Mercurial > repos > imgteam > colorize_labels

annotate colorize_labels.py @ 1:43c80f3c3b60 draft

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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels commit 98270c8f2805d406e0d88605fde778f8f182df9b
author imgteam
date Wed, 13 Mar 2024 19:08:34 +0000
parents 0afb17e107ff
children 2d1de6e7b113
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0afb17e107ff planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels commit ffedf4e17ecbb226657ccf8472b0572532e9aa8a
imgteam
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diff changeset
1 import argparse
0afb17e107ff planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels commit ffedf4e17ecbb226657ccf8472b0572532e9aa8a
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43c80f3c3b60 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels commit 98270c8f2805d406e0d88605fde778f8f182df9b
imgteam
parents: 0
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3 import matplotlib.colors as mpl
43c80f3c3b60 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels commit 98270c8f2805d406e0d88605fde778f8f182df9b
imgteam
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4 import networkx as nx
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0afb17e107ff planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels commit ffedf4e17ecbb226657ccf8472b0572532e9aa8a
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5 import numpy as np
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43c80f3c3b60 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels commit 98270c8f2805d406e0d88605fde778f8f182df9b
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6 import scipy.ndimage as ndi
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0afb17e107ff planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels commit ffedf4e17ecbb226657ccf8472b0572532e9aa8a
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7 import skimage.io
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43c80f3c3b60 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels commit 98270c8f2805d406e0d88605fde778f8f182df9b
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8 import skimage.morphology as morph
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0afb17e107ff planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels commit ffedf4e17ecbb226657ccf8472b0572532e9aa8a
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9 import skimage.util
0afb17e107ff planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels commit ffedf4e17ecbb226657ccf8472b0572532e9aa8a
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0afb17e107ff planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels commit ffedf4e17ecbb226657ccf8472b0572532e9aa8a
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0afb17e107ff planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels commit ffedf4e17ecbb226657ccf8472b0572532e9aa8a
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12 def color_hex_to_rgb_tuple(hex):
0afb17e107ff planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels commit ffedf4e17ecbb226657ccf8472b0572532e9aa8a
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13 if hex.startswith('#'):
0afb17e107ff planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels commit ffedf4e17ecbb226657ccf8472b0572532e9aa8a
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14 hex = hex[1:]
0afb17e107ff planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels commit ffedf4e17ecbb226657ccf8472b0572532e9aa8a
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15 return (
0afb17e107ff planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels commit ffedf4e17ecbb226657ccf8472b0572532e9aa8a
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16 int(hex[0:2], 16),
0afb17e107ff planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels commit ffedf4e17ecbb226657ccf8472b0572532e9aa8a
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17 int(hex[2:4], 16),
0afb17e107ff planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels commit ffedf4e17ecbb226657ccf8472b0572532e9aa8a
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18 int(hex[4:6], 16),
0afb17e107ff planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels commit ffedf4e17ecbb226657ccf8472b0572532e9aa8a
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19 )
0afb17e107ff planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels commit ffedf4e17ecbb226657ccf8472b0572532e9aa8a
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0afb17e107ff planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels commit ffedf4e17ecbb226657ccf8472b0572532e9aa8a
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43c80f3c3b60 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels commit 98270c8f2805d406e0d88605fde778f8f182df9b
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22 def build_label_adjacency_graph(im, radius, bg_label):
43c80f3c3b60 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels commit 98270c8f2805d406e0d88605fde778f8f182df9b
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23 G = nx.Graph()
43c80f3c3b60 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels commit 98270c8f2805d406e0d88605fde778f8f182df9b
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24 selem = morph.disk(radius)
43c80f3c3b60 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels commit 98270c8f2805d406e0d88605fde778f8f182df9b
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25 for label in np.unique(im):
43c80f3c3b60 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels commit 98270c8f2805d406e0d88605fde778f8f182df9b
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43c80f3c3b60 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels commit 98270c8f2805d406e0d88605fde778f8f182df9b
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27 if label == bg_label:
43c80f3c3b60 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels commit 98270c8f2805d406e0d88605fde778f8f182df9b
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28 continue
43c80f3c3b60 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels commit 98270c8f2805d406e0d88605fde778f8f182df9b
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43c80f3c3b60 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels commit 98270c8f2805d406e0d88605fde778f8f182df9b
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30 G.add_node(label)
43c80f3c3b60 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels commit 98270c8f2805d406e0d88605fde778f8f182df9b
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43c80f3c3b60 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels commit 98270c8f2805d406e0d88605fde778f8f182df9b
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32 cc = (im == label)
43c80f3c3b60 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels commit 98270c8f2805d406e0d88605fde778f8f182df9b
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33 neighborhood = ndi.binary_dilation(cc, selem)
43c80f3c3b60 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels commit 98270c8f2805d406e0d88605fde778f8f182df9b
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34 adjacent_labels = np.unique(im[neighborhood])
43c80f3c3b60 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels commit 98270c8f2805d406e0d88605fde778f8f182df9b
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43c80f3c3b60 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels commit 98270c8f2805d406e0d88605fde778f8f182df9b
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36 for adjacent_label in adjacent_labels:
43c80f3c3b60 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels commit 98270c8f2805d406e0d88605fde778f8f182df9b
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43c80f3c3b60 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels commit 98270c8f2805d406e0d88605fde778f8f182df9b
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38 if adjacent_label == bg_label or adjacent_label <= label:
43c80f3c3b60 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels commit 98270c8f2805d406e0d88605fde778f8f182df9b
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39 continue
43c80f3c3b60 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels commit 98270c8f2805d406e0d88605fde778f8f182df9b
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43c80f3c3b60 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels commit 98270c8f2805d406e0d88605fde778f8f182df9b
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41 G.add_edge(label, adjacent_label)
43c80f3c3b60 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels commit 98270c8f2805d406e0d88605fde778f8f182df9b
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42 G.add_edge(adjacent_label, label)
43c80f3c3b60 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels commit 98270c8f2805d406e0d88605fde778f8f182df9b
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43c80f3c3b60 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels commit 98270c8f2805d406e0d88605fde778f8f182df9b
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44 return G
43c80f3c3b60 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels commit 98270c8f2805d406e0d88605fde778f8f182df9b
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43c80f3c3b60 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels commit 98270c8f2805d406e0d88605fde778f8f182df9b
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0afb17e107ff planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels commit ffedf4e17ecbb226657ccf8472b0572532e9aa8a
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47 if __name__ == '__main__':
0afb17e107ff planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels commit ffedf4e17ecbb226657ccf8472b0572532e9aa8a
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0afb17e107ff planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels commit ffedf4e17ecbb226657ccf8472b0572532e9aa8a
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49 parser = argparse.ArgumentParser()
0afb17e107ff planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels commit ffedf4e17ecbb226657ccf8472b0572532e9aa8a
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50 parser.add_argument('input', type=str)
0afb17e107ff planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels commit ffedf4e17ecbb226657ccf8472b0572532e9aa8a
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51 parser.add_argument('--bg_label', type=int)
0afb17e107ff planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels commit ffedf4e17ecbb226657ccf8472b0572532e9aa8a
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52 parser.add_argument('--bg_color', type=str)
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43c80f3c3b60 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels commit 98270c8f2805d406e0d88605fde778f8f182df9b
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53 parser.add_argument('--radius', type=int)
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0afb17e107ff planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels commit ffedf4e17ecbb226657ccf8472b0572532e9aa8a
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54 parser.add_argument('--output', type=str)
0afb17e107ff planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels commit ffedf4e17ecbb226657ccf8472b0572532e9aa8a
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55 args = parser.parse_args()
0afb17e107ff planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels commit ffedf4e17ecbb226657ccf8472b0572532e9aa8a
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56
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43c80f3c3b60 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels commit 98270c8f2805d406e0d88605fde778f8f182df9b
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57 # Load image and normalize
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0afb17e107ff planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels commit ffedf4e17ecbb226657ccf8472b0572532e9aa8a
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58 im = skimage.io.imread(args.input)
0afb17e107ff planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels commit ffedf4e17ecbb226657ccf8472b0572532e9aa8a
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59 im = np.squeeze(im)
0afb17e107ff planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels commit ffedf4e17ecbb226657ccf8472b0572532e9aa8a
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60 assert im.ndim == 2
0afb17e107ff planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels commit ffedf4e17ecbb226657ccf8472b0572532e9aa8a
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62 # Build adjacency graph of the labels
43c80f3c3b60 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels commit 98270c8f2805d406e0d88605fde778f8f182df9b
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63 G = build_label_adjacency_graph(im, args.radius, args.bg_label)
43c80f3c3b60 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels commit 98270c8f2805d406e0d88605fde778f8f182df9b
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43c80f3c3b60 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels commit 98270c8f2805d406e0d88605fde778f8f182df9b
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65 # Apply greedy coloring
43c80f3c3b60 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels commit 98270c8f2805d406e0d88605fde778f8f182df9b
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66 graph_coloring = nx.greedy_color(G)
43c80f3c3b60 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels commit 98270c8f2805d406e0d88605fde778f8f182df9b
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67 unique_colors = frozenset(graph_coloring.values())
43c80f3c3b60 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels commit 98270c8f2805d406e0d88605fde778f8f182df9b
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43c80f3c3b60 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels commit 98270c8f2805d406e0d88605fde778f8f182df9b
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69 # Assign colors to nodes based on the greedy coloring
43c80f3c3b60 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels commit 98270c8f2805d406e0d88605fde778f8f182df9b
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70 graph_color_to_mpl_color = dict(zip(unique_colors, mpl.TABLEAU_COLORS.values()))
43c80f3c3b60 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels commit 98270c8f2805d406e0d88605fde778f8f182df9b
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71 node_colors = [graph_color_to_mpl_color[graph_coloring[n]] for n in G.nodes()]
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72
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73 # Render result
43c80f3c3b60 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels commit 98270c8f2805d406e0d88605fde778f8f182df9b
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74 bg_color_rgb = color_hex_to_rgb_tuple(args.bg_color)
43c80f3c3b60 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels commit 98270c8f2805d406e0d88605fde778f8f182df9b
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75 result = np.dstack([np.full(im.shape, bg_color_rgb[ch], np.uint8) for ch in range(3)])
43c80f3c3b60 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels commit 98270c8f2805d406e0d88605fde778f8f182df9b
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76 for label, label_color in zip(G.nodes(), node_colors):
43c80f3c3b60 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels commit 98270c8f2805d406e0d88605fde778f8f182df9b
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78 cc = (im == label)
43c80f3c3b60 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels commit 98270c8f2805d406e0d88605fde778f8f182df9b
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79 label_color = color_hex_to_rgb_tuple(label_color)
43c80f3c3b60 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels commit 98270c8f2805d406e0d88605fde778f8f182df9b
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80 for ch in range(3):
43c80f3c3b60 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels commit 98270c8f2805d406e0d88605fde778f8f182df9b
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81 result[:, :, ch][cc] = label_color[ch]
43c80f3c3b60 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels commit 98270c8f2805d406e0d88605fde778f8f182df9b
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43c80f3c3b60 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels commit 98270c8f2805d406e0d88605fde778f8f182df9b
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83 # Write result image
43c80f3c3b60 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels commit 98270c8f2805d406e0d88605fde778f8f182df9b
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84 skimage.io.imsave(args.output, result)