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annotate binary2label.py @ 0:b97a362ff321 draft

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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/binary2labelimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
author imgteam
date Sat, 09 Feb 2019 14:30:31 -0500
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children 6c92ac9ce868
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b97a362ff321 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/binary2labelimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
1 import argparse
b97a362ff321 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/binary2labelimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
2 import sys
b97a362ff321 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/binary2labelimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
3 import skimage.io
b97a362ff321 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
b97a362ff321 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/binary2labelimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
5 import numpy as np
b97a362ff321 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/binary2labelimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
6 import warnings
b97a362ff321 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/binary2labelimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
7 from PIL import Image
b97a362ff321 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/binary2labelimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
8
b97a362ff321 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/binary2labelimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
9 parser = argparse.ArgumentParser()
b97a362ff321 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/binary2labelimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
10 parser.add_argument('input_file', type=argparse.FileType('r'), default=sys.stdin, help='input file')
b97a362ff321 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/binary2labelimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
11 parser.add_argument('out_file', type=argparse.FileType('w'), default=sys.stdin, help='out file (TIFF)')
b97a362ff321 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/binary2labelimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
12 args = parser.parse_args()
b97a362ff321 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/binary2labelimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
13
b97a362ff321 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/binary2labelimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
14 img_in = skimage.io.imread(args.input_file.name) > 0
b97a362ff321 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/binary2labelimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
15 res = label(img_in).astype(np.int32)
b97a362ff321 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/binary2labelimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
16
b97a362ff321 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/binary2labelimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
17 res = Image.fromarray(res)
b97a362ff321 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/binary2labelimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
18 res.save(args.out_file.name, "tiff")