Mercurial > repos > thomaswollmann > mergeneighboursinlabelimage

comparison mergeneighboursinlabelimage.py @ 1:3536648d0a93 draft default tip

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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/\mergeneighboursinlabelimage commit d93e1dd276027cfc3fb518236110395a23d96f66
author thomaswollmann
date Wed, 16 Jan 2019 15:35:29 -0500
parents 66f7e94db2e6
children
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0:66f7e94db2e6 1:3536648d0a93
1 #!/usr/bin/python
2
3 import argparse 1 import argparse
4 import sys 2 import sys
5 import skimage.io 3 import skimage.io
6 import skimage.util 4 import skimage.util
7 from skimage.measure import regionprops 5 from skimage.measure import regionprops
44 42
45 label_image = skimage.io.imread(args.input_file.name) 43 label_image = skimage.io.imread(args.input_file.name)
46 label_image = merge_n(label_image, args.cluster_merge) 44 label_image = merge_n(label_image, args.cluster_merge)
47 with warnings.catch_warnings(): 45 with warnings.catch_warnings():
48 warnings.simplefilter("ignore") 46 warnings.simplefilter("ignore")
49 res = skimage.util.img_as_uint(res) 47 res = skimage.util.img_as_uint(label_image)
50 skimage.io.imsave("tmp.tiff", res) 48 skimage.io.imsave(args.out_file.name, res, plugin="tifffile")
51 os.rename("tmp.tiff", args.output_file.name)