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import math
import os
import shutil
size = 512
well = "A1"
tileNum = 6
def create_canvas():
return canvas.PlateWellCanvas(size, size)
def write_to_png_file(canvas, filename):
canvas.write_png_file(filename)
def drawRect(canvas, r, g, b, start, isUnfilled = 0):
canvas.draw_inset_rect(r, g, b, start, isUnfilled)
def drawText(canvas, x, y, text):
canvas.draw_text(x, y, text)
def drawMatrix(coordsList, dir, channel, isOverlay):
nonemptyTiles = set([ calcTile(coords) for coords in coordsList ])
for tile in range(1, 10):
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
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):
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)
if os.path.exists(dir):
shutil.rmtree(dir)
os.mkdir(dir)
# -------------------------------
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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")