Mercurial > repos > imgteam > permutate_axis
diff permutate_axis.py @ 3:ce64e2e4afd2 draft default tip
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/permutate_axis/ commit 4afe0015d92913952714d0695b0fb46ea004171f
| author | imgteam |
|---|---|
| date | Wed, 17 Dec 2025 15:34:17 +0000 |
| parents | 21168547d572 |
| children |
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--- a/permutate_axis.py Wed Dec 18 09:58:57 2019 +0000 +++ b/permutate_axis.py Wed Dec 17 15:34:17 2025 +0000 @@ -1,32 +1,34 @@ import argparse -import sys import warnings + import numpy as np import skimage.io -import skimage.util +import skimage.util + def permutate_axis(input_image_path, output_image_path, axis, permutate): images = [] raw_image = skimage.io.imread(input_image_path, plugin='tifffile') for i in permutate: - # TODO generalise + # TODO generalise if axis == 0: a_slice = raw_image[i] elif axis == 1: - a_slice = raw_image[:,i] + a_slice = raw_image[:, i] elif axis == 2: - a_slice = raw_image[:,:,i] + a_slice = raw_image[:, :, i] elif axis == 3: - a_slice = raw_image[:,:,:,i] + a_slice = raw_image[:, :, :, i] elif axis == 4: - a_slice = raw_image[:,:,:,:,i] + a_slice = raw_image[:, :, :, :, i] images.append(np.expand_dims(a_slice, axis)) res = np.concatenate(images, axis) with warnings.catch_warnings(): - warnings.simplefilter("ignore") - res = skimage.util.img_as_uint(res) #Attention: precision loss - skimage.io.imsave(output_image_path, res, plugin='tifffile') + warnings.simplefilter("ignore") + res = skimage.util.img_as_uint(res) # Attention: precision loss + skimage.io.imsave(output_image_path, res, plugin='tifffile') + if __name__ == "__main__": parser = argparse.ArgumentParser()