From 16c608d161e86d311659ad0ff594d87c3f97305d Mon Sep 17 00:00:00 2001
From: cramakri <cramakri>
Date: Wed, 24 Aug 2011 13:52:29 +0000
Subject: [PATCH] LMS-2472 Initial check-in of Tomek's script
SVN: 22625
---
.../python/screening/generate-test-images.py | 284 ++++++++++++++++++
1 file changed, 284 insertions(+)
create mode 100644 test-data/source/python/screening/generate-test-images.py
diff --git a/test-data/source/python/screening/generate-test-images.py b/test-data/source/python/screening/generate-test-images.py
new file mode 100644
index 00000000000..69f758eef8d
--- /dev/null
+++ b/test-data/source/python/screening/generate-test-images.py
@@ -0,0 +1,284 @@
+#!/usr/bin/python
+
+from CoreGraphics import *
+import math
+import os
+import shutil
+
+size = 512
+well = "A1"
+tileNum = 6
+
+def drawRect(context, r, g, b, start, isUnfilled = 0):
+ context.saveGState ()
+ context.setRGBStrokeColor (r,g,b,1)
+ if isUnfilled:
+ context.setRGBFillColor (0,0,0,0) # transparent
+ else:
+ context.setRGBFillColor (r,g,b,1)
+ context.setLineWidth (40)
+ context.addRect (CGRectMake (start, start, size - 2*start, size - 2*start))
+ context.drawPath (kCGPathFillStroke);
+ context.restoreGState ()
+
+def createContext():
+ cs = CGColorSpaceCreateDeviceRGB ()
+ return CGBitmapContextCreateWithColor (size, size, cs, (0,0,0,0))
+
+# -------------------------
+"""
+def drawMatrixRect(context, isOverlay, x,y):
+ if isOverlay < 2:
+ context.saveGState ()
+ if isOverlay == 0:
+ context.setRGBFillColor (0.5,0.5,0.5,1)
+ context.setLineWidth (40)
+ ident = 0
+ else:
+ context.setRGBFillColor (0,0,0,0)
+ context.setLineWidth (5)
+ context.setRGBStrokeColor (1,1,1,1)
+ ident = 10
+ context.addRect (CGRectMake (ident+(x-1)*(size/3), ident+(y-1)*(size/3),
+ size/3 - ident*2, size/3 - ident*2))
+ context.drawPath (kCGPathFillStroke);
+ context.restoreGState ()
+ else:
+ drawText(context, (x-0.5)*(size/3), (y-0.5)*(size/3), "X")
+"""
+
+def calcTile(coords):
+ x,y = coords
+ return (y-1)*3+x
+
+def drawMatrix(coordsList, dir, channel, isOverlay):
+ nonemptyTiles = set([ calcTile(coords) for coords in coordsList ])
+ for tile in range(1, 10):
+ c = createContext()
+ if tile in nonemptyTiles:
+ if not isOverlay:
+ drawRect(c, 0, 0, 0, 0)
+ drawRect(c, 0.5, 0.5, 0.5, 70, isUnfilled = 0)
+ elif isOverlay == 1:
+ drawRect(c, 1, 1, 1, 30, isUnfilled = 1)
+ else:
+ drawText(c, size/2, size/2, "X")
+ destFile = dir + "/c"+channel + "_s" + str(tile) +".png"
+ c.writeToFile (destFile, kCGImageFormatPNG)
+
+def overlayTests(sampleCode):
+ rootDir = "targets/generated-images"
+ recreateDir(rootDir)
+
+ dir = rootDir + "/" + sampleCode+".basic"
+ recreateDir(dir)
+ drawMatrix(((1,1), (1,2), (1,3), (3,1)), dir, "NUCLEUS", 0);
+ drawMatrix(((1,2), (2,2), (2,3), (3,1)), dir, "CELL", 0);
+ drawMatrix(((1,3), (2,3), (3,3), (3,1)), dir, "MITOCHONDRION", 0);
+
+ dir = rootDir + "/" + sampleCode+".overlay-surround"
+ recreateDir(dir)
+ drawMatrix(((1,1), (1,2), (1,3), (3,1)), dir, "NUCLEUS", 1);
+ drawMatrix(((1,2), (2,2), (2,3), (3,1)), dir, "CELL", 1);
+ drawMatrix(((1,3), (2,3), (3,3), (3,1)), dir, "MITOCHONDRION", 1);
+
+ dir = rootDir + "/" + sampleCode+".overlay-text"
+ recreateDir(dir)
+ drawMatrix(((1,1), (1,2), (1,3), (3,1)), dir, "NUCLEUS-TEXT", 2);
+ drawMatrix(((1,2), (2,2), (2,3), (3,1)), dir, "CELL-TEXT", 2);
+ drawMatrix(((1,3), (2,3), (3,3), (3,1)), dir, "MITOCHONDRION-TEXT", 2);
+
+# ---------------------------
+def drawText(c, x, y, text):
+ c.saveGState ()
+ c.setRGBStrokeColor (0,0,0,1)
+ c.setRGBFillColor (1,1,1,1)
+ c.selectFont ("Helvetica", 70, kCGEncodingMacRoman)
+ c.setTextPosition (x, y)
+ c.setTextDrawingMode (kCGTextFillStroke)
+ c.showText (text, len(text))
+ c.restoreGState ()
+
+def save(dir, filename, text, r, g, b, merged = 0):
+ c = createContext()
+ drawRect(c, 0, 0, 0, 0) # fill with black
+
+ zero = 0
+ if merged:
+ zero = 1
+ if r:
+ drawRect(c, 1, zero, zero, 20) # red
+ if g:
+ drawRect(c, zero, 1, zero, 70) # green
+ if b:
+ drawRect(c, zero, zero, 1, 120) # blue
+
+ # text annotation
+ drawText(c, 5, size / 2, text)
+
+ # Write the bitmap to disk in PNG format
+ c.writeToFile (dir + "/" + filename, kCGImageFormatPNG)
+
+def recreateDir(dir):
+ if os.path.exists(dir):
+ shutil.rmtree(dir)
+ os.mkdir(dir)
+
+# -------------------------------
+
+def generateMicroscopy3D(dir, channelName, r, g, b, merged = 0):
+ timePoints = [ 5, 10, 15 ]
+ depthPoints = [ 3, 6, 9 ]
+ series = [1,2,3]
+ for seriesNum in series:
+ for tile in range(1, tileNum+1):
+ for time in timePoints:
+ for depth in depthPoints:
+ desc = "s"+str(tile)+"_z"+str(depth)+"_t"+str(time)+"_n"+str(seriesNum)
+ file = desc+"_c"+channelName+".png"
+ save(dir, file, desc, r, g, b, merged)
+
+def generateMicroscopySeries(dir, channelName, r, g, b, merged = 0):
+ for seriesNum in range(1,11):
+ for tile in range(1, tileNum+1):
+ desc = "s"+str(tile)+"_n"+str(seriesNum)
+ file = desc+"_c"+channelName+".png"
+ save(dir, file, desc, r, g, b, merged)
+
+def generateMicroscopySeriesBrokenTiles(dir, channelName, r, g, b, merged = 0):
+ tiles = [1,3,5]
+ for seriesNum in range(1,11):
+ for tile in tiles:
+ desc = "s"+str(tile)+"_n"+str(seriesNum)
+ file = desc+"_c"+channelName+".png"
+ save(dir, file, desc, r, g, b, merged)
+
+def generateMicroscopyChannel(dir, channelName, r, g, b, merged = 0):
+ #timePoints = [ 1 ]
+ #tileNum = 1
+ #depthPoints = [ 1 ]
+
+ timePoints = [ 5, 10, 15 ]
+ depthPoints = [ 3, 6, 9 ]
+ for tile in range(1, tileNum+1):
+ for time in timePoints:
+ for depth in depthPoints:
+ desc = "s"+str(tile)+"_z"+str(depth)+"_t"+str(time)
+ file = desc+"_c"+channelName+".png"
+ save(dir, file, desc, r, g, b, merged)
+
+def generateMicroscopyChannelNoDepth(dir, channelName, r, g, b):
+ timePoints = [ 5, 10, 15 ]
+ for tile in range(1, tileNum+1):
+ for time in timePoints:
+ desc = "s"+str(tile)+"_t"+str(time)
+ file = desc+"_c"+channelName+".png"
+ save(dir, file, desc, r, g, b)
+
+def generateMicroscopyChannelNoTimeNoDepth(dir, channelName, r, g, b):
+ for tile in range(1, tileNum+1):
+ desc = "s"+str(tile)
+ file = desc+"_c"+channelName+".png"
+ save(dir, file, desc, r, g, b)
+
+# -------------------------------
+
+def generatePlateChannel(dir, channelName, r, g, b, merged = 0):
+ timePoints = [ 5, 10, 15 ]
+ depthPoints = [ 3, 6, 9 ]
+ for tile in range(1, tileNum+1):
+ for time in timePoints:
+ for depth in depthPoints:
+ desc = "s"+str(tile)+"_z"+str(depth)+"_t"+str(time)
+ file = "bPLATE_w"+well+"_"+desc+"_c"+channelName+".png"
+ save(dir, file, desc, r, g, b, merged)
+
+def generatePlateChannelNoDepth(dir, channelName, r, g, b):
+ timePoints = [ 5, 10, 15 ]
+ for tile in range(1, tileNum+1):
+ for time in timePoints:
+ desc = "s"+str(tile)+"_t"+str(time)
+ file = "bPLATE_w"+well+"_"+desc+"_c"+channelName+".png"
+ save(dir, file, desc, r, g, b)
+
+def generatePlateChannelNoTimeNoDepth(dir, channelName, r, g, b):
+ for tile in range(1, tileNum+1):
+ desc = "s"+str(tile)
+ file = "bPLATE_w"+well+"_"+desc+"_c"+channelName+".png"
+ save(dir, file, desc, r, g, b)
+
+
+def generatePlateSplitChannels(dir):
+ recreateDir(dir)
+ generatePlateChannel(dir, "RED", 1, 0, 0, 1)
+ generatePlateChannel(dir, "GREEN", 0, 1, 0, 1)
+ generatePlateChannel(dir, "BLUE", 0, 0, 1, 1)
+
+def generatePlateMergedChannels(dir):
+ recreateDir(dir)
+ generatePlateChannel(dir, "RGB", 1, 1, 1)
+
+# -------------------------------
+
+def generateMicroscopySplitChannels(dir):
+ recreateDir(dir)
+ generateMicroscopyChannel(dir, "RED", 1, 0, 0, 1)
+ generateMicroscopyChannel(dir, "GREEN", 0, 1, 0, 1)
+ generateMicroscopyChannel(dir, "BLUE", 0, 0, 1, 1)
+
+def generateMicroscopyMergedChannels(dir):
+ recreateDir(dir)
+ generateMicroscopyChannel(dir, "RGB", 1, 1, 1)
+
+def generateMicroscopyMergedChannelsNoTimeNoDepth():
+ dir = "TEST.microscopy.mergedChannels_tile_noTime_noDepth"
+ recreateDir(dir)
+ generateMicroscopyChannelNoTimeNoDepth(dir, "RGB", 1, 1, 1)
+
+def generateMicroscopyMergedChannelsNoDepth():
+ dir = "TEST.microscopy.mergedChannels_tile_time_noDepth"
+ recreateDir(dir)
+ generateMicroscopyChannelNoDepth(dir, "RGB", 1, 1, 1)
+
+def generateMicroscopySplitChannelsSeriesBrokenTiles():
+ dir = "TEST.microscopy.splitChannels_someTiles_series"
+ recreateDir(dir)
+ generateMicroscopySeriesBrokenTiles(dir, "AAA", 1, 0, 0, 1)
+ generateMicroscopySeriesBrokenTiles(dir, "BBB", 0, 1, 0, 1)
+ generateMicroscopySeriesBrokenTiles(dir, "CCC", 0, 0, 1, 1)
+
+def generateMicroscopySplitChannels3D():
+ dir = "TEST.microscopy.splitChannels_3D"
+ recreateDir(dir)
+ generateMicroscopy3D(dir, "AAA", 1, 0, 0, 1)
+ generateMicroscopy3D(dir, "DDD", 0, 1, 0, 1)
+ generateMicroscopy3D(dir, "EEE", 0, 0, 1, 1)
+
+def generateMicroscopySplitChannelsSeries():
+ dir = "TEST.microscopy.splitChannels_series"
+ recreateDir(dir)
+ generateMicroscopySeries(dir, "AAA", 1, 0, 0, 1)
+ generateMicroscopySeries(dir, "CCC", 0, 1, 0, 1)
+ generateMicroscopySeries(dir, "FFF", 0, 0, 1, 1)
+
+def generateMicroscopySplitChannelsSeries():
+ dir = "TEST.microscopy.splitChannels_series"
+ recreateDir(dir)
+ generateMicroscopySeries(dir, "AAA", 1, 0, 0, 1)
+ generateMicroscopySeries(dir, "BBB", 0, 1, 0, 1)
+ generateMicroscopySeries(dir, "CCC", 0, 0, 1, 1)
+ generateMicroscopySeries(dir, "DDD", 1, 1, 0, 1)
+ generateMicroscopySeries(dir, "EEE", 0, 1, 1, 1)
+ generateMicroscopySeries(dir, "FFF", 1, 0, 1, 1)
+
+#generatePlateSplitChannels("PLATE.splitChannels_tile_time_depth")
+#generatePlateMergedChannels("PLATE.mergedChannels_tile_time_depth")
+#generateMicroscopySplitChannels("TEST.microscopy.splitChannels_tile_time_depth")
+#generateMicroscopyMergedChannels("TEST.microscopy.mergedChannels_tile_time_depth")
+#generateMicroscopyMergedChannels3D("TEST.microscopy.mergedChannels_tile_time_depth_series")
+#generateMicroscopyMergedChannelsNoTimeNoDepth()
+#generateMicroscopyMergedChannelsNoDepth()
+#generateMicroscopySplitChannelsSeriesBrokenTiles()
+#generateMicroscopySplitChannelsSeries()
+#generateMicroscopySplitChannels3D()
+overlayTests("OVERLAY-TEST")
\ No newline at end of file
--
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