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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
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d5ab37450c44 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/permutate_axis/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
1 import argparse
d5ab37450c44 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/permutate_axis/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
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2 import warnings
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ce64e2e4afd2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/permutate_axis/ commit 4afe0015d92913952714d0695b0fb46ea004171f
imgteam
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d5ab37450c44 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/permutate_axis/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
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4 import numpy as np
d5ab37450c44 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/permutate_axis/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
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5 import skimage.io
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ce64e2e4afd2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/permutate_axis/ commit 4afe0015d92913952714d0695b0fb46ea004171f
imgteam
parents: 2
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6 import skimage.util
ce64e2e4afd2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/permutate_axis/ commit 4afe0015d92913952714d0695b0fb46ea004171f
imgteam
parents: 2
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d5ab37450c44 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/permutate_axis/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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d5ab37450c44 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/permutate_axis/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
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9 def permutate_axis(input_image_path, output_image_path, axis, permutate):
d5ab37450c44 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/permutate_axis/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
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10 images = []
d5ab37450c44 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')
d5ab37450c44 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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ce64e2e4afd2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/permutate_axis/ commit 4afe0015d92913952714d0695b0fb46ea004171f
imgteam
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13 # TODO generalise
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d5ab37450c44 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:
d5ab37450c44 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]
d5ab37450c44 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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ce64e2e4afd2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/permutate_axis/ commit 4afe0015d92913952714d0695b0fb46ea004171f
imgteam
parents: 2
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17 a_slice = raw_image[:, i]
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d5ab37450c44 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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ce64e2e4afd2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/permutate_axis/ commit 4afe0015d92913952714d0695b0fb46ea004171f
imgteam
parents: 2
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19 a_slice = raw_image[:, :, i]
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d5ab37450c44 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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ce64e2e4afd2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/permutate_axis/ commit 4afe0015d92913952714d0695b0fb46ea004171f
imgteam
parents: 2
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21 a_slice = raw_image[:, :, :, i]
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d5ab37450c44 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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ce64e2e4afd2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/permutate_axis/ commit 4afe0015d92913952714d0695b0fb46ea004171f
imgteam
parents: 2
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23 a_slice = raw_image[:, :, :, :, i]
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d5ab37450c44 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/permutate_axis/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
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24 images.append(np.expand_dims(a_slice, axis))
d5ab37450c44 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/permutate_axis/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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d5ab37450c44 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/permutate_axis/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
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26 res = np.concatenate(images, axis)
d5ab37450c44 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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ce64e2e4afd2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/permutate_axis/ commit 4afe0015d92913952714d0695b0fb46ea004171f
imgteam
parents: 2
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28 warnings.simplefilter("ignore")
ce64e2e4afd2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/permutate_axis/ commit 4afe0015d92913952714d0695b0fb46ea004171f
imgteam
parents: 2
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29 res = skimage.util.img_as_uint(res) # Attention: precision loss
ce64e2e4afd2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/permutate_axis/ commit 4afe0015d92913952714d0695b0fb46ea004171f
imgteam
parents: 2
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30 skimage.io.imsave(output_image_path, res, plugin='tifffile')
ce64e2e4afd2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/permutate_axis/ commit 4afe0015d92913952714d0695b0fb46ea004171f
imgteam
parents: 2
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d5ab37450c44 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/permutate_axis/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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d5ab37450c44 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/permutate_axis/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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33 if __name__ == "__main__":
d5ab37450c44 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()
d5ab37450c44 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/permutate_axis/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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35 parser.add_argument('input_file', type=argparse.FileType('r'), help='input file')
d5ab37450c44 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)')
d5ab37450c44 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)
d5ab37450c44 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/permutate_axis/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
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38 parser.add_argument('--axis', dest='axis', type=int, default=0, help='concatenation axis')
d5ab37450c44 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()
d5ab37450c44 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/permutate_axis/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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d5ab37450c44 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/permutate_axis/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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41 permutate = [int(item) for item in args.permutate.split(',')]
d5ab37450c44 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)