Update function for getting center coordinates

Author: anwai98

micro_sam/util.py

@@ -288,7 +288,7 @@ def compute_iou(mask1, mask2):
     return iou
 
 
-def get_cell_center_coordinates(gt, mode="p"):
+def get_cell_center_coordinates(gt, mode="v"):
     """
     Returns the center coordinates of the foreground instances in the ground-truth
     """
@@ -300,6 +300,7 @@ def get_cell_center_coordinates(gt, mode="p"):
         center_coordinates = [prop.centroid for prop in properties]
     elif mode == "v":
         center_coordinates = vigra.filters.eccentricityCenters(gt.astype('float32'))
+        center_coordinates.pop(0)
 
     bbox_coordinates = [prop.bbox for prop in properties]
 

test/test_prompt_generators.py

@@ -19,10 +19,7 @@ def test_point_prompt_generator(self):
         labels = self._get_test_data()
         label_ids = np.unique(labels)
 
-        mode = "v"  # this gets center points using vigra - regionprops throws error for asymmetrical blobs
-        centers, boxes = get_cell_center_coordinates(labels, mode=mode)
-        if mode == "v":
-            centers.pop(0)   # to avoid the background element
+        centers, boxes = get_cell_center_coordinates(labels)
 
         test_point_pairs = [(1, 0), (1, 1), (2, 4), (3, 9)]
         for (n_pos, n_neg) in test_point_pairs: