comparison binary2label.py @ 0:668f8dabb346 draft

planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/\binary2labelimage commit 77f1ea5beca40d8b5851fe366e84c32d5df5d6f8
author thomaswollmann
date Sat, 11 Feb 2017 17:28:57 -0500
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-1:000000000000 0:668f8dabb346
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")