def extractChannel(imp, nChannel, nFrame):
""" Extract a stack for a specific color channel and time frame """
stack = imp.getImageStack()
ch = ImageStack(imp.width, imp.height)
for i in range(1, imp.getNSlices() + 1):
index = imp.getStackIndex(nChannel, i, nFrame)
ch.addSlice(str(i), stack.getProcessor(index))
stack_to_return = ImagePlus("Channel " + str(nChannel), ch)
stack_to_return.copyScale(imp)
return stack_to_return
def decon(seriesNumber, imgP, psfP):
nChannels = imgP.getNChannels()
if nChannels>1:
imgPc = ChannelSplitter.split(imgP)
else:
imgPc = [imgP]
if psfP.getNChannels()>1:
psfPc = ChannelSplitter.split(psfP)
if len(psfPc)<nChannels:
log("PSF image has fewer channels! Skipping image's trailing channels {} to {}".format(psfP.getNChannels()+1,nChannels))
imgPc = imgPc[:psfP.getNChannels()]
else:
psfPc = [psfP]*nChannels
nChannels = len(imgPc)
if combinedChannels:
deconChannels = None
for channelNumber in range(nChannels):
log("Processing image {} series {} channel {}..".format(inputFile.getAbsolutePath(),seriesNumber,channelNumber))
imgP = imgPc[channelNumber]
psfP = psfPc[channelNumber]
img = ImageJFunctions.wrap(imgP)
psf = ImageJFunctions.wrap(psfP)
# convert to float (TODO: make sure deconvolution op works on other types)
imgF=ops.convert().float32(img)
psfF=ops.convert().float32(psf)
# make psf same size as image
psfSize=FinalDimensions([img.dimension(0), img.dimension(1), img.dimension(2)]);
# add border in z direction
#borderSize=[0,0,psfSize.dimension(2)/2];
borderSize=[0,0,0];
deconvolved = ops.deconvolve().richardsonLucy(imgF, psfF, numIterations);
# Create the ImagePlus, copy scale and dimensions
deconvolvedImp = ImageJFunctions.wrapFloat(deconvolved,inputFile.getName()+'-series{}-channel{}-deconvolvedWith-{}-{}iterations.tiff'.format(seriesNumber,channelNumber,psfFile.getName(),numIterations))
deconvolvedImp.copyScale(imgP)
width, height, nChannelz, nSlices, nFrames = imgP.getDimensions()
deconvolvedImp.setDimensions(nChannelz, nSlices, nFrames)
if combinedChannels:
if deconChannels is None:
deconChannels = ImageStack(width,height)
for z in range(nSlices):
deconChannels.addSlice(deconvolvedImp.getStack().getProcessor(z))
else:
IJ.saveAsTiff(deconvolvedImp,os.path.join(outputDirectory.getAbsolutePath(),deconvolvedImp.getTitle()))
if combinedChannels:
final = ImageStack(width,height)
for z in range(nSlices):
for c in range(nChannels):
i = c*nSlices+z
final.addSlice(deconChannels.getProcessor(i+1))
hyperstack = ImagePlus(inputFile.getName()+'-series{}-deconvolvedWith-{}-{}iterations.tiff'.format(seriesNumber,psfFile.getName(),numIterations),final)
hyperstack = HyperStackConverter.toHyperStack(hyperstack,nChannels,nSlices,1)
hyperstack.copyScale(imgP)
IJ.saveAsTiff(hyperstack,os.path.join(outputDirectory.getAbsolutePath(),hyperstack.getTitle()))
