Mercurial > repos > imgteam > 2d_split_binaryimage_by_watershed
diff 2d_split_binaryimage_by_watershed.py @ 0:5e21d7342593 draft
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_split_binaryimage_by_watershed/ commit b2acc1845a25828181597fe5b6982fe116a7796d
author | imgteam |
---|---|
date | Mon, 22 Jul 2019 05:00:37 -0400 |
parents | |
children | f8f7987586b7 |
line wrap: on
line diff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/2d_split_binaryimage_by_watershed.py Mon Jul 22 05:00:37 2019 -0400 @@ -0,0 +1,26 @@ +import argparse +import sys +import skimage.io +from skimage.morphology import watershed +from skimage.feature import peak_local_max +from scipy import ndimage as ndi +import skimage.util + +if __name__ == "__main__": + parser = argparse.ArgumentParser(description='Split binaryimage by watershed') + parser.add_argument('input_file', type=argparse.FileType('r'), default=sys.stdin, help='input file') + parser.add_argument('out_file', type=argparse.FileType('w'), default=sys.stdin, help='out file (TIFF)') + parser.add_argument('min_distance', type=int, default=100, help='Minimum distance to next object') + args = parser.parse_args() + + img_in = skimage.io.imread(args.input_file.name) + distance = ndi.distance_transform_edt(img_in) + local_maxi = peak_local_max(distance, + indices=False, + min_distance=args.min_distance, + labels=img_in) + markers = ndi.label(local_maxi)[0] + res = watershed(-distance, markers, mask=img_in) + + res = skimage.util.img_as_uint(res) + skimage.io.imsave(args.out_file.name, res, plugin="tifffile")