Mercurial > repos > thomaswollmann > permutate_axis

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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/permutate_axis/ commit 27a6350188f687411bdd6bfe0d569c0803389ca0
author thomaswollmann
date Wed, 12 Dec 2018 04:50:51 -0500
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8fb82d514666 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/permutate_axis/ commit 27a6350188f687411bdd6bfe0d569c0803389ca0
thomaswollmann
parents:
diff changeset
1 import argparse
8fb82d514666 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/permutate_axis/ commit 27a6350188f687411bdd6bfe0d569c0803389ca0
thomaswollmann
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2 import sys
8fb82d514666 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/permutate_axis/ commit 27a6350188f687411bdd6bfe0d569c0803389ca0
thomaswollmann
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3 import warnings
8fb82d514666 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/permutate_axis/ commit 27a6350188f687411bdd6bfe0d569c0803389ca0
thomaswollmann
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4 import numpy as np
8fb82d514666 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/permutate_axis/ commit 27a6350188f687411bdd6bfe0d569c0803389ca0
thomaswollmann
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5 import skimage.io
8fb82d514666 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/permutate_axis/ commit 27a6350188f687411bdd6bfe0d569c0803389ca0
thomaswollmann
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6 import skimage.util
8fb82d514666 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/permutate_axis/ commit 27a6350188f687411bdd6bfe0d569c0803389ca0
thomaswollmann
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7
8fb82d514666 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/permutate_axis/ commit 27a6350188f687411bdd6bfe0d569c0803389ca0
thomaswollmann
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8 def permutate_axis(input_image_path, output_image_path, axis, permutate):
8fb82d514666 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/permutate_axis/ commit 27a6350188f687411bdd6bfe0d569c0803389ca0
thomaswollmann
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9 images = []
8fb82d514666 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/permutate_axis/ commit 27a6350188f687411bdd6bfe0d569c0803389ca0
thomaswollmann
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10 raw_image = skimage.io.imread(input_image_path, plugin='tifffile')
8fb82d514666 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/permutate_axis/ commit 27a6350188f687411bdd6bfe0d569c0803389ca0
thomaswollmann
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11 for i in permutate:
8fb82d514666 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/permutate_axis/ commit 27a6350188f687411bdd6bfe0d569c0803389ca0
thomaswollmann
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12 # TODO generalise
8fb82d514666 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/permutate_axis/ commit 27a6350188f687411bdd6bfe0d569c0803389ca0
thomaswollmann
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13 if axis == 0:
8fb82d514666 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/permutate_axis/ commit 27a6350188f687411bdd6bfe0d569c0803389ca0
thomaswollmann
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14 a_slice = raw_image[i]
8fb82d514666 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/permutate_axis/ commit 27a6350188f687411bdd6bfe0d569c0803389ca0
thomaswollmann
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15 elif axis == 1:
8fb82d514666 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/permutate_axis/ commit 27a6350188f687411bdd6bfe0d569c0803389ca0
thomaswollmann
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16 a_slice = raw_image[:,i]
8fb82d514666 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/permutate_axis/ commit 27a6350188f687411bdd6bfe0d569c0803389ca0
thomaswollmann
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17 elif axis == 2:
8fb82d514666 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/permutate_axis/ commit 27a6350188f687411bdd6bfe0d569c0803389ca0
thomaswollmann
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18 a_slice = raw_image[:,:,i]
8fb82d514666 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/permutate_axis/ commit 27a6350188f687411bdd6bfe0d569c0803389ca0
thomaswollmann
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19 elif axis == 3:
8fb82d514666 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/permutate_axis/ commit 27a6350188f687411bdd6bfe0d569c0803389ca0
thomaswollmann
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20 a_slice = raw_image[:,:,:,i]
8fb82d514666 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/permutate_axis/ commit 27a6350188f687411bdd6bfe0d569c0803389ca0
thomaswollmann
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21 elif axis == 4:
8fb82d514666 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/permutate_axis/ commit 27a6350188f687411bdd6bfe0d569c0803389ca0
thomaswollmann
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22 a_slice = raw_image[:,:,:,:,i]
8fb82d514666 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/permutate_axis/ commit 27a6350188f687411bdd6bfe0d569c0803389ca0
thomaswollmann
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23 images.append(np.expand_dims(a_slice, axis))
8fb82d514666 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/permutate_axis/ commit 27a6350188f687411bdd6bfe0d569c0803389ca0
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8fb82d514666 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/permutate_axis/ commit 27a6350188f687411bdd6bfe0d569c0803389ca0
thomaswollmann
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25 res = np.concatenate(images, axis)
8fb82d514666 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/permutate_axis/ commit 27a6350188f687411bdd6bfe0d569c0803389ca0
thomaswollmann
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26 with warnings.catch_warnings():
8fb82d514666 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/permutate_axis/ commit 27a6350188f687411bdd6bfe0d569c0803389ca0
thomaswollmann
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27 warnings.simplefilter("ignore")
8fb82d514666 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/permutate_axis/ commit 27a6350188f687411bdd6bfe0d569c0803389ca0
thomaswollmann
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28 res = skimage.util.img_as_uint(res) #Attention: precision loss
8fb82d514666 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/permutate_axis/ commit 27a6350188f687411bdd6bfe0d569c0803389ca0
thomaswollmann
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29 skimage.io.imsave(output_image_path, res, plugin='tifffile')
8fb82d514666 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/permutate_axis/ commit 27a6350188f687411bdd6bfe0d569c0803389ca0
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30
8fb82d514666 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/permutate_axis/ commit 27a6350188f687411bdd6bfe0d569c0803389ca0
thomaswollmann
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31 if __name__ == "__main__":
8fb82d514666 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/permutate_axis/ commit 27a6350188f687411bdd6bfe0d569c0803389ca0
thomaswollmann
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32 parser = argparse.ArgumentParser()
8fb82d514666 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/permutate_axis/ commit 27a6350188f687411bdd6bfe0d569c0803389ca0
thomaswollmann
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33 parser.add_argument('input_file', type=argparse.FileType('r'), help='input file')
8fb82d514666 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/permutate_axis/ commit 27a6350188f687411bdd6bfe0d569c0803389ca0
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34 parser.add_argument('out_file', type=argparse.FileType('w'), help='out file (TIFF)')
8fb82d514666 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/permutate_axis/ commit 27a6350188f687411bdd6bfe0d569c0803389ca0
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35 parser.add_argument('permutate', help='new channel order', default='0,1,2', type=str)
8fb82d514666 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/permutate_axis/ commit 27a6350188f687411bdd6bfe0d569c0803389ca0
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36 parser.add_argument('--axis', dest='axis', type=int, default=0, help='concatenation axis')
8fb82d514666 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/permutate_axis/ commit 27a6350188f687411bdd6bfe0d569c0803389ca0
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37 args = parser.parse_args()
8fb82d514666 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/permutate_axis/ commit 27a6350188f687411bdd6bfe0d569c0803389ca0
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38
8fb82d514666 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/permutate_axis/ commit 27a6350188f687411bdd6bfe0d569c0803389ca0
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39 permutate = [int(item) for item in args.permutate.split(',')]
8fb82d514666 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/permutate_axis/ commit 27a6350188f687411bdd6bfe0d569c0803389ca0
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40 permutate_axis(args.input_file.name, args.out_file.name, args.axis, permutate)