Added ih-write-sql script, updated ih-seed script to optionally allow thresh value.

docs/source/index.rst

@@ -9,7 +9,7 @@ To obtain access to a larger set of rice images (RGB, FLUO, NIR, IR), please con
 
 * Publications:
     * Campbell MT, Knecht AC, Berger B, Brien CJ, Wang D, Walia H. Integrating Image-Based Phenomics and Association Analysis to Dissect the Genetic Architecture of Temporal Salinity Responses in Rice. 2015, Plant Physiology. `Link <http://www.plantphysiol.org/content/early/2015/06/25/pp.15.00450.short>`_.
-    * Knecht AC, Campbell MT, Caprez A, Swanson DR, Walia H. Image Harvest: An open source platform for high-throughput plant image processing and analysis.  2016, JXB.  (In press).
+    * Knecht AC, Campbell MT, Caprez A, Swanson DR, Walia H. Image Harvest: An open source platform for high-throughput plant image processing and analysis.  2016, JXB.  (In prep).
         * `Developing a processing workflow on a local computer <http://cropstressgenomics.org/data/html/ex_script_camera2.html>`_
         * `Executing processing workflows on a computing cluster <http://cropstressgenomics.org/data/html/ex_workflow_1.html>`_
 

ih/statistics.py

@@ -765,10 +765,6 @@ class Stats:
         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

scripts/ih-seed

@@ -9,6 +9,7 @@ parser.add_argument("--input", dest="input", help="Path to input seed scan image
 parser.add_argument("--output", dest="output", help="Path to output csv file.", required = True)
 parser.add_argument("--dpi", dest="dpi", help="dpi of the image.", type = float, default = 600)
 parser.add_argument("--roi", dest="roi", help="roi file")
+parser.add_argument("--thresh", dest="thresh", type=int, default=230, help="Threshold value.")
 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.")
@@ -29,7 +30,8 @@ if args.writesteps:
 seed.convertColor("bgr", "gray")
 
 seed.equalizeHist()
-seed.threshold(230)
+seed.threshold(args.thresh)
+seed.save("thresh")
 if args.writesteps:
   seed.write(prefix + "_thresh.png")
 

scripts/ih-write-sql

+#!python
+"""
+A helper script as a workaround for >1000 column sqlite joins.
+The script itself walks through the current directory, and
+creates an sql file that will join all possible databases.
+"""
+import os
+import argparse
+
+parser = argparse.ArgumentParser(description = "Creates an sql script to join many databse files.")
+parser.add_argument("--prefix", dest="prefix", help="Optional prefix to match for db names.")
+parser.add_argument("--output", dest="output", default="combine.sql", help="Output file name.")
+args = parser.parse_args()
+
+# The required lines to write for each database
+lines = [
+"begin;",
+"insert into images select * from to_merge.images;",
+"commit;",
+"detach to_merge;"
+]
+
+# Writes the resulting combine.sql
+with open("combine.sql", "w") as wh:
+    for root, dirs, files in os.walk("."):
+        for f in files:
+            # Matches all db files
+            if f[-2:] == "db":
+                if not args.prefix or f[-len(args.prefix):] == prefix:
+                    first_line = ["attach \"%s\" as to_merge;" % (f,)]
+                    write_lines = first_line + std_lines
+                    for line in write_lines:
+                        wh.write(line + "\n")
+                    wh.write("\n")
+        break
+
+"""
+You may want to optionally filter based on the type of the data if different
+imtypes have different processing results.
+After creating the combine.sql file, you can aggregate data the following way:
+1. Copy a sample database to maintain original structure.
+    > cp fluosv0.db fluosv_all.db
+2. Load up the final database in sqlite:
+    > sqlite3 fluosv_all.db
+3. Within sqlite, read in the created sql file:
+    > .read combine.sql
+"""

setup.py

@@ -34,6 +34,7 @@ setup(
 		"scripts/ih-flood-fill",
 
 		"scripts/ih-seed",
+        "scripts/ih-write-sql",
 
 		"scripts/ih-setup",
 		"scripts/ih-crawl",