Mercurial > repos > imgteam > binary2labelimage

annotate binary2label.py @ 2:938e2358eb80 draft

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"planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/binary2labelimage/ commit 3d389fdec0db29cf6fbd783c0501455bf624fa90"
author imgteam
date Wed, 18 Dec 2019 09:56:41 +0000
parents 37b99b904027
children a041e4e9d449
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1cde6ba34356 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/binary2labelimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
1 import argparse
1cde6ba34356 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/binary2labelimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
2 import sys
1cde6ba34356 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/binary2labelimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
3 import skimage.io
1cde6ba34356 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/binary2labelimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
4 from skimage.measure import label
1cde6ba34356 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/binary2labelimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
5 import numpy as np
1cde6ba34356 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/binary2labelimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
6 import warnings
1cde6ba34356 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/binary2labelimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
7 from PIL import Image
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37b99b904027 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/binary2labelimage/ commit b2acc1845a25828181597fe5b6982fe116a7796d
imgteam
parents: 0
diff changeset
8 import skimage.util
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1cde6ba34356 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/binary2labelimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
9
1cde6ba34356 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/binary2labelimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
10 parser = argparse.ArgumentParser()
1cde6ba34356 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/binary2labelimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
11 parser.add_argument('input_file', type=argparse.FileType('r'), default=sys.stdin, help='input file')
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938e2358eb80 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/binary2labelimage/ commit 3d389fdec0db29cf6fbd783c0501455bf624fa90"
imgteam
parents: 1
diff changeset
12 parser.add_argument('out_file', type=argparse.FileType('w'), default=sys.stdin, help='out file (TIFF)')
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1cde6ba34356 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/binary2labelimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
13 args = parser.parse_args()
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37b99b904027 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/binary2labelimage/ commit b2acc1845a25828181597fe5b6982fe116a7796d
imgteam
parents: 0
diff changeset
14
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1cde6ba34356 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/binary2labelimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
15 img_in = skimage.io.imread(args.input_file.name) > 0
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37b99b904027 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/binary2labelimage/ commit b2acc1845a25828181597fe5b6982fe116a7796d
imgteam
parents: 0
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16 res = label(img_in)
37b99b904027 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/binary2labelimage/ commit b2acc1845a25828181597fe5b6982fe116a7796d
imgteam
parents: 0
diff changeset
17 res = skimage.util.img_as_uint(res)
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1cde6ba34356 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/binary2labelimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
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1cde6ba34356 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/binary2labelimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
19 res = Image.fromarray(res)
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37b99b904027 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/binary2labelimage/ commit b2acc1845a25828181597fe5b6982fe116a7796d
imgteam
parents: 0
diff changeset
20 res.save(args.out_file.name, "tiff")