Mercurial > repos > imgteam > mergeneighboursinlabelimage
comparison mergeneighboursinlabelimage.py @ 0:07ac39c0e949 draft
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/\mergeneighboursinlabelimage commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
| author | imgteam |
|---|---|
| date | Sat, 09 Feb 2019 14:38:38 -0500 |
| parents | |
| children | c6a6ab7c9940 |
comparison
equal
deleted
inserted
replaced
| -1:000000000000 | 0:07ac39c0e949 |
|---|---|
| 1 import argparse | |
| 2 import sys | |
| 3 import skimage.io | |
| 4 import skimage.util | |
| 5 from skimage.measure import regionprops | |
| 6 import scipy.spatial.distance | |
| 7 import numpy as np | |
| 8 import warnings | |
| 9 | |
| 10 def merge_n(img, dist=50): | |
| 11 props = regionprops(img) | |
| 12 found = False | |
| 13 for i in range(0, len(props)): | |
| 14 i_coords = props[i].coords | |
| 15 for q in range(0, len(props)): | |
| 16 if i==q: | |
| 17 continue | |
| 18 q_coords = props[q].coords | |
| 19 iq_dist = np.min(scipy.spatial.distance.cdist(i_coords, q_coords, 'euclidean')) | |
| 20 if iq_dist <= dist: | |
| 21 props[q].label = props[i].label | |
| 22 for a_point in range(0, q_coords.shape[0]): | |
| 23 img[q_coords[a_point, 0], q_coords[a_point, 1]] = props[i].label | |
| 24 found = True | |
| 25 if found: | |
| 26 merge_n(img, dist) | |
| 27 return img | |
| 28 | |
| 29 if __name__ == "__main__": | |
| 30 parser = argparse.ArgumentParser() | |
| 31 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)') | |
| 33 parser.add_argument( | |
| 34 '-c', | |
| 35 dest='cluster_merge', | |
| 36 type=int, | |
| 37 required=False, | |
| 38 default=50, | |
| 39 help='Distance in pixel of clusters which are merged', | |
| 40 ) | |
| 41 args = parser.parse_args() | |
| 42 | |
| 43 label_image = skimage.io.imread(args.input_file.name) | |
| 44 label_image = merge_n(label_image, args.cluster_merge) | |
| 45 with warnings.catch_warnings(): | |
| 46 warnings.simplefilter("ignore") | |
| 47 res = skimage.util.img_as_uint(label_image) | |
| 48 skimage.io.imsave(args.out_file.name, res, plugin="tifffile") |