Mercurial > repos > imgteam > permutate_axis
view permutate_axis.py @ 0:0bbe34198e24 draft
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/permutate_axis/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
author | imgteam |
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date | Sat, 09 Feb 2019 14:42:29 -0500 |
parents | |
children | 5b82f2186244 |
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import argparse import sys import warnings import numpy as np import skimage.io 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 if axis == 0: a_slice = raw_image[i] elif axis == 1: a_slice = raw_image[:,i] elif axis == 2: a_slice = raw_image[:,:,i] elif axis == 3: a_slice = raw_image[:,:,:,i] elif axis == 4: 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') if __name__ == "__main__": parser = argparse.ArgumentParser() parser.add_argument('input_file', type=argparse.FileType('r'), help='input file') parser.add_argument('out_file', type=argparse.FileType('w'), help='out file (TIFF)') parser.add_argument('permutate', help='new channel order', default='0,1,2', type=str) parser.add_argument('--axis', dest='axis', type=int, default=0, help='concatenation axis') args = parser.parse_args() permutate = [int(item) for item in args.permutate.split(',')] permutate_axis(args.input_file.name, args.out_file.name, args.axis, permutate)