parts );
+ });
+ }, null, value, arguments.length > 1, null, false );
+ },
+
+ removeData: function( key ) {
+ return this.each(function() {
+ jQuery.removeData( this, key );
+ });
+ }
+});
+
+function dataAttr( elem, key, data ) {
+ // If nothing was found internally, try to fetch any
+ // data from the HTML5 data-* attribute
+ if ( data === undefined && elem.nodeType === 1 ) {
+
+ var name = "data-" + key.replace( rmultiDash, "-$1" ).toLowerCase();
+
+ data = elem.getAttribute( name );
+
+ if ( typeof data === "string" ) {
+ try {
+ data = data === "true" ? true :
+ data === "false" ? false :
+ data === "null" ? null :
+ // Only convert to a number if it doesn't change the string
+ +data + "" === data ? +data :
+ rbrace.test( data ) ? jQuery.parseJSON( data ) :
+ data;
+ } catch( e ) {}
+
+ // Make sure we set the data so it isn't changed later
+ jQuery.data( elem, key, data );
+
+ } else {
+ data = undefined;
+ }
+ }
+
+ return data;
+}
+
+// checks a cache object for emptiness
+function isEmptyDataObject( obj ) {
+ var name;
+ for ( name in obj ) {
+
+ // if the public data object is empty, the private is still empty
+ if ( name === "data" && jQuery.isEmptyObject( obj[name] ) ) {
+ continue;
+ }
+ if ( name !== "toJSON" ) {
+ return false;
+ }
+ }
+
+ return true;
+}
+jQuery.extend({
+ queue: function( elem, type, data ) {
+ var queue;
+
+ if ( elem ) {
+ type = ( type || "fx" ) + "queue";
+ queue = jQuery._data( elem, type );
+
+ // Speed up dequeue by getting out quickly if this is just a lookup
+ if ( data ) {
+ if ( !queue || jQuery.isArray(data) ) {
+ queue = jQuery._data( elem, type, jQuery.makeArray(data) );
+ } else {
+ queue.push( data );
+ }
+ }
+ return queue || [];
+ }
+ },
+
+ dequeue: function( elem, type ) {
+ type = type || "fx";
+
+ var queue = jQuery.queue( elem, type ),
+ startLength = queue.length,
+ fn = queue.shift(),
+ hooks = jQuery._queueHooks( elem, type ),
+ next = function() {
+ jQuery.dequeue( elem, type );
+ };
+
+ // If the fx queue is dequeued, always remove the progress sentinel
+ if ( fn === "inprogress" ) {
+ fn = queue.shift();
+ startLength--;
+ }
+
+ if ( fn ) {
+
+ // Add a progress sentinel to prevent the fx queue from being
+ // automatically dequeued
+ if ( type === "fx" ) {
+ queue.unshift( "inprogress" );
+ }
+
+ // clear up the last queue stop function
+ delete hooks.stop;
+ fn.call( elem, next, hooks );
+ }
+
+ if ( !startLength && hooks ) {
+ hooks.empty.fire();
+ }
+ },
+
+ // not intended for public consumption - generates a queueHooks object, or returns the current one
+ _queueHooks: function( elem, type ) {
+ var key = type + "queueHooks";
+ return jQuery._data( elem, key ) || jQuery._data( elem, key, {
+ empty: jQuery.Callbacks("once memory").add(function() {
+ jQuery.removeData( elem, type + "queue", true );
+ jQuery.removeData( elem, key, true );
+ })
+ });
+ }
+});
+
+jQuery.fn.extend({
+ queue: function( type, data ) {
+ var setter = 2;
+
+ if ( typeof type !== "string" ) {
+ data = type;
+ type = "fx";
+ setter--;
+ }
+
+ if ( arguments.length < setter ) {
+ return jQuery.queue( this[0], type );
+ }
+
+ return data === undefined ?
+ this :
+ this.each(function() {
+ var queue = jQuery.queue( this, type, data );
+
+ // ensure a hooks for this queue
+ jQuery._queueHooks( this, type );
+
+ if ( type === "fx" && queue[0] !== "inprogress" ) {
+ jQuery.dequeue( this, type );
+ }
+ });
+ },
+ dequeue: function( type ) {
+ return this.each(function() {
+ jQuery.dequeue( this, type );
+ });
+ },
+ // Based off of the plugin by Clint Helfers, with permission.
+ // http://blindsignals.com/index.php/2009/07/jquery-delay/
+ delay: function( time, type ) {
+ time = jQuery.fx ? jQuery.fx.speeds[ time ] || time : time;
+ type = type || "fx";
+
+ return this.queue( type, function( next, hooks ) {
+ var timeout = setTimeout( next, time );
+ hooks.stop = function() {
+ clearTimeout( timeout );
+ };
+ });
+ },
+ clearQueue: function( type ) {
+ return this.queue( type || "fx", [] );
+ },
+ // Get a promise resolved when queues of a certain type
+ // are emptied (fx is the type by default)
+ promise: function( type, obj ) {
+ var tmp,
+ count = 1,
+ defer = jQuery.Deferred(),
+ elements = this,
+ i = this.length,
+ resolve = function() {
+ if ( !( --count ) ) {
+ defer.resolveWith( elements, [ elements ] );
+ }
+ };
+
+ if ( typeof type !== "string" ) {
+ obj = type;
+ type = undefined;
+ }
+ type = type || "fx";
+
+ while( i-- ) {
+ tmp = jQuery._data( elements[ i ], type + "queueHooks" );
+ if ( tmp && tmp.empty ) {
+ count++;
+ tmp.empty.add( resolve );
+ }
+ }
+ resolve();
+ return defer.promise( obj );
+ }
+});
+var nodeHook, boolHook, fixSpecified,
+ rclass = /[\t\r\n]/g,
+ rreturn = /\r/g,
+ rtype = /^(?:button|input)$/i,
+ rfocusable = /^(?:button|input|object|select|textarea)$/i,
+ rclickable = /^a(?:rea|)$/i,
+ rboolean = /^(?:autofocus|autoplay|async|checked|controls|defer|disabled|hidden|loop|multiple|open|readonly|required|scoped|selected)$/i,
+ getSetAttribute = jQuery.support.getSetAttribute;
+
+jQuery.fn.extend({
+ attr: function( name, value ) {
+ return jQuery.access( this, jQuery.attr, name, value, arguments.length > 1 );
+ },
+
+ removeAttr: function( name ) {
+ return this.each(function() {
+ jQuery.removeAttr( this, name );
+ });
+ },
+
+ prop: function( name, value ) {
+ return jQuery.access( this, jQuery.prop, name, value, arguments.length > 1 );
+ },
+
+ removeProp: function( name ) {
+ name = jQuery.propFix[ name ] || name;
+ return this.each(function() {
+ // try/catch handles cases where IE balks (such as removing a property on window)
+ try {
+ this[ name ] = undefined;
+ delete this[ name ];
+ } catch( e ) {}
+ });
+ },
+
+ addClass: function( value ) {
+ var classNames, i, l, elem,
+ setClass, c, cl;
+
+ if ( jQuery.isFunction( value ) ) {
+ return this.each(function( j ) {
+ jQuery( this ).addClass( value.call(this, j, this.className) );
+ });
+ }
+
+ if ( value && typeof value === "string" ) {
+ classNames = value.split( core_rspace );
+
+ for ( i = 0, l = this.length; i < l; i++ ) {
+ elem = this[ i ];
+
+ if ( elem.nodeType === 1 ) {
+ if ( !elem.className && classNames.length === 1 ) {
+ elem.className = value;
+
+ } else {
+ setClass = " " + elem.className + " ";
+
+ for ( c = 0, cl = classNames.length; c < cl; c++ ) {
+ if ( setClass.indexOf( " " + classNames[ c ] + " " ) < 0 ) {
+ setClass += classNames[ c ] + " ";
+ }
+ }
+ elem.className = jQuery.trim( setClass );
+ }
+ }
+ }
+ }
+
+ return this;
+ },
+
+ removeClass: function( value ) {
+ var removes, className, elem, c, cl, i, l;
+
+ if ( jQuery.isFunction( value ) ) {
+ return this.each(function( j ) {
+ jQuery( this ).removeClass( value.call(this, j, this.className) );
+ });
+ }
+ if ( (value && typeof value === "string") || value === undefined ) {
+ removes = ( value || "" ).split( core_rspace );
+
+ for ( i = 0, l = this.length; i < l; i++ ) {
+ elem = this[ i ];
+ if ( elem.nodeType === 1 && elem.className ) {
+
+ className = (" " + elem.className + " ").replace( rclass, " " );
+
+ // loop over each item in the removal list
+ for ( c = 0, cl = removes.length; c < cl; c++ ) {
+ // Remove until there is nothing to remove,
+ while ( className.indexOf(" " + removes[ c ] + " ") >= 0 ) {
+ className = className.replace( " " + removes[ c ] + " " , " " );
+ }
+ }
+ elem.className = value ? jQuery.trim( className ) : "";
+ }
+ }
+ }
+
+ return this;
+ },
+
+ toggleClass: function( value, stateVal ) {
+ var type = typeof value,
+ isBool = typeof stateVal === "boolean";
+
+ if ( jQuery.isFunction( value ) ) {
+ return this.each(function( i ) {
+ jQuery( this ).toggleClass( value.call(this, i, this.className, stateVal), stateVal );
+ });
+ }
+
+ return this.each(function() {
+ if ( type === "string" ) {
+ // toggle individual class names
+ var className,
+ i = 0,
+ self = jQuery( this ),
+ state = stateVal,
+ classNames = value.split( core_rspace );
+
+ while ( (className = classNames[ i++ ]) ) {
+ // check each className given, space separated list
+ state = isBool ? state : !self.hasClass( className );
+ self[ state ? "addClass" : "removeClass" ]( className );
+ }
+
+ } else if ( type === "undefined" || type === "boolean" ) {
+ if ( this.className ) {
+ // store className if set
+ jQuery._data( this, "__className__", this.className );
+ }
+
+ // toggle whole className
+ this.className = this.className || value === false ? "" : jQuery._data( this, "__className__" ) || "";
+ }
+ });
+ },
+
+ hasClass: function( selector ) {
+ var className = " " + selector + " ",
+ i = 0,
+ l = this.length;
+ for ( ; i < l; i++ ) {
+ if ( this[i].nodeType === 1 && (" " + this[i].className + " ").replace(rclass, " ").indexOf( className ) >= 0 ) {
+ return true;
+ }
+ }
+
+ return false;
+ },
+
+ val: function( value ) {
+ var hooks, ret, isFunction,
+ elem = this[0];
+
+ if ( !arguments.length ) {
+ if ( elem ) {
+ hooks = jQuery.valHooks[ elem.type ] || jQuery.valHooks[ elem.nodeName.toLowerCase() ];
+
+ if ( hooks && "get" in hooks && (ret = hooks.get( elem, "value" )) !== undefined ) {
+ return ret;
+ }
+
+ ret = elem.value;
+
+ return typeof ret === "string" ?
+ // handle most common string cases
+ ret.replace(rreturn, "") :
+ // handle cases where value is null/undef or number
+ ret == null ? "" : ret;
+ }
+
+ return;
+ }
+
+ isFunction = jQuery.isFunction( value );
+
+ return this.each(function( i ) {
+ var val,
+ self = jQuery(this);
+
+ if ( this.nodeType !== 1 ) {
+ return;
+ }
+
+ if ( isFunction ) {
+ val = value.call( this, i, self.val() );
+ } else {
+ val = value;
+ }
+
+ // Treat null/undefined as ""; convert numbers to string
+ if ( val == null ) {
+ val = "";
+ } else if ( typeof val === "number" ) {
+ val += "";
+ } else if ( jQuery.isArray( val ) ) {
+ val = jQuery.map(val, function ( value ) {
+ return value == null ? "" : value + "";
+ });
+ }
+
+ hooks = jQuery.valHooks[ this.type ] || jQuery.valHooks[ this.nodeName.toLowerCase() ];
+
+ // If set returns undefined, fall back to normal setting
+ if ( !hooks || !("set" in hooks) || hooks.set( this, val, "value" ) === undefined ) {
+ this.value = val;
+ }
+ });
+ }
+});
+
+jQuery.extend({
+ valHooks: {
+ option: {
+ get: function( elem ) {
+ // attributes.value is undefined in Blackberry 4.7 but
+ // uses .value. See #6932
+ var val = elem.attributes.value;
+ return !val || val.specified ? elem.value : elem.text;
+ }
+ },
+ select: {
+ get: function( elem ) {
+ var value, option,
+ options = elem.options,
+ index = elem.selectedIndex,
+ one = elem.type === "select-one" || index < 0,
+ values = one ? null : [],
+ max = one ? index + 1 : options.length,
+ i = index < 0 ?
+ max :
+ one ? index : 0;
+
+ // Loop through all the selected options
+ for ( ; i < max; i++ ) {
+ option = options[ i ];
+
+ // oldIE doesn't update selected after form reset (#2551)
+ if ( ( option.selected || i === index ) &&
+ // Don't return options that are disabled or in a disabled optgroup
+ ( jQuery.support.optDisabled ? !option.disabled : option.getAttribute("disabled") === null ) &&
+ ( !option.parentNode.disabled || !jQuery.nodeName( option.parentNode, "optgroup" ) ) ) {
+
+ // Get the specific value for the option
+ value = jQuery( option ).val();
+
+ // We don't need an array for one selects
+ if ( one ) {
+ return value;
+ }
+
+ // Multi-Selects return an array
+ values.push( value );
+ }
+ }
+
+ return values;
+ },
+
+ set: function( elem, value ) {
+ var values = jQuery.makeArray( value );
+
+ jQuery(elem).find("option").each(function() {
+ this.selected = jQuery.inArray( jQuery(this).val(), values ) >= 0;
+ });
+
+ if ( !values.length ) {
+ elem.selectedIndex = -1;
+ }
+ return values;
+ }
+ }
+ },
+
+ // Unused in 1.8, left in so attrFn-stabbers won't die; remove in 1.9
+ attrFn: {},
+
+ attr: function( elem, name, value, pass ) {
+ var ret, hooks, notxml,
+ nType = elem.nodeType;
+
+ // don't get/set attributes on text, comment and attribute nodes
+ if ( !elem || nType === 3 || nType === 8 || nType === 2 ) {
+ return;
+ }
+
+ if ( pass && jQuery.isFunction( jQuery.fn[ name ] ) ) {
+ return jQuery( elem )[ name ]( value );
+ }
+
+ // Fallback to prop when attributes are not supported
+ if ( typeof elem.getAttribute === "undefined" ) {
+ return jQuery.prop( elem, name, value );
+ }
+
+ notxml = nType !== 1 || !jQuery.isXMLDoc( elem );
+
+ // All attributes are lowercase
+ // Grab necessary hook if one is defined
+ if ( notxml ) {
+ name = name.toLowerCase();
+ hooks = jQuery.attrHooks[ name ] || ( rboolean.test( name ) ? boolHook : nodeHook );
+ }
+
+ if ( value !== undefined ) {
+
+ if ( value === null ) {
+ jQuery.removeAttr( elem, name );
+ return;
+
+ } else if ( hooks && "set" in hooks && notxml && (ret = hooks.set( elem, value, name )) !== undefined ) {
+ return ret;
+
+ } else {
+ elem.setAttribute( name, value + "" );
+ return value;
+ }
+
+ } else if ( hooks && "get" in hooks && notxml && (ret = hooks.get( elem, name )) !== null ) {
+ return ret;
+
+ } else {
+
+ ret = elem.getAttribute( name );
+
+ // Non-existent attributes return null, we normalize to undefined
+ return ret === null ?
+ undefined :
+ ret;
+ }
+ },
+
+ removeAttr: function( elem, value ) {
+ var propName, attrNames, name, isBool,
+ i = 0;
+
+ if ( value && elem.nodeType === 1 ) {
+
+ attrNames = value.split( core_rspace );
+
+ for ( ; i < attrNames.length; i++ ) {
+ name = attrNames[ i ];
+
+ if ( name ) {
+ propName = jQuery.propFix[ name ] || name;
+ isBool = rboolean.test( name );
+
+ // See #9699 for explanation of this approach (setting first, then removal)
+ // Do not do this for boolean attributes (see #10870)
+ if ( !isBool ) {
+ jQuery.attr( elem, name, "" );
+ }
+ elem.removeAttribute( getSetAttribute ? name : propName );
+
+ // Set corresponding property to false for boolean attributes
+ if ( isBool && propName in elem ) {
+ elem[ propName ] = false;
+ }
+ }
+ }
+ }
+ },
+
+ attrHooks: {
+ type: {
+ set: function( elem, value ) {
+ // We can't allow the type property to be changed (since it causes problems in IE)
+ if ( rtype.test( elem.nodeName ) && elem.parentNode ) {
+ jQuery.error( "type property can't be changed" );
+ } else if ( !jQuery.support.radioValue && value === "radio" && jQuery.nodeName(elem, "input") ) {
+ // Setting the type on a radio button after the value resets the value in IE6-9
+ // Reset value to it's default in case type is set after value
+ // This is for element creation
+ var val = elem.value;
+ elem.setAttribute( "type", value );
+ if ( val ) {
+ elem.value = val;
+ }
+ return value;
+ }
+ }
+ },
+ // Use the value property for back compat
+ // Use the nodeHook for button elements in IE6/7 (#1954)
+ value: {
+ get: function( elem, name ) {
+ if ( nodeHook && jQuery.nodeName( elem, "button" ) ) {
+ return nodeHook.get( elem, name );
+ }
+ return name in elem ?
+ elem.value :
+ null;
+ },
+ set: function( elem, value, name ) {
+ if ( nodeHook && jQuery.nodeName( elem, "button" ) ) {
+ return nodeHook.set( elem, value, name );
+ }
+ // Does not return so that setAttribute is also used
+ elem.value = value;
+ }
+ }
+ },
+
+ propFix: {
+ tabindex: "tabIndex",
+ readonly: "readOnly",
+ "for": "htmlFor",
+ "class": "className",
+ maxlength: "maxLength",
+ cellspacing: "cellSpacing",
+ cellpadding: "cellPadding",
+ rowspan: "rowSpan",
+ colspan: "colSpan",
+ usemap: "useMap",
+ frameborder: "frameBorder",
+ contenteditable: "contentEditable"
+ },
+
+ prop: function( elem, name, value ) {
+ var ret, hooks, notxml,
+ nType = elem.nodeType;
+
+ // don't get/set properties on text, comment and attribute nodes
+ if ( !elem || nType === 3 || nType === 8 || nType === 2 ) {
+ return;
+ }
+
+ notxml = nType !== 1 || !jQuery.isXMLDoc( elem );
+
+ if ( notxml ) {
+ // Fix name and attach hooks
+ name = jQuery.propFix[ name ] || name;
+ hooks = jQuery.propHooks[ name ];
+ }
+
+ if ( value !== undefined ) {
+ if ( hooks && "set" in hooks && (ret = hooks.set( elem, value, name )) !== undefined ) {
+ return ret;
+
+ } else {
+ return ( elem[ name ] = value );
+ }
+
+ } else {
+ if ( hooks && "get" in hooks && (ret = hooks.get( elem, name )) !== null ) {
+ return ret;
+
+ } else {
+ return elem[ name ];
+ }
+ }
+ },
+
+ propHooks: {
+ tabIndex: {
+ get: function( elem ) {
+ // elem.tabIndex doesn't always return the correct value when it hasn't been explicitly set
+ // http://fluidproject.org/blog/2008/01/09/getting-setting-and-removing-tabindex-values-with-javascript/
+ var attributeNode = elem.getAttributeNode("tabindex");
+
+ return attributeNode && attributeNode.specified ?
+ parseInt( attributeNode.value, 10 ) :
+ rfocusable.test( elem.nodeName ) || rclickable.test( elem.nodeName ) && elem.href ?
+ 0 :
+ undefined;
+ }
+ }
+ }
+});
+
+// Hook for boolean attributes
+boolHook = {
+ get: function( elem, name ) {
+ // Align boolean attributes with corresponding properties
+ // Fall back to attribute presence where some booleans are not supported
+ var attrNode,
+ property = jQuery.prop( elem, name );
+ return property === true || typeof property !== "boolean" && ( attrNode = elem.getAttributeNode(name) ) && attrNode.nodeValue !== false ?
+ name.toLowerCase() :
+ undefined;
+ },
+ set: function( elem, value, name ) {
+ var propName;
+ if ( value === false ) {
+ // Remove boolean attributes when set to false
+ jQuery.removeAttr( elem, name );
+ } else {
+ // value is true since we know at this point it's type boolean and not false
+ // Set boolean attributes to the same name and set the DOM property
+ propName = jQuery.propFix[ name ] || name;
+ if ( propName in elem ) {
+ // Only set the IDL specifically if it already exists on the element
+ elem[ propName ] = true;
+ }
+
+ elem.setAttribute( name, name.toLowerCase() );
+ }
+ return name;
+ }
+};
+
+// IE6/7 do not support getting/setting some attributes with get/setAttribute
+if ( !getSetAttribute ) {
+
+ fixSpecified = {
+ name: true,
+ id: true,
+ coords: true
+ };
+
+ // Use this for any attribute in IE6/7
+ // This fixes almost every IE6/7 issue
+ nodeHook = jQuery.valHooks.button = {
+ get: function( elem, name ) {
+ var ret;
+ ret = elem.getAttributeNode( name );
+ return ret && ( fixSpecified[ name ] ? ret.value !== "" : ret.specified ) ?
+ ret.value :
+ undefined;
+ },
+ set: function( elem, value, name ) {
+ // Set the existing or create a new attribute node
+ var ret = elem.getAttributeNode( name );
+ if ( !ret ) {
+ ret = document.createAttribute( name );
+ elem.setAttributeNode( ret );
+ }
+ return ( ret.value = value + "" );
+ }
+ };
+
+ // Set width and height to auto instead of 0 on empty string( Bug #8150 )
+ // This is for removals
+ jQuery.each([ "width", "height" ], function( i, name ) {
+ jQuery.attrHooks[ name ] = jQuery.extend( jQuery.attrHooks[ name ], {
+ set: function( elem, value ) {
+ if ( value === "" ) {
+ elem.setAttribute( name, "auto" );
+ return value;
+ }
+ }
+ });
+ });
+
+ // Set contenteditable to false on removals(#10429)
+ // Setting to empty string throws an error as an invalid value
+ jQuery.attrHooks.contenteditable = {
+ get: nodeHook.get,
+ set: function( elem, value, name ) {
+ if ( value === "" ) {
+ value = "false";
+ }
+ nodeHook.set( elem, value, name );
+ }
+ };
+}
+
+
+// Some attributes require a special call on IE
+if ( !jQuery.support.hrefNormalized ) {
+ jQuery.each([ "href", "src", "width", "height" ], function( i, name ) {
+ jQuery.attrHooks[ name ] = jQuery.extend( jQuery.attrHooks[ name ], {
+ get: function( elem ) {
+ var ret = elem.getAttribute( name, 2 );
+ return ret === null ? undefined : ret;
+ }
+ });
+ });
+}
+
+if ( !jQuery.support.style ) {
+ jQuery.attrHooks.style = {
+ get: function( elem ) {
+ // Return undefined in the case of empty string
+ // Normalize to lowercase since IE uppercases css property names
+ return elem.style.cssText.toLowerCase() || undefined;
+ },
+ set: function( elem, value ) {
+ return ( elem.style.cssText = value + "" );
+ }
+ };
+}
+
+// Safari mis-reports the default selected property of an option
+// Accessing the parent's selectedIndex property fixes it
+if ( !jQuery.support.optSelected ) {
+ jQuery.propHooks.selected = jQuery.extend( jQuery.propHooks.selected, {
+ get: function( elem ) {
+ var parent = elem.parentNode;
+
+ if ( parent ) {
+ parent.selectedIndex;
+
+ // Make sure that it also works with optgroups, see #5701
+ if ( parent.parentNode ) {
+ parent.parentNode.selectedIndex;
+ }
+ }
+ return null;
+ }
+ });
+}
+
+// IE6/7 call enctype encoding
+if ( !jQuery.support.enctype ) {
+ jQuery.propFix.enctype = "encoding";
+}
+
+// Radios and checkboxes getter/setter
+if ( !jQuery.support.checkOn ) {
+ jQuery.each([ "radio", "checkbox" ], function() {
+ jQuery.valHooks[ this ] = {
+ get: function( elem ) {
+ // Handle the case where in Webkit "" is returned instead of "on" if a value isn't specified
+ return elem.getAttribute("value") === null ? "on" : elem.value;
+ }
+ };
+ });
+}
+jQuery.each([ "radio", "checkbox" ], function() {
+ jQuery.valHooks[ this ] = jQuery.extend( jQuery.valHooks[ this ], {
+ set: function( elem, value ) {
+ if ( jQuery.isArray( value ) ) {
+ return ( elem.checked = jQuery.inArray( jQuery(elem).val(), value ) >= 0 );
+ }
+ }
+ });
+});
+var rformElems = /^(?:textarea|input|select)$/i,
+ rtypenamespace = /^([^\.]*|)(?:\.(.+)|)$/,
+ rhoverHack = /(?:^|\s)hover(\.\S+|)\b/,
+ rkeyEvent = /^key/,
+ rmouseEvent = /^(?:mouse|contextmenu)|click/,
+ rfocusMorph = /^(?:focusinfocus|focusoutblur)$/,
+ hoverHack = function( events ) {
+ return jQuery.event.special.hover ? events : events.replace( rhoverHack, "mouseenter$1 mouseleave$1" );
+ };
+
+/*
+ * Helper functions for managing events -- not part of the public interface.
+ * Props to Dean Edwards' addEvent library for many of the ideas.
+ */
+jQuery.event = {
+
+ add: function( elem, types, handler, data, selector ) {
+
+ var elemData, eventHandle, events,
+ t, tns, type, namespaces, handleObj,
+ handleObjIn, handlers, special;
+
+ // Don't attach events to noData or text/comment nodes (allow plain objects tho)
+ if ( elem.nodeType === 3 || elem.nodeType === 8 || !types || !handler || !(elemData = jQuery._data( elem )) ) {
+ return;
+ }
+
+ // Caller can pass in an object of custom data in lieu of the handler
+ if ( handler.handler ) {
+ handleObjIn = handler;
+ handler = handleObjIn.handler;
+ selector = handleObjIn.selector;
+ }
+
+ // Make sure that the handler has a unique ID, used to find/remove it later
+ if ( !handler.guid ) {
+ handler.guid = jQuery.guid++;
+ }
+
+ // Init the element's event structure and main handler, if this is the first
+ events = elemData.events;
+ if ( !events ) {
+ elemData.events = events = {};
+ }
+ eventHandle = elemData.handle;
+ if ( !eventHandle ) {
+ elemData.handle = eventHandle = function( e ) {
+ // Discard the second event of a jQuery.event.trigger() and
+ // when an event is called after a page has unloaded
+ return typeof jQuery !== "undefined" && (!e || jQuery.event.triggered !== e.type) ?
+ jQuery.event.dispatch.apply( eventHandle.elem, arguments ) :
+ undefined;
+ };
+ // Add elem as a property of the handle fn to prevent a memory leak with IE non-native events
+ eventHandle.elem = elem;
+ }
+
+ // Handle multiple events separated by a space
+ // jQuery(...).bind("mouseover mouseout", fn);
+ types = jQuery.trim( hoverHack(types) ).split( " " );
+ for ( t = 0; t < types.length; t++ ) {
+
+ tns = rtypenamespace.exec( types[t] ) || [];
+ type = tns[1];
+ namespaces = ( tns[2] || "" ).split( "." ).sort();
+
+ // If event changes its type, use the special event handlers for the changed type
+ special = jQuery.event.special[ type ] || {};
+
+ // If selector defined, determine special event api type, otherwise given type
+ type = ( selector ? special.delegateType : special.bindType ) || type;
+
+ // Update special based on newly reset type
+ special = jQuery.event.special[ type ] || {};
+
+ // handleObj is passed to all event handlers
+ handleObj = jQuery.extend({
+ type: type,
+ origType: tns[1],
+ data: data,
+ handler: handler,
+ guid: handler.guid,
+ selector: selector,
+ needsContext: selector && jQuery.expr.match.needsContext.test( selector ),
+ namespace: namespaces.join(".")
+ }, handleObjIn );
+
+ // Init the event handler queue if we're the first
+ handlers = events[ type ];
+ if ( !handlers ) {
+ handlers = events[ type ] = [];
+ handlers.delegateCount = 0;
+
+ // Only use addEventListener/attachEvent if the special events handler returns false
+ if ( !special.setup || special.setup.call( elem, data, namespaces, eventHandle ) === false ) {
+ // Bind the global event handler to the element
+ if ( elem.addEventListener ) {
+ elem.addEventListener( type, eventHandle, false );
+
+ } else if ( elem.attachEvent ) {
+ elem.attachEvent( "on" + type, eventHandle );
+ }
+ }
+ }
+
+ if ( special.add ) {
+ special.add.call( elem, handleObj );
+
+ if ( !handleObj.handler.guid ) {
+ handleObj.handler.guid = handler.guid;
+ }
+ }
+
+ // Add to the element's handler list, delegates in front
+ if ( selector ) {
+ handlers.splice( handlers.delegateCount++, 0, handleObj );
+ } else {
+ handlers.push( handleObj );
+ }
+
+ // Keep track of which events have ever been used, for event optimization
+ jQuery.event.global[ type ] = true;
+ }
+
+ // Nullify elem to prevent memory leaks in IE
+ elem = null;
+ },
+
+ global: {},
+
+ // Detach an event or set of events from an element
+ remove: function( elem, types, handler, selector, mappedTypes ) {
+
+ var t, tns, type, origType, namespaces, origCount,
+ j, events, special, eventType, handleObj,
+ elemData = jQuery.hasData( elem ) && jQuery._data( elem );
+
+ if ( !elemData || !(events = elemData.events) ) {
+ return;
+ }
+
+ // Once for each type.namespace in types; type may be omitted
+ types = jQuery.trim( hoverHack( types || "" ) ).split(" ");
+ for ( t = 0; t < types.length; t++ ) {
+ tns = rtypenamespace.exec( types[t] ) || [];
+ type = origType = tns[1];
+ namespaces = tns[2];
+
+ // Unbind all events (on this namespace, if provided) for the element
+ if ( !type ) {
+ for ( type in events ) {
+ jQuery.event.remove( elem, type + types[ t ], handler, selector, true );
+ }
+ continue;
+ }
+
+ special = jQuery.event.special[ type ] || {};
+ type = ( selector? special.delegateType : special.bindType ) || type;
+ eventType = events[ type ] || [];
+ origCount = eventType.length;
+ namespaces = namespaces ? new RegExp("(^|\\.)" + namespaces.split(".").sort().join("\\.(?:.*\\.|)") + "(\\.|$)") : null;
+
+ // Remove matching events
+ for ( j = 0; j < eventType.length; j++ ) {
+ handleObj = eventType[ j ];
+
+ if ( ( mappedTypes || origType === handleObj.origType ) &&
+ ( !handler || handler.guid === handleObj.guid ) &&
+ ( !namespaces || namespaces.test( handleObj.namespace ) ) &&
+ ( !selector || selector === handleObj.selector || selector === "**" && handleObj.selector ) ) {
+ eventType.splice( j--, 1 );
+
+ if ( handleObj.selector ) {
+ eventType.delegateCount--;
+ }
+ if ( special.remove ) {
+ special.remove.call( elem, handleObj );
+ }
+ }
+ }
+
+ // Remove generic event handler if we removed something and no more handlers exist
+ // (avoids potential for endless recursion during removal of special event handlers)
+ if ( eventType.length === 0 && origCount !== eventType.length ) {
+ if ( !special.teardown || special.teardown.call( elem, namespaces, elemData.handle ) === false ) {
+ jQuery.removeEvent( elem, type, elemData.handle );
+ }
+
+ delete events[ type ];
+ }
+ }
+
+ // Remove the expando if it's no longer used
+ if ( jQuery.isEmptyObject( events ) ) {
+ delete elemData.handle;
+
+ // removeData also checks for emptiness and clears the expando if empty
+ // so use it instead of delete
+ jQuery.removeData( elem, "events", true );
+ }
+ },
+
+ // Events that are safe to short-circuit if no handlers are attached.
+ // Native DOM events should not be added, they may have inline handlers.
+ customEvent: {
+ "getData": true,
+ "setData": true,
+ "changeData": true
+ },
+
+ trigger: function( event, data, elem, onlyHandlers ) {
+ // Don't do events on text and comment nodes
+ if ( elem && (elem.nodeType === 3 || elem.nodeType === 8) ) {
+ return;
+ }
+
+ // Event object or event type
+ var cache, exclusive, i, cur, old, ontype, special, handle, eventPath, bubbleType,
+ type = event.type || event,
+ namespaces = [];
+
+ // focus/blur morphs to focusin/out; ensure we're not firing them right now
+ if ( rfocusMorph.test( type + jQuery.event.triggered ) ) {
+ return;
+ }
+
+ if ( type.indexOf( "!" ) >= 0 ) {
+ // Exclusive events trigger only for the exact event (no namespaces)
+ type = type.slice(0, -1);
+ exclusive = true;
+ }
+
+ if ( type.indexOf( "." ) >= 0 ) {
+ // Namespaced trigger; create a regexp to match event type in handle()
+ namespaces = type.split(".");
+ type = namespaces.shift();
+ namespaces.sort();
+ }
+
+ if ( (!elem || jQuery.event.customEvent[ type ]) && !jQuery.event.global[ type ] ) {
+ // No jQuery handlers for this event type, and it can't have inline handlers
+ return;
+ }
+
+ // Caller can pass in an Event, Object, or just an event type string
+ event = typeof event === "object" ?
+ // jQuery.Event object
+ event[ jQuery.expando ] ? event :
+ // Object literal
+ new jQuery.Event( type, event ) :
+ // Just the event type (string)
+ new jQuery.Event( type );
+
+ event.type = type;
+ event.isTrigger = true;
+ event.exclusive = exclusive;
+ event.namespace = namespaces.join( "." );
+ event.namespace_re = event.namespace? new RegExp("(^|\\.)" + namespaces.join("\\.(?:.*\\.|)") + "(\\.|$)") : null;
+ ontype = type.indexOf( ":" ) < 0 ? "on" + type : "";
+
+ // Handle a global trigger
+ if ( !elem ) {
+
+ // TODO: Stop taunting the data cache; remove global events and always attach to document
+ cache = jQuery.cache;
+ for ( i in cache ) {
+ if ( cache[ i ].events && cache[ i ].events[ type ] ) {
+ jQuery.event.trigger( event, data, cache[ i ].handle.elem, true );
+ }
+ }
+ return;
+ }
+
+ // Clean up the event in case it is being reused
+ event.result = undefined;
+ if ( !event.target ) {
+ event.target = elem;
+ }
+
+ // Clone any incoming data and prepend the event, creating the handler arg list
+ data = data != null ? jQuery.makeArray( data ) : [];
+ data.unshift( event );
+
+ // Allow special events to draw outside the lines
+ special = jQuery.event.special[ type ] || {};
+ if ( special.trigger && special.trigger.apply( elem, data ) === false ) {
+ return;
+ }
+
+ // Determine event propagation path in advance, per W3C events spec (#9951)
+ // Bubble up to document, then to window; watch for a global ownerDocument var (#9724)
+ eventPath = [[ elem, special.bindType || type ]];
+ if ( !onlyHandlers && !special.noBubble && !jQuery.isWindow( elem ) ) {
+
+ bubbleType = special.delegateType || type;
+ cur = rfocusMorph.test( bubbleType + type ) ? elem : elem.parentNode;
+ for ( old = elem; cur; cur = cur.parentNode ) {
+ eventPath.push([ cur, bubbleType ]);
+ old = cur;
+ }
+
+ // Only add window if we got to document (e.g., not plain obj or detached DOM)
+ if ( old === (elem.ownerDocument || document) ) {
+ eventPath.push([ old.defaultView || old.parentWindow || window, bubbleType ]);
+ }
+ }
+
+ // Fire handlers on the event path
+ for ( i = 0; i < eventPath.length && !event.isPropagationStopped(); i++ ) {
+
+ cur = eventPath[i][0];
+ event.type = eventPath[i][1];
+
+ handle = ( jQuery._data( cur, "events" ) || {} )[ event.type ] && jQuery._data( cur, "handle" );
+ if ( handle ) {
+ handle.apply( cur, data );
+ }
+ // Note that this is a bare JS function and not a jQuery handler
+ handle = ontype && cur[ ontype ];
+ if ( handle && jQuery.acceptData( cur ) && handle.apply && handle.apply( cur, data ) === false ) {
+ event.preventDefault();
+ }
+ }
+ event.type = type;
+
+ // If nobody prevented the default action, do it now
+ if ( !onlyHandlers && !event.isDefaultPrevented() ) {
+
+ if ( (!special._default || special._default.apply( elem.ownerDocument, data ) === false) &&
+ !(type === "click" && jQuery.nodeName( elem, "a" )) && jQuery.acceptData( elem ) ) {
+
+ // Call a native DOM method on the target with the same name name as the event.
+ // Can't use an .isFunction() check here because IE6/7 fails that test.
+ // Don't do default actions on window, that's where global variables be (#6170)
+ // IE<9 dies on focus/blur to hidden element (#1486)
+ if ( ontype && elem[ type ] && ((type !== "focus" && type !== "blur") || event.target.offsetWidth !== 0) && !jQuery.isWindow( elem ) ) {
+
+ // Don't re-trigger an onFOO event when we call its FOO() method
+ old = elem[ ontype ];
+
+ if ( old ) {
+ elem[ ontype ] = null;
+ }
+
+ // Prevent re-triggering of the same event, since we already bubbled it above
+ jQuery.event.triggered = type;
+ elem[ type ]();
+ jQuery.event.triggered = undefined;
+
+ if ( old ) {
+ elem[ ontype ] = old;
+ }
+ }
+ }
+ }
+
+ return event.result;
+ },
+
+ dispatch: function( event ) {
+
+ // Make a writable jQuery.Event from the native event object
+ event = jQuery.event.fix( event || window.event );
+
+ var i, j, cur, ret, selMatch, matched, matches, handleObj, sel, related,
+ handlers = ( (jQuery._data( this, "events" ) || {} )[ event.type ] || []),
+ delegateCount = handlers.delegateCount,
+ args = core_slice.call( arguments ),
+ run_all = !event.exclusive && !event.namespace,
+ special = jQuery.event.special[ event.type ] || {},
+ handlerQueue = [];
+
+ // Use the fix-ed jQuery.Event rather than the (read-only) native event
+ args[0] = event;
+ event.delegateTarget = this;
+
+ // Call the preDispatch hook for the mapped type, and let it bail if desired
+ if ( special.preDispatch && special.preDispatch.call( this, event ) === false ) {
+ return;
+ }
+
+ // Determine handlers that should run if there are delegated events
+ // Avoid non-left-click bubbling in Firefox (#3861)
+ if ( delegateCount && !(event.button && event.type === "click") ) {
+
+ for ( cur = event.target; cur != this; cur = cur.parentNode || this ) {
+
+ // Don't process clicks (ONLY) on disabled elements (#6911, #8165, #11382, #11764)
+ if ( cur.disabled !== true || event.type !== "click" ) {
+ selMatch = {};
+ matches = [];
+ for ( i = 0; i < delegateCount; i++ ) {
+ handleObj = handlers[ i ];
+ sel = handleObj.selector;
+
+ if ( selMatch[ sel ] === undefined ) {
+ selMatch[ sel ] = handleObj.needsContext ?
+ jQuery( sel, this ).index( cur ) >= 0 :
+ jQuery.find( sel, this, null, [ cur ] ).length;
+ }
+ if ( selMatch[ sel ] ) {
+ matches.push( handleObj );
+ }
+ }
+ if ( matches.length ) {
+ handlerQueue.push({ elem: cur, matches: matches });
+ }
+ }
+ }
+ }
+
+ // Add the remaining (directly-bound) handlers
+ if ( handlers.length > delegateCount ) {
+ handlerQueue.push({ elem: this, matches: handlers.slice( delegateCount ) });
+ }
+
+ // Run delegates first; they may want to stop propagation beneath us
+ for ( i = 0; i < handlerQueue.length && !event.isPropagationStopped(); i++ ) {
+ matched = handlerQueue[ i ];
+ event.currentTarget = matched.elem;
+
+ for ( j = 0; j < matched.matches.length && !event.isImmediatePropagationStopped(); j++ ) {
+ handleObj = matched.matches[ j ];
+
+ // Triggered event must either 1) be non-exclusive and have no namespace, or
+ // 2) have namespace(s) a subset or equal to those in the bound event (both can have no namespace).
+ if ( run_all || (!event.namespace && !handleObj.namespace) || event.namespace_re && event.namespace_re.test( handleObj.namespace ) ) {
+
+ event.data = handleObj.data;
+ event.handleObj = handleObj;
+
+ ret = ( (jQuery.event.special[ handleObj.origType ] || {}).handle || handleObj.handler )
+ .apply( matched.elem, args );
+
+ if ( ret !== undefined ) {
+ event.result = ret;
+ if ( ret === false ) {
+ event.preventDefault();
+ event.stopPropagation();
+ }
+ }
+ }
+ }
+ }
+
+ // Call the postDispatch hook for the mapped type
+ if ( special.postDispatch ) {
+ special.postDispatch.call( this, event );
+ }
+
+ return event.result;
+ },
+
+ // Includes some event props shared by KeyEvent and MouseEvent
+ // *** attrChange attrName relatedNode srcElement are not normalized, non-W3C, deprecated, will be removed in 1.8 ***
+ props: "attrChange attrName relatedNode srcElement altKey bubbles cancelable ctrlKey currentTarget eventPhase metaKey relatedTarget shiftKey target timeStamp view which".split(" "),
+
+ fixHooks: {},
+
+ keyHooks: {
+ props: "char charCode key keyCode".split(" "),
+ filter: function( event, original ) {
+
+ // Add which for key events
+ if ( event.which == null ) {
+ event.which = original.charCode != null ? original.charCode : original.keyCode;
+ }
+
+ return event;
+ }
+ },
+
+ mouseHooks: {
+ props: "button buttons clientX clientY fromElement offsetX offsetY pageX pageY screenX screenY toElement".split(" "),
+ filter: function( event, original ) {
+ var eventDoc, doc, body,
+ button = original.button,
+ fromElement = original.fromElement;
+
+ // Calculate pageX/Y if missing and clientX/Y available
+ if ( event.pageX == null && original.clientX != null ) {
+ eventDoc = event.target.ownerDocument || document;
+ doc = eventDoc.documentElement;
+ body = eventDoc.body;
+
+ event.pageX = original.clientX + ( doc && doc.scrollLeft || body && body.scrollLeft || 0 ) - ( doc && doc.clientLeft || body && body.clientLeft || 0 );
+ event.pageY = original.clientY + ( doc && doc.scrollTop || body && body.scrollTop || 0 ) - ( doc && doc.clientTop || body && body.clientTop || 0 );
+ }
+
+ // Add relatedTarget, if necessary
+ if ( !event.relatedTarget && fromElement ) {
+ event.relatedTarget = fromElement === event.target ? original.toElement : fromElement;
+ }
+
+ // Add which for click: 1 === left; 2 === middle; 3 === right
+ // Note: button is not normalized, so don't use it
+ if ( !event.which && button !== undefined ) {
+ event.which = ( button & 1 ? 1 : ( button & 2 ? 3 : ( button & 4 ? 2 : 0 ) ) );
+ }
+
+ return event;
+ }
+ },
+
+ fix: function( event ) {
+ if ( event[ jQuery.expando ] ) {
+ return event;
+ }
+
+ // Create a writable copy of the event object and normalize some properties
+ var i, prop,
+ originalEvent = event,
+ fixHook = jQuery.event.fixHooks[ event.type ] || {},
+ copy = fixHook.props ? this.props.concat( fixHook.props ) : this.props;
+
+ event = jQuery.Event( originalEvent );
+
+ for ( i = copy.length; i; ) {
+ prop = copy[ --i ];
+ event[ prop ] = originalEvent[ prop ];
+ }
+
+ // Fix target property, if necessary (#1925, IE 6/7/8 & Safari2)
+ if ( !event.target ) {
+ event.target = originalEvent.srcElement || document;
+ }
+
+ // Target should not be a text node (#504, Safari)
+ if ( event.target.nodeType === 3 ) {
+ event.target = event.target.parentNode;
+ }
+
+ // For mouse/key events, metaKey==false if it's undefined (#3368, #11328; IE6/7/8)
+ event.metaKey = !!event.metaKey;
+
+ return fixHook.filter? fixHook.filter( event, originalEvent ) : event;
+ },
+
+ special: {
+ load: {
+ // Prevent triggered image.load events from bubbling to window.load
+ noBubble: true
+ },
+
+ focus: {
+ delegateType: "focusin"
+ },
+ blur: {
+ delegateType: "focusout"
+ },
+
+ beforeunload: {
+ setup: function( data, namespaces, eventHandle ) {
+ // We only want to do this special case on windows
+ if ( jQuery.isWindow( this ) ) {
+ this.onbeforeunload = eventHandle;
+ }
+ },
+
+ teardown: function( namespaces, eventHandle ) {
+ if ( this.onbeforeunload === eventHandle ) {
+ this.onbeforeunload = null;
+ }
+ }
+ }
+ },
+
+ simulate: function( type, elem, event, bubble ) {
+ // Piggyback on a donor event to simulate a different one.
+ // Fake originalEvent to avoid donor's stopPropagation, but if the
+ // simulated event prevents default then we do the same on the donor.
+ var e = jQuery.extend(
+ new jQuery.Event(),
+ event,
+ { type: type,
+ isSimulated: true,
+ originalEvent: {}
+ }
+ );
+ if ( bubble ) {
+ jQuery.event.trigger( e, null, elem );
+ } else {
+ jQuery.event.dispatch.call( elem, e );
+ }
+ if ( e.isDefaultPrevented() ) {
+ event.preventDefault();
+ }
+ }
+};
+
+// Some plugins are using, but it's undocumented/deprecated and will be removed.
+// The 1.7 special event interface should provide all the hooks needed now.
+jQuery.event.handle = jQuery.event.dispatch;
+
+jQuery.removeEvent = document.removeEventListener ?
+ function( elem, type, handle ) {
+ if ( elem.removeEventListener ) {
+ elem.removeEventListener( type, handle, false );
+ }
+ } :
+ function( elem, type, handle ) {
+ var name = "on" + type;
+
+ if ( elem.detachEvent ) {
+
+ // #8545, #7054, preventing memory leaks for custom events in IE6-8
+ // detachEvent needed property on element, by name of that event, to properly expose it to GC
+ if ( typeof elem[ name ] === "undefined" ) {
+ elem[ name ] = null;
+ }
+
+ elem.detachEvent( name, handle );
+ }
+ };
+
+jQuery.Event = function( src, props ) {
+ // Allow instantiation without the 'new' keyword
+ if ( !(this instanceof jQuery.Event) ) {
+ return new jQuery.Event( src, props );
+ }
+
+ // Event object
+ if ( src && src.type ) {
+ this.originalEvent = src;
+ this.type = src.type;
+
+ // Events bubbling up the document may have been marked as prevented
+ // by a handler lower down the tree; reflect the correct value.
+ this.isDefaultPrevented = ( src.defaultPrevented || src.returnValue === false ||
+ src.getPreventDefault && src.getPreventDefault() ) ? returnTrue : returnFalse;
+
+ // Event type
+ } else {
+ this.type = src;
+ }
+
+ // Put explicitly provided properties onto the event object
+ if ( props ) {
+ jQuery.extend( this, props );
+ }
+
+ // Create a timestamp if incoming event doesn't have one
+ this.timeStamp = src && src.timeStamp || jQuery.now();
+
+ // Mark it as fixed
+ this[ jQuery.expando ] = true;
+};
+
+function returnFalse() {
+ return false;
+}
+function returnTrue() {
+ return true;
+}
+
+// jQuery.Event is based on DOM3 Events as specified by the ECMAScript Language Binding
+// http://www.w3.org/TR/2003/WD-DOM-Level-3-Events-20030331/ecma-script-binding.html
+jQuery.Event.prototype = {
+ preventDefault: function() {
+ this.isDefaultPrevented = returnTrue;
+
+ var e = this.originalEvent;
+ if ( !e ) {
+ return;
+ }
+
+ // if preventDefault exists run it on the original event
+ if ( e.preventDefault ) {
+ e.preventDefault();
+
+ // otherwise set the returnValue property of the original event to false (IE)
+ } else {
+ e.returnValue = false;
+ }
+ },
+ stopPropagation: function() {
+ this.isPropagationStopped = returnTrue;
+
+ var e = this.originalEvent;
+ if ( !e ) {
+ return;
+ }
+ // if stopPropagation exists run it on the original event
+ if ( e.stopPropagation ) {
+ e.stopPropagation();
+ }
+ // otherwise set the cancelBubble property of the original event to true (IE)
+ e.cancelBubble = true;
+ },
+ stopImmediatePropagation: function() {
+ this.isImmediatePropagationStopped = returnTrue;
+ this.stopPropagation();
+ },
+ isDefaultPrevented: returnFalse,
+ isPropagationStopped: returnFalse,
+ isImmediatePropagationStopped: returnFalse
+};
+
+// Create mouseenter/leave events using mouseover/out and event-time checks
+jQuery.each({
+ mouseenter: "mouseover",
+ mouseleave: "mouseout"
+}, function( orig, fix ) {
+ jQuery.event.special[ orig ] = {
+ delegateType: fix,
+ bindType: fix,
+
+ handle: function( event ) {
+ var ret,
+ target = this,
+ related = event.relatedTarget,
+ handleObj = event.handleObj,
+ selector = handleObj.selector;
+
+ // For mousenter/leave call the handler if related is outside the target.
+ // NB: No relatedTarget if the mouse left/entered the browser window
+ if ( !related || (related !== target && !jQuery.contains( target, related )) ) {
+ event.type = handleObj.origType;
+ ret = handleObj.handler.apply( this, arguments );
+ event.type = fix;
+ }
+ return ret;
+ }
+ };
+});
+
+// IE submit delegation
+if ( !jQuery.support.submitBubbles ) {
+
+ jQuery.event.special.submit = {
+ setup: function() {
+ // Only need this for delegated form submit events
+ if ( jQuery.nodeName( this, "form" ) ) {
+ return false;
+ }
+
+ // Lazy-add a submit handler when a descendant form may potentially be submitted
+ jQuery.event.add( this, "click._submit keypress._submit", function( e ) {
+ // Node name check avoids a VML-related crash in IE (#9807)
+ var elem = e.target,
+ form = jQuery.nodeName( elem, "input" ) || jQuery.nodeName( elem, "button" ) ? elem.form : undefined;
+ if ( form && !jQuery._data( form, "_submit_attached" ) ) {
+ jQuery.event.add( form, "submit._submit", function( event ) {
+ event._submit_bubble = true;
+ });
+ jQuery._data( form, "_submit_attached", true );
+ }
+ });
+ // return undefined since we don't need an event listener
+ },
+
+ postDispatch: function( event ) {
+ // If form was submitted by the user, bubble the event up the tree
+ if ( event._submit_bubble ) {
+ delete event._submit_bubble;
+ if ( this.parentNode && !event.isTrigger ) {
+ jQuery.event.simulate( "submit", this.parentNode, event, true );
+ }
+ }
+ },
+
+ teardown: function() {
+ // Only need this for delegated form submit events
+ if ( jQuery.nodeName( this, "form" ) ) {
+ return false;
+ }
+
+ // Remove delegated handlers; cleanData eventually reaps submit handlers attached above
+ jQuery.event.remove( this, "._submit" );
+ }
+ };
+}
+
+// IE change delegation and checkbox/radio fix
+if ( !jQuery.support.changeBubbles ) {
+
+ jQuery.event.special.change = {
+
+ setup: function() {
+
+ if ( rformElems.test( this.nodeName ) ) {
+ // IE doesn't fire change on a check/radio until blur; trigger it on click
+ // after a propertychange. Eat the blur-change in special.change.handle.
+ // This still fires onchange a second time for check/radio after blur.
+ if ( this.type === "checkbox" || this.type === "radio" ) {
+ jQuery.event.add( this, "propertychange._change", function( event ) {
+ if ( event.originalEvent.propertyName === "checked" ) {
+ this._just_changed = true;
+ }
+ });
+ jQuery.event.add( this, "click._change", function( event ) {
+ if ( this._just_changed && !event.isTrigger ) {
+ this._just_changed = false;
+ }
+ // Allow triggered, simulated change events (#11500)
+ jQuery.event.simulate( "change", this, event, true );
+ });
+ }
+ return false;
+ }
+ // Delegated event; lazy-add a change handler on descendant inputs
+ jQuery.event.add( this, "beforeactivate._change", function( e ) {
+ var elem = e.target;
+
+ if ( rformElems.test( elem.nodeName ) && !jQuery._data( elem, "_change_attached" ) ) {
+ jQuery.event.add( elem, "change._change", function( event ) {
+ if ( this.parentNode && !event.isSimulated && !event.isTrigger ) {
+ jQuery.event.simulate( "change", this.parentNode, event, true );
+ }
+ });
+ jQuery._data( elem, "_change_attached", true );
+ }
+ });
+ },
+
+ handle: function( event ) {
+ var elem = event.target;
+
+ // Swallow native change events from checkbox/radio, we already triggered them above
+ if ( this !== elem || event.isSimulated || event.isTrigger || (elem.type !== "radio" && elem.type !== "checkbox") ) {
+ return event.handleObj.handler.apply( this, arguments );
+ }
+ },
+
+ teardown: function() {
+ jQuery.event.remove( this, "._change" );
+
+ return !rformElems.test( this.nodeName );
+ }
+ };
+}
+
+// Create "bubbling" focus and blur events
+if ( !jQuery.support.focusinBubbles ) {
+ jQuery.each({ focus: "focusin", blur: "focusout" }, function( orig, fix ) {
+
+ // Attach a single capturing handler while someone wants focusin/focusout
+ var attaches = 0,
+ handler = function( event ) {
+ jQuery.event.simulate( fix, event.target, jQuery.event.fix( event ), true );
+ };
+
+ jQuery.event.special[ fix ] = {
+ setup: function() {
+ if ( attaches++ === 0 ) {
+ document.addEventListener( orig, handler, true );
+ }
+ },
+ teardown: function() {
+ if ( --attaches === 0 ) {
+ document.removeEventListener( orig, handler, true );
+ }
+ }
+ };
+ });
+}
+
+jQuery.fn.extend({
+
+ on: function( types, selector, data, fn, /*INTERNAL*/ one ) {
+ var origFn, type;
+
+ // Types can be a map of types/handlers
+ if ( typeof types === "object" ) {
+ // ( types-Object, selector, data )
+ if ( typeof selector !== "string" ) { // && selector != null
+ // ( types-Object, data )
+ data = data || selector;
+ selector = undefined;
+ }
+ for ( type in types ) {
+ this.on( type, selector, data, types[ type ], one );
+ }
+ return this;
+ }
+
+ if ( data == null && fn == null ) {
+ // ( types, fn )
+ fn = selector;
+ data = selector = undefined;
+ } else if ( fn == null ) {
+ if ( typeof selector === "string" ) {
+ // ( types, selector, fn )
+ fn = data;
+ data = undefined;
+ } else {
+ // ( types, data, fn )
+ fn = data;
+ data = selector;
+ selector = undefined;
+ }
+ }
+ if ( fn === false ) {
+ fn = returnFalse;
+ } else if ( !fn ) {
+ return this;
+ }
+
+ if ( one === 1 ) {
+ origFn = fn;
+ fn = function( event ) {
+ // Can use an empty set, since event contains the info
+ jQuery().off( event );
+ return origFn.apply( this, arguments );
+ };
+ // Use same guid so caller can remove using origFn
+ fn.guid = origFn.guid || ( origFn.guid = jQuery.guid++ );
+ }
+ return this.each( function() {
+ jQuery.event.add( this, types, fn, data, selector );
+ });
+ },
+ one: function( types, selector, data, fn ) {
+ return this.on( types, selector, data, fn, 1 );
+ },
+ off: function( types, selector, fn ) {
+ var handleObj, type;
+ if ( types && types.preventDefault && types.handleObj ) {
+ // ( event ) dispatched jQuery.Event
+ handleObj = types.handleObj;
+ jQuery( types.delegateTarget ).off(
+ handleObj.namespace ? handleObj.origType + "." + handleObj.namespace : handleObj.origType,
+ handleObj.selector,
+ handleObj.handler
+ );
+ return this;
+ }
+ if ( typeof types === "object" ) {
+ // ( types-object [, selector] )
+ for ( type in types ) {
+ this.off( type, selector, types[ type ] );
+ }
+ return this;
+ }
+ if ( selector === false || typeof selector === "function" ) {
+ // ( types [, fn] )
+ fn = selector;
+ selector = undefined;
+ }
+ if ( fn === false ) {
+ fn = returnFalse;
+ }
+ return this.each(function() {
+ jQuery.event.remove( this, types, fn, selector );
+ });
+ },
+
+ bind: function( types, data, fn ) {
+ return this.on( types, null, data, fn );
+ },
+ unbind: function( types, fn ) {
+ return this.off( types, null, fn );
+ },
+
+ live: function( types, data, fn ) {
+ jQuery( this.context ).on( types, this.selector, data, fn );
+ return this;
+ },
+ die: function( types, fn ) {
+ jQuery( this.context ).off( types, this.selector || "**", fn );
+ return this;
+ },
+
+ delegate: function( selector, types, data, fn ) {
+ return this.on( types, selector, data, fn );
+ },
+ undelegate: function( selector, types, fn ) {
+ // ( namespace ) or ( selector, types [, fn] )
+ return arguments.length === 1 ? this.off( selector, "**" ) : this.off( types, selector || "**", fn );
+ },
+
+ trigger: function( type, data ) {
+ return this.each(function() {
+ jQuery.event.trigger( type, data, this );
+ });
+ },
+ triggerHandler: function( type, data ) {
+ if ( this[0] ) {
+ return jQuery.event.trigger( type, data, this[0], true );
+ }
+ },
+
+ toggle: function( fn ) {
+ // Save reference to arguments for access in closure
+ var args = arguments,
+ guid = fn.guid || jQuery.guid++,
+ i = 0,
+ toggler = function( event ) {
+ // Figure out which function to execute
+ var lastToggle = ( jQuery._data( this, "lastToggle" + fn.guid ) || 0 ) % i;
+ jQuery._data( this, "lastToggle" + fn.guid, lastToggle + 1 );
+
+ // Make sure that clicks stop
+ event.preventDefault();
+
+ // and execute the function
+ return args[ lastToggle ].apply( this, arguments ) || false;
+ };
+
+ // link all the functions, so any of them can unbind this click handler
+ toggler.guid = guid;
+ while ( i < args.length ) {
+ args[ i++ ].guid = guid;
+ }
+
+ return this.click( toggler );
+ },
+
+ hover: function( fnOver, fnOut ) {
+ return this.mouseenter( fnOver ).mouseleave( fnOut || fnOver );
+ }
+});
+
+jQuery.each( ("blur focus focusin focusout load resize scroll unload click dblclick " +
+ "mousedown mouseup mousemove mouseover mouseout mouseenter mouseleave " +
+ "change select submit keydown keypress keyup error contextmenu").split(" "), function( i, name ) {
+
+ // Handle event binding
+ jQuery.fn[ name ] = function( data, fn ) {
+ if ( fn == null ) {
+ fn = data;
+ data = null;
+ }
+
+ return arguments.length > 0 ?
+ this.on( name, null, data, fn ) :
+ this.trigger( name );
+ };
+
+ if ( rkeyEvent.test( name ) ) {
+ jQuery.event.fixHooks[ name ] = jQuery.event.keyHooks;
+ }
+
+ if ( rmouseEvent.test( name ) ) {
+ jQuery.event.fixHooks[ name ] = jQuery.event.mouseHooks;
+ }
+});
+/*!
+ * Sizzle CSS Selector Engine
+ * Copyright 2012 jQuery Foundation and other contributors
+ * Released under the MIT license
+ * http://sizzlejs.com/
+ */
+(function( window, undefined ) {
+
+var cachedruns,
+ assertGetIdNotName,
+ Expr,
+ getText,
+ isXML,
+ contains,
+ compile,
+ sortOrder,
+ hasDuplicate,
+ outermostContext,
+
+ baseHasDuplicate = true,
+ strundefined = "undefined",
+
+ expando = ( "sizcache" + Math.random() ).replace( ".", "" ),
+
+ Token = String,
+ document = window.document,
+ docElem = document.documentElement,
+ dirruns = 0,
+ done = 0,
+ pop = [].pop,
+ push = [].push,
+ slice = [].slice,
+ // Use a stripped-down indexOf if a native one is unavailable
+ indexOf = [].indexOf || function( elem ) {
+ var i = 0,
+ len = this.length;
+ for ( ; i < len; i++ ) {
+ if ( this[i] === elem ) {
+ return i;
+ }
+ }
+ return -1;
+ },
+
+ // Augment a function for special use by Sizzle
+ markFunction = function( fn, value ) {
+ fn[ expando ] = value == null || value;
+ return fn;
+ },
+
+ createCache = function() {
+ var cache = {},
+ keys = [];
+
+ return markFunction(function( key, value ) {
+ // Only keep the most recent entries
+ if ( keys.push( key ) > Expr.cacheLength ) {
+ delete cache[ keys.shift() ];
+ }
+
+ // Retrieve with (key + " ") to avoid collision with native Object.prototype properties (see Issue #157)
+ return (cache[ key + " " ] = value);
+ }, cache );
+ },
+
+ classCache = createCache(),
+ tokenCache = createCache(),
+ compilerCache = createCache(),
+
+ // Regex
+
+ // Whitespace characters http://www.w3.org/TR/css3-selectors/#whitespace
+ whitespace = "[\\x20\\t\\r\\n\\f]",
+ // http://www.w3.org/TR/css3-syntax/#characters
+ characterEncoding = "(?:\\\\.|[-\\w]|[^\\x00-\\xa0])+",
+
+ // Loosely modeled on CSS identifier characters
+ // An unquoted value should be a CSS identifier (http://www.w3.org/TR/css3-selectors/#attribute-selectors)
+ // Proper syntax: http://www.w3.org/TR/CSS21/syndata.html#value-def-identifier
+ identifier = characterEncoding.replace( "w", "w#" ),
+
+ // Acceptable operators http://www.w3.org/TR/selectors/#attribute-selectors
+ operators = "([*^$|!~]?=)",
+ attributes = "\\[" + whitespace + "*(" + characterEncoding + ")" + whitespace +
+ "*(?:" + operators + whitespace + "*(?:(['\"])((?:\\\\.|[^\\\\])*?)\\3|(" + identifier + ")|)|)" + whitespace + "*\\]",
+
+ // Prefer arguments not in parens/brackets,
+ // then attribute selectors and non-pseudos (denoted by :),
+ // then anything else
+ // These preferences are here to reduce the number of selectors
+ // needing tokenize in the PSEUDO preFilter
+ pseudos = ":(" + characterEncoding + ")(?:\\((?:(['\"])((?:\\\\.|[^\\\\])*?)\\2|([^()[\\]]*|(?:(?:" + attributes + ")|[^:]|\\\\.)*|.*))\\)|)",
+
+ // For matchExpr.POS and matchExpr.needsContext
+ pos = ":(even|odd|eq|gt|lt|nth|first|last)(?:\\(" + whitespace +
+ "*((?:-\\d)?\\d*)" + whitespace + "*\\)|)(?=[^-]|$)",
+
+ // Leading and non-escaped trailing whitespace, capturing some non-whitespace characters preceding the latter
+ rtrim = new RegExp( "^" + whitespace + "+|((?:^|[^\\\\])(?:\\\\.)*)" + whitespace + "+$", "g" ),
+
+ rcomma = new RegExp( "^" + whitespace + "*," + whitespace + "*" ),
+ rcombinators = new RegExp( "^" + whitespace + "*([\\x20\\t\\r\\n\\f>+~])" + whitespace + "*" ),
+ rpseudo = new RegExp( pseudos ),
+
+ // Easily-parseable/retrievable ID or TAG or CLASS selectors
+ rquickExpr = /^(?:#([\w\-]+)|(\w+)|\.([\w\-]+))$/,
+
+ rnot = /^:not/,
+ rsibling = /[\x20\t\r\n\f]*[+~]/,
+ rendsWithNot = /:not\($/,
+
+ rheader = /h\d/i,
+ rinputs = /input|select|textarea|button/i,
+
+ rbackslash = /\\(?!\\)/g,
+
+ matchExpr = {
+ "ID": new RegExp( "^#(" + characterEncoding + ")" ),
+ "CLASS": new RegExp( "^\\.(" + characterEncoding + ")" ),
+ "NAME": new RegExp( "^\\[name=['\"]?(" + characterEncoding + ")['\"]?\\]" ),
+ "TAG": new RegExp( "^(" + characterEncoding.replace( "w", "w*" ) + ")" ),
+ "ATTR": new RegExp( "^" + attributes ),
+ "PSEUDO": new RegExp( "^" + pseudos ),
+ "POS": new RegExp( pos, "i" ),
+ "CHILD": new RegExp( "^:(only|nth|first|last)-child(?:\\(" + whitespace +
+ "*(even|odd|(([+-]|)(\\d*)n|)" + whitespace + "*(?:([+-]|)" + whitespace +
+ "*(\\d+)|))" + whitespace + "*\\)|)", "i" ),
+ // For use in libraries implementing .is()
+ "needsContext": new RegExp( "^" + whitespace + "*[>+~]|" + pos, "i" )
+ },
+
+ // Support
+
+ // Used for testing something on an element
+ assert = function( fn ) {
+ var div = document.createElement("div");
+
+ try {
+ return fn( div );
+ } catch (e) {
+ return false;
+ } finally {
+ // release memory in IE
+ div = null;
+ }
+ },
+
+ // Check if getElementsByTagName("*") returns only elements
+ assertTagNameNoComments = assert(function( div ) {
+ div.appendChild( document.createComment("") );
+ return !div.getElementsByTagName("*").length;
+ }),
+
+ // Check if getAttribute returns normalized href attributes
+ assertHrefNotNormalized = assert(function( div ) {
+ div.innerHTML = "<a href='#'></a>";
+ return div.firstChild && typeof div.firstChild.getAttribute !== strundefined &&
+ div.firstChild.getAttribute("href") === "#";
+ }),
+
+ // Check if attributes should be retrieved by attribute nodes
+ assertAttributes = assert(function( div ) {
+ div.innerHTML = "<select></select>";
+ var type = typeof div.lastChild.getAttribute("multiple");
+ // IE8 returns a string for some attributes even when not present
+ return type !== "boolean" && type !== "string";
+ }),
+
+ // Check if getElementsByClassName can be trusted
+ assertUsableClassName = assert(function( div ) {
+ // Opera can't find a second classname (in 9.6)
+ div.innerHTML = "<div class='hidden e'></div><div class='hidden'></div>";
+ if ( !div.getElementsByClassName || !div.getElementsByClassName("e").length ) {
+ return false;
+ }
+
+ // Safari 3.2 caches class attributes and doesn't catch changes
+ div.lastChild.className = "e";
+ return div.getElementsByClassName("e").length === 2;
+ }),
+
+ // Check if getElementById returns elements by name
+ // Check if getElementsByName privileges form controls or returns elements by ID
+ assertUsableName = assert(function( div ) {
+ // Inject content
+ div.id = expando + 0;
+ div.innerHTML = "<a name='" + expando + "'></a><div name='" + expando + "'></div>";
+ docElem.insertBefore( div, docElem.firstChild );
+
+ // Test
+ var pass = document.getElementsByName &&
+ // buggy browsers will return fewer than the correct 2
+ document.getElementsByName( expando ).length === 2 +
+ // buggy browsers will return more than the correct 0
+ document.getElementsByName( expando + 0 ).length;
+ assertGetIdNotName = !document.getElementById( expando );
+
+ // Cleanup
+ docElem.removeChild( div );
+
+ return pass;
+ });
+
+// If slice is not available, provide a backup
+try {
+ slice.call( docElem.childNodes, 0 )[0].nodeType;
+} catch ( e ) {
+ slice = function( i ) {
+ var elem,
+ results = [];
+ for ( ; (elem = this[i]); i++ ) {
+ results.push( elem );
+ }
+ return results;
+ };
+}
+
+function Sizzle( selector, context, results, seed ) {
+ results = results || [];
+ context = context || document;
+ var match, elem, xml, m,
+ nodeType = context.nodeType;
+
+ if ( !selector || typeof selector !== "string" ) {
+ return results;
+ }
+
+ if ( nodeType !== 1 && nodeType !== 9 ) {
+ return [];
+ }
+
+ xml = isXML( context );
+
+ if ( !xml && !seed ) {
+ if ( (match = rquickExpr.exec( selector )) ) {
+ // Speed-up: Sizzle("#ID")
+ if ( (m = match[1]) ) {
+ if ( nodeType === 9 ) {
+ elem = context.getElementById( m );
+ // Check parentNode to catch when Blackberry 4.6 returns
+ // nodes that are no longer in the document #6963
+ if ( elem && elem.parentNode ) {
+ // Handle the case where IE, Opera, and Webkit return items
+ // by name instead of ID
+ if ( elem.id === m ) {
+ results.push( elem );
+ return results;
+ }
+ } else {
+ return results;
+ }
+ } else {
+ // Context is not a document
+ if ( context.ownerDocument && (elem = context.ownerDocument.getElementById( m )) &&
+ contains( context, elem ) && elem.id === m ) {
+ results.push( elem );
+ return results;
+ }
+ }
+
+ // Speed-up: Sizzle("TAG")
+ } else if ( match[2] ) {
+ push.apply( results, slice.call(context.getElementsByTagName( selector ), 0) );
+ return results;
+
+ // Speed-up: Sizzle(".CLASS")
+ } else if ( (m = match[3]) && assertUsableClassName && context.getElementsByClassName ) {
+ push.apply( results, slice.call(context.getElementsByClassName( m ), 0) );
+ return results;
+ }
+ }
+ }
+
+ // All others
+ return select( selector.replace( rtrim, "$1" ), context, results, seed, xml );
+}
+
+Sizzle.matches = function( expr, elements ) {
+ return Sizzle( expr, null, null, elements );
+};
+
+Sizzle.matchesSelector = function( elem, expr ) {
+ return Sizzle( expr, null, null, [ elem ] ).length > 0;
+};
+
+// Returns a function to use in pseudos for input types
+function createInputPseudo( type ) {
+ return function( elem ) {
+ var name = elem.nodeName.toLowerCase();
+ return name === "input" && elem.type === type;
+ };
+}
+
+// Returns a function to use in pseudos for buttons
+function createButtonPseudo( type ) {
+ return function( elem ) {
+ var name = elem.nodeName.toLowerCase();
+ return (name === "input" || name === "button") && elem.type === type;
+ };
+}
+
+// Returns a function to use in pseudos for positionals
+function createPositionalPseudo( fn ) {
+ return markFunction(function( argument ) {
+ argument = +argument;
+ return markFunction(function( seed, matches ) {
+ var j,
+ matchIndexes = fn( [], seed.length, argument ),
+ i = matchIndexes.length;
+
+ // Match elements found at the specified indexes
+ while ( i-- ) {
+ if ( seed[ (j = matchIndexes[i]) ] ) {
+ seed[j] = !(matches[j] = seed[j]);
+ }
+ }
+ });
+ });
+}
+
+/**
+ * Utility function for retrieving the text value of an array of DOM nodes
+ * @param {Array|Element} elem
+ */
+getText = Sizzle.getText = function( elem ) {
+ var node,
+ ret = "",
+ i = 0,
+ nodeType = elem.nodeType;
+
+ if ( nodeType ) {
+ if ( nodeType === 1 || nodeType === 9 || nodeType === 11 ) {
+ // Use textContent for elements
+ // innerText usage removed for consistency of new lines (see #11153)
+ if ( typeof elem.textContent === "string" ) {
+ return elem.textContent;
+ } else {
+ // Traverse its children
+ for ( elem = elem.firstChild; elem; elem = elem.nextSibling ) {
+ ret += getText( elem );
+ }
+ }
+ } else if ( nodeType === 3 || nodeType === 4 ) {
+ return elem.nodeValue;
+ }
+ // Do not include comment or processing instruction nodes
+ } else {
+
+ // If no nodeType, this is expected to be an array
+ for ( ; (node = elem[i]); i++ ) {
+ // Do not traverse comment nodes
+ ret += getText( node );
+ }
+ }
+ return ret;
+};
+
+isXML = Sizzle.isXML = function( elem ) {
+ // documentElement is verified for cases where it doesn't yet exist
+ // (such as loading iframes in IE - #4833)
+ var documentElement = elem && (elem.ownerDocument || elem).documentElement;
+ return documentElement ? documentElement.nodeName !== "HTML" : false;
+};
+
+// Element contains another
+contains = Sizzle.contains = docElem.contains ?
+ function( a, b ) {
+ var adown = a.nodeType === 9 ? a.documentElement : a,
+ bup = b && b.parentNode;
+ return a === bup || !!( bup && bup.nodeType === 1 && adown.contains && adown.contains(bup) );
+ } :
+ docElem.compareDocumentPosition ?
+ function( a, b ) {
+ return b && !!( a.compareDocumentPosition( b ) & 16 );
+ } :
+ function( a, b ) {
+ while ( (b = b.parentNode) ) {
+ if ( b === a ) {
+ return true;
+ }
+ }
+ return false;
+ };
+
+Sizzle.attr = function( elem, name ) {
+ var val,
+ xml = isXML( elem );
+
+ if ( !xml ) {
+ name = name.toLowerCase();
+ }
+ if ( (val = Expr.attrHandle[ name ]) ) {
+ return val( elem );
+ }
+ if ( xml || assertAttributes ) {
+ return elem.getAttribute( name );
+ }
+ val = elem.getAttributeNode( name );
+ return val ?
+ typeof elem[ name ] === "boolean" ?
+ elem[ name ] ? name : null :
+ val.specified ? val.value : null :
+ null;
+};
+
+Expr = Sizzle.selectors = {
+
+ // Can be adjusted by the user
+ cacheLength: 50,
+
+ createPseudo: markFunction,
+
+ match: matchExpr,
+
+ // IE6/7 return a modified href
+ attrHandle: assertHrefNotNormalized ?
+ {} :
+ {
+ "href": function( elem ) {
+ return elem.getAttribute( "href", 2 );
+ },
+ "type": function( elem ) {
+ return elem.getAttribute("type");
+ }
+ },
+
+ find: {
+ "ID": assertGetIdNotName ?
+ function( id, context, xml ) {
+ if ( typeof context.getElementById !== strundefined && !xml ) {
+ var m = context.getElementById( id );
+ // Check parentNode to catch when Blackberry 4.6 returns
+ // nodes that are no longer in the document #6963
+ return m && m.parentNode ? [m] : [];
+ }
+ } :
+ function( id, context, xml ) {
+ if ( typeof context.getElementById !== strundefined && !xml ) {
+ var m = context.getElementById( id );
+
+ return m ?
+ m.id === id || typeof m.getAttributeNode !== strundefined && m.getAttributeNode("id").value === id ?
+ [m] :
+ undefined :
+ [];
+ }
+ },
+
+ "TAG": assertTagNameNoComments ?
+ function( tag, context ) {
+ if ( typeof context.getElementsByTagName !== strundefined ) {
+ return context.getElementsByTagName( tag );
+ }
+ } :
+ function( tag, context ) {
+ var results = context.getElementsByTagName( tag );
+
+ // Filter out possible comments
+ if ( tag === "*" ) {
+ var elem,
+ tmp = [],
+ i = 0;
+
+ for ( ; (elem = results[i]); i++ ) {
+ if ( elem.nodeType === 1 ) {
+ tmp.push( elem );
+ }
+ }
+
+ return tmp;
+ }
+ return results;
+ },
+
+ "NAME": assertUsableName && function( tag, context ) {
+ if ( typeof context.getElementsByName !== strundefined ) {
+ return context.getElementsByName( name );
+ }
+ },
+
+ "CLASS": assertUsableClassName && function( className, context, xml ) {
+ if ( typeof context.getElementsByClassName !== strundefined && !xml ) {
+ return context.getElementsByClassName( className );
+ }
+ }
+ },
+
+ relative: {
+ ">": { dir: "parentNode", first: true },
+ " ": { dir: "parentNode" },
+ "+": { dir: "previousSibling", first: true },
+ "~": { dir: "previousSibling" }
+ },
+
+ preFilter: {
+ "ATTR": function( match ) {
+ match[1] = match[1].replace( rbackslash, "" );
+
+ // Move the given value to match[3] whether quoted or unquoted
+ match[3] = ( match[4] || match[5] || "" ).replace( rbackslash, "" );
+
+ if ( match[2] === "~=" ) {
+ match[3] = " " + match[3] + " ";
+ }
+
+ return match.slice( 0, 4 );
+ },
+
+ "CHILD": function( match ) {
+ /* matches from matchExpr["CHILD"]
+ 1 type (only|nth|...)
+ 2 argument (even|odd|\d*|\d*n([+-]\d+)?|...)
+ 3 xn-component of xn+y argument ([+-]?\d*n|)
+ 4 sign of xn-component
+ 5 x of xn-component
+ 6 sign of y-component
+ 7 y of y-component
+ */
+ match[1] = match[1].toLowerCase();
+
+ if ( match[1] === "nth" ) {
+ // nth-child requires argument
+ if ( !match[2] ) {
+ Sizzle.error( match[0] );
+ }
+
+ // numeric x and y parameters for Expr.filter.CHILD
+ // remember that false/true cast respectively to 0/1
+ match[3] = +( match[3] ? match[4] + (match[5] || 1) : 2 * ( match[2] === "even" || match[2] === "odd" ) );
+ match[4] = +( ( match[6] + match[7] ) || match[2] === "odd" );
+
+ // other types prohibit arguments
+ } else if ( match[2] ) {
+ Sizzle.error( match[0] );
+ }
+
+ return match;
+ },
+
+ "PSEUDO": function( match ) {
+ var unquoted, excess;
+ if ( matchExpr["CHILD"].test( match[0] ) ) {
+ return null;
+ }
+
+ if ( match[3] ) {
+ match[2] = match[3];
+ } else if ( (unquoted = match[4]) ) {
+ // Only check arguments that contain a pseudo
+ if ( rpseudo.test(unquoted) &&
+ // Get excess from tokenize (recursively)
+ (excess = tokenize( unquoted, true )) &&
+ // advance to the next closing parenthesis
+ (excess = unquoted.indexOf( ")", unquoted.length - excess ) - unquoted.length) ) {
+
+ // excess is a negative index
+ unquoted = unquoted.slice( 0, excess );
+ match[0] = match[0].slice( 0, excess );
+ }
+ match[2] = unquoted;
+ }
+
+ // Return only captures needed by the pseudo filter method (type and argument)
+ return match.slice( 0, 3 );
+ }
+ },
+
+ filter: {
+ "ID": assertGetIdNotName ?
+ function( id ) {
+ id = id.replace( rbackslash, "" );
+ return function( elem ) {
+ return elem.getAttribute("id") === id;
+ };
+ } :
+ function( id ) {
+ id = id.replace( rbackslash, "" );
+ return function( elem ) {
+ var node = typeof elem.getAttributeNode !== strundefined && elem.getAttributeNode("id");
+ return node && node.value === id;
+ };
+ },
+
+ "TAG": function( nodeName ) {
+ if ( nodeName === "*" ) {
+ return function() { return true; };
+ }
+ nodeName = nodeName.replace( rbackslash, "" ).toLowerCase();
+
+ return function( elem ) {
+ return elem.nodeName && elem.nodeName.toLowerCase() === nodeName;
+ };
+ },
+
+ "CLASS": function( className ) {
+ var pattern = classCache[ expando ][ className + " " ];
+
+ return pattern ||
+ (pattern = new RegExp( "(^|" + whitespace + ")" + className + "(" + whitespace + "|$)" )) &&
+ classCache( className, function( elem ) {
+ return pattern.test( elem.className || (typeof elem.getAttribute !== strundefined && elem.getAttribute("class")) || "" );
+ });
+ },
+
+ "ATTR": function( name, operator, check ) {
+ return function( elem, context ) {
+ var result = Sizzle.attr( elem, name );
+
+ if ( result == null ) {
+ return operator === "!=";
+ }
+ if ( !operator ) {
+ return true;
+ }
+
+ result += "";
+
+ return operator === "=" ? result === check :
+ operator === "!=" ? result !== check :
+ operator === "^=" ? check && result.indexOf( check ) === 0 :
+ operator === "*=" ? check && result.indexOf( check ) > -1 :
+ operator === "$=" ? check && result.substr( result.length - check.length ) === check :
+ operator === "~=" ? ( " " + result + " " ).indexOf( check ) > -1 :
+ operator === "|=" ? result === check || result.substr( 0, check.length + 1 ) === check + "-" :
+ false;
+ };
+ },
+
+ "CHILD": function( type, argument, first, last ) {
+
+ if ( type === "nth" ) {
+ return function( elem ) {
+ var node, diff,
+ parent = elem.parentNode;
+
+ if ( first === 1 && last === 0 ) {
+ return true;
+ }
+
+ if ( parent ) {
+ diff = 0;
+ for ( node = parent.firstChild; node; node = node.nextSibling ) {
+ if ( node.nodeType === 1 ) {
+ diff++;
+ if ( elem === node ) {
+ break;
+ }
+ }
+ }
+ }
+
+ // Incorporate the offset (or cast to NaN), then check against cycle size
+ diff -= last;
+ return diff === first || ( diff % first === 0 && diff / first >= 0 );
+ };
+ }
+
+ return function( elem ) {
+ var node = elem;
+
+ switch ( type ) {
+ case "only":
+ case "first":
+ while ( (node = node.previousSibling) ) {
+ if ( node.nodeType === 1 ) {
+ return false;
+ }
+ }
+
+ if ( type === "first" ) {
+ return true;
+ }
+
+ node = elem;
+
+ /* falls through */
+ case "last":
+ while ( (node = node.nextSibling) ) {
+ if ( node.nodeType === 1 ) {
+ return false;
+ }
+ }
+
+ return true;
+ }
+ };
+ },
+
+ "PSEUDO": function( pseudo, argument ) {
+ // pseudo-class names are case-insensitive
+ // http://www.w3.org/TR/selectors/#pseudo-classes
+ // Prioritize by case sensitivity in case custom pseudos are added with uppercase letters
+ // Remember that setFilters inherits from pseudos
+ var args,
+ fn = Expr.pseudos[ pseudo ] || Expr.setFilters[ pseudo.toLowerCase() ] ||
+ Sizzle.error( "unsupported pseudo: " + pseudo );
+
+ // The user may use createPseudo to indicate that
+ // arguments are needed to create the filter function
+ // just as Sizzle does
+ if ( fn[ expando ] ) {
+ return fn( argument );
+ }
+
+ // But maintain support for old signatures
+ if ( fn.length > 1 ) {
+ args = [ pseudo, pseudo, "", argument ];
+ return Expr.setFilters.hasOwnProperty( pseudo.toLowerCase() ) ?
+ markFunction(function( seed, matches ) {
+ var idx,
+ matched = fn( seed, argument ),
+ i = matched.length;
+ while ( i-- ) {
+ idx = indexOf.call( seed, matched[i] );
+ seed[ idx ] = !( matches[ idx ] = matched[i] );
+ }
+ }) :
+ function( elem ) {
+ return fn( elem, 0, args );
+ };
+ }
+
+ return fn;
+ }
+ },
+
+ pseudos: {
+ "not": markFunction(function( selector ) {
+ // Trim the selector passed to compile
+ // to avoid treating leading and trailing
+ // spaces as combinators
+ var input = [],
+ results = [],
+ matcher = compile( selector.replace( rtrim, "$1" ) );
+
+ return matcher[ expando ] ?
+ markFunction(function( seed, matches, context, xml ) {
+ var elem,
+ unmatched = matcher( seed, null, xml, [] ),
+ i = seed.length;
+
+ // Match elements unmatched by `matcher`
+ while ( i-- ) {
+ if ( (elem = unmatched[i]) ) {
+ seed[i] = !(matches[i] = elem);
+ }
+ }
+ }) :
+ function( elem, context, xml ) {
+ input[0] = elem;
+ matcher( input, null, xml, results );
+ return !results.pop();
+ };
+ }),
+
+ "has": markFunction(function( selector ) {
+ return function( elem ) {
+ return Sizzle( selector, elem ).length > 0;
+ };
+ }),
+
+ "contains": markFunction(function( text ) {
+ return function( elem ) {
+ return ( elem.textContent || elem.innerText || getText( elem ) ).indexOf( text ) > -1;
+ };
+ }),
+
+ "enabled": function( elem ) {
+ return elem.disabled === false;
+ },
+
+ "disabled": function( elem ) {
+ return elem.disabled === true;
+ },
+
+ "checked": function( elem ) {
+ // In CSS3, :checked should return both checked and selected elements
+ // http://www.w3.org/TR/2011/REC-css3-selectors-20110929/#checked
+ var nodeName = elem.nodeName.toLowerCase();
+ return (nodeName === "input" && !!elem.checked) || (nodeName === "option" && !!elem.selected);
+ },
+
+ "selected": function( elem ) {
+ // Accessing this property makes selected-by-default
+ // options in Safari work properly
+ if ( elem.parentNode ) {
+ elem.parentNode.selectedIndex;
+ }
+
+ return elem.selected === true;
+ },
+
+ "parent": function( elem ) {
+ return !Expr.pseudos["empty"]( elem );
+ },
+
+ "empty": function( elem ) {
+ // http://www.w3.org/TR/selectors/#empty-pseudo
+ // :empty is only affected by element nodes and content nodes(including text(3), cdata(4)),
+ // not comment, processing instructions, or others
+ // Thanks to Diego Perini for the nodeName shortcut
+ // Greater than "@" means alpha characters (specifically not starting with "#" or "?")
+ var nodeType;
+ elem = elem.firstChild;
+ while ( elem ) {
+ if ( elem.nodeName > "@" || (nodeType = elem.nodeType) === 3 || nodeType === 4 ) {
+ return false;
+ }
+ elem = elem.nextSibling;
+ }
+ return true;
+ },
+
+ "header": function( elem ) {
+ return rheader.test( elem.nodeName );
+ },
+
+ "text": function( elem ) {
+ var type, attr;
+ // IE6 and 7 will map elem.type to 'text' for new HTML5 types (search, etc)
+ // use getAttribute instead to test this case
+ return elem.nodeName.toLowerCase() === "input" &&
+ (type = elem.type) === "text" &&
+ ( (attr = elem.getAttribute("type")) == null || attr.toLowerCase() === type );
+ },
+
+ // Input types
+ "radio": createInputPseudo("radio"),
+ "checkbox": createInputPseudo("checkbox"),
+ "file": createInputPseudo("file"),
+ "password": createInputPseudo("password"),
+ "image": createInputPseudo("image"),
+
+ "submit": createButtonPseudo("submit"),
+ "reset": createButtonPseudo("reset"),
+
+ "button": function( elem ) {
+ var name = elem.nodeName.toLowerCase();
+ return name === "input" && elem.type === "button" || name === "button";
+ },
+
+ "input": function( elem ) {
+ return rinputs.test( elem.nodeName );
+ },
+
+ "focus": function( elem ) {
+ var doc = elem.ownerDocument;
+ return elem === doc.activeElement && (!doc.hasFocus || doc.hasFocus()) && !!(elem.type || elem.href || ~elem.tabIndex);
+ },
+
+ "active": function( elem ) {
+ return elem === elem.ownerDocument.activeElement;
+ },
+
+ // Positional types
+ "first": createPositionalPseudo(function() {
+ return [ 0 ];
+ }),
+
+ "last": createPositionalPseudo(function( matchIndexes, length ) {
+ return [ length - 1 ];
+ }),
+
+ "eq": createPositionalPseudo(function( matchIndexes, length, argument ) {
+ return [ argument < 0 ? argument + length : argument ];
+ }),
+
+ "even": createPositionalPseudo(function( matchIndexes, length ) {
+ for ( var i = 0; i < length; i += 2 ) {
+ matchIndexes.push( i );
+ }
+ return matchIndexes;
+ }),
+
+ "odd": createPositionalPseudo(function( matchIndexes, length ) {
+ for ( var i = 1; i < length; i += 2 ) {
+ matchIndexes.push( i );
+ }
+ return matchIndexes;
+ }),
+
+ "lt": createPositionalPseudo(function( matchIndexes, length, argument ) {
+ for ( var i = argument < 0 ? argument + length : argument; --i >= 0; ) {
+ matchIndexes.push( i );
+ }
+ return matchIndexes;
+ }),
+
+ "gt": createPositionalPseudo(function( matchIndexes, length, argument ) {
+ for ( var i = argument < 0 ? argument + length : argument; ++i < length; ) {
+ matchIndexes.push( i );
+ }
+ return matchIndexes;
+ })
+ }
+};
+
+function siblingCheck( a, b, ret ) {
+ if ( a === b ) {
+ return ret;
+ }
+
+ var cur = a.nextSibling;
+
+ while ( cur ) {
+ if ( cur === b ) {
+ return -1;
+ }
+
+ cur = cur.nextSibling;
+ }
+
+ return 1;
+}
+
+sortOrder = docElem.compareDocumentPosition ?
+ function( a, b ) {
+ if ( a === b ) {
+ hasDuplicate = true;
+ return 0;
+ }
+
+ return ( !a.compareDocumentPosition || !b.compareDocumentPosition ?
+ a.compareDocumentPosition :
+ a.compareDocumentPosition(b) & 4
+ ) ? -1 : 1;
+ } :
+ function( a, b ) {
+ // The nodes are identical, we can exit early
+ if ( a === b ) {
+ hasDuplicate = true;
+ return 0;
+
+ // Fallback to using sourceIndex (in IE) if it's available on both nodes
+ } else if ( a.sourceIndex && b.sourceIndex ) {
+ return a.sourceIndex - b.sourceIndex;
+ }
+
+ var al, bl,
+ ap = [],
+ bp = [],
+ aup = a.parentNode,
+ bup = b.parentNode,
+ cur = aup;
+
+ // If the nodes are siblings (or identical) we can do a quick check
+ if ( aup === bup ) {
+ return siblingCheck( a, b );
+
+ // If no parents were found then the nodes are disconnected
+ } else if ( !aup ) {
+ return -1;
+
+ } else if ( !bup ) {
+ return 1;
+ }
+
+ // Otherwise they're somewhere else in the tree so we need
+ // to build up a full list of the parentNodes for comparison
+ while ( cur ) {
+ ap.unshift( cur );
+ cur = cur.parentNode;
+ }
+
+ cur = bup;
+
+ while ( cur ) {
+ bp.unshift( cur );
+ cur = cur.parentNode;
+ }
+
+ al = ap.length;
+ bl = bp.length;
+
+ // Start walking down the tree looking for a discrepancy
+ for ( var i = 0; i < al && i < bl; i++ ) {
+ if ( ap[i] !== bp[i] ) {
+ return siblingCheck( ap[i], bp[i] );
+ }
+ }
+
+ // We ended someplace up the tree so do a sibling check
+ return i === al ?
+ siblingCheck( a, bp[i], -1 ) :
+ siblingCheck( ap[i], b, 1 );
+ };
+
+// Always assume the presence of duplicates if sort doesn't
+// pass them to our comparison function (as in Google Chrome).
+[0, 0].sort( sortOrder );
+baseHasDuplicate = !hasDuplicate;
+
+// Document sorting and removing duplicates
+Sizzle.uniqueSort = function( results ) {
+ var elem,
+ duplicates = [],
+ i = 1,
+ j = 0;
+
+ hasDuplicate = baseHasDuplicate;
+ results.sort( sortOrder );
+
+ if ( hasDuplicate ) {
+ for ( ; (elem = results[i]); i++ ) {
+ if ( elem === results[ i - 1 ] ) {
+ j = duplicates.push( i );
+ }
+ }
+ while ( j-- ) {
+ results.splice( duplicates[ j ], 1 );
+ }
+ }
+
+ return results;
+};
+
+Sizzle.error = function( msg ) {
+ throw new Error( "Syntax error, unrecognized expression: " + msg );
+};
+
+function tokenize( selector, parseOnly ) {
+ var matched, match, tokens, type,
+ soFar, groups, preFilters,
+ cached = tokenCache[ expando ][ selector + " " ];
+
+ if ( cached ) {
+ return parseOnly ? 0 : cached.slice( 0 );
+ }
+
+ soFar = selector;
+ groups = [];
+ preFilters = Expr.preFilter;
+
+ while ( soFar ) {
+
+ // Comma and first run
+ if ( !matched || (match = rcomma.exec( soFar )) ) {
+ if ( match ) {
+ // Don't consume trailing commas as valid
+ soFar = soFar.slice( match[0].length ) || soFar;
+ }
+ groups.push( tokens = [] );
+ }
+
+ matched = false;
+
+ // Combinators
+ if ( (match = rcombinators.exec( soFar )) ) {
+ tokens.push( matched = new Token( match.shift() ) );
+ soFar = soFar.slice( matched.length );
+
+ // Cast descendant combinators to space
+ matched.type = match[0].replace( rtrim, " " );
+ }
+
+ // Filters
+ for ( type in Expr.filter ) {
+ if ( (match = matchExpr[ type ].exec( soFar )) && (!preFilters[ type ] ||
+ (match = preFilters[ type ]( match ))) ) {
+
+ tokens.push( matched = new Token( match.shift() ) );
+ soFar = soFar.slice( matched.length );
+ matched.type = type;
+ matched.matches = match;
+ }
+ }
+
+ if ( !matched ) {
+ break;
+ }
+ }
+
+ // Return the length of the invalid excess
+ // if we're just parsing
+ // Otherwise, throw an error or return tokens
+ return parseOnly ?
+ soFar.length :
+ soFar ?
+ Sizzle.error( selector ) :
+ // Cache the tokens
+ tokenCache( selector, groups ).slice( 0 );
+}
+
+function addCombinator( matcher, combinator, base ) {
+ var dir = combinator.dir,
+ checkNonElements = base && combinator.dir === "parentNode",
+ doneName = done++;
+
+ return combinator.first ?
+ // Check against closest ancestor/preceding element
+ function( elem, context, xml ) {
+ while ( (elem = elem[ dir ]) ) {
+ if ( checkNonElements || elem.nodeType === 1 ) {
+ return matcher( elem, context, xml );
+ }
+ }
+ } :
+
+ // Check against all ancestor/preceding elements
+ function( elem, context, xml ) {
+ // We can't set arbitrary data on XML nodes, so they don't benefit from dir caching
+ if ( !xml ) {
+ var cache,
+ dirkey = dirruns + " " + doneName + " ",
+ cachedkey = dirkey + cachedruns;
+ while ( (elem = elem[ dir ]) ) {
+ if ( checkNonElements || elem.nodeType === 1 ) {
+ if ( (cache = elem[ expando ]) === cachedkey ) {
+ return elem.sizset;
+ } else if ( typeof cache === "string" && cache.indexOf(dirkey) === 0 ) {
+ if ( elem.sizset ) {
+ return elem;
+ }
+ } else {
+ elem[ expando ] = cachedkey;
+ if ( matcher( elem, context, xml ) ) {
+ elem.sizset = true;
+ return elem;
+ }
+ elem.sizset = false;
+ }
+ }
+ }
+ } else {
+ while ( (elem = elem[ dir ]) ) {
+ if ( checkNonElements || elem.nodeType === 1 ) {
+ if ( matcher( elem, context, xml ) ) {
+ return elem;
+ }
+ }
+ }
+ }
+ };
+}
+
+function elementMatcher( matchers ) {
+ return matchers.length > 1 ?
+ function( elem, context, xml ) {
+ var i = matchers.length;
+ while ( i-- ) {
+ if ( !matchers[i]( elem, context, xml ) ) {
+ return false;
+ }
+ }
+ return true;
+ } :
+ matchers[0];
+}
+
+function condense( unmatched, map, filter, context, xml ) {
+ var elem,
+ newUnmatched = [],
+ i = 0,
+ len = unmatched.length,
+ mapped = map != null;
+
+ for ( ; i < len; i++ ) {
+ if ( (elem = unmatched[i]) ) {
+ if ( !filter || filter( elem, context, xml ) ) {
+ newUnmatched.push( elem );
+ if ( mapped ) {
+ map.push( i );
+ }
+ }
+ }
+ }
+
+ return newUnmatched;
+}
+
+function setMatcher( preFilter, selector, matcher, postFilter, postFinder, postSelector ) {
+ if ( postFilter && !postFilter[ expando ] ) {
+ postFilter = setMatcher( postFilter );
+ }
+ if ( postFinder && !postFinder[ expando ] ) {
+ postFinder = setMatcher( postFinder, postSelector );
+ }
+ return markFunction(function( seed, results, context, xml ) {
+ var temp, i, elem,
+ preMap = [],
+ postMap = [],
+ preexisting = results.length,
+
+ // Get initial elements from seed or context
+ elems = seed || multipleContexts( selector || "*", context.nodeType ? [ context ] : context, [] ),
+
+ // Prefilter to get matcher input, preserving a map for seed-results synchronization
+ matcherIn = preFilter && ( seed || !selector ) ?
+ condense( elems, preMap, preFilter, context, xml ) :
+ elems,
+
+ matcherOut = matcher ?
+ // If we have a postFinder, or filtered seed, or non-seed postFilter or preexisting results,
+ postFinder || ( seed ? preFilter : preexisting || postFilter ) ?
+
+ // ...intermediate processing is necessary
+ [] :
+
+ // ...otherwise use results directly
+ results :
+ matcherIn;
+
+ // Find primary matches
+ if ( matcher ) {
+ matcher( matcherIn, matcherOut, context, xml );
+ }
+
+ // Apply postFilter
+ if ( postFilter ) {
+ temp = condense( matcherOut, postMap );
+ postFilter( temp, [], context, xml );
+
+ // Un-match failing elements by moving them back to matcherIn
+ i = temp.length;
+ while ( i-- ) {
+ if ( (elem = temp[i]) ) {
+ matcherOut[ postMap[i] ] = !(matcherIn[ postMap[i] ] = elem);
+ }
+ }
+ }
+
+ if ( seed ) {
+ if ( postFinder || preFilter ) {
+ if ( postFinder ) {
+ // Get the final matcherOut by condensing this intermediate into postFinder contexts
+ temp = [];
+ i = matcherOut.length;
+ while ( i-- ) {
+ if ( (elem = matcherOut[i]) ) {
+ // Restore matcherIn since elem is not yet a final match
+ temp.push( (matcherIn[i] = elem) );
+ }
+ }
+ postFinder( null, (matcherOut = []), temp, xml );
+ }
+
+ // Move matched elements from seed to results to keep them synchronized
+ i = matcherOut.length;
+ while ( i-- ) {
+ if ( (elem = matcherOut[i]) &&
+ (temp = postFinder ? indexOf.call( seed, elem ) : preMap[i]) > -1 ) {
+
+ seed[temp] = !(results[temp] = elem);
+ }
+ }
+ }
+
+ // Add elements to results, through postFinder if defined
+ } else {
+ matcherOut = condense(
+ matcherOut === results ?
+ matcherOut.splice( preexisting, matcherOut.length ) :
+ matcherOut
+ );
+ if ( postFinder ) {
+ postFinder( null, results, matcherOut, xml );
+ } else {
+ push.apply( results, matcherOut );
+ }
+ }
+ });
+}
+
+function matcherFromTokens( tokens ) {
+ var checkContext, matcher, j,
+ len = tokens.length,
+ leadingRelative = Expr.relative[ tokens[0].type ],
+ implicitRelative = leadingRelative || Expr.relative[" "],
+ i = leadingRelative ? 1 : 0,
+
+ // The foundational matcher ensures that elements are reachable from top-level context(s)
+ matchContext = addCombinator( function( elem ) {
+ return elem === checkContext;
+ }, implicitRelative, true ),
+ matchAnyContext = addCombinator( function( elem ) {
+ return indexOf.call( checkContext, elem ) > -1;
+ }, implicitRelative, true ),
+ matchers = [ function( elem, context, xml ) {
+ return ( !leadingRelative && ( xml || context !== outermostContext ) ) || (
+ (checkContext = context).nodeType ?
+ matchContext( elem, context, xml ) :
+ matchAnyContext( elem, context, xml ) );
+ } ];
+
+ for ( ; i < len; i++ ) {
+ if ( (matcher = Expr.relative[ tokens[i].type ]) ) {
+ matchers = [ addCombinator( elementMatcher( matchers ), matcher ) ];
+ } else {
+ matcher = Expr.filter[ tokens[i].type ].apply( null, tokens[i].matches );
+
+ // Return special upon seeing a positional matcher
+ if ( matcher[ expando ] ) {
+ // Find the next relative operator (if any) for proper handling
+ j = ++i;
+ for ( ; j < len; j++ ) {
+ if ( Expr.relative[ tokens[j].type ] ) {
+ break;
+ }
+ }
+ return setMatcher(
+ i > 1 && elementMatcher( matchers ),
+ i > 1 && tokens.slice( 0, i - 1 ).join("").replace( rtrim, "$1" ),
+ matcher,
+ i < j && matcherFromTokens( tokens.slice( i, j ) ),
+ j < len && matcherFromTokens( (tokens = tokens.slice( j )) ),
+ j < len && tokens.join("")
+ );
+ }
+ matchers.push( matcher );
+ }
+ }
+
+ return elementMatcher( matchers );
+}
+
+function matcherFromGroupMatchers( elementMatchers, setMatchers ) {
+ var bySet = setMatchers.length > 0,
+ byElement = elementMatchers.length > 0,
+ superMatcher = function( seed, context, xml, results, expandContext ) {
+ var elem, j, matcher,
+ setMatched = [],
+ matchedCount = 0,
+ i = "0",
+ unmatched = seed && [],
+ outermost = expandContext != null,
+ contextBackup = outermostContext,
+ // We must always have either seed elements or context
+ elems = seed || byElement && Expr.find["TAG"]( "*", expandContext && context.parentNode || context ),
+ // Nested matchers should use non-integer dirruns
+ dirrunsUnique = (dirruns += contextBackup == null ? 1 : Math.E);
+
+ if ( outermost ) {
+ outermostContext = context !== document && context;
+ cachedruns = superMatcher.el;
+ }
+
+ // Add elements passing elementMatchers directly to results
+ for ( ; (elem = elems[i]) != null; i++ ) {
+ if ( byElement && elem ) {
+ for ( j = 0; (matcher = elementMatchers[j]); j++ ) {
+ if ( matcher( elem, context, xml ) ) {
+ results.push( elem );
+ break;
+ }
+ }
+ if ( outermost ) {
+ dirruns = dirrunsUnique;
+ cachedruns = ++superMatcher.el;
+ }
+ }
+
+ // Track unmatched elements for set filters
+ if ( bySet ) {
+ // They will have gone through all possible matchers
+ if ( (elem = !matcher && elem) ) {
+ matchedCount--;
+ }
+
+ // Lengthen the array for every element, matched or not
+ if ( seed ) {
+ unmatched.push( elem );
+ }
+ }
+ }
+
+ // Apply set filters to unmatched elements
+ matchedCount += i;
+ if ( bySet && i !== matchedCount ) {
+ for ( j = 0; (matcher = setMatchers[j]); j++ ) {
+ matcher( unmatched, setMatched, context, xml );
+ }
+
+ if ( seed ) {
+ // Reintegrate element matches to eliminate the need for sorting
+ if ( matchedCount > 0 ) {
+ while ( i-- ) {
+ if ( !(unmatched[i] || setMatched[i]) ) {
+ setMatched[i] = pop.call( results );
+ }
+ }
+ }
+
+ // Discard index placeholder values to get only actual matches
+ setMatched = condense( setMatched );
+ }
+
+ // Add matches to results
+ push.apply( results, setMatched );
+
+ // Seedless set matches succeeding multiple successful matchers stipulate sorting
+ if ( outermost && !seed && setMatched.length > 0 &&
+ ( matchedCount + setMatchers.length ) > 1 ) {
+
+ Sizzle.uniqueSort( results );
+ }
+ }
+
+ // Override manipulation of globals by nested matchers
+ if ( outermost ) {
+ dirruns = dirrunsUnique;
+ outermostContext = contextBackup;
+ }
+
+ return unmatched;
+ };
+
+ superMatcher.el = 0;
+ return bySet ?
+ markFunction( superMatcher ) :
+ superMatcher;
+}
+
+compile = Sizzle.compile = function( selector, group /* Internal Use Only */ ) {
+ var i,
+ setMatchers = [],
+ elementMatchers = [],
+ cached = compilerCache[ expando ][ selector + " " ];
+
+ if ( !cached ) {
+ // Generate a function of recursive functions that can be used to check each element
+ if ( !group ) {
+ group = tokenize( selector );
+ }
+ i = group.length;
+ while ( i-- ) {
+ cached = matcherFromTokens( group[i] );
+ if ( cached[ expando ] ) {
+ setMatchers.push( cached );
+ } else {
+ elementMatchers.push( cached );
+ }
+ }
+
+ // Cache the compiled function
+ cached = compilerCache( selector, matcherFromGroupMatchers( elementMatchers, setMatchers ) );
+ }
+ return cached;
+};
+
+function multipleContexts( selector, contexts, results ) {
+ var i = 0,
+ len = contexts.length;
+ for ( ; i < len; i++ ) {
+ Sizzle( selector, contexts[i], results );
+ }
+ return results;
+}
+
+function select( selector, context, results, seed, xml ) {
+ var i, tokens, token, type, find,
+ match = tokenize( selector ),
+ j = match.length;
+
+ if ( !seed ) {
+ // Try to minimize operations if there is only one group
+ if ( match.length === 1 ) {
+
+ // Take a shortcut and set the context if the root selector is an ID
+ tokens = match[0] = match[0].slice( 0 );
+ if ( tokens.length > 2 && (token = tokens[0]).type === "ID" &&
+ context.nodeType === 9 && !xml &&
+ Expr.relative[ tokens[1].type ] ) {
+
+ context = Expr.find["ID"]( token.matches[0].replace( rbackslash, "" ), context, xml )[0];
+ if ( !context ) {
+ return results;
+ }
+
+ selector = selector.slice( tokens.shift().length );
+ }
+
+ // Fetch a seed set for right-to-left matching
+ for ( i = matchExpr["POS"].test( selector ) ? -1 : tokens.length - 1; i >= 0; i-- ) {
+ token = tokens[i];
+
+ // Abort if we hit a combinator
+ if ( Expr.relative[ (type = token.type) ] ) {
+ break;
+ }
+ if ( (find = Expr.find[ type ]) ) {
+ // Search, expanding context for leading sibling combinators
+ if ( (seed = find(
+ token.matches[0].replace( rbackslash, "" ),
+ rsibling.test( tokens[0].type ) && context.parentNode || context,
+ xml
+ )) ) {
+
+ // If seed is empty or no tokens remain, we can return early
+ tokens.splice( i, 1 );
+ selector = seed.length && tokens.join("");
+ if ( !selector ) {
+ push.apply( results, slice.call( seed, 0 ) );
+ return results;
+ }
+
+ break;
+ }
+ }
+ }
+ }
+ }
+
+ // Compile and execute a filtering function
+ // Provide `match` to avoid retokenization if we modified the selector above
+ compile( selector, match )(
+ seed,
+ context,
+ xml,
+ results,
+ rsibling.test( selector )
+ );
+ return results;
+}
+
+if ( document.querySelectorAll ) {
+ (function() {
+ var disconnectedMatch,
+ oldSelect = select,
+ rescape = /'|\\/g,
+ rattributeQuotes = /\=[\x20\t\r\n\f]*([^'"\]]*)[\x20\t\r\n\f]*\]/g,
+
+ // qSa(:focus) reports false when true (Chrome 21), no need to also add to buggyMatches since matches checks buggyQSA
+ // A support test would require too much code (would include document ready)
+ rbuggyQSA = [ ":focus" ],
+
+ // matchesSelector(:active) reports false when true (IE9/Opera 11.5)
+ // A support test would require too much code (would include document ready)
+ // just skip matchesSelector for :active
+ rbuggyMatches = [ ":active" ],
+ matches = docElem.matchesSelector ||
+ docElem.mozMatchesSelector ||
+ docElem.webkitMatchesSelector ||
+ docElem.oMatchesSelector ||
+ docElem.msMatchesSelector;
+
+ // Build QSA regex
+ // Regex strategy adopted from Diego Perini
+ assert(function( div ) {
+ // Select is set to empty string on purpose
+ // This is to test IE's treatment of not explictly
+ // setting a boolean content attribute,
+ // since its presence should be enough
+ // http://bugs.jquery.com/ticket/12359
+ div.innerHTML = "<select><option selected=''></option></select>";
+
+ // IE8 - Some boolean attributes are not treated correctly
+ if ( !div.querySelectorAll("[selected]").length ) {
+ rbuggyQSA.push( "\\[" + whitespace + "*(?:checked|disabled|ismap|multiple|readonly|selected|value)" );
+ }
+
+ // Webkit/Opera - :checked should return selected option elements
+ // http://www.w3.org/TR/2011/REC-css3-selectors-20110929/#checked
+ // IE8 throws error here (do not put tests after this one)
+ if ( !div.querySelectorAll(":checked").length ) {
+ rbuggyQSA.push(":checked");
+ }
+ });
+
+ assert(function( div ) {
+
+ // Opera 10-12/IE9 - ^= $= *= and empty values
+ // Should not select anything
+ div.innerHTML = "<p test=''></p>";
+ if ( div.querySelectorAll("[test^='']").length ) {
+ rbuggyQSA.push( "[*^$]=" + whitespace + "*(?:\"\"|'')" );
+ }
+
+ // FF 3.5 - :enabled/:disabled and hidden elements (hidden elements are still enabled)
+ // IE8 throws error here (do not put tests after this one)
+ div.innerHTML = "<input type='hidden'/>";
+ if ( !div.querySelectorAll(":enabled").length ) {
+ rbuggyQSA.push(":enabled", ":disabled");
+ }
+ });
+
+ // rbuggyQSA always contains :focus, so no need for a length check
+ rbuggyQSA = /* rbuggyQSA.length && */ new RegExp( rbuggyQSA.join("|") );
+
+ select = function( selector, context, results, seed, xml ) {
+ // Only use querySelectorAll when not filtering,
+ // when this is not xml,
+ // and when no QSA bugs apply
+ if ( !seed && !xml && !rbuggyQSA.test( selector ) ) {
+ var groups, i,
+ old = true,
+ nid = expando,
+ newContext = context,
+ newSelector = context.nodeType === 9 && selector;
+
+ // qSA works strangely on Element-rooted queries
+ // We can work around this by specifying an extra ID on the root
+ // and working up from there (Thanks to Andrew Dupont for the technique)
+ // IE 8 doesn't work on object elements
+ if ( context.nodeType === 1 && context.nodeName.toLowerCase() !== "object" ) {
+ groups = tokenize( selector );
+
+ if ( (old = context.getAttribute("id")) ) {
+ nid = old.replace( rescape, "\\$&" );
+ } else {
+ context.setAttribute( "id", nid );
+ }
+ nid = "[id='" + nid + "'] ";
+
+ i = groups.length;
+ while ( i-- ) {
+ groups[i] = nid + groups[i].join("");
+ }
+ newContext = rsibling.test( selector ) && context.parentNode || context;
+ newSelector = groups.join(",");
+ }
+
+ if ( newSelector ) {
+ try {
+ push.apply( results, slice.call( newContext.querySelectorAll(
+ newSelector
+ ), 0 ) );
+ return results;
+ } catch(qsaError) {
+ } finally {
+ if ( !old ) {
+ context.removeAttribute("id");
+ }
+ }
+ }
+ }
+
+ return oldSelect( selector, context, results, seed, xml );
+ };
+
+ if ( matches ) {
+ assert(function( div ) {
+ // Check to see if it's possible to do matchesSelector
+ // on a disconnected node (IE 9)
+ disconnectedMatch = matches.call( div, "div" );
+
+ // This should fail with an exception
+ // Gecko does not error, returns false instead
+ try {
+ matches.call( div, "[test!='']:sizzle" );
+ rbuggyMatches.push( "!=", pseudos );
+ } catch ( e ) {}
+ });
+
+ // rbuggyMatches always contains :active and :focus, so no need for a length check
+ rbuggyMatches = /* rbuggyMatches.length && */ new RegExp( rbuggyMatches.join("|") );
+
+ Sizzle.matchesSelector = function( elem, expr ) {
+ // Make sure that attribute selectors are quoted
+ expr = expr.replace( rattributeQuotes, "='$1']" );
+
+ // rbuggyMatches always contains :active, so no need for an existence check
+ if ( !isXML( elem ) && !rbuggyMatches.test( expr ) && !rbuggyQSA.test( expr ) ) {
+ try {
+ var ret = matches.call( elem, expr );
+
+ // IE 9's matchesSelector returns false on disconnected nodes
+ if ( ret || disconnectedMatch ||
+ // As well, disconnected nodes are said to be in a document
+ // fragment in IE 9
+ elem.document && elem.document.nodeType !== 11 ) {
+ return ret;
+ }
+ } catch(e) {}
+ }
+
+ return Sizzle( expr, null, null, [ elem ] ).length > 0;
+ };
+ }
+ })();
+}
+
+// Deprecated
+Expr.pseudos["nth"] = Expr.pseudos["eq"];
+
+// Back-compat
+function setFilters() {}
+Expr.filters = setFilters.prototype = Expr.pseudos;
+Expr.setFilters = new setFilters();
+
+// Override sizzle attribute retrieval
+Sizzle.attr = jQuery.attr;
+jQuery.find = Sizzle;
+jQuery.expr = Sizzle.selectors;
+jQuery.expr[":"] = jQuery.expr.pseudos;
+jQuery.unique = Sizzle.uniqueSort;
+jQuery.text = Sizzle.getText;
+jQuery.isXMLDoc = Sizzle.isXML;
+jQuery.contains = Sizzle.contains;
+
+
+})( window );
+var runtil = /Until$/,
+ rparentsprev = /^(?:parents|prev(?:Until|All))/,
+ isSimple = /^.[^:#\[\.,]*$/,
+ rneedsContext = jQuery.expr.match.needsContext,
+ // methods guaranteed to produce a unique set when starting from a unique set
+ guaranteedUnique = {
+ children: true,
+ contents: true,
+ next: true,
+ prev: true
+ };
+
+jQuery.fn.extend({
+ find: function( selector ) {
+ var i, l, length, n, r, ret,
+ self = this;
+
+ if ( typeof selector !== "string" ) {
+ return jQuery( selector ).filter(function() {
+ for ( i = 0, l = self.length; i < l; i++ ) {
+ if ( jQuery.contains( self[ i ], this ) ) {
+ return true;
+ }
+ }
+ });
+ }
+
+ ret = this.pushStack( "", "find", selector );
+
+ for ( i = 0, l = this.length; i < l; i++ ) {
+ length = ret.length;
+ jQuery.find( selector, this[i], ret );
+
+ if ( i > 0 ) {
+ // Make sure that the results are unique
+ for ( n = length; n < ret.length; n++ ) {
+ for ( r = 0; r < length; r++ ) {
+ if ( ret[r] === ret[n] ) {
+ ret.splice(n--, 1);
+ break;
+ }
+ }
+ }
+ }
+ }
+
+ return ret;
+ },
+
+ has: function( target ) {
+ var i,
+ targets = jQuery( target, this ),
+ len = targets.length;
+
+ return this.filter(function() {
+ for ( i = 0; i < len; i++ ) {
+ if ( jQuery.contains( this, targets[i] ) ) {
+ return true;
+ }
+ }
+ });
+ },
+
+ not: function( selector ) {
+ return this.pushStack( winnow(this, selector, false), "not", selector);
+ },
+
+ filter: function( selector ) {
+ return this.pushStack( winnow(this, selector, true), "filter", selector );
+ },
+
+ is: function( selector ) {
+ return !!selector && (
+ typeof selector === "string" ?
+ // If this is a positional/relative selector, check membership in the returned set
+ // so $("p:first").is("p:last") won't return true for a doc with two "p".
+ rneedsContext.test( selector ) ?
+ jQuery( selector, this.context ).index( this[0] ) >= 0 :
+ jQuery.filter( selector, this ).length > 0 :
+ this.filter( selector ).length > 0 );
+ },
+
+ closest: function( selectors, context ) {
+ var cur,
+ i = 0,
+ l = this.length,
+ ret = [],
+ pos = rneedsContext.test( selectors ) || typeof selectors !== "string" ?
+ jQuery( selectors, context || this.context ) :
+ 0;
+
+ for ( ; i < l; i++ ) {
+ cur = this[i];
+
+ while ( cur && cur.ownerDocument && cur !== context && cur.nodeType !== 11 ) {
+ if ( pos ? pos.index(cur) > -1 : jQuery.find.matchesSelector(cur, selectors) ) {
+ ret.push( cur );
+ break;
+ }
+ cur = cur.parentNode;
+ }
+ }
+
+ ret = ret.length > 1 ? jQuery.unique( ret ) : ret;
+
+ return this.pushStack( ret, "closest", selectors );
+ },
+
+ // Determine the position of an element within
+ // the matched set of elements
+ index: function( elem ) {
+
+ // No argument, return index in parent
+ if ( !elem ) {
+ return ( this[0] && this[0].parentNode ) ? this.prevAll().length : -1;
+ }
+
+ // index in selector
+ if ( typeof elem === "string" ) {
+ return jQuery.inArray( this[0], jQuery( elem ) );
+ }
+
+ // Locate the position of the desired element
+ return jQuery.inArray(
+ // If it receives a jQuery object, the first element is used
+ elem.jquery ? elem[0] : elem, this );
+ },
+
+ add: function( selector, context ) {
+ var set = typeof selector === "string" ?
+ jQuery( selector, context ) :
+ jQuery.makeArray( selector && selector.nodeType ? [ selector ] : selector ),
+ all = jQuery.merge( this.get(), set );
+
+ return this.pushStack( isDisconnected( set[0] ) || isDisconnected( all[0] ) ?
+ all :
+ jQuery.unique( all ) );
+ },
+
+ addBack: function( selector ) {
+ return this.add( selector == null ?
+ this.prevObject : this.prevObject.filter(selector)
+ );
+ }
+});
+
+jQuery.fn.andSelf = jQuery.fn.addBack;
+
+// A painfully simple check to see if an element is disconnected
+// from a document (should be improved, where feasible).
+function isDisconnected( node ) {
+ return !node || !node.parentNode || node.parentNode.nodeType === 11;
+}
+
+function sibling( cur, dir ) {
+ do {
+ cur = cur[ dir ];
+ } while ( cur && cur.nodeType !== 1 );
+
+ return cur;
+}
+
+jQuery.each({
+ parent: function( elem ) {
+ var parent = elem.parentNode;
+ return parent && parent.nodeType !== 11 ? parent : null;
+ },
+ parents: function( elem ) {
+ return jQuery.dir( elem, "parentNode" );
+ },
+ parentsUntil: function( elem, i, until ) {
+ return jQuery.dir( elem, "parentNode", until );
+ },
+ next: function( elem ) {
+ return sibling( elem, "nextSibling" );
+ },
+ prev: function( elem ) {
+ return sibling( elem, "previousSibling" );
+ },
+ nextAll: function( elem ) {
+ return jQuery.dir( elem, "nextSibling" );
+ },
+ prevAll: function( elem ) {
+ return jQuery.dir( elem, "previousSibling" );
+ },
+ nextUntil: function( elem, i, until ) {
+ return jQuery.dir( elem, "nextSibling", until );
+ },
+ prevUntil: function( elem, i, until ) {
+ return jQuery.dir( elem, "previousSibling", until );
+ },
+ siblings: function( elem ) {
+ return jQuery.sibling( ( elem.parentNode || {} ).firstChild, elem );
+ },
+ children: function( elem ) {
+ return jQuery.sibling( elem.firstChild );
+ },
+ contents: function( elem ) {
+ return jQuery.nodeName( elem, "iframe" ) ?
+ elem.contentDocument || elem.contentWindow.document :
+ jQuery.merge( [], elem.childNodes );
+ }
+}, function( name, fn ) {
+ jQuery.fn[ name ] = function( until, selector ) {
+ var ret = jQuery.map( this, fn, until );
+
+ if ( !runtil.test( name ) ) {
+ selector = until;
+ }
+
+ if ( selector && typeof selector === "string" ) {
+ ret = jQuery.filter( selector, ret );
+ }
+
+ ret = this.length > 1 && !guaranteedUnique[ name ] ? jQuery.unique( ret ) : ret;
+
+ if ( this.length > 1 && rparentsprev.test( name ) ) {
+ ret = ret.reverse();
+ }
+
+ return this.pushStack( ret, name, core_slice.call( arguments ).join(",") );
+ };
+});
+
+jQuery.extend({
+ filter: function( expr, elems, not ) {
+ if ( not ) {
+ expr = ":not(" + expr + ")";
+ }
+
+ return elems.length === 1 ?
+ jQuery.find.matchesSelector(elems[0], expr) ? [ elems[0] ] : [] :
+ jQuery.find.matches(expr, elems);
+ },
+
+ dir: function( elem, dir, until ) {
+ var matched = [],
+ cur = elem[ dir ];
+
+ while ( cur && cur.nodeType !== 9 && (until === undefined || cur.nodeType !== 1 || !jQuery( cur ).is( until )) ) {
+ if ( cur.nodeType === 1 ) {
+ matched.push( cur );
+ }
+ cur = cur[dir];
+ }
+ return matched;
+ },
+
+ sibling: function( n, elem ) {
+ var r = [];
+
+ for ( ; n; n = n.nextSibling ) {
+ if ( n.nodeType === 1 && n !== elem ) {
+ r.push( n );
+ }
+ }
+
+ return r;
+ }
+});
+
+// Implement the identical functionality for filter and not
+function winnow( elements, qualifier, keep ) {
+
+ // Can't pass null or undefined to indexOf in Firefox 4
+ // Set to 0 to skip string check
+ qualifier = qualifier || 0;
+
+ if ( jQuery.isFunction( qualifier ) ) {
+ return jQuery.grep(elements, function( elem, i ) {
+ var retVal = !!qualifier.call( elem, i, elem );
+ return retVal === keep;
+ });
+
+ } else if ( qualifier.nodeType ) {
+ return jQuery.grep(elements, function( elem, i ) {
+ return ( elem === qualifier ) === keep;
+ });
+
+ } else if ( typeof qualifier === "string" ) {
+ var filtered = jQuery.grep(elements, function( elem ) {
+ return elem.nodeType === 1;
+ });
+
+ if ( isSimple.test( qualifier ) ) {
+ return jQuery.filter(qualifier, filtered, !keep);
+ } else {
+ qualifier = jQuery.filter( qualifier, filtered );
+ }
+ }
+
+ return jQuery.grep(elements, function( elem, i ) {
+ return ( jQuery.inArray( elem, qualifier ) >= 0 ) === keep;
+ });
+}
+function createSafeFragment( document ) {
+ var list = nodeNames.split( "|" ),
+ safeFrag = document.createDocumentFragment();
+
+ if ( safeFrag.createElement ) {
+ while ( list.length ) {
+ safeFrag.createElement(
+ list.pop()
+ );
+ }
+ }
+ return safeFrag;
+}
+
+var nodeNames = "abbr|article|aside|audio|bdi|canvas|data|datalist|details|figcaption|figure|footer|" +
+ "header|hgroup|mark|meter|nav|output|progress|section|summary|time|video",
+ rinlinejQuery = / jQuery\d+="(?:null|\d+)"/g,
+ rleadingWhitespace = /^\s+/,
+ rxhtmlTag = /<(?!area|br|col|embed|hr|img|input|link|meta|param)(([\w:]+)[^>]*)\/>/gi,
+ rtagName = /<([\w:]+)/,
+ rtbody = /<tbody/i,
+ rhtml = /<|&#?\w+;/,
+ rnoInnerhtml = /<(?:script|style|link)/i,
+ rnocache = /<(?:script|object|embed|option|style)/i,
+ rnoshimcache = new RegExp("<(?:" + nodeNames + ")[\\s/>]", "i"),
+ rcheckableType = /^(?:checkbox|radio)$/,
+ // checked="checked" or checked
+ rchecked = /checked\s*(?:[^=]|=\s*.checked.)/i,
+ rscriptType = /\/(java|ecma)script/i,
+ rcleanScript = /^\s*<!(?:\[CDATA\[|\-\-)|[\]\-]{2}>\s*$/g,
+ wrapMap = {
+ option: [ 1, "<select multiple='multiple'>", "</select>" ],
+ legend: [ 1, "<fieldset>", "</fieldset>" ],
+ thead: [ 1, "<table>", "</table>" ],
+ tr: [ 2, "<table><tbody>", "</tbody></table>" ],
+ td: [ 3, "<table><tbody><tr>", "</tr></tbody></table>" ],
+ col: [ 2, "<table><tbody></tbody><colgroup>", "</colgroup></table>" ],
+ area: [ 1, "<map>", "</map>" ],
+ _default: [ 0, "", "" ]
+ },
+ safeFragment = createSafeFragment( document ),
+ fragmentDiv = safeFragment.appendChild( document.createElement("div") );
+
+wrapMap.optgroup = wrapMap.option;
+wrapMap.tbody = wrapMap.tfoot = wrapMap.colgroup = wrapMap.caption = wrapMap.thead;
+wrapMap.th = wrapMap.td;
+
+// IE6-8 can't serialize link, script, style, or any html5 (NoScope) tags,
+// unless wrapped in a div with non-breaking characters in front of it.
+if ( !jQuery.support.htmlSerialize ) {
+ wrapMap._default = [ 1, "X<div>", "</div>" ];
+}
+
+jQuery.fn.extend({
+ text: function( value ) {
+ return jQuery.access( this, function( value ) {
+ return value === undefined ?
+ jQuery.text( this ) :
+ this.empty().append( ( this[0] && this[0].ownerDocument || document ).createTextNode( value ) );
+ }, null, value, arguments.length );
+ },
+
+ wrapAll: function( html ) {
+ if ( jQuery.isFunction( html ) ) {
+ return this.each(function(i) {
+ jQuery(this).wrapAll( html.call(this, i) );
+ });
+ }
+
+ if ( this[0] ) {
+ // The elements to wrap the target around
+ var wrap = jQuery( html, this[0].ownerDocument ).eq(0).clone(true);
+
+ if ( this[0].parentNode ) {
+ wrap.insertBefore( this[0] );
+ }
+
+ wrap.map(function() {
+ var elem = this;
+
+ while ( elem.firstChild && elem.firstChild.nodeType === 1 ) {
+ elem = elem.firstChild;
+ }
+
+ return elem;
+ }).append( this );
+ }
+
+ return this;
+ },
+
+ wrapInner: function( html ) {
+ if ( jQuery.isFunction( html ) ) {
+ return this.each(function(i) {
+ jQuery(this).wrapInner( html.call(this, i) );
+ });
+ }
+
+ return this.each(function() {
+ var self = jQuery( this ),
+ contents = self.contents();
+
+ if ( contents.length ) {
+ contents.wrapAll( html );
+
+ } else {
+ self.append( html );
+ }
+ });
+ },
+
+ wrap: function( html ) {
+ var isFunction = jQuery.isFunction( html );
+
+ return this.each(function(i) {
+ jQuery( this ).wrapAll( isFunction ? html.call(this, i) : html );
+ });
+ },
+
+ unwrap: function() {
+ return this.parent().each(function() {
+ if ( !jQuery.nodeName( this, "body" ) ) {
+ jQuery( this ).replaceWith( this.childNodes );
+ }
+ }).end();
+ },
+
+ append: function() {
+ return this.domManip(arguments, true, function( elem ) {
+ if ( this.nodeType === 1 || this.nodeType === 11 ) {
+ this.appendChild( elem );
+ }
+ });
+ },
+
+ prepend: function() {
+ return this.domManip(arguments, true, function( elem ) {
+ if ( this.nodeType === 1 || this.nodeType === 11 ) {
+ this.insertBefore( elem, this.firstChild );
+ }
+ });
+ },
+
+ before: function() {
+ if ( !isDisconnected( this[0] ) ) {
+ return this.domManip(arguments, false, function( elem ) {
+ this.parentNode.insertBefore( elem, this );
+ });
+ }
+
+ if ( arguments.length ) {
+ var set = jQuery.clean( arguments );
+ return this.pushStack( jQuery.merge( set, this ), "before", this.selector );
+ }
+ },
+
+ after: function() {
+ if ( !isDisconnected( this[0] ) ) {
+ return this.domManip(arguments, false, function( elem ) {
+ this.parentNode.insertBefore( elem, this.nextSibling );
+ });
+ }
+
+ if ( arguments.length ) {
+ var set = jQuery.clean( arguments );
+ return this.pushStack( jQuery.merge( this, set ), "after", this.selector );
+ }
+ },
+
+ // keepData is for internal use only--do not document
+ remove: function( selector, keepData ) {
+ var elem,
+ i = 0;
+
+ for ( ; (elem = this[i]) != null; i++ ) {
+ if ( !selector || jQuery.filter( selector, [ elem ] ).length ) {
+ if ( !keepData && elem.nodeType === 1 ) {
+ jQuery.cleanData( elem.getElementsByTagName("*") );
+ jQuery.cleanData( [ elem ] );
+ }
+
+ if ( elem.parentNode ) {
+ elem.parentNode.removeChild( elem );
+ }
+ }
+ }
+
+ return this;
+ },
+
+ empty: function() {
+ var elem,
+ i = 0;
+
+ for ( ; (elem = this[i]) != null; i++ ) {
+ // Remove element nodes and prevent memory leaks
+ if ( elem.nodeType === 1 ) {
+ jQuery.cleanData( elem.getElementsByTagName("*") );
+ }
+
+ // Remove any remaining nodes
+ while ( elem.firstChild ) {
+ elem.removeChild( elem.firstChild );
+ }
+ }
+
+ return this;
+ },
+
+ clone: function( dataAndEvents, deepDataAndEvents ) {
+ dataAndEvents = dataAndEvents == null ? false : dataAndEvents;
+ deepDataAndEvents = deepDataAndEvents == null ? dataAndEvents : deepDataAndEvents;
+
+ return this.map( function () {
+ return jQuery.clone( this, dataAndEvents, deepDataAndEvents );
+ });
+ },
+
+ html: function( value ) {
+ return jQuery.access( this, function( value ) {
+ var elem = this[0] || {},
+ i = 0,
+ l = this.length;
+
+ if ( value === undefined ) {
+ return elem.nodeType === 1 ?
+ elem.innerHTML.replace( rinlinejQuery, "" ) :
+ undefined;
+ }
+
+ // See if we can take a shortcut and just use innerHTML
+ if ( typeof value === "string" && !rnoInnerhtml.test( value ) &&
+ ( jQuery.support.htmlSerialize || !rnoshimcache.test( value ) ) &&
+ ( jQuery.support.leadingWhitespace || !rleadingWhitespace.test( value ) ) &&
+ !wrapMap[ ( rtagName.exec( value ) || ["", ""] )[1].toLowerCase() ] ) {
+
+ value = value.replace( rxhtmlTag, "<$1></$2>" );
+
+ try {
+ for (; i < l; i++ ) {
+ // Remove element nodes and prevent memory leaks
+ elem = this[i] || {};
+ if ( elem.nodeType === 1 ) {
+ jQuery.cleanData( elem.getElementsByTagName( "*" ) );
+ elem.innerHTML = value;
+ }
+ }
+
+ elem = 0;
+
+ // If using innerHTML throws an exception, use the fallback method
+ } catch(e) {}
+ }
+
+ if ( elem ) {
+ this.empty().append( value );
+ }
+ }, null, value, arguments.length );
+ },
+
+ replaceWith: function( value ) {
+ if ( !isDisconnected( this[0] ) ) {
+ // Make sure that the elements are removed from the DOM before they are inserted
+ // this can help fix replacing a parent with child elements
+ if ( jQuery.isFunction( value ) ) {
+ return this.each(function(i) {
+ var self = jQuery(this), old = self.html();
+ self.replaceWith( value.call( this, i, old ) );
+ });
+ }
+
+ if ( typeof value !== "string" ) {
+ value = jQuery( value ).detach();
+ }
+
+ return this.each(function() {
+ var next = this.nextSibling,
+ parent = this.parentNode;
+
+ jQuery( this ).remove();
+
+ if ( next ) {
+ jQuery(next).before( value );
+ } else {
+ jQuery(parent).append( value );
+ }
+ });
+ }
+
+ return this.length ?
+ this.pushStack( jQuery(jQuery.isFunction(value) ? value() : value), "replaceWith", value ) :
+ this;
+ },
+
+ detach: function( selector ) {
+ return this.remove( selector, true );
+ },
+
+ domManip: function( args, table, callback ) {
+
+ // Flatten any nested arrays
+ args = [].concat.apply( [], args );
+
+ var results, first, fragment, iNoClone,
+ i = 0,
+ value = args[0],
+ scripts = [],
+ l = this.length;
+
+ // We can't cloneNode fragments that contain checked, in WebKit
+ if ( !jQuery.support.checkClone && l > 1 && typeof value === "string" && rchecked.test( value ) ) {
+ return this.each(function() {
+ jQuery(this).domManip( args, table, callback );
+ });
+ }
+
+ if ( jQuery.isFunction(value) ) {
+ return this.each(function(i) {
+ var self = jQuery(this);
+ args[0] = value.call( this, i, table ? self.html() : undefined );
+ self.domManip( args, table, callback );
+ });
+ }
+
+ if ( this[0] ) {
+ results = jQuery.buildFragment( args, this, scripts );
+ fragment = results.fragment;
+ first = fragment.firstChild;
+
+ if ( fragment.childNodes.length === 1 ) {
+ fragment = first;
+ }
+
+ if ( first ) {
+ table = table && jQuery.nodeName( first, "tr" );
+
+ // Use the original fragment for the last item instead of the first because it can end up
+ // being emptied incorrectly in certain situations (#8070).
+ // Fragments from the fragment cache must always be cloned and never used in place.
+ for ( iNoClone = results.cacheable || l - 1; i < l; i++ ) {
+ callback.call(
+ table && jQuery.nodeName( this[i], "table" ) ?
+ findOrAppend( this[i], "tbody" ) :
+ this[i],
+ i === iNoClone ?
+ fragment :
+ jQuery.clone( fragment, true, true )
+ );
+ }
+ }
+
+ // Fix #11809: Avoid leaking memory
+ fragment = first = null;
+
+ if ( scripts.length ) {
+ jQuery.each( scripts, function( i, elem ) {
+ if ( elem.src ) {
+ if ( jQuery.ajax ) {
+ jQuery.ajax({
+ url: elem.src,
+ type: "GET",
+ dataType: "script",
+ async: false,
+ global: false,
+ "throws": true
+ });
+ } else {
+ jQuery.error("no ajax");
+ }
+ } else {
+ jQuery.globalEval( ( elem.text || elem.textContent || elem.innerHTML || "" ).replace( rcleanScript, "" ) );
+ }
+
+ if ( elem.parentNode ) {
+ elem.parentNode.removeChild( elem );
+ }
+ });
+ }
+ }
+
+ return this;
+ }
+});
+
+function findOrAppend( elem, tag ) {
+ return elem.getElementsByTagName( tag )[0] || elem.appendChild( elem.ownerDocument.createElement( tag ) );
+}
+
+function cloneCopyEvent( src, dest ) {
+
+ if ( dest.nodeType !== 1 || !jQuery.hasData( src ) ) {
+ return;
+ }
+
+ var type, i, l,
+ oldData = jQuery._data( src ),
+ curData = jQuery._data( dest, oldData ),
+ events = oldData.events;
+
+ if ( events ) {
+ delete curData.handle;
+ curData.events = {};
+
+ for ( type in events ) {
+ for ( i = 0, l = events[ type ].length; i < l; i++ ) {
+ jQuery.event.add( dest, type, events[ type ][ i ] );
+ }
+ }
+ }
+
+ // make the cloned public data object a copy from the original
+ if ( curData.data ) {
+ curData.data = jQuery.extend( {}, curData.data );
+ }
+}
+
+function cloneFixAttributes( src, dest ) {
+ var nodeName;
+
+ // We do not need to do anything for non-Elements
+ if ( dest.nodeType !== 1 ) {
+ return;
+ }
+
+ // clearAttributes removes the attributes, which we don't want,
+ // but also removes the attachEvent events, which we *do* want
+ if ( dest.clearAttributes ) {
+ dest.clearAttributes();
+ }
+
+ // mergeAttributes, in contrast, only merges back on the
+ // original attributes, not the events
+ if ( dest.mergeAttributes ) {
+ dest.mergeAttributes( src );
+ }
+
+ nodeName = dest.nodeName.toLowerCase();
+
+ if ( nodeName === "object" ) {
+ // IE6-10 improperly clones children of object elements using classid.
+ // IE10 throws NoModificationAllowedError if parent is null, #12132.
+ if ( dest.parentNode ) {
+ dest.outerHTML = src.outerHTML;
+ }
+
+ // This path appears unavoidable for IE9. When cloning an object
+ // element in IE9, the outerHTML strategy above is not sufficient.
+ // If the src has innerHTML and the destination does not,
+ // copy the src.innerHTML into the dest.innerHTML. #10324
+ if ( jQuery.support.html5Clone && (src.innerHTML && !jQuery.trim(dest.innerHTML)) ) {
+ dest.innerHTML = src.innerHTML;
+ }
+
+ } else if ( nodeName === "input" && rcheckableType.test( src.type ) ) {
+ // IE6-8 fails to persist the checked state of a cloned checkbox
+ // or radio button. Worse, IE6-7 fail to give the cloned element
+ // a checked appearance if the defaultChecked value isn't also set
+
+ dest.defaultChecked = dest.checked = src.checked;
+
+ // IE6-7 get confused and end up setting the value of a cloned
+ // checkbox/radio button to an empty string instead of "on"
+ if ( dest.value !== src.value ) {
+ dest.value = src.value;
+ }
+
+ // IE6-8 fails to return the selected option to the default selected
+ // state when cloning options
+ } else if ( nodeName === "option" ) {
+ dest.selected = src.defaultSelected;
+
+ // IE6-8 fails to set the defaultValue to the correct value when
+ // cloning other types of input fields
+ } else if ( nodeName === "input" || nodeName === "textarea" ) {
+ dest.defaultValue = src.defaultValue;
+
+ // IE blanks contents when cloning scripts
+ } else if ( nodeName === "script" && dest.text !== src.text ) {
+ dest.text = src.text;
+ }
+
+ // Event data gets referenced instead of copied if the expando
+ // gets copied too
+ dest.removeAttribute( jQuery.expando );
+}
+
+jQuery.buildFragment = function( args, context, scripts ) {
+ var fragment, cacheable, cachehit,
+ first = args[ 0 ];
+
+ // Set context from what may come in as undefined or a jQuery collection or a node
+ // Updated to fix #12266 where accessing context[0] could throw an exception in IE9/10 &
+ // also doubles as fix for #8950 where plain objects caused createDocumentFragment exception
+ context = context || document;
+ context = !context.nodeType && context[0] || context;
+ context = context.ownerDocument || context;
+
+ // Only cache "small" (1/2 KB) HTML strings that are associated with the main document
+ // Cloning options loses the selected state, so don't cache them
+ // IE 6 doesn't like it when you put <object> or <embed> elements in a fragment
+ // Also, WebKit does not clone 'checked' attributes on cloneNode, so don't cache
+ // Lastly, IE6,7,8 will not correctly reuse cached fragments that were created from unknown elems #10501
+ if ( args.length === 1 && typeof first === "string" && first.length < 512 && context === document &&
+ first.charAt(0) === "<" && !rnocache.test( first ) &&
+ (jQuery.support.checkClone || !rchecked.test( first )) &&
+ (jQuery.support.html5Clone || !rnoshimcache.test( first )) ) {
+
+ // Mark cacheable and look for a hit
+ cacheable = true;
+ fragment = jQuery.fragments[ first ];
+ cachehit = fragment !== undefined;
+ }
+
+ if ( !fragment ) {
+ fragment = context.createDocumentFragment();
+ jQuery.clean( args, context, fragment, scripts );
+
+ // Update the cache, but only store false
+ // unless this is a second parsing of the same content
+ if ( cacheable ) {
+ jQuery.fragments[ first ] = cachehit && fragment;
+ }
+ }
+
+ return { fragment: fragment, cacheable: cacheable };
+};
+
+jQuery.fragments = {};
+
+jQuery.each({
+ appendTo: "append",
+ prependTo: "prepend",
+ insertBefore: "before",
+ insertAfter: "after",
+ replaceAll: "replaceWith"
+}, function( name, original ) {
+ jQuery.fn[ name ] = function( selector ) {
+ var elems,
+ i = 0,
+ ret = [],
+ insert = jQuery( selector ),
+ l = insert.length,
+ parent = this.length === 1 && this[0].parentNode;
+
+ if ( (parent == null || parent && parent.nodeType === 11 && parent.childNodes.length === 1) && l === 1 ) {
+ insert[ original ]( this[0] );
+ return this;
+ } else {
+ for ( ; i < l; i++ ) {
+ elems = ( i > 0 ? this.clone(true) : this ).get();
+ jQuery( insert[i] )[ original ]( elems );
+ ret = ret.concat( elems );
+ }
+
+ return this.pushStack( ret, name, insert.selector );
+ }
+ };
+});
+
+function getAll( elem ) {
+ if ( typeof elem.getElementsByTagName !== "undefined" ) {
+ return elem.getElementsByTagName( "*" );
+
+ } else if ( typeof elem.querySelectorAll !== "undefined" ) {
+ return elem.querySelectorAll( "*" );
+
+ } else {
+ return [];
+ }
+}
+
+// Used in clean, fixes the defaultChecked property
+function fixDefaultChecked( elem ) {
+ if ( rcheckableType.test( elem.type ) ) {
+ elem.defaultChecked = elem.checked;
+ }
+}
+
+jQuery.extend({
+ clone: function( elem, dataAndEvents, deepDataAndEvents ) {
+ var srcElements,
+ destElements,
+ i,
+ clone;
+
+ if ( jQuery.support.html5Clone || jQuery.isXMLDoc(elem) || !rnoshimcache.test( "<" + elem.nodeName + ">" ) ) {
+ clone = elem.cloneNode( true );
+
+ // IE<=8 does not properly clone detached, unknown element nodes
+ } else {
+ fragmentDiv.innerHTML = elem.outerHTML;
+ fragmentDiv.removeChild( clone = fragmentDiv.firstChild );
+ }
+
+ if ( (!jQuery.support.noCloneEvent || !jQuery.support.noCloneChecked) &&
+ (elem.nodeType === 1 || elem.nodeType === 11) && !jQuery.isXMLDoc(elem) ) {
+ // IE copies events bound via attachEvent when using cloneNode.
+ // Calling detachEvent on the clone will also remove the events
+ // from the original. In order to get around this, we use some
+ // proprietary methods to clear the events. Thanks to MooTools
+ // guys for this hotness.
+
+ cloneFixAttributes( elem, clone );
+
+ // Using Sizzle here is crazy slow, so we use getElementsByTagName instead
+ srcElements = getAll( elem );
+ destElements = getAll( clone );
+
+ // Weird iteration because IE will replace the length property
+ // with an element if you are cloning the body and one of the
+ // elements on the page has a name or id of "length"
+ for ( i = 0; srcElements[i]; ++i ) {
+ // Ensure that the destination node is not null; Fixes #9587
+ if ( destElements[i] ) {
+ cloneFixAttributes( srcElements[i], destElements[i] );
+ }
+ }
+ }
+
+ // Copy the events from the original to the clone
+ if ( dataAndEvents ) {
+ cloneCopyEvent( elem, clone );
+
+ if ( deepDataAndEvents ) {
+ srcElements = getAll( elem );
+ destElements = getAll( clone );
+
+ for ( i = 0; srcElements[i]; ++i ) {
+ cloneCopyEvent( srcElements[i], destElements[i] );
+ }
+ }
+ }
+
+ srcElements = destElements = null;
+
+ // Return the cloned set
+ return clone;
+ },
+
+ clean: function( elems, context, fragment, scripts ) {
+ var i, j, elem, tag, wrap, depth, div, hasBody, tbody, len, handleScript, jsTags,
+ safe = context === document && safeFragment,
+ ret = [];
+
+ // Ensure that context is a document
+ if ( !context || typeof context.createDocumentFragment === "undefined" ) {
+ context = document;
+ }
+
+ // Use the already-created safe fragment if context permits
+ for ( i = 0; (elem = elems[i]) != null; i++ ) {
+ if ( typeof elem === "number" ) {
+ elem += "";
+ }
+
+ if ( !elem ) {
+ continue;
+ }
+
+ // Convert html string into DOM nodes
+ if ( typeof elem === "string" ) {
+ if ( !rhtml.test( elem ) ) {
+ elem = context.createTextNode( elem );
+ } else {
+ // Ensure a safe container in which to render the html
+ safe = safe || createSafeFragment( context );
+ div = context.createElement("div");
+ safe.appendChild( div );
+
+ // Fix "XHTML"-style tags in all browsers
+ elem = elem.replace(rxhtmlTag, "<$1></$2>");
+
+ // Go to html and back, then peel off extra wrappers
+ tag = ( rtagName.exec( elem ) || ["", ""] )[1].toLowerCase();
+ wrap = wrapMap[ tag ] || wrapMap._default;
+ depth = wrap[0];
+ div.innerHTML = wrap[1] + elem + wrap[2];
+
+ // Move to the right depth
+ while ( depth-- ) {
+ div = div.lastChild;
+ }
+
+ // Remove IE's autoinserted <tbody> from table fragments
+ if ( !jQuery.support.tbody ) {
+
+ // String was a <table>, *may* have spurious <tbody>
+ hasBody = rtbody.test(elem);
+ tbody = tag === "table" && !hasBody ?
+ div.firstChild && div.firstChild.childNodes :
+
+ // String was a bare <thead> or <tfoot>
+ wrap[1] === "<table>" && !hasBody ?
+ div.childNodes :
+ [];
+
+ for ( j = tbody.length - 1; j >= 0 ; --j ) {
+ if ( jQuery.nodeName( tbody[ j ], "tbody" ) && !tbody[ j ].childNodes.length ) {
+ tbody[ j ].parentNode.removeChild( tbody[ j ] );
+ }
+ }
+ }
+
+ // IE completely kills leading whitespace when innerHTML is used
+ if ( !jQuery.support.leadingWhitespace && rleadingWhitespace.test( elem ) ) {
+ div.insertBefore( context.createTextNode( rleadingWhitespace.exec(elem)[0] ), div.firstChild );
+ }
+
+ elem = div.childNodes;
+
+ // Take out of fragment container (we need a fresh div each time)
+ div.parentNode.removeChild( div );
+ }
+ }
+
+ if ( elem.nodeType ) {
+ ret.push( elem );
+ } else {
+ jQuery.merge( ret, elem );
+ }
+ }
+
+ // Fix #11356: Clear elements from safeFragment
+ if ( div ) {
+ elem = div = safe = null;
+ }
+
+ // Reset defaultChecked for any radios and checkboxes
+ // about to be appended to the DOM in IE 6/7 (#8060)
+ if ( !jQuery.support.appendChecked ) {
+ for ( i = 0; (elem = ret[i]) != null; i++ ) {
+ if ( jQuery.nodeName( elem, "input" ) ) {
+ fixDefaultChecked( elem );
+ } else if ( typeof elem.getElementsByTagName !== "undefined" ) {
+ jQuery.grep( elem.getElementsByTagName("input"), fixDefaultChecked );
+ }
+ }
+ }
+
+ // Append elements to a provided document fragment
+ if ( fragment ) {
+ // Special handling of each script element
+ handleScript = function( elem ) {
+ // Check if we consider it executable
+ if ( !elem.type || rscriptType.test( elem.type ) ) {
+ // Detach the script and store it in the scripts array (if provided) or the fragment
+ // Return truthy to indicate that it has been handled
+ return scripts ?
+ scripts.push( elem.parentNode ? elem.parentNode.removeChild( elem ) : elem ) :
+ fragment.appendChild( elem );
+ }
+ };
+
+ for ( i = 0; (elem = ret[i]) != null; i++ ) {
+ // Check if we're done after handling an executable script
+ if ( !( jQuery.nodeName( elem, "script" ) && handleScript( elem ) ) ) {
+ // Append to fragment and handle embedded scripts
+ fragment.appendChild( elem );
+ if ( typeof elem.getElementsByTagName !== "undefined" ) {
+ // handleScript alters the DOM, so use jQuery.merge to ensure snapshot iteration
+ jsTags = jQuery.grep( jQuery.merge( [], elem.getElementsByTagName("script") ), handleScript );
+
+ // Splice the scripts into ret after their former ancestor and advance our index beyond them
+ ret.splice.apply( ret, [i + 1, 0].concat( jsTags ) );
+ i += jsTags.length;
+ }
+ }
+ }
+ }
+
+ return ret;
+ },
+
+ cleanData: function( elems, /* internal */ acceptData ) {
+ var data, id, elem, type,
+ i = 0,
+ internalKey = jQuery.expando,
+ cache = jQuery.cache,
+ deleteExpando = jQuery.support.deleteExpando,
+ special = jQuery.event.special;
+
+ for ( ; (elem = elems[i]) != null; i++ ) {
+
+ if ( acceptData || jQuery.acceptData( elem ) ) {
+
+ id = elem[ internalKey ];
+ data = id && cache[ id ];
+
+ if ( data ) {
+ if ( data.events ) {
+ for ( type in data.events ) {
+ if ( special[ type ] ) {
+ jQuery.event.remove( elem, type );
+
+ // This is a shortcut to avoid jQuery.event.remove's overhead
+ } else {
+ jQuery.removeEvent( elem, type, data.handle );
+ }
+ }
+ }
+
+ // Remove cache only if it was not already removed by jQuery.event.remove
+ if ( cache[ id ] ) {
+
+ delete cache[ id ];
+
+ // IE does not allow us to delete expando properties from nodes,
+ // nor does it have a removeAttribute function on Document nodes;
+ // we must handle all of these cases
+ if ( deleteExpando ) {
+ delete elem[ internalKey ];
+
+ } else if ( elem.removeAttribute ) {
+ elem.removeAttribute( internalKey );
+
+ } else {
+ elem[ internalKey ] = null;
+ }
+
+ jQuery.deletedIds.push( id );
+ }
+ }
+ }
+ }
+ }
+});
+// Limit scope pollution from any deprecated API
+(function() {
+
+var matched, browser;
+
+// Use of jQuery.browser is frowned upon.
+// More details: http://api.jquery.com/jQuery.browser
+// jQuery.uaMatch maintained for back-compat
+jQuery.uaMatch = function( ua ) {
+ ua = ua.toLowerCase();
+
+ var match = /(chrome)[ \/]([\w.]+)/.exec( ua ) ||
+ /(webkit)[ \/]([\w.]+)/.exec( ua ) ||
+ /(opera)(?:.*version|)[ \/]([\w.]+)/.exec( ua ) ||
+ /(msie) ([\w.]+)/.exec( ua ) ||
+ ua.indexOf("compatible") < 0 && /(mozilla)(?:.*? rv:([\w.]+)|)/.exec( ua ) ||
+ [];
+
+ return {
+ browser: match[ 1 ] || "",
+ version: match[ 2 ] || "0"
+ };
+};
+
+matched = jQuery.uaMatch( navigator.userAgent );
+browser = {};
+
+if ( matched.browser ) {
+ browser[ matched.browser ] = true;
+ browser.version = matched.version;
+}
+
+// Chrome is Webkit, but Webkit is also Safari.
+if ( browser.chrome ) {
+ browser.webkit = true;
+} else if ( browser.webkit ) {
+ browser.safari = true;
+}
+
+jQuery.browser = browser;
+
+jQuery.sub = function() {
+ function jQuerySub( selector, context ) {
+ return new jQuerySub.fn.init( selector, context );
+ }
+ jQuery.extend( true, jQuerySub, this );
+ jQuerySub.superclass = this;
+ jQuerySub.fn = jQuerySub.prototype = this();
+ jQuerySub.fn.constructor = jQuerySub;
+ jQuerySub.sub = this.sub;
+ jQuerySub.fn.init = function init( selector, context ) {
+ if ( context && context instanceof jQuery && !(context instanceof jQuerySub) ) {
+ context = jQuerySub( context );
+ }
+
+ return jQuery.fn.init.call( this, selector, context, rootjQuerySub );
+ };
+ jQuerySub.fn.init.prototype = jQuerySub.fn;
+ var rootjQuerySub = jQuerySub(document);
+ return jQuerySub;
+};
+
+})();
+var curCSS, iframe, iframeDoc,
+ ralpha = /alpha\([^)]*\)/i,
+ ropacity = /opacity=([^)]*)/,
+ rposition = /^(top|right|bottom|left)$/,
+ // swappable if display is none or starts with table except "table", "table-cell", or "table-caption"
+ // see here for display values: https://developer.mozilla.org/en-US/docs/CSS/display
+ rdisplayswap = /^(none|table(?!-c[ea]).+)/,
+ rmargin = /^margin/,
+ rnumsplit = new RegExp( "^(" + core_pnum + ")(.*)$", "i" ),
+ rnumnonpx = new RegExp( "^(" + core_pnum + ")(?!px)[a-z%]+$", "i" ),
+ rrelNum = new RegExp( "^([-+])=(" + core_pnum + ")", "i" ),
+ elemdisplay = { BODY: "block" },
+
+ cssShow = { position: "absolute", visibility: "hidden", display: "block" },
+ cssNormalTransform = {
+ letterSpacing: 0,
+ fontWeight: 400
+ },
+
+ cssExpand = [ "Top", "Right", "Bottom", "Left" ],
+ cssPrefixes = [ "Webkit", "O", "Moz", "ms" ],
+
+ eventsToggle = jQuery.fn.toggle;
+
+// return a css property mapped to a potentially vendor prefixed property
+function vendorPropName( style, name ) {
+
+ // shortcut for names that are not vendor prefixed
+ if ( name in style ) {
+ return name;
+ }
+
+ // check for vendor prefixed names
+ var capName = name.charAt(0).toUpperCase() + name.slice(1),
+ origName = name,
+ i = cssPrefixes.length;
+
+ while ( i-- ) {
+ name = cssPrefixes[ i ] + capName;
+ if ( name in style ) {
+ return name;
+ }
+ }
+
+ return origName;
+}
+
+function isHidden( elem, el ) {
+ elem = el || elem;
+ return jQuery.css( elem, "display" ) === "none" || !jQuery.contains( elem.ownerDocument, elem );
+}
+
+function showHide( elements, show ) {
+ var elem, display,
+ values = [],
+ index = 0,
+ length = elements.length;
+
+ for ( ; index < length; index++ ) {
+ elem = elements[ index ];
+ if ( !elem.style ) {
+ continue;
+ }
+ values[ index ] = jQuery._data( elem, "olddisplay" );
+ if ( show ) {
+ // Reset the inline display of this element to learn if it is
+ // being hidden by cascaded rules or not
+ if ( !values[ index ] && elem.style.display === "none" ) {
+ elem.style.display = "";
+ }
+
+ // Set elements which have been overridden with display: none
+ // in a stylesheet to whatever the default browser style is
+ // for such an element
+ if ( elem.style.display === "" && isHidden( elem ) ) {
+ values[ index ] = jQuery._data( elem, "olddisplay", css_defaultDisplay(elem.nodeName) );
+ }
+ } else {
+ display = curCSS( elem, "display" );
+
+ if ( !values[ index ] && display !== "none" ) {
+ jQuery._data( elem, "olddisplay", display );
+ }
+ }
+ }
+
+ // Set the display of most of the elements in a second loop
+ // to avoid the constant reflow
+ for ( index = 0; index < length; index++ ) {
+ elem = elements[ index ];
+ if ( !elem.style ) {
+ continue;
+ }
+ if ( !show || elem.style.display === "none" || elem.style.display === "" ) {
+ elem.style.display = show ? values[ index ] || "" : "none";
+ }
+ }
+
+ return elements;
+}
+
+jQuery.fn.extend({
+ css: function( name, value ) {
+ return jQuery.access( this, function( elem, name, value ) {
+ return value !== undefined ?
+ jQuery.style( elem, name, value ) :
+ jQuery.css( elem, name );
+ }, name, value, arguments.length > 1 );
+ },
+ show: function() {
+ return showHide( this, true );
+ },
+ hide: function() {
+ return showHide( this );
+ },
+ toggle: function( state, fn2 ) {
+ var bool = typeof state === "boolean";
+
+ if ( jQuery.isFunction( state ) && jQuery.isFunction( fn2 ) ) {
+ return eventsToggle.apply( this, arguments );
+ }
+
+ return this.each(function() {
+ if ( bool ? state : isHidden( this ) ) {
+ jQuery( this ).show();
+ } else {
+ jQuery( this ).hide();
+ }
+ });
+ }
+});
+
+jQuery.extend({
+ // Add in style property hooks for overriding the default
+ // behavior of getting and setting a style property
+ cssHooks: {
+ opacity: {
+ get: function( elem, computed ) {
+ if ( computed ) {
+ // We should always get a number back from opacity
+ var ret = curCSS( elem, "opacity" );
+ return ret === "" ? "1" : ret;
+
+ }
+ }
+ }
+ },
+
+ // Exclude the following css properties to add px
+ cssNumber: {
+ "fillOpacity": true,
+ "fontWeight": true,
+ "lineHeight": true,
+ "opacity": true,
+ "orphans": true,
+ "widows": true,
+ "zIndex": true,
+ "zoom": true
+ },
+
+ // Add in properties whose names you wish to fix before
+ // setting or getting the value
+ cssProps: {
+ // normalize float css property
+ "float": jQuery.support.cssFloat ? "cssFloat" : "styleFloat"
+ },
+
+ // Get and set the style property on a DOM Node
+ style: function( elem, name, value, extra ) {
+ // Don't set styles on text and comment nodes
+ if ( !elem || elem.nodeType === 3 || elem.nodeType === 8 || !elem.style ) {
+ return;
+ }
+
+ // Make sure that we're working with the right name
+ var ret, type, hooks,
+ origName = jQuery.camelCase( name ),
+ style = elem.style;
+
+ name = jQuery.cssProps[ origName ] || ( jQuery.cssProps[ origName ] = vendorPropName( style, origName ) );
+
+ // gets hook for the prefixed version
+ // followed by the unprefixed version
+ hooks = jQuery.cssHooks[ name ] || jQuery.cssHooks[ origName ];
+
+ // Check if we're setting a value
+ if ( value !== undefined ) {
+ type = typeof value;
+
+ // convert relative number strings (+= or -=) to relative numbers. #7345
+ if ( type === "string" && (ret = rrelNum.exec( value )) ) {
+ value = ( ret[1] + 1 ) * ret[2] + parseFloat( jQuery.css( elem, name ) );
+ // Fixes bug #9237
+ type = "number";
+ }
+
+ // Make sure that NaN and null values aren't set. See: #7116
+ if ( value == null || type === "number" && isNaN( value ) ) {
+ return;
+ }
+
+ // If a number was passed in, add 'px' to the (except for certain CSS properties)
+ if ( type === "number" && !jQuery.cssNumber[ origName ] ) {
+ value += "px";
+ }
+
+ // If a hook was provided, use that value, otherwise just set the specified value
+ if ( !hooks || !("set" in hooks) || (value = hooks.set( elem, value, extra )) !== undefined ) {
+ // Wrapped to prevent IE from throwing errors when 'invalid' values are provided
+ // Fixes bug #5509
+ try {
+ style[ name ] = value;
+ } catch(e) {}
+ }
+
+ } else {
+ // If a hook was provided get the non-computed value from there
+ if ( hooks && "get" in hooks && (ret = hooks.get( elem, false, extra )) !== undefined ) {
+ return ret;
+ }
+
+ // Otherwise just get the value from the style object
+ return style[ name ];
+ }
+ },
+
+ css: function( elem, name, numeric, extra ) {
+ var val, num, hooks,
+ origName = jQuery.camelCase( name );
+
+ // Make sure that we're working with the right name
+ name = jQuery.cssProps[ origName ] || ( jQuery.cssProps[ origName ] = vendorPropName( elem.style, origName ) );
+
+ // gets hook for the prefixed version
+ // followed by the unprefixed version
+ hooks = jQuery.cssHooks[ name ] || jQuery.cssHooks[ origName ];
+
+ // If a hook was provided get the computed value from there
+ if ( hooks && "get" in hooks ) {
+ val = hooks.get( elem, true, extra );
+ }
+
+ // Otherwise, if a way to get the computed value exists, use that
+ if ( val === undefined ) {
+ val = curCSS( elem, name );
+ }
+
+ //convert "normal" to computed value
+ if ( val === "normal" && name in cssNormalTransform ) {
+ val = cssNormalTransform[ name ];
+ }
+
+ // Return, converting to number if forced or a qualifier was provided and val looks numeric
+ if ( numeric || extra !== undefined ) {
+ num = parseFloat( val );
+ return numeric || jQuery.isNumeric( num ) ? num || 0 : val;
+ }
+ return val;
+ },
+
+ // A method for quickly swapping in/out CSS properties to get correct calculations
+ swap: function( elem, options, callback ) {
+ var ret, name,
+ old = {};
+
+ // Remember the old values, and insert the new ones
+ for ( name in options ) {
+ old[ name ] = elem.style[ name ];
+ elem.style[ name ] = options[ name ];
+ }
+
+ ret = callback.call( elem );
+
+ // Revert the old values
+ for ( name in options ) {
+ elem.style[ name ] = old[ name ];
+ }
+
+ return ret;
+ }
+});
+
+// NOTE: To any future maintainer, we've window.getComputedStyle
+// because jsdom on node.js will break without it.
+if ( window.getComputedStyle ) {
+ curCSS = function( elem, name ) {
+ var ret, width, minWidth, maxWidth,
+ computed = window.getComputedStyle( elem, null ),
+ style = elem.style;
+
+ if ( computed ) {
+
+ // getPropertyValue is only needed for .css('filter') in IE9, see #12537
+ ret = computed.getPropertyValue( name ) || computed[ name ];
+
+ if ( ret === "" && !jQuery.contains( elem.ownerDocument, elem ) ) {
+ ret = jQuery.style( elem, name );
+ }
+
+ // A tribute to the "awesome hack by Dean Edwards"
+ // Chrome < 17 and Safari 5.0 uses "computed value" instead of "used value" for margin-right
+ // Safari 5.1.7 (at least) returns percentage for a larger set of values, but width seems to be reliably pixels
+ // this is against the CSSOM draft spec: http://dev.w3.org/csswg/cssom/#resolved-values
+ if ( rnumnonpx.test( ret ) && rmargin.test( name ) ) {
+ width = style.width;
+ minWidth = style.minWidth;
+ maxWidth = style.maxWidth;
+
+ style.minWidth = style.maxWidth = style.width = ret;
+ ret = computed.width;
+
+ style.width = width;
+ style.minWidth = minWidth;
+ style.maxWidth = maxWidth;
+ }
+ }
+
+ return ret;
+ };
+} else if ( document.documentElement.currentStyle ) {
+ curCSS = function( elem, name ) {
+ var left, rsLeft,
+ ret = elem.currentStyle && elem.currentStyle[ name ],
+ style = elem.style;
+
+ // Avoid setting ret to empty string here
+ // so we don't default to auto
+ if ( ret == null && style && style[ name ] ) {
+ ret = style[ name ];
+ }
+
+ // From the awesome hack by Dean Edwards
+ // http://erik.eae.net/archives/2007/07/27/18.54.15/#comment-102291
+
+ // If we're not dealing with a regular pixel number
+ // but a number that has a weird ending, we need to convert it to pixels
+ // but not position css attributes, as those are proportional to the parent element instead
+ // and we can't measure the parent instead because it might trigger a "stacking dolls" problem
+ if ( rnumnonpx.test( ret ) && !rposition.test( name ) ) {
+
+ // Remember the original values
+ left = style.left;
+ rsLeft = elem.runtimeStyle && elem.runtimeStyle.left;
+
+ // Put in the new values to get a computed value out
+ if ( rsLeft ) {
+ elem.runtimeStyle.left = elem.currentStyle.left;
+ }
+ style.left = name === "fontSize" ? "1em" : ret;
+ ret = style.pixelLeft + "px";
+
+ // Revert the changed values
+ style.left = left;
+ if ( rsLeft ) {
+ elem.runtimeStyle.left = rsLeft;
+ }
+ }
+
+ return ret === "" ? "auto" : ret;
+ };
+}
+
+function setPositiveNumber( elem, value, subtract ) {
+ var matches = rnumsplit.exec( value );
+ return matches ?
+ Math.max( 0, matches[ 1 ] - ( subtract || 0 ) ) + ( matches[ 2 ] || "px" ) :
+ value;
+}
+
+function augmentWidthOrHeight( elem, name, extra, isBorderBox ) {
+ var i = extra === ( isBorderBox ? "border" : "content" ) ?
+ // If we already have the right measurement, avoid augmentation
+ 4 :
+ // Otherwise initialize for horizontal or vertical properties
+ name === "width" ? 1 : 0,
+
+ val = 0;
+
+ for ( ; i < 4; i += 2 ) {
+ // both box models exclude margin, so add it if we want it
+ if ( extra === "margin" ) {
+ // we use jQuery.css instead of curCSS here
+ // because of the reliableMarginRight CSS hook!
+ val += jQuery.css( elem, extra + cssExpand[ i ], true );
+ }
+
+ // From this point on we use curCSS for maximum performance (relevant in animations)
+ if ( isBorderBox ) {
+ // border-box includes padding, so remove it if we want content
+ if ( extra === "content" ) {
+ val -= parseFloat( curCSS( elem, "padding" + cssExpand[ i ] ) ) || 0;
+ }
+
+ // at this point, extra isn't border nor margin, so remove border
+ if ( extra !== "margin" ) {
+ val -= parseFloat( curCSS( elem, "border" + cssExpand[ i ] + "Width" ) ) || 0;
+ }
+ } else {
+ // at this point, extra isn't content, so add padding
+ val += parseFloat( curCSS( elem, "padding" + cssExpand[ i ] ) ) || 0;
+
+ // at this point, extra isn't content nor padding, so add border
+ if ( extra !== "padding" ) {
+ val += parseFloat( curCSS( elem, "border" + cssExpand[ i ] + "Width" ) ) || 0;
+ }
+ }
+ }
+
+ return val;
+}
+
+function getWidthOrHeight( elem, name, extra ) {
+
+ // Start with offset property, which is equivalent to the border-box value
+ var val = name === "width" ? elem.offsetWidth : elem.offsetHeight,
+ valueIsBorderBox = true,
+ isBorderBox = jQuery.support.boxSizing && jQuery.css( elem, "boxSizing" ) === "border-box";
+
+ // some non-html elements return undefined for offsetWidth, so check for null/undefined
+ // svg - https://bugzilla.mozilla.org/show_bug.cgi?id=649285
+ // MathML - https://bugzilla.mozilla.org/show_bug.cgi?id=491668
+ if ( val <= 0 || val == null ) {
+ // Fall back to computed then uncomputed css if necessary
+ val = curCSS( elem, name );
+ if ( val < 0 || val == null ) {
+ val = elem.style[ name ];
+ }
+
+ // Computed unit is not pixels. Stop here and return.
+ if ( rnumnonpx.test(val) ) {
+ return val;
+ }
+
+ // we need the check for style in case a browser which returns unreliable values
+ // for getComputedStyle silently falls back to the reliable elem.style
+ valueIsBorderBox = isBorderBox && ( jQuery.support.boxSizingReliable || val === elem.style[ name ] );
+
+ // Normalize "", auto, and prepare for extra
+ val = parseFloat( val ) || 0;
+ }
+
+ // use the active box-sizing model to add/subtract irrelevant styles
+ return ( val +
+ augmentWidthOrHeight(
+ elem,
+ name,
+ extra || ( isBorderBox ? "border" : "content" ),
+ valueIsBorderBox
+ )
+ ) + "px";
+}
+
+
+// Try to determine the default display value of an element
+function css_defaultDisplay( nodeName ) {
+ if ( elemdisplay[ nodeName ] ) {
+ return elemdisplay[ nodeName ];
+ }
+
+ var elem = jQuery( "<" + nodeName + ">" ).appendTo( document.body ),
+ display = elem.css("display");
+ elem.remove();
+
+ // If the simple way fails,
+ // get element's real default display by attaching it to a temp iframe
+ if ( display === "none" || display === "" ) {
+ // Use the already-created iframe if possible
+ iframe = document.body.appendChild(
+ iframe || jQuery.extend( document.createElement("iframe"), {
+ frameBorder: 0,
+ width: 0,
+ height: 0
+ })
+ );
+
+ // Create a cacheable copy of the iframe document on first call.
+ // IE and Opera will allow us to reuse the iframeDoc without re-writing the fake HTML
+ // document to it; WebKit & Firefox won't allow reusing the iframe document.
+ if ( !iframeDoc || !iframe.createElement ) {
+ iframeDoc = ( iframe.contentWindow || iframe.contentDocument ).document;
+ iframeDoc.write("<!doctype html><html><body>");
+ iframeDoc.close();
+ }
+
+ elem = iframeDoc.body.appendChild( iframeDoc.createElement(nodeName) );
+
+ display = curCSS( elem, "display" );
+ document.body.removeChild( iframe );
+ }
+
+ // Store the correct default display
+ elemdisplay[ nodeName ] = display;
+
+ return display;
+}
+
+jQuery.each([ "height", "width" ], function( i, name ) {
+ jQuery.cssHooks[ name ] = {
+ get: function( elem, computed, extra ) {
+ if ( computed ) {
+ // certain elements can have dimension info if we invisibly show them
+ // however, it must have a current display style that would benefit from this
+ if ( elem.offsetWidth === 0 && rdisplayswap.test( curCSS( elem, "display" ) ) ) {
+ return jQuery.swap( elem, cssShow, function() {
+ return getWidthOrHeight( elem, name, extra );
+ });
+ } else {
+ return getWidthOrHeight( elem, name, extra );
+ }
+ }
+ },
+
+ set: function( elem, value, extra ) {
+ return setPositiveNumber( elem, value, extra ?
+ augmentWidthOrHeight(
+ elem,
+ name,
+ extra,
+ jQuery.support.boxSizing && jQuery.css( elem, "boxSizing" ) === "border-box"
+ ) : 0
+ );
+ }
+ };
+});
+
+if ( !jQuery.support.opacity ) {
+ jQuery.cssHooks.opacity = {
+ get: function( elem, computed ) {
+ // IE uses filters for opacity
+ return ropacity.test( (computed && elem.currentStyle ? elem.currentStyle.filter : elem.style.filter) || "" ) ?
+ ( 0.01 * parseFloat( RegExp.$1 ) ) + "" :
+ computed ? "1" : "";
+ },
+
+ set: function( elem, value ) {
+ var style = elem.style,
+ currentStyle = elem.currentStyle,
+ opacity = jQuery.isNumeric( value ) ? "alpha(opacity=" + value * 100 + ")" : "",
+ filter = currentStyle && currentStyle.filter || style.filter || "";
+
+ // IE has trouble with opacity if it does not have layout
+ // Force it by setting the zoom level
+ style.zoom = 1;
+
+ // if setting opacity to 1, and no other filters exist - attempt to remove filter attribute #6652
+ if ( value >= 1 && jQuery.trim( filter.replace( ralpha, "" ) ) === "" &&
+ style.removeAttribute ) {
+
+ // Setting style.filter to null, "" & " " still leave "filter:" in the cssText
+ // if "filter:" is present at all, clearType is disabled, we want to avoid this
+ // style.removeAttribute is IE Only, but so apparently is this code path...
+ style.removeAttribute( "filter" );
+
+ // if there there is no filter style applied in a css rule, we are done
+ if ( currentStyle && !currentStyle.filter ) {
+ return;
+ }
+ }
+
+ // otherwise, set new filter values
+ style.filter = ralpha.test( filter ) ?
+ filter.replace( ralpha, opacity ) :
+ filter + " " + opacity;
+ }
+ };
+}
+
+// These hooks cannot be added until DOM ready because the support test
+// for it is not run until after DOM ready
+jQuery(function() {
+ if ( !jQuery.support.reliableMarginRight ) {
+ jQuery.cssHooks.marginRight = {
+ get: function( elem, computed ) {
+ // WebKit Bug 13343 - getComputedStyle returns wrong value for margin-right
+ // Work around by temporarily setting element display to inline-block
+ return jQuery.swap( elem, { "display": "inline-block" }, function() {
+ if ( computed ) {
+ return curCSS( elem, "marginRight" );
+ }
+ });
+ }
+ };
+ }
+
+ // Webkit bug: https://bugs.webkit.org/show_bug.cgi?id=29084
+ // getComputedStyle returns percent when specified for top/left/bottom/right
+ // rather than make the css module depend on the offset module, we just check for it here
+ if ( !jQuery.support.pixelPosition && jQuery.fn.position ) {
+ jQuery.each( [ "top", "left" ], function( i, prop ) {
+ jQuery.cssHooks[ prop ] = {
+ get: function( elem, computed ) {
+ if ( computed ) {
+ var ret = curCSS( elem, prop );
+ // if curCSS returns percentage, fallback to offset
+ return rnumnonpx.test( ret ) ? jQuery( elem ).position()[ prop ] + "px" : ret;
+ }
+ }
+ };
+ });
+ }
+
+});
+
+if ( jQuery.expr && jQuery.expr.filters ) {
+ jQuery.expr.filters.hidden = function( elem ) {
+ return ( elem.offsetWidth === 0 && elem.offsetHeight === 0 ) || (!jQuery.support.reliableHiddenOffsets && ((elem.style && elem.style.display) || curCSS( elem, "display" )) === "none");
+ };
+
+ jQuery.expr.filters.visible = function( elem ) {
+ return !jQuery.expr.filters.hidden( elem );
+ };
+}
+
+// These hooks are used by animate to expand properties
+jQuery.each({
+ margin: "",
+ padding: "",
+ border: "Width"
+}, function( prefix, suffix ) {
+ jQuery.cssHooks[ prefix + suffix ] = {
+ expand: function( value ) {
+ var i,
+
+ // assumes a single number if not a string
+ parts = typeof value === "string" ? value.split(" ") : [ value ],
+ expanded = {};
+
+ for ( i = 0; i < 4; i++ ) {
+ expanded[ prefix + cssExpand[ i ] + suffix ] =
+ parts[ i ] || parts[ i - 2 ] || parts[ 0 ];
+ }
+
+ return expanded;
+ }
+ };
+
+ if ( !rmargin.test( prefix ) ) {
+ jQuery.cssHooks[ prefix + suffix ].set = setPositiveNumber;
+ }
+});
+var r20 = /%20/g,
+ rbracket = /\[\]$/,
+ rCRLF = /\r?\n/g,
+ rinput = /^(?:color|date|datetime|datetime-local|email|hidden|month|number|password|range|search|tel|text|time|url|week)$/i,
+ rselectTextarea = /^(?:select|textarea)/i;
+
+jQuery.fn.extend({
+ serialize: function() {
+ return jQuery.param( this.serializeArray() );
+ },
+ serializeArray: function() {
+ return this.map(function(){
+ return this.elements ? jQuery.makeArray( this.elements ) : this;
+ })
+ .filter(function(){
+ return this.name && !this.disabled &&
+ ( this.checked || rselectTextarea.test( this.nodeName ) ||
+ rinput.test( this.type ) );
+ })
+ .map(function( i, elem ){
+ var val = jQuery( this ).val();
+
+ return val == null ?
+ null :
+ jQuery.isArray( val ) ?
+ jQuery.map( val, function( val, i ){
+ return { name: elem.name, value: val.replace( rCRLF, "\r\n" ) };
+ }) :
+ { name: elem.name, value: val.replace( rCRLF, "\r\n" ) };
+ }).get();
+ }
+});
+
+//Serialize an array of form elements or a set of
+//key/values into a query string
+jQuery.param = function( a, traditional ) {
+ var prefix,
+ s = [],
+ add = function( key, value ) {
+ // If value is a function, invoke it and return its value
+ value = jQuery.isFunction( value ) ? value() : ( value == null ? "" : value );
+ s[ s.length ] = encodeURIComponent( key ) + "=" + encodeURIComponent( value );
+ };
+
+ // Set traditional to true for jQuery <= 1.3.2 behavior.
+ if ( traditional === undefined ) {
+ traditional = jQuery.ajaxSettings && jQuery.ajaxSettings.traditional;
+ }
+
+ // If an array was passed in, assume that it is an array of form elements.
+ if ( jQuery.isArray( a ) || ( a.jquery && !jQuery.isPlainObject( a ) ) ) {
+ // Serialize the form elements
+ jQuery.each( a, function() {
+ add( this.name, this.value );
+ });
+
+ } else {
+ // If traditional, encode the "old" way (the way 1.3.2 or older
+ // did it), otherwise encode params recursively.
+ for ( prefix in a ) {
+ buildParams( prefix, a[ prefix ], traditional, add );
+ }
+ }
+
+ // Return the resulting serialization
+ return s.join( "&" ).replace( r20, "+" );
+};
+
+function buildParams( prefix, obj, traditional, add ) {
+ var name;
+
+ if ( jQuery.isArray( obj ) ) {
+ // Serialize array item.
+ jQuery.each( obj, function( i, v ) {
+ if ( traditional || rbracket.test( prefix ) ) {
+ // Treat each array item as a scalar.
+ add( prefix, v );
+
+ } else {
+ // If array item is non-scalar (array or object), encode its
+ // numeric index to resolve deserialization ambiguity issues.
+ // Note that rack (as of 1.0.0) can't currently deserialize
+ // nested arrays properly, and attempting to do so may cause
+ // a server error. Possible fixes are to modify rack's
+ // deserialization algorithm or to provide an option or flag
+ // to force array serialization to be shallow.
+ buildParams( prefix + "[" + ( typeof v === "object" ? i : "" ) + "]", v, traditional, add );
+ }
+ });
+
+ } else if ( !traditional && jQuery.type( obj ) === "object" ) {
+ // Serialize object item.
+ for ( name in obj ) {
+ buildParams( prefix + "[" + name + "]", obj[ name ], traditional, add );
+ }
+
+ } else {
+ // Serialize scalar item.
+ add( prefix, obj );
+ }
+}
+var
+ // Document location
+ ajaxLocParts,
+ ajaxLocation,
+
+ rhash = /#.*$/,
+ rheaders = /^(.*?):[ \t]*([^\r\n]*)\r?$/mg, // IE leaves an \r character at EOL
+ // #7653, #8125, #8152: local protocol detection
+ rlocalProtocol = /^(?:about|app|app\-storage|.+\-extension|file|res|widget):$/,
+ rnoContent = /^(?:GET|HEAD)$/,
+ rprotocol = /^\/\//,
+ rquery = /\?/,
+ rscript = /<script\b[^<]*(?:(?!<\/script>)<[^<]*)*<\/script>/gi,
+ rts = /([?&])_=[^&]*/,
+ rurl = /^([\w\+\.\-]+:)(?:\/\/([^\/?#:]*)(?::(\d+)|)|)/,
+
+ // Keep a copy of the old load method
+ _load = jQuery.fn.load,
+
+ /* Prefilters
+ * 1) They are useful to introduce custom dataTypes (see ajax/jsonp.js for an example)
+ * 2) These are called:
+ * - BEFORE asking for a transport
+ * - AFTER param serialization (s.data is a string if s.processData is true)
+ * 3) key is the dataType
+ * 4) the catchall symbol "*" can be used
+ * 5) execution will start with transport dataType and THEN continue down to "*" if needed
+ */
+ prefilters = {},
+
+ /* Transports bindings
+ * 1) key is the dataType
+ * 2) the catchall symbol "*" can be used
+ * 3) selection will start with transport dataType and THEN go to "*" if needed
+ */
+ transports = {},
+
+ // Avoid comment-prolog char sequence (#10098); must appease lint and evade compression
+ allTypes = ["*/"] + ["*"];
+
+// #8138, IE may throw an exception when accessing
+// a field from window.location if document.domain has been set
+try {
+ ajaxLocation = location.href;
+} catch( e ) {
+ // Use the href attribute of an A element
+ // since IE will modify it given document.location
+ ajaxLocation = document.createElement( "a" );
+ ajaxLocation.href = "";
+ ajaxLocation = ajaxLocation.href;
+}
+
+// Segment location into parts
+ajaxLocParts = rurl.exec( ajaxLocation.toLowerCase() ) || [];
+
+// Base "constructor" for jQuery.ajaxPrefilter and jQuery.ajaxTransport
+function addToPrefiltersOrTransports( structure ) {
+
+ // dataTypeExpression is optional and defaults to "*"
+ return function( dataTypeExpression, func ) {
+
+ if ( typeof dataTypeExpression !== "string" ) {
+ func = dataTypeExpression;
+ dataTypeExpression = "*";
+ }
+
+ var dataType, list, placeBefore,
+ dataTypes = dataTypeExpression.toLowerCase().split( core_rspace ),
+ i = 0,
+ length = dataTypes.length;
+
+ if ( jQuery.isFunction( func ) ) {
+ // For each dataType in the dataTypeExpression
+ for ( ; i < length; i++ ) {
+ dataType = dataTypes[ i ];
+ // We control if we're asked to add before
+ // any existing element
+ placeBefore = /^\+/.test( dataType );
+ if ( placeBefore ) {
+ dataType = dataType.substr( 1 ) || "*";
+ }
+ list = structure[ dataType ] = structure[ dataType ] || [];
+ // then we add to the structure accordingly
+ list[ placeBefore ? "unshift" : "push" ]( func );
+ }
+ }
+ };
+}
+
+// Base inspection function for prefilters and transports
+function inspectPrefiltersOrTransports( structure, options, originalOptions, jqXHR,
+ dataType /* internal */, inspected /* internal */ ) {
+
+ dataType = dataType || options.dataTypes[ 0 ];
+ inspected = inspected || {};
+
+ inspected[ dataType ] = true;
+
+ var selection,
+ list = structure[ dataType ],
+ i = 0,
+ length = list ? list.length : 0,
+ executeOnly = ( structure === prefilters );
+
+ for ( ; i < length && ( executeOnly || !selection ); i++ ) {
+ selection = list[ i ]( options, originalOptions, jqXHR );
+ // If we got redirected to another dataType
+ // we try there if executing only and not done already
+ if ( typeof selection === "string" ) {
+ if ( !executeOnly || inspected[ selection ] ) {
+ selection = undefined;
+ } else {
+ options.dataTypes.unshift( selection );
+ selection = inspectPrefiltersOrTransports(
+ structure, options, originalOptions, jqXHR, selection, inspected );
+ }
+ }
+ }
+ // If we're only executing or nothing was selected
+ // we try the catchall dataType if not done already
+ if ( ( executeOnly || !selection ) && !inspected[ "*" ] ) {
+ selection = inspectPrefiltersOrTransports(
+ structure, options, originalOptions, jqXHR, "*", inspected );
+ }
+ // unnecessary when only executing (prefilters)
+ // but it'll be ignored by the caller in that case
+ return selection;
+}
+
+// A special extend for ajax options
+// that takes "flat" options (not to be deep extended)
+// Fixes #9887
+function ajaxExtend( target, src ) {
+ var key, deep,
+ flatOptions = jQuery.ajaxSettings.flatOptions || {};
+ for ( key in src ) {
+ if ( src[ key ] !== undefined ) {
+ ( flatOptions[ key ] ? target : ( deep || ( deep = {} ) ) )[ key ] = src[ key ];
+ }
+ }
+ if ( deep ) {
+ jQuery.extend( true, target, deep );
+ }
+}
+
+jQuery.fn.load = function( url, params, callback ) {
+ if ( typeof url !== "string" && _load ) {
+ return _load.apply( this, arguments );
+ }
+
+ // Don't do a request if no elements are being requested
+ if ( !this.length ) {
+ return this;
+ }
+
+ var selector, type, response,
+ self = this,
+ off = url.indexOf(" ");
+
+ if ( off >= 0 ) {
+ selector = url.slice( off, url.length );
+ url = url.slice( 0, off );
+ }
+
+ // If it's a function
+ if ( jQuery.isFunction( params ) ) {
+
+ // We assume that it's the callback
+ callback = params;
+ params = undefined;
+
+ // Otherwise, build a param string
+ } else if ( params && typeof params === "object" ) {
+ type = "POST";
+ }
+
+ // Request the remote document
+ jQuery.ajax({
+ url: url,
+
+ // if "type" variable is undefined, then "GET" method will be used
+ type: type,
+ dataType: "html",
+ data: params,
+ complete: function( jqXHR, status ) {
+ if ( callback ) {
+ self.each( callback, response || [ jqXHR.responseText, status, jqXHR ] );
+ }
+ }
+ }).done(function( responseText ) {
+
+ // Save response for use in complete callback
+ response = arguments;
+
+ // See if a selector was specified
+ self.html( selector ?
+
+ // Create a dummy div to hold the results
+ jQuery("<div>")
+
+ // inject the contents of the document in, removing the scripts
+ // to avoid any 'Permission Denied' errors in IE
+ .append( responseText.replace( rscript, "" ) )
+
+ // Locate the specified elements
+ .find( selector ) :
+
+ // If not, just inject the full result
+ responseText );
+
+ });
+
+ return this;
+};
+
+// Attach a bunch of functions for handling common AJAX events
+jQuery.each( "ajaxStart ajaxStop ajaxComplete ajaxError ajaxSuccess ajaxSend".split( " " ), function( i, o ){
+ jQuery.fn[ o ] = function( f ){
+ return this.on( o, f );
+ };
+});
+
+jQuery.each( [ "get", "post" ], function( i, method ) {
+ jQuery[ method ] = function( url, data, callback, type ) {
+ // shift arguments if data argument was omitted
+ if ( jQuery.isFunction( data ) ) {
+ type = type || callback;
+ callback = data;
+ data = undefined;
+ }
+
+ return jQuery.ajax({
+ type: method,
+ url: url,
+ data: data,
+ success: callback,
+ dataType: type
+ });
+ };
+});
+
+jQuery.extend({
+
+ getScript: function( url, callback ) {
+ return jQuery.get( url, undefined, callback, "script" );
+ },
+
+ getJSON: function( url, data, callback ) {
+ return jQuery.get( url, data, callback, "json" );
+ },
+
+ // Creates a full fledged settings object into target
+ // with both ajaxSettings and settings fields.
+ // If target is omitted, writes into ajaxSettings.
+ ajaxSetup: function( target, settings ) {
+ if ( settings ) {
+ // Building a settings object
+ ajaxExtend( target, jQuery.ajaxSettings );
+ } else {
+ // Extending ajaxSettings
+ settings = target;
+ target = jQuery.ajaxSettings;
+ }
+ ajaxExtend( target, settings );
+ return target;
+ },
+
+ ajaxSettings: {
+ url: ajaxLocation,
+ isLocal: rlocalProtocol.test( ajaxLocParts[ 1 ] ),
+ global: true,
+ type: "GET",
+ contentType: "application/x-www-form-urlencoded; charset=UTF-8",
+ processData: true,
+ async: true,
+ /*
+ timeout: 0,
+ data: null,
+ dataType: null,
+ username: null,
+ password: null,
+ cache: null,
+ throws: false,
+ traditional: false,
+ headers: {},
+ */
+
+ accepts: {
+ xml: "application/xml, text/xml",
+ html: "text/html",
+ text: "text/plain",
+ json: "application/json, text/javascript",
+ "*": allTypes
+ },
+
+ contents: {
+ xml: /xml/,
+ html: /html/,
+ json: /json/
+ },
+
+ responseFields: {
+ xml: "responseXML",
+ text: "responseText"
+ },
+
+ // List of data converters
+ // 1) key format is "source_type destination_type" (a single space in-between)
+ // 2) the catchall symbol "*" can be used for source_type
+ converters: {
+
+ // Convert anything to text
+ "* text": window.String,
+
+ // Text to html (true = no transformation)
+ "text html": true,
+
+ // Evaluate text as a json expression
+ "text json": jQuery.parseJSON,
+
+ // Parse text as xml
+ "text xml": jQuery.parseXML
+ },
+
+ // For options that shouldn't be deep extended:
+ // you can add your own custom options here if
+ // and when you create one that shouldn't be
+ // deep extended (see ajaxExtend)
+ flatOptions: {
+ context: true,
+ url: true
+ }
+ },
+
+ ajaxPrefilter: addToPrefiltersOrTransports( prefilters ),
+ ajaxTransport: addToPrefiltersOrTransports( transports ),
+
+ // Main method
+ ajax: function( url, options ) {
+
+ // If url is an object, simulate pre-1.5 signature
+ if ( typeof url === "object" ) {
+ options = url;
+ url = undefined;
+ }
+
+ // Force options to be an object
+ options = options || {};
+
+ var // ifModified key
+ ifModifiedKey,
+ // Response headers
+ responseHeadersString,
+ responseHeaders,
+ // transport
+ transport,
+ // timeout handle
+ timeoutTimer,
+ // Cross-domain detection vars
+ parts,
+ // To know if global events are to be dispatched
+ fireGlobals,
+ // Loop variable
+ i,
+ // Create the final options object
+ s = jQuery.ajaxSetup( {}, options ),
+ // Callbacks context
+ callbackContext = s.context || s,
+ // Context for global events
+ // It's the callbackContext if one was provided in the options
+ // and if it's a DOM node or a jQuery collection
+ globalEventContext = callbackContext !== s &&
+ ( callbackContext.nodeType || callbackContext instanceof jQuery ) ?
+ jQuery( callbackContext ) : jQuery.event,
+ // Deferreds
+ deferred = jQuery.Deferred(),
+ completeDeferred = jQuery.Callbacks( "once memory" ),
+ // Status-dependent callbacks
+ statusCode = s.statusCode || {},
+ // Headers (they are sent all at once)
+ requestHeaders = {},
+ requestHeadersNames = {},
+ // The jqXHR state
+ state = 0,
+ // Default abort message
+ strAbort = "canceled",
+ // Fake xhr
+ jqXHR = {
+
+ readyState: 0,
+
+ // Caches the header
+ setRequestHeader: function( name, value ) {
+ if ( !state ) {
+ var lname = name.toLowerCase();
+ name = requestHeadersNames[ lname ] = requestHeadersNames[ lname ] || name;
+ requestHeaders[ name ] = value;
+ }
+ return this;
+ },
+
+ // Raw string
+ getAllResponseHeaders: function() {
+ return state === 2 ? responseHeadersString : null;
+ },
+
+ // Builds headers hashtable if needed
+ getResponseHeader: function( key ) {
+ var match;
+ if ( state === 2 ) {
+ if ( !responseHeaders ) {
+ responseHeaders = {};
+ while( ( match = rheaders.exec( responseHeadersString ) ) ) {
+ responseHeaders[ match[1].toLowerCase() ] = match[ 2 ];
+ }
+ }
+ match = responseHeaders[ key.toLowerCase() ];
+ }
+ return match === undefined ? null : match;
+ },
+
+ // Overrides response content-type header
+ overrideMimeType: function( type ) {
+ if ( !state ) {
+ s.mimeType = type;
+ }
+ return this;
+ },
+
+ // Cancel the request
+ abort: function( statusText ) {
+ statusText = statusText || strAbort;
+ if ( transport ) {
+ transport.abort( statusText );
+ }
+ done( 0, statusText );
+ return this;
+ }
+ };
+
+ // Callback for when everything is done
+ // It is defined here because jslint complains if it is declared
+ // at the end of the function (which would be more logical and readable)
+ function done( status, nativeStatusText, responses, headers ) {
+ var isSuccess, success, error, response, modified,
+ statusText = nativeStatusText;
+
+ // Called once
+ if ( state === 2 ) {
+ return;
+ }
+
+ // State is "done" now
+ state = 2;
+
+ // Clear timeout if it exists
+ if ( timeoutTimer ) {
+ clearTimeout( timeoutTimer );
+ }
+
+ // Dereference transport for early garbage collection
+ // (no matter how long the jqXHR object will be used)
+ transport = undefined;
+
+ // Cache response headers
+ responseHeadersString = headers || "";
+
+ // Set readyState
+ jqXHR.readyState = status > 0 ? 4 : 0;
+
+ // Get response data
+ if ( responses ) {
+ response = ajaxHandleResponses( s, jqXHR, responses );
+ }
+
+ // If successful, handle type chaining
+ if ( status >= 200 && status < 300 || status === 304 ) {
+
+ // Set the If-Modified-Since and/or If-None-Match header, if in ifModified mode.
+ if ( s.ifModified ) {
+
+ modified = jqXHR.getResponseHeader("Last-Modified");
+ if ( modified ) {
+ jQuery.lastModified[ ifModifiedKey ] = modified;
+ }
+ modified = jqXHR.getResponseHeader("Etag");
+ if ( modified ) {
+ jQuery.etag[ ifModifiedKey ] = modified;
+ }
+ }
+
+ // If not modified
+ if ( status === 304 ) {
+
+ statusText = "notmodified";
+ isSuccess = true;
+
+ // If we have data
+ } else {
+
+ isSuccess = ajaxConvert( s, response );
+ statusText = isSuccess.state;
+ success = isSuccess.data;
+ error = isSuccess.error;
+ isSuccess = !error;
+ }
+ } else {
+ // We extract error from statusText
+ // then normalize statusText and status for non-aborts
+ error = statusText;
+ if ( !statusText || status ) {
+ statusText = "error";
+ if ( status < 0 ) {
+ status = 0;
+ }
+ }
+ }
+
+ // Set data for the fake xhr object
+ jqXHR.status = status;
+ jqXHR.statusText = ( nativeStatusText || statusText ) + "";
+
+ // Success/Error
+ if ( isSuccess ) {
+ deferred.resolveWith( callbackContext, [ success, statusText, jqXHR ] );
+ } else {
+ deferred.rejectWith( callbackContext, [ jqXHR, statusText, error ] );
+ }
+
+ // Status-dependent callbacks
+ jqXHR.statusCode( statusCode );
+ statusCode = undefined;
+
+ if ( fireGlobals ) {
+ globalEventContext.trigger( "ajax" + ( isSuccess ? "Success" : "Error" ),
+ [ jqXHR, s, isSuccess ? success : error ] );
+ }
+
+ // Complete
+ completeDeferred.fireWith( callbackContext, [ jqXHR, statusText ] );
+
+ if ( fireGlobals ) {
+ globalEventContext.trigger( "ajaxComplete", [ jqXHR, s ] );
+ // Handle the global AJAX counter
+ if ( !( --jQuery.active ) ) {
+ jQuery.event.trigger( "ajaxStop" );
+ }
+ }
+ }
+
+ // Attach deferreds
+ deferred.promise( jqXHR );
+ jqXHR.success = jqXHR.done;
+ jqXHR.error = jqXHR.fail;
+ jqXHR.complete = completeDeferred.add;
+
+ // Status-dependent callbacks
+ jqXHR.statusCode = function( map ) {
+ if ( map ) {
+ var tmp;
+ if ( state < 2 ) {
+ for ( tmp in map ) {
+ statusCode[ tmp ] = [ statusCode[tmp], map[tmp] ];
+ }
+ } else {
+ tmp = map[ jqXHR.status ];
+ jqXHR.always( tmp );
+ }
+ }
+ return this;
+ };
+
+ // Remove hash character (#7531: and string promotion)
+ // Add protocol if not provided (#5866: IE7 issue with protocol-less urls)
+ // We also use the url parameter if available
+ s.url = ( ( url || s.url ) + "" ).replace( rhash, "" ).replace( rprotocol, ajaxLocParts[ 1 ] + "//" );
+
+ // Extract dataTypes list
+ s.dataTypes = jQuery.trim( s.dataType || "*" ).toLowerCase().split( core_rspace );
+
+ // A cross-domain request is in order when we have a protocol:host:port mismatch
+ if ( s.crossDomain == null ) {
+ parts = rurl.exec( s.url.toLowerCase() );
+ s.crossDomain = !!( parts &&
+ ( parts[ 1 ] !== ajaxLocParts[ 1 ] || parts[ 2 ] !== ajaxLocParts[ 2 ] ||
+ ( parts[ 3 ] || ( parts[ 1 ] === "http:" ? 80 : 443 ) ) !=
+ ( ajaxLocParts[ 3 ] || ( ajaxLocParts[ 1 ] === "http:" ? 80 : 443 ) ) )
+ );
+ }
+
+ // Convert data if not already a string
+ if ( s.data && s.processData && typeof s.data !== "string" ) {
+ s.data = jQuery.param( s.data, s.traditional );
+ }
+
+ // Apply prefilters
+ inspectPrefiltersOrTransports( prefilters, s, options, jqXHR );
+
+ // If request was aborted inside a prefilter, stop there
+ if ( state === 2 ) {
+ return jqXHR;
+ }
+
+ // We can fire global events as of now if asked to
+ fireGlobals = s.global;
+
+ // Uppercase the type
+ s.type = s.type.toUpperCase();
+
+ // Determine if request has content
+ s.hasContent = !rnoContent.test( s.type );
+
+ // Watch for a new set of requests
+ if ( fireGlobals && jQuery.active++ === 0 ) {
+ jQuery.event.trigger( "ajaxStart" );
+ }
+
+ // More options handling for requests with no content
+ if ( !s.hasContent ) {
+
+ // If data is available, append data to url
+ if ( s.data ) {
+ s.url += ( rquery.test( s.url ) ? "&" : "?" ) + s.data;
+ // #9682: remove data so that it's not used in an eventual retry
+ delete s.data;
+ }
+
+ // Get ifModifiedKey before adding the anti-cache parameter
+ ifModifiedKey = s.url;
+
+ // Add anti-cache in url if needed
+ if ( s.cache === false ) {
+
+ var ts = jQuery.now(),
+ // try replacing _= if it is there
+ ret = s.url.replace( rts, "$1_=" + ts );
+
+ // if nothing was replaced, add timestamp to the end
+ s.url = ret + ( ( ret === s.url ) ? ( rquery.test( s.url ) ? "&" : "?" ) + "_=" + ts : "" );
+ }
+ }
+
+ // Set the correct header, if data is being sent
+ if ( s.data && s.hasContent && s.contentType !== false || options.contentType ) {
+ jqXHR.setRequestHeader( "Content-Type", s.contentType );
+ }
+
+ // Set the If-Modified-Since and/or If-None-Match header, if in ifModified mode.
+ if ( s.ifModified ) {
+ ifModifiedKey = ifModifiedKey || s.url;
+ if ( jQuery.lastModified[ ifModifiedKey ] ) {
+ jqXHR.setRequestHeader( "If-Modified-Since", jQuery.lastModified[ ifModifiedKey ] );
+ }
+ if ( jQuery.etag[ ifModifiedKey ] ) {
+ jqXHR.setRequestHeader( "If-None-Match", jQuery.etag[ ifModifiedKey ] );
+ }
+ }
+
+ // Set the Accepts header for the server, depending on the dataType
+ jqXHR.setRequestHeader(
+ "Accept",
+ s.dataTypes[ 0 ] && s.accepts[ s.dataTypes[0] ] ?
+ s.accepts[ s.dataTypes[0] ] + ( s.dataTypes[ 0 ] !== "*" ? ", " + allTypes + "; q=0.01" : "" ) :
+ s.accepts[ "*" ]
+ );
+
+ // Check for headers option
+ for ( i in s.headers ) {
+ jqXHR.setRequestHeader( i, s.headers[ i ] );
+ }
+
+ // Allow custom headers/mimetypes and early abort
+ if ( s.beforeSend && ( s.beforeSend.call( callbackContext, jqXHR, s ) === false || state === 2 ) ) {
+ // Abort if not done already and return
+ return jqXHR.abort();
+
+ }
+
+ // aborting is no longer a cancellation
+ strAbort = "abort";
+
+ // Install callbacks on deferreds
+ for ( i in { success: 1, error: 1, complete: 1 } ) {
+ jqXHR[ i ]( s[ i ] );
+ }
+
+ // Get transport
+ transport = inspectPrefiltersOrTransports( transports, s, options, jqXHR );
+
+ // If no transport, we auto-abort
+ if ( !transport ) {
+ done( -1, "No Transport" );
+ } else {
+ jqXHR.readyState = 1;
+ // Send global event
+ if ( fireGlobals ) {
+ globalEventContext.trigger( "ajaxSend", [ jqXHR, s ] );
+ }
+ // Timeout
+ if ( s.async && s.timeout > 0 ) {
+ timeoutTimer = setTimeout( function(){
+ jqXHR.abort( "timeout" );
+ }, s.timeout );
+ }
+
+ try {
+ state = 1;
+ transport.send( requestHeaders, done );
+ } catch (e) {
+ // Propagate exception as error if not done
+ if ( state < 2 ) {
+ done( -1, e );
+ // Simply rethrow otherwise
+ } else {
+ throw e;
+ }
+ }
+ }
+
+ return jqXHR;
+ },
+
+ // Counter for holding the number of active queries
+ active: 0,
+
+ // Last-Modified header cache for next request
+ lastModified: {},
+ etag: {}
+
+});
+
+/* Handles responses to an ajax request:
+ * - sets all responseXXX fields accordingly
+ * - finds the right dataType (mediates between content-type and expected dataType)
+ * - returns the corresponding response
+ */
+function ajaxHandleResponses( s, jqXHR, responses ) {
+
+ var ct, type, finalDataType, firstDataType,
+ contents = s.contents,
+ dataTypes = s.dataTypes,
+ responseFields = s.responseFields;
+
+ // Fill responseXXX fields
+ for ( type in responseFields ) {
+ if ( type in responses ) {
+ jqXHR[ responseFields[type] ] = responses[ type ];
+ }
+ }
+
+ // Remove auto dataType and get content-type in the process
+ while( dataTypes[ 0 ] === "*" ) {
+ dataTypes.shift();
+ if ( ct === undefined ) {
+ ct = s.mimeType || jqXHR.getResponseHeader( "content-type" );
+ }
+ }
+
+ // Check if we're dealing with a known content-type
+ if ( ct ) {
+ for ( type in contents ) {
+ if ( contents[ type ] && contents[ type ].test( ct ) ) {
+ dataTypes.unshift( type );
+ break;
+ }
+ }
+ }
+
+ // Check to see if we have a response for the expected dataType
+ if ( dataTypes[ 0 ] in responses ) {
+ finalDataType = dataTypes[ 0 ];
+ } else {
+ // Try convertible dataTypes
+ for ( type in responses ) {
+ if ( !dataTypes[ 0 ] || s.converters[ type + " " + dataTypes[0] ] ) {
+ finalDataType = type;
+ break;
+ }
+ if ( !firstDataType ) {
+ firstDataType = type;
+ }
+ }
+ // Or just use first one
+ finalDataType = finalDataType || firstDataType;
+ }
+
+ // If we found a dataType
+ // We add the dataType to the list if needed
+ // and return the corresponding response
+ if ( finalDataType ) {
+ if ( finalDataType !== dataTypes[ 0 ] ) {
+ dataTypes.unshift( finalDataType );
+ }
+ return responses[ finalDataType ];
+ }
+}
+
+// Chain conversions given the request and the original response
+function ajaxConvert( s, response ) {
+
+ var conv, conv2, current, tmp,
+ // Work with a copy of dataTypes in case we need to modify it for conversion
+ dataTypes = s.dataTypes.slice(),
+ prev = dataTypes[ 0 ],
+ converters = {},
+ i = 0;
+
+ // Apply the dataFilter if provided
+ if ( s.dataFilter ) {
+ response = s.dataFilter( response, s.dataType );
+ }
+
+ // Create converters map with lowercased keys
+ if ( dataTypes[ 1 ] ) {
+ for ( conv in s.converters ) {
+ converters[ conv.toLowerCase() ] = s.converters[ conv ];
+ }
+ }
+
+ // Convert to each sequential dataType, tolerating list modification
+ for ( ; (current = dataTypes[++i]); ) {
+
+ // There's only work to do if current dataType is non-auto
+ if ( current !== "*" ) {
+
+ // Convert response if prev dataType is non-auto and differs from current
+ if ( prev !== "*" && prev !== current ) {
+
+ // Seek a direct converter
+ conv = converters[ prev + " " + current ] || converters[ "* " + current ];
+
+ // If none found, seek a pair
+ if ( !conv ) {
+ for ( conv2 in converters ) {
+
+ // If conv2 outputs current
+ tmp = conv2.split(" ");
+ if ( tmp[ 1 ] === current ) {
+
+ // If prev can be converted to accepted input
+ conv = converters[ prev + " " + tmp[ 0 ] ] ||
+ converters[ "* " + tmp[ 0 ] ];
+ if ( conv ) {
+ // Condense equivalence converters
+ if ( conv === true ) {
+ conv = converters[ conv2 ];
+
+ // Otherwise, insert the intermediate dataType
+ } else if ( converters[ conv2 ] !== true ) {
+ current = tmp[ 0 ];
+ dataTypes.splice( i--, 0, current );
+ }
+
+ break;
+ }
+ }
+ }
+ }
+
+ // Apply converter (if not an equivalence)
+ if ( conv !== true ) {
+
+ // Unless errors are allowed to bubble, catch and return them
+ if ( conv && s["throws"] ) {
+ response = conv( response );
+ } else {
+ try {
+ response = conv( response );
+ } catch ( e ) {
+ return { state: "parsererror", error: conv ? e : "No conversion from " + prev + " to " + current };
+ }
+ }
+ }
+ }
+
+ // Update prev for next iteration
+ prev = current;
+ }
+ }
+
+ return { state: "success", data: response };
+}
+var oldCallbacks = [],
+ rquestion = /\?/,
+ rjsonp = /(=)\?(?=&|$)|\?\?/,
+ nonce = jQuery.now();
+
+// Default jsonp settings
+jQuery.ajaxSetup({
+ jsonp: "callback",
+ jsonpCallback: function() {
+ var callback = oldCallbacks.pop() || ( jQuery.expando + "_" + ( nonce++ ) );
+ this[ callback ] = true;
+ return callback;
+ }
+});
+
+// Detect, normalize options and install callbacks for jsonp requests
+jQuery.ajaxPrefilter( "json jsonp", function( s, originalSettings, jqXHR ) {
+
+ var callbackName, overwritten, responseContainer,
+ data = s.data,
+ url = s.url,
+ hasCallback = s.jsonp !== false,
+ replaceInUrl = hasCallback && rjsonp.test( url ),
+ replaceInData = hasCallback && !replaceInUrl && typeof data === "string" &&
+ !( s.contentType || "" ).indexOf("application/x-www-form-urlencoded") &&
+ rjsonp.test( data );
+
+ // Handle iff the expected data type is "jsonp" or we have a parameter to set
+ if ( s.dataTypes[ 0 ] === "jsonp" || replaceInUrl || replaceInData ) {
+
+ // Get callback name, remembering preexisting value associated with it
+ callbackName = s.jsonpCallback = jQuery.isFunction( s.jsonpCallback ) ?
+ s.jsonpCallback() :
+ s.jsonpCallback;
+ overwritten = window[ callbackName ];
+
+ // Insert callback into url or form data
+ if ( replaceInUrl ) {
+ s.url = url.replace( rjsonp, "$1" + callbackName );
+ } else if ( replaceInData ) {
+ s.data = data.replace( rjsonp, "$1" + callbackName );
+ } else if ( hasCallback ) {
+ s.url += ( rquestion.test( url ) ? "&" : "?" ) + s.jsonp + "=" + callbackName;
+ }
+
+ // Use data converter to retrieve json after script execution
+ s.converters["script json"] = function() {
+ if ( !responseContainer ) {
+ jQuery.error( callbackName + " was not called" );
+ }
+ return responseContainer[ 0 ];
+ };
+
+ // force json dataType
+ s.dataTypes[ 0 ] = "json";
+
+ // Install callback
+ window[ callbackName ] = function() {
+ responseContainer = arguments;
+ };
+
+ // Clean-up function (fires after converters)
+ jqXHR.always(function() {
+ // Restore preexisting value
+ window[ callbackName ] = overwritten;
+
+ // Save back as free
+ if ( s[ callbackName ] ) {
+ // make sure that re-using the options doesn't screw things around
+ s.jsonpCallback = originalSettings.jsonpCallback;
+
+ // save the callback name for future use
+ oldCallbacks.push( callbackName );
+ }
+
+ // Call if it was a function and we have a response
+ if ( responseContainer && jQuery.isFunction( overwritten ) ) {
+ overwritten( responseContainer[ 0 ] );
+ }
+
+ responseContainer = overwritten = undefined;
+ });
+
+ // Delegate to script
+ return "script";
+ }
+});
+// Install script dataType
+jQuery.ajaxSetup({
+ accepts: {
+ script: "text/javascript, application/javascript, application/ecmascript, application/x-ecmascript"
+ },
+ contents: {
+ script: /javascript|ecmascript/
+ },
+ converters: {
+ "text script": function( text ) {
+ jQuery.globalEval( text );
+ return text;
+ }
+ }
+});
+
+// Handle cache's special case and global
+jQuery.ajaxPrefilter( "script", function( s ) {
+ if ( s.cache === undefined ) {
+ s.cache = false;
+ }
+ if ( s.crossDomain ) {
+ s.type = "GET";
+ s.global = false;
+ }
+});
+
+// Bind script tag hack transport
+jQuery.ajaxTransport( "script", function(s) {
+
+ // This transport only deals with cross domain requests
+ if ( s.crossDomain ) {
+
+ var script,
+ head = document.head || document.getElementsByTagName( "head" )[0] || document.documentElement;
+
+ return {
+
+ send: function( _, callback ) {
+
+ script = document.createElement( "script" );
+
+ script.async = "async";
+
+ if ( s.scriptCharset ) {
+ script.charset = s.scriptCharset;
+ }
+
+ script.src = s.url;
+
+ // Attach handlers for all browsers
+ script.onload = script.onreadystatechange = function( _, isAbort ) {
+
+ if ( isAbort || !script.readyState || /loaded|complete/.test( script.readyState ) ) {
+
+ // Handle memory leak in IE
+ script.onload = script.onreadystatechange = null;
+
+ // Remove the script
+ if ( head && script.parentNode ) {
+ head.removeChild( script );
+ }
+
+ // Dereference the script
+ script = undefined;
+
+ // Callback if not abort
+ if ( !isAbort ) {
+ callback( 200, "success" );
+ }
+ }
+ };
+ // Use insertBefore instead of appendChild to circumvent an IE6 bug.
+ // This arises when a base node is used (#2709 and #4378).
+ head.insertBefore( script, head.firstChild );
+ },
+
+ abort: function() {
+ if ( script ) {
+ script.onload( 0, 1 );
+ }
+ }
+ };
+ }
+});
+var xhrCallbacks,
+ // #5280: Internet Explorer will keep connections alive if we don't abort on unload
+ xhrOnUnloadAbort = window.ActiveXObject ? function() {
+ // Abort all pending requests
+ for ( var key in xhrCallbacks ) {
+ xhrCallbacks[ key ]( 0, 1 );
+ }
+ } : false,
+ xhrId = 0;
+
+// Functions to create xhrs
+function createStandardXHR() {
+ try {
+ return new window.XMLHttpRequest();
+ } catch( e ) {}
+}
+
+function createActiveXHR() {
+ try {
+ return new window.ActiveXObject( "Microsoft.XMLHTTP" );
+ } catch( e ) {}
+}
+
+// Create the request object
+// (This is still attached to ajaxSettings for backward compatibility)
+jQuery.ajaxSettings.xhr = window.ActiveXObject ?
+ /* Microsoft failed to properly
+ * implement the XMLHttpRequest in IE7 (can't request local files),
+ * so we use the ActiveXObject when it is available
+ * Additionally XMLHttpRequest can be disabled in IE7/IE8 so
+ * we need a fallback.
+ */
+ function() {
+ return !this.isLocal && createStandardXHR() || createActiveXHR();
+ } :
+ // For all other browsers, use the standard XMLHttpRequest object
+ createStandardXHR;
+
+// Determine support properties
+(function( xhr ) {
+ jQuery.extend( jQuery.support, {
+ ajax: !!xhr,
+ cors: !!xhr && ( "withCredentials" in xhr )
+ });
+})( jQuery.ajaxSettings.xhr() );
+
+// Create transport if the browser can provide an xhr
+if ( jQuery.support.ajax ) {
+
+ jQuery.ajaxTransport(function( s ) {
+ // Cross domain only allowed if supported through XMLHttpRequest
+ if ( !s.crossDomain || jQuery.support.cors ) {
+
+ var callback;
+
+ return {
+ send: function( headers, complete ) {
+
+ // Get a new xhr
+ var handle, i,
+ xhr = s.xhr();
+
+ // Open the socket
+ // Passing null username, generates a login popup on Opera (#2865)
+ if ( s.username ) {
+ xhr.open( s.type, s.url, s.async, s.username, s.password );
+ } else {
+ xhr.open( s.type, s.url, s.async );
+ }
+
+ // Apply custom fields if provided
+ if ( s.xhrFields ) {
+ for ( i in s.xhrFields ) {
+ xhr[ i ] = s.xhrFields[ i ];
+ }
+ }
+
+ // Override mime type if needed
+ if ( s.mimeType && xhr.overrideMimeType ) {
+ xhr.overrideMimeType( s.mimeType );
+ }
+
+ // X-Requested-With header
+ // For cross-domain requests, seeing as conditions for a preflight are
+ // akin to a jigsaw puzzle, we simply never set it to be sure.
+ // (it can always be set on a per-request basis or even using ajaxSetup)
+ // For same-domain requests, won't change header if already provided.
+ if ( !s.crossDomain && !headers["X-Requested-With"] ) {
+ headers[ "X-Requested-With" ] = "XMLHttpRequest";
+ }
+
+ // Need an extra try/catch for cross domain requests in Firefox 3
+ try {
+ for ( i in headers ) {
+ xhr.setRequestHeader( i, headers[ i ] );
+ }
+ } catch( _ ) {}
+
+ // Do send the request
+ // This may raise an exception which is actually
+ // handled in jQuery.ajax (so no try/catch here)
+ xhr.send( ( s.hasContent && s.data ) || null );
+
+ // Listener
+ callback = function( _, isAbort ) {
+
+ var status,
+ statusText,
+ responseHeaders,
+ responses,
+ xml;
+
+ // Firefox throws exceptions when accessing properties
+ // of an xhr when a network error occurred
+ // http://helpful.knobs-dials.com/index.php/Component_returned_failure_code:_0x80040111_(NS_ERROR_NOT_AVAILABLE)
+ try {
+
+ // Was never called and is aborted or complete
+ if ( callback && ( isAbort || xhr.readyState === 4 ) ) {
+
+ // Only called once
+ callback = undefined;
+
+ // Do not keep as active anymore
+ if ( handle ) {
+ xhr.onreadystatechange = jQuery.noop;
+ if ( xhrOnUnloadAbort ) {
+ delete xhrCallbacks[ handle ];
+ }
+ }
+
+ // If it's an abort
+ if ( isAbort ) {
+ // Abort it manually if needed
+ if ( xhr.readyState !== 4 ) {
+ xhr.abort();
+ }
+ } else {
+ status = xhr.status;
+ responseHeaders = xhr.getAllResponseHeaders();
+ responses = {};
+ xml = xhr.responseXML;
+
+ // Construct response list
+ if ( xml && xml.documentElement /* #4958 */ ) {
+ responses.xml = xml;
+ }
+
+ // When requesting binary data, IE6-9 will throw an exception
+ // on any attempt to access responseText (#11426)
+ try {
+ responses.text = xhr.responseText;
+ } catch( e ) {
+ }
+
+ // Firefox throws an exception when accessing
+ // statusText for faulty cross-domain requests
+ try {
+ statusText = xhr.statusText;
+ } catch( e ) {
+ // We normalize with Webkit giving an empty statusText
+ statusText = "";
+ }
+
+ // Filter status for non standard behaviors
+
+ // If the request is local and we have data: assume a success
+ // (success with no data won't get notified, that's the best we
+ // can do given current implementations)
+ if ( !status && s.isLocal && !s.crossDomain ) {
+ status = responses.text ? 200 : 404;
+ // IE - #1450: sometimes returns 1223 when it should be 204
+ } else if ( status === 1223 ) {
+ status = 204;
+ }
+ }
+ }
+ } catch( firefoxAccessException ) {
+ if ( !isAbort ) {
+ complete( -1, firefoxAccessException );
+ }
+ }
+
+ // Call complete if needed
+ if ( responses ) {
+ complete( status, statusText, responses, responseHeaders );
+ }
+ };
+
+ if ( !s.async ) {
+ // if we're in sync mode we fire the callback
+ callback();
+ } else if ( xhr.readyState === 4 ) {
+ // (IE6 & IE7) if it's in cache and has been
+ // retrieved directly we need to fire the callback
+ setTimeout( callback, 0 );
+ } else {
+ handle = ++xhrId;
+ if ( xhrOnUnloadAbort ) {
+ // Create the active xhrs callbacks list if needed
+ // and attach the unload handler
+ if ( !xhrCallbacks ) {
+ xhrCallbacks = {};
+ jQuery( window ).unload( xhrOnUnloadAbort );
+ }
+ // Add to list of active xhrs callbacks
+ xhrCallbacks[ handle ] = callback;
+ }
+ xhr.onreadystatechange = callback;
+ }
+ },
+
+ abort: function() {
+ if ( callback ) {
+ callback(0,1);
+ }
+ }
+ };
+ }
+ });
+}
+var fxNow, timerId,
+ rfxtypes = /^(?:toggle|show|hide)$/,
+ rfxnum = new RegExp( "^(?:([-+])=|)(" + core_pnum + ")([a-z%]*)$", "i" ),
+ rrun = /queueHooks$/,
+ animationPrefilters = [ defaultPrefilter ],
+ tweeners = {
+ "*": [function( prop, value ) {
+ var end, unit,
+ tween = this.createTween( prop, value ),
+ parts = rfxnum.exec( value ),
+ target = tween.cur(),
+ start = +target || 0,
+ scale = 1,
+ maxIterations = 20;
+
+ if ( parts ) {
+ end = +parts[2];
+ unit = parts[3] || ( jQuery.cssNumber[ prop ] ? "" : "px" );
+
+ // We need to compute starting value
+ if ( unit !== "px" && start ) {
+ // Iteratively approximate from a nonzero starting point
+ // Prefer the current property, because this process will be trivial if it uses the same units
+ // Fallback to end or a simple constant
+ start = jQuery.css( tween.elem, prop, true ) || end || 1;
+
+ do {
+ // If previous iteration zeroed out, double until we get *something*
+ // Use a string for doubling factor so we don't accidentally see scale as unchanged below
+ scale = scale || ".5";
+
+ // Adjust and apply
+ start = start / scale;
+ jQuery.style( tween.elem, prop, start + unit );
+
+ // Update scale, tolerating zero or NaN from tween.cur()
+ // And breaking the loop if scale is unchanged or perfect, or if we've just had enough
+ } while ( scale !== (scale = tween.cur() / target) && scale !== 1 && --maxIterations );
+ }
+
+ tween.unit = unit;
+ tween.start = start;
+ // If a +=/-= token was provided, we're doing a relative animation
+ tween.end = parts[1] ? start + ( parts[1] + 1 ) * end : end;
+ }
+ return tween;
+ }]
+ };
+
+// Animations created synchronously will run synchronously
+function createFxNow() {
+ setTimeout(function() {
+ fxNow = undefined;
+ }, 0 );
+ return ( fxNow = jQuery.now() );
+}
+
+function createTweens( animation, props ) {
+ jQuery.each( props, function( prop, value ) {
+ var collection = ( tweeners[ prop ] || [] ).concat( tweeners[ "*" ] ),
+ index = 0,
+ length = collection.length;
+ for ( ; index < length; index++ ) {
+ if ( collection[ index ].call( animation, prop, value ) ) {
+
+ // we're done with this property
+ return;
+ }
+ }
+ });
+}
+
+function Animation( elem, properties, options ) {
+ var result,
+ index = 0,
+ tweenerIndex = 0,
+ length = animationPrefilters.length,
+ deferred = jQuery.Deferred().always( function() {
+ // don't match elem in the :animated selector
+ delete tick.elem;
+ }),
+ tick = function() {
+ var currentTime = fxNow || createFxNow(),
+ remaining = Math.max( 0, animation.startTime + animation.duration - currentTime ),
+ // archaic crash bug won't allow us to use 1 - ( 0.5 || 0 ) (#12497)
+ temp = remaining / animation.duration || 0,
+ percent = 1 - temp,
+ index = 0,
+ length = animation.tweens.length;
+
+ for ( ; index < length ; index++ ) {
+ animation.tweens[ index ].run( percent );
+ }
+
+ deferred.notifyWith( elem, [ animation, percent, remaining ]);
+
+ if ( percent < 1 && length ) {
+ return remaining;
+ } else {
+ deferred.resolveWith( elem, [ animation ] );
+ return false;
+ }
+ },
+ animation = deferred.promise({
+ elem: elem,
+ props: jQuery.extend( {}, properties ),
+ opts: jQuery.extend( true, { specialEasing: {} }, options ),
+ originalProperties: properties,
+ originalOptions: options,
+ startTime: fxNow || createFxNow(),
+ duration: options.duration,
+ tweens: [],
+ createTween: function( prop, end, easing ) {
+ var tween = jQuery.Tween( elem, animation.opts, prop, end,
+ animation.opts.specialEasing[ prop ] || animation.opts.easing );
+ animation.tweens.push( tween );
+ return tween;
+ },
+ stop: function( gotoEnd ) {
+ var index = 0,
+ // if we are going to the end, we want to run all the tweens
+ // otherwise we skip this part
+ length = gotoEnd ? animation.tweens.length : 0;
+
+ for ( ; index < length ; index++ ) {
+ animation.tweens[ index ].run( 1 );
+ }
+
+ // resolve when we played the last frame
+ // otherwise, reject
+ if ( gotoEnd ) {
+ deferred.resolveWith( elem, [ animation, gotoEnd ] );
+ } else {
+ deferred.rejectWith( elem, [ animation, gotoEnd ] );
+ }
+ return this;
+ }
+ }),
+ props = animation.props;
+
+ propFilter( props, animation.opts.specialEasing );
+
+ for ( ; index < length ; index++ ) {
+ result = animationPrefilters[ index ].call( animation, elem, props, animation.opts );
+ if ( result ) {
+ return result;
+ }
+ }
+
+ createTweens( animation, props );
+
+ if ( jQuery.isFunction( animation.opts.start ) ) {
+ animation.opts.start.call( elem, animation );
+ }
+
+ jQuery.fx.timer(
+ jQuery.extend( tick, {
+ anim: animation,
+ queue: animation.opts.queue,
+ elem: elem
+ })
+ );
+
+ // attach callbacks from options
+ return animation.progress( animation.opts.progress )
+ .done( animation.opts.done, animation.opts.complete )
+ .fail( animation.opts.fail )
+ .always( animation.opts.always );
+}
+
+function propFilter( props, specialEasing ) {
+ var index, name, easing, value, hooks;
+
+ // camelCase, specialEasing and expand cssHook pass
+ for ( index in props ) {
+ name = jQuery.camelCase( index );
+ easing = specialEasing[ name ];
+ value = props[ index ];
+ if ( jQuery.isArray( value ) ) {
+ easing = value[ 1 ];
+ value = props[ index ] = value[ 0 ];
+ }
+
+ if ( index !== name ) {
+ props[ name ] = value;
+ delete props[ index ];
+ }
+
+ hooks = jQuery.cssHooks[ name ];
+ if ( hooks && "expand" in hooks ) {
+ value = hooks.expand( value );
+ delete props[ name ];
+
+ // not quite $.extend, this wont overwrite keys already present.
+ // also - reusing 'index' from above because we have the correct "name"
+ for ( index in value ) {
+ if ( !( index in props ) ) {
+ props[ index ] = value[ index ];
+ specialEasing[ index ] = easing;
+ }
+ }
+ } else {
+ specialEasing[ name ] = easing;
+ }
+ }
+}
+
+jQuery.Animation = jQuery.extend( Animation, {
+
+ tweener: function( props, callback ) {
+ if ( jQuery.isFunction( props ) ) {
+ callback = props;
+ props = [ "*" ];
+ } else {
+ props = props.split(" ");
+ }
+
+ var prop,
+ index = 0,
+ length = props.length;
+
+ for ( ; index < length ; index++ ) {
+ prop = props[ index ];
+ tweeners[ prop ] = tweeners[ prop ] || [];
+ tweeners[ prop ].unshift( callback );
+ }
+ },
+
+ prefilter: function( callback, prepend ) {
+ if ( prepend ) {
+ animationPrefilters.unshift( callback );
+ } else {
+ animationPrefilters.push( callback );
+ }
+ }
+});
+
+function defaultPrefilter( elem, props, opts ) {
+ var index, prop, value, length, dataShow, toggle, tween, hooks, oldfire,
+ anim = this,
+ style = elem.style,
+ orig = {},
+ handled = [],
+ hidden = elem.nodeType && isHidden( elem );
+
+ // handle queue: false promises
+ if ( !opts.queue ) {
+ hooks = jQuery._queueHooks( elem, "fx" );
+ if ( hooks.unqueued == null ) {
+ hooks.unqueued = 0;
+ oldfire = hooks.empty.fire;
+ hooks.empty.fire = function() {
+ if ( !hooks.unqueued ) {
+ oldfire();
+ }
+ };
+ }
+ hooks.unqueued++;
+
+ anim.always(function() {
+ // doing this makes sure that the complete handler will be called
+ // before this completes
+ anim.always(function() {
+ hooks.unqueued--;
+ if ( !jQuery.queue( elem, "fx" ).length ) {
+ hooks.empty.fire();
+ }
+ });
+ });
+ }
+
+ // height/width overflow pass
+ if ( elem.nodeType === 1 && ( "height" in props || "width" in props ) ) {
+ // Make sure that nothing sneaks out
+ // Record all 3 overflow attributes because IE does not
+ // change the overflow attribute when overflowX and
+ // overflowY are set to the same value
+ opts.overflow = [ style.overflow, style.overflowX, style.overflowY ];
+
+ // Set display property to inline-block for height/width
+ // animations on inline elements that are having width/height animated
+ if ( jQuery.css( elem, "display" ) === "inline" &&
+ jQuery.css( elem, "float" ) === "none" ) {
+
+ // inline-level elements accept inline-block;
+ // block-level elements need to be inline with layout
+ if ( !jQuery.support.inlineBlockNeedsLayout || css_defaultDisplay( elem.nodeName ) === "inline" ) {
+ style.display = "inline-block";
+
+ } else {
+ style.zoom = 1;
+ }
+ }
+ }
+
+ if ( opts.overflow ) {
+ style.overflow = "hidden";
+ if ( !jQuery.support.shrinkWrapBlocks ) {
+ anim.done(function() {
+ style.overflow = opts.overflow[ 0 ];
+ style.overflowX = opts.overflow[ 1 ];
+ style.overflowY = opts.overflow[ 2 ];
+ });
+ }
+ }
+
+
+ // show/hide pass
+ for ( index in props ) {
+ value = props[ index ];
+ if ( rfxtypes.exec( value ) ) {
+ delete props[ index ];
+ toggle = toggle || value === "toggle";
+ if ( value === ( hidden ? "hide" : "show" ) ) {
+ continue;
+ }
+ handled.push( index );
+ }
+ }
+
+ length = handled.length;
+ if ( length ) {
+ dataShow = jQuery._data( elem, "fxshow" ) || jQuery._data( elem, "fxshow", {} );
+ if ( "hidden" in dataShow ) {
+ hidden = dataShow.hidden;
+ }
+
+ // store state if its toggle - enables .stop().toggle() to "reverse"
+ if ( toggle ) {
+ dataShow.hidden = !hidden;
+ }
+ if ( hidden ) {
+ jQuery( elem ).show();
+ } else {
+ anim.done(function() {
+ jQuery( elem ).hide();
+ });
+ }
+ anim.done(function() {
+ var prop;
+ jQuery.removeData( elem, "fxshow", true );
+ for ( prop in orig ) {
+ jQuery.style( elem, prop, orig[ prop ] );
+ }
+ });
+ for ( index = 0 ; index < length ; index++ ) {
+ prop = handled[ index ];
+ tween = anim.createTween( prop, hidden ? dataShow[ prop ] : 0 );
+ orig[ prop ] = dataShow[ prop ] || jQuery.style( elem, prop );
+
+ if ( !( prop in dataShow ) ) {
+ dataShow[ prop ] = tween.start;
+ if ( hidden ) {
+ tween.end = tween.start;
+ tween.start = prop === "width" || prop === "height" ? 1 : 0;
+ }
+ }
+ }
+ }
+}
+
+function Tween( elem, options, prop, end, easing ) {
+ return new Tween.prototype.init( elem, options, prop, end, easing );
+}
+jQuery.Tween = Tween;
+
+Tween.prototype = {
+ constructor: Tween,
+ init: function( elem, options, prop, end, easing, unit ) {
+ this.elem = elem;
+ this.prop = prop;
+ this.easing = easing || "swing";
+ this.options = options;
+ this.start = this.now = this.cur();
+ this.end = end;
+ this.unit = unit || ( jQuery.cssNumber[ prop ] ? "" : "px" );
+ },
+ cur: function() {
+ var hooks = Tween.propHooks[ this.prop ];
+
+ return hooks && hooks.get ?
+ hooks.get( this ) :
+ Tween.propHooks._default.get( this );
+ },
+ run: function( percent ) {
+ var eased,
+ hooks = Tween.propHooks[ this.prop ];
+
+ if ( this.options.duration ) {
+ this.pos = eased = jQuery.easing[ this.easing ](
+ percent, this.options.duration * percent, 0, 1, this.options.duration
+ );
+ } else {
+ this.pos = eased = percent;
+ }
+ this.now = ( this.end - this.start ) * eased + this.start;
+
+ if ( this.options.step ) {
+ this.options.step.call( this.elem, this.now, this );
+ }
+
+ if ( hooks && hooks.set ) {
+ hooks.set( this );
+ } else {
+ Tween.propHooks._default.set( this );
+ }
+ return this;
+ }
+};
+
+Tween.prototype.init.prototype = Tween.prototype;
+
+Tween.propHooks = {
+ _default: {
+ get: function( tween ) {
+ var result;
+
+ if ( tween.elem[ tween.prop ] != null &&
+ (!tween.elem.style || tween.elem.style[ tween.prop ] == null) ) {
+ return tween.elem[ tween.prop ];
+ }
+
+ // passing any value as a 4th parameter to .css will automatically
+ // attempt a parseFloat and fallback to a string if the parse fails
+ // so, simple values such as "10px" are parsed to Float.
+ // complex values such as "rotate(1rad)" are returned as is.
+ result = jQuery.css( tween.elem, tween.prop, false, "" );
+ // Empty strings, null, undefined and "auto" are converted to 0.
+ return !result || result === "auto" ? 0 : result;
+ },
+ set: function( tween ) {
+ // use step hook for back compat - use cssHook if its there - use .style if its
+ // available and use plain properties where available
+ if ( jQuery.fx.step[ tween.prop ] ) {
+ jQuery.fx.step[ tween.prop ]( tween );
+ } else if ( tween.elem.style && ( tween.elem.style[ jQuery.cssProps[ tween.prop ] ] != null || jQuery.cssHooks[ tween.prop ] ) ) {
+ jQuery.style( tween.elem, tween.prop, tween.now + tween.unit );
+ } else {
+ tween.elem[ tween.prop ] = tween.now;
+ }
+ }
+ }
+};
+
+// Remove in 2.0 - this supports IE8's panic based approach
+// to setting things on disconnected nodes
+
+Tween.propHooks.scrollTop = Tween.propHooks.scrollLeft = {
+ set: function( tween ) {
+ if ( tween.elem.nodeType && tween.elem.parentNode ) {
+ tween.elem[ tween.prop ] = tween.now;
+ }
+ }
+};
+
+jQuery.each([ "toggle", "show", "hide" ], function( i, name ) {
+ var cssFn = jQuery.fn[ name ];
+ jQuery.fn[ name ] = function( speed, easing, callback ) {
+ return speed == null || typeof speed === "boolean" ||
+ // special check for .toggle( handler, handler, ... )
+ ( !i && jQuery.isFunction( speed ) && jQuery.isFunction( easing ) ) ?
+ cssFn.apply( this, arguments ) :
+ this.animate( genFx( name, true ), speed, easing, callback );
+ };
+});
+
+jQuery.fn.extend({
+ fadeTo: function( speed, to, easing, callback ) {
+
+ // show any hidden elements after setting opacity to 0
+ return this.filter( isHidden ).css( "opacity", 0 ).show()
+
+ // animate to the value specified
+ .end().animate({ opacity: to }, speed, easing, callback );
+ },
+ animate: function( prop, speed, easing, callback ) {
+ var empty = jQuery.isEmptyObject( prop ),
+ optall = jQuery.speed( speed, easing, callback ),
+ doAnimation = function() {
+ // Operate on a copy of prop so per-property easing won't be lost
+ var anim = Animation( this, jQuery.extend( {}, prop ), optall );
+
+ // Empty animations resolve immediately
+ if ( empty ) {
+ anim.stop( true );
+ }
+ };
+
+ return empty || optall.queue === false ?
+ this.each( doAnimation ) :
+ this.queue( optall.queue, doAnimation );
+ },
+ stop: function( type, clearQueue, gotoEnd ) {
+ var stopQueue = function( hooks ) {
+ var stop = hooks.stop;
+ delete hooks.stop;
+ stop( gotoEnd );
+ };
+
+ if ( typeof type !== "string" ) {
+ gotoEnd = clearQueue;
+ clearQueue = type;
+ type = undefined;
+ }
+ if ( clearQueue && type !== false ) {
+ this.queue( type || "fx", [] );
+ }
+
+ return this.each(function() {
+ var dequeue = true,
+ index = type != null && type + "queueHooks",
+ timers = jQuery.timers,
+ data = jQuery._data( this );
+
+ if ( index ) {
+ if ( data[ index ] && data[ index ].stop ) {
+ stopQueue( data[ index ] );
+ }
+ } else {
+ for ( index in data ) {
+ if ( data[ index ] && data[ index ].stop && rrun.test( index ) ) {
+ stopQueue( data[ index ] );
+ }
+ }
+ }
+
+ for ( index = timers.length; index--; ) {
+ if ( timers[ index ].elem === this && (type == null || timers[ index ].queue === type) ) {
+ timers[ index ].anim.stop( gotoEnd );
+ dequeue = false;
+ timers.splice( index, 1 );
+ }
+ }
+
+ // start the next in the queue if the last step wasn't forced
+ // timers currently will call their complete callbacks, which will dequeue
+ // but only if they were gotoEnd
+ if ( dequeue || !gotoEnd ) {
+ jQuery.dequeue( this, type );
+ }
+ });
+ }
+});
+
+// Generate parameters to create a standard animation
+function genFx( type, includeWidth ) {
+ var which,
+ attrs = { height: type },
+ i = 0;
+
+ // if we include width, step value is 1 to do all cssExpand values,
+ // if we don't include width, step value is 2 to skip over Left and Right
+ includeWidth = includeWidth? 1 : 0;
+ for( ; i < 4 ; i += 2 - includeWidth ) {
+ which = cssExpand[ i ];
+ attrs[ "margin" + which ] = attrs[ "padding" + which ] = type;
+ }
+
+ if ( includeWidth ) {
+ attrs.opacity = attrs.width = type;
+ }
+
+ return attrs;
+}
+
+// Generate shortcuts for custom animations
+jQuery.each({
+ slideDown: genFx("show"),
+ slideUp: genFx("hide"),
+ slideToggle: genFx("toggle"),
+ fadeIn: { opacity: "show" },
+ fadeOut: { opacity: "hide" },
+ fadeToggle: { opacity: "toggle" }
+}, function( name, props ) {
+ jQuery.fn[ name ] = function( speed, easing, callback ) {
+ return this.animate( props, speed, easing, callback );
+ };
+});
+
+jQuery.speed = function( speed, easing, fn ) {
+ var opt = speed && typeof speed === "object" ? jQuery.extend( {}, speed ) : {
+ complete: fn || !fn && easing ||
+ jQuery.isFunction( speed ) && speed,
+ duration: speed,
+ easing: fn && easing || easing && !jQuery.isFunction( easing ) && easing
+ };
+
+ opt.duration = jQuery.fx.off ? 0 : typeof opt.duration === "number" ? opt.duration :
+ opt.duration in jQuery.fx.speeds ? jQuery.fx.speeds[ opt.duration ] : jQuery.fx.speeds._default;
+
+ // normalize opt.queue - true/undefined/null -> "fx"
+ if ( opt.queue == null || opt.queue === true ) {
+ opt.queue = "fx";
+ }
+
+ // Queueing
+ opt.old = opt.complete;
+
+ opt.complete = function() {
+ if ( jQuery.isFunction( opt.old ) ) {
+ opt.old.call( this );
+ }
+
+ if ( opt.queue ) {
+ jQuery.dequeue( this, opt.queue );
+ }
+ };
+
+ return opt;
+};
+
+jQuery.easing = {
+ linear: function( p ) {
+ return p;
+ },
+ swing: function( p ) {
+ return 0.5 - Math.cos( p*Math.PI ) / 2;
+ }
+};
+
+jQuery.timers = [];
+jQuery.fx = Tween.prototype.init;
+jQuery.fx.tick = function() {
+ var timer,
+ timers = jQuery.timers,
+ i = 0;
+
+ fxNow = jQuery.now();
+
+ for ( ; i < timers.length; i++ ) {
+ timer = timers[ i ];
+ // Checks the timer has not already been removed
+ if ( !timer() && timers[ i ] === timer ) {
+ timers.splice( i--, 1 );
+ }
+ }
+
+ if ( !timers.length ) {
+ jQuery.fx.stop();
+ }
+ fxNow = undefined;
+};
+
+jQuery.fx.timer = function( timer ) {
+ if ( timer() && jQuery.timers.push( timer ) && !timerId ) {
+ timerId = setInterval( jQuery.fx.tick, jQuery.fx.interval );
+ }
+};
+
+jQuery.fx.interval = 13;
+
+jQuery.fx.stop = function() {
+ clearInterval( timerId );
+ timerId = null;
+};
+
+jQuery.fx.speeds = {
+ slow: 600,
+ fast: 200,
+ // Default speed
+ _default: 400
+};
+
+// Back Compat <1.8 extension point
+jQuery.fx.step = {};
+
+if ( jQuery.expr && jQuery.expr.filters ) {
+ jQuery.expr.filters.animated = function( elem ) {
+ return jQuery.grep(jQuery.timers, function( fn ) {
+ return elem === fn.elem;
+ }).length;
+ };
+}
+var rroot = /^(?:body|html)$/i;
+
+jQuery.fn.offset = function( options ) {
+ if ( arguments.length ) {
+ return options === undefined ?
+ this :
+ this.each(function( i ) {
+ jQuery.offset.setOffset( this, options, i );
+ });
+ }
+
+ var docElem, body, win, clientTop, clientLeft, scrollTop, scrollLeft,
+ box = { top: 0, left: 0 },
+ elem = this[ 0 ],
+ doc = elem && elem.ownerDocument;
+
+ if ( !doc ) {
+ return;
+ }
+
+ if ( (body = doc.body) === elem ) {
+ return jQuery.offset.bodyOffset( elem );
+ }
+
+ docElem = doc.documentElement;
+
+ // Make sure it's not a disconnected DOM node
+ if ( !jQuery.contains( docElem, elem ) ) {
+ return box;
+ }
+
+ // If we don't have gBCR, just use 0,0 rather than error
+ // BlackBerry 5, iOS 3 (original iPhone)
+ if ( typeof elem.getBoundingClientRect !== "undefined" ) {
+ box = elem.getBoundingClientRect();
+ }
+ win = getWindow( doc );
+ clientTop = docElem.clientTop || body.clientTop || 0;
+ clientLeft = docElem.clientLeft || body.clientLeft || 0;
+ scrollTop = win.pageYOffset || docElem.scrollTop;
+ scrollLeft = win.pageXOffset || docElem.scrollLeft;
+ return {
+ top: box.top + scrollTop - clientTop,
+ left: box.left + scrollLeft - clientLeft
+ };
+};
+
+jQuery.offset = {
+
+ bodyOffset: function( body ) {
+ var top = body.offsetTop,
+ left = body.offsetLeft;
+
+ if ( jQuery.support.doesNotIncludeMarginInBodyOffset ) {
+ top += parseFloat( jQuery.css(body, "marginTop") ) || 0;
+ left += parseFloat( jQuery.css(body, "marginLeft") ) || 0;
+ }
+
+ return { top: top, left: left };
+ },
+
+ setOffset: function( elem, options, i ) {
+ var position = jQuery.css( elem, "position" );
+
+ // set position first, in-case top/left are set even on static elem
+ if ( position === "static" ) {
+ elem.style.position = "relative";
+ }
+
+ var curElem = jQuery( elem ),
+ curOffset = curElem.offset(),
+ curCSSTop = jQuery.css( elem, "top" ),
+ curCSSLeft = jQuery.css( elem, "left" ),
+ calculatePosition = ( position === "absolute" || position === "fixed" ) && jQuery.inArray("auto", [curCSSTop, curCSSLeft]) > -1,
+ props = {}, curPosition = {}, curTop, curLeft;
+
+ // need to be able to calculate position if either top or left is auto and position is either absolute or fixed
+ if ( calculatePosition ) {
+ curPosition = curElem.position();
+ curTop = curPosition.top;
+ curLeft = curPosition.left;
+ } else {
+ curTop = parseFloat( curCSSTop ) || 0;
+ curLeft = parseFloat( curCSSLeft ) || 0;
+ }
+
+ if ( jQuery.isFunction( options ) ) {
+ options = options.call( elem, i, curOffset );
+ }
+
+ if ( options.top != null ) {
+ props.top = ( options.top - curOffset.top ) + curTop;
+ }
+ if ( options.left != null ) {
+ props.left = ( options.left - curOffset.left ) + curLeft;
+ }
+
+ if ( "using" in options ) {
+ options.using.call( elem, props );
+ } else {
+ curElem.css( props );
+ }
+ }
+};
+
+
+jQuery.fn.extend({
+
+ position: function() {
+ if ( !this[0] ) {
+ return;
+ }
+
+ var elem = this[0],
+
+ // Get *real* offsetParent
+ offsetParent = this.offsetParent(),
+
+ // Get correct offsets
+ offset = this.offset(),
+ parentOffset = rroot.test(offsetParent[0].nodeName) ? { top: 0, left: 0 } : offsetParent.offset();
+
+ // Subtract element margins
+ // note: when an element has margin: auto the offsetLeft and marginLeft
+ // are the same in Safari causing offset.left to incorrectly be 0
+ offset.top -= parseFloat( jQuery.css(elem, "marginTop") ) || 0;
+ offset.left -= parseFloat( jQuery.css(elem, "marginLeft") ) || 0;
+
+ // Add offsetParent borders
+ parentOffset.top += parseFloat( jQuery.css(offsetParent[0], "borderTopWidth") ) || 0;
+ parentOffset.left += parseFloat( jQuery.css(offsetParent[0], "borderLeftWidth") ) || 0;
+
+ // Subtract the two offsets
+ return {
+ top: offset.top - parentOffset.top,
+ left: offset.left - parentOffset.left
+ };
+ },
+
+ offsetParent: function() {
+ return this.map(function() {
+ var offsetParent = this.offsetParent || document.body;
+ while ( offsetParent && (!rroot.test(offsetParent.nodeName) && jQuery.css(offsetParent, "position") === "static") ) {
+ offsetParent = offsetParent.offsetParent;
+ }
+ return offsetParent || document.body;
+ });
+ }
+});
+
+
+// Create scrollLeft and scrollTop methods
+jQuery.each( {scrollLeft: "pageXOffset", scrollTop: "pageYOffset"}, function( method, prop ) {
+ var top = /Y/.test( prop );
+
+ jQuery.fn[ method ] = function( val ) {
+ return jQuery.access( this, function( elem, method, val ) {
+ var win = getWindow( elem );
+
+ if ( val === undefined ) {
+ return win ? (prop in win) ? win[ prop ] :
+ win.document.documentElement[ method ] :
+ elem[ method ];
+ }
+
+ if ( win ) {
+ win.scrollTo(
+ !top ? val : jQuery( win ).scrollLeft(),
+ top ? val : jQuery( win ).scrollTop()
+ );
+
+ } else {
+ elem[ method ] = val;
+ }
+ }, method, val, arguments.length, null );
+ };
+});
+
+function getWindow( elem ) {
+ return jQuery.isWindow( elem ) ?
+ elem :
+ elem.nodeType === 9 ?
+ elem.defaultView || elem.parentWindow :
+ false;
+}
+// Create innerHeight, innerWidth, height, width, outerHeight and outerWidth methods
+jQuery.each( { Height: "height", Width: "width" }, function( name, type ) {
+ jQuery.each( { padding: "inner" + name, content: type, "": "outer" + name }, function( defaultExtra, funcName ) {
+ // margin is only for outerHeight, outerWidth
+ jQuery.fn[ funcName ] = function( margin, value ) {
+ var chainable = arguments.length && ( defaultExtra || typeof margin !== "boolean" ),
+ extra = defaultExtra || ( margin === true || value === true ? "margin" : "border" );
+
+ return jQuery.access( this, function( elem, type, value ) {
+ var doc;
+
+ if ( jQuery.isWindow( elem ) ) {
+ // As of 5/8/2012 this will yield incorrect results for Mobile Safari, but there
+ // isn't a whole lot we can do. See pull request at this URL for discussion:
+ // https://github.com/jquery/jquery/pull/764
+ return elem.document.documentElement[ "client" + name ];
+ }
+
+ // Get document width or height
+ if ( elem.nodeType === 9 ) {
+ doc = elem.documentElement;
+
+ // Either scroll[Width/Height] or offset[Width/Height] or client[Width/Height], whichever is greatest
+ // unfortunately, this causes bug #3838 in IE6/8 only, but there is currently no good, small way to fix it.
+ return Math.max(
+ elem.body[ "scroll" + name ], doc[ "scroll" + name ],
+ elem.body[ "offset" + name ], doc[ "offset" + name ],
+ doc[ "client" + name ]
+ );
+ }
+
+ return value === undefined ?
+ // Get width or height on the element, requesting but not forcing parseFloat
+ jQuery.css( elem, type, value, extra ) :
+
+ // Set width or height on the element
+ jQuery.style( elem, type, value, extra );
+ }, type, chainable ? margin : undefined, chainable, null );
+ };
+ });
+});
+// Expose jQuery to the global object
+window.jQuery = window.$ = jQuery;
+
+// Expose jQuery as an AMD module, but only for AMD loaders that
+// understand the issues with loading multiple versions of jQuery
+// in a page that all might call define(). The loader will indicate
+// they have special allowances for multiple jQuery versions by
+// specifying define.amd.jQuery = true. Register as a named module,
+// since jQuery can be concatenated with other files that may use define,
+// but not use a proper concatenation script that understands anonymous
+// AMD modules. A named AMD is safest and most robust way to register.
+// Lowercase jquery is used because AMD module names are derived from
+// file names, and jQuery is normally delivered in a lowercase file name.
+// Do this after creating the global so that if an AMD module wants to call
+// noConflict to hide this version of jQuery, it will work.
+if ( typeof define === "function" && define.amd && define.amd.jQuery ) {
+ define( "jquery", [], function () { return jQuery; } );
+}
+
+})( window );
diff --git a/docs/build/html/_static/jquery.js b/docs/build/html/_static/jquery.js
new file mode 100644
index 0000000000000000000000000000000000000000..83589daa707a25a1fb3e4112075d382e9a1611ab
--- /dev/null
+++ b/docs/build/html/_static/jquery.js
@@ -0,0 +1,2 @@
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+// No Conflict in later (our) version of jQuery
+window.$jqTheme = jQuery.noConflict(true);
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+.highlight .hll { background-color: #ffffcc }
+.highlight { background: #eeffcc; }
+.highlight .c { color: #408090; font-style: italic } /* Comment */
+.highlight .err { border: 1px solid #FF0000 } /* Error */
+.highlight .k { color: #007020; font-weight: bold } /* Keyword */
+.highlight .o { color: #666666 } /* Operator */
+.highlight .cm { color: #408090; font-style: italic } /* Comment.Multiline */
+.highlight .cp { color: #007020 } /* Comment.Preproc */
+.highlight .c1 { color: #408090; font-style: italic } /* Comment.Single */
+.highlight .cs { color: #408090; background-color: #fff0f0 } /* Comment.Special */
+.highlight .gd { color: #A00000 } /* Generic.Deleted */
+.highlight .ge { font-style: italic } /* Generic.Emph */
+.highlight .gr { color: #FF0000 } /* Generic.Error */
+.highlight .gh { color: #000080; font-weight: bold } /* Generic.Heading */
+.highlight .gi { color: #00A000 } /* Generic.Inserted */
+.highlight .go { color: #333333 } /* Generic.Output */
+.highlight .gp { color: #c65d09; font-weight: bold } /* Generic.Prompt */
+.highlight .gs { font-weight: bold } /* Generic.Strong */
+.highlight .gu { color: #800080; font-weight: bold } /* Generic.Subheading */
+.highlight .gt { color: #0044DD } /* Generic.Traceback */
+.highlight .kc { color: #007020; font-weight: bold } /* Keyword.Constant */
+.highlight .kd { color: #007020; font-weight: bold } /* Keyword.Declaration */
+.highlight .kn { color: #007020; font-weight: bold } /* Keyword.Namespace */
+.highlight .kp { color: #007020 } /* Keyword.Pseudo */
+.highlight .kr { color: #007020; font-weight: bold } /* Keyword.Reserved */
+.highlight .kt { color: #902000 } /* Keyword.Type */
+.highlight .m { color: #208050 } /* Literal.Number */
+.highlight .s { color: #4070a0 } /* Literal.String */
+.highlight .na { color: #4070a0 } /* Name.Attribute */
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+.highlight .nf { color: #06287e } /* Name.Function */
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+.highlight .nt { color: #062873; font-weight: bold } /* Name.Tag */
+.highlight .nv { color: #bb60d5 } /* Name.Variable */
+.highlight .ow { color: #007020; font-weight: bold } /* Operator.Word */
+.highlight .w { color: #bbbbbb } /* Text.Whitespace */
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+++ b/docs/build/html/_static/searchtools.js
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+/*
+ * searchtools.js_t
+ * ~~~~~~~~~~~~~~~~
+ *
+ * Sphinx JavaScript utilties for the full-text search.
+ *
+ * :copyright: Copyright 2007-2014 by the Sphinx team, see AUTHORS.
+ * :license: BSD, see LICENSE for details.
+ *
+ */
+
+
+/**
+ * Porter Stemmer
+ */
+var Stemmer = function() {
+
+ var step2list = {
+ ational: 'ate',
+ tional: 'tion',
+ enci: 'ence',
+ anci: 'ance',
+ izer: 'ize',
+ bli: 'ble',
+ alli: 'al',
+ entli: 'ent',
+ eli: 'e',
+ ousli: 'ous',
+ ization: 'ize',
+ ation: 'ate',
+ ator: 'ate',
+ alism: 'al',
+ iveness: 'ive',
+ fulness: 'ful',
+ ousness: 'ous',
+ aliti: 'al',
+ iviti: 'ive',
+ biliti: 'ble',
+ logi: 'log'
+ };
+
+ var step3list = {
+ icate: 'ic',
+ ative: '',
+ alize: 'al',
+ iciti: 'ic',
+ ical: 'ic',
+ ful: '',
+ ness: ''
+ };
+
+ var c = "[^aeiou]"; // consonant
+ var v = "[aeiouy]"; // vowel
+ var C = c + "[^aeiouy]*"; // consonant sequence
+ var V = v + "[aeiou]*"; // vowel sequence
+
+ var mgr0 = "^(" + C + ")?" + V + C; // [C]VC... is m>0
+ var meq1 = "^(" + C + ")?" + V + C + "(" + V + ")?$"; // [C]VC[V] is m=1
+ var mgr1 = "^(" + C + ")?" + V + C + V + C; // [C]VCVC... is m>1
+ var s_v = "^(" + C + ")?" + v; // vowel in stem
+
+ this.stemWord = function (w) {
+ var stem;
+ var suffix;
+ var firstch;
+ var origword = w;
+
+ if (w.length < 3)
+ return w;
+
+ var re;
+ var re2;
+ var re3;
+ var re4;
+
+ firstch = w.substr(0,1);
+ if (firstch == "y")
+ w = firstch.toUpperCase() + w.substr(1);
+
+ // Step 1a
+ re = /^(.+?)(ss|i)es$/;
+ re2 = /^(.+?)([^s])s$/;
+
+ if (re.test(w))
+ w = w.replace(re,"$1$2");
+ else if (re2.test(w))
+ w = w.replace(re2,"$1$2");
+
+ // Step 1b
+ re = /^(.+?)eed$/;
+ re2 = /^(.+?)(ed|ing)$/;
+ if (re.test(w)) {
+ var fp = re.exec(w);
+ re = new RegExp(mgr0);
+ if (re.test(fp[1])) {
+ re = /.$/;
+ w = w.replace(re,"");
+ }
+ }
+ else if (re2.test(w)) {
+ var fp = re2.exec(w);
+ stem = fp[1];
+ re2 = new RegExp(s_v);
+ if (re2.test(stem)) {
+ w = stem;
+ re2 = /(at|bl|iz)$/;
+ re3 = new RegExp("([^aeiouylsz])\\1$");
+ re4 = new RegExp("^" + C + v + "[^aeiouwxy]$");
+ if (re2.test(w))
+ w = w + "e";
+ else if (re3.test(w)) {
+ re = /.$/;
+ w = w.replace(re,"");
+ }
+ else if (re4.test(w))
+ w = w + "e";
+ }
+ }
+
+ // Step 1c
+ re = /^(.+?)y$/;
+ if (re.test(w)) {
+ var fp = re.exec(w);
+ stem = fp[1];
+ re = new RegExp(s_v);
+ if (re.test(stem))
+ w = stem + "i";
+ }
+
+ // Step 2
+ re = /^(.+?)(ational|tional|enci|anci|izer|bli|alli|entli|eli|ousli|ization|ation|ator|alism|iveness|fulness|ousness|aliti|iviti|biliti|logi)$/;
+ if (re.test(w)) {
+ var fp = re.exec(w);
+ stem = fp[1];
+ suffix = fp[2];
+ re = new RegExp(mgr0);
+ if (re.test(stem))
+ w = stem + step2list[suffix];
+ }
+
+ // Step 3
+ re = /^(.+?)(icate|ative|alize|iciti|ical|ful|ness)$/;
+ if (re.test(w)) {
+ var fp = re.exec(w);
+ stem = fp[1];
+ suffix = fp[2];
+ re = new RegExp(mgr0);
+ if (re.test(stem))
+ w = stem + step3list[suffix];
+ }
+
+ // Step 4
+ re = /^(.+?)(al|ance|ence|er|ic|able|ible|ant|ement|ment|ent|ou|ism|ate|iti|ous|ive|ize)$/;
+ re2 = /^(.+?)(s|t)(ion)$/;
+ if (re.test(w)) {
+ var fp = re.exec(w);
+ stem = fp[1];
+ re = new RegExp(mgr1);
+ if (re.test(stem))
+ w = stem;
+ }
+ else if (re2.test(w)) {
+ var fp = re2.exec(w);
+ stem = fp[1] + fp[2];
+ re2 = new RegExp(mgr1);
+ if (re2.test(stem))
+ w = stem;
+ }
+
+ // Step 5
+ re = /^(.+?)e$/;
+ if (re.test(w)) {
+ var fp = re.exec(w);
+ stem = fp[1];
+ re = new RegExp(mgr1);
+ re2 = new RegExp(meq1);
+ re3 = new RegExp("^" + C + v + "[^aeiouwxy]$");
+ if (re.test(stem) || (re2.test(stem) && !(re3.test(stem))))
+ w = stem;
+ }
+ re = /ll$/;
+ re2 = new RegExp(mgr1);
+ if (re.test(w) && re2.test(w)) {
+ re = /.$/;
+ w = w.replace(re,"");
+ }
+
+ // and turn initial Y back to y
+ if (firstch == "y")
+ w = firstch.toLowerCase() + w.substr(1);
+ return w;
+ }
+}
+
+
+
+/**
+ * Simple result scoring code.
+ */
+var Scorer = {
+ // Implement the following function to further tweak the score for each result
+ // The function takes a result array [filename, title, anchor, descr, score]
+ // and returns the new score.
+ /*
+ score: function(result) {
+ return result[4];
+ },
+ */
+
+ // query matches the full name of an object
+ objNameMatch: 11,
+ // or matches in the last dotted part of the object name
+ objPartialMatch: 6,
+ // Additive scores depending on the priority of the object
+ objPrio: {0: 15, // used to be importantResults
+ 1: 5, // used to be objectResults
+ 2: -5}, // used to be unimportantResults
+ // Used when the priority is not in the mapping.
+ objPrioDefault: 0,
+
+ // query found in title
+ title: 15,
+ // query found in terms
+ term: 5
+};
+
+
+/**
+ * Search Module
+ */
+var Search = {
+
+ _index : null,
+ _queued_query : null,
+ _pulse_status : -1,
+
+ init : function() {
+ var params = $.getQueryParameters();
+ if (params.q) {
+ var query = params.q[0];
+ $('input[name="q"]')[0].value = query;
+ this.performSearch(query);
+ }
+ },
+
+ loadIndex : function(url) {
+ $.ajax({type: "GET", url: url, data: null,
+ dataType: "script", cache: true,
+ complete: function(jqxhr, textstatus) {
+ if (textstatus != "success") {
+ document.getElementById("searchindexloader").src = url;
+ }
+ }});
+ },
+
+ setIndex : function(index) {
+ var q;
+ this._index = index;
+ if ((q = this._queued_query) !== null) {
+ this._queued_query = null;
+ Search.query(q);
+ }
+ },
+
+ hasIndex : function() {
+ return this._index !== null;
+ },
+
+ deferQuery : function(query) {
+ this._queued_query = query;
+ },
+
+ stopPulse : function() {
+ this._pulse_status = 0;
+ },
+
+ startPulse : function() {
+ if (this._pulse_status >= 0)
+ return;
+ function pulse() {
+ var i;
+ Search._pulse_status = (Search._pulse_status + 1) % 4;
+ var dotString = '';
+ for (i = 0; i < Search._pulse_status; i++)
+ dotString += '.';
+ Search.dots.text(dotString);
+ if (Search._pulse_status > -1)
+ window.setTimeout(pulse, 500);
+ }
+ pulse();
+ },
+
+ /**
+ * perform a search for something (or wait until index is loaded)
+ */
+ performSearch : function(query) {
+ // create the required interface elements
+ this.out = $('#search-results');
+ this.title = $('<h2>' + _('Searching') + '</h2>').appendTo(this.out);
+ this.dots = $('<span></span>').appendTo(this.title);
+ this.status = $('<p style="display: none"></p>').appendTo(this.out);
+ this.output = $('<ul class="search"/>').appendTo(this.out);
+
+ $('#search-progress').text(_('Preparing search...'));
+ this.startPulse();
+
+ // index already loaded, the browser was quick!
+ if (this.hasIndex())
+ this.query(query);
+ else
+ this.deferQuery(query);
+ },
+
+ /**
+ * execute search (requires search index to be loaded)
+ */
+ query : function(query) {
+ var i;
+ var stopwords = ["a","and","are","as","at","be","but","by","for","if","in","into","is","it","near","no","not","of","on","or","such","that","the","their","then","there","these","they","this","to","was","will","with"];
+
+ // stem the searchterms and add them to the correct list
+ var stemmer = new Stemmer();
+ var searchterms = [];
+ var excluded = [];
+ var hlterms = [];
+ var tmp = query.split(/\s+/);
+ var objectterms = [];
+ for (i = 0; i < tmp.length; i++) {
+ if (tmp[i] !== "") {
+ objectterms.push(tmp[i].toLowerCase());
+ }
+
+ if ($u.indexOf(stopwords, tmp[i].toLowerCase()) != -1 || tmp[i].match(/^\d+$/) ||
+ tmp[i] === "") {
+ // skip this "word"
+ continue;
+ }
+ // stem the word
+ var word = stemmer.stemWord(tmp[i].toLowerCase());
+ var toAppend;
+ // select the correct list
+ if (word[0] == '-') {
+ toAppend = excluded;
+ word = word.substr(1);
+ }
+ else {
+ toAppend = searchterms;
+ hlterms.push(tmp[i].toLowerCase());
+ }
+ // only add if not already in the list
+ if (!$u.contains(toAppend, word))
+ toAppend.push(word);
+ }
+ var highlightstring = '?highlight=' + $.urlencode(hlterms.join(" "));
+
+ // console.debug('SEARCH: searching for:');
+ // console.info('required: ', searchterms);
+ // console.info('excluded: ', excluded);
+
+ // prepare search
+ var terms = this._index.terms;
+ var titleterms = this._index.titleterms;
+
+ // array of [filename, title, anchor, descr, score]
+ var results = [];
+ $('#search-progress').empty();
+
+ // lookup as object
+ for (i = 0; i < objectterms.length; i++) {
+ var others = [].concat(objectterms.slice(0, i),
+ objectterms.slice(i+1, objectterms.length));
+ results = results.concat(this.performObjectSearch(objectterms[i], others));
+ }
+
+ // lookup as search terms in fulltext
+ results = results.concat(this.performTermsSearch(searchterms, excluded, terms, Scorer.term))
+ .concat(this.performTermsSearch(searchterms, excluded, titleterms, Scorer.title));
+
+ // let the scorer override scores with a custom scoring function
+ if (Scorer.score) {
+ for (i = 0; i < results.length; i++)
+ results[i][4] = Scorer.score(results[i]);
+ }
+
+ // now sort the results by score (in opposite order of appearance, since the
+ // display function below uses pop() to retrieve items) and then
+ // alphabetically
+ results.sort(function(a, b) {
+ var left = a[4];
+ var right = b[4];
+ if (left > right) {
+ return 1;
+ } else if (left < right) {
+ return -1;
+ } else {
+ // same score: sort alphabetically
+ left = a[1].toLowerCase();
+ right = b[1].toLowerCase();
+ return (left > right) ? -1 : ((left < right) ? 1 : 0);
+ }
+ });
+
+ // for debugging
+ //Search.lastresults = results.slice(); // a copy
+ //console.info('search results:', Search.lastresults);
+
+ // print the results
+ var resultCount = results.length;
+ function displayNextItem() {
+ // results left, load the summary and display it
+ if (results.length) {
+ var item = results.pop();
+ var listItem = $('<li style="display:none"></li>');
+ if (DOCUMENTATION_OPTIONS.FILE_SUFFIX === '') {
+ // dirhtml builder
+ var dirname = item[0] + '/';
+ if (dirname.match(/\/index\/$/)) {
+ dirname = dirname.substring(0, dirname.length-6);
+ } else if (dirname == 'index/') {
+ dirname = '';
+ }
+ listItem.append($('<a/>').attr('href',
+ DOCUMENTATION_OPTIONS.URL_ROOT + dirname +
+ highlightstring + item[2]).html(item[1]));
+ } else {
+ // normal html builders
+ listItem.append($('<a/>').attr('href',
+ item[0] + DOCUMENTATION_OPTIONS.FILE_SUFFIX +
+ highlightstring + item[2]).html(item[1]));
+ }
+ if (item[3]) {
+ listItem.append($('<span> (' + item[3] + ')</span>'));
+ Search.output.append(listItem);
+ listItem.slideDown(5, function() {
+ displayNextItem();
+ });
+ } else if (DOCUMENTATION_OPTIONS.HAS_SOURCE) {
+ $.ajax({url: DOCUMENTATION_OPTIONS.URL_ROOT + '_sources/' + item[0] + '.txt',
+ dataType: "text",
+ complete: function(jqxhr, textstatus) {
+ var data = jqxhr.responseText;
+ if (data !== '') {
+ listItem.append(Search.makeSearchSummary(data, searchterms, hlterms));
+ }
+ Search.output.append(listItem);
+ listItem.slideDown(5, function() {
+ displayNextItem();
+ });
+ }});
+ } else {
+ // no source available, just display title
+ Search.output.append(listItem);
+ listItem.slideDown(5, function() {
+ displayNextItem();
+ });
+ }
+ }
+ // search finished, update title and status message
+ else {
+ Search.stopPulse();
+ Search.title.text(_('Search Results'));
+ if (!resultCount)
+ Search.status.text(_('Your search did not match any documents. Please make sure that all words are spelled correctly and that you\'ve selected enough categories.'));
+ else
+ Search.status.text(_('Search finished, found %s page(s) matching the search query.').replace('%s', resultCount));
+ Search.status.fadeIn(500);
+ }
+ }
+ displayNextItem();
+ },
+
+ /**
+ * search for object names
+ */
+ performObjectSearch : function(object, otherterms) {
+ var filenames = this._index.filenames;
+ var objects = this._index.objects;
+ var objnames = this._index.objnames;
+ var titles = this._index.titles;
+
+ var i;
+ var results = [];
+
+ for (var prefix in objects) {
+ for (var name in objects[prefix]) {
+ var fullname = (prefix ? prefix + '.' : '') + name;
+ if (fullname.toLowerCase().indexOf(object) > -1) {
+ var score = 0;
+ var parts = fullname.split('.');
+ // check for different match types: exact matches of full name or
+ // "last name" (i.e. last dotted part)
+ if (fullname == object || parts[parts.length - 1] == object) {
+ score += Scorer.objNameMatch;
+ // matches in last name
+ } else if (parts[parts.length - 1].indexOf(object) > -1) {
+ score += Scorer.objPartialMatch;
+ }
+ var match = objects[prefix][name];
+ var objname = objnames[match[1]][2];
+ var title = titles[match[0]];
+ // If more than one term searched for, we require other words to be
+ // found in the name/title/description
+ if (otherterms.length > 0) {
+ var haystack = (prefix + ' ' + name + ' ' +
+ objname + ' ' + title).toLowerCase();
+ var allfound = true;
+ for (i = 0; i < otherterms.length; i++) {
+ if (haystack.indexOf(otherterms[i]) == -1) {
+ allfound = false;
+ break;
+ }
+ }
+ if (!allfound) {
+ continue;
+ }
+ }
+ var descr = objname + _(', in ') + title;
+
+ var anchor = match[3];
+ if (anchor === '')
+ anchor = fullname;
+ else if (anchor == '-')
+ anchor = objnames[match[1]][1] + '-' + fullname;
+ // add custom score for some objects according to scorer
+ if (Scorer.objPrio.hasOwnProperty(match[2])) {
+ score += Scorer.objPrio[match[2]];
+ } else {
+ score += Scorer.objPrioDefault;
+ }
+ results.push([filenames[match[0]], fullname, '#'+anchor, descr, score]);
+ }
+ }
+ }
+
+ return results;
+ },
+
+ /**
+ * search for full-text terms in the index
+ */
+ performTermsSearch : function(searchterms, excluded, terms, score) {
+ var filenames = this._index.filenames;
+ var titles = this._index.titles;
+
+ var i, j, file, files;
+ var fileMap = {};
+ var results = [];
+
+ // perform the search on the required terms
+ for (i = 0; i < searchterms.length; i++) {
+ var word = searchterms[i];
+ // no match but word was a required one
+ if ((files = terms[word]) === undefined)
+ break;
+ if (files.length === undefined) {
+ files = [files];
+ }
+ // create the mapping
+ for (j = 0; j < files.length; j++) {
+ file = files[j];
+ if (file in fileMap)
+ fileMap[file].push(word);
+ else
+ fileMap[file] = [word];
+ }
+ }
+
+ // now check if the files don't contain excluded terms
+ for (file in fileMap) {
+ var valid = true;
+
+ // check if all requirements are matched
+ if (fileMap[file].length != searchterms.length)
+ continue;
+
+ // ensure that none of the excluded terms is in the search result
+ for (i = 0; i < excluded.length; i++) {
+ if (terms[excluded[i]] == file ||
+ $u.contains(terms[excluded[i]] || [], file)) {
+ valid = false;
+ break;
+ }
+ }
+
+ // if we have still a valid result we can add it to the result list
+ if (valid) {
+ results.push([filenames[file], titles[file], '', null, score]);
+ }
+ }
+ return results;
+ },
+
+ /**
+ * helper function to return a node containing the
+ * search summary for a given text. keywords is a list
+ * of stemmed words, hlwords is the list of normal, unstemmed
+ * words. the first one is used to find the occurance, the
+ * latter for highlighting it.
+ */
+ makeSearchSummary : function(text, keywords, hlwords) {
+ var textLower = text.toLowerCase();
+ var start = 0;
+ $.each(keywords, function() {
+ var i = textLower.indexOf(this.toLowerCase());
+ if (i > -1)
+ start = i;
+ });
+ start = Math.max(start - 120, 0);
+ var excerpt = ((start > 0) ? '...' : '') +
+ $.trim(text.substr(start, 240)) +
+ ((start + 240 - text.length) ? '...' : '');
+ var rv = $('<div class="context"></div>').text(excerpt);
+ $.each(hlwords, function() {
+ rv = rv.highlightText(this, 'highlighted');
+ });
+ return rv;
+ }
+};
+
+$(document).ready(function() {
+ Search.init();
+});
\ No newline at end of file
diff --git a/docs/build/html/_static/sidebar.js b/docs/build/html/_static/sidebar.js
new file mode 100644
index 0000000000000000000000000000000000000000..4f09a0df1f433af4e045a62871ebb12169557710
--- /dev/null
+++ b/docs/build/html/_static/sidebar.js
@@ -0,0 +1,159 @@
+/*
+ * sidebar.js
+ * ~~~~~~~~~~
+ *
+ * This script makes the Sphinx sidebar collapsible.
+ *
+ * .sphinxsidebar contains .sphinxsidebarwrapper. This script adds
+ * in .sphixsidebar, after .sphinxsidebarwrapper, the #sidebarbutton
+ * used to collapse and expand the sidebar.
+ *
+ * When the sidebar is collapsed the .sphinxsidebarwrapper is hidden
+ * and the width of the sidebar and the margin-left of the document
+ * are decreased. When the sidebar is expanded the opposite happens.
+ * This script saves a per-browser/per-session cookie used to
+ * remember the position of the sidebar among the pages.
+ * Once the browser is closed the cookie is deleted and the position
+ * reset to the default (expanded).
+ *
+ * :copyright: Copyright 2007-2014 by the Sphinx team, see AUTHORS.
+ * :license: BSD, see LICENSE for details.
+ *
+ */
+
+$(function() {
+
+
+
+
+
+
+
+
+ // global elements used by the functions.
+ // the 'sidebarbutton' element is defined as global after its
+ // creation, in the add_sidebar_button function
+ var bodywrapper = $('.bodywrapper');
+ var sidebar = $('.sphinxsidebar');
+ var sidebarwrapper = $('.sphinxsidebarwrapper');
+
+ // for some reason, the document has no sidebar; do not run into errors
+ if (!sidebar.length) return;
+
+ // original margin-left of the bodywrapper and width of the sidebar
+ // with the sidebar expanded
+ var bw_margin_expanded = bodywrapper.css('margin-left');
+ var ssb_width_expanded = sidebar.width();
+
+ // margin-left of the bodywrapper and width of the sidebar
+ // with the sidebar collapsed
+ var bw_margin_collapsed = '.8em';
+ var ssb_width_collapsed = '.8em';
+
+ // colors used by the current theme
+ var dark_color = $('.related').css('background-color');
+ var light_color = $('.document').css('background-color');
+
+ function sidebar_is_collapsed() {
+ return sidebarwrapper.is(':not(:visible)');
+ }
+
+ function toggle_sidebar() {
+ if (sidebar_is_collapsed())
+ expand_sidebar();
+ else
+ collapse_sidebar();
+ }
+
+ function collapse_sidebar() {
+ sidebarwrapper.hide();
+ sidebar.css('width', ssb_width_collapsed);
+ bodywrapper.css('margin-left', bw_margin_collapsed);
+ sidebarbutton.css({
+ 'margin-left': '0',
+ 'height': bodywrapper.height()
+ });
+ sidebarbutton.find('span').text('»');
+ sidebarbutton.attr('title', _('Expand sidebar'));
+ document.cookie = 'sidebar=collapsed';
+ }
+
+ function expand_sidebar() {
+ bodywrapper.css('margin-left', bw_margin_expanded);
+ sidebar.css('width', ssb_width_expanded);
+ sidebarwrapper.show();
+ sidebarbutton.css({
+ 'margin-left': ssb_width_expanded-12,
+ 'height': bodywrapper.height()
+ });
+ sidebarbutton.find('span').text('«');
+ sidebarbutton.attr('title', _('Collapse sidebar'));
+ document.cookie = 'sidebar=expanded';
+ }
+
+ function add_sidebar_button() {
+ sidebarwrapper.css({
+ 'float': 'left',
+ 'margin-right': '0',
+ 'width': ssb_width_expanded - 28
+ });
+ // create the button
+ sidebar.append(
+ '<div id="sidebarbutton"><span>«</span></div>'
+ );
+ var sidebarbutton = $('#sidebarbutton');
+ light_color = sidebarbutton.css('background-color');
+ // find the height of the viewport to center the '<<' in the page
+ var viewport_height;
+ if (window.innerHeight)
+ viewport_height = window.innerHeight;
+ else
+ viewport_height = $(window).height();
+ sidebarbutton.find('span').css({
+ 'display': 'block',
+ 'margin-top': (viewport_height - sidebar.position().top - 20) / 2
+ });
+
+ sidebarbutton.click(toggle_sidebar);
+ sidebarbutton.attr('title', _('Collapse sidebar'));
+ sidebarbutton.css({
+ 'color': '#FFFFFF',
+ 'border-left': '1px solid ' + dark_color,
+ 'font-size': '1.2em',
+ 'cursor': 'pointer',
+ 'height': bodywrapper.height(),
+ 'padding-top': '1px',
+ 'margin-left': ssb_width_expanded - 12
+ });
+
+ sidebarbutton.hover(
+ function () {
+ $(this).css('background-color', dark_color);
+ },
+ function () {
+ $(this).css('background-color', light_color);
+ }
+ );
+ }
+
+ function set_position_from_cookie() {
+ if (!document.cookie)
+ return;
+ var items = document.cookie.split(';');
+ for(var k=0; k<items.length; k++) {
+ var key_val = items[k].split('=');
+ var key = key_val[0].replace(/ /, ""); // strip leading spaces
+ if (key == 'sidebar') {
+ var value = key_val[1];
+ if ((value == 'collapsed') && (!sidebar_is_collapsed()))
+ collapse_sidebar();
+ else if ((value == 'expanded') && (sidebar_is_collapsed()))
+ expand_sidebar();
+ }
+ }
+ }
+
+ add_sidebar_button();
+ var sidebarbutton = $('#sidebarbutton');
+ set_position_from_cookie();
+});
\ No newline at end of file
diff --git a/docs/build/html/_static/underscore-1.3.1.js b/docs/build/html/_static/underscore-1.3.1.js
new file mode 100644
index 0000000000000000000000000000000000000000..208d4cd890c3183d946092ebe982738ade565061
--- /dev/null
+++ b/docs/build/html/_static/underscore-1.3.1.js
@@ -0,0 +1,999 @@
+// Underscore.js 1.3.1
+// (c) 2009-2012 Jeremy Ashkenas, DocumentCloud Inc.
+// Underscore is freely distributable under the MIT license.
+// Portions of Underscore are inspired or borrowed from Prototype,
+// Oliver Steele's Functional, and John Resig's Micro-Templating.
+// For all details and documentation:
+// http://documentcloud.github.com/underscore
+
+(function() {
+
+ // Baseline setup
+ // --------------
+
+ // Establish the root object, `window` in the browser, or `global` on the server.
+ var root = this;
+
+ // Save the previous value of the `_` variable.
+ var previousUnderscore = root._;
+
+ // Establish the object that gets returned to break out of a loop iteration.
+ var breaker = {};
+
+ // Save bytes in the minified (but not gzipped) version:
+ var ArrayProto = Array.prototype, ObjProto = Object.prototype, FuncProto = Function.prototype;
+
+ // Create quick reference variables for speed access to core prototypes.
+ var slice = ArrayProto.slice,
+ unshift = ArrayProto.unshift,
+ toString = ObjProto.toString,
+ hasOwnProperty = ObjProto.hasOwnProperty;
+
+ // All **ECMAScript 5** native function implementations that we hope to use
+ // are declared here.
+ var
+ nativeForEach = ArrayProto.forEach,
+ nativeMap = ArrayProto.map,
+ nativeReduce = ArrayProto.reduce,
+ nativeReduceRight = ArrayProto.reduceRight,
+ nativeFilter = ArrayProto.filter,
+ nativeEvery = ArrayProto.every,
+ nativeSome = ArrayProto.some,
+ nativeIndexOf = ArrayProto.indexOf,
+ nativeLastIndexOf = ArrayProto.lastIndexOf,
+ nativeIsArray = Array.isArray,
+ nativeKeys = Object.keys,
+ nativeBind = FuncProto.bind;
+
+ // Create a safe reference to the Underscore object for use below.
+ var _ = function(obj) { return new wrapper(obj); };
+
+ // Export the Underscore object for **Node.js**, with
+ // backwards-compatibility for the old `require()` API. If we're in
+ // the browser, add `_` as a global object via a string identifier,
+ // for Closure Compiler "advanced" mode.
+ if (typeof exports !== 'undefined') {
+ if (typeof module !== 'undefined' && module.exports) {
+ exports = module.exports = _;
+ }
+ exports._ = _;
+ } else {
+ root['_'] = _;
+ }
+
+ // Current version.
+ _.VERSION = '1.3.1';
+
+ // Collection Functions
+ // --------------------
+
+ // The cornerstone, an `each` implementation, aka `forEach`.
+ // Handles objects with the built-in `forEach`, arrays, and raw objects.
+ // Delegates to **ECMAScript 5**'s native `forEach` if available.
+ var each = _.each = _.forEach = function(obj, iterator, context) {
+ if (obj == null) return;
+ if (nativeForEach && obj.forEach === nativeForEach) {
+ obj.forEach(iterator, context);
+ } else if (obj.length === +obj.length) {
+ for (var i = 0, l = obj.length; i < l; i++) {
+ if (i in obj && iterator.call(context, obj[i], i, obj) === breaker) return;
+ }
+ } else {
+ for (var key in obj) {
+ if (_.has(obj, key)) {
+ if (iterator.call(context, obj[key], key, obj) === breaker) return;
+ }
+ }
+ }
+ };
+
+ // Return the results of applying the iterator to each element.
+ // Delegates to **ECMAScript 5**'s native `map` if available.
+ _.map = _.collect = function(obj, iterator, context) {
+ var results = [];
+ if (obj == null) return results;
+ if (nativeMap && obj.map === nativeMap) return obj.map(iterator, context);
+ each(obj, function(value, index, list) {
+ results[results.length] = iterator.call(context, value, index, list);
+ });
+ if (obj.length === +obj.length) results.length = obj.length;
+ return results;
+ };
+
+ // **Reduce** builds up a single result from a list of values, aka `inject`,
+ // or `foldl`. Delegates to **ECMAScript 5**'s native `reduce` if available.
+ _.reduce = _.foldl = _.inject = function(obj, iterator, memo, context) {
+ var initial = arguments.length > 2;
+ if (obj == null) obj = [];
+ if (nativeReduce && obj.reduce === nativeReduce) {
+ if (context) iterator = _.bind(iterator, context);
+ return initial ? obj.reduce(iterator, memo) : obj.reduce(iterator);
+ }
+ each(obj, function(value, index, list) {
+ if (!initial) {
+ memo = value;
+ initial = true;
+ } else {
+ memo = iterator.call(context, memo, value, index, list);
+ }
+ });
+ if (!initial) throw new TypeError('Reduce of empty array with no initial value');
+ return memo;
+ };
+
+ // The right-associative version of reduce, also known as `foldr`.
+ // Delegates to **ECMAScript 5**'s native `reduceRight` if available.
+ _.reduceRight = _.foldr = function(obj, iterator, memo, context) {
+ var initial = arguments.length > 2;
+ if (obj == null) obj = [];
+ if (nativeReduceRight && obj.reduceRight === nativeReduceRight) {
+ if (context) iterator = _.bind(iterator, context);
+ return initial ? obj.reduceRight(iterator, memo) : obj.reduceRight(iterator);
+ }
+ var reversed = _.toArray(obj).reverse();
+ if (context && !initial) iterator = _.bind(iterator, context);
+ return initial ? _.reduce(reversed, iterator, memo, context) : _.reduce(reversed, iterator);
+ };
+
+ // Return the first value which passes a truth test. Aliased as `detect`.
+ _.find = _.detect = function(obj, iterator, context) {
+ var result;
+ any(obj, function(value, index, list) {
+ if (iterator.call(context, value, index, list)) {
+ result = value;
+ return true;
+ }
+ });
+ return result;
+ };
+
+ // Return all the elements that pass a truth test.
+ // Delegates to **ECMAScript 5**'s native `filter` if available.
+ // Aliased as `select`.
+ _.filter = _.select = function(obj, iterator, context) {
+ var results = [];
+ if (obj == null) return results;
+ if (nativeFilter && obj.filter === nativeFilter) return obj.filter(iterator, context);
+ each(obj, function(value, index, list) {
+ if (iterator.call(context, value, index, list)) results[results.length] = value;
+ });
+ return results;
+ };
+
+ // Return all the elements for which a truth test fails.
+ _.reject = function(obj, iterator, context) {
+ var results = [];
+ if (obj == null) return results;
+ each(obj, function(value, index, list) {
+ if (!iterator.call(context, value, index, list)) results[results.length] = value;
+ });
+ return results;
+ };
+
+ // Determine whether all of the elements match a truth test.
+ // Delegates to **ECMAScript 5**'s native `every` if available.
+ // Aliased as `all`.
+ _.every = _.all = function(obj, iterator, context) {
+ var result = true;
+ if (obj == null) return result;
+ if (nativeEvery && obj.every === nativeEvery) return obj.every(iterator, context);
+ each(obj, function(value, index, list) {
+ if (!(result = result && iterator.call(context, value, index, list))) return breaker;
+ });
+ return result;
+ };
+
+ // Determine if at least one element in the object matches a truth test.
+ // Delegates to **ECMAScript 5**'s native `some` if available.
+ // Aliased as `any`.
+ var any = _.some = _.any = function(obj, iterator, context) {
+ iterator || (iterator = _.identity);
+ var result = false;
+ if (obj == null) return result;
+ if (nativeSome && obj.some === nativeSome) return obj.some(iterator, context);
+ each(obj, function(value, index, list) {
+ if (result || (result = iterator.call(context, value, index, list))) return breaker;
+ });
+ return !!result;
+ };
+
+ // Determine if a given value is included in the array or object using `===`.
+ // Aliased as `contains`.
+ _.include = _.contains = function(obj, target) {
+ var found = false;
+ if (obj == null) return found;
+ if (nativeIndexOf && obj.indexOf === nativeIndexOf) return obj.indexOf(target) != -1;
+ found = any(obj, function(value) {
+ return value === target;
+ });
+ return found;
+ };
+
+ // Invoke a method (with arguments) on every item in a collection.
+ _.invoke = function(obj, method) {
+ var args = slice.call(arguments, 2);
+ return _.map(obj, function(value) {
+ return (_.isFunction(method) ? method || value : value[method]).apply(value, args);
+ });
+ };
+
+ // Convenience version of a common use case of `map`: fetching a property.
+ _.pluck = function(obj, key) {
+ return _.map(obj, function(value){ return value[key]; });
+ };
+
+ // Return the maximum element or (element-based computation).
+ _.max = function(obj, iterator, context) {
+ if (!iterator && _.isArray(obj)) return Math.max.apply(Math, obj);
+ if (!iterator && _.isEmpty(obj)) return -Infinity;
+ var result = {computed : -Infinity};
+ each(obj, function(value, index, list) {
+ var computed = iterator ? iterator.call(context, value, index, list) : value;
+ computed >= result.computed && (result = {value : value, computed : computed});
+ });
+ return result.value;
+ };
+
+ // Return the minimum element (or element-based computation).
+ _.min = function(obj, iterator, context) {
+ if (!iterator && _.isArray(obj)) return Math.min.apply(Math, obj);
+ if (!iterator && _.isEmpty(obj)) return Infinity;
+ var result = {computed : Infinity};
+ each(obj, function(value, index, list) {
+ var computed = iterator ? iterator.call(context, value, index, list) : value;
+ computed < result.computed && (result = {value : value, computed : computed});
+ });
+ return result.value;
+ };
+
+ // Shuffle an array.
+ _.shuffle = function(obj) {
+ var shuffled = [], rand;
+ each(obj, function(value, index, list) {
+ if (index == 0) {
+ shuffled[0] = value;
+ } else {
+ rand = Math.floor(Math.random() * (index + 1));
+ shuffled[index] = shuffled[rand];
+ shuffled[rand] = value;
+ }
+ });
+ return shuffled;
+ };
+
+ // Sort the object's values by a criterion produced by an iterator.
+ _.sortBy = function(obj, iterator, context) {
+ return _.pluck(_.map(obj, function(value, index, list) {
+ return {
+ value : value,
+ criteria : iterator.call(context, value, index, list)
+ };
+ }).sort(function(left, right) {
+ var a = left.criteria, b = right.criteria;
+ return a < b ? -1 : a > b ? 1 : 0;
+ }), 'value');
+ };
+
+ // Groups the object's values by a criterion. Pass either a string attribute
+ // to group by, or a function that returns the criterion.
+ _.groupBy = function(obj, val) {
+ var result = {};
+ var iterator = _.isFunction(val) ? val : function(obj) { return obj[val]; };
+ each(obj, function(value, index) {
+ var key = iterator(value, index);
+ (result[key] || (result[key] = [])).push(value);
+ });
+ return result;
+ };
+
+ // Use a comparator function to figure out at what index an object should
+ // be inserted so as to maintain order. Uses binary search.
+ _.sortedIndex = function(array, obj, iterator) {
+ iterator || (iterator = _.identity);
+ var low = 0, high = array.length;
+ while (low < high) {
+ var mid = (low + high) >> 1;
+ iterator(array[mid]) < iterator(obj) ? low = mid + 1 : high = mid;
+ }
+ return low;
+ };
+
+ // Safely convert anything iterable into a real, live array.
+ _.toArray = function(iterable) {
+ if (!iterable) return [];
+ if (iterable.toArray) return iterable.toArray();
+ if (_.isArray(iterable)) return slice.call(iterable);
+ if (_.isArguments(iterable)) return slice.call(iterable);
+ return _.values(iterable);
+ };
+
+ // Return the number of elements in an object.
+ _.size = function(obj) {
+ return _.toArray(obj).length;
+ };
+
+ // Array Functions
+ // ---------------
+
+ // Get the first element of an array. Passing **n** will return the first N
+ // values in the array. Aliased as `head`. The **guard** check allows it to work
+ // with `_.map`.
+ _.first = _.head = function(array, n, guard) {
+ return (n != null) && !guard ? slice.call(array, 0, n) : array[0];
+ };
+
+ // Returns everything but the last entry of the array. Especcialy useful on
+ // the arguments object. Passing **n** will return all the values in
+ // the array, excluding the last N. The **guard** check allows it to work with
+ // `_.map`.
+ _.initial = function(array, n, guard) {
+ return slice.call(array, 0, array.length - ((n == null) || guard ? 1 : n));
+ };
+
+ // Get the last element of an array. Passing **n** will return the last N
+ // values in the array. The **guard** check allows it to work with `_.map`.
+ _.last = function(array, n, guard) {
+ if ((n != null) && !guard) {
+ return slice.call(array, Math.max(array.length - n, 0));
+ } else {
+ return array[array.length - 1];
+ }
+ };
+
+ // Returns everything but the first entry of the array. Aliased as `tail`.
+ // Especially useful on the arguments object. Passing an **index** will return
+ // the rest of the values in the array from that index onward. The **guard**
+ // check allows it to work with `_.map`.
+ _.rest = _.tail = function(array, index, guard) {
+ return slice.call(array, (index == null) || guard ? 1 : index);
+ };
+
+ // Trim out all falsy values from an array.
+ _.compact = function(array) {
+ return _.filter(array, function(value){ return !!value; });
+ };
+
+ // Return a completely flattened version of an array.
+ _.flatten = function(array, shallow) {
+ return _.reduce(array, function(memo, value) {
+ if (_.isArray(value)) return memo.concat(shallow ? value : _.flatten(value));
+ memo[memo.length] = value;
+ return memo;
+ }, []);
+ };
+
+ // Return a version of the array that does not contain the specified value(s).
+ _.without = function(array) {
+ return _.difference(array, slice.call(arguments, 1));
+ };
+
+ // Produce a duplicate-free version of the array. If the array has already
+ // been sorted, you have the option of using a faster algorithm.
+ // Aliased as `unique`.
+ _.uniq = _.unique = function(array, isSorted, iterator) {
+ var initial = iterator ? _.map(array, iterator) : array;
+ var result = [];
+ _.reduce(initial, function(memo, el, i) {
+ if (0 == i || (isSorted === true ? _.last(memo) != el : !_.include(memo, el))) {
+ memo[memo.length] = el;
+ result[result.length] = array[i];
+ }
+ return memo;
+ }, []);
+ return result;
+ };
+
+ // Produce an array that contains the union: each distinct element from all of
+ // the passed-in arrays.
+ _.union = function() {
+ return _.uniq(_.flatten(arguments, true));
+ };
+
+ // Produce an array that contains every item shared between all the
+ // passed-in arrays. (Aliased as "intersect" for back-compat.)
+ _.intersection = _.intersect = function(array) {
+ var rest = slice.call(arguments, 1);
+ return _.filter(_.uniq(array), function(item) {
+ return _.every(rest, function(other) {
+ return _.indexOf(other, item) >= 0;
+ });
+ });
+ };
+
+ // Take the difference between one array and a number of other arrays.
+ // Only the elements present in just the first array will remain.
+ _.difference = function(array) {
+ var rest = _.flatten(slice.call(arguments, 1));
+ return _.filter(array, function(value){ return !_.include(rest, value); });
+ };
+
+ // Zip together multiple lists into a single array -- elements that share
+ // an index go together.
+ _.zip = function() {
+ var args = slice.call(arguments);
+ var length = _.max(_.pluck(args, 'length'));
+ var results = new Array(length);
+ for (var i = 0; i < length; i++) results[i] = _.pluck(args, "" + i);
+ return results;
+ };
+
+ // If the browser doesn't supply us with indexOf (I'm looking at you, **MSIE**),
+ // we need this function. Return the position of the first occurrence of an
+ // item in an array, or -1 if the item is not included in the array.
+ // Delegates to **ECMAScript 5**'s native `indexOf` if available.
+ // If the array is large and already in sort order, pass `true`
+ // for **isSorted** to use binary search.
+ _.indexOf = function(array, item, isSorted) {
+ if (array == null) return -1;
+ var i, l;
+ if (isSorted) {
+ i = _.sortedIndex(array, item);
+ return array[i] === item ? i : -1;
+ }
+ if (nativeIndexOf && array.indexOf === nativeIndexOf) return array.indexOf(item);
+ for (i = 0, l = array.length; i < l; i++) if (i in array && array[i] === item) return i;
+ return -1;
+ };
+
+ // Delegates to **ECMAScript 5**'s native `lastIndexOf` if available.
+ _.lastIndexOf = function(array, item) {
+ if (array == null) return -1;
+ if (nativeLastIndexOf && array.lastIndexOf === nativeLastIndexOf) return array.lastIndexOf(item);
+ var i = array.length;
+ while (i--) if (i in array && array[i] === item) return i;
+ return -1;
+ };
+
+ // Generate an integer Array containing an arithmetic progression. A port of
+ // the native Python `range()` function. See
+ // [the Python documentation](http://docs.python.org/library/functions.html#range).
+ _.range = function(start, stop, step) {
+ if (arguments.length <= 1) {
+ stop = start || 0;
+ start = 0;
+ }
+ step = arguments[2] || 1;
+
+ var len = Math.max(Math.ceil((stop - start) / step), 0);
+ var idx = 0;
+ var range = new Array(len);
+
+ while(idx < len) {
+ range[idx++] = start;
+ start += step;
+ }
+
+ return range;
+ };
+
+ // Function (ahem) Functions
+ // ------------------
+
+ // Reusable constructor function for prototype setting.
+ var ctor = function(){};
+
+ // Create a function bound to a given object (assigning `this`, and arguments,
+ // optionally). Binding with arguments is also known as `curry`.
+ // Delegates to **ECMAScript 5**'s native `Function.bind` if available.
+ // We check for `func.bind` first, to fail fast when `func` is undefined.
+ _.bind = function bind(func, context) {
+ var bound, args;
+ if (func.bind === nativeBind && nativeBind) return nativeBind.apply(func, slice.call(arguments, 1));
+ if (!_.isFunction(func)) throw new TypeError;
+ args = slice.call(arguments, 2);
+ return bound = function() {
+ if (!(this instanceof bound)) return func.apply(context, args.concat(slice.call(arguments)));
+ ctor.prototype = func.prototype;
+ var self = new ctor;
+ var result = func.apply(self, args.concat(slice.call(arguments)));
+ if (Object(result) === result) return result;
+ return self;
+ };
+ };
+
+ // Bind all of an object's methods to that object. Useful for ensuring that
+ // all callbacks defined on an object belong to it.
+ _.bindAll = function(obj) {
+ var funcs = slice.call(arguments, 1);
+ if (funcs.length == 0) funcs = _.functions(obj);
+ each(funcs, function(f) { obj[f] = _.bind(obj[f], obj); });
+ return obj;
+ };
+
+ // Memoize an expensive function by storing its results.
+ _.memoize = function(func, hasher) {
+ var memo = {};
+ hasher || (hasher = _.identity);
+ return function() {
+ var key = hasher.apply(this, arguments);
+ return _.has(memo, key) ? memo[key] : (memo[key] = func.apply(this, arguments));
+ };
+ };
+
+ // Delays a function for the given number of milliseconds, and then calls
+ // it with the arguments supplied.
+ _.delay = function(func, wait) {
+ var args = slice.call(arguments, 2);
+ return setTimeout(function(){ return func.apply(func, args); }, wait);
+ };
+
+ // Defers a function, scheduling it to run after the current call stack has
+ // cleared.
+ _.defer = function(func) {
+ return _.delay.apply(_, [func, 1].concat(slice.call(arguments, 1)));
+ };
+
+ // Returns a function, that, when invoked, will only be triggered at most once
+ // during a given window of time.
+ _.throttle = function(func, wait) {
+ var context, args, timeout, throttling, more;
+ var whenDone = _.debounce(function(){ more = throttling = false; }, wait);
+ return function() {
+ context = this; args = arguments;
+ var later = function() {
+ timeout = null;
+ if (more) func.apply(context, args);
+ whenDone();
+ };
+ if (!timeout) timeout = setTimeout(later, wait);
+ if (throttling) {
+ more = true;
+ } else {
+ func.apply(context, args);
+ }
+ whenDone();
+ throttling = true;
+ };
+ };
+
+ // Returns a function, that, as long as it continues to be invoked, will not
+ // be triggered. The function will be called after it stops being called for
+ // N milliseconds.
+ _.debounce = function(func, wait) {
+ var timeout;
+ return function() {
+ var context = this, args = arguments;
+ var later = function() {
+ timeout = null;
+ func.apply(context, args);
+ };
+ clearTimeout(timeout);
+ timeout = setTimeout(later, wait);
+ };
+ };
+
+ // Returns a function that will be executed at most one time, no matter how
+ // often you call it. Useful for lazy initialization.
+ _.once = function(func) {
+ var ran = false, memo;
+ return function() {
+ if (ran) return memo;
+ ran = true;
+ return memo = func.apply(this, arguments);
+ };
+ };
+
+ // Returns the first function passed as an argument to the second,
+ // allowing you to adjust arguments, run code before and after, and
+ // conditionally execute the original function.
+ _.wrap = function(func, wrapper) {
+ return function() {
+ var args = [func].concat(slice.call(arguments, 0));
+ return wrapper.apply(this, args);
+ };
+ };
+
+ // Returns a function that is the composition of a list of functions, each
+ // consuming the return value of the function that follows.
+ _.compose = function() {
+ var funcs = arguments;
+ return function() {
+ var args = arguments;
+ for (var i = funcs.length - 1; i >= 0; i--) {
+ args = [funcs[i].apply(this, args)];
+ }
+ return args[0];
+ };
+ };
+
+ // Returns a function that will only be executed after being called N times.
+ _.after = function(times, func) {
+ if (times <= 0) return func();
+ return function() {
+ if (--times < 1) { return func.apply(this, arguments); }
+ };
+ };
+
+ // Object Functions
+ // ----------------
+
+ // Retrieve the names of an object's properties.
+ // Delegates to **ECMAScript 5**'s native `Object.keys`
+ _.keys = nativeKeys || function(obj) {
+ if (obj !== Object(obj)) throw new TypeError('Invalid object');
+ var keys = [];
+ for (var key in obj) if (_.has(obj, key)) keys[keys.length] = key;
+ return keys;
+ };
+
+ // Retrieve the values of an object's properties.
+ _.values = function(obj) {
+ return _.map(obj, _.identity);
+ };
+
+ // Return a sorted list of the function names available on the object.
+ // Aliased as `methods`
+ _.functions = _.methods = function(obj) {
+ var names = [];
+ for (var key in obj) {
+ if (_.isFunction(obj[key])) names.push(key);
+ }
+ return names.sort();
+ };
+
+ // Extend a given object with all the properties in passed-in object(s).
+ _.extend = function(obj) {
+ each(slice.call(arguments, 1), function(source) {
+ for (var prop in source) {
+ obj[prop] = source[prop];
+ }
+ });
+ return obj;
+ };
+
+ // Fill in a given object with default properties.
+ _.defaults = function(obj) {
+ each(slice.call(arguments, 1), function(source) {
+ for (var prop in source) {
+ if (obj[prop] == null) obj[prop] = source[prop];
+ }
+ });
+ return obj;
+ };
+
+ // Create a (shallow-cloned) duplicate of an object.
+ _.clone = function(obj) {
+ if (!_.isObject(obj)) return obj;
+ return _.isArray(obj) ? obj.slice() : _.extend({}, obj);
+ };
+
+ // Invokes interceptor with the obj, and then returns obj.
+ // The primary purpose of this method is to "tap into" a method chain, in
+ // order to perform operations on intermediate results within the chain.
+ _.tap = function(obj, interceptor) {
+ interceptor(obj);
+ return obj;
+ };
+
+ // Internal recursive comparison function.
+ function eq(a, b, stack) {
+ // Identical objects are equal. `0 === -0`, but they aren't identical.
+ // See the Harmony `egal` proposal: http://wiki.ecmascript.org/doku.php?id=harmony:egal.
+ if (a === b) return a !== 0 || 1 / a == 1 / b;
+ // A strict comparison is necessary because `null == undefined`.
+ if (a == null || b == null) return a === b;
+ // Unwrap any wrapped objects.
+ if (a._chain) a = a._wrapped;
+ if (b._chain) b = b._wrapped;
+ // Invoke a custom `isEqual` method if one is provided.
+ if (a.isEqual && _.isFunction(a.isEqual)) return a.isEqual(b);
+ if (b.isEqual && _.isFunction(b.isEqual)) return b.isEqual(a);
+ // Compare `[[Class]]` names.
+ var className = toString.call(a);
+ if (className != toString.call(b)) return false;
+ switch (className) {
+ // Strings, numbers, dates, and booleans are compared by value.
+ case '[object String]':
+ // Primitives and their corresponding object wrappers are equivalent; thus, `"5"` is
+ // equivalent to `new String("5")`.
+ return a == String(b);
+ case '[object Number]':
+ // `NaN`s are equivalent, but non-reflexive. An `egal` comparison is performed for
+ // other numeric values.
+ return a != +a ? b != +b : (a == 0 ? 1 / a == 1 / b : a == +b);
+ case '[object Date]':
+ case '[object Boolean]':
+ // Coerce dates and booleans to numeric primitive values. Dates are compared by their
+ // millisecond representations. Note that invalid dates with millisecond representations
+ // of `NaN` are not equivalent.
+ return +a == +b;
+ // RegExps are compared by their source patterns and flags.
+ case '[object RegExp]':
+ return a.source == b.source &&
+ a.global == b.global &&
+ a.multiline == b.multiline &&
+ a.ignoreCase == b.ignoreCase;
+ }
+ if (typeof a != 'object' || typeof b != 'object') return false;
+ // Assume equality for cyclic structures. The algorithm for detecting cyclic
+ // structures is adapted from ES 5.1 section 15.12.3, abstract operation `JO`.
+ var length = stack.length;
+ while (length--) {
+ // Linear search. Performance is inversely proportional to the number of
+ // unique nested structures.
+ if (stack[length] == a) return true;
+ }
+ // Add the first object to the stack of traversed objects.
+ stack.push(a);
+ var size = 0, result = true;
+ // Recursively compare objects and arrays.
+ if (className == '[object Array]') {
+ // Compare array lengths to determine if a deep comparison is necessary.
+ size = a.length;
+ result = size == b.length;
+ if (result) {
+ // Deep compare the contents, ignoring non-numeric properties.
+ while (size--) {
+ // Ensure commutative equality for sparse arrays.
+ if (!(result = size in a == size in b && eq(a[size], b[size], stack))) break;
+ }
+ }
+ } else {
+ // Objects with different constructors are not equivalent.
+ if ('constructor' in a != 'constructor' in b || a.constructor != b.constructor) return false;
+ // Deep compare objects.
+ for (var key in a) {
+ if (_.has(a, key)) {
+ // Count the expected number of properties.
+ size++;
+ // Deep compare each member.
+ if (!(result = _.has(b, key) && eq(a[key], b[key], stack))) break;
+ }
+ }
+ // Ensure that both objects contain the same number of properties.
+ if (result) {
+ for (key in b) {
+ if (_.has(b, key) && !(size--)) break;
+ }
+ result = !size;
+ }
+ }
+ // Remove the first object from the stack of traversed objects.
+ stack.pop();
+ return result;
+ }
+
+ // Perform a deep comparison to check if two objects are equal.
+ _.isEqual = function(a, b) {
+ return eq(a, b, []);
+ };
+
+ // Is a given array, string, or object empty?
+ // An "empty" object has no enumerable own-properties.
+ _.isEmpty = function(obj) {
+ if (_.isArray(obj) || _.isString(obj)) return obj.length === 0;
+ for (var key in obj) if (_.has(obj, key)) return false;
+ return true;
+ };
+
+ // Is a given value a DOM element?
+ _.isElement = function(obj) {
+ return !!(obj && obj.nodeType == 1);
+ };
+
+ // Is a given value an array?
+ // Delegates to ECMA5's native Array.isArray
+ _.isArray = nativeIsArray || function(obj) {
+ return toString.call(obj) == '[object Array]';
+ };
+
+ // Is a given variable an object?
+ _.isObject = function(obj) {
+ return obj === Object(obj);
+ };
+
+ // Is a given variable an arguments object?
+ _.isArguments = function(obj) {
+ return toString.call(obj) == '[object Arguments]';
+ };
+ if (!_.isArguments(arguments)) {
+ _.isArguments = function(obj) {
+ return !!(obj && _.has(obj, 'callee'));
+ };
+ }
+
+ // Is a given value a function?
+ _.isFunction = function(obj) {
+ return toString.call(obj) == '[object Function]';
+ };
+
+ // Is a given value a string?
+ _.isString = function(obj) {
+ return toString.call(obj) == '[object String]';
+ };
+
+ // Is a given value a number?
+ _.isNumber = function(obj) {
+ return toString.call(obj) == '[object Number]';
+ };
+
+ // Is the given value `NaN`?
+ _.isNaN = function(obj) {
+ // `NaN` is the only value for which `===` is not reflexive.
+ return obj !== obj;
+ };
+
+ // Is a given value a boolean?
+ _.isBoolean = function(obj) {
+ return obj === true || obj === false || toString.call(obj) == '[object Boolean]';
+ };
+
+ // Is a given value a date?
+ _.isDate = function(obj) {
+ return toString.call(obj) == '[object Date]';
+ };
+
+ // Is the given value a regular expression?
+ _.isRegExp = function(obj) {
+ return toString.call(obj) == '[object RegExp]';
+ };
+
+ // Is a given value equal to null?
+ _.isNull = function(obj) {
+ return obj === null;
+ };
+
+ // Is a given variable undefined?
+ _.isUndefined = function(obj) {
+ return obj === void 0;
+ };
+
+ // Has own property?
+ _.has = function(obj, key) {
+ return hasOwnProperty.call(obj, key);
+ };
+
+ // Utility Functions
+ // -----------------
+
+ // Run Underscore.js in *noConflict* mode, returning the `_` variable to its
+ // previous owner. Returns a reference to the Underscore object.
+ _.noConflict = function() {
+ root._ = previousUnderscore;
+ return this;
+ };
+
+ // Keep the identity function around for default iterators.
+ _.identity = function(value) {
+ return value;
+ };
+
+ // Run a function **n** times.
+ _.times = function (n, iterator, context) {
+ for (var i = 0; i < n; i++) iterator.call(context, i);
+ };
+
+ // Escape a string for HTML interpolation.
+ _.escape = function(string) {
+ return (''+string).replace(/&/g, '&').replace(/</g, '<').replace(/>/g, '>').replace(/"/g, '"').replace(/'/g, ''').replace(/\//g,'/');
+ };
+
+ // Add your own custom functions to the Underscore object, ensuring that
+ // they're correctly added to the OOP wrapper as well.
+ _.mixin = function(obj) {
+ each(_.functions(obj), function(name){
+ addToWrapper(name, _[name] = obj[name]);
+ });
+ };
+
+ // Generate a unique integer id (unique within the entire client session).
+ // Useful for temporary DOM ids.
+ var idCounter = 0;
+ _.uniqueId = function(prefix) {
+ var id = idCounter++;
+ return prefix ? prefix + id : id;
+ };
+
+ // By default, Underscore uses ERB-style template delimiters, change the
+ // following template settings to use alternative delimiters.
+ _.templateSettings = {
+ evaluate : /<%([\s\S]+?)%>/g,
+ interpolate : /<%=([\s\S]+?)%>/g,
+ escape : /<%-([\s\S]+?)%>/g
+ };
+
+ // When customizing `templateSettings`, if you don't want to define an
+ // interpolation, evaluation or escaping regex, we need one that is
+ // guaranteed not to match.
+ var noMatch = /.^/;
+
+ // Within an interpolation, evaluation, or escaping, remove HTML escaping
+ // that had been previously added.
+ var unescape = function(code) {
+ return code.replace(/\\\\/g, '\\').replace(/\\'/g, "'");
+ };
+
+ // JavaScript micro-templating, similar to John Resig's implementation.
+ // Underscore templating handles arbitrary delimiters, preserves whitespace,
+ // and correctly escapes quotes within interpolated code.
+ _.template = function(str, data) {
+ var c = _.templateSettings;
+ var tmpl = 'var __p=[],print=function(){__p.push.apply(__p,arguments);};' +
+ 'with(obj||{}){__p.push(\'' +
+ str.replace(/\\/g, '\\\\')
+ .replace(/'/g, "\\'")
+ .replace(c.escape || noMatch, function(match, code) {
+ return "',_.escape(" + unescape(code) + "),'";
+ })
+ .replace(c.interpolate || noMatch, function(match, code) {
+ return "'," + unescape(code) + ",'";
+ })
+ .replace(c.evaluate || noMatch, function(match, code) {
+ return "');" + unescape(code).replace(/[\r\n\t]/g, ' ') + ";__p.push('";
+ })
+ .replace(/\r/g, '\\r')
+ .replace(/\n/g, '\\n')
+ .replace(/\t/g, '\\t')
+ + "');}return __p.join('');";
+ var func = new Function('obj', '_', tmpl);
+ if (data) return func(data, _);
+ return function(data) {
+ return func.call(this, data, _);
+ };
+ };
+
+ // Add a "chain" function, which will delegate to the wrapper.
+ _.chain = function(obj) {
+ return _(obj).chain();
+ };
+
+ // The OOP Wrapper
+ // ---------------
+
+ // If Underscore is called as a function, it returns a wrapped object that
+ // can be used OO-style. This wrapper holds altered versions of all the
+ // underscore functions. Wrapped objects may be chained.
+ var wrapper = function(obj) { this._wrapped = obj; };
+
+ // Expose `wrapper.prototype` as `_.prototype`
+ _.prototype = wrapper.prototype;
+
+ // Helper function to continue chaining intermediate results.
+ var result = function(obj, chain) {
+ return chain ? _(obj).chain() : obj;
+ };
+
+ // A method to easily add functions to the OOP wrapper.
+ var addToWrapper = function(name, func) {
+ wrapper.prototype[name] = function() {
+ var args = slice.call(arguments);
+ unshift.call(args, this._wrapped);
+ return result(func.apply(_, args), this._chain);
+ };
+ };
+
+ // Add all of the Underscore functions to the wrapper object.
+ _.mixin(_);
+
+ // Add all mutator Array functions to the wrapper.
+ each(['pop', 'push', 'reverse', 'shift', 'sort', 'splice', 'unshift'], function(name) {
+ var method = ArrayProto[name];
+ wrapper.prototype[name] = function() {
+ var wrapped = this._wrapped;
+ method.apply(wrapped, arguments);
+ var length = wrapped.length;
+ if ((name == 'shift' || name == 'splice') && length === 0) delete wrapped[0];
+ return result(wrapped, this._chain);
+ };
+ });
+
+ // Add all accessor Array functions to the wrapper.
+ each(['concat', 'join', 'slice'], function(name) {
+ var method = ArrayProto[name];
+ wrapper.prototype[name] = function() {
+ return result(method.apply(this._wrapped, arguments), this._chain);
+ };
+ });
+
+ // Start chaining a wrapped Underscore object.
+ wrapper.prototype.chain = function() {
+ this._chain = true;
+ return this;
+ };
+
+ // Extracts the result from a wrapped and chained object.
+ wrapper.prototype.value = function() {
+ return this._wrapped;
+ };
+
+}).call(this);
diff --git a/docs/build/html/_static/underscore.js b/docs/build/html/_static/underscore.js
new file mode 100644
index 0000000000000000000000000000000000000000..5b55f32beaca186f84cca115514f02cddbd1bbd5
--- /dev/null
+++ b/docs/build/html/_static/underscore.js
@@ -0,0 +1,31 @@
+// Underscore.js 1.3.1
+// (c) 2009-2012 Jeremy Ashkenas, DocumentCloud Inc.
+// Underscore is freely distributable under the MIT license.
+// Portions of Underscore are inspired or borrowed from Prototype,
+// Oliver Steele's Functional, and John Resig's Micro-Templating.
+// For all details and documentation:
+// http://documentcloud.github.com/underscore
+(function(){function q(a,c,d){if(a===c)return a!==0||1/a==1/c;if(a==null||c==null)return a===c;if(a._chain)a=a._wrapped;if(c._chain)c=c._wrapped;if(a.isEqual&&b.isFunction(a.isEqual))return a.isEqual(c);if(c.isEqual&&b.isFunction(c.isEqual))return c.isEqual(a);var e=l.call(a);if(e!=l.call(c))return false;switch(e){case "[object String]":return a==String(c);case "[object Number]":return a!=+a?c!=+c:a==0?1/a==1/c:a==+c;case "[object Date]":case "[object Boolean]":return+a==+c;case "[object RegExp]":return a.source==
+c.source&&a.global==c.global&&a.multiline==c.multiline&&a.ignoreCase==c.ignoreCase}if(typeof a!="object"||typeof c!="object")return false;for(var f=d.length;f--;)if(d[f]==a)return true;d.push(a);var f=0,g=true;if(e=="[object Array]"){if(f=a.length,g=f==c.length)for(;f--;)if(!(g=f in a==f in c&&q(a[f],c[f],d)))break}else{if("constructor"in a!="constructor"in c||a.constructor!=c.constructor)return false;for(var h in a)if(b.has(a,h)&&(f++,!(g=b.has(c,h)&&q(a[h],c[h],d))))break;if(g){for(h in c)if(b.has(c,
+h)&&!f--)break;g=!f}}d.pop();return g}var r=this,G=r._,n={},k=Array.prototype,o=Object.prototype,i=k.slice,H=k.unshift,l=o.toString,I=o.hasOwnProperty,w=k.forEach,x=k.map,y=k.reduce,z=k.reduceRight,A=k.filter,B=k.every,C=k.some,p=k.indexOf,D=k.lastIndexOf,o=Array.isArray,J=Object.keys,s=Function.prototype.bind,b=function(a){return new m(a)};if(typeof exports!=="undefined"){if(typeof module!=="undefined"&&module.exports)exports=module.exports=b;exports._=b}else r._=b;b.VERSION="1.3.1";var j=b.each=
+b.forEach=function(a,c,d){if(a!=null)if(w&&a.forEach===w)a.forEach(c,d);else if(a.length===+a.length)for(var e=0,f=a.length;e<f;e++){if(e in a&&c.call(d,a[e],e,a)===n)break}else for(e in a)if(b.has(a,e)&&c.call(d,a[e],e,a)===n)break};b.map=b.collect=function(a,c,b){var e=[];if(a==null)return e;if(x&&a.map===x)return a.map(c,b);j(a,function(a,g,h){e[e.length]=c.call(b,a,g,h)});if(a.length===+a.length)e.length=a.length;return e};b.reduce=b.foldl=b.inject=function(a,c,d,e){var f=arguments.length>2;a==
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+function(a,c){return b.map(a,function(a){return a[c]})};b.max=function(a,c,d){if(!c&&b.isArray(a))return Math.max.apply(Math,a);if(!c&&b.isEmpty(a))return-Infinity;var e={computed:-Infinity};j(a,function(a,b,h){b=c?c.call(d,a,b,h):a;b>=e.computed&&(e={value:a,computed:b})});return e.value};b.min=function(a,c,d){if(!c&&b.isArray(a))return Math.min.apply(Math,a);if(!c&&b.isEmpty(a))return Infinity;var e={computed:Infinity};j(a,function(a,b,h){b=c?c.call(d,a,b,h):a;b<e.computed&&(e={value:a,computed:b})});
+return e.value};b.shuffle=function(a){var b=[],d;j(a,function(a,f){f==0?b[0]=a:(d=Math.floor(Math.random()*(f+1)),b[f]=b[d],b[d]=a)});return b};b.sortBy=function(a,c,d){return b.pluck(b.map(a,function(a,b,g){return{value:a,criteria:c.call(d,a,b,g)}}).sort(function(a,b){var c=a.criteria,d=b.criteria;return c<d?-1:c>d?1:0}),"value")};b.groupBy=function(a,c){var d={},e=b.isFunction(c)?c:function(a){return a[c]};j(a,function(a,b){var c=e(a,b);(d[c]||(d[c]=[])).push(a)});return d};b.sortedIndex=function(a,
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+b.tail=function(a,b,d){return i.call(a,b==null||d?1:b)};b.compact=function(a){return b.filter(a,function(a){return!!a})};b.flatten=function(a,c){return b.reduce(a,function(a,e){if(b.isArray(e))return a.concat(c?e:b.flatten(e));a[a.length]=e;return a},[])};b.without=function(a){return b.difference(a,i.call(arguments,1))};b.uniq=b.unique=function(a,c,d){var d=d?b.map(a,d):a,e=[];b.reduce(d,function(d,g,h){if(0==h||(c===true?b.last(d)!=g:!b.include(d,g)))d[d.length]=g,e[e.length]=a[h];return d},[]);
+return e};b.union=function(){return b.uniq(b.flatten(arguments,true))};b.intersection=b.intersect=function(a){var c=i.call(arguments,1);return b.filter(b.uniq(a),function(a){return b.every(c,function(c){return b.indexOf(c,a)>=0})})};b.difference=function(a){var c=b.flatten(i.call(arguments,1));return b.filter(a,function(a){return!b.include(c,a)})};b.zip=function(){for(var a=i.call(arguments),c=b.max(b.pluck(a,"length")),d=Array(c),e=0;e<c;e++)d[e]=b.pluck(a,""+e);return d};b.indexOf=function(a,c,
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+var F=function(){};b.bind=function(a,c){var d,e;if(a.bind===s&&s)return s.apply(a,i.call(arguments,1));if(!b.isFunction(a))throw new TypeError;e=i.call(arguments,2);return d=function(){if(!(this instanceof d))return a.apply(c,e.concat(i.call(arguments)));F.prototype=a.prototype;var b=new F,g=a.apply(b,e.concat(i.call(arguments)));return Object(g)===g?g:b}};b.bindAll=function(a){var c=i.call(arguments,1);c.length==0&&(c=b.functions(a));j(c,function(c){a[c]=b.bind(a[c],a)});return a};b.memoize=function(a,
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+b.after=function(a,b){return a<=0?b():function(){if(--a<1)return b.apply(this,arguments)}};b.keys=J||function(a){if(a!==Object(a))throw new TypeError("Invalid object");var c=[],d;for(d in a)b.has(a,d)&&(c[c.length]=d);return c};b.values=function(a){return b.map(a,b.identity)};b.functions=b.methods=function(a){var c=[],d;for(d in a)b.isFunction(a[d])&&c.push(d);return c.sort()};b.extend=function(a){j(i.call(arguments,1),function(b){for(var d in b)a[d]=b[d]});return a};b.defaults=function(a){j(i.call(arguments,
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+b.isArguments=function(a){return l.call(a)=="[object Arguments]"};if(!b.isArguments(arguments))b.isArguments=function(a){return!(!a||!b.has(a,"callee"))};b.isFunction=function(a){return l.call(a)=="[object Function]"};b.isString=function(a){return l.call(a)=="[object String]"};b.isNumber=function(a){return l.call(a)=="[object Number]"};b.isNaN=function(a){return a!==a};b.isBoolean=function(a){return a===true||a===false||l.call(a)=="[object Boolean]"};b.isDate=function(a){return l.call(a)=="[object Date]"};
+b.isRegExp=function(a){return l.call(a)=="[object RegExp]"};b.isNull=function(a){return a===null};b.isUndefined=function(a){return a===void 0};b.has=function(a,b){return I.call(a,b)};b.noConflict=function(){r._=G;return this};b.identity=function(a){return a};b.times=function(a,b,d){for(var e=0;e<a;e++)b.call(d,e)};b.escape=function(a){return(""+a).replace(/&/g,"&").replace(/</g,"<").replace(/>/g,">").replace(/"/g,""").replace(/'/g,"'").replace(/\//g,"/")};b.mixin=function(a){j(b.functions(a),
+function(c){K(c,b[c]=a[c])})};var L=0;b.uniqueId=function(a){var b=L++;return a?a+b:b};b.templateSettings={evaluate:/<%([\s\S]+?)%>/g,interpolate:/<%=([\s\S]+?)%>/g,escape:/<%-([\s\S]+?)%>/g};var t=/.^/,u=function(a){return a.replace(/\\\\/g,"\\").replace(/\\'/g,"'")};b.template=function(a,c){var d=b.templateSettings,d="var __p=[],print=function(){__p.push.apply(__p,arguments);};with(obj||{}){__p.push('"+a.replace(/\\/g,"\\\\").replace(/'/g,"\\'").replace(d.escape||t,function(a,b){return"',_.escape("+
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+function(){var a=i.call(arguments);H.call(a,this._wrapped);return v(c.apply(b,a),this._chain)}};b.mixin(b);j("pop,push,reverse,shift,sort,splice,unshift".split(","),function(a){var b=k[a];m.prototype[a]=function(){var d=this._wrapped;b.apply(d,arguments);var e=d.length;(a=="shift"||a=="splice")&&e===0&&delete d[0];return v(d,this._chain)}});j(["concat","join","slice"],function(a){var b=k[a];m.prototype[a]=function(){return v(b.apply(this._wrapped,arguments),this._chain)}});m.prototype.chain=function(){this._chain=
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diff --git a/docs/build/html/_static/up-pressed.png b/docs/build/html/_static/up-pressed.png
new file mode 100644
index 0000000000000000000000000000000000000000..99e7210962b0667e47408b40fdb5dd14749a156e
Binary files /dev/null and b/docs/build/html/_static/up-pressed.png differ
diff --git a/docs/build/html/_static/up.png b/docs/build/html/_static/up.png
new file mode 100644
index 0000000000000000000000000000000000000000..26de002e85d3f5df53163e80b61af59bc4a6389b
Binary files /dev/null and b/docs/build/html/_static/up.png differ
diff --git a/docs/build/html/_static/websupport.js b/docs/build/html/_static/websupport.js
new file mode 100644
index 0000000000000000000000000000000000000000..9932afb99dc989f5e65c8003bd0c1f31f57e7665
--- /dev/null
+++ b/docs/build/html/_static/websupport.js
@@ -0,0 +1,808 @@
+/*
+ * websupport.js
+ * ~~~~~~~~~~~~~
+ *
+ * sphinx.websupport utilties for all documentation.
+ *
+ * :copyright: Copyright 2007-2014 by the Sphinx team, see AUTHORS.
+ * :license: BSD, see LICENSE for details.
+ *
+ */
+
+(function($) {
+ $.fn.autogrow = function() {
+ return this.each(function() {
+ var textarea = this;
+
+ $.fn.autogrow.resize(textarea);
+
+ $(textarea)
+ .focus(function() {
+ textarea.interval = setInterval(function() {
+ $.fn.autogrow.resize(textarea);
+ }, 500);
+ })
+ .blur(function() {
+ clearInterval(textarea.interval);
+ });
+ });
+ };
+
+ $.fn.autogrow.resize = function(textarea) {
+ var lineHeight = parseInt($(textarea).css('line-height'), 10);
+ var lines = textarea.value.split('\n');
+ var columns = textarea.cols;
+ var lineCount = 0;
+ $.each(lines, function() {
+ lineCount += Math.ceil(this.length / columns) || 1;
+ });
+ var height = lineHeight * (lineCount + 1);
+ $(textarea).css('height', height);
+ };
+})(jQuery);
+
+(function($) {
+ var comp, by;
+
+ function init() {
+ initEvents();
+ initComparator();
+ }
+
+ function initEvents() {
+ $('a.comment-close').live("click", function(event) {
+ event.preventDefault();
+ hide($(this).attr('id').substring(2));
+ });
+ $('a.vote').live("click", function(event) {
+ event.preventDefault();
+ handleVote($(this));
+ });
+ $('a.reply').live("click", function(event) {
+ event.preventDefault();
+ openReply($(this).attr('id').substring(2));
+ });
+ $('a.close-reply').live("click", function(event) {
+ event.preventDefault();
+ closeReply($(this).attr('id').substring(2));
+ });
+ $('a.sort-option').live("click", function(event) {
+ event.preventDefault();
+ handleReSort($(this));
+ });
+ $('a.show-proposal').live("click", function(event) {
+ event.preventDefault();
+ showProposal($(this).attr('id').substring(2));
+ });
+ $('a.hide-proposal').live("click", function(event) {
+ event.preventDefault();
+ hideProposal($(this).attr('id').substring(2));
+ });
+ $('a.show-propose-change').live("click", function(event) {
+ event.preventDefault();
+ showProposeChange($(this).attr('id').substring(2));
+ });
+ $('a.hide-propose-change').live("click", function(event) {
+ event.preventDefault();
+ hideProposeChange($(this).attr('id').substring(2));
+ });
+ $('a.accept-comment').live("click", function(event) {
+ event.preventDefault();
+ acceptComment($(this).attr('id').substring(2));
+ });
+ $('a.delete-comment').live("click", function(event) {
+ event.preventDefault();
+ deleteComment($(this).attr('id').substring(2));
+ });
+ $('a.comment-markup').live("click", function(event) {
+ event.preventDefault();
+ toggleCommentMarkupBox($(this).attr('id').substring(2));
+ });
+ }
+
+ /**
+ * Set comp, which is a comparator function used for sorting and
+ * inserting comments into the list.
+ */
+ function setComparator() {
+ // If the first three letters are "asc", sort in ascending order
+ // and remove the prefix.
+ if (by.substring(0,3) == 'asc') {
+ var i = by.substring(3);
+ comp = function(a, b) { return a[i] - b[i]; };
+ } else {
+ // Otherwise sort in descending order.
+ comp = function(a, b) { return b[by] - a[by]; };
+ }
+
+ // Reset link styles and format the selected sort option.
+ $('a.sel').attr('href', '#').removeClass('sel');
+ $('a.by' + by).removeAttr('href').addClass('sel');
+ }
+
+ /**
+ * Create a comp function. If the user has preferences stored in
+ * the sortBy cookie, use those, otherwise use the default.
+ */
+ function initComparator() {
+ by = 'rating'; // Default to sort by rating.
+ // If the sortBy cookie is set, use that instead.
+ if (document.cookie.length > 0) {
+ var start = document.cookie.indexOf('sortBy=');
+ if (start != -1) {
+ start = start + 7;
+ var end = document.cookie.indexOf(";", start);
+ if (end == -1) {
+ end = document.cookie.length;
+ by = unescape(document.cookie.substring(start, end));
+ }
+ }
+ }
+ setComparator();
+ }
+
+ /**
+ * Show a comment div.
+ */
+ function show(id) {
+ $('#ao' + id).hide();
+ $('#ah' + id).show();
+ var context = $.extend({id: id}, opts);
+ var popup = $(renderTemplate(popupTemplate, context)).hide();
+ popup.find('textarea[name="proposal"]').hide();
+ popup.find('a.by' + by).addClass('sel');
+ var form = popup.find('#cf' + id);
+ form.submit(function(event) {
+ event.preventDefault();
+ addComment(form);
+ });
+ $('#s' + id).after(popup);
+ popup.slideDown('fast', function() {
+ getComments(id);
+ });
+ }
+
+ /**
+ * Hide a comment div.
+ */
+ function hide(id) {
+ $('#ah' + id).hide();
+ $('#ao' + id).show();
+ var div = $('#sc' + id);
+ div.slideUp('fast', function() {
+ div.remove();
+ });
+ }
+
+ /**
+ * Perform an ajax request to get comments for a node
+ * and insert the comments into the comments tree.
+ */
+ function getComments(id) {
+ $.ajax({
+ type: 'GET',
+ url: opts.getCommentsURL,
+ data: {node: id},
+ success: function(data, textStatus, request) {
+ var ul = $('#cl' + id);
+ var speed = 100;
+ $('#cf' + id)
+ .find('textarea[name="proposal"]')
+ .data('source', data.source);
+
+ if (data.comments.length === 0) {
+ ul.html('<li>No comments yet.</li>');
+ ul.data('empty', true);
+ } else {
+ // If there are comments, sort them and put them in the list.
+ var comments = sortComments(data.comments);
+ speed = data.comments.length * 100;
+ appendComments(comments, ul);
+ ul.data('empty', false);
+ }
+ $('#cn' + id).slideUp(speed + 200);
+ ul.slideDown(speed);
+ },
+ error: function(request, textStatus, error) {
+ showError('Oops, there was a problem retrieving the comments.');
+ },
+ dataType: 'json'
+ });
+ }
+
+ /**
+ * Add a comment via ajax and insert the comment into the comment tree.
+ */
+ function addComment(form) {
+ var node_id = form.find('input[name="node"]').val();
+ var parent_id = form.find('input[name="parent"]').val();
+ var text = form.find('textarea[name="comment"]').val();
+ var proposal = form.find('textarea[name="proposal"]').val();
+
+ if (text == '') {
+ showError('Please enter a comment.');
+ return;
+ }
+
+ // Disable the form that is being submitted.
+ form.find('textarea,input').attr('disabled', 'disabled');
+
+ // Send the comment to the server.
+ $.ajax({
+ type: "POST",
+ url: opts.addCommentURL,
+ dataType: 'json',
+ data: {
+ node: node_id,
+ parent: parent_id,
+ text: text,
+ proposal: proposal
+ },
+ success: function(data, textStatus, error) {
+ // Reset the form.
+ if (node_id) {
+ hideProposeChange(node_id);
+ }
+ form.find('textarea')
+ .val('')
+ .add(form.find('input'))
+ .removeAttr('disabled');
+ var ul = $('#cl' + (node_id || parent_id));
+ if (ul.data('empty')) {
+ $(ul).empty();
+ ul.data('empty', false);
+ }
+ insertComment(data.comment);
+ var ao = $('#ao' + node_id);
+ ao.find('img').attr({'src': opts.commentBrightImage});
+ if (node_id) {
+ // if this was a "root" comment, remove the commenting box
+ // (the user can get it back by reopening the comment popup)
+ $('#ca' + node_id).slideUp();
+ }
+ },
+ error: function(request, textStatus, error) {
+ form.find('textarea,input').removeAttr('disabled');
+ showError('Oops, there was a problem adding the comment.');
+ }
+ });
+ }
+
+ /**
+ * Recursively append comments to the main comment list and children
+ * lists, creating the comment tree.
+ */
+ function appendComments(comments, ul) {
+ $.each(comments, function() {
+ var div = createCommentDiv(this);
+ ul.append($(document.createElement('li')).html(div));
+ appendComments(this.children, div.find('ul.comment-children'));
+ // To avoid stagnating data, don't store the comments children in data.
+ this.children = null;
+ div.data('comment', this);
+ });
+ }
+
+ /**
+ * After adding a new comment, it must be inserted in the correct
+ * location in the comment tree.
+ */
+ function insertComment(comment) {
+ var div = createCommentDiv(comment);
+
+ // To avoid stagnating data, don't store the comments children in data.
+ comment.children = null;
+ div.data('comment', comment);
+
+ var ul = $('#cl' + (comment.node || comment.parent));
+ var siblings = getChildren(ul);
+
+ var li = $(document.createElement('li'));
+ li.hide();
+
+ // Determine where in the parents children list to insert this comment.
+ for(i=0; i < siblings.length; i++) {
+ if (comp(comment, siblings[i]) <= 0) {
+ $('#cd' + siblings[i].id)
+ .parent()
+ .before(li.html(div));
+ li.slideDown('fast');
+ return;
+ }
+ }
+
+ // If we get here, this comment rates lower than all the others,
+ // or it is the only comment in the list.
+ ul.append(li.html(div));
+ li.slideDown('fast');
+ }
+
+ function acceptComment(id) {
+ $.ajax({
+ type: 'POST',
+ url: opts.acceptCommentURL,
+ data: {id: id},
+ success: function(data, textStatus, request) {
+ $('#cm' + id).fadeOut('fast');
+ $('#cd' + id).removeClass('moderate');
+ },
+ error: function(request, textStatus, error) {
+ showError('Oops, there was a problem accepting the comment.');
+ }
+ });
+ }
+
+ function deleteComment(id) {
+ $.ajax({
+ type: 'POST',
+ url: opts.deleteCommentURL,
+ data: {id: id},
+ success: function(data, textStatus, request) {
+ var div = $('#cd' + id);
+ if (data == 'delete') {
+ // Moderator mode: remove the comment and all children immediately
+ div.slideUp('fast', function() {
+ div.remove();
+ });
+ return;
+ }
+ // User mode: only mark the comment as deleted
+ div
+ .find('span.user-id:first')
+ .text('[deleted]').end()
+ .find('div.comment-text:first')
+ .text('[deleted]').end()
+ .find('#cm' + id + ', #dc' + id + ', #ac' + id + ', #rc' + id +
+ ', #sp' + id + ', #hp' + id + ', #cr' + id + ', #rl' + id)
+ .remove();
+ var comment = div.data('comment');
+ comment.username = '[deleted]';
+ comment.text = '[deleted]';
+ div.data('comment', comment);
+ },
+ error: function(request, textStatus, error) {
+ showError('Oops, there was a problem deleting the comment.');
+ }
+ });
+ }
+
+ function showProposal(id) {
+ $('#sp' + id).hide();
+ $('#hp' + id).show();
+ $('#pr' + id).slideDown('fast');
+ }
+
+ function hideProposal(id) {
+ $('#hp' + id).hide();
+ $('#sp' + id).show();
+ $('#pr' + id).slideUp('fast');
+ }
+
+ function showProposeChange(id) {
+ $('#pc' + id).hide();
+ $('#hc' + id).show();
+ var textarea = $('#pt' + id);
+ textarea.val(textarea.data('source'));
+ $.fn.autogrow.resize(textarea[0]);
+ textarea.slideDown('fast');
+ }
+
+ function hideProposeChange(id) {
+ $('#hc' + id).hide();
+ $('#pc' + id).show();
+ var textarea = $('#pt' + id);
+ textarea.val('').removeAttr('disabled');
+ textarea.slideUp('fast');
+ }
+
+ function toggleCommentMarkupBox(id) {
+ $('#mb' + id).toggle();
+ }
+
+ /** Handle when the user clicks on a sort by link. */
+ function handleReSort(link) {
+ var classes = link.attr('class').split(/\s+/);
+ for (var i=0; i<classes.length; i++) {
+ if (classes[i] != 'sort-option') {
+ by = classes[i].substring(2);
+ }
+ }
+ setComparator();
+ // Save/update the sortBy cookie.
+ var expiration = new Date();
+ expiration.setDate(expiration.getDate() + 365);
+ document.cookie= 'sortBy=' + escape(by) +
+ ';expires=' + expiration.toUTCString();
+ $('ul.comment-ul').each(function(index, ul) {
+ var comments = getChildren($(ul), true);
+ comments = sortComments(comments);
+ appendComments(comments, $(ul).empty());
+ });
+ }
+
+ /**
+ * Function to process a vote when a user clicks an arrow.
+ */
+ function handleVote(link) {
+ if (!opts.voting) {
+ showError("You'll need to login to vote.");
+ return;
+ }
+
+ var id = link.attr('id');
+ if (!id) {
+ // Didn't click on one of the voting arrows.
+ return;
+ }
+ // If it is an unvote, the new vote value is 0,
+ // Otherwise it's 1 for an upvote, or -1 for a downvote.
+ var value = 0;
+ if (id.charAt(1) != 'u') {
+ value = id.charAt(0) == 'u' ? 1 : -1;
+ }
+ // The data to be sent to the server.
+ var d = {
+ comment_id: id.substring(2),
+ value: value
+ };
+
+ // Swap the vote and unvote links.
+ link.hide();
+ $('#' + id.charAt(0) + (id.charAt(1) == 'u' ? 'v' : 'u') + d.comment_id)
+ .show();
+
+ // The div the comment is displayed in.
+ var div = $('div#cd' + d.comment_id);
+ var data = div.data('comment');
+
+ // If this is not an unvote, and the other vote arrow has
+ // already been pressed, unpress it.
+ if ((d.value !== 0) && (data.vote === d.value * -1)) {
+ $('#' + (d.value == 1 ? 'd' : 'u') + 'u' + d.comment_id).hide();
+ $('#' + (d.value == 1 ? 'd' : 'u') + 'v' + d.comment_id).show();
+ }
+
+ // Update the comments rating in the local data.
+ data.rating += (data.vote === 0) ? d.value : (d.value - data.vote);
+ data.vote = d.value;
+ div.data('comment', data);
+
+ // Change the rating text.
+ div.find('.rating:first')
+ .text(data.rating + ' point' + (data.rating == 1 ? '' : 's'));
+
+ // Send the vote information to the server.
+ $.ajax({
+ type: "POST",
+ url: opts.processVoteURL,
+ data: d,
+ error: function(request, textStatus, error) {
+ showError('Oops, there was a problem casting that vote.');
+ }
+ });
+ }
+
+ /**
+ * Open a reply form used to reply to an existing comment.
+ */
+ function openReply(id) {
+ // Swap out the reply link for the hide link
+ $('#rl' + id).hide();
+ $('#cr' + id).show();
+
+ // Add the reply li to the children ul.
+ var div = $(renderTemplate(replyTemplate, {id: id})).hide();
+ $('#cl' + id)
+ .prepend(div)
+ // Setup the submit handler for the reply form.
+ .find('#rf' + id)
+ .submit(function(event) {
+ event.preventDefault();
+ addComment($('#rf' + id));
+ closeReply(id);
+ })
+ .find('input[type=button]')
+ .click(function() {
+ closeReply(id);
+ });
+ div.slideDown('fast', function() {
+ $('#rf' + id).find('textarea').focus();
+ });
+ }
+
+ /**
+ * Close the reply form opened with openReply.
+ */
+ function closeReply(id) {
+ // Remove the reply div from the DOM.
+ $('#rd' + id).slideUp('fast', function() {
+ $(this).remove();
+ });
+
+ // Swap out the hide link for the reply link
+ $('#cr' + id).hide();
+ $('#rl' + id).show();
+ }
+
+ /**
+ * Recursively sort a tree of comments using the comp comparator.
+ */
+ function sortComments(comments) {
+ comments.sort(comp);
+ $.each(comments, function() {
+ this.children = sortComments(this.children);
+ });
+ return comments;
+ }
+
+ /**
+ * Get the children comments from a ul. If recursive is true,
+ * recursively include childrens' children.
+ */
+ function getChildren(ul, recursive) {
+ var children = [];
+ ul.children().children("[id^='cd']")
+ .each(function() {
+ var comment = $(this).data('comment');
+ if (recursive)
+ comment.children = getChildren($(this).find('#cl' + comment.id), true);
+ children.push(comment);
+ });
+ return children;
+ }
+
+ /** Create a div to display a comment in. */
+ function createCommentDiv(comment) {
+ if (!comment.displayed && !opts.moderator) {
+ return $('<div class="moderate">Thank you! Your comment will show up '
+ + 'once it is has been approved by a moderator.</div>');
+ }
+ // Prettify the comment rating.
+ comment.pretty_rating = comment.rating + ' point' +
+ (comment.rating == 1 ? '' : 's');
+ // Make a class (for displaying not yet moderated comments differently)
+ comment.css_class = comment.displayed ? '' : ' moderate';
+ // Create a div for this comment.
+ var context = $.extend({}, opts, comment);
+ var div = $(renderTemplate(commentTemplate, context));
+
+ // If the user has voted on this comment, highlight the correct arrow.
+ if (comment.vote) {
+ var direction = (comment.vote == 1) ? 'u' : 'd';
+ div.find('#' + direction + 'v' + comment.id).hide();
+ div.find('#' + direction + 'u' + comment.id).show();
+ }
+
+ if (opts.moderator || comment.text != '[deleted]') {
+ div.find('a.reply').show();
+ if (comment.proposal_diff)
+ div.find('#sp' + comment.id).show();
+ if (opts.moderator && !comment.displayed)
+ div.find('#cm' + comment.id).show();
+ if (opts.moderator || (opts.username == comment.username))
+ div.find('#dc' + comment.id).show();
+ }
+ return div;
+ }
+
+ /**
+ * A simple template renderer. Placeholders such as <%id%> are replaced
+ * by context['id'] with items being escaped. Placeholders such as <#id#>
+ * are not escaped.
+ */
+ function renderTemplate(template, context) {
+ var esc = $(document.createElement('div'));
+
+ function handle(ph, escape) {
+ var cur = context;
+ $.each(ph.split('.'), function() {
+ cur = cur[this];
+ });
+ return escape ? esc.text(cur || "").html() : cur;
+ }
+
+ return template.replace(/<([%#])([\w\.]*)\1>/g, function() {
+ return handle(arguments[2], arguments[1] == '%' ? true : false);
+ });
+ }
+
+ /** Flash an error message briefly. */
+ function showError(message) {
+ $(document.createElement('div')).attr({'class': 'popup-error'})
+ .append($(document.createElement('div'))
+ .attr({'class': 'error-message'}).text(message))
+ .appendTo('body')
+ .fadeIn("slow")
+ .delay(2000)
+ .fadeOut("slow");
+ }
+
+ /** Add a link the user uses to open the comments popup. */
+ $.fn.comment = function() {
+ return this.each(function() {
+ var id = $(this).attr('id').substring(1);
+ var count = COMMENT_METADATA[id];
+ var title = count + ' comment' + (count == 1 ? '' : 's');
+ var image = count > 0 ? opts.commentBrightImage : opts.commentImage;
+ var addcls = count == 0 ? ' nocomment' : '';
+ $(this)
+ .append(
+ $(document.createElement('a')).attr({
+ href: '#',
+ 'class': 'sphinx-comment-open' + addcls,
+ id: 'ao' + id
+ })
+ .append($(document.createElement('img')).attr({
+ src: image,
+ alt: 'comment',
+ title: title
+ }))
+ .click(function(event) {
+ event.preventDefault();
+ show($(this).attr('id').substring(2));
+ })
+ )
+ .append(
+ $(document.createElement('a')).attr({
+ href: '#',
+ 'class': 'sphinx-comment-close hidden',
+ id: 'ah' + id
+ })
+ .append($(document.createElement('img')).attr({
+ src: opts.closeCommentImage,
+ alt: 'close',
+ title: 'close'
+ }))
+ .click(function(event) {
+ event.preventDefault();
+ hide($(this).attr('id').substring(2));
+ })
+ );
+ });
+ };
+
+ var opts = {
+ processVoteURL: '/_process_vote',
+ addCommentURL: '/_add_comment',
+ getCommentsURL: '/_get_comments',
+ acceptCommentURL: '/_accept_comment',
+ deleteCommentURL: '/_delete_comment',
+ commentImage: '/static/_static/comment.png',
+ closeCommentImage: '/static/_static/comment-close.png',
+ loadingImage: '/static/_static/ajax-loader.gif',
+ commentBrightImage: '/static/_static/comment-bright.png',
+ upArrow: '/static/_static/up.png',
+ downArrow: '/static/_static/down.png',
+ upArrowPressed: '/static/_static/up-pressed.png',
+ downArrowPressed: '/static/_static/down-pressed.png',
+ voting: false,
+ moderator: false
+ };
+
+ if (typeof COMMENT_OPTIONS != "undefined") {
+ opts = jQuery.extend(opts, COMMENT_OPTIONS);
+ }
+
+ var popupTemplate = '\
+ <div class="sphinx-comments" id="sc<%id%>">\
+ <p class="sort-options">\
+ Sort by:\
+ <a href="#" class="sort-option byrating">best rated</a>\
+ <a href="#" class="sort-option byascage">newest</a>\
+ <a href="#" class="sort-option byage">oldest</a>\
+ </p>\
+ <div class="comment-header">Comments</div>\
+ <div class="comment-loading" id="cn<%id%>">\
+ loading comments... <img src="<%loadingImage%>" alt="" /></div>\
+ <ul id="cl<%id%>" class="comment-ul"></ul>\
+ <div id="ca<%id%>">\
+ <p class="add-a-comment">Add a comment\
+ (<a href="#" class="comment-markup" id="ab<%id%>">markup</a>):</p>\
+ <div class="comment-markup-box" id="mb<%id%>">\
+ reStructured text markup: <i>*emph*</i>, <b>**strong**</b>, \
+ <code>``code``</code>, \
+ code blocks: <code>::</code> and an indented block after blank line</div>\
+ <form method="post" id="cf<%id%>" class="comment-form" action="">\
+ <textarea name="comment" cols="80"></textarea>\
+ <p class="propose-button">\
+ <a href="#" id="pc<%id%>" class="show-propose-change">\
+ Propose a change ▹\
+ </a>\
+ <a href="#" id="hc<%id%>" class="hide-propose-change">\
+ Propose a change ▿\
+ </a>\
+ </p>\
+ <textarea name="proposal" id="pt<%id%>" cols="80"\
+ spellcheck="false"></textarea>\
+ <input type="submit" value="Add comment" />\
+ <input type="hidden" name="node" value="<%id%>" />\
+ <input type="hidden" name="parent" value="" />\
+ </form>\
+ </div>\
+ </div>';
+
+ var commentTemplate = '\
+ <div id="cd<%id%>" class="sphinx-comment<%css_class%>">\
+ <div class="vote">\
+ <div class="arrow">\
+ <a href="#" id="uv<%id%>" class="vote" title="vote up">\
+ <img src="<%upArrow%>" />\
+ </a>\
+ <a href="#" id="uu<%id%>" class="un vote" title="vote up">\
+ <img src="<%upArrowPressed%>" />\
+ </a>\
+ </div>\
+ <div class="arrow">\
+ <a href="#" id="dv<%id%>" class="vote" title="vote down">\
+ <img src="<%downArrow%>" id="da<%id%>" />\
+ </a>\
+ <a href="#" id="du<%id%>" class="un vote" title="vote down">\
+ <img src="<%downArrowPressed%>" />\
+ </a>\
+ </div>\
+ </div>\
+ <div class="comment-content">\
+ <p class="tagline comment">\
+ <span class="user-id"><%username%></span>\
+ <span class="rating"><%pretty_rating%></span>\
+ <span class="delta"><%time.delta%></span>\
+ </p>\
+ <div class="comment-text comment"><#text#></div>\
+ <p class="comment-opts comment">\
+ <a href="#" class="reply hidden" id="rl<%id%>">reply ▹</a>\
+ <a href="#" class="close-reply" id="cr<%id%>">reply ▿</a>\
+ <a href="#" id="sp<%id%>" class="show-proposal">proposal ▹</a>\
+ <a href="#" id="hp<%id%>" class="hide-proposal">proposal ▿</a>\
+ <a href="#" id="dc<%id%>" class="delete-comment hidden">delete</a>\
+ <span id="cm<%id%>" class="moderation hidden">\
+ <a href="#" id="ac<%id%>" class="accept-comment">accept</a>\
+ </span>\
+ </p>\
+ <pre class="proposal" id="pr<%id%>">\
+<#proposal_diff#>\
+ </pre>\
+ <ul class="comment-children" id="cl<%id%>"></ul>\
+ </div>\
+ <div class="clearleft"></div>\
+ </div>\
+ </div>';
+
+ var replyTemplate = '\
+ <li>\
+ <div class="reply-div" id="rd<%id%>">\
+ <form id="rf<%id%>">\
+ <textarea name="comment" cols="80"></textarea>\
+ <input type="submit" value="Add reply" />\
+ <input type="button" value="Cancel" />\
+ <input type="hidden" name="parent" value="<%id%>" />\
+ <input type="hidden" name="node" value="" />\
+ </form>\
+ </div>\
+ </li>';
+
+ $(document).ready(function() {
+ init();
+ });
+})(jQuery);
+
+$(document).ready(function() {
+ // add comment anchors for all paragraphs that are commentable
+ $('.sphinx-has-comment').comment();
+
+ // highlight search words in search results
+ $("div.context").each(function() {
+ var params = $.getQueryParameters();
+ var terms = (params.q) ? params.q[0].split(/\s+/) : [];
+ var result = $(this);
+ $.each(terms, function() {
+ result.highlightText(this.toLowerCase(), 'highlighted');
+ });
+ });
+
+ // directly open comment window if requested
+ var anchor = document.location.hash;
+ if (anchor.substring(0, 9) == '#comment-') {
+ $('#ao' + anchor.substring(9)).click();
+ document.location.hash = '#s' + anchor.substring(9);
+ }
+});
diff --git a/docs/build/html/ex_script_color1.html b/docs/build/html/ex_script_color1.html
new file mode 100644
index 0000000000000000000000000000000000000000..a5e9f23773f3d46564b068a192d7bc23893d0e9f
--- /dev/null
+++ b/docs/build/html/ex_script_color1.html
@@ -0,0 +1,453 @@
+<!DOCTYPE html>
+
+
+<html xmlns="http://www.w3.org/1999/xhtml">
+ <head>
+ <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
+
+ <title>Color Filter In Depth #1 — Image Harvest 1.0.1 documentation</title>
+
+ <link rel="stylesheet" href="_static/basic.css" type="text/css" />
+ <link rel="stylesheet" href="_static/pygments.css" type="text/css" />
+ <link rel="stylesheet" href="_static/bootstrap-3.2.0/css/bootstrap.min.css" type="text/css" />
+ <link rel="stylesheet" href="_static/bootstrap-3.2.0/css/bootstrap-theme.min.css" type="text/css" />
+ <link rel="stylesheet" href="_static/bootstrap-sphinx.css" type="text/css" />
+
+ <script type="text/javascript">
+ var DOCUMENTATION_OPTIONS = {
+ URL_ROOT: './',
+ VERSION: '1.0.1',
+ COLLAPSE_INDEX: false,
+ FILE_SUFFIX: '.html',
+ HAS_SOURCE: true
+ };
+ </script>
+ <script type="text/javascript" src="_static/jquery.js"></script>
+ <script type="text/javascript" src="_static/underscore.js"></script>
+ <script type="text/javascript" src="_static/doctools.js"></script>
+ <script type="text/javascript" src="https://c328740.ssl.cf1.rackcdn.com/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
+ <script type="text/javascript" src="_static/js/jquery-1.11.0.min.js"></script>
+ <script type="text/javascript" src="_static/js/jquery-fix.js"></script>
+ <script type="text/javascript" src="_static/bootstrap-3.2.0/js/bootstrap.min.js"></script>
+ <script type="text/javascript" src="_static/bootstrap-sphinx.js"></script>
+ <link rel="top" title="Image Harvest 1.0.1 documentation" href="index.html" />
+ <link rel="up" title="Examples" href="examples.html" />
+ <link rel="next" title="Workflow Example #1" href="ex_workflow_1.html" />
+ <link rel="prev" title="Core Processing Example #2" href="ex_script_core2.html" />
+<meta charset='utf-8'>
+<meta http-equiv='X-UA-Compatible' content='IE=edge,chrome=1'>
+<meta name='viewport' content='width=device-width, initial-scale=1.0, maximum-scale=1'>
+<meta name="apple-mobile-web-app-capable" content="yes">
+
+ </head>
+ <body role="document">
+
+ <div id="navbar" class="navbar navbar-default navbar-fixed-top">
+ <div class="container">
+ <div class="navbar-header">
+ <!-- .btn-navbar is used as the toggle for collapsed navbar content -->
+ <button type="button" class="navbar-toggle" data-toggle="collapse" data-target=".nav-collapse">
+ <span class="icon-bar"></span>
+ <span class="icon-bar"></span>
+ <span class="icon-bar"></span>
+ </button>
+ <a class="navbar-brand" href="index.html">
+ Image Harvest</a>
+ <span class="navbar-text navbar-version pull-left"><b>1.0</b></span>
+ </div>
+
+ <div class="collapse navbar-collapse nav-collapse">
+ <ul class="nav navbar-nav">
+
+
+ <li class="dropdown globaltoc-container">
+ <a role="button"
+ id="dLabelGlobalToc"
+ data-toggle="dropdown"
+ data-target="#"
+ href="index.html">Site <b class="caret"></b></a>
+ <ul class="dropdown-menu globaltoc"
+ role="menu"
+ aria-labelledby="dLabelGlobalToc"><ul class="current">
+<li class="toctree-l1"><a class="reference internal" href="introduction.html">Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="installation.html">Installation</a></li>
+<li class="toctree-l1"><a class="reference internal" href="start.html">Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="ex_script_core1.html">Core Processing Example #1</a></li>
+<li class="toctree-l1"><a class="reference internal" href="ex_script_core2.html">Core Processing Example #2</a></li>
+<li class="toctree-l1 current"><a class="current reference internal" href="">Color Filter In Depth #1</a></li>
+<li class="toctree-l1"><a class="reference internal" href="ex_workflow_1.html">Workflow Example #1</a></li>
+<li class="toctree-l1"><a class="reference internal" href="examples.html">Examples</a></li>
+<li class="toctree-l1"><a class="reference internal" href="processing.html">Image Processing</a></li>
+<li class="toctree-l1"><a class="reference internal" href="viewer.html">Image Processing Viewer</a></li>
+<li class="toctree-l1"><a class="reference internal" href="statistics.html">Statistics</a></li>
+<li class="toctree-l1"><a class="reference internal" href="indexing.html">Image Loading</a></li>
+<li class="toctree-l1"><a class="reference internal" href="workflowimage.html">Image Processing Workflows</a></li>
+<li class="toctree-l1"><a class="reference internal" href="workflowstats.html">Statistics Workflows</a></li>
+</ul>
+</ul>
+</li>
+
+ <li class="dropdown">
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+ aria-labelledby="dLabelLocalToc"><ul>
+<li><a class="reference internal" href="#">Color Filter In Depth #1</a><ul>
+<li><a class="reference internal" href="#python-script">Python Script</a></li>
+<li><a class="reference internal" href="#command-line-script">Command Line Script</a></li>
+</ul>
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+<div id="sourcelink">
+ <a href="_sources/ex_script_color1.txt"
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+
+ </ul>
+
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+<form class="navbar-form navbar-right" action="search.html" method="get">
+ <div class="form-group">
+ <input type="text" name="q" class="form-control" placeholder="Search" />
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+
+<div class="container">
+ <div class="row">
+ <div class="col-md-12">
+
+ <div class="section" id="color-filter-in-depth-1">
+<h1>Color Filter In Depth #1<a class="headerlink" href="#color-filter-in-depth-1" title="Permalink to this headline">¶</a></h1>
+<p>The <a class="reference internal" href="processing.html#ih.imgproc.Image.colorFilter" title="ih.imgproc.Image.colorFilter"><code class="xref py py-meth docutils literal"><span class="pre">colorFilter()</span></code></a> function is a very powerful and versatile function, that removes pixels
+from an image based on arbitrarily inputted logic. This example
+focuses solely on the uses and syntax of the <a class="reference internal" href="processing.html#ih.imgproc.Image.colorFilter" title="ih.imgproc.Image.colorFilter"><code class="xref py py-meth docutils literal"><span class="pre">colorFilter()</span></code></a> function. This function takes
+2 arguments. The first is the actual logic to solve, and this first argument will be the main focus of all
+color filter examples. The second argument is simply a region of interest – namely where you want
+to apply your specified logic. If left blank, it simply applies it to the entire image. Let’s talk
+about what we can do with logic. As stated under the function specific documentation, the supported
+characters for logic are: ‘+’, ‘-‘, ‘*’, ‘/’, ‘>’, ‘>=’,’==’, ‘<’, ‘<=’, ‘and’, ‘or’, ‘max’, ‘min’, ‘(‘, ‘)’, ‘r’, ‘g’, ‘b’, as well
+as any number.
+Excluding parenthesis, these can be broken down into 2 categories, operators and values. The operators
+are all the symbols before the parenthesis: ‘+’, ‘-‘, ‘*’, ‘/’, ‘>’, ‘>=’,’==’, ‘<’, ‘<=’, ‘and’, ‘or’, ‘max’, and ‘min’.
+The values are all the symbols after the parenthesis: ‘r’, ‘g’, ‘b’, and again, any number.
+Parenthesis are used to make sure your logic is well formed and easy to parse. Well formed logic means that each operator only acts
+on 2 values, and logic is surrounded by parenthesis. Thus ((r + g) + b) is well formed, but (r + g + b) is not. The logic argument for this function
+<strong>must be well formed</strong>. This is important to remember as we continue forward. Since we have fewer values than
+operators, let’s talk about values first.</p>
+<p>Values are simply numbers. Numbers that are input as raw text are interpreted literally – this is a dense way
+of saying that if a given number, say ‘15’, occurs in your logic string, it is translated to the number 15. However,
+the other values hold special meaning relating to the colors of the image in question. ‘r’ is the value of the
+red channel, ‘g’ is the value of the green channel, ‘b’ is the value of the blue channel. If we are considering a particular pixel
+of an image, and let’s say it has the following values for its channels in BGR order: [20, 30, 40]. For this pixel, ‘r’
+equates to 40, ‘g’ equates to 30, and ‘b’ equates to 20. We apply operators
+to these values to remove pixels.</p>
+<p>By applying operators, we look to convert our values into a true or false output. The arithmetic operators
+(‘+’, ‘-‘, ‘*’, ‘/’) do exactly what you’d expect to numbers. Thus, by themselves they do not return a true or false value.
+The comparison operators (‘>’, ‘>=’, ‘==’, ‘<’, ‘<=’) however, return true or false depending on what their comparison
+returns. ‘max’ and ‘min’ are used to select the maximum or minimum respectively of values. Thus (b max g) selects the
+maximum value between the blue and green channels. ((b min g) min r) selects the minimum of all three channels.
+Finally, ‘and’ and ‘or’ can be used to join together multiple pieces of logic. That’s a lot of text to absorb – let’s look at some examples.</p>
+<div class="section" id="python-script">
+<h2>Python Script<a class="headerlink" href="#python-script" title="Permalink to this headline">¶</a></h2>
+<p><a class="reference download internal" href="_downloads/color1.py"><code class="xref download docutils literal"><span class="pre">Download</span> <span class="pre">Script</span></code></a></p>
+<p><a class="reference download internal" href="_downloads/rgbtv1.png"><code class="xref download docutils literal"><span class="pre">Download</span> <span class="pre">Image</span></code></a></p>
+<div class="highlight-python"><div class="highlight"><pre><span class="kn">import</span> <span class="nn">ih.imgproc</span>
+
+<span class="n">plant</span> <span class="o">=</span> <span class="n">ih</span><span class="o">.</span><span class="n">imgproc</span><span class="o">.</span><span class="n">Image</span><span class="p">(</span><span class="s">"/path/to/your/image"</span><span class="p">)</span>
+<span class="n">plant</span><span class="o">.</span><span class="n">save</span><span class="p">(</span><span class="s">"base"</span><span class="p">)</span>
+
+<span class="n">logicList</span> <span class="o">=</span> <span class="p">[</span>
+ <span class="s">"(((r + g) + b) > 350)"</span><span class="p">,</span>
+ <span class="s">"(r >= 250)"</span><span class="p">,</span>
+ <span class="s">"((b > 150) and (b < 220))"</span><span class="p">,</span>
+ <span class="s">"((((b max g) max r) - ((b min g) min r)) > 20)"</span><span class="p">,</span>
+ <span class="s">"((((r + g) + b) > 700) or (((r + g) + b) < 100))"</span><span class="p">,</span>
+ <span class="s">"((r - g) > 50)"</span><span class="p">,</span>
+ <span class="s">"(((g - r) > 15) and (b < g))"</span>
+<span class="p">]</span>
+
+<span class="k">for</span> <span class="n">logic</span> <span class="ow">in</span> <span class="n">logicList</span><span class="p">:</span>
+ <span class="n">plant</span><span class="o">.</span><span class="n">restore</span><span class="p">(</span><span class="s">"base"</span><span class="p">)</span>
+ <span class="n">plant</span><span class="o">.</span><span class="n">show</span><span class="p">(</span><span class="s">"base"</span><span class="p">)</span>
+ <span class="n">plant</span><span class="o">.</span><span class="n">colorFilter</span><span class="p">(</span><span class="n">logic</span><span class="p">)</span>
+ <span class="n">plant</span><span class="o">.</span><span class="n">show</span><span class="p">(</span><span class="n">logic</span><span class="p">)</span>
+ <span class="n">plant</span><span class="o">.</span><span class="n">wait</span><span class="p">()</span>
+</pre></div>
+</div>
+<p>This script applies different logic to the same image, while displaying both the base image
+and the filtered image at the same time. Let’s talk about each individual piece of logic. First is “(((r + g) + b) > 350)”. This
+will sum up the value of each channel (the intensity of the pixel) and compare this sum to 350. If the value is greater
+than 350, it will keep the pixel, otherwise it writes it as black. Here’s the result:</p>
+<img alt="_images/rgbtv1_small.png" class="align-left" src="_images/rgbtv1_small.png" />
+<img alt="_images/logic0.png" class="align-right" src="_images/logic0.png" />
+<div class="line-block">
+<div class="line"><br /></div>
+<div class="line"><br /></div>
+<div class="line"><br /></div>
+<div class="line"><br /></div>
+<div class="line"><br /></div>
+<div class="line"><br /></div>
+<div class="line"><br /></div>
+<div class="line"><br /></div>
+<div class="line"><br /></div>
+<div class="line"><br /></div>
+<div class="line"><br /></div>
+<div class="line"><br /></div>
+<div class="line"><br /></div>
+<div class="line"><br /></div>
+<div class="line"><br /></div>
+<div class="line"><br /></div>
+<div class="line"><br /></div>
+<div class="line"><br /></div>
+<div class="line"><br /></div>
+<div class="line"><br /></div>
+<div class="line"><br /></div>
+<div class="line"><br /></div>
+<div class="line"><br /></div>
+</div>
+<p>Next is “(r >= 250)”. This simply keeps any pixel who has a red value greater than or equal
+to 250. Color channels range from 0 to 255, so 250 is very large. Here’s the result:</p>
+<img alt="_images/rgbtv1_small.png" class="align-left" src="_images/rgbtv1_small.png" />
+<img alt="_images/logic1.png" class="align-right" src="_images/logic1.png" />
+<div class="line-block">
+<div class="line"><br /></div>
+<div class="line"><br /></div>
+<div class="line"><br /></div>
+<div class="line"><br /></div>
+<div class="line"><br /></div>
+<div class="line"><br /></div>
+<div class="line"><br /></div>
+<div class="line"><br /></div>
+<div class="line"><br /></div>
+<div class="line"><br /></div>
+<div class="line"><br /></div>
+<div class="line"><br /></div>
+<div class="line"><br /></div>
+<div class="line"><br /></div>
+<div class="line"><br /></div>
+<div class="line"><br /></div>
+<div class="line"><br /></div>
+<div class="line"><br /></div>
+<div class="line"><br /></div>
+<div class="line"><br /></div>
+<div class="line"><br /></div>
+<div class="line"><br /></div>
+<div class="line"><br /></div>
+</div>
+<p>Next is “((b > 150) and (b < 220))”. This will keep any pixel that has a blue value
+that is greater than 150 and less than 220. Here’s the result:</p>
+<img alt="_images/rgbtv1_small.png" class="align-left" src="_images/rgbtv1_small.png" />
+<img alt="_images/logic2.png" class="align-right" src="_images/logic2.png" />
+<div class="line-block">
+<div class="line"><br /></div>
+<div class="line"><br /></div>
+<div class="line"><br /></div>
+<div class="line"><br /></div>
+<div class="line"><br /></div>
+<div class="line"><br /></div>
+<div class="line"><br /></div>
+<div class="line"><br /></div>
+<div class="line"><br /></div>
+<div class="line"><br /></div>
+<div class="line"><br /></div>
+<div class="line"><br /></div>
+<div class="line"><br /></div>
+<div class="line"><br /></div>
+<div class="line"><br /></div>
+<div class="line"><br /></div>
+<div class="line"><br /></div>
+<div class="line"><br /></div>
+<div class="line"><br /></div>
+<div class="line"><br /></div>
+<div class="line"><br /></div>
+<div class="line"><br /></div>
+<div class="line"><br /></div>
+</div>
+<p>Next is “”((((b max g) max r) - ((b min g) min r)) > 20)”,”. This will keep any pixel
+whose maximum channel value is at least 20 greater than its minimum channel value. Here’s the result:</p>
+<img alt="_images/rgbtv1_small.png" class="align-left" src="_images/rgbtv1_small.png" />
+<img alt="_images/logic3.png" class="align-right" src="_images/logic3.png" />
+<div class="line-block">
+<div class="line"><br /></div>
+<div class="line"><br /></div>
+<div class="line"><br /></div>
+<div class="line"><br /></div>
+<div class="line"><br /></div>
+<div class="line"><br /></div>
+<div class="line"><br /></div>
+<div class="line"><br /></div>
+<div class="line"><br /></div>
+<div class="line"><br /></div>
+<div class="line"><br /></div>
+<div class="line"><br /></div>
+<div class="line"><br /></div>
+<div class="line"><br /></div>
+<div class="line"><br /></div>
+<div class="line"><br /></div>
+<div class="line"><br /></div>
+<div class="line"><br /></div>
+<div class="line"><br /></div>
+<div class="line"><br /></div>
+<div class="line"><br /></div>
+<div class="line"><br /></div>
+<div class="line"><br /></div>
+</div>
+<p>Next is “((((r + g) + b) > 700) or (((r + g) + b) < 100))”. This will keep any pixel whose
+intensity is larger than 700 OR smaller than 100. Here’s the result:</p>
+<img alt="_images/rgbtv1_small.png" class="align-left" src="_images/rgbtv1_small.png" />
+<img alt="_images/logic4.png" class="align-right" src="_images/logic4.png" />
+<div class="line-block">
+<div class="line"><br /></div>
+<div class="line"><br /></div>
+<div class="line"><br /></div>
+<div class="line"><br /></div>
+<div class="line"><br /></div>
+<div class="line"><br /></div>
+<div class="line"><br /></div>
+<div class="line"><br /></div>
+<div class="line"><br /></div>
+<div class="line"><br /></div>
+<div class="line"><br /></div>
+<div class="line"><br /></div>
+<div class="line"><br /></div>
+<div class="line"><br /></div>
+<div class="line"><br /></div>
+<div class="line"><br /></div>
+<div class="line"><br /></div>
+<div class="line"><br /></div>
+<div class="line"><br /></div>
+<div class="line"><br /></div>
+<div class="line"><br /></div>
+<div class="line"><br /></div>
+<div class="line"><br /></div>
+</div>
+<p>Next is “((r - g) > 50)”. This will keep any pixel that has a red channel value
+that is at least 50 greater than its green channel value. Here’s the result:</p>
+<img alt="_images/rgbtv1_small.png" class="align-left" src="_images/rgbtv1_small.png" />
+<img alt="_images/logic5.png" class="align-right" src="_images/logic5.png" />
+<div class="line-block">
+<div class="line"><br /></div>
+<div class="line"><br /></div>
+<div class="line"><br /></div>
+<div class="line"><br /></div>
+<div class="line"><br /></div>
+<div class="line"><br /></div>
+<div class="line"><br /></div>
+<div class="line"><br /></div>
+<div class="line"><br /></div>
+<div class="line"><br /></div>
+<div class="line"><br /></div>
+<div class="line"><br /></div>
+<div class="line"><br /></div>
+<div class="line"><br /></div>
+<div class="line"><br /></div>
+<div class="line"><br /></div>
+<div class="line"><br /></div>
+<div class="line"><br /></div>
+<div class="line"><br /></div>
+<div class="line"><br /></div>
+<div class="line"><br /></div>
+<div class="line"><br /></div>
+<div class="line"><br /></div>
+</div>
+<p>Finally, is “(((g - r) > 15) and (b < g))”. This will keep any pixel that has a green channel value at least 15
+greater than the red channel value AND a blue channel value less than its green channel value. Here’s the result:</p>
+<img alt="_images/rgbtv1_small.png" class="align-left" src="_images/rgbtv1_small.png" />
+<img alt="_images/logic6.png" class="align-right" src="_images/logic6.png" />
+<div class="line-block">
+<div class="line"><br /></div>
+<div class="line"><br /></div>
+<div class="line"><br /></div>
+<div class="line"><br /></div>
+<div class="line"><br /></div>
+<div class="line"><br /></div>
+<div class="line"><br /></div>
+<div class="line"><br /></div>
+<div class="line"><br /></div>
+<div class="line"><br /></div>
+<div class="line"><br /></div>
+<div class="line"><br /></div>
+<div class="line"><br /></div>
+<div class="line"><br /></div>
+<div class="line"><br /></div>
+<div class="line"><br /></div>
+<div class="line"><br /></div>
+<div class="line"><br /></div>
+<div class="line"><br /></div>
+<div class="line"><br /></div>
+<div class="line"><br /></div>
+<div class="line"><br /></div>
+<div class="line"><br /></div>
+</div>
+</div>
+<div class="section" id="command-line-script">
+<h2>Command Line Script<a class="headerlink" href="#command-line-script" title="Permalink to this headline">¶</a></h2>
+<p><a class="reference download internal" href="_downloads/color1.sh"><code class="xref download docutils literal"><span class="pre">Download</span> <span class="pre">Script</span></code></a></p>
+<p><a class="reference download internal" href="_downloads/rgbtv1.png"><code class="xref download docutils literal"><span class="pre">Download</span> <span class="pre">Image</span></code></a> (The image is identical to the one above)</p>
+<div class="highlight-bash"><div class="highlight"><pre><span class="c">#!/bin/bash</span>
+
+ih-color-filter --input <span class="s2">"/path/to/your/image"</span> --output <span class="s2">"logic0.png"</span> --logic <span class="s2">"(((r + g) + b) > 350)"</span>
+ih-color-filter --input <span class="s2">"/path/to/your/image"</span> --output <span class="s2">"logic1.png"</span> --logic <span class="s2">"(r >= 250)"</span>
+ih-color-filter --input <span class="s2">"/path/to/your/image"</span> --output <span class="s2">"logic2.png"</span> --logic <span class="s2">"((b > 150) and (b < 220))"</span>
+ih-color-filter --input <span class="s2">"/path/to/your/image"</span> --output <span class="s2">"logic3.png"</span> --logic <span class="s2">"((((b max g) max r) - ((b min g) min r)) > 20)"</span>
+ih-color-filter --input <span class="s2">"/path/to/your/image"</span> --output <span class="s2">"logic4.png"</span> --logic <span class="s2">"((((r + g) + b) > 700) or (((r + g) + b) < 100))"</span>
+ih-color-filter --input <span class="s2">"/path/to/your/image"</span> --output <span class="s2">"logic5.png"</span> --logic <span class="s2">"((r - g) > 50)"</span>
+ih-color-filter --input <span class="s2">"/path/to/your/image"</span> --output <span class="s2">"logic6.png"</span> --logic <span class="s2">"(((g - r) > 15) and (b < g))"</span>
+</pre></div>
+</div>
+<p>This bash script performs the exact same color filtering as the above python script. Each color filter call
+must be done separately. Each takes in the same input file, and writes a separate output file.</p>
+</div>
+</div>
+
+
+ </div>
+
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+ <div class="section" id="core-processing-example-1">
+<h1>Core Processing Example #1<a class="headerlink" href="#core-processing-example-1" title="Permalink to this headline">¶</a></h1>
+<p>This section will detail a shorter script that provides details on how to get started with
+script form image processing. The script will detail how to use several core functions
+to load, save, and show images.</p>
+<div class="section" id="python-script">
+<h2>Python Script<a class="headerlink" href="#python-script" title="Permalink to this headline">¶</a></h2>
+<p><a class="reference download internal" href="_downloads/core1.py"><code class="xref download docutils literal"><span class="pre">Download</span> <span class="pre">Script</span></code></a></p>
+<p><a class="reference download internal" href="_downloads/base1.png"><code class="xref download docutils literal"><span class="pre">Download</span> <span class="pre">Image</span></code></a></p>
+<div class="highlight-python"><div class="highlight"><pre><span class="kn">import</span> <span class="nn">ih.imgproc</span>
+
+<span class="n">plant</span> <span class="o">=</span> <span class="n">ih</span><span class="o">.</span><span class="n">imgproc</span><span class="o">.</span><span class="n">Image</span><span class="p">(</span><span class="s">"/path/to/your/image"</span><span class="p">)</span>
+
+<span class="n">plant</span><span class="o">.</span><span class="n">save</span><span class="p">(</span><span class="s">"base"</span><span class="p">)</span>
+<span class="n">plant</span><span class="o">.</span><span class="n">show</span><span class="p">(</span><span class="s">"base"</span><span class="p">)</span>
+<span class="n">plant</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s">"base.png"</span><span class="p">)</span>
+
+<span class="n">plant</span><span class="o">.</span><span class="n">convertColor</span><span class="p">(</span><span class="s">"bgr"</span><span class="p">,</span> <span class="s">"gray"</span><span class="p">)</span>
+<span class="n">plant</span><span class="o">.</span><span class="n">save</span><span class="p">(</span><span class="s">"gray"</span><span class="p">)</span>
+<span class="n">plant</span><span class="o">.</span><span class="n">show</span><span class="p">(</span><span class="s">"gray"</span><span class="p">)</span>
+<span class="n">plant</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s">"gray.png"</span><span class="p">)</span>
+
+<span class="n">plant</span><span class="o">.</span><span class="n">threshold</span><span class="p">(</span><span class="mi">50</span><span class="p">)</span>
+<span class="n">plant</span><span class="o">.</span><span class="n">save</span><span class="p">(</span><span class="s">"thresh50"</span><span class="p">)</span>
+<span class="n">plant</span><span class="o">.</span><span class="n">show</span><span class="p">(</span><span class="s">"thresh50"</span><span class="p">)</span>
+<span class="n">plant</span><span class="o">.</span><span class="n">restore</span><span class="p">(</span><span class="s">"gray"</span><span class="p">)</span>
+
+<span class="n">plant</span><span class="o">.</span><span class="n">threshold</span><span class="p">(</span><span class="mi">75</span><span class="p">)</span>
+<span class="n">plant</span><span class="o">.</span><span class="n">save</span><span class="p">(</span><span class="s">"thresh75"</span><span class="p">)</span>
+<span class="n">plant</span><span class="o">.</span><span class="n">show</span><span class="p">(</span><span class="s">"thresh75"</span><span class="p">)</span>
+<span class="n">plant</span><span class="o">.</span><span class="n">restore</span><span class="p">(</span><span class="s">"gray"</span><span class="p">)</span>
+
+<span class="n">plant</span><span class="o">.</span><span class="n">threshold</span><span class="p">(</span><span class="mi">100</span><span class="p">)</span>
+<span class="n">plant</span><span class="o">.</span><span class="n">save</span><span class="p">(</span><span class="s">"thresh100"</span><span class="p">)</span>
+<span class="n">plant</span><span class="o">.</span><span class="n">show</span><span class="p">(</span><span class="s">"thresh100"</span><span class="p">)</span>
+<span class="n">plant</span><span class="o">.</span><span class="n">restore</span><span class="p">(</span><span class="s">"gray"</span><span class="p">)</span>
+
+<span class="n">plant</span><span class="o">.</span><span class="n">wait</span><span class="p">()</span>
+<span class="n">plant</span><span class="o">.</span><span class="n">restore</span><span class="p">(</span><span class="s">"thresh50"</span><span class="p">)</span>
+<span class="n">plant</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s">"thresh50.png"</span><span class="p">)</span>
+</pre></div>
+</div>
+<p>This script shows how to get started with ih. Let’s talk about it block by block:</p>
+<div class="highlight-python"><div class="highlight"><pre><span class="kn">import</span> <span class="nn">ih.imgproc</span>
+<span class="n">plant</span> <span class="o">=</span> <span class="n">ih</span><span class="o">.</span><span class="n">imgproc</span><span class="o">.</span><span class="n">Image</span><span class="p">(</span><span class="s">"/path/to/your/image"</span><span class="p">)</span>
+</pre></div>
+</div>
+<p>These two lines setup your image. The first line imports a module, which is simply
+a grouping of related in code. In this case, we import the ‘imgproc’ module, which
+is a grouping of functions related to image processing. This module contains
+all of ih’s image processing functionality, and as a result, is the code we want to import
+to process images. The second line creates an Image object named ‘plant’.
+Object Oriented Programming (OOP) can be a hard concept to understand at first.
+In a simplistic form, objects are like nouns, and the methods we perform on the objects
+are like verbs. Our Image object has certain properties that make it that type of object,
+just like plants have properties that define them. This line accomplishes translating
+the actual image into a form understandable by the code. The ‘plant’ object now has
+properties that define it, and actions (methods) we can perform on it. The rest of the script
+deals specifically with the methods we can perform on our image objects.</p>
+<div class="highlight-python"><div class="highlight"><pre><span class="n">plant</span><span class="o">.</span><span class="n">save</span><span class="p">(</span><span class="s">"base"</span><span class="p">)</span>
+<span class="n">plant</span><span class="o">.</span><span class="n">show</span><span class="p">(</span><span class="s">"base"</span><span class="p">)</span>
+<span class="n">plant</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s">"base.png"</span><span class="p">)</span>
+</pre></div>
+</div>
+<p>These three lines use three separate methods on our plant object, <a class="reference internal" href="processing.html#ih.imgproc.Image.save" title="ih.imgproc.Image.save"><code class="xref py py-meth docutils literal"><span class="pre">save()</span></code></a>,
+<a class="reference internal" href="processing.html#ih.imgproc.Image.show" title="ih.imgproc.Image.show"><code class="xref py py-meth docutils literal"><span class="pre">show()</span></code></a>, and <a class="reference internal" href="processing.html#ih.imgproc.Image.write" title="ih.imgproc.Image.write"><code class="xref py py-meth docutils literal"><span class="pre">write()</span></code></a>. Each of these
+methods performs exactly what its named – the save method saves the image for future use, the show method
+displays the image, and the write method writes the image to a file. Each method has an argument
+passed into it, determining the name to be used in each case. Calling plant.save(“base”) saves the image
+with the name base, plant.show(“base”) shows the image with the window title base, and plant.write(“base.png”)
+writes the image to a file named base.png. Here’s what our base image looks like:</p>
+<img alt="_images/base.png" class="align-center" src="_images/base.png" />
+<div class="line-block">
+<div class="line"><br /></div>
+</div>
+<div class="highlight-python"><div class="highlight"><pre><span class="n">plant</span><span class="o">.</span><span class="n">convertColor</span><span class="p">(</span><span class="s">"bgr"</span><span class="p">,</span> <span class="s">"gray"</span><span class="p">)</span>
+<span class="n">plant</span><span class="o">.</span><span class="n">save</span><span class="p">(</span><span class="s">"gray"</span><span class="p">)</span>
+<span class="n">plant</span><span class="o">.</span><span class="n">show</span><span class="p">(</span><span class="s">"gray"</span><span class="p">)</span>
+<span class="n">plant</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s">"gray.png"</span><span class="p">)</span>
+</pre></div>
+</div>
+<p>The <a class="reference internal" href="processing.html#ih.imgproc.Image.convertColor" title="ih.imgproc.Image.convertColor"><code class="xref py py-meth docutils literal"><span class="pre">convertColor()</span></code></a> method performs a color spectrum shift, changing our image from a color image i.e. “bgr”
+to a gray scale image i.e. “gray”. It should be noted, that all methods overwrite the current image – which is way the save / restore
+functionality is so important. Additionally, converting an image to gray scale from color is an important non-linear shift.
+A color image is called “bgr” because of the three colors in the image, blue, green, and red. Each pixel has a value for
+each of these colors, or channels. Converting to gray condenses the image to a single channel – intensity.
+This means that you <strong>cannot</strong> use <a class="reference internal" href="processing.html#ih.imgproc.Image.convertColor" title="ih.imgproc.Image.convertColor"><code class="xref py py-meth docutils literal"><span class="pre">convertColor()</span></code></a> to restore color to a gray scale image.
+Although we do not use it in this example, the reason for saving the base image is to restore color in a future step.
+The last three lines of this block of code perform the exact same function as the previous block, only using
+different names for saving, showing, and writing. Here’s what our gray scale image looks like:</p>
+<img alt="_images/gray.png" class="align-center" src="_images/gray.png" />
+<div class="line-block">
+<div class="line"><br /></div>
+</div>
+<div class="highlight-python"><div class="highlight"><pre><span class="n">plant</span><span class="o">.</span><span class="n">threshold</span><span class="p">(</span><span class="mi">50</span><span class="p">)</span>
+<span class="n">plant</span><span class="o">.</span><span class="n">save</span><span class="p">(</span><span class="s">"thresh50"</span><span class="p">)</span>
+<span class="n">plant</span><span class="o">.</span><span class="n">show</span><span class="p">(</span><span class="s">"thresh50"</span><span class="p">)</span>
+<span class="n">plant</span><span class="o">.</span><span class="n">restore</span><span class="p">(</span><span class="s">"gray"</span><span class="p">)</span>
+</pre></div>
+</div>
+<p>Now that we have a gray scale image, we perform a <a class="reference internal" href="processing.html#ih.imgproc.Image.threshold" title="ih.imgproc.Image.threshold"><code class="xref py py-meth docutils literal"><span class="pre">threshold()</span></code></a> on it. This simply
+checks the value of each pixels intensity, and checks to see if it beats the cutoff we specify. In this case,
+if the pixel has an intensity greater than 50, we keep it. Intensity values range from 0 to 255. The
+<a class="reference internal" href="processing.html#ih.imgproc.Image.save" title="ih.imgproc.Image.save"><code class="xref py py-meth docutils literal"><span class="pre">save()</span></code></a> and <a class="reference internal" href="processing.html#ih.imgproc.Image.show" title="ih.imgproc.Image.show"><code class="xref py py-meth docutils literal"><span class="pre">show()</span></code></a> methods should be familiar,
+but the fourth line contains a new method, <a class="reference internal" href="processing.html#ih.imgproc.Image.restore" title="ih.imgproc.Image.restore"><code class="xref py py-meth docutils literal"><span class="pre">restore()</span></code></a>. This method restores
+the image to a previously saved image. In the previous block we saved our gray scale image under the name ‘gray’.
+Here, we simply restore that image after thresholding. The purpose of this is to compare multiple threshold values.
+We restore the gray image at the end of each thresholding block to use the same image for thresholding. Here’s the
+result of thresholding by 50:</p>
+<img alt="_images/thresh50.png" class="align-center" src="_images/thresh50.png" />
+<div class="line-block">
+<div class="line"><br /></div>
+</div>
+<div class="highlight-python"><div class="highlight"><pre><span class="n">plant</span><span class="o">.</span><span class="n">threshold</span><span class="p">(</span><span class="mi">75</span><span class="p">)</span>
+<span class="n">plant</span><span class="o">.</span><span class="n">save</span><span class="p">(</span><span class="s">"thresh75"</span><span class="p">)</span>
+<span class="n">plant</span><span class="o">.</span><span class="n">show</span><span class="p">(</span><span class="s">"thresh75"</span><span class="p">)</span>
+<span class="n">plant</span><span class="o">.</span><span class="n">restore</span><span class="p">(</span><span class="s">"gray"</span><span class="p">)</span>
+</pre></div>
+</div>
+<p>This block is identical to the previous one, except we use a threshold value of 75 instead of 50,
+and we rename our saved image and displayed image accordingly. Here’s the result of thresholding
+by 75:</p>
+<img alt="_images/thresh75.png" class="align-center" src="_images/thresh75.png" />
+<div class="line-block">
+<div class="line"><br /></div>
+</div>
+<div class="highlight-python"><div class="highlight"><pre><span class="n">plant</span><span class="o">.</span><span class="n">threshold</span><span class="p">(</span><span class="mi">100</span><span class="p">)</span>
+<span class="n">plant</span><span class="o">.</span><span class="n">save</span><span class="p">(</span><span class="s">"thresh100"</span><span class="p">)</span>
+<span class="n">plant</span><span class="o">.</span><span class="n">show</span><span class="p">(</span><span class="s">"thresh100"</span><span class="p">)</span>
+<span class="n">plant</span><span class="o">.</span><span class="n">restore</span><span class="p">(</span><span class="s">"gray"</span><span class="p">)</span>
+</pre></div>
+</div>
+<p>This block is identical to the previous one, except we use a threshold value of 100 instead of 75,
+and we rename our saved image and displayed image accordingly. Here’s the result of thresholding
+by 100:</p>
+<img alt="_images/thresh100.png" class="align-center" src="_images/thresh100.png" />
+<div class="line-block">
+<div class="line"><br /></div>
+</div>
+<div class="highlight-python"><div class="highlight"><pre><span class="n">plant</span><span class="o">.</span><span class="n">wait</span><span class="p">()</span>
+<span class="n">plant</span><span class="o">.</span><span class="n">restore</span><span class="p">(</span><span class="s">"thresh50"</span><span class="p">)</span>
+<span class="n">plant</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s">"thresh50.png"</span><span class="p">)</span>
+</pre></div>
+</div>
+<p>The final block introduces a new method, <a class="reference internal" href="processing.html#ih.imgproc.Image.wait" title="ih.imgproc.Image.wait"><code class="xref py py-meth docutils literal"><span class="pre">wait()</span></code></a>. This method
+simply halts execution until a key is pressed, then destroys all displayed windows. This
+means that once this point in the script is hit, there should be 5 open windows, the base image,
+the gray image, and one for each of the three thresholds. After execution is resumed,
+we restore the threshold by 50, and write it to a file.</p>
+</div>
+<div class="section" id="command-line-script">
+<h2>Command Line Script<a class="headerlink" href="#command-line-script" title="Permalink to this headline">¶</a></h2>
+<p><a class="reference download internal" href="_downloads/core1.sh"><code class="xref download docutils literal"><span class="pre">Download</span> <span class="pre">Script</span></code></a></p>
+<p><a class="reference download internal" href="_downloads/base1.png"><code class="xref download docutils literal"><span class="pre">Download</span> <span class="pre">Image</span></code></a> (The image is identical to the one above)</p>
+<div class="highlight-bash"><div class="highlight"><pre><span class="c">#!/bin/bash</span>
+
+ih-convert-color --input <span class="s2">"/path/to/your/image"</span> --output <span class="s2">"gray.png"</span> --intype <span class="s2">"bgr"</span> --outtype <span class="s2">"gray"</span>
+ih-threshold --input <span class="s2">"gray.png"</span> --output <span class="s2">"thresh50.png"</span> --thresh 50
+ih-threshold --input <span class="s2">"gray.png"</span> --output <span class="s2">"thresh75.png"</span> --thresh 75
+ih-threshold --input <span class="s2">"gray.png"</span> --output <span class="s2">"thresh100.png"</span> --thresh 100
+</pre></div>
+</div>
+<p>This bash script performs the exact same workflow as the one above. Although not major, it is important to note the
+differences between library and command line access. Command line access loads and writes an image at each step,
+whereas library access loads once, and only writes when you tell it to. Additionally, script names are close to that
+of the method, and all follow lower case format, with words seperated by dashes, and ih prependening all commands.
+The most notable difference, is that a restore method is unnecessary with command-line input. We simply reuse the gray.png
+file we wrote once. Additionally, there is no initial setup, you simply begin processing. The arguments pased into the
+command line arguments match identically with the method arguments above.</p>
+</div>
+</div>
+
+
+ </div>
+
+ </div>
+</div>
+<footer class="footer">
+ <div class="container">
+ <p class="pull-right">
+ <a href="#">Back to top</a>
+
+ </p>
+ <p>
+ © Copyright 2015, Avi Knecht.<br/>
+ Created using <a href="http://sphinx.pocoo.org/">Sphinx</a> 1.3a0.<br/>
+ </p>
+ </div>
+</footer>
+ </body>
+</html>
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+ <div class="section" id="core-processing-example-2">
+<h1>Core Processing Example #2<a class="headerlink" href="#core-processing-example-2" title="Permalink to this headline">¶</a></h1>
+<p>This section will go over a longer script that provides details on many different image processing
+functions including blurring, thresholding, morphologies, color filtering, and contour cutting, as
+well as many core functions, such as save, restore, show, and write.</p>
+<div class="section" id="python-script">
+<h2>Python Script<a class="headerlink" href="#python-script" title="Permalink to this headline">¶</a></h2>
+<p><a class="reference download internal" href="_downloads/core2.py"><code class="xref download docutils literal"><span class="pre">Download</span> <span class="pre">Script</span></code></a></p>
+<p><a class="reference download internal" href="_downloads/base.png"><code class="xref download docutils literal"><span class="pre">Download</span> <span class="pre">Image</span></code></a></p>
+<div class="highlight-python"><div class="highlight"><pre><span class="kn">import</span> <span class="nn">ih.imgproc</span>
+<span class="n">plant</span> <span class="o">=</span> <span class="n">ih</span><span class="o">.</span><span class="n">imgproc</span><span class="o">.</span><span class="n">Image</span><span class="p">(</span><span class="s">"/path/to/your/image"</span><span class="p">)</span>
+
+<span class="n">plant</span><span class="o">.</span><span class="n">save</span><span class="p">(</span><span class="s">"base"</span><span class="p">)</span>
+<span class="n">plant</span><span class="o">.</span><span class="n">show</span><span class="p">(</span><span class="s">"base"</span><span class="p">)</span>
+
+<span class="n">plant</span><span class="o">.</span><span class="n">convertColor</span><span class="p">(</span><span class="s">"bgr"</span><span class="p">,</span> <span class="s">"gray"</span><span class="p">)</span>
+<span class="n">plant</span><span class="o">.</span><span class="n">show</span><span class="p">(</span><span class="s">"grayscale"</span><span class="p">)</span>
+
+<span class="n">plant</span><span class="o">.</span><span class="n">gaussianBlur</span><span class="p">((</span><span class="mi">5</span><span class="p">,</span> <span class="mi">5</span><span class="p">))</span>
+<span class="n">plant</span><span class="o">.</span><span class="n">show</span><span class="p">(</span><span class="s">"blur"</span><span class="p">)</span>
+
+<span class="n">plant</span><span class="o">.</span><span class="n">adaptiveThreshold</span><span class="p">(</span><span class="mi">255</span><span class="p">,</span> <span class="s">"mean"</span><span class="p">,</span> <span class="s">"binary"</span><span class="p">,</span> <span class="mi">15</span><span class="p">,</span> <span class="mi">3</span><span class="p">)</span>
+<span class="n">plant</span><span class="o">.</span><span class="n">show</span><span class="p">(</span><span class="s">"adaptive threshold"</span><span class="p">)</span>
+
+<span class="n">plant</span><span class="o">.</span><span class="n">bitwise_not</span><span class="p">()</span>
+<span class="n">plant</span><span class="o">.</span><span class="n">show</span><span class="p">(</span><span class="s">"invert"</span><span class="p">)</span>
+
+<span class="n">plant</span><span class="o">.</span><span class="n">convertColor</span><span class="p">(</span><span class="s">"gray"</span><span class="p">,</span> <span class="s">"bgr"</span><span class="p">)</span>
+<span class="n">plant</span><span class="o">.</span><span class="n">bitwise_and</span><span class="p">(</span><span class="s">"base"</span><span class="p">)</span>
+<span class="n">plant</span><span class="o">.</span><span class="n">show</span><span class="p">(</span><span class="s">"recolor"</span><span class="p">)</span>
+
+<span class="n">plant</span><span class="o">.</span><span class="n">morphology</span><span class="p">(</span><span class="s">"open"</span><span class="p">,</span> <span class="s">"rect"</span><span class="p">,</span> <span class="p">(</span><span class="mi">3</span><span class="p">,</span> <span class="mi">3</span><span class="p">))</span>
+<span class="n">plant</span><span class="o">.</span><span class="n">show</span><span class="p">(</span><span class="s">"morph"</span><span class="p">)</span>
+
+<span class="n">plant</span><span class="o">.</span><span class="n">colorFilter</span><span class="p">(</span><span class="s">"(((max - min) > 40) and ((b - g) < 30))"</span><span class="p">,</span> <span class="p">[</span><span class="n">plant</span><span class="o">.</span><span class="n">y</span> <span class="o">-</span> <span class="mi">350</span><span class="p">,</span> <span class="o">-</span><span class="mi">1</span><span class="p">,</span> <span class="o">-</span><span class="mi">1</span><span class="p">,</span> <span class="o">-</span><span class="mi">1</span><span class="p">])</span>
+<span class="n">plant</span><span class="o">.</span><span class="n">show</span><span class="p">(</span><span class="s">"filter"</span><span class="p">)</span>
+<span class="n">plant</span><span class="o">.</span><span class="n">save</span><span class="p">(</span><span class="s">"filter"</span><span class="p">)</span>
+
+<span class="n">plant</span><span class="o">.</span><span class="n">convertColor</span><span class="p">(</span><span class="s">"bgr"</span><span class="p">,</span> <span class="s">"gray"</span><span class="p">)</span>
+<span class="n">plant</span><span class="o">.</span><span class="n">threshold</span><span class="p">(</span><span class="mi">0</span><span class="p">)</span>
+<span class="n">plant</span><span class="o">.</span><span class="n">save</span><span class="p">(</span><span class="s">"binary"</span><span class="p">)</span>
+<span class="n">plant</span><span class="o">.</span><span class="n">restore</span><span class="p">(</span><span class="s">"filter"</span><span class="p">)</span>
+
+<span class="n">plant</span><span class="o">.</span><span class="n">contourCut</span><span class="p">(</span><span class="s">"binary"</span><span class="p">,</span> <span class="n">basemin</span> <span class="o">=</span> <span class="mi">500</span><span class="p">,</span> <span class="n">resize</span> <span class="o">=</span> <span class="bp">True</span><span class="p">)</span>
+<span class="n">plant</span><span class="o">.</span><span class="n">show</span><span class="p">(</span><span class="s">"final"</span><span class="p">)</span>
+<span class="n">plant</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s">"final.png"</span><span class="p">)</span>
+
+<span class="k">print</span> <span class="s">"total plant pixels = "</span><span class="p">,</span><span class="n">plant</span><span class="o">.</span><span class="n">extractPixels</span><span class="p">()</span>
+<span class="k">print</span> <span class="s">"[plant height, plant width] = "</span><span class="p">,</span><span class="n">plant</span><span class="o">.</span><span class="n">extractDimensions</span><span class="p">()</span>
+<span class="k">print</span> <span class="s">"Nonzero color data -- [ [bmean, bmed], [gmean, gmed], [rmean, rmed] ] = "</span><span class="p">,</span><span class="n">plant</span><span class="o">.</span><span class="n">extractColorData</span><span class="p">()</span>
+<span class="k">print</span> <span class="s">"With zero color data -- [ [bmean, bmed], [gmean, gmed], [rmean, rmed] ] = "</span><span class="p">,</span><span class="n">plant</span><span class="o">.</span><span class="n">extractColorData</span><span class="p">(</span><span class="n">nonzero</span> <span class="o">=</span> <span class="bp">False</span><span class="p">)</span>
+
+<span class="n">plant</span><span class="o">.</span><span class="n">wait</span><span class="p">()</span>
+</pre></div>
+</div>
+<p>This script show cases several features of ih, is fairly simple and fairly accurate. Let’s talk about it block by block:</p>
+<div class="highlight-python"><div class="highlight"><pre><span class="kn">import</span> <span class="nn">ih.imgproc</span>
+<span class="n">plant</span> <span class="o">=</span> <span class="n">ih</span><span class="o">.</span><span class="n">imgproc</span><span class="o">.</span><span class="n">Image</span><span class="p">(</span><span class="s">"/path/to/your/image"</span><span class="p">)</span>
+</pre></div>
+</div>
+<p>These two lines setup your image. The first line imports the actual library to be used, and in this case we
+want the imgproc module from ih. The second line creates an object of your image, named ‘plant’. Our image
+has been loaded in, so we are ready for processing.</p>
+<div class="highlight-python"><div class="highlight"><pre><span class="n">plant</span><span class="o">.</span><span class="n">save</span><span class="p">(</span><span class="s">"base"</span><span class="p">)</span>
+<span class="n">plant</span><span class="o">.</span><span class="n">show</span><span class="p">(</span><span class="s">"base"</span><span class="p">)</span>
+</pre></div>
+</div>
+<p>These two lines don’t do any actual processing yet. The <a class="reference internal" href="processing.html#ih.imgproc.Image.save" title="ih.imgproc.Image.save"><code class="xref py py-meth docutils literal"><span class="pre">save()</span></code></a> method saves what our image currently looks like
+for future use. This will be used in a later step to re-constitute the color of the image. We fed in the name
+‘base’, and that’s how we will refer to this saved image in the future. The ‘show’ method simply opens a window
+of the current image. Show automatically resizes an image down if it is too large (which it will be). We also
+fed in the name base which means our window will have the title ‘base’. If a name is not fed in, the titles
+will simply be numbered. Here’s what our base image looks like:</p>
+<img alt="_images/base_small.png" class="align-center" src="_images/base_small.png" />
+<p>For viewing purposes all images have been greatly reduced in size. On to the next block:</p>
+<div class="highlight-python"><div class="highlight"><pre><span class="n">plant</span><span class="o">.</span><span class="n">convertColor</span><span class="p">(</span><span class="s">"bgr"</span><span class="p">,</span> <span class="s">"gray"</span><span class="p">)</span>
+<span class="n">plant</span><span class="o">.</span><span class="n">show</span><span class="p">(</span><span class="s">"grayscale"</span><span class="p">)</span>
+</pre></div>
+</div>
+<p>Now we do some actual processing! The <a class="reference internal" href="processing.html#ih.imgproc.Image.convertColor" title="ih.imgproc.Image.convertColor"><code class="xref py py-meth docutils literal"><span class="pre">convertColor()</span></code></a> method does exactly that – changes the spectrum of the image.
+Currently, supported spectrums are “bgr”, “hsv”, “lab”, “ycrcb”, and “gray”. It is important to remember that
+many spectrum changes are one-directional. In this case, we convert “bgr” to “gray”, giving us a grayscale image.
+If we then called the same function in reverse i.e. plant.convertColor(“gray”, “bgr”), our image would look exactly the same.
+You can find more information on this in the <a class="reference internal" href="processing.html#ih.imgproc.Image.convertColor" title="ih.imgproc.Image.convertColor"><code class="xref py py-meth docutils literal"><span class="pre">convertColor()</span></code></a> method. Again, we use
+‘show’ to view the result of our step. Here’s what our gray scale image looks like:</p>
+<img alt="_images/gray_small.png" class="align-center" src="_images/gray_small.png" />
+<div class="line-block">
+<div class="line"><br /></div>
+</div>
+<div class="highlight-python"><div class="highlight"><pre><span class="n">plant</span><span class="o">.</span><span class="n">gaussianBlur</span><span class="p">((</span><span class="mi">5</span><span class="p">,</span> <span class="mi">5</span><span class="p">))</span>
+<span class="n">plant</span><span class="o">.</span><span class="n">show</span><span class="p">(</span><span class="s">"blur"</span><span class="p">)</span>
+</pre></div>
+</div>
+<p>Here we blur the image slightly, using <a class="reference internal" href="processing.html#ih.imgproc.Image.gaussianBlur" title="ih.imgproc.Image.gaussianBlur"><code class="xref py py-meth docutils literal"><span class="pre">gaussianBlur()</span></code></a> with a kernel of size 5 x 5.
+The first number specifies the height of the kernel, and the second the width of the kernel. Blurring an image
+before thresholding will help smooth the result, and remove more noise from the image. Here’s our result:</p>
+<img alt="_images/blur_small.png" class="align-center" src="_images/blur_small.png" />
+<div class="line-block">
+<div class="line"><br /></div>
+</div>
+<div class="highlight-python"><div class="highlight"><pre><span class="n">plant</span><span class="o">.</span><span class="n">adaptiveThreshold</span><span class="p">(</span><span class="mi">255</span><span class="p">,</span> <span class="s">"mean"</span><span class="p">,</span> <span class="s">"binary"</span><span class="p">,</span> <span class="mi">15</span><span class="p">,</span> <span class="mi">3</span><span class="p">)</span>
+<span class="n">plant</span><span class="o">.</span><span class="n">show</span><span class="p">(</span><span class="s">"adaptive threshold"</span><span class="p">)</span>
+</pre></div>
+</div>
+<p>Next, we threshold our gray image. Normal thresholding (see the <a class="reference internal" href="processing.html#ih.imgproc.Image.threshold" title="ih.imgproc.Image.threshold"><code class="xref py py-meth docutils literal"><span class="pre">threshold()</span></code></a> method) simply
+checks to see if each pixel in the image is greater than the specified threshold. The <a class="reference internal" href="processing.html#ih.imgproc.Image.adaptiveThreshold" title="ih.imgproc.Image.adaptiveThreshold"><code class="xref py py-meth docutils literal"><span class="pre">adaptiveThreshold()</span></code></a> method
+breaks up the image into windows, and considers each window separately. ‘255’ represents the value we assign to a pixel if it beats the
+threshold. “mean” is the adaptive method we use – we take the average of the pixels in a window to determine the threshold.
+“binary” is the threshold type. 15 is the window size – which means we consider 15 x 15 blocks of pixels as each window. 3
+is a constant that is subtracted from the calculated threshold for each window. Again, we use ‘show’ to view the result of our step.
+Here’s what our image looks like after adaptive thresholding:</p>
+<img alt="_images/thresh_small.png" class="align-center" src="_images/thresh_small.png" />
+<div class="line-block">
+<div class="line"><br /></div>
+</div>
+<div class="highlight-python"><div class="highlight"><pre><span class="n">plant</span><span class="o">.</span><span class="n">bitwise_not</span><span class="p">()</span>
+<span class="n">plant</span><span class="o">.</span><span class="n">show</span><span class="p">(</span><span class="s">"inverted"</span><span class="p">)</span>
+</pre></div>
+</div>
+<p>The <a class="reference internal" href="processing.html#ih.imgproc.Image.bitwise_not" title="ih.imgproc.Image.bitwise_not"><code class="xref py py-meth docutils literal"><span class="pre">bitwise_not()</span></code></a> method inverts an image. If the image is a color image it processes each channel separately.
+Inverting the image is going to be important for our next step. Here’s the inverted image:</p>
+<img alt="_images/invert_small.png" class="align-center" src="_images/invert_small.png" />
+<div class="line-block">
+<div class="line"><br /></div>
+</div>
+<div class="highlight-python"><div class="highlight"><pre><span class="n">plant</span><span class="o">.</span><span class="n">convertColor</span><span class="p">(</span><span class="s">"gray"</span><span class="p">,</span> <span class="s">"bgr"</span><span class="p">)</span>
+<span class="n">plant</span><span class="o">.</span><span class="n">bitwise_and</span><span class="p">(</span><span class="s">"base"</span><span class="p">)</span>
+<span class="n">plant</span><span class="o">.</span><span class="n">show</span><span class="p">(</span><span class="s">"recolor"</span><span class="p">)</span>
+</pre></div>
+</div>
+<p>This step recolors the image to the original colors which we saved under the name ‘base’. <a class="reference internal" href="processing.html#ih.imgproc.Image.bitwise_and" title="ih.imgproc.Image.bitwise_and"><code class="xref py py-meth docutils literal"><span class="pre">bitwise_and()</span></code></a>
+computes the logical and of two images. This function can only be used on two images of the same shape. In this case, our base
+image has 3 channels, an r, g, and b channel, but our gray image only has 1 channel, intensity. Even though <a class="reference internal" href="processing.html#ih.imgproc.Image.convertColor" title="ih.imgproc.Image.convertColor"><code class="xref py py-meth docutils literal"><span class="pre">convertColor()</span></code></a>
+won’t change what the image looks like, we need to ensure that both images have the same number of channels before computing the bitwise_and.
+This extra convertColor step doesn’t need to happen when using command-line scripts for processing, because images are saved and loaded as
+3 channel images. Here’s the recolored image:</p>
+<img alt="_images/recolor_small.png" class="align-center" src="_images/recolor_small.png" />
+<p>We’ve stripped a lot of the background out of image with pretty good accuracy.
+We need to clean up the noise around the bottom, and clean up the pot still.</p>
+<div class="highlight-python"><div class="highlight"><pre><span class="n">plant</span><span class="o">.</span><span class="n">morphology</span><span class="p">(</span><span class="s">"open"</span><span class="p">,</span> <span class="s">"rect"</span><span class="p">,</span> <span class="p">(</span><span class="mi">3</span><span class="p">,</span> <span class="mi">3</span><span class="p">))</span>
+<span class="n">plant</span><span class="o">.</span><span class="n">show</span><span class="p">(</span><span class="s">"morph"</span><span class="p">)</span>
+</pre></div>
+</div>
+<p><a class="reference internal" href="processing.html#ih.imgproc.Image.morphology" title="ih.imgproc.Image.morphology"><code class="xref py py-meth docutils literal"><span class="pre">morphology()</span></code></a> uses one of several different methods to adjust the structure of your image.
+In this case, we use morphological opening – this erodes all borders in the image, and then adds borders back on to
+the shapes still in the image. In this case, it removes a lot of the noise around the bottom without hurting the
+plant very much:</p>
+<img alt="_images/morph_small.png" class="align-center" src="_images/morph_small.png" />
+<p>Now we need to filter out the carrier, as well as the track from the bottom of the image.</p>
+<div class="highlight-python"><div class="highlight"><pre><span class="n">plant</span><span class="o">.</span><span class="n">colorFilter</span><span class="p">(</span><span class="s">"(((max - min) > 40) and ((b - g) < 30))"</span><span class="p">,</span> <span class="p">[</span><span class="n">plant</span><span class="o">.</span><span class="n">y</span> <span class="o">-</span> <span class="mi">350</span><span class="p">,</span> <span class="o">-</span><span class="mi">1</span><span class="p">,</span> <span class="o">-</span><span class="mi">1</span><span class="p">,</span> <span class="o">-</span><span class="mi">1</span><span class="p">])</span>
+<span class="n">plant</span><span class="o">.</span><span class="n">show</span><span class="p">(</span><span class="s">"filter"</span><span class="p">)</span>
+<span class="n">plant</span><span class="o">.</span><span class="n">save</span><span class="p">(</span><span class="s">"filter"</span><span class="p">)</span>
+</pre></div>
+</div>
+<p><a class="reference internal" href="processing.html#ih.imgproc.Image.colorFilter" title="ih.imgproc.Image.colorFilter"><code class="xref py py-meth docutils literal"><span class="pre">colorFilter()</span></code></a> is a powerful method that takes 2 arguments, the first is logic, the second is a region of interest.
+The logic argument to colorFilter must be well formed based on symbolic logic rules. This means that operators can only act on two operands,
+which means that your logic string may have more parenthesis than if it were in a standard language. You can find more information under the
+<a class="reference internal" href="processing.html#ih.imgproc.Image.colorFilter" title="ih.imgproc.Image.colorFilter"><code class="xref py py-meth docutils literal"><span class="pre">colorFilter()</span></code></a> docs. Based on our logic, we only keep a pixel if it meets both of the following conditions:
+the maximum value of the pixel (max([r, g, b])) minus the minimum value of the pixel (min([r, g, b])) is greater than 40, and the blue value
+of the pixel minus the green value of the pixel is less than 30. The first condition removes all gray pixels. Gray colors have lower variance between
+the three channels and we target them likewise. This piece will filter out the track and the bright colors of the pot. The second condition will remove
+the blue part of the part. The next argument is our region of interest. All roi’s have the following form [ystart, yend, xstart, xend], due to the order
+which opencv uses. Additionally, -1 can be used as a placeholder for any value in an roi, and represents the far edge for that value. For start values
+-1 is equivalent to 0, for end values -1 is equivalent to the maximal width or height of the image. Finally,
+the plant object internally maintains a width as ‘x’ and a height as ‘y’. plant.x will return the plant’s width, and plant.y will return the
+plant’s height. So, in this case our region of interest targets only the bottom 350 pixels of the image. ystart is at plant.y - 350, and we use the maximal
+height of the image for yend. We also target the entire width of the plant – we use -1 for both xstart and xend. Here’s the image after filtration:</p>
+<img alt="_images/filter_small.png" class="align-center" src="_images/filter_small.png" />
+<p>At this point we will call our image processing good, and crop the image down to just the plant, so we can get an accurate height and width.
+To do this, we will use the <a class="reference internal" href="processing.html#ih.imgproc.Image.contourCut" title="ih.imgproc.Image.contourCut"><code class="xref py py-meth docutils literal"><span class="pre">contourCut()</span></code></a> function. This function requires a color image, and a binary image.
+We have saved our current image under the name ‘filter’, so we need to prepare a binary image:</p>
+<div class="highlight-python"><div class="highlight"><pre><span class="n">plant</span><span class="o">.</span><span class="n">convertColor</span><span class="p">(</span><span class="s">"bgr"</span><span class="p">,</span> <span class="s">"gray"</span><span class="p">)</span>
+<span class="n">plant</span><span class="o">.</span><span class="n">threshold</span><span class="p">(</span><span class="mi">0</span><span class="p">)</span>
+<span class="n">plant</span><span class="o">.</span><span class="n">save</span><span class="p">(</span><span class="s">"binary"</span><span class="p">)</span>
+<span class="n">plant</span><span class="o">.</span><span class="n">restore</span><span class="p">(</span><span class="s">"filter"</span><span class="p">)</span>
+</pre></div>
+</div>
+<p>We can’t threshold color images, so we begin by using <a class="reference internal" href="processing.html#ih.imgproc.Image.convertColor" title="ih.imgproc.Image.convertColor"><code class="xref py py-meth docutils literal"><span class="pre">convertColor()</span></code></a> to convert our image to gray scale. Next, we
+use <a class="reference internal" href="processing.html#ih.imgproc.Image.threshold" title="ih.imgproc.Image.threshold"><code class="xref py py-meth docutils literal"><span class="pre">threshold()</span></code></a> with a thresh value of 0 to threshold our image. With a threshold of 0, as long as any pixel is
+non-zero, it will be kept. This means that we will create a binary image that is an exact structural replica of our current image. We save
+this image for later use under the name ‘binary’. Final, we :py:meth:<a href="#id1"><span class="problematic" id="id2">`</span></a>~ih.imgproc.Image.restore~ our color image we previously saved.
+The restore method changes the current image to a previously saved one. Here’s what our binary image looks like:</p>
+<img alt="_images/binary_small.png" class="align-center" src="_images/binary_small.png" />
+<div class="line-block">
+<div class="line"><br /></div>
+</div>
+<div class="highlight-python"><div class="highlight"><pre><span class="n">plant</span><span class="o">.</span><span class="n">contourCut</span><span class="p">(</span><span class="s">"binary"</span><span class="p">,</span> <span class="n">basemin</span> <span class="o">=</span> <span class="mi">500</span><span class="p">,</span> <span class="n">resize</span> <span class="o">=</span> <span class="bp">True</span><span class="p">)</span>
+<span class="n">plant</span><span class="o">.</span><span class="n">show</span><span class="p">(</span><span class="s">"final"</span><span class="p">)</span>
+<span class="n">plant</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s">"final.png"</span><span class="p">)</span>
+</pre></div>
+</div>
+<p>Finally, we use <a class="reference internal" href="processing.html#ih.imgproc.Image.contourCut" title="ih.imgproc.Image.contourCut"><code class="xref py py-meth docutils literal"><span class="pre">contourCut()</span></code></a> to crop our image. contourCut removes pieces of an
+image based on the size of contours, which are clusters of pixels in the image. Noise in the image is spread
+out in small clusters, but the plant is connected. Specifying a sufficiently large threshold value will cause
+the noise to get excluded from the image. The final roi of the image is determined by the contours that are
+larger than the threshold value, and the image is cropped such that all the contours remain in the image. The
+image calculates contours from the binary image, but returns a final image based on the colors of the current image.
+We feed in ‘binary’ as our binary image, specify a threshold area of 500 pixels, and specify resize = True. If resize
+is false, the image won’t be resized, and instead, all pixels outside the roi will be set off. We <a class="reference internal" href="processing.html#ih.imgproc.Image.write" title="ih.imgproc.Image.write"><code class="xref py py-meth docutils literal"><span class="pre">write()</span></code></a>
+our final image to “final.png”. By default, images are written to the current directory, unless you specify an outputdir when
+you create the plant object. Here’s the final, un-scaled image:</p>
+<img alt="_images/final.png" class="align-center" src="_images/final.png" />
+<p>Now that our image is processed, we extract data from it:</p>
+<div class="highlight-python"><div class="highlight"><pre><span class="k">print</span> <span class="s">"total plant pixels = "</span><span class="p">,</span><span class="n">plant</span><span class="o">.</span><span class="n">extractPixels</span><span class="p">()</span>
+<span class="k">print</span> <span class="s">"[plant height, plant width] = "</span><span class="p">,</span><span class="n">plant</span><span class="o">.</span><span class="n">extractDimensions</span><span class="p">()</span>
+<span class="k">print</span> <span class="s">"Nonzero color data -- [ [bmean, bmed], [gmean, gmed], [rmean, rmed] ] = "</span><span class="p">,</span><span class="n">plant</span><span class="o">.</span><span class="n">extractColorData</span><span class="p">()</span>
+<span class="k">print</span> <span class="s">"With zero color data -- [ [bmean, bmed], [gmean, gmed], [rmean, rmed] ] = "</span><span class="p">,</span><span class="n">plant</span><span class="o">.</span><span class="n">extractColorData</span><span class="p">(</span><span class="n">nonzero</span> <span class="o">=</span> <span class="bp">False</span><span class="p">)</span>
+</pre></div>
+</div>
+<p>Each of these lines print out information about our final image. <a class="reference internal" href="processing.html#ih.imgproc.Image.extractPixels" title="ih.imgproc.Image.extractPixels"><code class="xref py py-meth docutils literal"><span class="pre">extractPixels()</span></code></a> returns the
+total number of non-zero pixels in the image. <a class="reference internal" href="processing.html#ih.imgproc.Image.extractDimensions" title="ih.imgproc.Image.extractDimensions"><code class="xref py py-meth docutils literal"><span class="pre">extractDimensions()</span></code></a> returns the height and
+width of the plant. <a class="reference internal" href="processing.html#ih.imgproc.Image.extractColorData" title="ih.imgproc.Image.extractColorData"><code class="xref py py-meth docutils literal"><span class="pre">extractColorData()</span></code></a> calculates histograms for each individual color channel
+of the image, and returns the median and mean for each histogram. By default, it only uses non-zero values in its calculations,
+but you can specify nonzero = False to use all values. Your output should look something like this:</p>
+<div class="highlight-python"><div class="highlight"><pre><span class="n">total</span> <span class="n">plant</span> <span class="n">pixels</span> <span class="o">=</span> <span class="mi">21964</span>
+<span class="p">[</span><span class="n">plant</span> <span class="n">height</span><span class="p">,</span> <span class="n">plant</span> <span class="n">width</span><span class="p">]</span> <span class="o">=</span> <span class="p">[</span><span class="mi">637</span><span class="p">,</span> <span class="mi">668</span><span class="p">]</span>
+<span class="n">Nonzero</span> <span class="n">color</span> <span class="n">data</span> <span class="o">--</span> <span class="p">[</span> <span class="p">[</span><span class="n">bmean</span><span class="p">,</span> <span class="n">bmed</span><span class="p">],</span> <span class="p">[</span><span class="n">gmean</span><span class="p">,</span> <span class="n">gmed</span><span class="p">],</span> <span class="p">[</span><span class="n">rmean</span><span class="p">,</span> <span class="n">rmed</span><span class="p">]</span> <span class="p">]</span> <span class="o">=</span> <span class="p">[[</span><span class="mf">56.514124293785308</span><span class="p">,</span> <span class="mf">11.0</span><span class="p">],</span> <span class="p">[</span><span class="mf">71.787162162162161</span><span class="p">,</span> <span class="mf">34.5</span><span class="p">],</span> <span class="p">[</span><span class="mf">67.78235294117647</span><span class="p">,</span> <span class="mf">25.0</span><span class="p">]]</span>
+<span class="n">With</span> <span class="n">zero</span> <span class="n">color</span> <span class="n">data</span> <span class="o">--</span> <span class="p">[</span> <span class="p">[</span><span class="n">bmean</span><span class="p">,</span> <span class="n">bmed</span><span class="p">],</span> <span class="p">[</span><span class="n">gmean</span><span class="p">,</span> <span class="n">gmed</span><span class="p">],</span> <span class="p">[</span><span class="n">rmean</span><span class="p">,</span> <span class="n">rmed</span><span class="p">]</span> <span class="p">]</span> <span class="o">=</span> <span class="p">[[</span><span class="mf">35.67578125</span><span class="p">,</span> <span class="mf">10.0</span><span class="p">],</span> <span class="p">[</span><span class="mf">53.78515625</span><span class="p">,</span> <span class="mf">9.0</span><span class="p">],</span> <span class="p">[</span><span class="mf">44.4140625</span><span class="p">,</span> <span class="mf">9.0</span><span class="p">]]</span>
+</pre></div>
+</div>
+<p>Finally, hiding at the end is the following line:</p>
+<div class="highlight-python"><div class="highlight"><pre><span class="n">plant</span><span class="o">.</span><span class="n">wait</span><span class="p">()</span>
+</pre></div>
+</div>
+<p>The <a class="reference internal" href="processing.html#ih.imgproc.Image.wait" title="ih.imgproc.Image.wait"><code class="xref py py-meth docutils literal"><span class="pre">wait()</span></code></a> does exactly that, and is a wrapper to 2 opencv functions. First, the function
+will pause execution, and all of the images you displayed will stay open in the named windows you specified. Second,
+while focused on one of your displayed windows, if you press any key, it will remove all the windows, and continue execution
+of the program – which in this case means the program will stop.</p>
+</div>
+<div class="section" id="command-line-script">
+<h2>Command Line Script<a class="headerlink" href="#command-line-script" title="Permalink to this headline">¶</a></h2>
+<p><a class="reference download internal" href="_downloads/core2.sh"><code class="xref download docutils literal"><span class="pre">Download</span> <span class="pre">Script</span></code></a></p>
+<p><a class="reference download internal" href="_downloads/base.png"><code class="xref download docutils literal"><span class="pre">Download</span> <span class="pre">Image</span></code></a> (The image is identical to the one above)</p>
+<div class="highlight-bash"><div class="highlight"><pre><span class="c">#!/bin/bash</span>
+
+ih-convert-color --input <span class="s2">"/path/to/your/image"</span> --output <span class="s2">"gray.png"</span> --intype <span class="s2">"bgr"</span> --outtype <span class="s2">"gray"</span>
+ih-gaussian-blur --input <span class="s2">"gray.png"</span> --output <span class="s2">"blur.png"</span> --kwidth <span class="m">5</span> --kheight 5
+ih-adaptive-threshold --input <span class="s2">"blur.png"</span> --output <span class="s2">"thresh.png"</span> --value <span class="m">255</span> --adaptiveType <span class="s2">"mean"</span> --thresholdType <span class="s2">"binary"</span> --blockSize <span class="m">15</span> --C 3
+ih-bitwise-not --input <span class="s2">"thresh.png"</span> --output <span class="s2">"invert.png"</span>
+ih-bitwise-and --input1 <span class="s2">"base.png"</span> --input2 <span class="s2">"invert.png"</span> --output <span class="s2">"recolor.png"</span>
+ih-morphology --input <span class="s2">"recolor.png"</span> --output <span class="s2">"morph.png"</span> --morphType <span class="s2">"open"</span> --ktype <span class="s2">"rect"</span> --kwidth <span class="m">3</span> --kheight 3
+ih-color-filter --input <span class="s2">"morph.png"</span> --output <span class="s2">"filter.png"</span> --logic <span class="s2">"(((max - min) > 40) and ((b - g) < 30))"</span> --ystart <span class="s2">"y - 350"</span>
+ih-threshold --input <span class="s2">"filter.png"</span> --output <span class="s2">"binary.png"</span> --thresh 0
+ih-contour-cut --input <span class="s2">"filter.png"</span> --binary <span class="s2">"binary.png"</span> --output <span class="s2">"final.png"</span> --basemin <span class="m">500</span> --resize
+</pre></div>
+</div>
+<p>This bash script should perform the exact same workflow as the one above. Although not major, it is important to note the
+differences between library and command line access. Command line access loads and writes an image at each step,
+whereas library access loads once, and only writes when you tell it to. Additionally, script names are close to that
+of the method, and all follow lower case format, with words seperated by dashes, and ih prependening all commands.
+Most arguments are the same, but because we can’t specify tuples or lists from the command line, arguments like kernels and
+regions of interest have to change. Individual arguments are defined, as you can see in gaussian-blur, morphology, and
+color-fitler. kwidth and kheight have to specified individual, and ystart, yend, xstart, xend have to be specified individual.
+-1 is assumed as the default value for roi, so any value you don’t specify will be the edge for that position as specified
+above. For the contour-cut ‘resize’ argument, you don’t have to specify true, as simply adding –resize will imply
+you want to resize.</p>
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+ <input type="text" name="q" class="form-control" placeholder="Search" />
+ </div>
+ <input type="hidden" name="check_keywords" value="yes" />
+ <input type="hidden" name="area" value="default" />
+</form>
+
+ </div>
+ </div>
+ </div>
+
+<div class="container">
+ <div class="row">
+ <div class="col-md-12">
+
+ <style> .red {color:red} .blue {color:blue} .green {color:green} .orange {color:orange} </style><div class="section" id="workflow-example-1">
+<h1>Workflow Example #1<a class="headerlink" href="#workflow-example-1" title="Permalink to this headline">¶</a></h1>
+<p>This section will detail the steps involved with creating a super-computer
+workflow. It assumes that you have the proper environment setup
+already on a grid computer with Condor and Pegasus installed.
+Workflow generation is designed specifically for high throughput
+data sets – this example uses a data set of ~80,000 images. Additionally,
+this tutorial serves to show how to setup and run a workflow, not
+explaining the analysis choices made when designing a workflow. This workflow
+was created using experiment ‘0184 Uni Nebraska Rice 1’ data, on
+Tusker at the Holland Computing Center.</p>
+<div class="section" id="final-templates">
+<h2>Final Templates<a class="headerlink" href="#final-templates" title="Permalink to this headline">¶</a></h2>
+<p><a class="reference download internal" href="_downloads/crawl.json"><code class="xref download docutils literal"><span class="pre">Image</span> <span class="pre">Loading</span></code></a></p>
+<p><a class="reference download internal" href="_downloads/imgproc.json"><code class="xref download docutils literal"><span class="pre">Image</span> <span class="pre">Processing</span></code></a></p>
+<p><a class="reference download internal" href="_downloads/config.json"><code class="xref download docutils literal"><span class="pre">Configuration</span></code></a></p>
+<p><a class="reference download internal" href="_downloads/GenKey.csv"><code class="xref download docutils literal"><span class="pre">Genotype</span> <span class="pre">Key</span> <span class="pre">File</span></code></a></p>
+<p><a class="reference download internal" href="_downloads/roi.tar.gz"><code class="xref download docutils literal"><span class="pre">ROI</span> <span class="pre">files</span></code></a></p>
+</div>
+<div class="section" id="image-loading">
+<h2>Image Loading<a class="headerlink" href="#image-loading" title="Permalink to this headline">¶</a></h2>
+<p>In this workflow example, we will use data acquired from LemnaTec’s
+imaging system, for experiment 0184. The input data structure has been
+altered slightly from the raw LemnaTec data. Although none of the data
+changed, an extra directory was added to help break up the data set.
+Here are several examples of paths to images:</p>
+<div class="line-block">
+<div class="line">/work/walia/common/ih/rawdata/0184 Uni Nebraska Rice 1/strain3/0184 Uni Nebraska Rice 1_023542-C_2013-09-05_05-18-33_455640/RGB SV1/0_0.png</div>
+<div class="line">/work/walia/common/ih/rawdata/0184 Uni Nebraska Rice 1/strain5/0184 Uni Nebraska Rice 1_023546-C_2013-08-21_05-22-52_432942/FLUO SV1/0_0.png</div>
+<div class="line">/work/walia/common/ih/rawdata/0184 Uni Nebraska Rice 1/strain93/0184 Uni Nebraska Rice 1_023722-S_2013-09-09_10-56-45_462980/RGB TV/0_0.png</div>
+</div>
+<p>There are a total of 436 strain folders, 36 sub folders in each strain folder, and 12 additional image-type folders. For
+this experiment, we will be processing RGB SV1, RGB SV2, FLUO SV1, FLUO SV2, and RGB TV images for a total of 436 * 36 * 5 ~= 80,000 images.
+The image loading step takes care of two key problems posed by having large data sets (assuming correctly written template files). First,
+it tracks all images, and loads them into a single database, making it very easy to find and process files in the future. Second,
+all meta-data definitions are done as a result of the crawling – no manual definitions are required. Consider our directory structure.
+There is a lot of information about each image in the names of the directories – id numbers, whether or not the plant was stressed, the date, and the image
+type. With this motivation in mind, lets look at the loading template, crawl.json.</p>
+<div class="highlight-javascript"><div class="highlight"><pre><span class="p">{</span>
+ <span class="s2">"path"</span><span class="o">:</span> <span class="s2">"/work/walia/common/ih/rawdata/0184 Uni Nebraska Rice 1/%null%/%null%_%idnum%-%idchar%_%date%/%imgname%/0_0.png"</span><span class="p">,</span>
+ <span class="s2">"base"</span><span class="o">:</span> <span class="s2">"/work/walia/common/ih/rawdata/0184 Uni Nebraska Rice 1/"</span><span class="p">,</span>
+ <span class="s2">"filetype"</span><span class="o">:</span> <span class="s2">".png"</span><span class="p">,</span>
+ <span class="s2">"order"</span><span class="o">:</span> <span class="p">[</span><span class="s2">"experiment"</span><span class="p">,</span> <span class="s2">"id"</span><span class="p">,</span> <span class="s2">"genotype"</span><span class="p">,</span> <span class="s2">"date"</span><span class="p">,</span> <span class="s2">"treatment"</span><span class="p">,</span> <span class="s2">"imgname"</span><span class="p">,</span> <span class="s2">"imtype"</span><span class="p">,</span> <span class="s2">"path"</span><span class="p">],</span>
+ <span class="s2">"data"</span><span class="o">:</span> <span class="p">{</span>
+ <span class="s2">"experiment"</span><span class="o">:</span> <span class="p">{</span>
+ <span class="s2">"type"</span><span class="o">:</span> <span class="s2">"value"</span><span class="p">,</span>
+ <span class="s2">"value"</span><span class="o">:</span> <span class="s2">"0184"</span>
+ <span class="p">},</span>
+ <span class="s2">"id"</span><span class="o">:</span> <span class="p">{</span>
+ <span class="s2">"type"</span><span class="o">:</span> <span class="s2">"value"</span><span class="p">,</span>
+ <span class="s2">"value"</span><span class="o">:</span> <span class="s2">"%idnum%-%idchar%"</span>
+ <span class="p">},</span>
+ <span class="s2">"genotype"</span><span class="o">:</span> <span class="p">{</span>
+ <span class="s2">"type"</span><span class="o">:</span> <span class="s2">"file"</span><span class="p">,</span>
+ <span class="s2">"value"</span><span class="o">:</span> <span class="s2">"/Users/aknecht/git/ih/old_scripts/2014-09-03/GenKey.csv"</span><span class="p">,</span>
+ <span class="s2">"key"</span><span class="o">:</span> <span class="s2">"%idnum%-%idchar%"</span><span class="p">,</span>
+ <span class="s2">"keyColumn"</span><span class="o">:</span> <span class="mi">0</span><span class="p">,</span>
+ <span class="s2">"valueColumn"</span><span class="o">:</span> <span class="mi">1</span>
+ <span class="p">},</span>
+ <span class="s2">"date"</span><span class="o">:</span> <span class="p">{</span>
+ <span class="s2">"type"</span><span class="o">:</span> <span class="s2">"date"</span><span class="p">,</span>
+ <span class="s2">"value"</span><span class="o">:</span> <span class="s2">"%date%"</span><span class="p">,</span>
+ <span class="s2">"format"</span><span class="o">:</span> <span class="s2">"Y-m-d"</span>
+ <span class="p">},</span>
+ <span class="s2">"treatment"</span><span class="o">:</span> <span class="p">{</span>
+ <span class="s2">"type"</span><span class="o">:</span> <span class="s2">"value"</span><span class="p">,</span>
+ <span class="s2">"translate"</span><span class="o">:</span> <span class="s2">"true"</span><span class="p">,</span>
+ <span class="s2">"value"</span><span class="o">:</span> <span class="s2">"%idchar%"</span>
+ <span class="p">},</span>
+ <span class="s2">"imgname"</span><span class="o">:</span> <span class="p">{</span>
+ <span class="s2">"type"</span><span class="o">:</span> <span class="s2">"value"</span><span class="p">,</span>
+ <span class="s2">"value"</span><span class="o">:</span> <span class="s2">"%imgname%"</span>
+ <span class="p">},</span>
+ <span class="s2">"imtype"</span><span class="o">:</span> <span class="p">{</span>
+ <span class="s2">"type"</span><span class="o">:</span> <span class="s2">"value"</span><span class="p">,</span>
+ <span class="s2">"translate"</span><span class="o">:</span> <span class="s2">"true"</span><span class="p">,</span>
+ <span class="s2">"value"</span><span class="o">:</span> <span class="s2">"%imgname%"</span>
+ <span class="p">}</span>
+ <span class="p">},</span>
+ <span class="s2">"translations"</span><span class="o">:</span> <span class="p">{</span>
+ <span class="s2">"treatment"</span><span class="o">:</span> <span class="p">{</span>
+ <span class="s2">"S"</span><span class="o">:</span> <span class="s2">"Stress"</span><span class="p">,</span>
+ <span class="s2">"s"</span><span class="o">:</span> <span class="s2">"Stress"</span><span class="p">,</span>
+ <span class="s2">"C"</span><span class="o">:</span> <span class="s2">"Control"</span><span class="p">,</span>
+ <span class="s2">"c"</span><span class="o">:</span> <span class="s2">"Control"</span>
+ <span class="p">},</span>
+ <span class="s2">"imtype"</span><span class="o">:</span> <span class="p">{</span>
+ <span class="s2">"RGB SV1"</span><span class="o">:</span> <span class="s2">"rgbsv"</span><span class="p">,</span>
+ <span class="s2">"RGB SV2"</span><span class="o">:</span> <span class="s2">"rgbsv"</span><span class="p">,</span>
+ <span class="s2">"RGB TV"</span><span class="o">:</span> <span class="s2">"rgbtv"</span><span class="p">,</span>
+ <span class="s2">"FLUO SV1"</span><span class="o">:</span> <span class="s2">"fluosv"</span><span class="p">,</span>
+ <span class="s2">"FLUO SV2"</span><span class="o">:</span> <span class="s2">"fluosv"</span><span class="p">,</span>
+ <span class="s2">"FLUO TV"</span><span class="o">:</span> <span class="s2">"fluotv"</span><span class="p">,</span>
+ <span class="s2">"NIR SV1"</span><span class="o">:</span> <span class="s2">"nirsv"</span><span class="p">,</span>
+ <span class="s2">"NIR SV2"</span><span class="o">:</span> <span class="s2">"nirsv"</span><span class="p">,</span>
+ <span class="s2">"NIR TV"</span><span class="o">:</span> <span class="s2">"nirtv"</span><span class="p">,</span>
+ <span class="s2">"IR SV1"</span><span class="o">:</span> <span class="s2">"irsv"</span><span class="p">,</span>
+ <span class="s2">"IR SV2"</span><span class="o">:</span> <span class="s2">"irsv"</span><span class="p">,</span>
+ <span class="s2">"IR TV"</span><span class="o">:</span> <span class="s2">"irtv"</span>
+ <span class="p">}</span>
+ <span class="p">}</span>
+<span class="p">}</span>
+</pre></div>
+</div>
+<p>This template is fairly complex, so we will break it down into logical subunits. It should be noted,
+that the order of these definitions is not strict, the way they are written matches the thought process
+behind crawling.</p>
+<div class="highlight-javascript"><div class="highlight"><pre><span class="s2">"path"</span><span class="o">:</span> <span class="s2">"/work/walia/common/ih/rawdata/0184 Uni Nebraska Rice 1/%null%/%null%_%idnum%-%idchar%_%date%/%imgname%/0_0.png"</span><span class="p">,</span>
+<span class="s2">"base"</span><span class="o">:</span> <span class="s2">"/work/walia/common/ih/rawdata/0184 Uni Nebraska Rice 1/"</span><span class="p">,</span>
+</pre></div>
+</div>
+<p>The first two definitions map our way through the rest of the template. Above, we noted several important
+pieces of information in the name of the directories. We are doing exactly that here, except in a way that
+is more understandable to the computer. We mark important places in the directory structure by using % signs,
+along with names. The names themselves are not strictly checked, so use names that are easy to remember.
+Here we mark 4 places, with the identifiers ‘idnum’, ‘idchar’, ‘date’, and ‘imgname’. The ‘null’ name is for a
+piece of information that isn’t important, but still needs to be crawled. In this case, the ‘strain’ directories
+contain no information relevant to the images themselves. Also note the underscores and dashes in the definition.
+Path splitting to obtain information is possible by placing underscores (_), dashes (-), or spaces ( ) into your
+definition. To make it easier to see, look at our “path” definition side by side with an example path:</p>
+<div class="line-block">
+<div class="line">“path”: “/work/walia/common/ih/rawdata/0184 Uni Nebraska Rice 1/<strong>%null%</strong>/%null%_<span class="red">%idnum%</span>-<span class="blue">%idchar%</span>_<span class="green">%date%</span>/<span class="orange">%imgname%</span>/0_0.png”,</div>
+<div class="line">/work/walia/common/ih/rawdata/0184 Uni Nebraska Rice 1/<strong>strain3</strong>/0184 Uni Nebraska Rice 1_<span class="red">023542</span>-<span class="blue">C</span>_<span class="green">2013-09-05</span>_05-18-33_455640/<span class="orange">RGB SV1</span>/0_0.png</div>
+</div>
+<p>It becomes very apparent how each defined identifier lines up with the path. Creating this identifier string is
+a very key part of the template definition. It will likely take some time before you are completely comfortable
+writing identifier strings, and every workflow is different. The other workflow examples have different data paths
+for input files, so it is recommended you look at those as well. The identifiers will be used in further steps. The “base” definition
+is simply where crawling should start. It should be a subset of the “path” definition.</p>
+<div class="highlight-javascript"><div class="highlight"><pre><span class="s2">"filetype"</span><span class="o">:</span> <span class="s2">".png"</span><span class="p">,</span>
+<span class="s2">"order"</span><span class="o">:</span> <span class="p">[</span><span class="s2">"experiment"</span><span class="p">,</span> <span class="s2">"id"</span><span class="p">,</span> <span class="s2">"genotype"</span><span class="p">,</span> <span class="s2">"date"</span><span class="p">,</span> <span class="s2">"treatment"</span><span class="p">,</span> <span class="s2">"imgname"</span><span class="p">,</span> <span class="s2">"imtype"</span><span class="p">,</span> <span class="s2">"path"</span><span class="p">],</span>
+</pre></div>
+</div>
+<p>The “filetype” definition is exactly that. It searches for all files in the final path that end in the specified filetype.
+The “order” definition is the order in which values are stored in to the database. It serves two purposes. Thematically,
+you can organize your columns the same way you would data. More importantly, it specifies which values are saved to the database.
+You can define any value in the “order” definition, however, there are <strong>required</strong> definitions as well. In addition,
+although there are some optional column names, many of the statistics function expect a given format for data.
+The names included above are the names that the statistics functions expect. They relate directly to information about each image.
+“experiment” is required, although we simply use it as additional information to help keep things organized. Data that comes
+from LemnaTec has id’s assigned to them, in this case, “id” is the LemnaTec assigned value. “genotype” contains the identifier for
+which genotype the plant is. “date” is the date the plant was imaged. “treatment” is whether the plant is control or stressed.
+“imgname” is which type, shot, and number the plant is. Examples include RGB SV1, RGB SV2, RGB TV, FLUO SV1, FLUO SV2, FLUO TV e.t.c
+“imtype” is just which type and shot the plant is. Examples include rgbsv, rgbtv, fluosv, fluotv e.t.c. “imtype” is generally
+used more than it “imgname” counterpart. “path” is a required entry, and will be filed with the input path to the image.
+The final output path of the image is based on “experiment”, “id”, “date”, “imtype”, and “imgname”, so defining
+these is very important.
+The next section we talk about is the data section. The purpose of the data section is to convert the identifiers from
+our “path” definition, to the names used in our “order” definition. Let’s look at it one name at a time:</p>
+<div class="highlight-javascript"><div class="highlight"><pre><span class="s2">"data"</span><span class="o">:</span> <span class="p">{</span>
+ <span class="s2">"experiment"</span><span class="o">:</span> <span class="p">{</span>
+ <span class="s2">"type"</span><span class="o">:</span> <span class="s2">"value"</span><span class="p">,</span>
+ <span class="s2">"value"</span><span class="o">:</span> <span class="s2">"0184"</span>
+ <span class="p">},</span>
+</pre></div>
+</div>
+<p>The first line simply shows how to start the data section. Specifying ‘“data”: {‘ shows that all further entries
+are specifically related to data-mapping. Each value specified in the data section corresponds to a specific
+value in the “order” entry. The values defined in the data section are NOT order dependent, but we include
+them in the same order for ease of access. Finally, remember that each of these values is for <em>every</em> image.
+Our first example is defining a value for “experiment”. It’s important
+to note that “experiment” occurs in order. The names of entries in the data section must match the value
+in the “order” entry exactly. First we define the type of “experiment”. Type’s of data keys can be defined
+as “value”, “file”, or “date”. Here, we define the type of experiment as a value. This means that the value of
+experiment will be saved as some combination of hard-coded characters, and identifiers, based on the “value” definition.
+In this case, we do not use identifiers in our “value” definition. We simply save the value for experiment for every image
+as 0184.</p>
+<div class="highlight-javascript"><div class="highlight"><pre><span class="s2">"id"</span><span class="o">:</span> <span class="p">{</span>
+ <span class="s2">"type"</span><span class="o">:</span> <span class="s2">"value"</span><span class="p">,</span>
+ <span class="s2">"value"</span><span class="o">:</span> <span class="s2">"%idnum%-%idchar%"</span>
+<span class="p">},</span>
+</pre></div>
+</div>
+<p>Here, we define the “id” for each plant. We also define it as type “value”, but this time we use identifiers in
+the value. This will load the identifiers from the path directly into the value for id. Looking at our path definition and test path again:</p>
+<div class="line-block">
+<div class="line">“path”: “/work/walia/common/ih/rawdata/0184 Uni Nebraska Rice 1/<strong>%null%</strong>/%null%_<span class="red">%idnum%</span>-<span class="blue">%idchar%</span>_<span class="green">%date%</span>/<span class="orange">%imgname%</span>/0_0.png”,</div>
+<div class="line">/work/walia/common/ih/rawdata/0184 Uni Nebraska Rice 1/<strong>strain3</strong>/0184 Uni Nebraska Rice 1_<span class="red">023542</span>-<span class="blue">C</span>_<span class="green">2013-09-05</span>_05-18-33_455640/<span class="orange">RGB SV1</span>/0_0.png</div>
+</div>
+<p>For this example, the value of id would be loaded as “023542-C”. It may seem unnecessary to break up ‘idnum’ and ‘idchar’, since we use them together here,
+however, we use ‘idchar’ by itself in a later step. It’s important to make sure that the identifiers you use match exactly with those used in the path.
+Any value not surrounded by percent signs will be hard-coded into the output value. So the “-” between our “idnum” and “idchar” identifiers is hard-coded
+into the output value.</p>
+<div class="highlight-javascript"><div class="highlight"><pre><span class="s2">"genotype"</span><span class="o">:</span> <span class="p">{</span>
+ <span class="s2">"type"</span><span class="o">:</span> <span class="s2">"file"</span><span class="p">,</span>
+ <span class="s2">"value"</span><span class="o">:</span> <span class="s2">"GenKey.csv"</span><span class="p">,</span>
+ <span class="s2">"key"</span><span class="o">:</span> <span class="s2">"%idnum%-%idchar%"</span><span class="p">,</span>
+ <span class="s2">"keyColumn"</span><span class="o">:</span> <span class="mi">0</span><span class="p">,</span>
+ <span class="s2">"valueColumn"</span><span class="o">:</span> <span class="mi">1</span>
+<span class="p">},</span>
+</pre></div>
+</div>
+<p>Here, we define the “genotype” for each plant. This time, the type is “file”. This type of data key searches through the rows of a file,
+assuming that there is a mapping of key -> value in your row. If you look at the <a class="reference download internal" href="_downloads/GenKey.csv"><code class="xref download docutils literal"><span class="pre">Genotype</span> <span class="pre">Key</span> <span class="pre">File</span></code></a>,
+you can see that it is a csv file with two columns. We can see that the first column contains values that look like our “id” value. The second column
+contains our genotype string – our target value. The “file” type always assumes your input is some sort of value separated file. It doesn’t necessarily have to be
+separated by commas, but that is the default functionality. If your file is separated by something other than commas, specify the “separator” option. There are three
+other required definitions for “file” type data keys. You need to define “key”, “keyColumn”, and “valueColumn”. The columns themselves are 0-indexed. In this case, our “keyColumn” is 0, because
+our key is located in the 0th column. “valueColumn” is 1, because our key is located in the 1st column. Finally, our “key” value is the same as our “id”. This
+will sift through our file until it finds the row who’s 0th column is our “key” value. Then, it returns the value of 1st column. Looking at our path definition and test path again:</p>
+<div class="line-block">
+<div class="line">“path”: “/work/walia/common/ih/rawdata/0184 Uni Nebraska Rice 1/<strong>%null%</strong>/%null%_<span class="red">%idnum%</span>-<span class="blue">%idchar%</span>_<span class="green">%date%</span>/<span class="orange">%imgname%</span>/0_0.png”,</div>
+<div class="line">/work/walia/common/ih/rawdata/0184 Uni Nebraska Rice 1/<strong>strain3</strong>/0184 Uni Nebraska Rice 1_<span class="red">023542</span>-<span class="blue">C</span>_<span class="green">2013-09-05</span>_05-18-33_455640/<span class="orange">RGB SV1</span>/0_0.png</div>
+</div>
+<p>We will sift through our file looking for “023542-C” (which occurs in the 243rd line). It will then return the corresponding genotype string
+located in the same row, namely UNL032</p>
+<div class="highlight-javascript"><div class="highlight"><pre><span class="s2">"date"</span><span class="o">:</span> <span class="p">{</span>
+ <span class="s2">"type"</span><span class="o">:</span> <span class="s2">"date"</span><span class="p">,</span>
+ <span class="s2">"value"</span><span class="o">:</span> <span class="s2">"%date%"</span><span class="p">,</span>
+ <span class="s2">"format"</span><span class="o">:</span> <span class="s2">"Y-m-d"</span>
+ <span class="p">},</span>
+</pre></div>
+</div>
+<p>Here, we define the “date” for each plant. We use our final type, “date”. The only additional argument to the date type
+is “format”, which specifies the input format of the date. The date type loads in values based on a combination of identifiers and hard-coded values again,
+but afterwards, it converts the date to Y-m-d format. In this case, because the input type is defined as “Y-m-d” using a date type
+isn’t strictly required, we use it as an example though. The date input string can contain “Y”, “y”, “M”, “m”, “d”, “B”, “b” as format characters,
+and uses “-”, “/”, ” ”, and “_” as separators.</p>
+<blockquote>
+<div><div class="highlight-javascript"><div class="highlight"><pre><span class="s2">"treatment"</span><span class="o">:</span> <span class="p">{</span>
+ <span class="s2">"type"</span><span class="o">:</span> <span class="s2">"value"</span><span class="p">,</span>
+ <span class="s2">"translate"</span><span class="o">:</span> <span class="s2">"true"</span><span class="p">,</span>
+ <span class="s2">"value"</span><span class="o">:</span> <span class="s2">"%idchar%"</span>
+ <span class="p">},</span>
+ <span class="s2">"imgname"</span><span class="o">:</span> <span class="p">{</span>
+ <span class="s2">"type"</span><span class="o">:</span> <span class="s2">"value"</span><span class="p">,</span>
+ <span class="s2">"value"</span><span class="o">:</span> <span class="s2">"%imgname%"</span>
+ <span class="p">},</span>
+ <span class="s2">"imtype"</span><span class="o">:</span> <span class="p">{</span>
+ <span class="s2">"type"</span><span class="o">:</span> <span class="s2">"value"</span><span class="p">,</span>
+ <span class="s2">"translate"</span><span class="o">:</span> <span class="s2">"true"</span><span class="p">,</span>
+ <span class="s2">"value"</span><span class="o">:</span> <span class="s2">"%imgname%"</span>
+ <span class="p">}</span>
+</pre></div>
+</div>
+</div></blockquote>
+<p>We include the last three together, because they are all of type “value”, and simply use one of the identifiers from the base path in their value.
+However, it is important to note that two of these values have an additional option, namely “translate”: “true”. This specifies that the input value
+should be mapped to a different output value. This functions very similar to a file mapping, except the mapping is defined inside the template.
+It should be noted, that if the “translate” option exists in the data key, then it will check for a translation. Even if you specify “translate”: “false”,
+it will still check for a translation. Let’s look at the translation section:</p>
+<div class="highlight-javascript"><div class="highlight"><pre><span class="s2">"translations"</span><span class="o">:</span> <span class="p">{</span>
+ <span class="s2">"treatment"</span><span class="o">:</span> <span class="p">{</span>
+ <span class="s2">"S"</span><span class="o">:</span> <span class="s2">"Stress"</span><span class="p">,</span>
+ <span class="s2">"s"</span><span class="o">:</span> <span class="s2">"Stress"</span><span class="p">,</span>
+ <span class="s2">"C"</span><span class="o">:</span> <span class="s2">"Control"</span><span class="p">,</span>
+ <span class="s2">"c"</span><span class="o">:</span> <span class="s2">"Control"</span>
+ <span class="p">},</span>
+ <span class="s2">"imtype"</span><span class="o">:</span> <span class="p">{</span>
+ <span class="s2">"RGB SV1"</span><span class="o">:</span> <span class="s2">"rgbsv"</span><span class="p">,</span>
+ <span class="s2">"RGB SV2"</span><span class="o">:</span> <span class="s2">"rgbsv"</span><span class="p">,</span>
+ <span class="s2">"RGB TV"</span><span class="o">:</span> <span class="s2">"rgbtv"</span><span class="p">,</span>
+ <span class="s2">"FLUO SV1"</span><span class="o">:</span> <span class="s2">"fluosv"</span><span class="p">,</span>
+ <span class="s2">"FLUO SV2"</span><span class="o">:</span> <span class="s2">"fluosv"</span><span class="p">,</span>
+ <span class="s2">"FLUO TV"</span><span class="o">:</span> <span class="s2">"fluotv"</span><span class="p">,</span>
+ <span class="s2">"NIR SV1"</span><span class="o">:</span> <span class="s2">"nirsv"</span><span class="p">,</span>
+ <span class="s2">"NIR SV2"</span><span class="o">:</span> <span class="s2">"nirsv"</span><span class="p">,</span>
+ <span class="s2">"NIR TV"</span><span class="o">:</span> <span class="s2">"nirtv"</span><span class="p">,</span>
+ <span class="s2">"IR SV1"</span><span class="o">:</span> <span class="s2">"irsv"</span><span class="p">,</span>
+ <span class="s2">"IR SV2"</span><span class="o">:</span> <span class="s2">"irsv"</span><span class="p">,</span>
+ <span class="s2">"IR TV"</span><span class="o">:</span> <span class="s2">"irtv"</span>
+ <span class="p">}</span>
+<span class="p">}</span>
+</pre></div>
+</div>
+<p>The translation keys line up exactly with the data keys that have “translate”: “true” specified. The data-mapping to perform is simply defined in-line
+as key-value parings. This is effective for small sets, but is inefficient for large translation sets, such as the genotype file mapping.
+Here, the “treatment” translation takes a single character, and maps it to a word. We simply convert the 1 character idchar into the full word
+“Control” or “Stress”. Looking at our path definition and test path again:</p>
+<div class="line-block">
+<div class="line">“path”: “/work/walia/common/ih/rawdata/0184 Uni Nebraska Rice 1/<strong>%null%</strong>/%null%_<span class="red">%idnum%</span>-<span class="blue">%idchar%</span>_<span class="green">%date%</span>/<span class="orange">%imgname%</span>/0_0.png”,</div>
+<div class="line">/work/walia/common/ih/rawdata/0184 Uni Nebraska Rice 1/<strong>strain3</strong>/0184 Uni Nebraska Rice 1_<span class="red">023542</span>-<span class="blue">C</span>_<span class="green">2013-09-05</span>_05-18-33_455640/<span class="orange">RGB SV1</span>/0_0.png</div>
+</div>
+<p>In this case, our idchar is ‘C’, this means that the “treatment” data key, will get mapped to “Control”. We also have a translation defined for “imtype”. Looking at our test path,
+our imgname is “RGB SV1”. This means that the “imtype” data key will get mapped to “rgbsv”. Remember, the key difference between defining translations, and using file mapping is size.</p>
+<p>With our template written, we can now load the images. We do this using the ‘ih-setup’ command as follows:</p>
+<div class="highlight-bash"><div class="highlight"><pre>ih-setup --dir <span class="s2">"DIR_NAME"</span> --template <span class="s2">"crawl.json"</span>
+</pre></div>
+</div>
+<p>This will setup a workflow submission directory with the name “DIR_NAME”. It will create an input folder,
+and populate that input folder with the images database, the crawl.json template file, and empty template files required for job submission.
+Next we will look at defining the configuration file!</p>
+</div>
+<div class="section" id="configuration">
+<h2>Configuration<a class="headerlink" href="#configuration" title="Permalink to this headline">¶</a></h2>
+<p>The config file contains information that shouldn’t really change from run to run. It contains things like installation directories, environment
+variables, and job clustering. Let’s take a look.</p>
+<div class="highlight-javascript"><div class="highlight"><pre><span class="p">{</span>
+<span class="s2">"installdir"</span><span class="o">:</span> <span class="s2">"/work/walia/common/ih/pymodules/bin/"</span><span class="p">,</span>
+<span class="s2">"profile"</span><span class="o">:</span> <span class="p">{</span>
+ <span class="s2">"pegasus"</span><span class="o">:</span> <span class="p">{</span>
+ <span class="s2">"style"</span><span class="o">:</span> <span class="s2">"glite"</span>
+ <span class="p">},</span>
+ <span class="s2">"condor"</span><span class="o">:</span> <span class="p">{</span>
+ <span class="s2">"grid_resource"</span><span class="o">:</span> <span class="s2">"pbs"</span><span class="p">,</span>
+ <span class="s2">"universe"</span><span class="o">:</span> <span class="s2">"vanilla"</span>
+ <span class="p">},</span>
+ <span class="s2">"env"</span><span class="o">:</span> <span class="p">{</span>
+ <span class="s2">"PATH"</span><span class="o">:</span> <span class="s2">"/work/walia/common/ih/pymodules/bin/"</span><span class="p">,</span>
+ <span class="s2">"LD_LIBRARY_PATH"</span><span class="o">:</span> <span class="s2">"/work/walia/common/ih/pymodules/opencv_lib/"</span>
+ <span class="p">}</span>
+<span class="p">},</span>
+<span class="s2">"cluster"</span><span class="o">:</span> <span class="mi">100</span><span class="p">,</span>
+<span class="s2">"email"</span><span class="o">:</span> <span class="s2">"avi@kurtknecht.com"</span>
+<span class="p">}</span>
+</pre></div>
+</div>
+<p>The “installdir” definition is the location where all of ih’s scripts are installed. It may seem
+unnecessary to include this as well as a path, but it is important for pegasus to know the exact location
+of executable files. The “profile” defintion supports inclusion of any-possible profile variable for
+the sites.xml. This is taken directly from the pegasus docs. To run the workflow on HCC & OSG,
+we specify “pegasus”->”style”->”glite”, and “condor”->”grid_resource”->”pbs”. The “env” definition
+passes environment variables through to the script. In this case, we pass in two different path variables.
+One is the location of other executable scripts, in this case our custom python install. The LD_LIBRARY_PATH
+is for the location of the required libraries for opencv. It should be noted, that multiple path variables can be included
+by specifying the value as a list i.e. If you specify “PATH”: [“/test/path/1/”, “/test/path/2/”], both paths will
+be loaded into the sites.xml. “cluster” specifies how many jobs you want to clump together. Most jobs take
+seconds to run, so running-the entire workflow unclustered is very-inefficient. A cluster size of 100 is used here,
+which means that jobs will be run in batches of 100. The “email” option defines which email to send the results to upon
+completion of the workflow.</p>
+</div>
+<div class="section" id="processing">
+<h2>Processing<a class="headerlink" href="#processing" title="Permalink to this headline">¶</a></h2>
+<p>The image processing template contains what image processing functions to use and in what order. Separate workflows
+are defined for each image type – as a result the template is quite long. Here it is in full:</p>
+<div class="highlight-javascript"><div class="highlight"><pre><span class="p">{</span>
+ <span class="s2">"workflows"</span><span class="o">:</span> <span class="p">{</span>
+ <span class="s2">"fluosv"</span><span class="o">:</span> <span class="p">[</span>
+ <span class="p">{</span>
+ <span class="s2">"name"</span><span class="o">:</span> <span class="s2">"pot_filter_1"</span><span class="p">,</span>
+ <span class="s2">"executable"</span><span class="o">:</span> <span class="s2">"ih-color-filter"</span><span class="p">,</span>
+ <span class="s2">"inputs"</span><span class="o">:</span> <span class="p">[</span><span class="s2">"base"</span><span class="p">,</span> <span class="s2">"/work/walia/common/ih/workflows/0184/input/fluosv_pot1.json"</span><span class="p">],</span>
+ <span class="s2">"outputs"</span><span class="o">:</span> <span class="p">[</span><span class="s2">"pot1"</span><span class="p">],</span>
+ <span class="s2">"arguments"</span><span class="o">:</span> <span class="p">{</span>
+ <span class="s2">"--logic"</span><span class="o">:</span> <span class="s2">"(((((((r - g) < 30) and (((r + g) + b) < 110)) or ((((r + g) + b) > 110) and ((r - g) < 50))) or (((r - g) < 25) and ((g - r) < 25))) or (g > 60)) not 1)"</span>
+ <span class="p">}</span>
+ <span class="p">},</span>
+ <span class="p">{</span>
+ <span class="s2">"name"</span><span class="o">:</span> <span class="s2">"pot_filter_2"</span><span class="p">,</span>
+ <span class="s2">"executable"</span><span class="o">:</span> <span class="s2">"ih-color-filter"</span><span class="p">,</span>
+ <span class="s2">"inputs"</span><span class="o">:</span> <span class="p">[</span><span class="s2">"pot1"</span><span class="p">,</span> <span class="s2">"/work/walia/common/ih/workflows/0184/input/fluosv_pot2.json"</span><span class="p">],</span>
+ <span class="s2">"outputs"</span><span class="o">:</span> <span class="p">[</span><span class="s2">"pot2"</span><span class="p">],</span>
+ <span class="s2">"arguments"</span><span class="o">:</span> <span class="p">{</span>
+ <span class="s2">"--logic"</span><span class="o">:</span> <span class="s2">"(((r + g) + b) > 120)"</span>
+ <span class="p">},</span>
+ <span class="s2">"depends"</span><span class="o">:</span> <span class="p">[</span><span class="s2">"pot_filter_1"</span><span class="p">]</span>
+ <span class="p">},</span>
+ <span class="p">{</span>
+ <span class="s2">"name"</span><span class="o">:</span> <span class="s2">"main_filter"</span><span class="p">,</span>
+ <span class="s2">"executable"</span><span class="o">:</span> <span class="s2">"ih-color-filter"</span><span class="p">,</span>
+ <span class="s2">"inputs"</span><span class="o">:</span> <span class="p">[</span><span class="s2">"pot2"</span><span class="p">],</span>
+ <span class="s2">"outputs"</span><span class="o">:</span> <span class="p">[</span><span class="s2">"filter"</span><span class="p">],</span>
+ <span class="s2">"arguments"</span><span class="o">:</span> <span class="p">{</span>
+ <span class="s2">"--logic"</span><span class="o">:</span> <span class="s2">"((r - g) > 10)"</span>
+ <span class="p">},</span>
+ <span class="s2">"depends"</span><span class="o">:</span> <span class="p">[</span><span class="s2">"pot_filter_2"</span><span class="p">]</span>
+ <span class="p">},</span>
+ <span class="p">{</span>
+ <span class="s2">"name"</span><span class="o">:</span> <span class="s2">"crop"</span><span class="p">,</span>
+ <span class="s2">"executable"</span><span class="o">:</span> <span class="s2">"ih-crop"</span><span class="p">,</span>
+ <span class="s2">"inputs"</span><span class="o">:</span> <span class="p">[</span><span class="s2">"filter"</span><span class="p">,</span> <span class="s2">"/work/walia/common/ih/workflows/0184/input/fluosv_edge.json"</span><span class="p">],</span>
+ <span class="s2">"outputs"</span><span class="o">:</span> <span class="p">[</span><span class="s2">"edged"</span><span class="p">],</span>
+ <span class="s2">"arguments"</span><span class="o">:</span> <span class="p">{},</span>
+ <span class="s2">"depends"</span><span class="o">:</span> <span class="p">[</span><span class="s2">"main_filter"</span><span class="p">]</span>
+ <span class="p">},</span>
+ <span class="p">{</span>
+ <span class="s2">"name"</span><span class="o">:</span> <span class="s2">"cut"</span><span class="p">,</span>
+ <span class="s2">"executable"</span><span class="o">:</span> <span class="s2">"ih-contour-cut"</span><span class="p">,</span>
+ <span class="s2">"inputs"</span><span class="o">:</span> <span class="p">[</span><span class="s2">"edged"</span><span class="p">,</span> <span class="s2">"edged"</span><span class="p">],</span>
+ <span class="s2">"outputs"</span><span class="o">:</span> <span class="p">[</span><span class="s2">"final"</span><span class="p">],</span>
+ <span class="s2">"arguments"</span><span class="o">:</span> <span class="p">{</span>
+ <span class="s2">"--resize"</span><span class="o">:</span> <span class="s2">""</span><span class="p">,</span>
+ <span class="s2">"--basemin"</span><span class="o">:</span> <span class="mi">75</span>
+ <span class="p">},</span>
+ <span class="s2">"depends"</span><span class="o">:</span> <span class="p">[</span><span class="s2">"crop"</span><span class="p">]</span>
+ <span class="p">}</span>
+ <span class="p">],</span>
+ <span class="s2">"rgbtv"</span><span class="o">:</span> <span class="p">[</span>
+ <span class="p">{</span>
+ <span class="s2">"name"</span><span class="o">:</span> <span class="s2">"normalize"</span><span class="p">,</span>
+ <span class="s2">"executable"</span><span class="o">:</span> <span class="s2">"ih-normalize-intensity"</span><span class="p">,</span>
+ <span class="s2">"inputs"</span><span class="o">:</span> <span class="p">[</span><span class="s2">"base"</span><span class="p">],</span>
+ <span class="s2">"outputs"</span><span class="o">:</span> <span class="p">[</span><span class="s2">"normal"</span><span class="p">],</span>
+ <span class="s2">"arguments"</span><span class="o">:</span> <span class="p">{}</span>
+ <span class="p">},</span>
+ <span class="p">{</span>
+ <span class="s2">"name"</span><span class="o">:</span> <span class="s2">"meanshift"</span><span class="p">,</span>
+ <span class="s2">"executable"</span><span class="o">:</span> <span class="s2">"ih-meanshift"</span><span class="p">,</span>
+ <span class="s2">"inputs"</span><span class="o">:</span> <span class="p">[</span><span class="s2">"normal"</span><span class="p">],</span>
+ <span class="s2">"outputs"</span><span class="o">:</span> <span class="p">[</span><span class="s2">"shift"</span><span class="p">],</span>
+ <span class="s2">"arguments"</span><span class="o">:</span> <span class="p">{</span>
+ <span class="s2">"--spatial_radius"</span><span class="o">:</span> <span class="mi">4</span><span class="p">,</span>
+ <span class="s2">"--range_radius"</span><span class="o">:</span> <span class="mi">4</span><span class="p">,</span>
+ <span class="s2">"--min_density"</span><span class="o">:</span> <span class="mi">40</span>
+ <span class="p">},</span>
+ <span class="s2">"depends"</span><span class="o">:</span> <span class="p">[</span><span class="s2">"normalize"</span><span class="p">]</span>
+ <span class="p">},</span>
+ <span class="p">{</span>
+ <span class="s2">"name"</span><span class="o">:</span> <span class="s2">"main_filter"</span><span class="p">,</span>
+ <span class="s2">"executable"</span><span class="o">:</span> <span class="s2">"ih-color-filter"</span><span class="p">,</span>
+ <span class="s2">"inputs"</span><span class="o">:</span> <span class="p">[</span><span class="s2">"shift"</span><span class="p">],</span>
+ <span class="s2">"outputs"</span><span class="o">:</span> <span class="p">[</span><span class="s2">"filter"</span><span class="p">],</span>
+ <span class="s2">"arguments"</span><span class="o">:</span> <span class="p">{</span>
+ <span class="s2">"--logic"</span><span class="o">:</span> <span class="s2">"(((g > r) and (g > b)) and ((((b max g) max r) - ((b min g) min r)) > 20))"</span>
+ <span class="p">},</span>
+ <span class="s2">"depends"</span><span class="o">:</span> <span class="p">[</span><span class="s2">"meanshift"</span><span class="p">]</span>
+ <span class="p">},</span>
+ <span class="p">{</span>
+ <span class="s2">"name"</span><span class="o">:</span> <span class="s2">"closing"</span><span class="p">,</span>
+ <span class="s2">"executable"</span><span class="o">:</span> <span class="s2">"ih-morphology"</span><span class="p">,</span>
+ <span class="s2">"inputs"</span><span class="o">:</span> <span class="p">[</span><span class="s2">"filter"</span><span class="p">],</span>
+ <span class="s2">"outputs"</span><span class="o">:</span> <span class="p">[</span><span class="s2">"morphed"</span><span class="p">],</span>
+ <span class="s2">"arguments"</span><span class="o">:</span> <span class="p">{</span>
+ <span class="s2">"--ktype"</span><span class="o">:</span> <span class="s2">"ellipse"</span><span class="p">,</span>
+ <span class="s2">"--kwidth"</span><span class="o">:</span> <span class="mi">5</span><span class="p">,</span>
+ <span class="s2">"--kheight"</span><span class="o">:</span> <span class="mi">5</span><span class="p">,</span>
+ <span class="s2">"--morphType"</span><span class="o">:</span> <span class="s2">"close"</span>
+ <span class="p">},</span>
+ <span class="s2">"depends"</span><span class="o">:</span> <span class="p">[</span><span class="s2">"main_filter"</span><span class="p">]</span>
+ <span class="p">},</span>
+ <span class="p">{</span>
+ <span class="s2">"name"</span><span class="o">:</span> <span class="s2">"crop"</span><span class="p">,</span>
+ <span class="s2">"executable"</span><span class="o">:</span> <span class="s2">"ih-crop"</span><span class="p">,</span>
+ <span class="s2">"inputs"</span><span class="o">:</span> <span class="p">[</span><span class="s2">"morphed"</span><span class="p">,</span> <span class="s2">"/work/walia/common/ih/workflows/0184/input/rgbtv_edge.json"</span><span class="p">],</span>
+ <span class="s2">"outputs"</span><span class="o">:</span> <span class="p">[</span><span class="s2">"edged"</span><span class="p">],</span>
+ <span class="s2">"arguments"</span><span class="o">:</span> <span class="p">{},</span>
+ <span class="s2">"depends"</span><span class="o">:</span> <span class="p">[</span><span class="s2">"closing"</span><span class="p">]</span>
+ <span class="p">},</span>
+ <span class="p">{</span>
+ <span class="s2">"name"</span><span class="o">:</span> <span class="s2">"reconstitute"</span><span class="p">,</span>
+ <span class="s2">"executable"</span><span class="o">:</span> <span class="s2">"ih-bitwise-and"</span><span class="p">,</span>
+ <span class="s2">"inputs"</span><span class="o">:</span> <span class="p">[</span><span class="s2">"edged"</span><span class="p">,</span> <span class="s2">"base"</span><span class="p">],</span>
+ <span class="s2">"outputs"</span><span class="o">:</span> <span class="p">[</span><span class="s2">"recolor"</span><span class="p">],</span>
+ <span class="s2">"arguments"</span><span class="o">:</span> <span class="p">{},</span>
+ <span class="s2">"depends"</span><span class="o">:</span> <span class="p">[</span><span class="s2">"crop"</span><span class="p">]</span>
+ <span class="p">},</span>
+ <span class="p">{</span>
+ <span class="s2">"name"</span><span class="o">:</span> <span class="s2">"cut"</span><span class="p">,</span>
+ <span class="s2">"executable"</span><span class="o">:</span> <span class="s2">"ih-contour-cut"</span><span class="p">,</span>
+ <span class="s2">"inputs"</span><span class="o">:</span> <span class="p">[</span><span class="s2">"recolor"</span><span class="p">,</span> <span class="s2">"recolor"</span><span class="p">],</span>
+ <span class="s2">"outputs"</span><span class="o">:</span> <span class="p">[</span><span class="s2">"final"</span><span class="p">],</span>
+ <span class="s2">"arguments"</span><span class="o">:</span> <span class="p">{</span>
+ <span class="s2">"--basemin"</span><span class="o">:</span> <span class="mi">200</span><span class="p">,</span>
+ <span class="s2">"--resize"</span><span class="o">:</span> <span class="s2">""</span>
+ <span class="p">},</span>
+ <span class="s2">"depends"</span><span class="o">:</span> <span class="p">[</span><span class="s2">"reconstitute"</span><span class="p">]</span>
+ <span class="p">}</span>
+ <span class="p">],</span>
+ <span class="s2">"rgbsv"</span><span class="o">:</span> <span class="p">[</span>
+ <span class="p">{</span>
+ <span class="s2">"name"</span><span class="o">:</span> <span class="s2">"pot-detect"</span><span class="p">,</span>
+ <span class="s2">"executable"</span><span class="o">:</span> <span class="s2">"ih-color-filter"</span><span class="p">,</span>
+ <span class="s2">"inputs"</span><span class="o">:</span> <span class="p">[</span><span class="s2">"base"</span><span class="p">],</span>
+ <span class="s2">"outputs"</span><span class="o">:</span> <span class="p">[</span><span class="s2">"pot"</span><span class="p">],</span>
+ <span class="s2">"arguments"</span><span class="o">:</span> <span class="p">{</span>
+ <span class="s2">"--logic"</span><span class="o">:</span> <span class="s2">"((((r + g) + b) < 100) or (((b - r) > 40) and ((b - g) > 30)))"</span>
+ <span class="p">}</span>
+ <span class="p">},</span>
+ <span class="p">{</span>
+ <span class="s2">"name"</span><span class="o">:</span> <span class="s2">"pot-crop"</span><span class="p">,</span>
+ <span class="s2">"executable"</span><span class="o">:</span> <span class="s2">"ih-contour-cut"</span><span class="p">,</span>
+ <span class="s2">"inputs"</span><span class="o">:</span> <span class="p">[</span><span class="s2">"pot"</span><span class="p">,</span> <span class="s2">"pot"</span><span class="p">],</span>
+ <span class="s2">"outputs"</span><span class="o">:</span> <span class="p">[</span><span class="s2">"unused_1"</span><span class="p">,</span> <span class="s2">"pot_roi"</span><span class="p">],</span>
+ <span class="s2">"arguments"</span><span class="o">:</span> <span class="p">{</span>
+ <span class="s2">"--basemin"</span><span class="o">:</span> <span class="mi">100</span><span class="p">,</span>
+ <span class="s2">"--padminy"</span><span class="o">:</span> <span class="mi">100</span><span class="p">,</span>
+ <span class="s2">"--padmaxy"</span><span class="o">:</span> <span class="mi">2000</span><span class="p">,</span>
+ <span class="s2">"--padminx"</span><span class="o">:</span> <span class="o">-</span><span class="mi">25</span><span class="p">,</span>
+ <span class="s2">"--padmaxx"</span><span class="o">:</span> <span class="o">-</span><span class="mi">25</span><span class="p">,</span>
+ <span class="s2">"--returnBound"</span><span class="o">:</span> <span class="s2">""</span>
+ <span class="p">},</span>
+ <span class="s2">"depends"</span><span class="o">:</span> <span class="p">[</span><span class="s2">"pot-detect"</span><span class="p">]</span>
+ <span class="p">},</span>
+ <span class="p">{</span>
+ <span class="s2">"name"</span><span class="o">:</span> <span class="s2">"box-crop"</span><span class="p">,</span>
+ <span class="s2">"executable"</span><span class="o">:</span> <span class="s2">"ih-contour-cut"</span><span class="p">,</span>
+ <span class="s2">"inputs"</span><span class="o">:</span> <span class="p">[</span><span class="s2">"pot"</span><span class="p">,</span> <span class="s2">"pot"</span><span class="p">],</span>
+ <span class="s2">"outputs"</span><span class="o">:</span> <span class="p">[</span><span class="s2">"unused_2"</span><span class="p">,</span> <span class="s2">"box_roi"</span><span class="p">],</span>
+ <span class="s2">"arguments"</span><span class="o">:</span> <span class="p">{</span>
+ <span class="s2">"--basemin"</span><span class="o">:</span> <span class="mi">100</span><span class="p">,</span>
+ <span class="s2">"--padminy"</span><span class="o">:</span> <span class="mi">35</span><span class="p">,</span>
+ <span class="s2">"--padmaxy"</span><span class="o">:</span> <span class="mi">2000</span><span class="p">,</span>
+ <span class="s2">"--padminx"</span><span class="o">:</span> <span class="mi">25</span><span class="p">,</span>
+ <span class="s2">"--padmaxx"</span><span class="o">:</span> <span class="mi">25</span><span class="p">,</span>
+ <span class="s2">"--returnBound"</span><span class="o">:</span> <span class="s2">""</span>
+ <span class="p">},</span>
+ <span class="s2">"depends"</span><span class="o">:</span> <span class="p">[</span><span class="s2">"pot-detect"</span><span class="p">]</span>
+ <span class="p">},</span>
+ <span class="p">{</span>
+ <span class="s2">"name"</span><span class="o">:</span> <span class="s2">"gray"</span><span class="p">,</span>
+ <span class="s2">"executable"</span><span class="o">:</span> <span class="s2">"ih-convert-color"</span><span class="p">,</span>
+ <span class="s2">"inputs"</span><span class="o">:</span> <span class="p">[</span><span class="s2">"base"</span><span class="p">],</span>
+ <span class="s2">"outputs"</span><span class="o">:</span> <span class="p">[</span><span class="s2">"grayscale"</span><span class="p">],</span>
+ <span class="s2">"arguments"</span><span class="o">:</span> <span class="p">{</span>
+ <span class="s2">"--intype"</span><span class="o">:</span> <span class="s2">"bgr"</span><span class="p">,</span>
+ <span class="s2">"--outtype"</span><span class="o">:</span> <span class="s2">"gray"</span>
+ <span class="p">}</span>
+ <span class="p">},</span>
+ <span class="p">{</span>
+ <span class="s2">"name"</span><span class="o">:</span> <span class="s2">"blur"</span><span class="p">,</span>
+ <span class="s2">"executable"</span><span class="o">:</span> <span class="s2">"ih-gaussian-blur"</span><span class="p">,</span>
+ <span class="s2">"inputs"</span><span class="o">:</span> <span class="p">[</span><span class="s2">"grayscale"</span><span class="p">],</span>
+ <span class="s2">"outputs"</span><span class="o">:</span> <span class="p">[</span><span class="s2">"blurred"</span><span class="p">],</span>
+ <span class="s2">"arguments"</span><span class="o">:</span> <span class="p">{</span>
+ <span class="s2">"--kwidth"</span><span class="o">:</span> <span class="mi">5</span><span class="p">,</span>
+ <span class="s2">"--kheight"</span><span class="o">:</span> <span class="mi">5</span>
+ <span class="p">},</span>
+ <span class="s2">"depends"</span><span class="o">:</span> <span class="p">[</span><span class="s2">"gray"</span><span class="p">]</span>
+ <span class="p">},</span>
+ <span class="p">{</span>
+ <span class="s2">"name"</span><span class="o">:</span> <span class="s2">"thresh"</span><span class="p">,</span>
+ <span class="s2">"executable"</span><span class="o">:</span> <span class="s2">"ih-adaptive-threshold"</span><span class="p">,</span>
+ <span class="s2">"inputs"</span><span class="o">:</span> <span class="p">[</span><span class="s2">"blurred"</span><span class="p">],</span>
+ <span class="s2">"outputs"</span><span class="o">:</span> <span class="p">[</span><span class="s2">"thresh"</span><span class="p">],</span>
+ <span class="s2">"arguments"</span><span class="o">:</span> <span class="p">{</span>
+ <span class="s2">"--value"</span><span class="o">:</span> <span class="mi">200</span><span class="p">,</span>
+ <span class="s2">"--thresholdType"</span><span class="o">:</span> <span class="s2">"binary"</span><span class="p">,</span>
+ <span class="s2">"--adaptiveType"</span><span class="o">:</span> <span class="s2">"mean"</span><span class="p">,</span>
+ <span class="s2">"--blockSize"</span><span class="o">:</span> <span class="mi">15</span><span class="p">,</span>
+ <span class="s2">"--C"</span><span class="o">:</span> <span class="mi">3</span>
+ <span class="p">},</span>
+ <span class="s2">"depends"</span><span class="o">:</span> <span class="p">[</span><span class="s2">"blur"</span><span class="p">]</span>
+ <span class="p">},</span>
+ <span class="p">{</span>
+ <span class="s2">"name"</span><span class="o">:</span> <span class="s2">"reconstitute1"</span><span class="p">,</span>
+ <span class="s2">"executable"</span><span class="o">:</span> <span class="s2">"ih-bitwise-and"</span><span class="p">,</span>
+ <span class="s2">"inputs"</span><span class="o">:</span> <span class="p">[</span><span class="s2">"thresh"</span><span class="p">,</span> <span class="s2">"base"</span><span class="p">],</span>
+ <span class="s2">"outputs"</span><span class="o">:</span> <span class="p">[</span><span class="s2">"recolor1"</span><span class="p">],</span>
+ <span class="s2">"arguments"</span><span class="o">:</span> <span class="p">{},</span>
+ <span class="s2">"depends"</span><span class="o">:</span> <span class="p">[</span><span class="s2">"thresh"</span><span class="p">]</span>
+ <span class="p">},</span>
+ <span class="p">{</span>
+ <span class="s2">"name"</span><span class="o">:</span> <span class="s2">"meanshift"</span><span class="p">,</span>
+ <span class="s2">"executable"</span><span class="o">:</span> <span class="s2">"ih-meanshift"</span><span class="p">,</span>
+ <span class="s2">"inputs"</span><span class="o">:</span> <span class="p">[</span><span class="s2">"recolor1"</span><span class="p">],</span>
+ <span class="s2">"outputs"</span><span class="o">:</span> <span class="p">[</span><span class="s2">"shift"</span><span class="p">],</span>
+ <span class="s2">"arguments"</span><span class="o">:</span> <span class="p">{</span>
+ <span class="s2">"--spatial_radius"</span><span class="o">:</span> <span class="mi">2</span><span class="p">,</span>
+ <span class="s2">"--range_radius"</span><span class="o">:</span> <span class="mi">2</span><span class="p">,</span>
+ <span class="s2">"--min_density"</span><span class="o">:</span> <span class="mi">50</span>
+ <span class="p">},</span>
+ <span class="s2">"depends"</span><span class="o">:</span> <span class="p">[</span><span class="s2">"reconstitute1"</span><span class="p">]</span>
+ <span class="p">},</span>
+ <span class="p">{</span>
+ <span class="s2">"name"</span><span class="o">:</span> <span class="s2">"pot-filter"</span><span class="p">,</span>
+ <span class="s2">"executable"</span><span class="o">:</span> <span class="s2">"ih-color-filter"</span><span class="p">,</span>
+ <span class="s2">"inputs"</span><span class="o">:</span> <span class="p">[</span><span class="s2">"shift"</span><span class="p">,</span> <span class="s2">"pot_roi"</span><span class="p">],</span>
+ <span class="s2">"outputs"</span><span class="o">:</span> <span class="p">[</span><span class="s2">"pot_filtered"</span><span class="p">],</span>
+ <span class="s2">"arguments"</span><span class="o">:</span> <span class="p">{</span>
+ <span class="s2">"--logic"</span><span class="o">:</span> <span class="s2">"((((((((((r > g) and (r > b)) and (((b max g) - (b min g)) < (((r + g) + b) / 20))) or ((((b max g) max r) - ((b min g) min r)) < 10)) or ((b > r) and ((b > g) or (g > r)))) or (((r + g) + b) < 220)) or ((((r + g) + b) < 350) and ((((b max g) max r) - ((b min g) min r)) < 25))) or ((b > g) and (r > g))) or (((((r - g) > 5) and ((g - b) > 5)) and ((r - g) < 25)) and ((g - b) < 25))) not 1)"</span>
+ <span class="p">},</span>
+ <span class="s2">"depends"</span><span class="o">:</span> <span class="p">[</span><span class="s2">"meanshift"</span><span class="p">,</span> <span class="s2">"pot-crop"</span><span class="p">]</span>
+ <span class="p">},</span>
+ <span class="p">{</span>
+ <span class="s2">"name"</span><span class="o">:</span> <span class="s2">"box-filter"</span><span class="p">,</span>
+ <span class="s2">"executable"</span><span class="o">:</span> <span class="s2">"ih-color-filter"</span><span class="p">,</span>
+ <span class="s2">"inputs"</span><span class="o">:</span> <span class="p">[</span><span class="s2">"pot_filtered"</span><span class="p">,</span> <span class="s2">"box_roi"</span><span class="p">],</span>
+ <span class="s2">"outputs"</span><span class="o">:</span> <span class="p">[</span><span class="s2">"box_filtered"</span><span class="p">],</span>
+ <span class="s2">"arguments"</span><span class="o">:</span> <span class="p">{</span>
+ <span class="s2">"--logic"</span><span class="o">:</span> <span class="s2">"(((((r > g) and (r > b)) and (((b max g) - (b min g)) < (((r + g) + b) / 20))) or ((((b max g) max r) - ((b min g) min r)) < 10)) not 1)"</span>
+ <span class="p">},</span>
+ <span class="s2">"depends"</span><span class="o">:</span> <span class="p">[</span><span class="s2">"pot-filter"</span><span class="p">,</span> <span class="s2">"box-crop"</span><span class="p">]</span>
+ <span class="p">},</span>
+ <span class="p">{</span>
+ <span class="s2">"name"</span><span class="o">:</span> <span class="s2">"gfilter1"</span><span class="p">,</span>
+ <span class="s2">"executable"</span><span class="o">:</span> <span class="s2">"ih-color-filter"</span><span class="p">,</span>
+ <span class="s2">"inputs"</span><span class="o">:</span> <span class="p">[</span><span class="s2">"box_filtered"</span><span class="p">,</span> <span class="s2">"/work/walia/common/ih/workflows/0184/input/rgbsv_gray1.json"</span><span class="p">],</span>
+ <span class="s2">"outputs"</span><span class="o">:</span> <span class="p">[</span><span class="s2">"gray_filtered1"</span><span class="p">],</span>
+ <span class="s2">"arguments"</span><span class="o">:</span> <span class="p">{</span>
+ <span class="s2">"--logic"</span><span class="o">:</span> <span class="s2">"((((b max g) max r) - ((b min g) min r)) > 50)"</span>
+ <span class="p">},</span>
+ <span class="s2">"depends"</span><span class="o">:</span> <span class="p">[</span><span class="s2">"box-filter"</span><span class="p">,</span> <span class="s2">"box-crop"</span><span class="p">]</span>
+ <span class="p">},</span>
+ <span class="p">{</span>
+ <span class="s2">"name"</span><span class="o">:</span> <span class="s2">"gfilter2"</span><span class="p">,</span>
+ <span class="s2">"executable"</span><span class="o">:</span> <span class="s2">"ih-color-filter"</span><span class="p">,</span>
+ <span class="s2">"inputs"</span><span class="o">:</span> <span class="p">[</span><span class="s2">"gray_filtered1"</span><span class="p">,</span> <span class="s2">"/work/walia/common/ih/workflows/0184/input/rgbsv_gray2.json"</span><span class="p">],</span>
+ <span class="s2">"outputs"</span><span class="o">:</span> <span class="p">[</span><span class="s2">"gray_filtered2"</span><span class="p">],</span>
+ <span class="s2">"arguments"</span><span class="o">:</span> <span class="p">{</span>
+ <span class="s2">"--logic"</span><span class="o">:</span> <span class="s2">"((((b max g) max r) - ((b min g) min r)) > 100)"</span>
+ <span class="p">},</span>
+ <span class="s2">"depends"</span><span class="o">:</span> <span class="p">[</span><span class="s2">"gfilter1"</span><span class="p">]</span>
+ <span class="p">},</span>
+ <span class="p">{</span>
+ <span class="s2">"name"</span><span class="o">:</span> <span class="s2">"crop"</span><span class="p">,</span>
+ <span class="s2">"executable"</span><span class="o">:</span> <span class="s2">"ih-crop"</span><span class="p">,</span>
+ <span class="s2">"inputs"</span><span class="o">:</span> <span class="p">[</span><span class="s2">"gray_filtered2"</span><span class="p">,</span> <span class="s2">"/work/walia/common/ih/workflows/0184/input/rgbsv_edge.json"</span><span class="p">],</span>
+ <span class="s2">"outputs"</span><span class="o">:</span> <span class="p">[</span><span class="s2">"edged"</span><span class="p">],</span>
+ <span class="s2">"arguments"</span><span class="o">:</span> <span class="p">{},</span>
+ <span class="s2">"depends"</span><span class="o">:</span> <span class="p">[</span><span class="s2">"gfilter2"</span><span class="p">]</span>
+ <span class="p">},</span>
+ <span class="p">{</span>
+ <span class="s2">"name"</span><span class="o">:</span> <span class="s2">"reconstitute2"</span><span class="p">,</span>
+ <span class="s2">"executable"</span><span class="o">:</span> <span class="s2">"ih-bitwise-and"</span><span class="p">,</span>
+ <span class="s2">"inputs"</span><span class="o">:</span> <span class="p">[</span><span class="s2">"edged"</span><span class="p">,</span> <span class="s2">"base"</span><span class="p">],</span>
+ <span class="s2">"outputs"</span><span class="o">:</span> <span class="p">[</span><span class="s2">"recolor2"</span><span class="p">],</span>
+ <span class="s2">"arguments"</span><span class="o">:</span> <span class="p">{},</span>
+ <span class="s2">"depends"</span><span class="o">:</span> <span class="p">[</span><span class="s2">"crop"</span><span class="p">]</span>
+ <span class="p">},</span>
+ <span class="p">{</span>
+ <span class="s2">"name"</span><span class="o">:</span> <span class="s2">"cut"</span><span class="p">,</span>
+ <span class="s2">"executable"</span><span class="o">:</span> <span class="s2">"ih-contour-cut"</span><span class="p">,</span>
+ <span class="s2">"inputs"</span><span class="o">:</span> <span class="p">[</span><span class="s2">"recolor2"</span><span class="p">,</span> <span class="s2">"recolor2"</span><span class="p">],</span>
+ <span class="s2">"outputs"</span><span class="o">:</span> <span class="p">[</span><span class="s2">"final"</span><span class="p">],</span>
+ <span class="s2">"arguments"</span><span class="o">:</span> <span class="p">{</span>
+ <span class="s2">"--basemin"</span><span class="o">:</span> <span class="mi">50</span><span class="p">,</span>
+ <span class="s2">"--resize"</span><span class="o">:</span> <span class="s2">""</span>
+ <span class="p">},</span>
+ <span class="s2">"depends"</span><span class="o">:</span> <span class="p">[</span><span class="s2">"reconstitute2"</span><span class="p">]</span>
+ <span class="p">}</span>
+ <span class="p">]</span>
+ <span class="p">},</span>
+ <span class="s2">"options"</span><span class="o">:</span> <span class="p">{</span>
+
+ <span class="p">},</span>
+ <span class="s2">"extract"</span><span class="o">:</span> <span class="p">{</span>
+ <span class="s2">"histogram-bin"</span><span class="o">:</span> <span class="p">{</span>
+ <span class="s2">"--group"</span><span class="o">:</span> <span class="p">{</span><span class="s2">"rgb"</span><span class="o">:</span> <span class="p">[</span><span class="s2">"rgbsv"</span><span class="p">,</span> <span class="s2">"rgbtv"</span><span class="p">],</span> <span class="s2">"fluo"</span><span class="o">:</span> <span class="p">[</span><span class="s2">"fluosv"</span><span class="p">]},</span>
+ <span class="s2">"--chunks"</span><span class="o">:</span> <span class="p">{</span><span class="s2">"rgb"</span><span class="o">:</span> <span class="mi">5</span><span class="p">,</span> <span class="s2">"fluo"</span><span class="o">:</span> <span class="mi">6</span><span class="p">},</span>
+ <span class="s2">"--channels"</span><span class="o">:</span> <span class="p">{</span><span class="s2">"rgb"</span><span class="o">:</span> <span class="p">[</span><span class="mi">0</span><span class="p">,</span> <span class="mi">1</span><span class="p">,</span> <span class="mi">2</span><span class="p">],</span> <span class="s2">"fluo"</span><span class="o">:</span> <span class="p">[</span><span class="mi">1</span><span class="p">,</span> <span class="mi">2</span><span class="p">]}</span>
+ <span class="p">},</span>
+ <span class="s2">"workflows"</span><span class="o">:</span> <span class="p">{</span>
+ <span class="s2">"rgbsv"</span><span class="o">:</span> <span class="p">{</span>
+ <span class="s2">"inputs"</span><span class="o">:</span> <span class="p">[</span><span class="s2">"final"</span><span class="p">],</span>
+ <span class="s2">"arguments"</span><span class="o">:</span> <span class="p">{</span>
+ <span class="s2">"--dimensions"</span><span class="o">:</span> <span class="s2">""</span><span class="p">,</span>
+ <span class="s2">"--pixels"</span><span class="o">:</span> <span class="s2">""</span><span class="p">,</span>
+ <span class="s2">"--moments"</span><span class="o">:</span> <span class="s2">""</span>
+ <span class="p">},</span>
+ <span class="s2">"depends"</span><span class="o">:</span> <span class="p">[</span><span class="s2">"cut"</span><span class="p">]</span>
+ <span class="p">},</span>
+ <span class="s2">"rgbtv"</span><span class="o">:</span> <span class="p">{</span>
+ <span class="s2">"inputs"</span><span class="o">:</span> <span class="p">[</span><span class="s2">"final"</span><span class="p">],</span>
+ <span class="s2">"arguments"</span><span class="o">:</span> <span class="p">{</span>
+ <span class="s2">"--dimensions"</span><span class="o">:</span> <span class="s2">""</span><span class="p">,</span>
+ <span class="s2">"--pixels"</span><span class="o">:</span> <span class="s2">""</span><span class="p">,</span>
+ <span class="s2">"--moments"</span><span class="o">:</span> <span class="s2">""</span>
+ <span class="p">},</span>
+ <span class="s2">"depends"</span><span class="o">:</span> <span class="p">[</span><span class="s2">"cut"</span><span class="p">]</span>
+ <span class="p">},</span>
+ <span class="s2">"fluosv"</span><span class="o">:</span> <span class="p">{</span>
+ <span class="s2">"inputs"</span><span class="o">:</span> <span class="p">[</span><span class="s2">"final"</span><span class="p">],</span>
+ <span class="s2">"arguments"</span><span class="o">:</span> <span class="p">{</span>
+ <span class="s2">"--dimensions"</span><span class="o">:</span> <span class="s2">""</span><span class="p">,</span>
+ <span class="s2">"--pixels"</span><span class="o">:</span> <span class="s2">""</span><span class="p">,</span>
+ <span class="s2">"--moments"</span><span class="o">:</span> <span class="s2">""</span>
+ <span class="p">},</span>
+ <span class="s2">"depends"</span><span class="o">:</span> <span class="p">[</span><span class="s2">"cut"</span><span class="p">]</span>
+ <span class="p">}</span>
+ <span class="p">}</span>
+ <span class="p">}</span>
+<span class="p">}</span>
+</pre></div>
+</div>
+<p>Let’s break it down into more manageable chunks. We will look at a few jobs from the workflows.
+First, note that all workflow definitions must be under the “workflows” key. Secondly,
+note that the names of the workflows i.e. in this case “fluosv”, must match the image types
+of images in your database. Each workflow is defined as a list of jobs. The jobs aren’t
+necessarily executed in the order you specify them in the list, but you should structure
+your job definition such that it follows the list order as closely as possible for ease
+of reading. Each individual job has 5 required definitions, and 1 optional one. For each
+job you <strong>must</strong> define a name, an executable, the job inputs, the job outputs, and the job arguments.
+Note that you must include “arguments” even if it is left blank.
+For each job you may optionally define dependent jobs. Let’s look at the first job we define for fluosv:</p>
+<div class="highlight-javascript"><div class="highlight"><pre><span class="p">{</span>
+ <span class="s2">"name"</span><span class="o">:</span> <span class="s2">"pot_filter_1"</span><span class="p">,</span>
+ <span class="s2">"executable"</span><span class="o">:</span> <span class="s2">"ih-color-filter"</span><span class="p">,</span>
+ <span class="s2">"inputs"</span><span class="o">:</span> <span class="p">[</span><span class="s2">"base"</span><span class="p">,</span> <span class="s2">"/work/walia/common/ih/workflows/0184/input/fluosv_pot1.json"</span><span class="p">],</span>
+ <span class="s2">"outputs"</span><span class="o">:</span> <span class="p">[</span><span class="s2">"pot1"</span><span class="p">],</span>
+ <span class="s2">"arguments"</span><span class="o">:</span> <span class="p">{</span>
+ <span class="s2">"--logic"</span><span class="o">:</span> <span class="s2">"(((((((r - g) < 30) and (((r + g) + b) < 110)) or ((((r + g) + b) > 110) and ((r - g) < 50))) or (((r - g) < 25) and ((g - r) < 25))) or (g > 60)) not 1)"</span>
+ <span class="p">}</span>
+<span class="p">},</span>
+</pre></div>
+</div>
+<p>Here, we define the name as “pot_filter_1”. Names are used to apply a more meaningful label
+to each job for the user, as well as used for dependencies in later processing steps.
+We define the executable we want to use as “ih-color-filter” – This executable is used for
+processing user defined color logic, and will not be talked about in depth here. We define two inputs
+for our function. The first is “base” – which serves as a placeholder for raw images. You can use
+this input in any step and it will load in the starting image. This is important for steps such
+as reconstiuting the color of the image. The second argument we feed is a path to a roi file.
+Here are the contents of the file:</p>
+<div class="highlight-javascript"><div class="highlight"><pre><span class="p">{</span>
+ <span class="s2">"ystart"</span><span class="o">:</span> <span class="mi">1110</span><span class="p">,</span>
+ <span class="s2">"yend"</span><span class="o">:</span> <span class="s2">"y"</span><span class="p">,</span>
+ <span class="s2">"xstart"</span><span class="o">:</span> <span class="mi">369</span><span class="p">,</span>
+ <span class="s2">"xend"</span><span class="o">:</span> <span class="mi">669</span>
+<span class="p">}</span>
+</pre></div>
+</div>
+<p>The roi file simply defines the region we want to apply our color-filter to.
+The roi file will automatically convert “y” to the maximum height, and “x” to the maximum
+width. Additionally it supports simply arithmetic, thus you could enter “y - 300” for
+“yend”. If this input is left blank, it simply applies the color-filter to the entire image.
+We define the output as “pot1”. This means that the intermediate file will be saved with
+a name of “pot1”. Additionally, we can now use “pot1” as input in further steps. Finally
+we define the arguments of our processing functino – in this case only one, our logic
+string. This job is the first job in our processing workflow, so we define no dependencies.
+We now look at the second job for fluosv:</p>
+<div class="highlight-javascript"><div class="highlight"><pre><span class="p">{</span>
+ <span class="s2">"name"</span><span class="o">:</span> <span class="s2">"pot_filter_2"</span><span class="p">,</span>
+ <span class="s2">"executable"</span><span class="o">:</span> <span class="s2">"ih-color-filter"</span><span class="p">,</span>
+ <span class="s2">"inputs"</span><span class="o">:</span> <span class="p">[</span><span class="s2">"pot1"</span><span class="p">,</span> <span class="s2">"/work/walia/common/ih/workflows/0184/input/fluosv_pot2.json"</span><span class="p">],</span>
+ <span class="s2">"outputs"</span><span class="o">:</span> <span class="p">[</span><span class="s2">"pot2"</span><span class="p">],</span>
+ <span class="s2">"arguments"</span><span class="o">:</span> <span class="p">{</span>
+ <span class="s2">"--logic"</span><span class="o">:</span> <span class="s2">"(((r + g) + b) > 120)"</span>
+ <span class="p">},</span>
+ <span class="s2">"depends"</span><span class="o">:</span> <span class="p">[</span><span class="s2">"pot_filter_1"</span><span class="p">]</span>
+<span class="p">},</span>
+</pre></div>
+</div>
+<p>Note that the input image is now “pot1” instead of “base”. This chains the output
+of the previous step into the input of this step. To fully accomplish this, we must define
+dependency. Our first job was named “pot_filter_1”, and we can see this name in our
+dependency list. A job can have multiple dependencies, you simply separate the names with
+commas i.e. “depends”: [“job1”, “job2”, “job3”]. Whenever you use the output of a previous
+job, you must include it in the dependency list. Some functions output roi files instead of,
+or in addition to images. You can similarly use these roi files as input in future steps,
+provided that you include them in the proper location in your “inputs” definition. As a
+demonstration of this, we look at two jobs from the rgbsv workflow, “box-crop” and “box-filter”.
+“box-crop” outputs “box_roi” which we use as a roi for “box-filter”. There are two other definitions
+in the processing template. One is for “options” – which is left blank in this case. Currently,
+the only supported option is “save-steps”. If you specify:</p>
+<div class="highlight-javascript"><div class="highlight"><pre><span class="s2">"options"</span><span class="o">:</span> <span class="p">{</span>
+ <span class="s2">"save-step"</span><span class="o">:</span> <span class="s2">"true"</span>
+<span class="p">},</span>
+</pre></div>
+</div>
+<p>Each intermediary step (including roi files) will be saved to the final output folder. Otherwise,
+only the final processed image will be saved. Lastly, “extract” is required, and here you specify
+all the numeric information you want to extract from your final images. Let’s take a look:</p>
+<div class="highlight-javascript"><div class="highlight"><pre><span class="s2">"extract"</span><span class="o">:</span> <span class="p">{</span>
+ <span class="s2">"histogram-bin"</span><span class="o">:</span> <span class="p">{</span>
+ <span class="s2">"--group"</span><span class="o">:</span> <span class="p">{</span><span class="s2">"rgb"</span><span class="o">:</span> <span class="p">[</span><span class="s2">"rgbsv"</span><span class="p">,</span> <span class="s2">"rgbtv"</span><span class="p">],</span> <span class="s2">"fluo"</span><span class="o">:</span> <span class="p">[</span><span class="s2">"fluosv"</span><span class="p">]},</span>
+ <span class="s2">"--chunks"</span><span class="o">:</span> <span class="p">{</span><span class="s2">"rgb"</span><span class="o">:</span> <span class="mi">5</span><span class="p">,</span> <span class="s2">"fluo"</span><span class="o">:</span> <span class="mi">6</span><span class="p">},</span>
+ <span class="s2">"--channels"</span><span class="o">:</span> <span class="p">{</span><span class="s2">"rgb"</span><span class="o">:</span> <span class="p">[</span><span class="mi">0</span><span class="p">,</span> <span class="mi">1</span><span class="p">,</span> <span class="mi">2</span><span class="p">],</span> <span class="s2">"fluo"</span><span class="o">:</span> <span class="p">[</span><span class="mi">1</span><span class="p">,</span> <span class="mi">2</span><span class="p">]}</span>
+ <span class="p">},</span>
+ <span class="s2">"workflows"</span><span class="o">:</span> <span class="p">{</span>
+ <span class="s2">"rgbsv"</span><span class="o">:</span> <span class="p">{</span>
+ <span class="s2">"inputs"</span><span class="o">:</span> <span class="p">[</span><span class="s2">"final"</span><span class="p">],</span>
+ <span class="s2">"arguments"</span><span class="o">:</span> <span class="p">{</span>
+ <span class="s2">"--dimensions"</span><span class="o">:</span> <span class="s2">""</span><span class="p">,</span>
+ <span class="s2">"--pixels"</span><span class="o">:</span> <span class="s2">""</span><span class="p">,</span>
+ <span class="s2">"--moments"</span><span class="o">:</span> <span class="s2">""</span>
+ <span class="p">},</span>
+ <span class="s2">"depends"</span><span class="o">:</span> <span class="p">[</span><span class="s2">"cut"</span><span class="p">]</span>
+ <span class="p">},</span>
+ <span class="s2">"rgbtv"</span><span class="o">:</span> <span class="p">{</span>
+ <span class="s2">"inputs"</span><span class="o">:</span> <span class="p">[</span><span class="s2">"final"</span><span class="p">],</span>
+ <span class="s2">"arguments"</span><span class="o">:</span> <span class="p">{</span>
+ <span class="s2">"--dimensions"</span><span class="o">:</span> <span class="s2">""</span><span class="p">,</span>
+ <span class="s2">"--pixels"</span><span class="o">:</span> <span class="s2">""</span><span class="p">,</span>
+ <span class="s2">"--moments"</span><span class="o">:</span> <span class="s2">""</span>
+ <span class="p">},</span>
+ <span class="s2">"depends"</span><span class="o">:</span> <span class="p">[</span><span class="s2">"cut"</span><span class="p">]</span>
+ <span class="p">},</span>
+ <span class="s2">"fluosv"</span><span class="o">:</span> <span class="p">{</span>
+ <span class="s2">"inputs"</span><span class="o">:</span> <span class="p">[</span><span class="s2">"final"</span><span class="p">],</span>
+ <span class="s2">"arguments"</span><span class="o">:</span> <span class="p">{</span>
+ <span class="s2">"--dimensions"</span><span class="o">:</span> <span class="s2">""</span><span class="p">,</span>
+ <span class="s2">"--pixels"</span><span class="o">:</span> <span class="s2">""</span><span class="p">,</span>
+ <span class="s2">"--moments"</span><span class="o">:</span> <span class="s2">""</span>
+ <span class="p">},</span>
+ <span class="s2">"depends"</span><span class="o">:</span> <span class="p">[</span><span class="s2">"cut"</span><span class="p">]</span>
+ <span class="p">}</span>
+ <span class="p">}</span>
+<span class="p">}</span>
+</pre></div>
+</div>
+<p>There is an optional special key you can define – “histogram-bin” – in the
+extract section. Specifying this key allows you to perform an experiment-wise histogram
+calculation of color-channel information to generate relevant bins. It performs the
+following steps: 1. Calculate color histogram for each processed image. 2. Sum
+the histograms to get a histogram for the entire data set. 3. Segment the histogram
+into equal area pieces as based on the inputs. 4. Generate complete permutation
+of bins based on the divided histogram. In the “histogram-bin” section we
+first define “–group”. This allows us to group one or more imtypes from separate
+workflows together. In this case, we group “rgbsv” and “rgbtv” together. This
+allows us to consider color information from the RGB spectrum as a whole.
+We name this group “rgb” – group names are important for future “histogram-bin”
+definitions. Next is “–chunks”. For each group, you simply define how many
+pieces you want the total calculated histogram to be broken up into. Remember
+that color-space is 3 dimensional – this means that specifying chunks = 5
+will generate <span class="math">\(5^{3} = 125\)</span> bins. Finally, we define what channels to
+process for each group. Channel 0 corresponds to blue, channel 1 corresponds
+to green, and channel 2 corresponds to red. In this case, we leave channel 0
+out of fluorescence processing – this is because a majority of the blue values
+in the image are either 0 or 1. Any channel left out will simply be given a range of [0, 255]
+for every generated bin.</p>
+<p>The definitions in each individual “workflow” extract information from each individual
+image. You must define “inputs” and “depends” so that the extraction script
+can locate the image you want to extract data from (it does not necessarily have to be the
+final image, though it generally is). In the arguments section, you define a list of the
+numeric information you want to extract. For an example of all arguments you can specify,
+look at the ih-extract script. If you specify “histogram-bin” for a particular
+imtype, the “–colors” options is added automatically.</p>
+<p>Finally, to actually generate your workflow, use the ih-run command.
+You should have setup a directory from the crawling step when you executed</p>
+<div class="highlight-bash"><div class="highlight"><pre>ih-setup --dir <span class="s2">"DIR_NAME"</span> --template <span class="s2">"crawl.json"</span>
+</pre></div>
+</div>
+<p>The easiest way to run ih-run is to change directories to “DIR_NAME”, then
+simply run:</p>
+<div class="highlight-bash"><div class="highlight"><pre>ih-run
+</pre></div>
+</div>
+<p>with no arguments! Run with the -h option to see options. Additionally, the validator
+for processing workflows is very powerful. Use –validate to run in validate only mode
+to help debug your workflow as you create it. Depending on how many input images,
+it may take a while to write the necessary submission files (sometimes 10-20 minutes).</p>
+</div>
+<div class="section" id="submission">
+<h2>Submission<a class="headerlink" href="#submission" title="Permalink to this headline">¶</a></h2>
+<p>Upon sucessful completion of ih-run, a date and timestamped folder should be created
+with the following structure:</p>
+<div class="highlight-bash"><div class="highlight"><pre>date-timestamp/
+ input/
+ imgproc/
+ -sites.xml
+ -conf.rc
+ -map.rc
+ -extract.dax
+ -workflow.dax
+ -notify.sh
+ -submit.sh
+ rawfiles/
+ templates/
+ output/
+ -output.db
+ work/
+</pre></div>
+</div>
+<p>The work directory is where actual processing is done – but initially starts empty. The output
+folder starts only with the output database, but contains no images to start with. The input folder
+contains a copy of your submitted templates in the templates folder, and a copy of all non-image raw-input files
+in the rawfiles folder. Finally, within the imgproc folder are the actual files required to submit
+a pegasus workflow. All you need to do to submit is execute the submit.sh script. This will launch your
+workflow, as well as creating a status.sh script for easy monitoring, and a remove.sh script if you
+want to remove your workflow.</p>
+</div>
+</div>
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+<div class="section" id="examples">
+<h1>Examples<a class="headerlink" href="#examples" title="Permalink to this headline">¶</a></h1>
+<p>Working through examples is a much better way of learning how to use ih than
+reading implementation details. Additionally, creating workflows is a complicated
+multi-step process. As such, many examples are detailed below, falling into
+two broad categories. Script examples are those that deal with local computing.
+Each script example includes a test image to download, as well as scripts
+for library and command-line usage of ih. Workflow examples are those that
+deal with distributed computing. They include template files for download,
+but due to their nature, image sets are not available for download.
+However, data sets are available through the OSG (Open Science Grid). Workflow examples
+are very complex. Step by step instructions are provided, but it is <strong>highly</strong> recommended
+to work through script examples before jumping into workflow examples.</p>
+<div class="section" id="script-examples">
+<h2>Script Examples<a class="headerlink" href="#script-examples" title="Permalink to this headline">¶</a></h2>
+<p>There are many different script examples. Some are specific to functions,
+others cover a broad range of functions. If you are getting started,
+begin by working through the core processing examples. In particular,
+if you are unfamiliar with Python, the first core processing script attempts
+to explain some basic terms.</p>
+<div class="section" id="core-processing">
+<h3>Core Processing<a class="headerlink" href="#core-processing" title="Permalink to this headline">¶</a></h3>
+<p><a class="reference internal" href="ex_script_core1.html"><em>Core Processing #1</em></a>, difficulty = easy.</p>
+<p><a class="reference internal" href="ex_script_core2.html"><em>Core Processing #2</em></a>, difficulty = medium.</p>
+</div>
+<div class="section" id="color-filter">
+<h3>Color Filter<a class="headerlink" href="#color-filter" title="Permalink to this headline">¶</a></h3>
+<p><a class="reference internal" href="ex_script_color1.html"><em>Color Filter #1</em></a>, difficulty = medium.</p>
+</div>
+</div>
+<div class="section" id="workflow-examples">
+<h2>Workflow Examples<a class="headerlink" href="#workflow-examples" title="Permalink to this headline">¶</a></h2>
+<p><a class="reference internal" href="ex_workflow_1.html"><em>Workflow #1</em></a>, difficulty = complex.</p>
+</div>
+</div>
+
+
+ </div>
+
+ </div>
+</div>
+<footer class="footer">
+ <div class="container">
+ <p class="pull-right">
+ <a href="#">Back to top</a>
+
+ </p>
+ <p>
+ © Copyright 2015, Avi Knecht.<br/>
+ Created using <a href="http://sphinx.pocoo.org/">Sphinx</a> 1.3a0.<br/>
+ </p>
+ </div>
+</footer>
+ </body>
+</html>
\ No newline at end of file
diff --git a/docs/build/html/genindex.html b/docs/build/html/genindex.html
new file mode 100644
index 0000000000000000000000000000000000000000..fe57c3570f82718972a6c87b433f12a9704dba26
--- /dev/null
+++ b/docs/build/html/genindex.html
@@ -0,0 +1,494 @@
+
+<!DOCTYPE html>
+
+
+<html xmlns="http://www.w3.org/1999/xhtml">
+ <head>
+ <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
+
+ <title>Index — Image Harvest 1.0.1 documentation</title>
+
+ <link rel="stylesheet" href="_static/basic.css" type="text/css" />
+ <link rel="stylesheet" href="_static/pygments.css" type="text/css" />
+ <link rel="stylesheet" href="_static/bootstrap-3.2.0/css/bootstrap.min.css" type="text/css" />
+ <link rel="stylesheet" href="_static/bootstrap-3.2.0/css/bootstrap-theme.min.css" type="text/css" />
+ <link rel="stylesheet" href="_static/bootstrap-sphinx.css" type="text/css" />
+
+ <script type="text/javascript">
+ var DOCUMENTATION_OPTIONS = {
+ URL_ROOT: './',
+ VERSION: '1.0.1',
+ COLLAPSE_INDEX: false,
+ FILE_SUFFIX: '.html',
+ HAS_SOURCE: true
+ };
+ </script>
+ <script type="text/javascript" src="_static/jquery.js"></script>
+ <script type="text/javascript" src="_static/underscore.js"></script>
+ <script type="text/javascript" src="_static/doctools.js"></script>
+ <script type="text/javascript" src="https://c328740.ssl.cf1.rackcdn.com/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
+ <script type="text/javascript" src="_static/js/jquery-1.11.0.min.js"></script>
+ <script type="text/javascript" src="_static/js/jquery-fix.js"></script>
+ <script type="text/javascript" src="_static/bootstrap-3.2.0/js/bootstrap.min.js"></script>
+ <script type="text/javascript" src="_static/bootstrap-sphinx.js"></script>
+ <link rel="top" title="Image Harvest 1.0.1 documentation" href="index.html" />
+<meta charset='utf-8'>
+<meta http-equiv='X-UA-Compatible' content='IE=edge,chrome=1'>
+<meta name='viewport' content='width=device-width, initial-scale=1.0, maximum-scale=1'>
+<meta name="apple-mobile-web-app-capable" content="yes">
+
+ </head>
+ <body role="document">
+
+ <div id="navbar" class="navbar navbar-default navbar-fixed-top">
+ <div class="container">
+ <div class="navbar-header">
+ <!-- .btn-navbar is used as the toggle for collapsed navbar content -->
+ <button type="button" class="navbar-toggle" data-toggle="collapse" data-target=".nav-collapse">
+ <span class="icon-bar"></span>
+ <span class="icon-bar"></span>
+ <span class="icon-bar"></span>
+ </button>
+ <a class="navbar-brand" href="index.html">
+ Image Harvest</a>
+ <span class="navbar-text navbar-version pull-left"><b>1.0</b></span>
+ </div>
+
+ <div class="collapse navbar-collapse nav-collapse">
+ <ul class="nav navbar-nav">
+
+
+ <li class="dropdown globaltoc-container">
+ <a role="button"
+ id="dLabelGlobalToc"
+ data-toggle="dropdown"
+ data-target="#"
+ href="index.html">Site <b class="caret"></b></a>
+ <ul class="dropdown-menu globaltoc"
+ role="menu"
+ aria-labelledby="dLabelGlobalToc"><ul>
+<li class="toctree-l1"><a class="reference internal" href="introduction.html">Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="installation.html">Installation</a></li>
+<li class="toctree-l1"><a class="reference internal" href="start.html">Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="ex_script_core1.html">Core Processing Example #1</a></li>
+<li class="toctree-l1"><a class="reference internal" href="ex_script_core2.html">Core Processing Example #2</a></li>
+<li class="toctree-l1"><a class="reference internal" href="ex_script_color1.html">Color Filter In Depth #1</a></li>
+<li class="toctree-l1"><a class="reference internal" href="ex_workflow_1.html">Workflow Example #1</a></li>
+<li class="toctree-l1"><a class="reference internal" href="examples.html">Examples</a></li>
+<li class="toctree-l1"><a class="reference internal" href="processing.html">Image Processing</a></li>
+<li class="toctree-l1"><a class="reference internal" href="viewer.html">Image Processing Viewer</a></li>
+<li class="toctree-l1"><a class="reference internal" href="statistics.html">Statistics</a></li>
+<li class="toctree-l1"><a class="reference internal" href="indexing.html">Image Loading</a></li>
+<li class="toctree-l1"><a class="reference internal" href="workflowimage.html">Image Processing Workflows</a></li>
+<li class="toctree-l1"><a class="reference internal" href="workflowstats.html">Statistics Workflows</a></li>
+</ul>
+</ul>
+</li>
+
+ <li class="dropdown">
+ <a role="button"
+ id="dLabelLocalToc"
+ data-toggle="dropdown"
+ data-target="#"
+ href="#">Page <b class="caret"></b></a>
+ <ul class="dropdown-menu localtoc"
+ role="menu"
+ aria-labelledby="dLabelLocalToc"></ul>
+</li>
+
+
+
+
+
+
+
+
+
+
+ <li class="hidden-sm"></li>
+
+ </ul>
+
+
+
+<form class="navbar-form navbar-right" action="search.html" method="get">
+ <div class="form-group">
+ <input type="text" name="q" class="form-control" placeholder="Search" />
+ </div>
+ <input type="hidden" name="check_keywords" value="yes" />
+ <input type="hidden" name="area" value="default" />
+</form>
+
+ </div>
+ </div>
+ </div>
+
+<div class="container">
+ <div class="row">
+ <div class="col-md-12">
+
+
+<h1 id="index">Index</h1>
+
+<div class="genindex-jumpbox">
+ <a href="#A"><strong>A</strong></a>
+ | <a href="#B"><strong>B</strong></a>
+ | <a href="#C"><strong>C</strong></a>
+ | <a href="#D"><strong>D</strong></a>
+ | <a href="#E"><strong>E</strong></a>
+ | <a href="#G"><strong>G</strong></a>
+ | <a href="#I"><strong>I</strong></a>
+ | <a href="#K"><strong>K</strong></a>
+ | <a href="#L"><strong>L</strong></a>
+ | <a href="#M"><strong>M</strong></a>
+ | <a href="#N"><strong>N</strong></a>
+ | <a href="#R"><strong>R</strong></a>
+ | <a href="#S"><strong>S</strong></a>
+ | <a href="#T"><strong>T</strong></a>
+ | <a href="#W"><strong>W</strong></a>
+
+</div>
+<h2 id="A">A</h2>
+<table style="width: 100%" class="indextable genindextable"><tr>
+ <td style="width: 33%" valign="top"><dl>
+
+ <dt><a href="processing.html#ih.imgproc.Image.adaptiveThreshold">adaptiveThreshold() (ih.imgproc.Image method)</a>
+ </dt>
+
+ </dl></td>
+ <td style="width: 33%" valign="top"><dl>
+
+ <dt><a href="statistics.html#ih.statistics.Stats.anova">anova() (ih.statistics.Stats method)</a>
+ </dt>
+
+ </dl></td>
+</tr></table>
+
+<h2 id="B">B</h2>
+<table style="width: 100%" class="indextable genindextable"><tr>
+ <td style="width: 33%" valign="top"><dl>
+
+ <dt><a href="processing.html#ih.imgproc.Image.bitwise_and">bitwise_and() (ih.imgproc.Image method)</a>
+ </dt>
+
+
+ <dt><a href="processing.html#ih.imgproc.Image.bitwise_not">bitwise_not() (ih.imgproc.Image method)</a>
+ </dt>
+
+
+ <dt><a href="processing.html#ih.imgproc.Image.bitwise_or">bitwise_or() (ih.imgproc.Image method)</a>
+ </dt>
+
+ </dl></td>
+ <td style="width: 33%" valign="top"><dl>
+
+ <dt><a href="processing.html#ih.imgproc.Image.bitwise_xor">bitwise_xor() (ih.imgproc.Image method)</a>
+ </dt>
+
+
+ <dt><a href="processing.html#ih.imgproc.Image.blur">blur() (ih.imgproc.Image method)</a>
+ </dt>
+
+ </dl></td>
+</tr></table>
+
+<h2 id="C">C</h2>
+<table style="width: 100%" class="indextable genindextable"><tr>
+ <td style="width: 33%" valign="top"><dl>
+
+ <dt><a href="processing.html#ih.imgproc.Image.colorFilter">colorFilter() (ih.imgproc.Image method)</a>
+ </dt>
+
+
+ <dt><a href="processing.html#ih.imgproc.Image.contourCut">contourCut() (ih.imgproc.Image method)</a>
+ </dt>
+
+
+ <dt><a href="processing.html#ih.imgproc.Image.convertColor">convertColor() (ih.imgproc.Image method)</a>
+ </dt>
+
+
+ <dt><a href="statistics.html#ih.statistics.Stats.correlation">correlation() (ih.statistics.Stats method)</a>
+ </dt>
+
+ </dl></td>
+ <td style="width: 33%" valign="top"><dl>
+
+ <dt><a href="indexing.html#ih.workflow.ImageLoader.crawl">crawl() (ih.workflow.ImageLoader method)</a>
+ </dt>
+
+
+ <dt><a href="workflowimage.html#ih.workflow.ImageProcessor.create">create() (ih.workflow.ImageProcessor method)</a>
+ </dt>
+
+ <dd><dl>
+
+ <dt><a href="workflowstats.html#ih.workflow.Statistics.create">(ih.workflow.Statistics method)</a>
+ </dt>
+
+ </dl></dd>
+
+ <dt><a href="processing.html#ih.imgproc.Image.crop">crop() (ih.imgproc.Image method)</a>
+ </dt>
+
+ </dl></td>
+</tr></table>
+
+<h2 id="D">D</h2>
+<table style="width: 100%" class="indextable genindextable"><tr>
+ <td style="width: 33%" valign="top"><dl>
+
+ <dt><a href="processing.html#ih.imgproc.Image.destroy">destroy() (ih.imgproc.Image method)</a>
+ </dt>
+
+ </dl></td>
+</tr></table>
+
+<h2 id="E">E</h2>
+<table style="width: 100%" class="indextable genindextable"><tr>
+ <td style="width: 33%" valign="top"><dl>
+
+ <dt><a href="processing.html#ih.imgproc.Image.edges">edges() (ih.imgproc.Image method)</a>
+ </dt>
+
+
+ <dt><a href="statistics.html#ih.statistics.Stats.export">export() (ih.statistics.Stats method)</a>
+ </dt>
+
+
+ <dt><a href="processing.html#ih.imgproc.Image.extractBins">extractBins() (ih.imgproc.Image method)</a>
+ </dt>
+
+
+ <dt><a href="processing.html#ih.imgproc.Image.extractColorData">extractColorData() (ih.imgproc.Image method)</a>
+ </dt>
+
+ </dl></td>
+ <td style="width: 33%" valign="top"><dl>
+
+ <dt><a href="processing.html#ih.imgproc.Image.extractDimensions">extractDimensions() (ih.imgproc.Image method)</a>
+ </dt>
+
+
+ <dt><a href="processing.html#ih.imgproc.Image.extractFinalPath">extractFinalPath() (ih.imgproc.Image method)</a>
+ </dt>
+
+
+ <dt><a href="processing.html#ih.imgproc.Image.extractMoments">extractMoments() (ih.imgproc.Image method)</a>
+ </dt>
+
+
+ <dt><a href="processing.html#ih.imgproc.Image.extractPixels">extractPixels() (ih.imgproc.Image method)</a>
+ </dt>
+
+ </dl></td>
+</tr></table>
+
+<h2 id="G">G</h2>
+<table style="width: 100%" class="indextable genindextable"><tr>
+ <td style="width: 33%" valign="top"><dl>
+
+ <dt><a href="processing.html#ih.imgproc.Image.gaussianBlur">gaussianBlur() (ih.imgproc.Image method)</a>
+ </dt>
+
+ </dl></td>
+</tr></table>
+
+<h2 id="I">I</h2>
+<table style="width: 100%" class="indextable genindextable"><tr>
+ <td style="width: 33%" valign="top"><dl>
+
+ <dt><a href="processing.html#ih.imgproc.Image">Image (class in ih.imgproc)</a>
+ </dt>
+
+
+ <dt><a href="indexing.html#ih.workflow.ImageLoader">ImageLoader (class in ih.workflow)</a>
+ </dt>
+
+ </dl></td>
+ <td style="width: 33%" valign="top"><dl>
+
+ <dt><a href="workflowimage.html#ih.workflow.ImageProcessor">ImageProcessor (class in ih.workflow)</a>
+ </dt>
+
+ </dl></td>
+</tr></table>
+
+<h2 id="K">K</h2>
+<table style="width: 100%" class="indextable genindextable"><tr>
+ <td style="width: 33%" valign="top"><dl>
+
+ <dt><a href="processing.html#ih.imgproc.Image.kmeans">kmeans() (ih.imgproc.Image method)</a>
+ </dt>
+
+ </dl></td>
+</tr></table>
+
+<h2 id="L">L</h2>
+<table style="width: 100%" class="indextable genindextable"><tr>
+ <td style="width: 33%" valign="top"><dl>
+
+ <dt><a href="processing.html#ih.imgproc.Image.list">list() (ih.imgproc.Image method)</a>
+ </dt>
+
+ </dl></td>
+ <td style="width: 33%" valign="top"><dl>
+
+ <dt><a href="statistics.html#ih.statistics.Stats.logErrors">logErrors() (ih.statistics.Stats method)</a>
+ </dt>
+
+ </dl></td>
+</tr></table>
+
+<h2 id="M">M</h2>
+<table style="width: 100%" class="indextable genindextable"><tr>
+ <td style="width: 33%" valign="top"><dl>
+
+ <dt><a href="processing.html#ih.imgproc.Image.meanshift">meanshift() (ih.imgproc.Image method)</a>
+ </dt>
+
+
+ <dt><a href="processing.html#ih.imgproc.Image.medianBlur">medianBlur() (ih.imgproc.Image method)</a>
+ </dt>
+
+ </dl></td>
+ <td style="width: 33%" valign="top"><dl>
+
+ <dt><a href="processing.html#ih.imgproc.Image.morphology">morphology() (ih.imgproc.Image method)</a>
+ </dt>
+
+ </dl></td>
+</tr></table>
+
+<h2 id="N">N</h2>
+<table style="width: 100%" class="indextable genindextable"><tr>
+ <td style="width: 33%" valign="top"><dl>
+
+ <dt><a href="statistics.html#ih.statistics.Stats.normalize">normalize() (ih.statistics.Stats method)</a>
+ </dt>
+
+ </dl></td>
+ <td style="width: 33%" valign="top"><dl>
+
+ <dt><a href="processing.html#ih.imgproc.Image.normalizeByIntensity">normalizeByIntensity() (ih.imgproc.Image method)</a>
+ </dt>
+
+ </dl></td>
+</tr></table>
+
+<h2 id="R">R</h2>
+<table style="width: 100%" class="indextable genindextable"><tr>
+ <td style="width: 33%" valign="top"><dl>
+
+ <dt><a href="processing.html#ih.imgproc.Image.resize">resize() (ih.imgproc.Image method)</a>
+ </dt>
+
+
+ <dt><a href="processing.html#ih.imgproc.Image.resizeSelf">resizeSelf() (ih.imgproc.Image method)</a>
+ </dt>
+
+ </dl></td>
+ <td style="width: 33%" valign="top"><dl>
+
+ <dt><a href="processing.html#ih.imgproc.Image.restore">restore() (ih.imgproc.Image method)</a>
+ </dt>
+
+ </dl></td>
+</tr></table>
+
+<h2 id="S">S</h2>
+<table style="width: 100%" class="indextable genindextable"><tr>
+ <td style="width: 33%" valign="top"><dl>
+
+ <dt><a href="processing.html#ih.imgproc.Image.save">save() (ih.imgproc.Image method)</a>
+ </dt>
+
+
+ <dt><a href="statistics.html#ih.statistics.Stats.shootArea">shootArea() (ih.statistics.Stats method)</a>
+ </dt>
+
+
+ <dt><a href="processing.html#ih.imgproc.Image.show">show() (ih.imgproc.Image method)</a>
+ </dt>
+
+ </dl></td>
+ <td style="width: 33%" valign="top"><dl>
+
+ <dt><a href="workflowstats.html#ih.workflow.Statistics">Statistics (class in ih.workflow)</a>
+ </dt>
+
+
+ <dt><a href="statistics.html#ih.statistics.Stats">Stats (class in ih.statistics)</a>
+ </dt>
+
+ </dl></td>
+</tr></table>
+
+<h2 id="T">T</h2>
+<table style="width: 100%" class="indextable genindextable"><tr>
+ <td style="width: 33%" valign="top"><dl>
+
+ <dt><a href="processing.html#ih.imgproc.Image.threshold">threshold() (ih.imgproc.Image method)</a>
+ </dt>
+
+ <dd><dl>
+
+ <dt><a href="statistics.html#ih.statistics.Stats.threshold">(ih.statistics.Stats method)</a>
+ </dt>
+
+ </dl></dd>
+
+ <dt><a href="statistics.html#ih.statistics.Stats.treatmentComp">treatmentComp() (ih.statistics.Stats method)</a>
+ </dt>
+
+ </dl></td>
+ <td style="width: 33%" valign="top"><dl>
+
+ <dt><a href="statistics.html#ih.statistics.Stats.tTest">tTest() (ih.statistics.Stats method)</a>
+ </dt>
+
+ </dl></td>
+</tr></table>
+
+<h2 id="W">W</h2>
+<table style="width: 100%" class="indextable genindextable"><tr>
+ <td style="width: 33%" valign="top"><dl>
+
+ <dt><a href="processing.html#ih.imgproc.Image.wait">wait() (ih.imgproc.Image method)</a>
+ </dt>
+
+ </dl></td>
+ <td style="width: 33%" valign="top"><dl>
+
+ <dt><a href="processing.html#ih.imgproc.Image.write">write() (ih.imgproc.Image method)</a>
+ </dt>
+
+ <dd><dl>
+
+ <dt><a href="indexing.html#ih.workflow.ImageLoader.write">(ih.workflow.ImageLoader method)</a>
+ </dt>
+
+ </dl></dd>
+ </dl></td>
+</tr></table>
+
+
+
+ </div>
+
+ </div>
+</div>
+<footer class="footer">
+ <div class="container">
+ <p class="pull-right">
+ <a href="#">Back to top</a>
+
+ </p>
+ <p>
+ © Copyright 2015, Avi Knecht.<br/>
+ Created using <a href="http://sphinx.pocoo.org/">Sphinx</a> 1.3a0.<br/>
+ </p>
+ </div>
+</footer>
+ </body>
+</html>
\ No newline at end of file
diff --git a/docs/build/html/index.html b/docs/build/html/index.html
new file mode 100644
index 0000000000000000000000000000000000000000..b02b99cf48190c2356283d18075ef2ecd7d9ad44
--- /dev/null
+++ b/docs/build/html/index.html
@@ -0,0 +1,199 @@
+<!DOCTYPE html>
+
+
+<html xmlns="http://www.w3.org/1999/xhtml">
+ <head>
+ <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
+
+ <title>Welcome to Image Harvest documentation! — Image Harvest 1.0.1 documentation</title>
+
+ <link rel="stylesheet" href="_static/basic.css" type="text/css" />
+ <link rel="stylesheet" href="_static/pygments.css" type="text/css" />
+ <link rel="stylesheet" href="_static/bootstrap-3.2.0/css/bootstrap.min.css" type="text/css" />
+ <link rel="stylesheet" href="_static/bootstrap-3.2.0/css/bootstrap-theme.min.css" type="text/css" />
+ <link rel="stylesheet" href="_static/bootstrap-sphinx.css" type="text/css" />
+
+ <script type="text/javascript">
+ var DOCUMENTATION_OPTIONS = {
+ URL_ROOT: './',
+ VERSION: '1.0.1',
+ COLLAPSE_INDEX: false,
+ FILE_SUFFIX: '.html',
+ HAS_SOURCE: true
+ };
+ </script>
+ <script type="text/javascript" src="_static/jquery.js"></script>
+ <script type="text/javascript" src="_static/underscore.js"></script>
+ <script type="text/javascript" src="_static/doctools.js"></script>
+ <script type="text/javascript" src="https://c328740.ssl.cf1.rackcdn.com/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
+ <script type="text/javascript" src="_static/js/jquery-1.11.0.min.js"></script>
+ <script type="text/javascript" src="_static/js/jquery-fix.js"></script>
+ <script type="text/javascript" src="_static/bootstrap-3.2.0/js/bootstrap.min.js"></script>
+ <script type="text/javascript" src="_static/bootstrap-sphinx.js"></script>
+ <link rel="top" title="Image Harvest 1.0.1 documentation" href="#" />
+ <link rel="next" title="Introduction" href="introduction.html" />
+<meta charset='utf-8'>
+<meta http-equiv='X-UA-Compatible' content='IE=edge,chrome=1'>
+<meta name='viewport' content='width=device-width, initial-scale=1.0, maximum-scale=1'>
+<meta name="apple-mobile-web-app-capable" content="yes">
+
+ </head>
+ <body role="document">
+
+ <div id="navbar" class="navbar navbar-default navbar-fixed-top">
+ <div class="container">
+ <div class="navbar-header">
+ <!-- .btn-navbar is used as the toggle for collapsed navbar content -->
+ <button type="button" class="navbar-toggle" data-toggle="collapse" data-target=".nav-collapse">
+ <span class="icon-bar"></span>
+ <span class="icon-bar"></span>
+ <span class="icon-bar"></span>
+ </button>
+ <a class="navbar-brand" href="#">
+ Image Harvest</a>
+ <span class="navbar-text navbar-version pull-left"><b>1.0</b></span>
+ </div>
+
+ <div class="collapse navbar-collapse nav-collapse">
+ <ul class="nav navbar-nav">
+
+
+ <li class="dropdown globaltoc-container">
+ <a role="button"
+ id="dLabelGlobalToc"
+ data-toggle="dropdown"
+ data-target="#"
+ href="#">Site <b class="caret"></b></a>
+ <ul class="dropdown-menu globaltoc"
+ role="menu"
+ aria-labelledby="dLabelGlobalToc"><ul>
+<li class="toctree-l1"><a class="reference internal" href="introduction.html">Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="installation.html">Installation</a></li>
+<li class="toctree-l1"><a class="reference internal" href="start.html">Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="ex_script_core1.html">Core Processing Example #1</a></li>
+<li class="toctree-l1"><a class="reference internal" href="ex_script_core2.html">Core Processing Example #2</a></li>
+<li class="toctree-l1"><a class="reference internal" href="ex_script_color1.html">Color Filter In Depth #1</a></li>
+<li class="toctree-l1"><a class="reference internal" href="ex_workflow_1.html">Workflow Example #1</a></li>
+<li class="toctree-l1"><a class="reference internal" href="examples.html">Examples</a></li>
+<li class="toctree-l1"><a class="reference internal" href="processing.html">Image Processing</a></li>
+<li class="toctree-l1"><a class="reference internal" href="viewer.html">Image Processing Viewer</a></li>
+<li class="toctree-l1"><a class="reference internal" href="statistics.html">Statistics</a></li>
+<li class="toctree-l1"><a class="reference internal" href="indexing.html">Image Loading</a></li>
+<li class="toctree-l1"><a class="reference internal" href="workflowimage.html">Image Processing Workflows</a></li>
+<li class="toctree-l1"><a class="reference internal" href="workflowstats.html">Statistics Workflows</a></li>
+</ul>
+</ul>
+</li>
+
+ <li class="dropdown">
+ <a role="button"
+ id="dLabelLocalToc"
+ data-toggle="dropdown"
+ data-target="#"
+ href="#">Page <b class="caret"></b></a>
+ <ul class="dropdown-menu localtoc"
+ role="menu"
+ aria-labelledby="dLabelLocalToc"><ul>
+<li><a class="reference internal" href="#">Welcome to Image Harvest documentation!</a></li>
+<li><a class="reference internal" href="#indices-and-tables">Indices and tables</a></li>
+</ul>
+</ul>
+</li>
+
+
+
+
+
+ <li>
+ <a href="introduction.html" title="Next Chapter: Introduction"><span class="glyphicon glyphicon-chevron-right visible-sm"></span><span class="hidden-sm hidden-tablet">Introduction »</span>
+ </a>
+ </li>
+
+
+
+
+
+ <li class="hidden-sm">
+<div id="sourcelink">
+ <a href="_sources/index.txt"
+ rel="nofollow">Source</a>
+</div></li>
+
+ </ul>
+
+
+
+<form class="navbar-form navbar-right" action="search.html" method="get">
+ <div class="form-group">
+ <input type="text" name="q" class="form-control" placeholder="Search" />
+ </div>
+ <input type="hidden" name="check_keywords" value="yes" />
+ <input type="hidden" name="area" value="default" />
+</form>
+
+ </div>
+ </div>
+ </div>
+
+<div class="container">
+ <div class="row">
+ <div class="col-md-12">
+
+ <div class="section" id="welcome-to-image-harvest-documentation">
+<h1>Welcome to Image Harvest documentation!<a class="headerlink" href="#welcome-to-image-harvest-documentation" title="Permalink to this headline">¶</a></h1>
+<p>Link to GitHub: <a class="reference external" href="https://git.unl.edu/aknecht2/ih/">ih</a></p>
+<p>Contents:</p>
+<div class="toctree-wrapper compound">
+<ul>
+<li class="toctree-l1"><a class="reference internal" href="introduction.html">Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="installation.html">Installation</a><ul>
+<li class="toctree-l2"><a class="reference internal" href="installation.html#dependencies">Dependencies</a></li>
+<li class="toctree-l2"><a class="reference internal" href="installation.html#centos-6-5">Centos 6.5</a></li>
+<li class="toctree-l2"><a class="reference internal" href="installation.html#ubuntu-12-04">Ubuntu 12.04</a></li>
+<li class="toctree-l2"><a class="reference internal" href="installation.html#mac-osx">Mac OSX</a></li>
+<li class="toctree-l2"><a class="reference internal" href="installation.html#windows">Windows</a></li>
+</ul>
+</li>
+<li class="toctree-l1"><a class="reference internal" href="start.html">Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="examples.html">Examples</a><ul>
+<li class="toctree-l2"><a class="reference internal" href="examples.html#script-examples">Script Examples</a></li>
+<li class="toctree-l2"><a class="reference internal" href="examples.html#workflow-examples">Workflow Examples</a></li>
+</ul>
+</li>
+<li class="toctree-l1"><a class="reference internal" href="processing.html">Image Processing</a></li>
+<li class="toctree-l1"><a class="reference internal" href="viewer.html">Image Processing Viewer</a></li>
+<li class="toctree-l1"><a class="reference internal" href="statistics.html">Statistics</a></li>
+<li class="toctree-l1"><a class="reference internal" href="indexing.html">Image Loading</a></li>
+<li class="toctree-l1"><a class="reference internal" href="workflowimage.html">Image Processing Workflows</a></li>
+<li class="toctree-l1"><a class="reference internal" href="workflowstats.html">Statistics Workflows</a></li>
+</ul>
+</div>
+</div>
+<div class="section" id="indices-and-tables">
+<h1>Indices and tables<a class="headerlink" href="#indices-and-tables" title="Permalink to this headline">¶</a></h1>
+<ul class="simple">
+<li><a class="reference internal" href="genindex.html"><em>Index</em></a></li>
+<li><a class="reference internal" href="py-modindex.html"><em>Module Index</em></a></li>
+<li><a class="reference internal" href="search.html"><em>Search Page</em></a></li>
+</ul>
+</div>
+
+
+ </div>
+
+ </div>
+</div>
+<footer class="footer">
+ <div class="container">
+ <p class="pull-right">
+ <a href="#">Back to top</a>
+
+ </p>
+ <p>
+ © Copyright 2015, Avi Knecht.<br/>
+ Created using <a href="http://sphinx.pocoo.org/">Sphinx</a> 1.3a0.<br/>
+ </p>
+ </div>
+</footer>
+ </body>
+</html>
\ No newline at end of file
diff --git a/docs/build/html/indexing.html b/docs/build/html/indexing.html
new file mode 100644
index 0000000000000000000000000000000000000000..e6b89964cdc1dfd804103b53f7e180e20ddb2471
--- /dev/null
+++ b/docs/build/html/indexing.html
@@ -0,0 +1,187 @@
+<!DOCTYPE html>
+
+
+<html xmlns="http://www.w3.org/1999/xhtml">
+ <head>
+ <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
+
+ <title>Image Loading — Image Harvest 1.0.1 documentation</title>
+
+ <link rel="stylesheet" href="_static/basic.css" type="text/css" />
+ <link rel="stylesheet" href="_static/pygments.css" type="text/css" />
+ <link rel="stylesheet" href="_static/bootstrap-3.2.0/css/bootstrap.min.css" type="text/css" />
+ <link rel="stylesheet" href="_static/bootstrap-3.2.0/css/bootstrap-theme.min.css" type="text/css" />
+ <link rel="stylesheet" href="_static/bootstrap-sphinx.css" type="text/css" />
+
+ <script type="text/javascript">
+ var DOCUMENTATION_OPTIONS = {
+ URL_ROOT: './',
+ VERSION: '1.0.1',
+ COLLAPSE_INDEX: false,
+ FILE_SUFFIX: '.html',
+ HAS_SOURCE: true
+ };
+ </script>
+ <script type="text/javascript" src="_static/jquery.js"></script>
+ <script type="text/javascript" src="_static/underscore.js"></script>
+ <script type="text/javascript" src="_static/doctools.js"></script>
+ <script type="text/javascript" src="https://c328740.ssl.cf1.rackcdn.com/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
+ <script type="text/javascript" src="_static/js/jquery-1.11.0.min.js"></script>
+ <script type="text/javascript" src="_static/js/jquery-fix.js"></script>
+ <script type="text/javascript" src="_static/bootstrap-3.2.0/js/bootstrap.min.js"></script>
+ <script type="text/javascript" src="_static/bootstrap-sphinx.js"></script>
+ <link rel="top" title="Image Harvest 1.0.1 documentation" href="index.html" />
+ <link rel="next" title="Image Processing Workflows" href="workflowimage.html" />
+ <link rel="prev" title="Statistics" href="statistics.html" />
+<meta charset='utf-8'>
+<meta http-equiv='X-UA-Compatible' content='IE=edge,chrome=1'>
+<meta name='viewport' content='width=device-width, initial-scale=1.0, maximum-scale=1'>
+<meta name="apple-mobile-web-app-capable" content="yes">
+
+ </head>
+ <body role="document">
+
+ <div id="navbar" class="navbar navbar-default navbar-fixed-top">
+ <div class="container">
+ <div class="navbar-header">
+ <!-- .btn-navbar is used as the toggle for collapsed navbar content -->
+ <button type="button" class="navbar-toggle" data-toggle="collapse" data-target=".nav-collapse">
+ <span class="icon-bar"></span>
+ <span class="icon-bar"></span>
+ <span class="icon-bar"></span>
+ </button>
+ <a class="navbar-brand" href="index.html">
+ Image Harvest</a>
+ <span class="navbar-text navbar-version pull-left"><b>1.0</b></span>
+ </div>
+
+ <div class="collapse navbar-collapse nav-collapse">
+ <ul class="nav navbar-nav">
+
+
+ <li class="dropdown globaltoc-container">
+ <a role="button"
+ id="dLabelGlobalToc"
+ data-toggle="dropdown"
+ data-target="#"
+ href="index.html">Site <b class="caret"></b></a>
+ <ul class="dropdown-menu globaltoc"
+ role="menu"
+ aria-labelledby="dLabelGlobalToc"><ul class="current">
+<li class="toctree-l1"><a class="reference internal" href="introduction.html">Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="installation.html">Installation</a></li>
+<li class="toctree-l1"><a class="reference internal" href="start.html">Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="ex_script_core1.html">Core Processing Example #1</a></li>
+<li class="toctree-l1"><a class="reference internal" href="ex_script_core2.html">Core Processing Example #2</a></li>
+<li class="toctree-l1"><a class="reference internal" href="ex_script_color1.html">Color Filter In Depth #1</a></li>
+<li class="toctree-l1"><a class="reference internal" href="ex_workflow_1.html">Workflow Example #1</a></li>
+<li class="toctree-l1"><a class="reference internal" href="examples.html">Examples</a></li>
+<li class="toctree-l1"><a class="reference internal" href="processing.html">Image Processing</a></li>
+<li class="toctree-l1"><a class="reference internal" href="viewer.html">Image Processing Viewer</a></li>
+<li class="toctree-l1"><a class="reference internal" href="statistics.html">Statistics</a></li>
+<li class="toctree-l1 current"><a class="current reference internal" href="">Image Loading</a></li>
+<li class="toctree-l1"><a class="reference internal" href="workflowimage.html">Image Processing Workflows</a></li>
+<li class="toctree-l1"><a class="reference internal" href="workflowstats.html">Statistics Workflows</a></li>
+</ul>
+</ul>
+</li>
+
+ <li class="dropdown">
+ <a role="button"
+ id="dLabelLocalToc"
+ data-toggle="dropdown"
+ data-target="#"
+ href="#">Page <b class="caret"></b></a>
+ <ul class="dropdown-menu localtoc"
+ role="menu"
+ aria-labelledby="dLabelLocalToc"><ul>
+<li><a class="reference internal" href="#">Image Loading</a></li>
+</ul>
+</ul>
+</li>
+
+
+
+
+
+ <li>
+ <a href="statistics.html" title="Previous Chapter: Statistics"><span class="glyphicon glyphicon-chevron-left visible-sm"></span><span class="hidden-sm hidden-tablet">« Statistics</span>
+ </a>
+ </li>
+ <li>
+ <a href="workflowimage.html" title="Next Chapter: Image Processing Workflows"><span class="glyphicon glyphicon-chevron-right visible-sm"></span><span class="hidden-sm hidden-tablet">Image Processing... »</span>
+ </a>
+ </li>
+
+
+
+
+
+ <li class="hidden-sm">
+<div id="sourcelink">
+ <a href="_sources/indexing.txt"
+ rel="nofollow">Source</a>
+</div></li>
+
+ </ul>
+
+
+
+<form class="navbar-form navbar-right" action="search.html" method="get">
+ <div class="form-group">
+ <input type="text" name="q" class="form-control" placeholder="Search" />
+ </div>
+ <input type="hidden" name="check_keywords" value="yes" />
+ <input type="hidden" name="area" value="default" />
+</form>
+
+ </div>
+ </div>
+ </div>
+
+<div class="container">
+ <div class="row">
+ <div class="col-md-12">
+
+ <div class="section" id="image-loading">
+<h1>Image Loading<a class="headerlink" href="#image-loading" title="Permalink to this headline">¶</a></h1>
+<dl class="class">
+<dt id="ih.workflow.ImageLoader">
+<em class="property">class </em><code class="descclassname">ih.workflow.</code><code class="descname">ImageLoader</code><span class="sig-paren">(</span><em>template</em>, <em>output</em>, <em>validOnly=False</em>, <em>overwrite=False</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/ih/workflow.html#ImageLoader"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#ih.workflow.ImageLoader" title="Permalink to this definition">¶</a></dt>
+<dd><p>This should handle all meta-data definitions</p>
+<dl class="method">
+<dt id="ih.workflow.ImageLoader.crawl">
+<code class="descname">crawl</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="_modules/ih/workflow.html#ImageLoader.crawl"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#ih.workflow.ImageLoader.crawl" title="Permalink to this definition">¶</a></dt>
+<dd><p>Recursively walks through directories in base, and loads
+the appropriate data.</p>
+</dd></dl>
+
+<dl class="method">
+<dt id="ih.workflow.ImageLoader.write">
+<code class="descname">write</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="_modules/ih/workflow.html#ImageLoader.write"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#ih.workflow.ImageLoader.write" title="Permalink to this definition">¶</a></dt>
+<dd><p>Writes the data loaded from crawl into csv format based on ‘order’</p>
+</dd></dl>
+
+</dd></dl>
+
+</div>
+
+
+ </div>
+
+ </div>
+</div>
+<footer class="footer">
+ <div class="container">
+ <p class="pull-right">
+ <a href="#">Back to top</a>
+
+ </p>
+ <p>
+ © Copyright 2015, Avi Knecht.<br/>
+ Created using <a href="http://sphinx.pocoo.org/">Sphinx</a> 1.3a0.<br/>
+ </p>
+ </div>
+</footer>
+ </body>
+</html>
\ No newline at end of file
diff --git a/docs/build/html/installation.html b/docs/build/html/installation.html
new file mode 100644
index 0000000000000000000000000000000000000000..66441b68a193bb40441850ab2c2f05f077e3fcb6
--- /dev/null
+++ b/docs/build/html/installation.html
@@ -0,0 +1,407 @@
+<!DOCTYPE html>
+
+
+<html xmlns="http://www.w3.org/1999/xhtml">
+ <head>
+ <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
+
+ <title>Installation — Image Harvest 1.0.1 documentation</title>
+
+ <link rel="stylesheet" href="_static/basic.css" type="text/css" />
+ <link rel="stylesheet" href="_static/pygments.css" type="text/css" />
+ <link rel="stylesheet" href="_static/bootstrap-3.2.0/css/bootstrap.min.css" type="text/css" />
+ <link rel="stylesheet" href="_static/bootstrap-3.2.0/css/bootstrap-theme.min.css" type="text/css" />
+ <link rel="stylesheet" href="_static/bootstrap-sphinx.css" type="text/css" />
+
+ <script type="text/javascript">
+ var DOCUMENTATION_OPTIONS = {
+ URL_ROOT: './',
+ VERSION: '1.0.1',
+ COLLAPSE_INDEX: false,
+ FILE_SUFFIX: '.html',
+ HAS_SOURCE: true
+ };
+ </script>
+ <script type="text/javascript" src="_static/jquery.js"></script>
+ <script type="text/javascript" src="_static/underscore.js"></script>
+ <script type="text/javascript" src="_static/doctools.js"></script>
+ <script type="text/javascript" src="https://c328740.ssl.cf1.rackcdn.com/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
+ <script type="text/javascript" src="_static/js/jquery-1.11.0.min.js"></script>
+ <script type="text/javascript" src="_static/js/jquery-fix.js"></script>
+ <script type="text/javascript" src="_static/bootstrap-3.2.0/js/bootstrap.min.js"></script>
+ <script type="text/javascript" src="_static/bootstrap-sphinx.js"></script>
+ <link rel="top" title="Image Harvest 1.0.1 documentation" href="index.html" />
+ <link rel="next" title="Getting Started" href="start.html" />
+ <link rel="prev" title="Introduction" href="introduction.html" />
+<meta charset='utf-8'>
+<meta http-equiv='X-UA-Compatible' content='IE=edge,chrome=1'>
+<meta name='viewport' content='width=device-width, initial-scale=1.0, maximum-scale=1'>
+<meta name="apple-mobile-web-app-capable" content="yes">
+
+ </head>
+ <body role="document">
+
+ <div id="navbar" class="navbar navbar-default navbar-fixed-top">
+ <div class="container">
+ <div class="navbar-header">
+ <!-- .btn-navbar is used as the toggle for collapsed navbar content -->
+ <button type="button" class="navbar-toggle" data-toggle="collapse" data-target=".nav-collapse">
+ <span class="icon-bar"></span>
+ <span class="icon-bar"></span>
+ <span class="icon-bar"></span>
+ </button>
+ <a class="navbar-brand" href="index.html">
+ Image Harvest</a>
+ <span class="navbar-text navbar-version pull-left"><b>1.0</b></span>
+ </div>
+
+ <div class="collapse navbar-collapse nav-collapse">
+ <ul class="nav navbar-nav">
+
+
+ <li class="dropdown globaltoc-container">
+ <a role="button"
+ id="dLabelGlobalToc"
+ data-toggle="dropdown"
+ data-target="#"
+ href="index.html">Site <b class="caret"></b></a>
+ <ul class="dropdown-menu globaltoc"
+ role="menu"
+ aria-labelledby="dLabelGlobalToc"><ul class="current">
+<li class="toctree-l1"><a class="reference internal" href="introduction.html">Introduction</a></li>
+<li class="toctree-l1 current"><a class="current reference internal" href="">Installation</a></li>
+<li class="toctree-l1"><a class="reference internal" href="start.html">Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="ex_script_core1.html">Core Processing Example #1</a></li>
+<li class="toctree-l1"><a class="reference internal" href="ex_script_core2.html">Core Processing Example #2</a></li>
+<li class="toctree-l1"><a class="reference internal" href="ex_script_color1.html">Color Filter In Depth #1</a></li>
+<li class="toctree-l1"><a class="reference internal" href="ex_workflow_1.html">Workflow Example #1</a></li>
+<li class="toctree-l1"><a class="reference internal" href="examples.html">Examples</a></li>
+<li class="toctree-l1"><a class="reference internal" href="processing.html">Image Processing</a></li>
+<li class="toctree-l1"><a class="reference internal" href="viewer.html">Image Processing Viewer</a></li>
+<li class="toctree-l1"><a class="reference internal" href="statistics.html">Statistics</a></li>
+<li class="toctree-l1"><a class="reference internal" href="indexing.html">Image Loading</a></li>
+<li class="toctree-l1"><a class="reference internal" href="workflowimage.html">Image Processing Workflows</a></li>
+<li class="toctree-l1"><a class="reference internal" href="workflowstats.html">Statistics Workflows</a></li>
+</ul>
+</ul>
+</li>
+
+ <li class="dropdown">
+ <a role="button"
+ id="dLabelLocalToc"
+ data-toggle="dropdown"
+ data-target="#"
+ href="#">Page <b class="caret"></b></a>
+ <ul class="dropdown-menu localtoc"
+ role="menu"
+ aria-labelledby="dLabelLocalToc"><ul>
+<li><a class="reference internal" href="#">Installation</a><ul>
+<li><a class="reference internal" href="#dependencies">Dependencies</a></li>
+<li><a class="reference internal" href="#centos-6-5">Centos 6.5</a><ul>
+<li><a class="reference internal" href="#with-anaconda">With Anaconda</a></li>
+</ul>
+</li>
+<li><a class="reference internal" href="#ubuntu-12-04">Ubuntu 12.04</a><ul>
+<li><a class="reference internal" href="#id1">With Anaconda</a></li>
+</ul>
+</li>
+<li><a class="reference internal" href="#mac-osx">Mac OSX</a></li>
+<li><a class="reference internal" href="#windows">Windows</a></li>
+</ul>
+</li>
+</ul>
+</ul>
+</li>
+
+
+
+
+
+ <li>
+ <a href="introduction.html" title="Previous Chapter: Introduction"><span class="glyphicon glyphicon-chevron-left visible-sm"></span><span class="hidden-sm hidden-tablet">« Introduction</span>
+ </a>
+ </li>
+ <li>
+ <a href="start.html" title="Next Chapter: Getting Started"><span class="glyphicon glyphicon-chevron-right visible-sm"></span><span class="hidden-sm hidden-tablet">Getting Started »</span>
+ </a>
+ </li>
+
+
+
+
+
+ <li class="hidden-sm">
+<div id="sourcelink">
+ <a href="_sources/installation.txt"
+ rel="nofollow">Source</a>
+</div></li>
+
+ </ul>
+
+
+
+<form class="navbar-form navbar-right" action="search.html" method="get">
+ <div class="form-group">
+ <input type="text" name="q" class="form-control" placeholder="Search" />
+ </div>
+ <input type="hidden" name="check_keywords" value="yes" />
+ <input type="hidden" name="area" value="default" />
+</form>
+
+ </div>
+ </div>
+ </div>
+
+<div class="container">
+ <div class="row">
+ <div class="col-md-12">
+
+ <div class="section" id="installation">
+<h1>Installation<a class="headerlink" href="#installation" title="Permalink to this headline">¶</a></h1>
+<p>It is recommended to use the latest stable version for each of the dependencies. Package
+manager software is sometimes behind, so for some dependencies you may have to download and
+install a more recent version. Many systems come with a development tools package which
+should be installed. Most of the requirements below requires a c and c++ compiler, and some
+require a fortran compiler.</p>
+<div class="section" id="dependencies">
+<h2>Dependencies<a class="headerlink" href="#dependencies" title="Permalink to this headline">¶</a></h2>
+<ul>
+<li><p class="first"><a class="reference external" href="http://matplotlib.org/">Matplotlib</a> >= 1.3.1</p>
+</li>
+<li><p class="first"><a class="reference external" href="http://www.numpy.org/">NumPy</a> >= 1.7</p>
+</li>
+<li><dl class="first docutils">
+<dt><a class="reference external" href="http://opencv.org/">OpenCV</a> == 2.4.x</dt>
+<dd><ul class="first last simple">
+<li>GTK2 (including headers) >= 2.24</li>
+<li>blas >= 3.2.1</li>
+<li>lapack >= 3.2.1</li>
+<li>libav >= 0.5.3</li>
+<li>cmake >= 2.8.12</li>
+<li><a class="reference external" href="https://www.ffmpeg.org/">ffmpeg</a> >= 2.0.5</li>
+</ul>
+</dd>
+</dl>
+</li>
+<li><dl class="first docutils">
+<dt><a class="reference external" href="http://pandas.pydata.org/">Pandas</a> >= 0.13.1</dt>
+<dd><ul class="first last simple">
+<li><a class="reference external" href="http://cython.org/">Cython</a> >= 0.21.1</li>
+<li><a class="reference external" href="https://labix.org/python-dateutil">python-dateutil</a> >= 1.4.1</li>
+</ul>
+</dd>
+</dl>
+</li>
+<li><p class="first"><a class="reference external" href="https://code.google.com/p/pymeanshift/">PyMeanShift</a> >= 0.2.0</p>
+</li>
+<li><p class="first"><a class="reference external" href="http://www.scipy.org/">SciPy</a> >= 0.13.1</p>
+</li>
+<li><dl class="first docutils">
+<dt><a class="reference external" href="http://pegasus.isi.edu/">Pegasus</a> >= 4.4.0</dt>
+<dd><ul class="first last simple">
+<li>Java >= 1.8</li>
+<li>Perl >= 5.10</li>
+</ul>
+</dd>
+</dl>
+</li>
+<li><p class="first"><a class="reference external" href="http://research.cs.wisc.edu/htcondor/">HTCondor</a> >= 8.3.0</p>
+</li>
+</ul>
+<p>Pegasus and HTCondor are only required if you wish to use the super computer workflow generation functionality.
+Additionally, many super computing environments may already have Pegasus, HTCondor, and other
+dependencies installed. There are resources available for quickly installing the <a class="reference external" href="http://www.scipy.org/install.html">SciPy Stack</a>,
+which includes the NumPy, SciPy, Pandas, and Matplotlib. The installation tutorials for Mac OSX, and Windows
+specifically leave out Pegasus and HTCondor, as they are expected to be machines for local testing, not for
+submitting grid jobs. Finally, Image Harvest can be installed by downloading a zip file from the repo
+(<a class="reference external" href="https://git.unl.edu/aknecht2/ih">link</a>), and running ‘python setup.py install’.</p>
+</div>
+<div class="section" id="centos-6-5">
+<h2>Centos 6.5<a class="headerlink" href="#centos-6-5" title="Permalink to this headline">¶</a></h2>
+<p>It is <strong>highly</strong> recommended that you use anaconda (or another python package manager such as pip) to install the python packages. The installation
+process becomes much simpler and faster.</p>
+<div class="section" id="with-anaconda">
+<h3>With Anaconda<a class="headerlink" href="#with-anaconda" title="Permalink to this headline">¶</a></h3>
+<div class="highlight-bash"><div class="highlight"><pre><span class="c"># Update</span>
+sudo yum -y update
+
+<span class="c"># Set up condor repo</span>
+<span class="nb">cd</span> /etc/yum.repos.d
+sudo wget http://research.cs.wisc.edu/htcondor/yum/repo.d/htcondor-stable-rhel6.repo
+sudo wget http://research.cs.wisc.edu/htcondor/yum/RPM-GPG-KEY-HTCondor
+sudo rpm --import RPM-GPG-KEY-HTCondor
+
+<span class="c"># Install packages</span>
+sudo yum -y install java-1.8.0-* perl condor.x86_64
+
+<span class="c"># Download Pegasus</span>
+wget -O pegasus.tar.gz http://download.pegasus.isi.edu/pegasus/4.4.0/pegasus-worker-4.4.0-x86_64_rhel_6.tar.gz
+tar -zxvf pegasus.tar.gz
+
+<span class="c"># Download and install anaconda</span>
+wget -O anaconda.sh http://09c8d0b2229f813c1b93-c95ac804525aac4b6dba79b00b39d1d3.r79.cf1.rackcdn.com/Anaconda-2.1.0-Linux-x86_64.sh
+bash anaconda.sh -b
+
+<span class="c"># Install *almost* everything in one line</span>
+conda install numpy scipy pandas matplotlib opencv
+
+<span class="c"># Download PyMeanShift and install, assuming directory is 'pymeanshift'</span>
+<span class="nb">cd </span>pymeanshift
+sudo python setup.py install
+
+<span class="c"># Install Image Harvest, assuming directory is 'ih.git'</span>
+<span class="nb">cd </span>ih.git
+sudo python setup.py install
+
+<span class="c"># Make sure to move the pegasus python files into the anaconda package folder</span>
+<span class="c"># Update the following command as necessary</span>
+cp -r pegasus-4.4.0/lib64/python2.6/site-packages/Pegasus ~/anaconda/lib/python2.7/site-packages/
+<span class="c"># and to update your bash profile to include the pegasus commands,</span>
+<span class="c"># or cp the pegasus commands to /usr/bin or /usr/local/bin</span>
+cp pegasus-4.4.0/bin/* /usr/bin/
+</pre></div>
+</div>
+</div>
+</div>
+<div class="section" id="ubuntu-12-04">
+<h2>Ubuntu 12.04<a class="headerlink" href="#ubuntu-12-04" title="Permalink to this headline">¶</a></h2>
+<p>It is <strong>highly</strong> recommended that you use anaconda (or another python package manager such as pip) to install the python packages. The installation
+process becomes much simpler and faster.</p>
+<div class="section" id="id1">
+<h3>With Anaconda<a class="headerlink" href="#id1" title="Permalink to this headline">¶</a></h3>
+<div class="highlight-bash"><div class="highlight"><pre><span class="c"># Update</span>
+sudo apt-get -y update
+
+<span class="c"># Install build-essential</span>
+sudo apt-get -y install build-essential
+
+<span class="c"># Setup condor repository</span>
+sudo bash -c <span class="s1">'echo "deb http://research.cs.wisc.edu/htcondor/debian/stable/ wheezy contrib" >> /etc/apt/sources.list'</span>
+wget -qO - http://research.cs.wisc.edu/htcondor/debian/HTCondor-Release.gpg.key <span class="p">|</span> sudo apt-key add -
+sudo apt-get -y update
+sudo apt-get install condor
+
+<span class="c"># Install dependencies</span>
+sudo apt-get -y install software-properties-common python-software-properties perl
+sudo add-apt-repository -y ppa:webupd8team/java
+sudo apt-get update
+sudo apt-get -y install oracle-java8-installer
+<span class="c"># A license agrement will pop up here...</span>
+
+
+<span class="c"># Download pegasus</span>
+wget http://download.pegasus.isi.edu/pegasus/4.4.0/pegasus_4.4.0-1+deb7_amd64.deb
+tar -zxvf pegasus.tar.gz
+
+<span class="c"># Download and install anaconda</span>
+wget -O anaconda.sh http://09c8d0b2229f813c1b93-c95ac804525aac4b6dba79b00b39d1d3.r79.cf1.rackcdn.com/Anaconda-2.1.0-Linux-x86_64.sh
+bash anaconda.sh -b
+
+<span class="c"># Install *almost* everything in one line</span>
+conda install numpy scipy pandas matplotlib opencv
+
+<span class="c"># Download PyMeanShift and install, assuming directory is 'pymeanshift'</span>
+<span class="nb">cd </span>pymeanshift
+sudo python setup.py install
+
+<span class="c"># Install Image Harvest, assuming directory is 'ih.git'</span>
+<span class="nb">cd </span>ih.git
+sudo python setup.py install
+
+<span class="c"># Make sure to move the pegasus python files into the anaconda package folder</span>
+<span class="c"># Update the following command as necessary</span>
+cp -r pegasus-4.4.0/lib64/python2.6/site-packages/Pegasus ~/anaconda/lib/python2.7/site-packages/
+<span class="c"># and to update your bash profile to include the pegasus commands,</span>
+<span class="c"># or cp the pegasus commands to /usr/bin or /usr/local/bin</span>
+cp pegasus-4.4.0/bin/* /usr/bin/
+</pre></div>
+</div>
+</div>
+</div>
+<div class="section" id="mac-osx">
+<h2>Mac OSX<a class="headerlink" href="#mac-osx" title="Permalink to this headline">¶</a></h2>
+<p>Installation for local testing is a breeze with <a class="reference external" href="http://brew.sh">brew</a>. Installing
+brew simply requires copying a line into a terminal. The only two packages
+you need to manual download will be PyMeanShift and Image Harvest.
+NOTE: You will have to install XCode, and the XCode Command Line Tools if you have not already. It’s a free download
+from the App Store.
+After you have downloaded the packages and installed brew, run the following:</p>
+<div class="highlight-bash"><div class="highlight"><pre><span class="c"># Install *almost* everything in one line</span>
+brew tap homebrew/science
+brew tap homebrew/python
+brew update <span class="o">&&</span> brew upgrade
+brew install numpy scipy matplotlib pandaseq opencv
+<span class="c"># You need to make sure your PYTHONPATH</span>
+<span class="c"># points to the installed packages.</span>
+<span class="c"># We point to the brew installed packages first,</span>
+<span class="c"># to make sure there are no conflicts with system python.</span>
+<span class="nb">export </span><span class="nv">PYTHONPATH</span><span class="o">=</span><span class="sb">`</span>brew --prefix<span class="sb">`</span>/lib/python2.7/site-packages/:<span class="nv">$PYTHONPATH</span>
+
+<span class="c"># Download PyMeanShift and install, assuming directory is 'pymeanshift'</span>
+<span class="nb">cd </span>pymeanshift
+sudo python setup.py install
+
+<span class="c"># Download Image Harvest and install, assuming directory is 'ih.git'</span>
+<span class="nb">cd </span>ih.git
+sudo python setup.py install
+
+<span class="c"># That's it!</span>
+</pre></div>
+</div>
+</div>
+<div class="section" id="windows">
+<h2>Windows<a class="headerlink" href="#windows" title="Permalink to this headline">¶</a></h2>
+<p>Windows requires a little more work, and in fact, windows doesn’t even come with python.
+Installing requires adjusting some system settings as well. You will need to manually
+install several packages before <a class="reference external" href="https://pypi.python.org/pypi/pip">pip</a> can put
+in work. First, install <a class="reference external" href="https://www.python.org/downloads/">python2.7</a>. Next,
+you have to add python to your PATH environment variable.</p>
+<ul class="simple">
+<li>Windows 7: Right click on Computer > properties > Advanced system settings > Advanced Tab > Enviornment Variables</li>
+<li>Windows 8: Control Panel > System > Advanced system settings > Advanced Tab > Environment Variables</li>
+</ul>
+<p>You should see two boxes. One that says “User variables for <user>”, and the other that says
+“System variables”. Scroll through the “System variables” box until you find the ‘Path’ variable.
+It should look like lots of paths separated by semicolons. Edit Path, and add two new paths,
+‘C:\Python2.7\’ and ‘C:\Python2.7\Scripts\’. Make sure to keep each path separated by a semicolon.
+Next, you need to install a <a class="reference external" href="http://www.microsoft.com/en-us/download/details.aspx?id=44266">c++ compiler</a> –
+simply download the installer and run it.
+Finally, download and install <a class="reference external" href="https://pypi.python.org/pypi/pip">pip</a>. There should
+simply be a giant script you copy to a local file, and execute with python.</p>
+<p>Now, you can install all the dependent python packages by finding the correct version for your os,
+and downloading them from this <a class="reference external" href="http://www.lfd.uci.edu/~gohlke/pythonlibs/">link</a>. You will need the same
+list as above that is, numpy, scipy, pandas, matplotlib, and opencv.</p>
+<div class="highlight-bash"><div class="highlight"><pre><span class="c"># For each downloaded wheel file, you will</span>
+<span class="c"># need to run the following from a command prompt</span>
+pip install name.whl
+<span class="c"># Then, download pymeanshift and install, run installer.</span>
+<span class="c"># Then, download Image Harvest and install, assuming directory is 'ih.git'</span>
+<span class="nb">cd </span>ih.git
+python setup.py install
+</pre></div>
+</div>
+<p>One final note, when loading images, python expects forward slashes not back slashes,
+and does not expect the C: for absolute paths. If you have an image called “test.jpg”
+in your downloads folder, the correct path for python is “/Users/username/Downloads/test.jpg”.</p>
+</div>
+</div>
+
+
+ </div>
+
+ </div>
+</div>
+<footer class="footer">
+ <div class="container">
+ <p class="pull-right">
+ <a href="#">Back to top</a>
+
+ </p>
+ <p>
+ © Copyright 2015, Avi Knecht.<br/>
+ Created using <a href="http://sphinx.pocoo.org/">Sphinx</a> 1.3a0.<br/>
+ </p>
+ </div>
+</footer>
+ </body>
+</html>
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+<!DOCTYPE html>
+
+
+<html xmlns="http://www.w3.org/1999/xhtml">
+ <head>
+ <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
+
+ <title>Introduction — Image Harvest 1.0.1 documentation</title>
+
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+ <link rel="stylesheet" href="_static/bootstrap-sphinx.css" type="text/css" />
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+ var DOCUMENTATION_OPTIONS = {
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+<meta name='viewport' content='width=device-width, initial-scale=1.0, maximum-scale=1'>
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+
+ <div id="navbar" class="navbar navbar-default navbar-fixed-top">
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+ <span class="icon-bar"></span>
+ <span class="icon-bar"></span>
+ </button>
+ <a class="navbar-brand" href="index.html">
+ Image Harvest</a>
+ <span class="navbar-text navbar-version pull-left"><b>1.0</b></span>
+ </div>
+
+ <div class="collapse navbar-collapse nav-collapse">
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+
+
+ <li class="dropdown globaltoc-container">
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+<li class="toctree-l1 current"><a class="current reference internal" href="">Introduction</a></li>
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+<li class="toctree-l1"><a class="reference internal" href="start.html">Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="ex_script_core1.html">Core Processing Example #1</a></li>
+<li class="toctree-l1"><a class="reference internal" href="ex_script_core2.html">Core Processing Example #2</a></li>
+<li class="toctree-l1"><a class="reference internal" href="ex_script_color1.html">Color Filter In Depth #1</a></li>
+<li class="toctree-l1"><a class="reference internal" href="ex_workflow_1.html">Workflow Example #1</a></li>
+<li class="toctree-l1"><a class="reference internal" href="examples.html">Examples</a></li>
+<li class="toctree-l1"><a class="reference internal" href="processing.html">Image Processing</a></li>
+<li class="toctree-l1"><a class="reference internal" href="viewer.html">Image Processing Viewer</a></li>
+<li class="toctree-l1"><a class="reference internal" href="statistics.html">Statistics</a></li>
+<li class="toctree-l1"><a class="reference internal" href="indexing.html">Image Loading</a></li>
+<li class="toctree-l1"><a class="reference internal" href="workflowimage.html">Image Processing Workflows</a></li>
+<li class="toctree-l1"><a class="reference internal" href="workflowstats.html">Statistics Workflows</a></li>
+</ul>
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+ <li>
+ <a href="index.html" title="Previous Chapter: Welcome to Image Harvest documentation!"><span class="glyphicon glyphicon-chevron-left visible-sm"></span><span class="hidden-sm hidden-tablet">« Welcome to Image...</span>
+ </a>
+ </li>
+ <li>
+ <a href="installation.html" title="Next Chapter: Installation"><span class="glyphicon glyphicon-chevron-right visible-sm"></span><span class="hidden-sm hidden-tablet">Installation »</span>
+ </a>
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+
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+
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+<div id="sourcelink">
+ <a href="_sources/introduction.txt"
+ rel="nofollow">Source</a>
+</div></li>
+
+ </ul>
+
+
+
+<form class="navbar-form navbar-right" action="search.html" method="get">
+ <div class="form-group">
+ <input type="text" name="q" class="form-control" placeholder="Search" />
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+
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+
+<div class="container">
+ <div class="row">
+ <div class="col-md-12">
+
+ <div class="section" id="introduction">
+<h1>Introduction<a class="headerlink" href="#introduction" title="Permalink to this headline">¶</a></h1>
+<p>Image Harvest (ih) is an open-source <a class="reference external" href="https://www.python.org/">Python</a> library for processing and analyzing plant images.
+The software uses <a class="reference external" href="http://opencv.org/">OpenCV</a> for image processing, and <a class="reference external" href="http://www.scipy.org/">SciPy</a> for statistics.
+Besides inclusion of stand-alone scripts to access processing and statistics functions, ih is integrated with
+<a class="reference external" href="pegasus.isi.edu">Pegasus</a> to create and submit workflows to super computers.</p>
+<p>Many software tools already exist to perform image analysis. The ability to create distributed computing workflows
+is one of the features that makes ih distinct. Workflow generation is completely adaptable to any input, and can
+be customized using many different modular processing components.</p>
+<p>Image Harvest is a work in a progress. For any help, questions, or bugs, please contact: <a class="reference external" href="mailto:avi%40kurtknecht.com">avi<span>@</span>kurtknecht<span>.</span>com</a></p>
+</div>
+
+
+ </div>
+
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+ <div class="container">
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+
+ </p>
+ <p>
+ © Copyright 2015, Avi Knecht.<br/>
+ Created using <a href="http://sphinx.pocoo.org/">Sphinx</a> 1.3a0.<br/>
+ </p>
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+++ b/docs/build/html/processing.html
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+
+
+<html xmlns="http://www.w3.org/1999/xhtml">
+ <head>
+ <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
+
+ <title>Image Processing — Image Harvest 1.0.1 documentation</title>
+
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+ <link rel="stylesheet" href="_static/pygments.css" type="text/css" />
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+ <link rel="stylesheet" href="_static/bootstrap-sphinx.css" type="text/css" />
+
+ <script type="text/javascript">
+ var DOCUMENTATION_OPTIONS = {
+ URL_ROOT: './',
+ VERSION: '1.0.1',
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+ FILE_SUFFIX: '.html',
+ HAS_SOURCE: true
+ };
+ </script>
+ <script type="text/javascript" src="_static/jquery.js"></script>
+ <script type="text/javascript" src="_static/underscore.js"></script>
+ <script type="text/javascript" src="_static/doctools.js"></script>
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+ <link rel="top" title="Image Harvest 1.0.1 documentation" href="index.html" />
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+ <div class="section" id="image-processing">
+<h1>Image Processing<a class="headerlink" href="#image-processing" title="Permalink to this headline">¶</a></h1>
+<p>This page contains specific implementation details of image processing functions.
+Additionally, the next page contains an interactive image processing function viewer.
+It allows for adjusting inputs and seeing results of many different functions
+on several different sample input images.</p>
+<dl class="class">
+<dt id="ih.imgproc.Image">
+<em class="property">class </em><code class="descclassname">ih.imgproc.</code><code class="descname">Image</code><span class="sig-paren">(</span><em>input</em>, <em>outputdir='.'</em>, <em>writename=None</em>, <em>dev=False</em>, <em>db=None</em>, <em>dbid=None</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/ih/imgproc.html#Image"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#ih.imgproc.Image" title="Permalink to this definition">¶</a></dt>
+<dd><p>An individual image. Each image is loaded in as its own instance of the Image class for processing.</p>
+<dl class="method">
+<dt id="ih.imgproc.Image.adaptiveThreshold">
+<code class="descname">adaptiveThreshold</code><span class="sig-paren">(</span><em>value</em>, <em>adaptiveType</em>, <em>thresholdType</em>, <em>blockSize</em>, <em>C</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/ih/imgproc.html#Image.adaptiveThreshold"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#ih.imgproc.Image.adaptiveThreshold" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
+<li><strong>value</strong> – Intensity value for the pixels based on the thresholding conditions.</li>
+<li><strong>adaptiveType</strong> (<a class="reference external" href="http://docs.python.org/library/functions.html#str" title="(in Python v2.7)"><em>str</em></a>) – Adaptive algorithm to use, should be either ‘mean’ or ‘gaussian’.</li>
+<li><strong>thresholdType</strong> (<a class="reference external" href="http://docs.python.org/library/functions.html#str" title="(in Python v2.7)"><em>str</em></a>) – Threshold type, should be either ‘binary’ or ‘inverse’.</li>
+<li><strong>blockSize</strong> (<a class="reference external" href="http://docs.python.org/library/functions.html#int" title="(in Python v2.7)"><em>int</em></a>) – The window size to consider while thresholding, should only be an odd number.</li>
+<li><strong>C</strong> (<a class="reference external" href="http://docs.python.org/library/functions.html#int" title="(in Python v2.7)"><em>int</em></a>) – A constant subtracted from the calculated mean in each window.</li>
+</ul>
+</td>
+</tr>
+</tbody>
+</table>
+<p>Thresholds an image by considering the image in several different windows instead of the image
+as a whole. This function is a wrapper to the OpenCV function <a class="reference external" href="http://docs.opencv.org/modules/imgproc/doc/miscellaneous_transformations.html#adaptivethreshold">adaptiveThreshold</a>.
+Specifying ‘mean’ for adaptiveType calculates a simple mean of the area, wheras specifying ‘gaussian’ calculates a weighted sum
+based upon a <a class="reference external" href="http://docs.opencv.org/modules/imgproc/doc/filtering.html#MatgetGaussianKernel(intksize,doublesigma,intktype)">Gaussian Kernel</a>.
+Specifying ‘binary’ for thresholdType means that a particular intensity value must beat the threshold to be kept, whereas
+specifying ‘inverse’ means that a particular intensity value must lose to the threshold to be kept.
+Similar to a normal thresholding function, the image must be converted to grayscale first. This can be done using the
+<a class="reference internal" href="#ih.imgproc.Image.convertColor" title="ih.imgproc.Image.convertColor"><code class="xref py py-meth docutils literal"><span class="pre">convertColor()</span></code></a> function, however, if your image is of type ‘bgr’, this is handled automatically.</p>
+</dd></dl>
+
+<dl class="method">
+<dt id="ih.imgproc.Image.bitwise_and">
+<code class="descname">bitwise_and</code><span class="sig-paren">(</span><em>comp</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/ih/imgproc.html#Image.bitwise_and"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#ih.imgproc.Image.bitwise_and" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>comp</strong> (<em>str or np.ndarray</em>) – The comparison image.</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body">The resulting mask.</td>
+</tr>
+<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body">numpy.ndarray</td>
+</tr>
+</tbody>
+</table>
+<p>Performs logical AND between the input image and the comp image.
+The comp input is very versatile, and can be one of three input types,
+an image, a path, or a saved state. An image input is a raw numpy array,
+and this input type will be passed through to the function without modification.
+If a path is specified, ih attempts to load the file as an image, and pass it
+to the function. Finally, the input is checked against the currently saved
+image states. If it matches, the corresponding state is passed to the function.
+The function assumes that the two input images are of matching type –
+if they are not an error will be thrown. By default, images loaded from a
+path are loaded as ‘bgr’ type images.
+For more information on states, see <a class="reference internal" href="#ih.imgproc.Image.save" title="ih.imgproc.Image.save"><code class="xref py py-meth docutils literal"><span class="pre">save()</span></code></a>.</p>
+</dd></dl>
+
+<dl class="method">
+<dt id="ih.imgproc.Image.bitwise_not">
+<code class="descname">bitwise_not</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="_modules/ih/imgproc.html#Image.bitwise_not"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#ih.imgproc.Image.bitwise_not" title="Permalink to this definition">¶</a></dt>
+<dd><p>Inverts the image. If the given image has multiple channels (i.e. is a color image) each channel is processed independently.</p>
+</dd></dl>
+
+<dl class="method">
+<dt id="ih.imgproc.Image.bitwise_or">
+<code class="descname">bitwise_or</code><span class="sig-paren">(</span><em>comp</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/ih/imgproc.html#Image.bitwise_or"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#ih.imgproc.Image.bitwise_or" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>comp</strong> (<em>str or np.ndarray</em>) – The comparison image.</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body">The resulting mask.</td>
+</tr>
+<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body">numpy.ndarray</td>
+</tr>
+</tbody>
+</table>
+<p>Performs logical OR between the input image and the comp image.
+The comp input is very versatile, and can be one of three input types,
+an image, a path, or a saved state. An image input is a raw numpy array,
+and this input type will be passed through to the function without modification.
+If a path is specified, ih attempts to load the file as an image, and pass it
+to the function. Finally, the input is checked against the currently saved
+image states. If it matches, the corresponding state is passed to the function.
+The function assumes that the two input images are of matching type –
+if they are not an error will be thrown. By default, images loaded from a
+path are loaded as ‘bgr’ type images.
+For more information on states, see <a class="reference internal" href="#ih.imgproc.Image.save" title="ih.imgproc.Image.save"><code class="xref py py-meth docutils literal"><span class="pre">save()</span></code></a>.</p>
+</dd></dl>
+
+<dl class="method">
+<dt id="ih.imgproc.Image.bitwise_xor">
+<code class="descname">bitwise_xor</code><span class="sig-paren">(</span><em>comp</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/ih/imgproc.html#Image.bitwise_xor"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#ih.imgproc.Image.bitwise_xor" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>comp</strong> (<em>str or np.ndarray</em>) – The comparison image.</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body">The resulting mask.</td>
+</tr>
+<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body">numpy.ndarray</td>
+</tr>
+</tbody>
+</table>
+<p>Performs exclusive logical OR between the input image and the comp image.
+The comp input is very versatile, and can be one of three input types,
+an image, a path, or a saved state. An image input is a raw numpy array,
+and this input type will be passed through to the function without modification.
+If a path is specified, ih attempts to load the file as an image, and pass it
+to the function. Finally, the input is checked against the currently saved
+image states. If it matches, the corresponding state is passed to the function.
+The function assumes that the two input images are of matching type –
+if they are not an error will be thrown. By default, images loaded from a
+path are loaded as ‘bgr’ type images.
+For more information on states, see <a class="reference internal" href="#ih.imgproc.Image.save" title="ih.imgproc.Image.save"><code class="xref py py-meth docutils literal"><span class="pre">save()</span></code></a>.</p>
+</dd></dl>
+
+<dl class="method">
+<dt id="ih.imgproc.Image.blur">
+<code class="descname">blur</code><span class="sig-paren">(</span><em>ksize</em>, <em>anchor=(-1</em>, <em>-1)</em>, <em>borderType='default'</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/ih/imgproc.html#Image.blur"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#ih.imgproc.Image.blur" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
+<li><strong>ksize</strong> (<a class="reference external" href="http://docs.python.org/library/functions.html#tuple" title="(in Python v2.7)"><em>tuple</em></a>) – The size of the kernel represented by a tuple (width, height). Both numbers should be odd and positive.</li>
+<li><strong>anchor</strong> (<a class="reference external" href="http://docs.python.org/library/functions.html#tuple" title="(in Python v2.7)"><em>tuple</em></a>) – The anchor point for filtering. Default is (-1, -1) which is the center of the kernel.</li>
+<li><strong>borderType</strong> (<a class="reference external" href="http://docs.python.org/library/functions.html#str" title="(in Python v2.7)"><em>str</em></a>) – The type of border mode used to extrapolate pixels outside the image.</li>
+</ul>
+</td>
+</tr>
+</tbody>
+</table>
+<p>Smoothes an image using the normalized box filter. This function is a wrapper to the OpenCV function
+<a class="reference external" href="http://docs.opencv.org/modules/imgproc/doc/filtering.html#blur">blur</a>. Increasing the kernel size increase
+the window considered when applying a blur. The anchor by default is the center of the kernel,
+however you can alter the anchor to consider different areas of the kernel. When blurring on the edge
+of the image, values for pixels that would be outside of the image are extrapolated. The method
+of extrapolation depends on the specified ‘borderType’, and can be one of ‘default’, ‘constant’,
+‘reflect’, or ‘replicate’.</p>
+</dd></dl>
+
+<dl class="method">
+<dt id="ih.imgproc.Image.colorFilter">
+<code class="descname">colorFilter</code><span class="sig-paren">(</span><em>logic</em>, <em>roi=None</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/ih/imgproc.html#Image.colorFilter"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#ih.imgproc.Image.colorFilter" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
+<li><strong>logic</strong> (<a class="reference external" href="http://docs.python.org/library/functions.html#str" title="(in Python v2.7)"><em>str</em></a>) – The logic you want to run on the image.</li>
+<li><strong>roi</strong> (<em>list or roi file</em>) – The roi you want to apply the filter to</li>
+</ul>
+</td>
+</tr>
+</tbody>
+</table>
+<p>This function applies a color filter defined by the input logic, to a
+targeted region defined by the input roi. The roi is defined the same,
+[ystart, yend, xstart, xend]. The logic string itself is fairly complicated.
+The string supports the following characters: ‘+’, ‘-‘, ‘*’, ‘/’, ‘>’, ‘>=’,
+‘==’, ‘<’, ‘<=’, ‘and’, ‘or’, ‘(‘, ‘)’, ‘r’, ‘g’, ‘b’, ‘max’, and ‘min’ as well as any numeric
+value. The logic string itself must be well formed – each
+operation, arg1 operator arg2, must be surrounded by parenthesis, and the entire statement
+must be surrounded by parenthesis. For example,
+if you want to check the intensity of the pixel, your logic string would be:
+‘(((r + g) + b) < 100)’. This string in particular will only keep pixels whose
+intensity is less than 100. Similar rules apply for ‘and’ and ‘or’ operators.
+Let’s say we only want to keep pixels whose intensity is less than 100, OR both
+the red and blue channels are greater than 150, the logic string would be:
+‘((((r + g) + b) < 100) or ((r > 150) and (b > 150)))’. The more complex
+your logic is the harder it is to read, so you may want to consider breaking
+up complex filtering into multiple steps for readability. Finally, despite
+the fact this function solves arbitrary logic, it is very fast.</p>
+</dd></dl>
+
+<dl class="method">
+<dt id="ih.imgproc.Image.contourCut">
+<code class="descname">contourCut</code><span class="sig-paren">(</span><em>binary, basemin=100, padding=[0, 0, 0, 0], resize=False, returnBound=False, roiwrite='roi.json'</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/ih/imgproc.html#Image.contourCut"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#ih.imgproc.Image.contourCut" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
+<li><strong>binary</strong> (<em>str or np.ndarray</em>) – The binary image to find contours of.</li>
+<li><strong>basemin</strong> (<a class="reference external" href="http://docs.python.org/library/functions.html#int" title="(in Python v2.7)"><em>int</em></a>) – The minimum area a contour must have to be consider part of the foreground.</li>
+<li><strong>padding</strong> (<a class="reference external" href="http://docs.python.org/library/functions.html#int" title="(in Python v2.7)"><em>int</em></a>) – Padding add to all sides of the final roi.</li>
+<li><strong>returnBound</strong> (<a class="reference external" href="http://docs.python.org/library/functions.html#bool" title="(in Python v2.7)"><em>bool</em></a>) – If set, instead of cropping the image, simply write the detected roi.</li>
+<li><strong>resize</strong> (<a class="reference external" href="http://docs.python.org/library/functions.html#bool" title="(in Python v2.7)"><em>bool</em></a>) – Whether or not to resize the image.</li>
+</ul>
+</td>
+</tr>
+</tbody>
+</table>
+<p>This function crops an image based on the size of detected contours in the image –
+clusters of pixels in the image. The image is cropped such that all contours
+that are greater than the specified area are included in the final output image.
+image is cropped such that all contours that are greater than the specified area are
+included in the final output image. If returnBound is set, instead of actually
+cropping the image, the detected roi is written to a file instead. Otherwise,
+the detected roi is passed into the <a class="reference internal" href="#ih.imgproc.Image.crop" title="ih.imgproc.Image.crop"><code class="xref py py-meth docutils literal"><span class="pre">crop()</span></code></a> function,
+with the given resize value. This function is useful for getting accurate
+height and width of a specific plant, as well as removing outlying clusters
+of non-important pixels.</p>
+</dd></dl>
+
+<dl class="method">
+<dt id="ih.imgproc.Image.convertColor">
+<code class="descname">convertColor</code><span class="sig-paren">(</span><em>intype</em>, <em>outtype</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/ih/imgproc.html#Image.convertColor"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#ih.imgproc.Image.convertColor" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
+<li><strong>intype</strong> (<a class="reference external" href="http://docs.python.org/library/functions.html#str" title="(in Python v2.7)"><em>str</em></a>) – The input image type</li>
+<li><strong>outtype</strong> (<a class="reference external" href="http://docs.python.org/library/functions.html#str" title="(in Python v2.7)"><em>str</em></a>) – The output image type</li>
+</ul>
+</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">The converted image.</p>
+</td>
+</tr>
+<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><p class="first">numpy.ndarray</p>
+</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><p class="first last">KeyError</p>
+</td>
+</tr>
+</tbody>
+</table>
+<p>Converts the given image between color spaces, based on the given types.
+Supported types are: bgr, gray, hsv, lab, and ycrcb. Note, you cannot
+restore color to a gray image with this function, for that you must use
+bitwise_and with an appropriate mask + image.</p>
+</dd></dl>
+
+<dl class="method">
+<dt id="ih.imgproc.Image.crop">
+<code class="descname">crop</code><span class="sig-paren">(</span><em>roi</em>, <em>resize=False</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/ih/imgproc.html#Image.crop"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#ih.imgproc.Image.crop" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
+<li><strong>roi</strong> (<em>list or roi file</em>) – A list corresponding to the area of the image you want. List should be of the form [ystart, yend, xstart, xend]</li>
+<li><strong>resize</strong> (<a class="reference external" href="http://docs.python.org/library/functions.html#bool" title="(in Python v2.7)"><em>bool</em></a>) – If True, actually adjusts the size of the image, otherwise just draws over the part of the image not in the roi.</li>
+</ul>
+</td>
+</tr>
+</tbody>
+</table>
+<p>This function crops the image based on the given roi [ystart, yend, xstart, xend]. There are two crop options,
+by default, the function doesn’t actually resize the image. Instead, it sets each pixel not in the roi to black.
+If resize is set to True, the function will actually crop the image down to the roi.</p>
+</dd></dl>
+
+<dl class="method">
+<dt id="ih.imgproc.Image.destroy">
+<code class="descname">destroy</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="_modules/ih/imgproc.html#Image.destroy"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#ih.imgproc.Image.destroy" title="Permalink to this definition">¶</a></dt>
+<dd><p>Destroys all currently open windows.</p>
+</dd></dl>
+
+<dl class="method">
+<dt id="ih.imgproc.Image.edges">
+<code class="descname">edges</code><span class="sig-paren">(</span><em>threshold1</em>, <em>threshold2</em>, <em>apertureSize=3</em>, <em>L2gradient=False</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/ih/imgproc.html#Image.edges"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#ih.imgproc.Image.edges" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
+<li><strong>threshold1</strong> (<a class="reference external" href="http://docs.python.org/library/functions.html#int" title="(in Python v2.7)"><em>int</em></a>) – First threshold for the hysteresis procedure.</li>
+<li><strong>threshold2</strong> (<a class="reference external" href="http://docs.python.org/library/functions.html#int" title="(in Python v2.7)"><em>int</em></a>) – Second threshold for the hysteresis procedure.</li>
+<li><strong>apertureSize</strong> (<a class="reference external" href="http://docs.python.org/library/functions.html#int" title="(in Python v2.7)"><em>int</em></a>) – aperture size used for the Sobel algorithm. Must be odd, postive, and less than 8.</li>
+</ul>
+</td>
+</tr>
+<tr class="field-even field"><th class="field-name">L2gradient:</th><td class="field-body"><p class="first last">Used to calculate Image gradient magnitude, if true then <span class="math">\(L = \sqrt{(dI/dx)^2 + (dI/dy)^2}\)</span>, if false then <span class="math">\(L = dI/dx + dI/dy\)</span>.</p>
+</td>
+</tr>
+</tbody>
+</table>
+<p>This function calculates the edges of an image using the Canny edge detection algorithm, which is built upon the Sobel
+algorithm. This function is a wrapper to the OpenCV function <a class="reference external" href="http://docs.opencv.org/modules/imgproc/doc/feature_detection.html#canny">Canny</a>.</p>
+</dd></dl>
+
+<dl class="method">
+<dt id="ih.imgproc.Image.extractBins">
+<code class="descname">extractBins</code><span class="sig-paren">(</span><em>binlist</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/ih/imgproc.html#Image.extractBins"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#ih.imgproc.Image.extractBins" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>binlist</strong> (<a class="reference external" href="http://docs.python.org/library/functions.html#list" title="(in Python v2.7)"><em>list</em></a>) – The specified bins (color ranges) to count.</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body">The number of pixels that fall in each bin.</td>
+</tr>
+<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body">list</td>
+</tr>
+</tbody>
+</table>
+<p>This function counts the number of pixels that fall into the range as
+specified by each bin. This function expects the input to be a list of
+dictionaries as follows:</p>
+<div class="highlight-python"><div class="highlight"><pre> <span class="n">binlist</span> <span class="o">=</span> <span class="p">[</span>
+ <span class="p">{</span><span class="s">"name"</span><span class="p">:</span> <span class="s">"bin1"</span><span class="p">,</span>
+ <span class="s">"min"</span><span class="p">:</span> <span class="p">[</span><span class="n">B</span><span class="p">,</span> <span class="n">G</span><span class="p">,</span> <span class="n">R</span><span class="p">],</span>
+ <span class="s">"max"</span><span class="p">:</span> <span class="p">[</span><span class="n">B</span><span class="p">,</span> <span class="n">G</span><span class="p">,</span> <span class="n">R</span><span class="p">]</span>
+ <span class="p">},</span>
+ <span class="p">{</span><span class="s">"name"</span><span class="p">:</span> <span class="s">"bin2"</span><span class="p">,</span>
+ <span class="o">...</span>
+<span class="p">]</span>
+</pre></div>
+</div>
+<p>Each range is defined by 6 values. A minimum and maximum blue,
+green, and red value. The returned list is very similar to the
+input list, except a ‘count’ key is added to each dictionary:</p>
+<div class="highlight-python"><div class="highlight"><pre><span class="n">returnlist</span> <span class="o">=</span> <span class="p">[</span>
+ <span class="p">{</span><span class="s">"name"</span><span class="p">:</span> <span class="s">"bin1"</span><span class="p">,</span>
+ <span class="s">"min"</span><span class="p">:</span> <span class="p">[</span><span class="n">B</span><span class="p">,</span> <span class="n">G</span><span class="p">,</span> <span class="n">R</span><span class="p">],</span>
+ <span class="s">"max"</span><span class="p">:</span> <span class="p">[</span><span class="n">B</span><span class="p">,</span> <span class="n">G</span><span class="p">,</span> <span class="n">R</span><span class="p">],</span>
+ <span class="s">"count"</span><span class="p">:</span> <span class="n">VALUE</span>
+ <span class="p">},</span>
+ <span class="o">...</span>
+<span class="p">]</span>
+</pre></div>
+</div>
+<p>Where ‘VALUE’ is the number of pixels that fall into the
+corresponding range.
+A list is used instead of a dictionary as the base structure
+to maintain order for writing to the output database. When
+using this function within a workflow, the order you specify
+your bins is the order in which they will show up in the
+database, and the name you specify for you bin will be
+the column name in the database.</p>
+</dd></dl>
+
+<dl class="method">
+<dt id="ih.imgproc.Image.extractColorData">
+<code class="descname">extractColorData</code><span class="sig-paren">(</span><em>nonzero=True</em>, <em>returnhist=False</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/ih/imgproc.html#Image.extractColorData"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#ih.imgproc.Image.extractColorData" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>nonzero</strong> (<a class="reference external" href="http://docs.python.org/library/functions.html#bool" title="(in Python v2.7)"><em>bool</em></a>) – Whether or not to look at only nonzero pixels. Default true.</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body">Mean & median for each channel.</td>
+</tr>
+<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body">list</td>
+</tr>
+</tbody>
+</table>
+<p>This function calculates a normalized histogram of each individual color channel of
+the image, and returns the mean & median of the histograms for the channels
+specified. Because images are imported with the channels ordered as B,G,R,
+the output list is returned the same way. The returned list always looks like
+this: [ [BlueMean, BlueMedian], [GreenMean, GreenMedian], [RedMean, RedMedian] ].
+Mean values always come before median values. If nonzero is set to true (default)
+the function will only calculate mediapytn and means based on the non-black pixels.</p>
+</dd></dl>
+
+<dl class="method">
+<dt id="ih.imgproc.Image.extractDimensions">
+<code class="descname">extractDimensions</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="_modules/ih/imgproc.html#Image.extractDimensions"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#ih.imgproc.Image.extractDimensions" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">A list corresponding to the height and width of the image.</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body">list</td>
+</tr>
+</tbody>
+</table>
+<p>Returns a list with the following form: [height, width]</p>
+</dd></dl>
+
+<dl class="method">
+<dt id="ih.imgproc.Image.extractFinalPath">
+<code class="descname">extractFinalPath</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="_modules/ih/imgproc.html#Image.extractFinalPath"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#ih.imgproc.Image.extractFinalPath" title="Permalink to this definition">¶</a></dt>
+<dd><p>This function writes the absolute path of the output file to the database.</p>
+</dd></dl>
+
+<dl class="method">
+<dt id="ih.imgproc.Image.extractMoments">
+<code class="descname">extractMoments</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="_modules/ih/imgproc.html#Image.extractMoments"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#ih.imgproc.Image.extractMoments" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">A dictionary corresponding to the different moments of the image.</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body">dict</td>
+</tr>
+</tbody>
+</table>
+<p>Calculates the moments of the image, and returns a dicitonary based on them.
+Spatial moments are prefixed with ‘m’, central moments are prefixed with ‘mu’,
+and central normalized moments are prefixed with ‘nu’. This function
+is a wrapper to the OpenCV function <a class="reference external" href="http://docs.opencv.org/modules/imgproc/doc/structural_analysis_and_shape_descriptors.html#moments">moments</a>.</p>
+</dd></dl>
+
+<dl class="method">
+<dt id="ih.imgproc.Image.extractPixels">
+<code class="descname">extractPixels</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="_modules/ih/imgproc.html#Image.extractPixels"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#ih.imgproc.Image.extractPixels" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">The number of non-black pixels in the image.</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body">int</td>
+</tr>
+</tbody>
+</table>
+<p>Returns the number of non-black pixels in the image. Creates
+a temporary binary image to do this. The point of this function
+is not to threshold, so the binary image is created by all
+pixels that fall into the range [1, 1, 1], [255, 255, 255].</p>
+</dd></dl>
+
+<dl class="method">
+<dt id="ih.imgproc.Image.gaussianBlur">
+<code class="descname">gaussianBlur</code><span class="sig-paren">(</span><em>ksize</em>, <em>sigmaX=0</em>, <em>sigmaY=0</em>, <em>borderType='default'</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/ih/imgproc.html#Image.gaussianBlur"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#ih.imgproc.Image.gaussianBlur" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
+<li><strong>ksize</strong> (<a class="reference external" href="http://docs.python.org/library/functions.html#tuple" title="(in Python v2.7)"><em>tuple</em></a>) – The size of the kernel represented by a tuple (width, height). Both numers should be odd and positive.</li>
+<li><strong>sigmaX</strong> (<a class="reference external" href="http://docs.python.org/library/functions.html#float" title="(in Python v2.7)"><em>float</em></a>) – The standard deviation in the x direction. If 0, the value is calculated based on the kernel size.</li>
+<li><strong>sigmaY</strong> (<a class="reference external" href="http://docs.python.org/library/functions.html#float" title="(in Python v2.7)"><em>float</em></a>) – The standard deviation in the y direction. If 0, the value is equal to sigmaX.</li>
+<li><strong>borderType</strong> (<a class="reference external" href="http://docs.python.org/library/functions.html#str" title="(in Python v2.7)"><em>str</em></a>) – The type of border mode used to extrapolate pixels outside the image.</li>
+</ul>
+</td>
+</tr>
+</tbody>
+</table>
+<p>This function blurs an image based on a Gaussian kernel. When blurring on the edge
+of the image, values for pixels that would be outside of the image are extrapolated. The method
+of extrapolation depends on the specified ‘borderType’, and can be one of ‘default’, ‘constant’,
+‘reflect’, or ‘replicate’. This function is a wrapper to the OpenCV function <a class="reference external" href="http://docs.opencv.org/modules/imgproc/doc/filtering.html#gaussianblur">GaussianBlur</a>.</p>
+</dd></dl>
+
+<dl class="method">
+<dt id="ih.imgproc.Image.kmeans">
+<code class="descname">kmeans</code><span class="sig-paren">(</span><em>k</em>, <em>criteria</em>, <em>maxiter=10</em>, <em>accuracy=1.0</em>, <em>attempts=10</em>, <em>flags='random'</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/ih/imgproc.html#Image.kmeans"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#ih.imgproc.Image.kmeans" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
+<li><strong>k</strong> (<a class="reference external" href="http://docs.python.org/library/functions.html#int" title="(in Python v2.7)"><em>int</em></a>) – Number of colors in final image.</li>
+<li><strong>criteria</strong> (<a class="reference external" href="http://docs.python.org/library/functions.html#str" title="(in Python v2.7)"><em>str</em></a>) – Determination of how the algorithm stops execution. Should be one of ‘accuracy’, ‘iteration’, or ‘either’.</li>
+<li><strong>maxiter</strong> (<a class="reference external" href="http://docs.python.org/library/functions.html#int" title="(in Python v2.7)"><em>int</em></a>) – Maximum number of iterations of the algorithm.</li>
+<li><strong>accuracy</strong> (<a class="reference external" href="http://docs.python.org/library/functions.html#float" title="(in Python v2.7)"><em>float</em></a>) – Minimum accuracy before algorithm finishes executing.</li>
+<li><strong>attempts</strong> (<a class="reference external" href="http://docs.python.org/library/functions.html#int" title="(in Python v2.7)"><em>int</em></a>) – Number of times the algorithm is executed using different initial guesses.</li>
+<li><strong>flags</strong> (<a class="reference external" href="http://docs.python.org/library/functions.html#str" title="(in Python v2.7)"><em>str</em></a>) – How to determine initial centers should be either ‘random’ or ‘pp’.</li>
+</ul>
+</td>
+</tr>
+</tbody>
+</table>
+<p>This function is a wrapper to the OpenCV function <a class="reference external" href="http://docs.opencv.org/modules/core/doc/clustering.html">kmeans</a>
+Adjusts the colors in the image to find the most compact ‘central’ colors. The amount of colors
+in the resulting image is the specified value ‘k’. The colors are chosen based upon the minimum
+amount of adjustment in the image necessary. The criteria parameter determines when the algorithm
+stops. If ‘accuracy’ is specified, the algorithm runs until the specified accuracy is reached. If ‘iteration’
+is specified, the algorithm runs the specified number of iterations. If ‘either’ is specified, the algorithm
+runs until one of the conditions is satisfied. The flags parameter determines the initial central colors,
+and should be either ‘random’ – to generate a random initial guess – or ‘pp’ to use center initialization by Arthur and Vassilvitskii.</p>
+</dd></dl>
+
+<dl class="method">
+<dt id="ih.imgproc.Image.list">
+<code class="descname">list</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="_modules/ih/imgproc.html#Image.list"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#ih.imgproc.Image.list" title="Permalink to this definition">¶</a></dt>
+<dd><p>Lists all saved states.</p>
+</dd></dl>
+
+<dl class="method">
+<dt id="ih.imgproc.Image.meanshift">
+<code class="descname">meanshift</code><span class="sig-paren">(</span><em>spatial_radius</em>, <em>range_radius</em>, <em>min_density</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/ih/imgproc.html#Image.meanshift"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#ih.imgproc.Image.meanshift" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
+<li><strong>spatial_radius</strong> (<a class="reference external" href="http://docs.python.org/library/functions.html#float" title="(in Python v2.7)"><em>float</em></a>) – Spatial Radius</li>
+<li><strong>range_radius</strong> (<a class="reference external" href="http://docs.python.org/library/functions.html#float" title="(in Python v2.7)"><em>float</em></a>) – Range Radius.</li>
+<li><strong>min_density</strong> (<a class="reference external" href="http://docs.python.org/library/functions.html#int" title="(in Python v2.7)"><em>int</em></a>) – Minimum Density.</li>
+</ul>
+</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">The mean-shifted image.</p>
+</td>
+</tr>
+<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><p class="first last">numpy.ndarray</p>
+</td>
+</tr>
+</tbody>
+</table>
+<p>Segments the image into clusters based on nearest neighbors. This function
+is a wrapper to the <a class="reference external" href="https://code.google.com/p/pymeanshift/">pymeanshift</a>
+module. For details on the algorithm itself: <a class="reference external" href="http://dx.doi.org/10.1109/34.1000236">Mean shift: A robust approach toward feature space analysis</a>.</p>
+</dd></dl>
+
+<dl class="method">
+<dt id="ih.imgproc.Image.medianBlur">
+<code class="descname">medianBlur</code><span class="sig-paren">(</span><em>ksize</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/ih/imgproc.html#Image.medianBlur"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#ih.imgproc.Image.medianBlur" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>ksize</strong> (<a class="reference external" href="http://docs.python.org/library/functions.html#int" title="(in Python v2.7)"><em>int</em></a>) – The size of the kernel (ksize x ksize). Should be odd and positive.</td>
+</tr>
+</tbody>
+</table>
+<p>This function smoothes an image using the median filter. The kernel is set to size (ksize, ksize).
+The anchor position is assumed to be the center.
+REFERENCE OPENCV MEDIAN BLUR</p>
+</dd></dl>
+
+<dl class="method">
+<dt id="ih.imgproc.Image.morphology">
+<code class="descname">morphology</code><span class="sig-paren">(</span><em>morphType</em>, <em>ktype</em>, <em>ksize</em>, <em>anchor=(-1</em>, <em>-1)</em>, <em>iterations=1</em>, <em>borderType='default'</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/ih/imgproc.html#Image.morphology"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#ih.imgproc.Image.morphology" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
+<li><strong>morphType</strong> (<a class="reference external" href="http://docs.python.org/library/functions.html#str" title="(in Python v2.7)"><em>str</em></a>) – The type of morphology to perform. Should be dilate, erode, open, close, gradient, tophat, or blackhat.</li>
+<li><strong>ktype</strong> (<a class="reference external" href="http://docs.python.org/library/functions.html#str" title="(in Python v2.7)"><em>str</em></a>) – the type of the kernel, should be rect, ellipse, or cross.</li>
+<li><strong>ksize</strong> (<a class="reference external" href="http://docs.python.org/library/functions.html#tuple" title="(in Python v2.7)"><em>tuple</em></a>) – The size of the kernel represented by a tuple (width, height). Both numbers should be odd and positive.</li>
+<li><strong>anchor</strong> (<a class="reference external" href="http://docs.python.org/library/functions.html#tuple" title="(in Python v2.7)"><em>tuple</em></a>) – The anchor point for filtering. Default is (-1, -1) which is the center of the kernel.</li>
+<li><strong>iterations</strong> (<a class="reference external" href="http://docs.python.org/library/functions.html#int" title="(in Python v2.7)"><em>int</em></a>) – The number of times to perform the specified morphology.</li>
+<li><strong>borderType</strong> (<a class="reference external" href="http://docs.python.org/library/functions.html#str" title="(in Python v2.7)"><em>str</em></a>) – The type of border mode used to extrapolate pixels outside the image.</li>
+</ul>
+</td>
+</tr>
+</tbody>
+</table>
+<p>This function performs morphological operations based on the inputted values. This function is
+a wrapper to the OpenCv function <a class="reference external" href="http://docs.opencv.org/modules/imgproc/doc/filtering.html#morphologyex">morphologyEx</a>. When performing the morphology on the edges
+of the image, values for pixels that would be outside of the image are extrapolated. The method
+of extrapolation depends on the specified ‘borderType’, and can be one of ‘default’, ‘constant’,
+‘reflect’, or ‘replicate’.</p>
+</dd></dl>
+
+<dl class="method">
+<dt id="ih.imgproc.Image.normalizeByIntensity">
+<code class="descname">normalizeByIntensity</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="_modules/ih/imgproc.html#Image.normalizeByIntensity"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#ih.imgproc.Image.normalizeByIntensity" title="Permalink to this definition">¶</a></dt>
+<dd><p>Normalizes each channel of the pixel by its intensity. For each pixel, the intensity is defined as
+<span class="math">\(I = R + G + B\)</span>, where <span class="math">\(R,G,B\)</span> are the color values for that pixel. We calculate new color values by
+multiplying the original number by 255, and dividing by the intensity, that is, <span class="math">\(r = \frac{255 \cdot R}{I}
+, g = \frac{255 \cdot G}{I}, b = \frac{255 \cdot B}{I}\)</span>.</p>
+</dd></dl>
+
+<dl class="method">
+<dt id="ih.imgproc.Image.resize">
+<code class="descname">resize</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="_modules/ih/imgproc.html#Image.resize"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#ih.imgproc.Image.resize" title="Permalink to this definition">¶</a></dt>
+<dd><p>If the image is large than conf.maxArea, resize its total area down to conf.maxArea.
+This function is primarily used for viewing purposes, and as such, it does not resize
+the base image, but creates a copy to resize instead.</p>
+</dd></dl>
+
+<dl class="method">
+<dt id="ih.imgproc.Image.resizeSelf">
+<code class="descname">resizeSelf</code><span class="sig-paren">(</span><em>scale=None</em>, <em>width=None</em>, <em>height=None</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/ih/imgproc.html#Image.resizeSelf"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#ih.imgproc.Image.resizeSelf" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
+<li><strong>scale</strong> (<a class="reference external" href="http://docs.python.org/library/functions.html#float" title="(in Python v2.7)"><em>float</em></a>) – Value to scale image by.</li>
+<li><strong>width</strong> (<a class="reference external" href="http://docs.python.org/library/functions.html#int" title="(in Python v2.7)"><em>int</em></a>) – Target width of image.</li>
+<li><strong>height</strong> (<a class="reference external" href="http://docs.python.org/library/functions.html#int" title="(in Python v2.7)"><em>int</em></a>) – Target height of image.</li>
+</ul>
+</td>
+</tr>
+</tbody>
+</table>
+<p>Resizes the current image. If scale is set, it simply resizes the
+width and height of the image based on the scale. If only one of width
+or height is set, it scales the other accordingly. If both width
+and height are set, it scales the image to the exact size specified.</p>
+</dd></dl>
+
+<dl class="method">
+<dt id="ih.imgproc.Image.restore">
+<code class="descname">restore</code><span class="sig-paren">(</span><em>name</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/ih/imgproc.html#Image.restore"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#ih.imgproc.Image.restore" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>name</strong> (<em>str OR any hashable type.</em>) – The name the image is saved under.</td>
+</tr>
+</tbody>
+</table>
+<p>Reloads a previously saved image from the ‘states’ variable.</p>
+</dd></dl>
+
+<dl class="method">
+<dt id="ih.imgproc.Image.save">
+<code class="descname">save</code><span class="sig-paren">(</span><em>name</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/ih/imgproc.html#Image.save"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#ih.imgproc.Image.save" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>name</strong> (<em>str OR any hashable type.</em>) – The name to save the image under.</td>
+</tr>
+</tbody>
+</table>
+<p>This function saves the current image in the ‘states’ variable under
+the specified name. It can then be reloaded using the <a class="reference internal" href="#ih.imgproc.Image.restore" title="ih.imgproc.Image.restore"><code class="xref py py-meth docutils literal"><span class="pre">restore()</span></code></a>
+method.</p>
+</dd></dl>
+
+<dl class="method">
+<dt id="ih.imgproc.Image.show">
+<code class="descname">show</code><span class="sig-paren">(</span><em>title=None</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/ih/imgproc.html#Image.show"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#ih.imgproc.Image.show" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>title</strong> (<a class="reference external" href="http://docs.python.org/library/functions.html#str" title="(in Python v2.7)"><em>str</em></a>) – The title to give the display window, if left blank one will be created.</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body">None</td>
+</tr>
+</tbody>
+</table>
+<p>Displays the image in a window. Utilizes the <a class="reference internal" href="#ih.imgproc.Image.resize" title="ih.imgproc.Image.resize"><code class="xref py py-meth docutils literal"><span class="pre">resize()</span></code></a> function.
+If a title is not specified, the window will be named ‘windowX’ where X is the number of times
+show has been called.</p>
+</dd></dl>
+
+<dl class="method">
+<dt id="ih.imgproc.Image.threshold">
+<code class="descname">threshold</code><span class="sig-paren">(</span><em>thresh</em>, <em>max=255</em>, <em>type='binary'</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/ih/imgproc.html#Image.threshold"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#ih.imgproc.Image.threshold" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
+<li><strong>thresh</strong> (<a class="reference external" href="http://docs.python.org/library/functions.html#int" title="(in Python v2.7)"><em>int</em></a>) – Threshold value.</li>
+<li><strong>max</strong> (<a class="reference external" href="http://docs.python.org/library/functions.html#int" title="(in Python v2.7)"><em>int</em></a>) – Write value for binary threshold.</li>
+<li><strong>type</strong> (<a class="reference external" href="http://docs.python.org/library/functions.html#str" title="(in Python v2.7)"><em>str</em></a>) – Threhsold type.</li>
+</ul>
+</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">The thresholded image.</p>
+</td>
+</tr>
+<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><p class="first">numpy.ndarray</p>
+</td>
+</tr>
+<tr class="field-even field"><th class="field-name" colspan="2">Raises KeyError:</th></tr>
+<tr class="field-even field"><td> </td><td class="field-body"><p class="first last">if the specified threshold type doesn’t exist.</p>
+</td>
+</tr>
+</tbody>
+</table>
+<p>Thresholds the image based on the given type. The image must be
+grayscale to be thresholded. If the image is of type ‘bgr’ it is
+automatically converted to grayscale before thresholding.
+Supported types are: binary, truncate, tozero, and otsu.</p>
+</dd></dl>
+
+<dl class="method">
+<dt id="ih.imgproc.Image.wait">
+<code class="descname">wait</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="_modules/ih/imgproc.html#Image.wait"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#ih.imgproc.Image.wait" title="Permalink to this definition">¶</a></dt>
+<dd><p>Waits until a key is pressed, then destroys all windows and
+continues program execution.</p>
+</dd></dl>
+
+<dl class="method">
+<dt id="ih.imgproc.Image.write">
+<code class="descname">write</code><span class="sig-paren">(</span><em>name=None</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/ih/imgproc.html#Image.write"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#ih.imgproc.Image.write" title="Permalink to this definition">¶</a></dt>
+<dd><p>Writes the current image to the given output directory, with the given name.</p>
+</dd></dl>
+
+</dd></dl>
+
+</div>
+
+
+ </div>
+
+ </div>
+</div>
+<footer class="footer">
+ <div class="container">
+ <p class="pull-right">
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+
+ </p>
+ <p>
+ © Copyright 2015, Avi Knecht.<br/>
+ Created using <a href="http://sphinx.pocoo.org/">Sphinx</a> 1.3a0.<br/>
+ </p>
+ </div>
+</footer>
+ </body>
+</html>
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diff --git a/docs/build/html/searchindex.js b/docs/build/html/searchindex.js
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+
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+ <head>
+ <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
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+ <title>Getting Started — Image Harvest 1.0.1 documentation</title>
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+ Image Harvest</a>
+ <span class="navbar-text navbar-version pull-left"><b>1.0</b></span>
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+ <div class="collapse navbar-collapse nav-collapse">
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+<li class="toctree-l1"><a class="reference internal" href="introduction.html">Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="installation.html">Installation</a></li>
+<li class="toctree-l1 current"><a class="current reference internal" href="">Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="ex_script_core1.html">Core Processing Example #1</a></li>
+<li class="toctree-l1"><a class="reference internal" href="ex_script_core2.html">Core Processing Example #2</a></li>
+<li class="toctree-l1"><a class="reference internal" href="ex_script_color1.html">Color Filter In Depth #1</a></li>
+<li class="toctree-l1"><a class="reference internal" href="ex_workflow_1.html">Workflow Example #1</a></li>
+<li class="toctree-l1"><a class="reference internal" href="examples.html">Examples</a></li>
+<li class="toctree-l1"><a class="reference internal" href="processing.html">Image Processing</a></li>
+<li class="toctree-l1"><a class="reference internal" href="viewer.html">Image Processing Viewer</a></li>
+<li class="toctree-l1"><a class="reference internal" href="statistics.html">Statistics</a></li>
+<li class="toctree-l1"><a class="reference internal" href="indexing.html">Image Loading</a></li>
+<li class="toctree-l1"><a class="reference internal" href="workflowimage.html">Image Processing Workflows</a></li>
+<li class="toctree-l1"><a class="reference internal" href="workflowstats.html">Statistics Workflows</a></li>
+</ul>
+</ul>
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+<li><a class="reference internal" href="#">Getting Started</a></li>
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+ <a href="examples.html" title="Next Chapter: Examples"><span class="glyphicon glyphicon-chevron-right visible-sm"></span><span class="hidden-sm hidden-tablet">Examples »</span>
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+<div id="sourcelink">
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+<form class="navbar-form navbar-right" action="search.html" method="get">
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+ <input type="text" name="q" class="form-control" placeholder="Search" />
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+<div class="container">
+ <div class="row">
+ <div class="col-md-12">
+
+ <div class="section" id="getting-started">
+<h1>Getting Started<a class="headerlink" href="#getting-started" title="Permalink to this headline">¶</a></h1>
+<p>There are 3 main ways of accessing the software.</p>
+<ol class="arabic">
+<li><dl class="first docutils">
+<dt>Library Access</dt>
+<dd><p class="first">The image processing and statistics functions can be accessed by importing ih.
+Within your script you create objects out of individual plant images and process them
+directly. Ex:</p>
+<div class="highlight-python"><div class="highlight"><pre><span class="c"># import ih</span>
+<span class="kn">import</span> <span class="nn">ih.imgproc</span>
+<span class="c"># load your image as an object</span>
+<span class="n">plant</span> <span class="o">=</span> <span class="n">ih</span><span class="o">.</span><span class="n">imgproc</span><span class="o">.</span><span class="n">Image</span><span class="p">(</span><span class="s">"/home/user/image.png"</span><span class="p">,</span> <span class="n">outputdir</span> <span class="o">=</span> <span class="s">"/home/user/"</span><span class="p">)</span>
+<span class="c"># execute processing functions, in this simple case,</span>
+<span class="c"># the image is converted to grayscale, then thresholded.</span>
+<span class="n">plant</span><span class="o">.</span><span class="n">convertColor</span><span class="p">(</span><span class="s">"bgr"</span><span class="p">,</span> <span class="s">"gray"</span><span class="p">)</span>
+<span class="n">plant</span><span class="o">.</span><span class="n">threshold</span><span class="p">(</span><span class="mi">127</span><span class="p">)</span>
+<span class="c"># write the output</span>
+<span class="n">plant</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s">"threshold.png"</span><span class="p">)</span>
+</pre></div>
+</div>
+<p class="last">This method is good for testing and adjusting your image processing workflow,
+but does not scale well for large sets of images.</p>
+</dd>
+</dl>
+</li>
+<li><dl class="first docutils">
+<dt>Command Line Access</dt>
+<dd><p class="first">ih comes with dozens of micro-scripts providing individual access to each
+function. Each script takes an input image, and writes an output image. The
+previous example would be done with two commands as follows:</p>
+<div class="highlight-bash"><div class="highlight"><pre><span class="c">#!/bin/bash</span>
+ih-convert-color --input <span class="s2">"/home/user/image.png"</span> --output <span class="s2">"/home/user/gray.png"</span> --intype <span class="s2">"bgr"</span> --outtype <span class="s2">"gray"</span>
+ih-threshold --input <span class="s2">"/home/user/gray.png"</span> --output <span class="s2">"/home/user/threshold.png"</span> --thresh 127
+</pre></div>
+</div>
+<p class="last">This method is slightly different than the previous one in a few aspects. The names of the command line
+scripts will not exactly match the names of the functions. Because each script takes an image and
+writes an image, it is important to chain the output of one command into the input of the next command.
+This method can also be used to test your workflow. Super computer workflows use this method for processing,
+so familiarity with command-line arguments are helpful, and ensure your large-scale runs process correctly.</p>
+</dd>
+</dl>
+</li>
+<li><dl class="first docutils">
+<dt>Workflow Generation</dt>
+<dd><p class="first">Super computer workflow generation and submission is complicated enough that there isn’t a simple
+starter script, but it can be broken down into three major steps. Each step is handled by user defined
+json template files.</p>
+<ol class="last lowerroman">
+<li><dl class="first docutils">
+<dt>Image Loading</dt>
+<dd><p class="first last">Input images can range from automated systems such as LemnaTec, to pictures taken by hand.
+Besides the images themselves being different, the format of the input also differs greatly
+from source to source. This step sets up the base job submission directory, and loads
+images into a database, to keep the format consistent for all inputs. Loading requires
+a template that defines where and how to load images into the database, as well as metadata
+to load for each image. Metadata for images is not defined for each individual image, but
+rather, is loaded from the directory structure / names of the images.</p>
+</dd>
+</dl>
+</li>
+<li><dl class="first docutils">
+<dt>Image Processing</dt>
+<dd><p class="first last">This step requires two inputs, a workflow template file, and a config file. The workflow template
+file defines what image-processing scripts to use, and in what order. Additionally, which numeric
+variables to extract are defined in the workflow template files. The config file is for several
+pieces of system information, such as environment variables, and job cluster size.</p>
+</dd>
+</dl>
+</li>
+<li><dl class="first docutils">
+<dt>Statistics</dt>
+<dd><p class="first last">This step also requires two inputs, a workflow template file, and a config file. The workflow template
+file is identical to that of the previous step, except using statistic processing scripts. The
+config file for this step is completely identical to that of the previous step. Statistics workflows
+require that data has been processed, which means an image-processing workflow must be run first.
+Additionally, statistics workflows are still a work in progress.</p>
+</dd>
+</dl>
+</li>
+</ol>
+</dd>
+</dl>
+</li>
+</ol>
+<p>The next session details several tutorials of how to use ih, for both local and distributed computing. It
+is recommended that you familiarize yourself with local computing examples before jumping into generating
+super computer workflows. Implementation details of specific functions can be found in further sections.</p>
+</div>
+
+
+ </div>
+
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+ <span class="navbar-text navbar-version pull-left"><b>1.0</b></span>
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+<li class="toctree-l1"><a class="reference internal" href="start.html">Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="ex_script_core1.html">Core Processing Example #1</a></li>
+<li class="toctree-l1"><a class="reference internal" href="ex_script_core2.html">Core Processing Example #2</a></li>
+<li class="toctree-l1"><a class="reference internal" href="ex_script_color1.html">Color Filter In Depth #1</a></li>
+<li class="toctree-l1"><a class="reference internal" href="ex_workflow_1.html">Workflow Example #1</a></li>
+<li class="toctree-l1"><a class="reference internal" href="examples.html">Examples</a></li>
+<li class="toctree-l1"><a class="reference internal" href="processing.html">Image Processing</a></li>
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+<li class="toctree-l1 current"><a class="current reference internal" href="">Statistics</a></li>
+<li class="toctree-l1"><a class="reference internal" href="indexing.html">Image Loading</a></li>
+<li class="toctree-l1"><a class="reference internal" href="workflowimage.html">Image Processing Workflows</a></li>
+<li class="toctree-l1"><a class="reference internal" href="workflowstats.html">Statistics Workflows</a></li>
+</ul>
+</ul>
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+</li>
+
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+
+
+ <li>
+ <a href="viewer.html" title="Previous Chapter: Image Processing Viewer"><span class="glyphicon glyphicon-chevron-left visible-sm"></span><span class="hidden-sm hidden-tablet">« Image Processing...</span>
+ </a>
+ </li>
+ <li>
+ <a href="indexing.html" title="Next Chapter: Image Loading"><span class="glyphicon glyphicon-chevron-right visible-sm"></span><span class="hidden-sm hidden-tablet">Image Loading »</span>
+ </a>
+ </li>
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+
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+ <li class="hidden-sm">
+<div id="sourcelink">
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+ rel="nofollow">Source</a>
+</div></li>
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+
+
+
+<form class="navbar-form navbar-right" action="search.html" method="get">
+ <div class="form-group">
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+
+<div class="container">
+ <div class="row">
+ <div class="col-md-12">
+
+ <div class="section" id="statistics">
+<h1>Statistics<a class="headerlink" href="#statistics" title="Permalink to this headline">¶</a></h1>
+<p>Statistics analysis is currently being worked on!</p>
+<dl class="class">
+<dt id="ih.statistics.Stats">
+<em class="property">class </em><code class="descclassname">ih.statistics.</code><code class="descname">Stats</code><span class="sig-paren">(</span><em>db</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/ih/statistics.html#Stats"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#ih.statistics.Stats" title="Permalink to this definition">¶</a></dt>
+<dd><dl class="method">
+<dt id="ih.statistics.Stats.anova">
+<code class="descname">anova</code><span class="sig-paren">(</span><em>intable</em>, <em>outtable</em>, <em>grouping</em>, <em>overwrite=False</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/ih/statistics.html#Stats.anova"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#ih.statistics.Stats.anova" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
+<li><strong>intable</strong> (<a class="reference external" href="http://docs.python.org/library/functions.html#str" title="(in Python v2.7)"><em>str</em></a>) – The input table to load information from</li>
+<li><strong>outtable</strong> (<a class="reference external" href="http://docs.python.org/library/functions.html#str" title="(in Python v2.7)"><em>str</em></a>) – The output table to write information to.</li>
+<li><strong>grouping</strong> (<a class="reference external" href="http://docs.python.org/library/functions.html#list" title="(in Python v2.7)"><em>list</em></a>) – The list of image types to group by.</li>
+</ul>
+</td>
+</tr>
+</tbody>
+</table>
+<p>Computes the analysis of variation of all numeric information based on 3 factors,
+treatment, date, and the interaction between the two. Analysis of variation is
+different than the rest of the stats functions, in that a lot of information is
+lost after running it. The results themselves correspond to columns (pixels, rmed, binx...)
+instead of actual images.</p>
+</dd></dl>
+
+<dl class="method">
+<dt id="ih.statistics.Stats.correlation">
+<code class="descname">correlation</code><span class="sig-paren">(</span><em>intable</em>, <em>outtable</em>, <em>dataFile</em>, <em>dataHeaders</em>, <em>overwrite=False</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/ih/statistics.html#Stats.correlation"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#ih.statistics.Stats.correlation" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
+<li><strong>intable</strong> (<a class="reference external" href="http://docs.python.org/library/functions.html#str" title="(in Python v2.7)"><em>str</em></a>) – The input table to load information from</li>
+<li><strong>outtable</strong> (<a class="reference external" href="http://docs.python.org/library/functions.html#str" title="(in Python v2.7)"><em>str</em></a>) – The output table to write information to.</li>
+<li><strong>dataFile</strong> (<a class="reference external" href="http://docs.python.org/library/functions.html#str" title="(in Python v2.7)"><em>str</em></a>) – The csv data file to load</li>
+<li><strong>dataHeaders</strong> (<a class="reference external" href="http://docs.python.org/library/functions.html#str" title="(in Python v2.7)"><em>str</em></a>) – Column names for relevant table headers.</li>
+</ul>
+</td>
+</tr>
+</tbody>
+</table>
+<p>This function correlates all numeric values with values in the given file.
+The input data file is assumed to be in csv format. In dataHeaders, you must
+specify four keys, ‘id’, ‘date’, ‘dateFormat’, and ‘metric’. Each of these should
+be column names. Id corresponds to the lemnaTec style identifier ex: ‘023535-S’.
+All dates are converted into Y-m-d form, you must provide a valid format in ‘dateFormat’,
+that way the dates can be converted correctly. The ‘metric’ column is the actual value you
+want to correlate to.</p>
+</dd></dl>
+
+<dl class="method">
+<dt id="ih.statistics.Stats.export">
+<code class="descname">export</code><span class="sig-paren">(</span><em>table</em>, <em>processed=True</em>, <em>group=None</em>, <em>fname=None</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/ih/statistics.html#Stats.export"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#ih.statistics.Stats.export" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
+<li><strong>table</strong> (<a class="reference external" href="http://docs.python.org/library/functions.html#str" title="(in Python v2.7)"><em>str</em></a>) – The table to write to csv</li>
+<li><strong>processed</strong> (<a class="reference external" href="http://docs.python.org/library/functions.html#bool" title="(in Python v2.7)"><em>bool</em></a>) – Whether or not to extract processed data</li>
+<li><strong>group</strong> (<a class="reference external" href="http://docs.python.org/library/functions.html#list" title="(in Python v2.7)"><em>list</em></a>) – Which image types to extract from the database.</li>
+<li><strong>fname</strong> (<a class="reference external" href="http://docs.python.org/library/functions.html#str" title="(in Python v2.7)"><em>str</em></a>) – The file name to write to.</li>
+</ul>
+</td>
+</tr>
+</tbody>
+</table>
+<p>This function simply extracts data from a database and writes it to csv format.
+Default functionality is to extract only data that has been processed. This is
+checked by finding if an outputPath has been set. Additionally,
+you can specify a list of image types to extract, if not, the default list contains
+all rgb and fluo images. Finally, if no file name is specified, the name
+of the table is used as the filename.</p>
+</dd></dl>
+
+<dl class="method">
+<dt id="ih.statistics.Stats.logErrors">
+<code class="descname">logErrors</code><span class="sig-paren">(</span><em>logfile</em>, <em>table='images'</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/ih/statistics.html#Stats.logErrors"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#ih.statistics.Stats.logErrors" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
+<li><strong>logfile</strong> (<a class="reference external" href="http://docs.python.org/library/functions.html#str" title="(in Python v2.7)"><em>str</em></a>) – The logfile to write errors to</li>
+<li><strong>table</strong> (<a class="reference external" href="http://docs.python.org/library/functions.html#str" title="(in Python v2.7)"><em>str</em></a>) – The table to load errors from</li>
+</ul>
+</td>
+</tr>
+</tbody>
+</table>
+<p>This function writes all errors from a given table to a log file,
+usually used at the end of image processing to write all images that
+did not process correctly.</p>
+</dd></dl>
+
+<dl class="method">
+<dt id="ih.statistics.Stats.normalize">
+<code class="descname">normalize</code><span class="sig-paren">(</span><em>intable</em>, <em>outtable</em>, <em>column='pixels'</em>, <em>overwrite=False</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/ih/statistics.html#Stats.normalize"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#ih.statistics.Stats.normalize" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
+<li><strong>intable</strong> (<a class="reference external" href="http://docs.python.org/library/functions.html#str" title="(in Python v2.7)"><em>str</em></a>) – The input table to load information from</li>
+<li><strong>outtable</strong> (<a class="reference external" href="http://docs.python.org/library/functions.html#str" title="(in Python v2.7)"><em>str</em></a>) – The output table to write information to.</li>
+<li><strong>column</strong> (<a class="reference external" href="http://docs.python.org/library/functions.html#str" title="(in Python v2.7)"><em>str</em></a>) – The column to normalize information to</li>
+</ul>
+</td>
+</tr>
+</tbody>
+</table>
+<p>Normalizes all numerical information to the specific column. This
+function is usually used with ‘pixels’ as the specified column, which
+expresses all numeric information as a percentage of the total pixels
+in the image.</p>
+</dd></dl>
+
+<dl class="method">
+<dt id="ih.statistics.Stats.shootArea">
+<code class="descname">shootArea</code><span class="sig-paren">(</span><em>intable</em>, <em>outtable</em>, <em>grouping</em>, <em>overwrite=False</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/ih/statistics.html#Stats.shootArea"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#ih.statistics.Stats.shootArea" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
+<li><strong>intable</strong> (<a class="reference external" href="http://docs.python.org/library/functions.html#str" title="(in Python v2.7)"><em>str</em></a>) – The input table to load information from</li>
+<li><strong>outtable</strong> (<a class="reference external" href="http://docs.python.org/library/functions.html#str" title="(in Python v2.7)"><em>str</em></a>) – The output table to write information to.</li>
+<li><strong>grouping</strong> (<a class="reference external" href="http://docs.python.org/library/functions.html#list" title="(in Python v2.7)"><em>list</em></a>) – Which imtypes to group</li>
+</ul>
+</td>
+</tr>
+</tbody>
+</table>
+<p>This function adds the numeric values of multiple image types together.
+In general, it is used to combine side view + top view images of the same spectrum.
+If you plan on correlating your data to lemnaTec’s data, lemnaTec uses SV1 + SV2 + TV,
+so you should aggregate your data likewise.</p>
+</dd></dl>
+
+<dl class="method">
+<dt id="ih.statistics.Stats.tTest">
+<code class="descname">tTest</code><span class="sig-paren">(</span><em>intable</em>, <em>outtable</em>, <em>comp='imtype'</em>, <em>overwrite=False</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/ih/statistics.html#Stats.tTest"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#ih.statistics.Stats.tTest" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
+<li><strong>intable</strong> (<a class="reference external" href="http://docs.python.org/library/functions.html#str" title="(in Python v2.7)"><em>str</em></a>) – The input table to perform the T test on.</li>
+<li><strong>outtable</strong> (<a class="reference external" href="http://docs.python.org/library/functions.html#str" title="(in Python v2.7)"><em>str</em></a>) – The output table to write the results to.</li>
+<li><strong>comp</strong> (<a class="reference external" href="http://docs.python.org/library/functions.html#str" title="(in Python v2.7)"><em>str</em></a>) – Whether to compare image types or image names.</li>
+<li><strong>overwrite</strong> (<a class="reference external" href="http://docs.python.org/library/functions.html#bool" title="(in Python v2.7)"><em>bool</em></a>) – Whether or not to overwrite the output database</li>
+</ul>
+</td>
+</tr>
+</tbody>
+</table>
+<p>This function computes a ttest of the input table for all numeric headers.
+The comparison is either done based on image types or image names. Default
+functionality is a comparison between image types, specify comp = ‘imgname’
+to compare image names.</p>
+</dd></dl>
+
+<dl class="method">
+<dt id="ih.statistics.Stats.threshold">
+<code class="descname">threshold</code><span class="sig-paren">(</span><em>intable</em>, <em>outtable</em>, <em>thresh=0.01</em>, <em>overwrite=False</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/ih/statistics.html#Stats.threshold"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#ih.statistics.Stats.threshold" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
+<li><strong>intable</strong> (<a class="reference external" href="http://docs.python.org/library/functions.html#str" title="(in Python v2.7)"><em>str</em></a>) – The input table to load information from</li>
+<li><strong>outtable</strong> (<a class="reference external" href="http://docs.python.org/library/functions.html#str" title="(in Python v2.7)"><em>str</em></a>) – The output table to write information to.</li>
+<li><strong>thresh</strong> (<a class="reference external" href="http://docs.python.org/library/functions.html#float" title="(in Python v2.7)"><em>float</em></a>) – The threshold value.</li>
+</ul>
+</td>
+</tr>
+</tbody>
+</table>
+<p>This function thresholds the table based on the given value. All values
+that fall below the threhsold are ‘updated’ in place with ‘null’. Normalize
+is often called before thresholding.</p>
+</dd></dl>
+
+<dl class="method">
+<dt id="ih.statistics.Stats.treatmentComp">
+<code class="descname">treatmentComp</code><span class="sig-paren">(</span><em>intable</em>, <em>outtable</em>, <em>type='ratio'</em>, <em>direction='Control'</em>, <em>comp='imtype'</em>, <em>overwrite=False</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/ih/statistics.html#Stats.treatmentComp"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#ih.statistics.Stats.treatmentComp" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
+<li><strong>intable</strong> (<a class="reference external" href="http://docs.python.org/library/functions.html#str" title="(in Python v2.7)"><em>str</em></a>) – The input table to load information from</li>
+<li><strong>outtable</strong> (<a class="reference external" href="http://docs.python.org/library/functions.html#str" title="(in Python v2.7)"><em>str</em></a>) – The output table to write information to.</li>
+<li><strong>type</strong> (<a class="reference external" href="http://docs.python.org/library/functions.html#str" title="(in Python v2.7)"><em>str</em></a>) – The type of calculation to do between treatments. Should be ratio or difference.</li>
+<li><strong>direction</strong> (<a class="reference external" href="http://docs.python.org/library/functions.html#str" title="(in Python v2.7)"><em>str</em></a>) – Whether to compute C ~ S, or S ~ C, default is Control first.</li>
+<li><strong>comp</strong> (<a class="reference external" href="http://docs.python.org/library/functions.html#str" title="(in Python v2.7)"><em>str</em></a>) – Whether to compare by imtype or imgname</li>
+</ul>
+</td>
+</tr>
+</tbody>
+</table>
+<p>This function compares information between treatments – It finds plants that are identical
+except for treatment, and computes either a ratio or difference between them. Direction
+is specified as the column you want first, so direction = “Control” will compute C ~ S, and
+direction = “Stress” will compute S ~ C. If you have already normalized your table, difference
+will provide better information than ratio.</p>
+</dd></dl>
+
+</dd></dl>
+
+</div>
+
+
+ </div>
+
+ </div>
+</div>
+<footer class="footer">
+ <div class="container">
+ <p class="pull-right">
+ <a href="#">Back to top</a>
+
+ </p>
+ <p>
+ © Copyright 2015, Avi Knecht.<br/>
+ Created using <a href="http://sphinx.pocoo.org/">Sphinx</a> 1.3a0.<br/>
+ </p>
+ </div>
+</footer>
+ </body>
+</html>
\ No newline at end of file
diff --git a/docs/build/html/viewer.html b/docs/build/html/viewer.html
new file mode 100644
index 0000000000000000000000000000000000000000..cb601ce549de2eedcf3e92d6296998aee4549b34
--- /dev/null
+++ b/docs/build/html/viewer.html
@@ -0,0 +1,265 @@
+<!DOCTYPE html>
+
+
+<html xmlns="http://www.w3.org/1999/xhtml">
+ <head>
+ <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
+
+ <title>Image Processing Viewer — Image Harvest 1.0.1 documentation</title>
+
+ <link rel="stylesheet" href="_static/basic.css" type="text/css" />
+ <link rel="stylesheet" href="_static/pygments.css" type="text/css" />
+ <link rel="stylesheet" href="_static/bootstrap-3.2.0/css/bootstrap.min.css" type="text/css" />
+ <link rel="stylesheet" href="_static/bootstrap-3.2.0/css/bootstrap-theme.min.css" type="text/css" />
+ <link rel="stylesheet" href="_static/bootstrap-sphinx.css" type="text/css" />
+
+ <script type="text/javascript">
+ var DOCUMENTATION_OPTIONS = {
+ URL_ROOT: './',
+ VERSION: '1.0.1',
+ COLLAPSE_INDEX: false,
+ FILE_SUFFIX: '.html',
+ HAS_SOURCE: true
+ };
+ </script>
+ <script type="text/javascript" src="_static/jquery.js"></script>
+ <script type="text/javascript" src="_static/underscore.js"></script>
+ <script type="text/javascript" src="_static/doctools.js"></script>
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+ <script type="text/javascript" src="_static/js/jquery-1.11.0.min.js"></script>
+ <script type="text/javascript" src="_static/js/jquery-fix.js"></script>
+ <script type="text/javascript" src="_static/bootstrap-3.2.0/js/bootstrap.min.js"></script>
+ <script type="text/javascript" src="_static/bootstrap-sphinx.js"></script>
+ <link rel="top" title="Image Harvest 1.0.1 documentation" href="index.html" />
+ <link rel="next" title="Statistics" href="statistics.html" />
+ <link rel="prev" title="Image Processing" href="processing.html" />
+<meta charset='utf-8'>
+<meta http-equiv='X-UA-Compatible' content='IE=edge,chrome=1'>
+<meta name='viewport' content='width=device-width, initial-scale=1.0, maximum-scale=1'>
+<meta name="apple-mobile-web-app-capable" content="yes">
+
+ </head>
+ <body role="document">
+
+ <div id="navbar" class="navbar navbar-default navbar-fixed-top">
+ <div class="container">
+ <div class="navbar-header">
+ <!-- .btn-navbar is used as the toggle for collapsed navbar content -->
+ <button type="button" class="navbar-toggle" data-toggle="collapse" data-target=".nav-collapse">
+ <span class="icon-bar"></span>
+ <span class="icon-bar"></span>
+ <span class="icon-bar"></span>
+ </button>
+ <a class="navbar-brand" href="index.html">
+ Image Harvest</a>
+ <span class="navbar-text navbar-version pull-left"><b>1.0</b></span>
+ </div>
+
+ <div class="collapse navbar-collapse nav-collapse">
+ <ul class="nav navbar-nav">
+
+
+ <li class="dropdown globaltoc-container">
+ <a role="button"
+ id="dLabelGlobalToc"
+ data-toggle="dropdown"
+ data-target="#"
+ href="index.html">Site <b class="caret"></b></a>
+ <ul class="dropdown-menu globaltoc"
+ role="menu"
+ aria-labelledby="dLabelGlobalToc"><ul class="current">
+<li class="toctree-l1"><a class="reference internal" href="introduction.html">Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="installation.html">Installation</a></li>
+<li class="toctree-l1"><a class="reference internal" href="start.html">Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="ex_script_core1.html">Core Processing Example #1</a></li>
+<li class="toctree-l1"><a class="reference internal" href="ex_script_core2.html">Core Processing Example #2</a></li>
+<li class="toctree-l1"><a class="reference internal" href="ex_script_color1.html">Color Filter In Depth #1</a></li>
+<li class="toctree-l1"><a class="reference internal" href="ex_workflow_1.html">Workflow Example #1</a></li>
+<li class="toctree-l1"><a class="reference internal" href="examples.html">Examples</a></li>
+<li class="toctree-l1"><a class="reference internal" href="processing.html">Image Processing</a></li>
+<li class="toctree-l1 current"><a class="current reference internal" href="">Image Processing Viewer</a></li>
+<li class="toctree-l1"><a class="reference internal" href="statistics.html">Statistics</a></li>
+<li class="toctree-l1"><a class="reference internal" href="indexing.html">Image Loading</a></li>
+<li class="toctree-l1"><a class="reference internal" href="workflowimage.html">Image Processing Workflows</a></li>
+<li class="toctree-l1"><a class="reference internal" href="workflowstats.html">Statistics Workflows</a></li>
+</ul>
+</ul>
+</li>
+
+ <li class="dropdown">
+ <a role="button"
+ id="dLabelLocalToc"
+ data-toggle="dropdown"
+ data-target="#"
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+ <ul class="dropdown-menu localtoc"
+ role="menu"
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+<li><a class="reference internal" href="#">Image Processing Viewer</a></li>
+</ul>
+</ul>
+</li>
+
+
+
+
+
+ <li>
+ <a href="processing.html" title="Previous Chapter: Image Processing"><span class="glyphicon glyphicon-chevron-left visible-sm"></span><span class="hidden-sm hidden-tablet">« Image Processing</span>
+ </a>
+ </li>
+ <li>
+ <a href="statistics.html" title="Next Chapter: Statistics"><span class="glyphicon glyphicon-chevron-right visible-sm"></span><span class="hidden-sm hidden-tablet">Statistics »</span>
+ </a>
+ </li>
+
+
+
+
+
+ <li class="hidden-sm">
+<div id="sourcelink">
+ <a href="_sources/viewer.txt"
+ rel="nofollow">Source</a>
+</div></li>
+
+ </ul>
+
+
+
+<form class="navbar-form navbar-right" action="search.html" method="get">
+ <div class="form-group">
+ <input type="text" name="q" class="form-control" placeholder="Search" />
+ </div>
+ <input type="hidden" name="check_keywords" value="yes" />
+ <input type="hidden" name="area" value="default" />
+</form>
+
+ </div>
+ </div>
+ </div>
+
+<div class="container">
+ <div class="row">
+ <div class="col-md-12">
+
+ <div class="section" id="image-processing-viewer">
+<h1>Image Processing Viewer<a class="headerlink" href="#image-processing-viewer" title="Permalink to this headline">¶</a></h1>
+<script type="text/javascript" src="/Users/aknecht/git/ih/docs/images/viewer.json"></script>
+<script type="text/javascript">
+ base = "/Users/aknecht/git/ih/docs/images/"
+ // base = "/cropstressgenomics.org/data/viewerim/"
+ $(function() {
+ $("#function").on("change", function() {
+ optstr = ""
+ if ($("#function").val() == "bitwise_not" || $("#function").val() == "normalizeByIntensity") {
+ optstr += "<input type='hidden' class='imload' />";
+ }
+ for (var ordernum in data[$("#function").val()]["order"]) {
+ option = data[$("#function").val()]["order"][ordernum]
+ optstr += "<div class='form-group'>";
+ optstr += "<label for='" + option + "'>" + option + "</label>";
+ optstr += "<select class='form-control imload' name='" + option + "' id='load_" + ordernum + "'>";
+ for (var arg in data[$("#function").val()][option]) {
+ optstr += "<option value='" + data[$("#function").val()][option][arg] + "'>" + data[$("#function").val()][option][arg] + "</option>";
+ }
+ optstr += "</select>"
+ optstr += "</div>";
+ }
+ $("#options").html(optstr);
+ $("#options .imload").trigger("change");
+ });
+ $("#image").on("change", function() {
+ $("#inputImage").html("<img src='" + base + "sample/" + $("#image").val() + "' />");
+ $("#options .imload").trigger("change");
+ });
+ $("#options").on("change", ".imload", function() {
+ var l = $("#options > div").length;
+ var impath = base + "/" + $("#function").val() + "/"
+ for (var i = 0; i < l; i++) {
+ impath += $("#load_" + i).attr("name");
+ impath += $("#load_" + i).val()
+ }
+ impath += $("#image").val();
+ $("#outputImage").html("<img src='" + escape(impath) + "' />");
+ });
+ $("#function").trigger("change");
+ $("#image").trigger("change");
+ });
+</script>
+<div class="row">
+ <div style="height:613px;" class="col-md-2">
+ <form>
+ <div class="form-group">
+ <label for="function">Function</label>
+ <select class="form-control" id="function">
+ <option value="adaptiveThreshold">Adaptive Threshold</option>
+ <option value="bitwise_and">Bitwise And</option>
+ <option value="bitwise_not">Bitwise Not</option>
+ <option value="bitwise_or">Bitwise Or</option>
+ <option value="bitwise_xor">Bitwise XOr</option>
+ <option value="blur">Blur</option>
+ <option value="colorFilter">Color Filter</option>
+ <option value="convertColor">Convert Color</option>
+ <option value="crop">Crop</option>
+ <option value="edges">Edges</option>
+ <option value="gaussianBlur">Gaussian Blur</option>
+ <option value="kmeans">Kmeans</option>
+ <option value="meanshift">Mean Shift Segmentation</option>
+ <option value="morphology">Morphology</option>
+ <option value="normalizeByIntensity">Normalize By Intensity</option>
+ <option value="threshold">Threshold</option>
+ </select>
+ </div>
+ <div class="form-group">
+ <label for="image">Images</label>
+ <select class="form-control" id="image">
+ <option value="rgbsv1.png">rgbsv1</option>
+ <option value="rgbsv2.png">rgbsv2</option>
+ <option value="rgbsv3.png">rgbsv3</option>
+ <option value="rgbtv1.png">rgbtv1</option>
+ <option value="rgbtv2.png">rgbtv2</option>
+ <option value="rgbtv3.png">rgbtv3</option>
+ <option value="fluosv1.png">fluosv1</option>
+ <option value="fluosv2.png">fluosv2</option>
+ </select>
+ </div>
+ <div class="form-group">
+ <label for="options">Options</label>
+ <hr style="margin-top:0px;margin-bottom:5px;">
+ </div>
+ <div id="options">
+
+ </div>
+ </form>
+ </div>
+ <div id="inputImage" style="height:613px;" class="col-md-5">
+
+ </div>
+ <div id="outputImage" style="height:613px;" class="col-md-5">
+
+ </div>
+</div>
+<div class="row">
+ <br />
+</div></div>
+
+
+ </div>
+
+ </div>
+</div>
+<footer class="footer">
+ <div class="container">
+ <p class="pull-right">
+ <a href="#">Back to top</a>
+
+ </p>
+ <p>
+ © Copyright 2015, Avi Knecht.<br/>
+ Created using <a href="http://sphinx.pocoo.org/">Sphinx</a> 1.3a0.<br/>
+ </p>
+ </div>
+</footer>
+ </body>
+</html>
\ No newline at end of file
diff --git a/docs/build/html/workflowimage.html b/docs/build/html/workflowimage.html
new file mode 100644
index 0000000000000000000000000000000000000000..60f6275b50031bba52914e138d49b609010f4731
--- /dev/null
+++ b/docs/build/html/workflowimage.html
@@ -0,0 +1,182 @@
+<!DOCTYPE html>
+
+
+<html xmlns="http://www.w3.org/1999/xhtml">
+ <head>
+ <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
+
+ <title>Image Processing Workflows — Image Harvest 1.0.1 documentation</title>
+
+ <link rel="stylesheet" href="_static/basic.css" type="text/css" />
+ <link rel="stylesheet" href="_static/pygments.css" type="text/css" />
+ <link rel="stylesheet" href="_static/bootstrap-3.2.0/css/bootstrap.min.css" type="text/css" />
+ <link rel="stylesheet" href="_static/bootstrap-3.2.0/css/bootstrap-theme.min.css" type="text/css" />
+ <link rel="stylesheet" href="_static/bootstrap-sphinx.css" type="text/css" />
+
+ <script type="text/javascript">
+ var DOCUMENTATION_OPTIONS = {
+ URL_ROOT: './',
+ VERSION: '1.0.1',
+ COLLAPSE_INDEX: false,
+ FILE_SUFFIX: '.html',
+ HAS_SOURCE: true
+ };
+ </script>
+ <script type="text/javascript" src="_static/jquery.js"></script>
+ <script type="text/javascript" src="_static/underscore.js"></script>
+ <script type="text/javascript" src="_static/doctools.js"></script>
+ <script type="text/javascript" src="https://c328740.ssl.cf1.rackcdn.com/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
+ <script type="text/javascript" src="_static/js/jquery-1.11.0.min.js"></script>
+ <script type="text/javascript" src="_static/js/jquery-fix.js"></script>
+ <script type="text/javascript" src="_static/bootstrap-3.2.0/js/bootstrap.min.js"></script>
+ <script type="text/javascript" src="_static/bootstrap-sphinx.js"></script>
+ <link rel="top" title="Image Harvest 1.0.1 documentation" href="index.html" />
+ <link rel="next" title="Statistics Workflows" href="workflowstats.html" />
+ <link rel="prev" title="Image Loading" href="indexing.html" />
+<meta charset='utf-8'>
+<meta http-equiv='X-UA-Compatible' content='IE=edge,chrome=1'>
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+
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+ <body role="document">
+
+ <div id="navbar" class="navbar navbar-default navbar-fixed-top">
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+ <a class="navbar-brand" href="index.html">
+ Image Harvest</a>
+ <span class="navbar-text navbar-version pull-left"><b>1.0</b></span>
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+ <ul class="nav navbar-nav">
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+<li class="toctree-l1"><a class="reference internal" href="start.html">Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="ex_script_core1.html">Core Processing Example #1</a></li>
+<li class="toctree-l1"><a class="reference internal" href="ex_script_core2.html">Core Processing Example #2</a></li>
+<li class="toctree-l1"><a class="reference internal" href="ex_script_color1.html">Color Filter In Depth #1</a></li>
+<li class="toctree-l1"><a class="reference internal" href="ex_workflow_1.html">Workflow Example #1</a></li>
+<li class="toctree-l1"><a class="reference internal" href="examples.html">Examples</a></li>
+<li class="toctree-l1"><a class="reference internal" href="processing.html">Image Processing</a></li>
+<li class="toctree-l1"><a class="reference internal" href="viewer.html">Image Processing Viewer</a></li>
+<li class="toctree-l1"><a class="reference internal" href="statistics.html">Statistics</a></li>
+<li class="toctree-l1"><a class="reference internal" href="indexing.html">Image Loading</a></li>
+<li class="toctree-l1 current"><a class="current reference internal" href="">Image Processing Workflows</a></li>
+<li class="toctree-l1"><a class="reference internal" href="workflowstats.html">Statistics Workflows</a></li>
+</ul>
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+ data-toggle="dropdown"
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+ role="menu"
+ aria-labelledby="dLabelLocalToc"><ul>
+<li><a class="reference internal" href="#">Image Processing Workflows</a></li>
+</ul>
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+</li>
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+ <li>
+ <a href="indexing.html" title="Previous Chapter: Image Loading"><span class="glyphicon glyphicon-chevron-left visible-sm"></span><span class="hidden-sm hidden-tablet">« Image Loading</span>
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+<div id="sourcelink">
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+
+<div class="container">
+ <div class="row">
+ <div class="col-md-12">
+
+ <div class="section" id="image-processing-workflows">
+<h1>Image Processing Workflows<a class="headerlink" href="#image-processing-workflows" title="Permalink to this headline">¶</a></h1>
+<dl class="class">
+<dt id="ih.workflow.ImageProcessor">
+<em class="property">class </em><code class="descclassname">ih.workflow.</code><code class="descname">ImageProcessor</code><span class="sig-paren">(</span><em>jobhome</em>, <em>basename=None</em>, <em>validOnly=False</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/ih/workflow.html#ImageProcessor"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#ih.workflow.ImageProcessor" title="Permalink to this definition">¶</a></dt>
+<dd><p>A class specifically for image processing workflow
+validation and submission.</p>
+<dl class="method">
+<dt id="ih.workflow.ImageProcessor.create">
+<code class="descname">create</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="_modules/ih/workflow.html#ImageProcessor.create"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#ih.workflow.ImageProcessor.create" title="Permalink to this definition">¶</a></dt>
+<dd><p>Creates a new pegasus submission directory based on the current timestamp,
+and populates it with all required information to submit a pegasus job.</p>
+</dd></dl>
+
+</dd></dl>
+
+</div>
+
+
+ </div>
+
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+<footer class="footer">
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+ </p>
+ </div>
+</footer>
+ </body>
+</html>
\ No newline at end of file
diff --git a/docs/build/html/workflowstats.html b/docs/build/html/workflowstats.html
new file mode 100644
index 0000000000000000000000000000000000000000..4e739bfea4d9a5ed3c31d7a16f17f9b6717594ad
--- /dev/null
+++ b/docs/build/html/workflowstats.html
@@ -0,0 +1,177 @@
+<!DOCTYPE html>
+
+
+<html xmlns="http://www.w3.org/1999/xhtml">
+ <head>
+ <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
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+ <title>Statistics Workflows — Image Harvest 1.0.1 documentation</title>
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+ URL_ROOT: './',
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+ HAS_SOURCE: true
+ };
+ </script>
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+ <link rel="top" title="Image Harvest 1.0.1 documentation" href="index.html" />
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+ <span class="icon-bar"></span>
+ <span class="icon-bar"></span>
+ <span class="icon-bar"></span>
+ </button>
+ <a class="navbar-brand" href="index.html">
+ Image Harvest</a>
+ <span class="navbar-text navbar-version pull-left"><b>1.0</b></span>
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+ role="menu"
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+<li class="toctree-l1"><a class="reference internal" href="introduction.html">Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="installation.html">Installation</a></li>
+<li class="toctree-l1"><a class="reference internal" href="start.html">Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="ex_script_core1.html">Core Processing Example #1</a></li>
+<li class="toctree-l1"><a class="reference internal" href="ex_script_core2.html">Core Processing Example #2</a></li>
+<li class="toctree-l1"><a class="reference internal" href="ex_script_color1.html">Color Filter In Depth #1</a></li>
+<li class="toctree-l1"><a class="reference internal" href="ex_workflow_1.html">Workflow Example #1</a></li>
+<li class="toctree-l1"><a class="reference internal" href="examples.html">Examples</a></li>
+<li class="toctree-l1"><a class="reference internal" href="processing.html">Image Processing</a></li>
+<li class="toctree-l1"><a class="reference internal" href="viewer.html">Image Processing Viewer</a></li>
+<li class="toctree-l1"><a class="reference internal" href="statistics.html">Statistics</a></li>
+<li class="toctree-l1"><a class="reference internal" href="indexing.html">Image Loading</a></li>
+<li class="toctree-l1"><a class="reference internal" href="workflowimage.html">Image Processing Workflows</a></li>
+<li class="toctree-l1 current"><a class="current reference internal" href="">Statistics Workflows</a></li>
+</ul>
+</ul>
+</li>
+
+ <li class="dropdown">
+ <a role="button"
+ id="dLabelLocalToc"
+ data-toggle="dropdown"
+ data-target="#"
+ href="#">Page <b class="caret"></b></a>
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+ role="menu"
+ aria-labelledby="dLabelLocalToc"><ul>
+<li><a class="reference internal" href="#">Statistics Workflows</a></li>
+</ul>
+</ul>
+</li>
+
+
+
+
+
+ <li>
+ <a href="workflowimage.html" title="Previous Chapter: Image Processing Workflows"><span class="glyphicon glyphicon-chevron-left visible-sm"></span><span class="hidden-sm hidden-tablet">« Image Processing...</span>
+ </a>
+ </li>
+
+
+
+
+
+ <li class="hidden-sm">
+<div id="sourcelink">
+ <a href="_sources/workflowstats.txt"
+ rel="nofollow">Source</a>
+</div></li>
+
+ </ul>
+
+
+
+<form class="navbar-form navbar-right" action="search.html" method="get">
+ <div class="form-group">
+ <input type="text" name="q" class="form-control" placeholder="Search" />
+ </div>
+ <input type="hidden" name="check_keywords" value="yes" />
+ <input type="hidden" name="area" value="default" />
+</form>
+
+ </div>
+ </div>
+ </div>
+
+<div class="container">
+ <div class="row">
+ <div class="col-md-12">
+
+ <div class="section" id="statistics-workflows">
+<h1>Statistics Workflows<a class="headerlink" href="#statistics-workflows" title="Permalink to this headline">¶</a></h1>
+<dl class="class">
+<dt id="ih.workflow.Statistics">
+<em class="property">class </em><code class="descclassname">ih.workflow.</code><code class="descname">Statistics</code><span class="sig-paren">(</span><em>jobhome</em>, <em>basename</em>, <em>validOnly=False</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/ih/workflow.html#Statistics"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#ih.workflow.Statistics" title="Permalink to this definition">¶</a></dt>
+<dd><p>A class specifically for statistics workflow
+validation and submission.</p>
+<dl class="method">
+<dt id="ih.workflow.Statistics.create">
+<code class="descname">create</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="_modules/ih/workflow.html#Statistics.create"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#ih.workflow.Statistics.create" title="Permalink to this definition">¶</a></dt>
+<dd><p>Creates a new pegasus submission directory based on the current timestamp,
+and populates it with all required information to submit a pegasus job.</p>
+</dd></dl>
+
+</dd></dl>
+
+</div>
+
+
+ </div>
+
+ </div>
+</div>
+<footer class="footer">
+ <div class="container">
+ <p class="pull-right">
+ <a href="#">Back to top</a>
+
+ </p>
+ <p>
+ © Copyright 2015, Avi Knecht.<br/>
+ Created using <a href="http://sphinx.pocoo.org/">Sphinx</a> 1.3a0.<br/>
+ </p>
+ </div>
+</footer>
+ </body>
+</html>
\ No newline at end of file
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diff --git a/docs/images/info.py b/docs/images/info.py
new file mode 100644
index 0000000000000000000000000000000000000000..2263246383a86afc429f360443d8bb943be524db
--- /dev/null
+++ b/docs/images/info.py
@@ -0,0 +1,5 @@
+rgbsv = ["rgbsv" + str(i) + ".png" for i in range(1,4)]
+rgbtv = ["rgbtv" + str(i) + ".png" for i in range(1,4)]
+fluosv = ["fluosv" + str(i) + ".png" for i in range(1, 3)]
+all = rgbsv + rgbtv + fluosv
+
diff --git a/docs/images/info.pyc b/docs/images/info.pyc
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diff --git a/docs/images/sample/fluosvmask1.png b/docs/images/sample/fluosvmask1.png
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diff --git a/docs/images/sample/fluosvmask2.png b/docs/images/sample/fluosvmask2.png
new file mode 100644
index 0000000000000000000000000000000000000000..da5f268a26c05aa29f79d2fda70bf36f45de8a35
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diff --git a/docs/images/sample/fluosvmask3.png b/docs/images/sample/fluosvmask3.png
new file mode 100644
index 0000000000000000000000000000000000000000..57b0f404c619d8491ee5c2fdd3227d34a218afe4
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diff --git a/docs/images/sample/fluosvmask4.png b/docs/images/sample/fluosvmask4.png
new file mode 100644
index 0000000000000000000000000000000000000000..7bb1927a1c59efec70a4f11e2c5ac2f112f584fa
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diff --git a/docs/images/sample/mask.py b/docs/images/sample/mask.py
new file mode 100644
index 0000000000000000000000000000000000000000..52efbd2ad0777cc6845544530e4a24d0523827cb
--- /dev/null
+++ b/docs/images/sample/mask.py
@@ -0,0 +1,25 @@
+import ih.imgproc
+import numpy as np
+import cv2
+
+type = "rgbsv"
+infile = type + "1.png"
+plant = ih.imgproc.Image(infile)
+
+m = np.zeros(plant.image.shape)
+
+mask1 = ih.imgproc.Image(m)
+mask1.image[:plant.y / 2,:,:] = 255
+mask1.write(type + "mask1.png")
+
+mask2 = ih.imgproc.Image(m)
+mask2.image[plant.y / 2:,:,:] = 255
+mask2.write(type + "mask2.png")
+
+mask3 = ih.imgproc.Image(m)
+mask3.image[:,:plant.x/2,:] = 255
+mask3.write(type + "mask3.png")
+
+mask4 = ih.imgproc.Image(m)
+mask4.image[:,plant.x/2:,:] = 255
+mask4.write(type + "mask4.png")
diff --git a/docs/images/sample/resize.py b/docs/images/sample/resize.py
new file mode 100644
index 0000000000000000000000000000000000000000..43407acbab0083c0ebb473290a5dc6484d4b0878
--- /dev/null
+++ b/docs/images/sample/resize.py
@@ -0,0 +1,5 @@
+import ih.imgproc
+
+plant = ih.imgproc.Image("save_rgbsv1.png")
+plant.resizeSelf(scale = 0.4)
+plant.write("test.png")
diff --git a/docs/images/sample/rgbsv1.png b/docs/images/sample/rgbsv1.png
new file mode 100755
index 0000000000000000000000000000000000000000..7238c6a4f41bcfd565b8e22c0deedab91d9902b7
Binary files /dev/null and b/docs/images/sample/rgbsv1.png differ
diff --git a/docs/images/sample/rgbsv2.png b/docs/images/sample/rgbsv2.png
new file mode 100644
index 0000000000000000000000000000000000000000..2f6e7e470681f26ea65f6fdcc4418d3b5cadbb46
Binary files /dev/null and b/docs/images/sample/rgbsv2.png differ
diff --git a/docs/images/sample/rgbsv3.png b/docs/images/sample/rgbsv3.png
new file mode 100644
index 0000000000000000000000000000000000000000..6e794ac5af13d6c513cf54793eb60c05e6d136b3
Binary files /dev/null and b/docs/images/sample/rgbsv3.png differ
diff --git a/docs/images/sample/rgbsvmask1.png b/docs/images/sample/rgbsvmask1.png
new file mode 100644
index 0000000000000000000000000000000000000000..80b39f75c787a38f316d2f1a72b962ce0d247f13
Binary files /dev/null and b/docs/images/sample/rgbsvmask1.png differ
diff --git a/docs/images/sample/rgbsvmask2.png b/docs/images/sample/rgbsvmask2.png
new file mode 100644
index 0000000000000000000000000000000000000000..f0760724fd745e4e84a81967486b403ef4bd5fa5
Binary files /dev/null and b/docs/images/sample/rgbsvmask2.png differ
diff --git a/docs/images/sample/rgbsvmask3.png b/docs/images/sample/rgbsvmask3.png
new file mode 100644
index 0000000000000000000000000000000000000000..817fc60d6036c0c95b222c9eee2087759f7176a0
Binary files /dev/null and b/docs/images/sample/rgbsvmask3.png differ
diff --git a/docs/images/sample/rgbsvmask4.png b/docs/images/sample/rgbsvmask4.png
new file mode 100644
index 0000000000000000000000000000000000000000..158afa43ac2e07b86cc84d5f4a1f7362706b56f5
Binary files /dev/null and b/docs/images/sample/rgbsvmask4.png differ
diff --git a/docs/images/sample/rgbtv1.png b/docs/images/sample/rgbtv1.png
new file mode 100644
index 0000000000000000000000000000000000000000..3e511ecd79ce64e0184b1ca2abeef1d6ae5fd71c
Binary files /dev/null and b/docs/images/sample/rgbtv1.png differ
diff --git a/docs/images/sample/rgbtv1_small.png b/docs/images/sample/rgbtv1_small.png
new file mode 100644
index 0000000000000000000000000000000000000000..58e869084fd10951625e9b0ac960ac7fa9fa5a5e
Binary files /dev/null and b/docs/images/sample/rgbtv1_small.png differ
diff --git a/docs/images/sample/rgbtv2.png b/docs/images/sample/rgbtv2.png
new file mode 100644
index 0000000000000000000000000000000000000000..10ccb5e282aa55de4b956a5a23c64b4d710538ef
Binary files /dev/null and b/docs/images/sample/rgbtv2.png differ
diff --git a/docs/images/sample/rgbtv3.png b/docs/images/sample/rgbtv3.png
new file mode 100644
index 0000000000000000000000000000000000000000..d43591223048d88797b33cf10dddccb8eed9f17f
Binary files /dev/null and b/docs/images/sample/rgbtv3.png differ
diff --git a/docs/images/sample/rgbtvmask1.png b/docs/images/sample/rgbtvmask1.png
new file mode 100644
index 0000000000000000000000000000000000000000..c44b9ceae8f498d9180073cd0fa36802abc732c5
Binary files /dev/null and b/docs/images/sample/rgbtvmask1.png differ
diff --git a/docs/images/sample/rgbtvmask2.png b/docs/images/sample/rgbtvmask2.png
new file mode 100644
index 0000000000000000000000000000000000000000..e546e3cf5b88adfca9daf4c2c384e5516d49b5a7
Binary files /dev/null and b/docs/images/sample/rgbtvmask2.png differ
diff --git a/docs/images/sample/rgbtvmask3.png b/docs/images/sample/rgbtvmask3.png
new file mode 100644
index 0000000000000000000000000000000000000000..ef0d19062ab1d5b3e306912a56cc407467339d5b
Binary files /dev/null and b/docs/images/sample/rgbtvmask3.png differ
diff --git a/docs/images/sample/rgbtvmask4.png b/docs/images/sample/rgbtvmask4.png
new file mode 100644
index 0000000000000000000000000000000000000000..6fb42b3507944de386922b6c4dfdd48db6747888
Binary files /dev/null and b/docs/images/sample/rgbtvmask4.png differ
diff --git a/docs/images/sample/save_rgbsv1.png b/docs/images/sample/save_rgbsv1.png
new file mode 100755
index 0000000000000000000000000000000000000000..a5614cdf0d60fa48b1472271a6ea9260a6a8102e
Binary files /dev/null and b/docs/images/sample/save_rgbsv1.png differ
diff --git a/docs/images/sample/test.png b/docs/images/sample/test.png
new file mode 100644
index 0000000000000000000000000000000000000000..b4bbf64a79b86bc2f1abab96d2a615315a083143
Binary files /dev/null and b/docs/images/sample/test.png differ
diff --git a/examples/workflows/current/GenKey239.csv b/examples/workflows/current/GenKey239.csv
new file mode 100644
index 0000000000000000000000000000000000000000..0886d4a04d9bb5a2724c163dcc7c610d067cdbd7
--- /dev/null
+++ b/examples/workflows/current/GenKey239.csv
@@ -0,0 +1 @@
+Snapshot ID Tag,UNL ID
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041324-S,UNL250
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