Mercurial > repos > thomaswollmann > mergeneighboursinlabelimage

annotate mergeneighboursinlabelimage.py @ 0:66f7e94db2e6 draft

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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/\mergeneighboursinlabelimage commit d0759a055484abd42bba38b2fa46f2a7b8f96259
author thomaswollmann
date Tue, 08 Jan 2019 08:54:16 -0500
parents
children 3536648d0a93
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66f7e94db2e6 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/\mergeneighboursinlabelimage commit d0759a055484abd42bba38b2fa46f2a7b8f96259
thomaswollmann
parents:
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1 #!/usr/bin/python
66f7e94db2e6 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/\mergeneighboursinlabelimage commit d0759a055484abd42bba38b2fa46f2a7b8f96259
thomaswollmann
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2
66f7e94db2e6 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/\mergeneighboursinlabelimage commit d0759a055484abd42bba38b2fa46f2a7b8f96259
thomaswollmann
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3 import argparse
66f7e94db2e6 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/\mergeneighboursinlabelimage commit d0759a055484abd42bba38b2fa46f2a7b8f96259
thomaswollmann
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4 import sys
66f7e94db2e6 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/\mergeneighboursinlabelimage commit d0759a055484abd42bba38b2fa46f2a7b8f96259
thomaswollmann
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5 import skimage.io
66f7e94db2e6 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/\mergeneighboursinlabelimage commit d0759a055484abd42bba38b2fa46f2a7b8f96259
thomaswollmann
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6 import skimage.util
66f7e94db2e6 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/\mergeneighboursinlabelimage commit d0759a055484abd42bba38b2fa46f2a7b8f96259
thomaswollmann
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7 from skimage.measure import regionprops
66f7e94db2e6 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/\mergeneighboursinlabelimage commit d0759a055484abd42bba38b2fa46f2a7b8f96259
thomaswollmann
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8 import scipy.spatial.distance
66f7e94db2e6 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/\mergeneighboursinlabelimage commit d0759a055484abd42bba38b2fa46f2a7b8f96259
thomaswollmann
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9 import numpy as np
66f7e94db2e6 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/\mergeneighboursinlabelimage commit d0759a055484abd42bba38b2fa46f2a7b8f96259
thomaswollmann
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10 import warnings
66f7e94db2e6 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/\mergeneighboursinlabelimage commit d0759a055484abd42bba38b2fa46f2a7b8f96259
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11
66f7e94db2e6 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/\mergeneighboursinlabelimage commit d0759a055484abd42bba38b2fa46f2a7b8f96259
thomaswollmann
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12 def merge_n(img, dist=50):
66f7e94db2e6 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/\mergeneighboursinlabelimage commit d0759a055484abd42bba38b2fa46f2a7b8f96259
thomaswollmann
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13 props = regionprops(img)
66f7e94db2e6 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/\mergeneighboursinlabelimage commit d0759a055484abd42bba38b2fa46f2a7b8f96259
thomaswollmann
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14 found = False
66f7e94db2e6 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/\mergeneighboursinlabelimage commit d0759a055484abd42bba38b2fa46f2a7b8f96259
thomaswollmann
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15 for i in range(0, len(props)):
66f7e94db2e6 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/\mergeneighboursinlabelimage commit d0759a055484abd42bba38b2fa46f2a7b8f96259
thomaswollmann
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16 i_coords = props[i].coords
66f7e94db2e6 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/\mergeneighboursinlabelimage commit d0759a055484abd42bba38b2fa46f2a7b8f96259
thomaswollmann
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17 for q in range(0, len(props)):
66f7e94db2e6 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/\mergeneighboursinlabelimage commit d0759a055484abd42bba38b2fa46f2a7b8f96259
thomaswollmann
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18 if i==q:
66f7e94db2e6 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/\mergeneighboursinlabelimage commit d0759a055484abd42bba38b2fa46f2a7b8f96259
thomaswollmann
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19 continue
66f7e94db2e6 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/\mergeneighboursinlabelimage commit d0759a055484abd42bba38b2fa46f2a7b8f96259
thomaswollmann
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20 q_coords = props[q].coords
66f7e94db2e6 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/\mergeneighboursinlabelimage commit d0759a055484abd42bba38b2fa46f2a7b8f96259
thomaswollmann
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21 iq_dist = np.min(scipy.spatial.distance.cdist(i_coords, q_coords, 'euclidean'))
66f7e94db2e6 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/\mergeneighboursinlabelimage commit d0759a055484abd42bba38b2fa46f2a7b8f96259
thomaswollmann
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22 if iq_dist <= dist:
66f7e94db2e6 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/\mergeneighboursinlabelimage commit d0759a055484abd42bba38b2fa46f2a7b8f96259
thomaswollmann
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23 props[q].label = props[i].label
66f7e94db2e6 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/\mergeneighboursinlabelimage commit d0759a055484abd42bba38b2fa46f2a7b8f96259
thomaswollmann
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24 for a_point in range(0, q_coords.shape[0]):
66f7e94db2e6 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/\mergeneighboursinlabelimage commit d0759a055484abd42bba38b2fa46f2a7b8f96259
thomaswollmann
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25 img[q_coords[a_point, 0], q_coords[a_point, 1]] = props[i].label
66f7e94db2e6 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/\mergeneighboursinlabelimage commit d0759a055484abd42bba38b2fa46f2a7b8f96259
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26 found = True
66f7e94db2e6 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/\mergeneighboursinlabelimage commit d0759a055484abd42bba38b2fa46f2a7b8f96259
thomaswollmann
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27 if found:
66f7e94db2e6 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/\mergeneighboursinlabelimage commit d0759a055484abd42bba38b2fa46f2a7b8f96259
thomaswollmann
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28 merge_n(img, dist)
66f7e94db2e6 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/\mergeneighboursinlabelimage commit d0759a055484abd42bba38b2fa46f2a7b8f96259
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29 return img
66f7e94db2e6 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/\mergeneighboursinlabelimage commit d0759a055484abd42bba38b2fa46f2a7b8f96259
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30
66f7e94db2e6 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/\mergeneighboursinlabelimage commit d0759a055484abd42bba38b2fa46f2a7b8f96259
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31 if __name__ == "__main__":
66f7e94db2e6 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/\mergeneighboursinlabelimage commit d0759a055484abd42bba38b2fa46f2a7b8f96259
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32 parser = argparse.ArgumentParser()
66f7e94db2e6 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/\mergeneighboursinlabelimage commit d0759a055484abd42bba38b2fa46f2a7b8f96259
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33 parser.add_argument('input_file', type=argparse.FileType('r'), default=sys.stdin, help='input file')
66f7e94db2e6 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/\mergeneighboursinlabelimage commit d0759a055484abd42bba38b2fa46f2a7b8f96259
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34 parser.add_argument('out_file', type=argparse.FileType('w'), default=sys.stdin, help='out file (TIFF)')
66f7e94db2e6 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/\mergeneighboursinlabelimage commit d0759a055484abd42bba38b2fa46f2a7b8f96259
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35 parser.add_argument(
66f7e94db2e6 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/\mergeneighboursinlabelimage commit d0759a055484abd42bba38b2fa46f2a7b8f96259
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36 '-c',
66f7e94db2e6 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/\mergeneighboursinlabelimage commit d0759a055484abd42bba38b2fa46f2a7b8f96259
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37 dest='cluster_merge',
66f7e94db2e6 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/\mergeneighboursinlabelimage commit d0759a055484abd42bba38b2fa46f2a7b8f96259
thomaswollmann
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38 type=int,
66f7e94db2e6 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/\mergeneighboursinlabelimage commit d0759a055484abd42bba38b2fa46f2a7b8f96259
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39 required=False,
66f7e94db2e6 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/\mergeneighboursinlabelimage commit d0759a055484abd42bba38b2fa46f2a7b8f96259
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40 default=50,
66f7e94db2e6 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/\mergeneighboursinlabelimage commit d0759a055484abd42bba38b2fa46f2a7b8f96259
thomaswollmann
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41 help='Distance in pixel of clusters which are merged',
66f7e94db2e6 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/\mergeneighboursinlabelimage commit d0759a055484abd42bba38b2fa46f2a7b8f96259
thomaswollmann
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42 )
66f7e94db2e6 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/\mergeneighboursinlabelimage commit d0759a055484abd42bba38b2fa46f2a7b8f96259
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43 args = parser.parse_args()
66f7e94db2e6 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/\mergeneighboursinlabelimage commit d0759a055484abd42bba38b2fa46f2a7b8f96259
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44
66f7e94db2e6 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/\mergeneighboursinlabelimage commit d0759a055484abd42bba38b2fa46f2a7b8f96259
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45 label_image = skimage.io.imread(args.input_file.name)
66f7e94db2e6 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/\mergeneighboursinlabelimage commit d0759a055484abd42bba38b2fa46f2a7b8f96259
thomaswollmann
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46 label_image = merge_n(label_image, args.cluster_merge)
66f7e94db2e6 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/\mergeneighboursinlabelimage commit d0759a055484abd42bba38b2fa46f2a7b8f96259
thomaswollmann
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47 with warnings.catch_warnings():
66f7e94db2e6 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/\mergeneighboursinlabelimage commit d0759a055484abd42bba38b2fa46f2a7b8f96259
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48 warnings.simplefilter("ignore")
66f7e94db2e6 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/\mergeneighboursinlabelimage commit d0759a055484abd42bba38b2fa46f2a7b8f96259
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49 res = skimage.util.img_as_uint(res)
66f7e94db2e6 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/\mergeneighboursinlabelimage commit d0759a055484abd42bba38b2fa46f2a7b8f96259
thomaswollmann
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50 skimage.io.imsave("tmp.tiff", res)
66f7e94db2e6 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/\mergeneighboursinlabelimage commit d0759a055484abd42bba38b2fa46f2a7b8f96259
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51 os.rename("tmp.tiff", args.output_file.name)