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 |
|---|---|
| date | Tue, 12 Mar 2024 23:00:45 +0000 |
| parents | |
| children | 43c80f3c3b60 |
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| -1:000000000000 | 0:0afb17e107ff |
|---|---|
| 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) |