diff --git a/test-data/source/python/screening/generate-test-images.py b/test-data/source/python/screening/generate-test-images.py
index 69f758eef8dfb75eefaef0e619fe9da092467033..3240aba80d800617daae178620768eff6c68036e 100644
--- a/test-data/source/python/screening/generate-test-images.py
+++ b/test-data/source/python/screening/generate-test-images.py
@@ -1,6 +1,8 @@
#!/usr/bin/python
-from CoreGraphics import *
+from Quartz import *
+from Cocoa import *
+from LaunchServices import * # for kUTTypePNG
import math
import os
import shutil
@@ -9,267 +11,261 @@ 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")
-"""
+ cs = CGColorSpaceCreateDeviceRGB ()
+ pixelsWide = size
+ pixelsHigh = size
+ bits_per_component = 8
+ number_of_components = 4 # r,g,b,a
+ # Convert bits per component to bytes per pixel, rounding up to the next int if necessary
+ bytes_per_pixel = (bits_per_component * number_of_components + 7)/8
+ bitmapBytesPerRow = (pixelsWide * bytes_per_pixel);
+ bitmapByteCount = (bitmapBytesPerRow * pixelsHigh);
+ # Create an RGB bitmap, let CoreGraphics deal with allocating and managing memory
+ ctx = CGBitmapContextCreate(None, pixelsWide, pixelsHigh, bits_per_component, bitmapBytesPerRow, cs, kCGImageAlphaPremultipliedLast)
+ return ctx
+
+def write_to_png_file(ctx, filename):
+ image = CGBitmapContextCreateImage(ctx)
+ fileUrl = NSURL.fileURLWithPath_(filename)
+ dest = CGImageDestinationCreateWithURL(fileUrl, kUTTypePNG, 1, None);
+ CGImageDestinationAddImage(dest, image, None);
+ CGImageDestinationFinalize(dest);
+
+def drawRect(ctx, r, g, b, start, isUnfilled = 0):
+ with CGSavedGState(ctx):
+ CGContextSetRGBStrokeColor(ctx, r, g, b, 1)
+ if isUnfilled:
+ CGContextSetRGBFillColor(ctx, 0, 0, 0, 0) # transparent
+ else:
+ CGContextSetRGBFillColor(ctx, r, g, b, 1)
+ CGContextSetLineWidth(ctx, 40)
+ CGContextAddRect(ctx, CGRectMake(start, start, size - 2 * start, size - 2 * start))
+ CGContextDrawPath(ctx, kCGPathFillStroke)
+
+def drawText(ctx, x, y, text):
+ with CGSavedGState(ctx):
+ CGContextSetRGBStrokeColor(ctx, 0, 0, 0, 1) # black
+ CGContextSetRGBFillColor(ctx, 1, 1, 1, 1) # white
+ CGContextSetTextMatrix(ctx, CGAffineTransformIdentity)
+ CGContextSelectFont(ctx, "Helvetica Neue", 70, kCGEncodingMacRoman)
+ CGContextSetTextDrawingMode(ctx, kCGTextFillStroke)
+ CGContextShowTextAtPoint(ctx, x, y, text, len(text))
-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)
+ 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"
+ write_to_png_file(c, destFile)
+
+def calcTile(coords):
+ x,y = coords
+ return (y-1)*3+x
+
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 ()
-
+ 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 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)
+ 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
+ write_to_png_file(c, dir + "/" + filename)
def recreateDir(dir):
- if os.path.exists(dir):
- shutil.rmtree(dir)
- os.mkdir(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 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)
-
+ #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)
+ 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)
-
+ 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)
+ 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)
+ 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)
+ 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)
+ 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)
+ 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)
+ 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)
+ 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)
+ 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)
+ 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)
+ 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)
-
+ 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)
+ 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)
+ 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")