LMS-2472 Initial check-in of Tomek's script

SVN: 22625

test-data/source/python/screening/generate-test-images.py

+#!/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")
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