Mercurial > repos > imgteam > colorize_labels

comparison colorize_labels.py @ 3:2d1de6e7b113 draft default tip

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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels commit c86a1b93cb7732f7331a981d13465653cc1a2790
author imgteam
date Wed, 24 Apr 2024 08:12:15 +0000
parents 43c80f3c3b60
children
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2:3aa2d054848a 3:2d1de6e7b113
1 import argparse 1 import argparse
2 2
3 import giatools.io
3 import matplotlib.colors as mpl 4 import matplotlib.colors as mpl
4 import networkx as nx 5 import networkx as nx
5 import numpy as np 6 import numpy as np
6 import scipy.ndimage as ndi 7 import scipy.ndimage as ndi
7 import skimage.io 8 import skimage.io
53 parser.add_argument('--radius', type=int) 54 parser.add_argument('--radius', type=int)
54 parser.add_argument('--output', type=str) 55 parser.add_argument('--output', type=str)
55 args = parser.parse_args() 56 args = parser.parse_args()
56 57
57 # Load image and normalize 58 # Load image and normalize
58 im = skimage.io.imread(args.input) 59 im = giatools.io.imread(args.input)
59 im = np.squeeze(im) 60 im = np.squeeze(im)
60 assert im.ndim == 2 61 assert im.ndim == 2
61 62
62 # Build adjacency graph of the labels 63 # Build adjacency graph of the labels
63 G = build_label_adjacency_graph(im, args.radius, args.bg_label) 64 G = build_label_adjacency_graph(im, args.radius, args.bg_label)