Mercurial > repos > imgteam > colorize_labels

annotate colorize_labels.py @ 0:6f09b367cd9a draft default tip

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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels commit 4344f548f365dba87c20188d6e3c2df8630d2313
author imgteam
date Tue, 24 Sep 2024 17:30:11 +0000
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6f09b367cd9a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels commit 4344f548f365dba87c20188d6e3c2df8630d2313
imgteam
parents:
diff changeset
1 import argparse
6f09b367cd9a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels commit 4344f548f365dba87c20188d6e3c2df8630d2313
imgteam
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6f09b367cd9a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels commit 4344f548f365dba87c20188d6e3c2df8630d2313
imgteam
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3 import giatools.io
6f09b367cd9a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels commit 4344f548f365dba87c20188d6e3c2df8630d2313
imgteam
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4 import matplotlib.pyplot as plt
6f09b367cd9a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels commit 4344f548f365dba87c20188d6e3c2df8630d2313
imgteam
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5 import networkx as nx
6f09b367cd9a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels commit 4344f548f365dba87c20188d6e3c2df8630d2313
imgteam
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6 import numpy as np
6f09b367cd9a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels commit 4344f548f365dba87c20188d6e3c2df8630d2313
imgteam
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7 import scipy.ndimage as ndi
6f09b367cd9a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels commit 4344f548f365dba87c20188d6e3c2df8630d2313
imgteam
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8 import skimage.io
6f09b367cd9a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels commit 4344f548f365dba87c20188d6e3c2df8630d2313
imgteam
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9 import skimage.util
6f09b367cd9a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels commit 4344f548f365dba87c20188d6e3c2df8630d2313
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6f09b367cd9a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels commit 4344f548f365dba87c20188d6e3c2df8630d2313
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6f09b367cd9a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels commit 4344f548f365dba87c20188d6e3c2df8630d2313
imgteam
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12 def color_hex_to_rgb_tuple(hex):
6f09b367cd9a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels commit 4344f548f365dba87c20188d6e3c2df8630d2313
imgteam
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13 if hex.startswith('#'):
6f09b367cd9a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels commit 4344f548f365dba87c20188d6e3c2df8630d2313
imgteam
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14 hex = hex[1:]
6f09b367cd9a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels commit 4344f548f365dba87c20188d6e3c2df8630d2313
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15 return (
6f09b367cd9a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels commit 4344f548f365dba87c20188d6e3c2df8630d2313
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16 int(hex[0:2], 16),
6f09b367cd9a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels commit 4344f548f365dba87c20188d6e3c2df8630d2313
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17 int(hex[2:4], 16),
6f09b367cd9a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels commit 4344f548f365dba87c20188d6e3c2df8630d2313
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18 int(hex[4:6], 16),
6f09b367cd9a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels commit 4344f548f365dba87c20188d6e3c2df8630d2313
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19 )
6f09b367cd9a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels commit 4344f548f365dba87c20188d6e3c2df8630d2313
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6f09b367cd9a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels commit 4344f548f365dba87c20188d6e3c2df8630d2313
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6f09b367cd9a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels commit 4344f548f365dba87c20188d6e3c2df8630d2313
imgteam
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22 def build_label_adjacency_graph(im, radius, bg_label):
6f09b367cd9a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels commit 4344f548f365dba87c20188d6e3c2df8630d2313
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23 G = nx.Graph()
6f09b367cd9a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels commit 4344f548f365dba87c20188d6e3c2df8630d2313
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24 for label in np.unique(im):
6f09b367cd9a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels commit 4344f548f365dba87c20188d6e3c2df8630d2313
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6f09b367cd9a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels commit 4344f548f365dba87c20188d6e3c2df8630d2313
imgteam
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26 if label == bg_label:
6f09b367cd9a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels commit 4344f548f365dba87c20188d6e3c2df8630d2313
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27 continue
6f09b367cd9a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels commit 4344f548f365dba87c20188d6e3c2df8630d2313
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6f09b367cd9a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels commit 4344f548f365dba87c20188d6e3c2df8630d2313
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29 G.add_node(label)
6f09b367cd9a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels commit 4344f548f365dba87c20188d6e3c2df8630d2313
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6f09b367cd9a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels commit 4344f548f365dba87c20188d6e3c2df8630d2313
imgteam
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31 cc = (im == label)
6f09b367cd9a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels commit 4344f548f365dba87c20188d6e3c2df8630d2313
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32 neighborhood = (ndi.distance_transform_edt(~cc) <= radius)
6f09b367cd9a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels commit 4344f548f365dba87c20188d6e3c2df8630d2313
imgteam
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33 adjacent_labels = np.unique(im[neighborhood])
6f09b367cd9a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels commit 4344f548f365dba87c20188d6e3c2df8630d2313
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6f09b367cd9a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels commit 4344f548f365dba87c20188d6e3c2df8630d2313
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35 for adjacent_label in adjacent_labels:
6f09b367cd9a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels commit 4344f548f365dba87c20188d6e3c2df8630d2313
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6f09b367cd9a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels commit 4344f548f365dba87c20188d6e3c2df8630d2313
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37 if adjacent_label == bg_label or adjacent_label <= label:
6f09b367cd9a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels commit 4344f548f365dba87c20188d6e3c2df8630d2313
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38 continue
6f09b367cd9a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels commit 4344f548f365dba87c20188d6e3c2df8630d2313
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6f09b367cd9a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels commit 4344f548f365dba87c20188d6e3c2df8630d2313
imgteam
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40 G.add_edge(label, adjacent_label)
6f09b367cd9a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels commit 4344f548f365dba87c20188d6e3c2df8630d2313
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41 G.add_edge(adjacent_label, label)
6f09b367cd9a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels commit 4344f548f365dba87c20188d6e3c2df8630d2313
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6f09b367cd9a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels commit 4344f548f365dba87c20188d6e3c2df8630d2313
imgteam
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43 return G
6f09b367cd9a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels commit 4344f548f365dba87c20188d6e3c2df8630d2313
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6f09b367cd9a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels commit 4344f548f365dba87c20188d6e3c2df8630d2313
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6f09b367cd9a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels commit 4344f548f365dba87c20188d6e3c2df8630d2313
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46 def get_n_unique_mpl_colors(n, colormap='jet', cyclic=False):
6f09b367cd9a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels commit 4344f548f365dba87c20188d6e3c2df8630d2313
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47 """
6f09b367cd9a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels commit 4344f548f365dba87c20188d6e3c2df8630d2313
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48 Yields `n` unique colors from the given `colormap`.
6f09b367cd9a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels commit 4344f548f365dba87c20188d6e3c2df8630d2313
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49
6f09b367cd9a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels commit 4344f548f365dba87c20188d6e3c2df8630d2313
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50 Set `cyclic` to `True` if the `colormap` is cyclic.
6f09b367cd9a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels commit 4344f548f365dba87c20188d6e3c2df8630d2313
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51 """
6f09b367cd9a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels commit 4344f548f365dba87c20188d6e3c2df8630d2313
imgteam
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52 cmap = plt.get_cmap(colormap)
6f09b367cd9a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels commit 4344f548f365dba87c20188d6e3c2df8630d2313
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53 m = n if cyclic else n - 1
6f09b367cd9a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels commit 4344f548f365dba87c20188d6e3c2df8630d2313
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54 for i in range(n):
6f09b367cd9a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels commit 4344f548f365dba87c20188d6e3c2df8630d2313
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55 yield np.multiply(255, cmap(i / m))
6f09b367cd9a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels commit 4344f548f365dba87c20188d6e3c2df8630d2313
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56
6f09b367cd9a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels commit 4344f548f365dba87c20188d6e3c2df8630d2313
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57
6f09b367cd9a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels commit 4344f548f365dba87c20188d6e3c2df8630d2313
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58 if __name__ == '__main__':
6f09b367cd9a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels commit 4344f548f365dba87c20188d6e3c2df8630d2313
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59
6f09b367cd9a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels commit 4344f548f365dba87c20188d6e3c2df8630d2313
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60 parser = argparse.ArgumentParser()
6f09b367cd9a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels commit 4344f548f365dba87c20188d6e3c2df8630d2313
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61 parser.add_argument('input', type=str)
6f09b367cd9a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels commit 4344f548f365dba87c20188d6e3c2df8630d2313
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62 parser.add_argument('--bg_label', type=int)
6f09b367cd9a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels commit 4344f548f365dba87c20188d6e3c2df8630d2313
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63 parser.add_argument('--bg_color', type=str)
6f09b367cd9a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels commit 4344f548f365dba87c20188d6e3c2df8630d2313
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64 parser.add_argument('--radius', type=int)
6f09b367cd9a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels commit 4344f548f365dba87c20188d6e3c2df8630d2313
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65 parser.add_argument('--output', type=str)
6f09b367cd9a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels commit 4344f548f365dba87c20188d6e3c2df8630d2313
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66 args = parser.parse_args()
6f09b367cd9a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels commit 4344f548f365dba87c20188d6e3c2df8630d2313
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67
6f09b367cd9a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels commit 4344f548f365dba87c20188d6e3c2df8630d2313
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68 # Load image and normalize
6f09b367cd9a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels commit 4344f548f365dba87c20188d6e3c2df8630d2313
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69 im = giatools.io.imread(args.input)
6f09b367cd9a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels commit 4344f548f365dba87c20188d6e3c2df8630d2313
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70 im = np.squeeze(im)
6f09b367cd9a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels commit 4344f548f365dba87c20188d6e3c2df8630d2313
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71 assert im.ndim == 2
6f09b367cd9a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels commit 4344f548f365dba87c20188d6e3c2df8630d2313
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6f09b367cd9a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels commit 4344f548f365dba87c20188d6e3c2df8630d2313
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73 # Build adjacency graph of the labels
6f09b367cd9a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels commit 4344f548f365dba87c20188d6e3c2df8630d2313
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74 G = build_label_adjacency_graph(im, args.radius, args.bg_label)
6f09b367cd9a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels commit 4344f548f365dba87c20188d6e3c2df8630d2313
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75
6f09b367cd9a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels commit 4344f548f365dba87c20188d6e3c2df8630d2313
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76 # Apply greedy coloring
6f09b367cd9a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels commit 4344f548f365dba87c20188d6e3c2df8630d2313
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77 graph_coloring = nx.greedy_color(G)
6f09b367cd9a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels commit 4344f548f365dba87c20188d6e3c2df8630d2313
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78 unique_colors = frozenset(graph_coloring.values())
6f09b367cd9a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels commit 4344f548f365dba87c20188d6e3c2df8630d2313
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6f09b367cd9a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels commit 4344f548f365dba87c20188d6e3c2df8630d2313
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80 # Assign colors to nodes based on the greedy coloring
6f09b367cd9a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels commit 4344f548f365dba87c20188d6e3c2df8630d2313
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81 graph_color_to_mpl_color = dict(zip(unique_colors, get_n_unique_mpl_colors(len(unique_colors))))
6f09b367cd9a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels commit 4344f548f365dba87c20188d6e3c2df8630d2313
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82 node_colors = [graph_color_to_mpl_color[graph_coloring[n]] for n in G.nodes()]
6f09b367cd9a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels commit 4344f548f365dba87c20188d6e3c2df8630d2313
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83
6f09b367cd9a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels commit 4344f548f365dba87c20188d6e3c2df8630d2313
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84 # Render result
6f09b367cd9a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels commit 4344f548f365dba87c20188d6e3c2df8630d2313
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85 bg_color_rgb = color_hex_to_rgb_tuple(args.bg_color)
6f09b367cd9a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels commit 4344f548f365dba87c20188d6e3c2df8630d2313
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86 result = np.dstack([np.full(im.shape, bg_color_rgb[ch], np.uint8) for ch in range(3)])
6f09b367cd9a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels commit 4344f548f365dba87c20188d6e3c2df8630d2313
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87 for label, label_color in zip(G.nodes(), node_colors):
6f09b367cd9a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels commit 4344f548f365dba87c20188d6e3c2df8630d2313
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88
6f09b367cd9a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels commit 4344f548f365dba87c20188d6e3c2df8630d2313
imgteam
parents:
diff changeset
89 cc = (im == label)
6f09b367cd9a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels commit 4344f548f365dba87c20188d6e3c2df8630d2313
imgteam
parents:
diff changeset
90 for ch in range(3):
6f09b367cd9a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels commit 4344f548f365dba87c20188d6e3c2df8630d2313
imgteam
parents:
diff changeset
91 result[:, :, ch][cc] = label_color[ch]
6f09b367cd9a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels commit 4344f548f365dba87c20188d6e3c2df8630d2313
imgteam
parents:
diff changeset
92
6f09b367cd9a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels commit 4344f548f365dba87c20188d6e3c2df8630d2313
imgteam
parents:
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93 # Write result image
6f09b367cd9a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels commit 4344f548f365dba87c20188d6e3c2df8630d2313
imgteam
parents:
diff changeset
94 skimage.io.imsave(args.output, result)