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

--- /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")