Mercurial > repos > imgteam > colorize_labels
view 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 |
line wrap: on
line source
import argparse import numpy as np import skimage.io import skimage.util import superdsm.render def color_hex_to_rgb_tuple(hex): if hex.startswith('#'): hex = hex[1:] return ( int(hex[0:2], 16), int(hex[2:4], 16), int(hex[4:6], 16), ) if __name__ == '__main__': parser = argparse.ArgumentParser() parser.add_argument('input', type=str) parser.add_argument('--bg_label', type=int) parser.add_argument('--bg_color', type=str) parser.add_argument('--cmap', type=str, default='hsv') parser.add_argument('--seed', type=int) parser.add_argument('--output', type=str) args = parser.parse_args() im = skimage.io.imread(args.input) im = np.squeeze(im) assert im.ndim == 2 im_colorized = superdsm.render.colorize_labels( labels=im, bg_label=args.bg_label, cmap=args.cmap, bg_color=np.divide(color_hex_to_rgb_tuple(args.bg_color), 255), shuffle=args.seed, ) im_colorized = skimage.util.img_as_ubyte(im_colorized) skimage.io.imsave(args.output, im_colorized)