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kmader/AverageSliceValue.py

Created March 5, 2014 15:46
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Calculate the average value in each slice
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AverageSliceValue.py
image = WindowManager.getCurrentImage()
stack = image.getStack() # get the stack within the ImagePlus
n_slices = stack.getSize() # get the number of slices
# iterate over every slice
for sliceIndex in range(1,n_slices+1):
curSlice=stack.getProcessor(sliceIndex)
sumVal=0;countPixel=0
# iterate over every pixel in the slice
for cPixel in curSlice.toFloatArrays()[0]:
sumVal+=cPixel
countPixel+=1
IJ.log("Slice:"+str(sliceIndex)+", Mean:"+str(sumVal/countPixel))
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