Mercurial > repos > imgteam > permutate_axis

annotate permutate_axis.py @ 2:91e255c78eb5 draft

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"planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/permutate_axis/ commit 3d389fdec0db29cf6fbd783c0501455bf624fa90"
author imgteam
date Wed, 18 Dec 2019 05:02:53 -0500
parents 5b82f2186244
children 7e7215e721af
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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
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2 import sys
0bbe34198e24 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/permutate_axis/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
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3 import warnings
0bbe34198e24 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
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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91e255c78eb5 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/permutate_axis/ commit 3d389fdec0db29cf6fbd783c0501455bf624fa90"
imgteam
parents: 1
diff changeset
6 import skimage.util
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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
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8 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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9 images = []
0bbe34198e24 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/permutate_axis/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
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10 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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11 for i in permutate:
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5b82f2186244 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/permutate_axis/ commit b2acc1845a25828181597fe5b6982fe116a7796d
imgteam
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12 # 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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13 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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14 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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15 elif axis == 1:
0bbe34198e24 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/permutate_axis/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
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16 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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17 elif axis == 2:
0bbe34198e24 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/permutate_axis/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
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18 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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19 elif axis == 3:
0bbe34198e24 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/permutate_axis/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
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20 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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21 elif axis == 4:
0bbe34198e24 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/permutate_axis/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
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22 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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23 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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24
0bbe34198e24 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/permutate_axis/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
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25 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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26 with warnings.catch_warnings():
0bbe34198e24 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/permutate_axis/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
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27 warnings.simplefilter("ignore")
0bbe34198e24 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/permutate_axis/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
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28 res = skimage.util.img_as_uint(res) #Attention: precision loss
0bbe34198e24 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/permutate_axis/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
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29 skimage.io.imsave(output_image_path, res, plugin='tifffile')
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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31 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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32 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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33 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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34 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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35 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
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36 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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37 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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38
0bbe34198e24 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/permutate_axis/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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39 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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40 permutate_axis(args.input_file.name, args.out_file.name, args.axis, permutate)