fix removal of closeby clusters

clustering.py

@@ -47,6 +47,7 @@ def get_centroids(image : np.ndarray, image_threshold = 20,
 
 
     centroids = []
+    #print('Threshold: ', image_threshold)
 
     # apply the threshold to identify regions of "dark" pixels
     # the result is a binary mask (true/false) whether a given pixel is above or below the threshold
@@ -98,6 +99,13 @@ def get_centroids(image : np.ndarray, image_threshold = 20,
         proximity_tree = KDTree(centroids)
         pairs = proximity_tree.query_pairs(filter_radius)
         for p in pairs:
-            item = centroids.pop(p[0])
+            #print('pair: ', p, ' p[0]: ', p[0], ' p[1]:', p[1])
+            #print('coords: ', proximity_tree.data[p[0]], '  ', proximity_tree.data[p[1]])
+            coords_to_remove = [proximity_tree.data[p[0]][0], proximity_tree.data[p[0]][1]]
+            try:
+                idx = centroids.index(coords_to_remove)
+                centroids.pop(idx)
+            except ValueError:
+                pass
 
     return centroids