Merge pull request #63 from computational-cell-analytics/fix-track2

Fix issue in tracking with points and set default projection mode to …

Author: constantinpape

micro_sam/sam_annotator/annotator_tracking.py

@@ -222,7 +222,7 @@ def track_objet_widget(
 
     # we use the bounding box projection method as default which generally seems to work better for larger changes
     # between frames (which is pretty tyipical for tracking compared to 3d segmentation)
-    projection_ = "bounding_box" if projection == "default" else projection
+    projection_ = "mask" if projection == "default" else projection
 
     with progress(total=shape[0]) as progress_bar:
         # step 1: segment all slices with prompts

micro_sam/sam_annotator/util.py

@@ -221,9 +221,10 @@ def segment_slices_with_prompts(
         assert len(track_ids_points) == len(z_values)
         z_values = z_values[track_ids_points == track_id]
 
-        track_ids_boxes = np.array(list(map(int, box_prompts.properties["track_id"])))
-        assert len(track_ids_boxes) == len(z_values_boxes), f"{len(track_ids_boxes)}, {len(z_values_boxes)}"
-        z_values_boxes = z_values_boxes[track_ids_boxes == track_id]
+        if len(z_values_boxes) > 0:
+            track_ids_boxes = np.array(list(map(int, box_prompts.properties["track_id"])))
+            assert len(track_ids_boxes) == len(z_values_boxes), f"{len(track_ids_boxes)}, {len(z_values_boxes)}"
+            z_values_boxes = z_values_boxes[track_ids_boxes == track_id]
 
     slices = np.unique(np.concatenate([z_values, z_values_boxes])).astype("int")
     stop_lower, stop_upper = False, False