updates "Merge neighbors in label map" tool

BMCV · Nov 1, 2023 · 3929102 · 3929102
1 parent bb6952a
commit 3929102
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Showing 2 changed files with 18 additions and 9 deletions.
diff --git a/tools/mergeneighboursinlabelimage/mergeneighboursinlabelimage.py b/tools/mergeneighboursinlabelimage/mergeneighboursinlabelimage.py
@@ -1,19 +1,21 @@
 import argparse
 import sys
+import warnings
+
+import numpy as np
+import scipy.spatial.distance
 import skimage.io
 import skimage.util
 from skimage.measure import regionprops
-import scipy.spatial.distance
-import numpy as np
-import warnings 
+
 
 def merge_n(img, dist=50):
     props = regionprops(img)
     found = False
     for i in range(0, len(props)):
         i_coords = props[i].coords
         for q in range(0, len(props)):
-            if i==q:
+            if i == q:
                 continue
             q_coords = props[q].coords
             iq_dist = np.min(scipy.spatial.distance.cdist(i_coords, q_coords, 'euclidean'))
@@ -26,6 +28,7 @@ def merge_n(img, dist=50):
         merge_n(img, dist)
     return img
 
+
 if __name__ == "__main__":
     parser = argparse.ArgumentParser()
     parser.add_argument('input_file', type=argparse.FileType('r'), default=sys.stdin, help='input file')
@@ -43,6 +46,6 @@ def merge_n(img, dist=50):
     label_image = skimage.io.imread(args.input_file.name)
     label_image = merge_n(label_image, args.cluster_merge)
     with warnings.catch_warnings():
-    	warnings.simplefilter("ignore")
-    	res = skimage.util.img_as_uint(label_image)
-    	skimage.io.imsave(args.out_file.name, res, plugin="tifffile")
+        warnings.simplefilter("ignore")
+        res = skimage.util.img_as_uint(label_image)
+        skimage.io.imsave(args.out_file.name, res, plugin="tifffile")
diff --git a/tools/mergeneighboursinlabelimage/mergeneighboursinlabelimage.xml b/tools/mergeneighboursinlabelimage/mergeneighboursinlabelimage.xml
@@ -1,5 +1,11 @@
-<tool id="ip_merge_neighbours_in_label" name="Merge Neighbours in Label" version="0.3"> 
-    <description>Merge Neighbours in Label Image</description>
+<tool id="ip_merge_neighbours_in_label" name="Merge neighbors in label map" version="0.3-2"> 
+    <description></description>
+    <edam_operations>
+        <edam_operation>operation_3443</edam_operation>
+    </edam_operations>
+    <xrefs>
+        <xref type="bio.tools">galaxy_image_analysis</xref>
+    </xrefs>
     <requirements>
         <requirement type="package" version="0.14.2">scikit-image</requirement>
         <requirement type="package" version="1.15.4">numpy</requirement>