Mercurial > repos > imgteam > permutate_axis

comparison permutate_axis.py @ 0:0bbe34198e24 draft

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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/permutate_axis/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
author imgteam
date Sat, 09 Feb 2019 14:42:29 -0500
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children 5b82f2186244
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-1:000000000000 0:0bbe34198e24
1 import argparse
2 import sys
3 import warnings
4 import numpy as np
5 import skimage.io
6 import skimage.util
7
8 def permutate_axis(input_image_path, output_image_path, axis, permutate):
9 images = []
10 raw_image = skimage.io.imread(input_image_path, plugin='tifffile')
11 for i in permutate:
12 # TODO generalise
13 if axis == 0:
14 a_slice = raw_image[i]
15 elif axis == 1:
16 a_slice = raw_image[:,i]
17 elif axis == 2:
18 a_slice = raw_image[:,:,i]
19 elif axis == 3:
20 a_slice = raw_image[:,:,:,i]
21 elif axis == 4:
22 a_slice = raw_image[:,:,:,:,i]
23 images.append(np.expand_dims(a_slice, axis))
24
25 res = np.concatenate(images, axis)
26 with warnings.catch_warnings():
27 warnings.simplefilter("ignore")
28 res = skimage.util.img_as_uint(res) #Attention: precision loss
29 skimage.io.imsave(output_image_path, res, plugin='tifffile')
30
31 if __name__ == "__main__":
32 parser = argparse.ArgumentParser()
33 parser.add_argument('input_file', type=argparse.FileType('r'), help='input file')
34 parser.add_argument('out_file', type=argparse.FileType('w'), help='out file (TIFF)')
35 parser.add_argument('permutate', help='new channel order', default='0,1,2', type=str)
36 parser.add_argument('--axis', dest='axis', type=int, default=0, help='concatenation axis')
37 args = parser.parse_args()
38
39 permutate = [int(item) for item in args.permutate.split(',')]
40 permutate_axis(args.input_file.name, args.out_file.name, args.axis, permutate)