Mercurial > repos > imgteam > binary2labelimage

annotate 2d_split_binaryimage_by_watershed.py @ 4:984358e43242 draft

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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binary2labelimage/ commit 00199464fa2aa1928a49e2379edf199c3db91533
author imgteam
date Tue, 14 Nov 2023 08:27:27 +0000
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children 7f8102bdbfa1
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984358e43242 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binary2labelimage/ commit 00199464fa2aa1928a49e2379edf199c3db91533
imgteam
parents:
diff changeset
1 import argparse
984358e43242 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binary2labelimage/ commit 00199464fa2aa1928a49e2379edf199c3db91533
imgteam
parents:
diff changeset
2 import sys
984358e43242 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binary2labelimage/ commit 00199464fa2aa1928a49e2379edf199c3db91533
imgteam
parents:
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3
984358e43242 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binary2labelimage/ commit 00199464fa2aa1928a49e2379edf199c3db91533
imgteam
parents:
diff changeset
4 import skimage.io
984358e43242 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binary2labelimage/ commit 00199464fa2aa1928a49e2379edf199c3db91533
imgteam
parents:
diff changeset
5 import skimage.util
984358e43242 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binary2labelimage/ commit 00199464fa2aa1928a49e2379edf199c3db91533
imgteam
parents:
diff changeset
6 from scipy import ndimage as ndi
984358e43242 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binary2labelimage/ commit 00199464fa2aa1928a49e2379edf199c3db91533
imgteam
parents:
diff changeset
7 from skimage.feature import peak_local_max
984358e43242 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binary2labelimage/ commit 00199464fa2aa1928a49e2379edf199c3db91533
imgteam
parents:
diff changeset
8 from skimage.morphology import watershed
984358e43242 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binary2labelimage/ commit 00199464fa2aa1928a49e2379edf199c3db91533
imgteam
parents:
diff changeset
9
984358e43242 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binary2labelimage/ commit 00199464fa2aa1928a49e2379edf199c3db91533
imgteam
parents:
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10
984358e43242 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binary2labelimage/ commit 00199464fa2aa1928a49e2379edf199c3db91533
imgteam
parents:
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11 if __name__ == "__main__":
984358e43242 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binary2labelimage/ commit 00199464fa2aa1928a49e2379edf199c3db91533
imgteam
parents:
diff changeset
12 parser = argparse.ArgumentParser(description='Split binaryimage by watershed')
984358e43242 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binary2labelimage/ commit 00199464fa2aa1928a49e2379edf199c3db91533
imgteam
parents:
diff changeset
13 parser.add_argument('input_file', type=argparse.FileType('r'), default=sys.stdin, help='input file')
984358e43242 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binary2labelimage/ commit 00199464fa2aa1928a49e2379edf199c3db91533
imgteam
parents:
diff changeset
14 parser.add_argument('out_file', type=argparse.FileType('w'), default=sys.stdin, help='out file (TIFF)')
984358e43242 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binary2labelimage/ commit 00199464fa2aa1928a49e2379edf199c3db91533
imgteam
parents:
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15 parser.add_argument('min_distance', type=int, default=100, help='Minimum distance to next object')
984358e43242 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binary2labelimage/ commit 00199464fa2aa1928a49e2379edf199c3db91533
imgteam
parents:
diff changeset
16 args = parser.parse_args()
984358e43242 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binary2labelimage/ commit 00199464fa2aa1928a49e2379edf199c3db91533
imgteam
parents:
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984358e43242 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binary2labelimage/ commit 00199464fa2aa1928a49e2379edf199c3db91533
imgteam
parents:
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18 img_in = skimage.io.imread(args.input_file.name)
984358e43242 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binary2labelimage/ commit 00199464fa2aa1928a49e2379edf199c3db91533
imgteam
parents:
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19 distance = ndi.distance_transform_edt(img_in)
984358e43242 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binary2labelimage/ commit 00199464fa2aa1928a49e2379edf199c3db91533
imgteam
parents:
diff changeset
20 local_maxi = peak_local_max(distance,
984358e43242 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binary2labelimage/ commit 00199464fa2aa1928a49e2379edf199c3db91533
imgteam
parents:
diff changeset
21 indices=False,
984358e43242 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binary2labelimage/ commit 00199464fa2aa1928a49e2379edf199c3db91533
imgteam
parents:
diff changeset
22 min_distance=args.min_distance,
984358e43242 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binary2labelimage/ commit 00199464fa2aa1928a49e2379edf199c3db91533
imgteam
parents:
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23 labels=img_in)
984358e43242 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binary2labelimage/ commit 00199464fa2aa1928a49e2379edf199c3db91533
imgteam
parents:
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24 markers = ndi.label(local_maxi)[0]
984358e43242 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binary2labelimage/ commit 00199464fa2aa1928a49e2379edf199c3db91533
imgteam
parents:
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25 res = watershed(-distance, markers, mask=img_in)
984358e43242 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binary2labelimage/ commit 00199464fa2aa1928a49e2379edf199c3db91533
imgteam
parents:
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984358e43242 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binary2labelimage/ commit 00199464fa2aa1928a49e2379edf199c3db91533
imgteam
parents:
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27 res = skimage.util.img_as_uint(res)
984358e43242 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binary2labelimage/ commit 00199464fa2aa1928a49e2379edf199c3db91533
imgteam
parents:
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28 skimage.io.imsave(args.out_file.name, res, plugin="tifffile")