Mercurial > repos > imgteam > voronoi_tesselation

annotate voronoi_tessellation.py @ 3:1944b0fccdbd draft default tip

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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/voronoi_tesselation commit 60cf803236ef94f414056823688e6fd008b7a1b6
author imgteam
date Thu, 25 Apr 2024 10:58:05 +0000
parents 412d7478ec92
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8b74843c136e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/voronoi_tesselation commit 43f036ed5341c36a1e076f9df9f47a3743ef4e6f
imgteam
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diff changeset
1 import argparse
8b74843c136e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/voronoi_tesselation commit 43f036ed5341c36a1e076f9df9f47a3743ef4e6f
imgteam
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412d7478ec92 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/voronoi_tesselation commit c86a1b93cb7732f7331a981d13465653cc1a2790
imgteam
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3 import giatools.io
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8b74843c136e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/voronoi_tesselation commit 43f036ed5341c36a1e076f9df9f47a3743ef4e6f
imgteam
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4 import numpy as np
8b74843c136e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/voronoi_tesselation commit 43f036ed5341c36a1e076f9df9f47a3743ef4e6f
imgteam
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5 import scipy.ndimage as ndi
8b74843c136e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/voronoi_tesselation commit 43f036ed5341c36a1e076f9df9f47a3743ef4e6f
imgteam
parents:
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6 import skimage.io
8b74843c136e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/voronoi_tesselation commit 43f036ed5341c36a1e076f9df9f47a3743ef4e6f
imgteam
parents:
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7 from skimage.segmentation import watershed
8b74843c136e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/voronoi_tesselation commit 43f036ed5341c36a1e076f9df9f47a3743ef4e6f
imgteam
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8b74843c136e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/voronoi_tesselation commit 43f036ed5341c36a1e076f9df9f47a3743ef4e6f
imgteam
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8b74843c136e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/voronoi_tesselation commit 43f036ed5341c36a1e076f9df9f47a3743ef4e6f
imgteam
parents:
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10 if __name__ == '__main__':
8b74843c136e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/voronoi_tesselation commit 43f036ed5341c36a1e076f9df9f47a3743ef4e6f
imgteam
parents:
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8b74843c136e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/voronoi_tesselation commit 43f036ed5341c36a1e076f9df9f47a3743ef4e6f
imgteam
parents:
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12 parser = argparse.ArgumentParser()
8b74843c136e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/voronoi_tesselation commit 43f036ed5341c36a1e076f9df9f47a3743ef4e6f
imgteam
parents:
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13 parser.add_argument('input')
8b74843c136e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/voronoi_tesselation commit 43f036ed5341c36a1e076f9df9f47a3743ef4e6f
imgteam
parents:
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14 parser.add_argument('output')
8b74843c136e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/voronoi_tesselation commit 43f036ed5341c36a1e076f9df9f47a3743ef4e6f
imgteam
parents:
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15 args = parser.parse_args()
8b74843c136e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/voronoi_tesselation commit 43f036ed5341c36a1e076f9df9f47a3743ef4e6f
imgteam
parents:
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412d7478ec92 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/voronoi_tesselation commit c86a1b93cb7732f7331a981d13465653cc1a2790
imgteam
parents: 0
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17 im = giatools.io.imread(args.input)
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8b74843c136e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/voronoi_tesselation commit 43f036ed5341c36a1e076f9df9f47a3743ef4e6f
imgteam
parents:
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18 im = im.squeeze()
8b74843c136e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/voronoi_tesselation commit 43f036ed5341c36a1e076f9df9f47a3743ef4e6f
imgteam
parents:
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19 assert im.ndim == 2
8b74843c136e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/voronoi_tesselation commit 43f036ed5341c36a1e076f9df9f47a3743ef4e6f
imgteam
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8b74843c136e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/voronoi_tesselation commit 43f036ed5341c36a1e076f9df9f47a3743ef4e6f
imgteam
parents:
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21 distances = np.full(im.shape, np.inf)
8b74843c136e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/voronoi_tesselation commit 43f036ed5341c36a1e076f9df9f47a3743ef4e6f
imgteam
parents:
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22 for label in np.unique(im):
8b74843c136e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/voronoi_tesselation commit 43f036ed5341c36a1e076f9df9f47a3743ef4e6f
imgteam
parents:
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23 if label == 0:
8b74843c136e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/voronoi_tesselation commit 43f036ed5341c36a1e076f9df9f47a3743ef4e6f
imgteam
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24 continue
8b74843c136e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/voronoi_tesselation commit 43f036ed5341c36a1e076f9df9f47a3743ef4e6f
imgteam
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8b74843c136e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/voronoi_tesselation commit 43f036ed5341c36a1e076f9df9f47a3743ef4e6f
imgteam
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26 label_distances = ndi.distance_transform_edt(im != label)
8b74843c136e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/voronoi_tesselation commit 43f036ed5341c36a1e076f9df9f47a3743ef4e6f
imgteam
parents:
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27 distances = np.min((distances, label_distances), axis=0)
8b74843c136e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/voronoi_tesselation commit 43f036ed5341c36a1e076f9df9f47a3743ef4e6f
imgteam
parents:
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8b74843c136e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/voronoi_tesselation commit 43f036ed5341c36a1e076f9df9f47a3743ef4e6f
imgteam
parents:
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29 result = watershed(
8b74843c136e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/voronoi_tesselation commit 43f036ed5341c36a1e076f9df9f47a3743ef4e6f
imgteam
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30 image=distances,
8b74843c136e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/voronoi_tesselation commit 43f036ed5341c36a1e076f9df9f47a3743ef4e6f
imgteam
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31 markers=im,
8b74843c136e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/voronoi_tesselation commit 43f036ed5341c36a1e076f9df9f47a3743ef4e6f
imgteam
parents:
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32 )
8b74843c136e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/voronoi_tesselation commit 43f036ed5341c36a1e076f9df9f47a3743ef4e6f
imgteam
parents:
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8b74843c136e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/voronoi_tesselation commit 43f036ed5341c36a1e076f9df9f47a3743ef4e6f
imgteam
parents:
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34 skimage.io.imsave(args.output, result)