OSG Documentation Update

MANIFEST

+# file GENERATED by distutils, do NOT edit
+setup.py
+ih/__init__.py
+ih/conf.py
+ih/imgproc.py
+ih/statistics.py
+ih/validator.py
+ih/workflow.py
+scripts/ih-adaptive-threshold
+scripts/ih-bitwise-and
+scripts/ih-bitwise-not
+scripts/ih-bitwise-or
+scripts/ih-bitwise-xor
+scripts/ih-blur
+scripts/ih-color-filter
+scripts/ih-contour-cut
+scripts/ih-convert-color
+scripts/ih-crawl
+scripts/ih-crop
+scripts/ih-data
+scripts/ih-edges
+scripts/ih-error-log
+scripts/ih-extract
+scripts/ih-extract-all
+scripts/ih-extract-multi
+scripts/ih-gaussian-blur
+scripts/ih-meanshift
+scripts/ih-median-blur
+scripts/ih-morphology
+scripts/ih-normalize-intensity
+scripts/ih-resize
+scripts/ih-run
+scripts/ih-setup
+scripts/ih-sql-aggregate
+scripts/ih-stats-anova
+scripts/ih-stats-correlate
+scripts/ih-stats-export
+scripts/ih-stats-histogram-bin
+scripts/ih-stats-normalize
+scripts/ih-stats-shoot-area
+scripts/ih-stats-threshold
+scripts/ih-stats-treatment-comp
+scripts/ih-stats-ttest
+scripts/ih-threshold
+scripts/osg-wrapper.sh

build/scripts-2.7/ih-adaptive-threshold

+#!/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()

build/scripts-2.7/ih-bitwise-and

+#!/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.")
+parser.add_argument("--mask", default=False, dest="mask", action="store_true", help="Convert the first input image to a mask.")
+args = parser.parse_args()
+
+try:
+    plant = ih.imgproc.Image(args.input1, args.outputdir, args.output, False)
+    if args.mask:
+    	plant.mask()
+    plant.bitwise_and(args.input2)
+    plant.write()
+except Exception as e:
+    print traceback.format_exc()

build/scripts-2.7/ih-bitwise-not

+#!/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()

build/scripts-2.7/ih-bitwise-or

+#!/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()

build/scripts-2.7/ih-bitwise-xor

+#!/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()

build/scripts-2.7/ih-blur

+#!/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()

build/scripts-2.7/ih-color-filter

+#!/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()

build/scripts-2.7/ih-contour-cut

+#!/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()

build/scripts-2.7/ih-convert-color

+#!/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()

build/scripts-2.7/ih-crawl

+#!/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()

build/scripts-2.7/ih-crop

+#!/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()

build/scripts-2.7/ih-data

+#!/usr/bin/python
+import argparse
+import traceback
+import ih.statistics
+import os
+import json
+
+parser = argparse.ArgumentParser(description = "Change input data format.")
+parser.add_argument("--db", dest="db", help="Database to run statistics on.", required = True)
+parser.add_argument("--dir", dest="dir", required = True, help="Folder to move files to.")
+parser.add_argument("--type", dest="type", required = True, help="Type of translation.  Should be one of [pcv, iap]")
+parser.add_argument("--ids", dest="ids", nargs="+", default=None, help="List of ids to extract from db.")
+parser.add_argument("--idfile", dest="idfile", default=None, help="Path to file containing list of ids.")
+parser.add_argument("--imtypes", dest="imtypes", nargs="+", default=None, help="List of imtypes to extract from db.")
+parser.add_argument("--imtypefile", dest="imtypefile", default=None, help="Path to file containing list of imtypes.")
+parser.add_argument("--dates", dest="dates", nargs="+", default=None, help="List of dates to extract from db.")
+parser.add_argument("--datefile", dest="datefile", default=None, help="Path to file containing list of dates.")
+args = parser.parse_args()
+
+try:
+    if args.idfile:
+        with open(args.idfile, "r") as rh:
+            ids = []
+            for line in rh.readlines():
+                ids.append(line.strip())
+    else:
+        ids = args.ids
+        
+    if args.imtypefile:
+        with open(args.idfile, "r") as rh:
+            imtypes = []
+            for line in rh.readlines():
+                imtypes.append(line.strip())
+    else:
+        imtypes = args.imtypes
+        
+    if args.datefile:
+        with open(args.datefile, "r") as rh:
+            dates = []
+            for line in rh.readlines():
+                dates.append(line.strip())
+    else:
+        dates = args.dates
+            
+    stats = ih.statistics.Stats(args.db)
+    if args.type == "pcv":
+        stats.dataToPlantcv(args.dir, ids, imtypes, dates)
+    elif args.type == "iap":
+        stats.dataToIAP(args.dir, ids, imtypes, dates)
+    stats._closeConnection()
+except Exception as e:
+    print traceback.format_exc()
\ No newline at end of file

build/scripts-2.7/ih-edges

+#!/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()