Mercurial > repos > thomaswollmann > binary2labelimage
view binary2label.py @ 1:f772af27a6de draft
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/\binary2labelimage commit 7c8ef45ea41aa832628cfd1d2931992a2340d7b7
author | thomaswollmann |
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date | Sun, 12 Feb 2017 05:20:09 -0500 |
parents | 668f8dabb346 |
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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")