Mercurial > repos > imgteam > permutate_axis

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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/permutate_axis/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
author imgteam
date Mon, 13 Nov 2023 22:11:38 +0000
parents 91e255c78eb5
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0bbe34198e24 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/permutate_axis/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
1 import argparse
0bbe34198e24 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/permutate_axis/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
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2 import warnings
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7e7215e721af planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/permutate_axis/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
imgteam
parents: 2
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0bbe34198e24 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/permutate_axis/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
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4 import numpy as np
0bbe34198e24 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/permutate_axis/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
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5 import skimage.io
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7e7215e721af planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/permutate_axis/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
imgteam
parents: 2
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6 import skimage.util
7e7215e721af planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/permutate_axis/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
imgteam
parents: 2
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0bbe34198e24 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/permutate_axis/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
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0bbe34198e24 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/permutate_axis/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
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9 def permutate_axis(input_image_path, output_image_path, axis, permutate):
0bbe34198e24 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/permutate_axis/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
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10 images = []
0bbe34198e24 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/permutate_axis/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
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11 raw_image = skimage.io.imread(input_image_path, plugin='tifffile')
0bbe34198e24 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/permutate_axis/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
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12 for i in permutate:
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7e7215e721af planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/permutate_axis/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
imgteam
parents: 2
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13 # TODO generalise
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0bbe34198e24 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/permutate_axis/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
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14 if axis == 0:
0bbe34198e24 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/permutate_axis/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
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15 a_slice = raw_image[i]
0bbe34198e24 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/permutate_axis/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
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16 elif axis == 1:
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7e7215e721af planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/permutate_axis/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
imgteam
parents: 2
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17 a_slice = raw_image[:, i]
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0bbe34198e24 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/permutate_axis/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
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18 elif axis == 2:
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7e7215e721af planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/permutate_axis/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
imgteam
parents: 2
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19 a_slice = raw_image[:, :, i]
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0bbe34198e24 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/permutate_axis/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
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20 elif axis == 3:
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7e7215e721af planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/permutate_axis/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
imgteam
parents: 2
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21 a_slice = raw_image[:, :, :, i]
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0bbe34198e24 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/permutate_axis/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
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22 elif axis == 4:
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7e7215e721af planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/permutate_axis/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
imgteam
parents: 2
diff changeset
23 a_slice = raw_image[:, :, :, :, i]
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0bbe34198e24 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/permutate_axis/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
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24 images.append(np.expand_dims(a_slice, axis))
0bbe34198e24 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/permutate_axis/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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0bbe34198e24 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/permutate_axis/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
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26 res = np.concatenate(images, axis)
0bbe34198e24 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/permutate_axis/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
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27 with warnings.catch_warnings():
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7e7215e721af planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/permutate_axis/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
imgteam
parents: 2
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28 warnings.simplefilter("ignore")
7e7215e721af planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/permutate_axis/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
imgteam
parents: 2
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29 res = skimage.util.img_as_uint(res) # Attention: precision loss
7e7215e721af planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/permutate_axis/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
imgteam
parents: 2
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30 skimage.io.imsave(output_image_path, res, plugin='tifffile')
7e7215e721af planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/permutate_axis/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
imgteam
parents: 2
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0bbe34198e24 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/permutate_axis/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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0bbe34198e24 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/permutate_axis/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
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33 if __name__ == "__main__":
0bbe34198e24 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/permutate_axis/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
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34 parser = argparse.ArgumentParser()
0bbe34198e24 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/permutate_axis/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
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35 parser.add_argument('input_file', type=argparse.FileType('r'), help='input file')
0bbe34198e24 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/permutate_axis/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
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36 parser.add_argument('out_file', type=argparse.FileType('w'), help='out file (TIFF)')
0bbe34198e24 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/permutate_axis/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
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37 parser.add_argument('permutate', help='new channel order', default='0,1,2', type=str)
0bbe34198e24 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/permutate_axis/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
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38 parser.add_argument('--axis', dest='axis', type=int, default=0, help='concatenation axis')
0bbe34198e24 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/permutate_axis/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
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39 args = parser.parse_args()
0bbe34198e24 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/permutate_axis/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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0bbe34198e24 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/permutate_axis/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
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41 permutate = [int(item) for item in args.permutate.split(',')]
0bbe34198e24 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/permutate_axis/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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42 permutate_axis(args.input_file.name, args.out_file.name, args.axis, permutate)