Mercurial > repos > imgteam > binary2labelimage
comparison binary2label.py @ 0:b97a362ff321 draft
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 |
| parents | |
| children | 6c92ac9ce868 |
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| -1:000000000000 | 0:b97a362ff321 |
|---|---|
| 1 import argparse | |
| 2 import sys | |
| 3 import skimage.io | |
| 4 from skimage.measure import label | |
| 5 import numpy as np | |
| 6 import warnings | |
| 7 from PIL import Image | |
| 8 | |
| 9 parser = argparse.ArgumentParser() | |
| 10 parser.add_argument('input_file', type=argparse.FileType('r'), default=sys.stdin, help='input file') | |
| 11 parser.add_argument('out_file', type=argparse.FileType('w'), default=sys.stdin, help='out file (TIFF)') | |
| 12 args = parser.parse_args() | |
| 13 | |
| 14 img_in = skimage.io.imread(args.input_file.name) > 0 | |
| 15 res = label(img_in).astype(np.int32) | |
| 16 | |
| 17 res = Image.fromarray(res) | |
| 18 res.save(args.out_file.name, "tiff") |