Mercurial > repos > thomaswollmann > binary2labelimage
diff binary2label.py @ 0:668f8dabb346 draft
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/\binary2labelimage commit 77f1ea5beca40d8b5851fe366e84c32d5df5d6f8
author | thomaswollmann |
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date | Sat, 11 Feb 2017 17:28:57 -0500 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/binary2label.py Sat Feb 11 17:28:57 2017 -0500 @@ -0,0 +1,18 @@ +import argparse +import sys +import skimage.io +from skimage.measure import label +import numpy as np +import warnings +from PIL import Image + +parser = argparse.ArgumentParser() +parser.add_argument('input_file', type=argparse.FileType('r'), default=sys.stdin, help='input file') +parser.add_argument('out_file', type=argparse.FileType('w'), default=sys.stdin, help='out file (TIFF)') +args = parser.parse_args() + +img_in = skimage.io.imread(args.input_file.name) > 0 +res = label(img_in).astype(np.int32) + +res = Image.fromarray(res) +res.save(args.out_file.name, "tiff") \ No newline at end of file