Mercurial > repos > imgteam > binary2labelimage
comparison 2d_split_binaryimage_by_watershed.py @ 3:a041e4e9d449 draft default tip
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binary2labelimage/ commit 48df7d9c58fb88e472caeb4d4a1e14170d79b643
| author | imgteam |
|---|---|
| date | Mon, 12 May 2025 08:15:32 +0000 |
| parents | |
| children |
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| 2:938e2358eb80 | 3:a041e4e9d449 |
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| 1 import argparse | |
| 2 import sys | |
| 3 | |
| 4 import numpy as np | |
| 5 import skimage.io | |
| 6 import skimage.util | |
| 7 from scipy import ndimage as ndi | |
| 8 from skimage.feature import peak_local_max | |
| 9 from skimage.segmentation import watershed | |
| 10 | |
| 11 | |
| 12 if __name__ == "__main__": | |
| 13 parser = argparse.ArgumentParser(description='Split binaryimage by watershed') | |
| 14 parser.add_argument('input_file', type=argparse.FileType('r'), default=sys.stdin, help='input file') | |
| 15 parser.add_argument('out_file', type=argparse.FileType('w'), default=sys.stdin, help='out file (TIFF)') | |
| 16 parser.add_argument('min_distance', type=int, default=100, help='Minimum distance to next object') | |
| 17 args = parser.parse_args() | |
| 18 | |
| 19 img_in = skimage.io.imread(args.input_file.name) | |
| 20 distance = ndi.distance_transform_edt(img_in) | |
| 21 | |
| 22 local_max_indices = peak_local_max( | |
| 23 distance, | |
| 24 min_distance=args.min_distance, | |
| 25 labels=img_in, | |
| 26 ) | |
| 27 local_max_mask = np.zeros(img_in.shape, dtype=bool) | |
| 28 local_max_mask[tuple(local_max_indices.T)] = True | |
| 29 markers = ndi.label(local_max_mask)[0] | |
| 30 res = watershed(-distance, markers, mask=img_in) | |
| 31 | |
| 32 res = skimage.util.img_as_uint(res) | |
| 33 skimage.io.imsave(args.out_file.name, res, plugin="tifffile") |