bug: merge site near boundary

Author: anna-grim

src/segmentation_skeleton_metrics/skeleton_metric.py

@@ -554,13 +554,11 @@ def localize(self, swc_id_1, swc_id_2, label):
                     xyz_pair = [xyz_1, xyz_2]
         return xyz_pair, min_dist
 
-    def near_bdd(self, xyz_pair):
+    def near_bdd(self, xyz):
         near_bdd_bool = False
         if self.ignore_boundary_mistakes:
-            merge_site = utils.get_midpoint(xyz_pair[0], xyz_pair[1])
-            dims = self.labels.shape
-            above = [merge_site[i] > dims[i] - 32 for i in range(3)]
-            below = [merge_site[i] < 32 for i in range(3)]
+            above = [xyz[i] >= self.labels.shape[i] - 32 for i in range(3)]
+            below = [xyz[i] < 32 for i in range(3)]
             near_bdd_bool = True if any(above) or any(below) else False
         return near_bdd_bool
 

src/segmentation_skeleton_metrics/utils.py

@@ -186,7 +186,7 @@ def get_midpoint(xyz_1, xyz_2):
     xyz_2 : numpy.ndarray
         n-dimensional coordinate.
     """
-    return np.mean([xyz_1, xyz_2], axis=0)
+    return np.array([np.mean([xyz_1[i], xyz_2[i]]) for i in range(3)])
 
 
 def to_world(xyz, anisotropy):