def resizeAndSave(filePaths, l):
while l.get() < min(len(filePaths), currentWrittenLayer + nTilesAtATime + 1) :
k = l.getAndIncrement()
if k < min(len(filePaths), currentWrittenLayer + nTilesAtATime):
filePath = filePaths[k]
imageName = os.path.basename(filePath)
resizedImageName = os.path.splitext(imageName)[0] + '_resized_' + factorString + os.path.splitext(imageName)[1]
imageFolderName = os.path.basename(os.path.dirname(filePath))
resizedFilePath = fc.cleanLinuxPath(os.path.join(downSampledEMFolder, imageFolderName, resizedImageName))
im = Opener().openImage(filePath)
IJ.log('Am I going to process the image: im.height = ' + str(im.height) + ' - tileHeight = ' + str(tileHeight) + ' tile number ' + str(k))
if im.height == tileHeight: # crop a few lines at the top only if it has not already been done (sometimes the pipeline gets rerun)
im = fc.crop(im,cropRoi)
im = fc.normLocalContrast(im, normLocalContrastSize, normLocalContrastSize, 3, True, True)
# IJ.run(im, 'Replace value', 'pattern=0 replacement=1') # only for final waferOverview
FileSaver(im).saveAsTiff(filePath)
if not os.path.isfile(resizedFilePath):
im = fc.resize(im, scaleFactor)
FileSaver(im).saveAsTiff(resizedFilePath)
IJ.log('Image resized to ' + resizedFilePath)
im.close()
def contrastImage(): while atomicI.get() < nPaths: k = atomicI.getAndIncrement() if k < nPaths: im = IJ.openImage(toContrastPaths[k][0]) im = fc.normLocalContrast(im, normLocalContrastSize, normLocalContrastSize, 3, True, True) IJ.save(im, toContrastPaths[k][1]) im.close()
im = IJ.openImage(imPath)
im = fc.minMax(im, meanMin, meanMax)
IJ.run(im, '8-bit', '')
IJ.run(im, 'Flip Horizontally',
'') # {Leica DMI, NikonTiEclipse} to Merlin
IJ.save(im, imPath)
IJ.log('Image ' + imPath + ' thresholded 8-bited')
# process all other channels that are not refChannel: normLocalContrast, threshold, 8-bit
for (dirpath, dirnames, filenames) in os.walk(LMDataFolder):
for filename in filenames:
if (os.path.splitext(filename)[1]
== '.tif') and not (refChannel in filename):
imPath = os.path.join(dirpath, filename)
im = IJ.openImage(imPath)
im = fc.normLocalContrast(im, normLocalContrastSizeFluo,
normLocalContrastSizeFluo, 3, True, True)
im = fc.minMax(im, minMaxFluo[0], minMaxFluo[1])
IJ.run(im, '8-bit', '')
if flipHorizontally:
IJ.run(im, 'Flip Horizontally', '') # Leica DMI to Merlin
IJ.save(im, imPath)
IJ.log('Image ' + imPath + ' processed')
# add a contrasted reference channel (e.g., contrast the brightfield channel)
IJ.log('Adding a contrasted channel')
contrastedChannel = 'contrasted' + refChannel
channels.append(contrastedChannel)
toContrastPaths = []
for (dirpath, dirnames, filenames) in os.walk(LMDataFolder):
for filename in filenames:
LMFolder, 'exported_downscaled_1_' + channel,
'exported_downscaled_1_' + channel + '_' +
str(l).zfill(4) + '.tif'))
patch = Patch.createPatch(pZ, LMMosaicsPath)
layerZ.add(patch)
IJ.log('Setting the affineTransform ' + str(affTransform))
patch.setAffineTransform(affTransform)
patch.updateBucket()
bb = Rectangle(0, 0, widthEM, heightEM)
affineCroppedIm = loaderZ.getFlatImage(layerZ, bb, 1, 0x7fffffff,
ImagePlus.GRAY8, Patch,
layerZ.getAll(Patch), True,
Color.black, None)
affineCroppedIm = fc.normLocalContrast(affineCroppedIm, 50, 50, 3,
True, True)
IJ.run(affineCroppedIm, 'Median...', 'radius=2')
affineCroppedImPath = os.path.join(
affineCroppedFolder,
'affineCropped_' + channel + '_' + str(l).zfill(4) + '.tif')
IJ.save(affineCroppedIm, affineCroppedImPath)
affineCroppedIm.close()
layerZ.remove(patch)
layerZ.recreateBuckets()
IJ.log('Has been written: ' + str(affineCroppedImPath))
fc.closeProject(pZ) # close dummy trakem
# # # # # # create the median folders
# # # # # for channel in channels[:-2]: # the fluorescent channels, excluding the brightfield and contrastedBrightfield channels
# # # # # affineCroppedFolder = os.path.join(LMFolder, 'affineCropped_' + channel)