Mercurial > repos > imgteam > colorize_labels
comparison colorize_labels.py @ 0:0afb17e107ff draft
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels commit ffedf4e17ecbb226657ccf8472b0572532e9aa8a
author | imgteam |
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date | Tue, 12 Mar 2024 23:00:45 +0000 |
parents | |
children | 43c80f3c3b60 |
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-1:000000000000 | 0:0afb17e107ff |
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1 import argparse | |
2 | |
3 import numpy as np | |
4 import skimage.io | |
5 import skimage.util | |
6 import superdsm.render | |
7 | |
8 | |
9 def color_hex_to_rgb_tuple(hex): | |
10 if hex.startswith('#'): | |
11 hex = hex[1:] | |
12 return ( | |
13 int(hex[0:2], 16), | |
14 int(hex[2:4], 16), | |
15 int(hex[4:6], 16), | |
16 ) | |
17 | |
18 | |
19 if __name__ == '__main__': | |
20 | |
21 parser = argparse.ArgumentParser() | |
22 parser.add_argument('input', type=str) | |
23 parser.add_argument('--bg_label', type=int) | |
24 parser.add_argument('--bg_color', type=str) | |
25 parser.add_argument('--cmap', type=str, default='hsv') | |
26 parser.add_argument('--seed', type=int) | |
27 parser.add_argument('--output', type=str) | |
28 args = parser.parse_args() | |
29 | |
30 im = skimage.io.imread(args.input) | |
31 im = np.squeeze(im) | |
32 assert im.ndim == 2 | |
33 | |
34 im_colorized = superdsm.render.colorize_labels( | |
35 labels=im, | |
36 bg_label=args.bg_label, | |
37 cmap=args.cmap, | |
38 bg_color=np.divide(color_hex_to_rgb_tuple(args.bg_color), 255), | |
39 shuffle=args.seed, | |
40 ) | |
41 | |
42 im_colorized = skimage.util.img_as_ubyte(im_colorized) | |
43 skimage.io.imsave(args.output, im_colorized) |