Mercurial > repos > imgteam > mergeneighboursinlabelimage
comparison mergeneighboursinlabelimage.py @ 2:9cbddb13fb9e draft default tip
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/\mergeneighboursinlabelimage commit 2286a6c9da88596349ed9d967c51541409c0a7bf
author | imgteam |
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date | Mon, 13 Nov 2023 22:11:27 +0000 |
parents | c6a6ab7c9940 |
children |
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1:c6a6ab7c9940 | 2:9cbddb13fb9e |
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1 import argparse | 1 import argparse |
2 import sys | 2 import sys |
3 import warnings | |
4 | |
5 import numpy as np | |
6 import scipy.spatial.distance | |
3 import skimage.io | 7 import skimage.io |
4 import skimage.util | 8 import skimage.util |
5 from skimage.measure import regionprops | 9 from skimage.measure import regionprops |
6 import scipy.spatial.distance | 10 |
7 import numpy as np | |
8 import warnings | |
9 | 11 |
10 def merge_n(img, dist=50): | 12 def merge_n(img, dist=50): |
11 props = regionprops(img) | 13 props = regionprops(img) |
12 found = False | 14 found = False |
13 for i in range(0, len(props)): | 15 for i in range(0, len(props)): |
14 i_coords = props[i].coords | 16 i_coords = props[i].coords |
15 for q in range(0, len(props)): | 17 for q in range(0, len(props)): |
16 if i==q: | 18 if i == q: |
17 continue | 19 continue |
18 q_coords = props[q].coords | 20 q_coords = props[q].coords |
19 iq_dist = np.min(scipy.spatial.distance.cdist(i_coords, q_coords, 'euclidean')) | 21 iq_dist = np.min(scipy.spatial.distance.cdist(i_coords, q_coords, 'euclidean')) |
20 if iq_dist <= dist: | 22 if iq_dist <= dist: |
21 props[q].label = props[i].label | 23 props[q].label = props[i].label |
23 img[q_coords[a_point, 0], q_coords[a_point, 1]] = props[i].label | 25 img[q_coords[a_point, 0], q_coords[a_point, 1]] = props[i].label |
24 found = True | 26 found = True |
25 if found: | 27 if found: |
26 merge_n(img, dist) | 28 merge_n(img, dist) |
27 return img | 29 return img |
30 | |
28 | 31 |
29 if __name__ == "__main__": | 32 if __name__ == "__main__": |
30 parser = argparse.ArgumentParser() | 33 parser = argparse.ArgumentParser() |
31 parser.add_argument('input_file', type=argparse.FileType('r'), default=sys.stdin, help='input file') | 34 parser.add_argument('input_file', type=argparse.FileType('r'), default=sys.stdin, help='input file') |
32 parser.add_argument('out_file', type=argparse.FileType('w'), default=sys.stdin, help='out file (TIFF)') | 35 parser.add_argument('out_file', type=argparse.FileType('w'), default=sys.stdin, help='out file (TIFF)') |
41 args = parser.parse_args() | 44 args = parser.parse_args() |
42 | 45 |
43 label_image = skimage.io.imread(args.input_file.name) | 46 label_image = skimage.io.imread(args.input_file.name) |
44 label_image = merge_n(label_image, args.cluster_merge) | 47 label_image = merge_n(label_image, args.cluster_merge) |
45 with warnings.catch_warnings(): | 48 with warnings.catch_warnings(): |
46 warnings.simplefilter("ignore") | 49 warnings.simplefilter("ignore") |
47 res = skimage.util.img_as_uint(label_image) | 50 res = skimage.util.img_as_uint(label_image) |
48 skimage.io.imsave(args.out_file.name, res, plugin="tifffile") | 51 skimage.io.imsave(args.out_file.name, res, plugin="tifffile") |