Mercurial > repos > imgteam > binary2labelimage

annotate binary2label.py @ 0:1cde6ba34356 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/binary2labelimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
author imgteam
date Sat, 09 Feb 2019 14:13:08 -0500
parents
children 37b99b904027
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
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
1cde6ba34356 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/binary2labelimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
8
1cde6ba34356 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/binary2labelimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
9 parser = argparse.ArgumentParser()
1cde6ba34356 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')
1cde6ba34356 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)')
1cde6ba34356 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/binary2labelimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
12 args = parser.parse_args()
1cde6ba34356 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/binary2labelimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
13
1cde6ba34356 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
1cde6ba34356 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)
1cde6ba34356 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/binary2labelimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
16
1cde6ba34356 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/binary2labelimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
17 res = Image.fromarray(res)
1cde6ba34356 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")