Updates to the image series annotator (#549)

Author: constantinpape

micro_sam/napari.yaml

@@ -4,9 +4,13 @@ contributions:
   commands:
 
     # Commands for sample data.
-    - id: micro-sam.sample_data_image_series
-      python_name: micro_sam.sample_data:sample_data_image_series
-      title: Load image series sample data from micro-sam plugin
+    # We don't provide the sample data for image series via napari for now,
+    # because the image series annotator cannot be called for image layers in napari (yet),
+    # but it has to be called with the path to the folder where the images are stored.
+    # So providing the sample data in napari would be confusing.
+    # - id: micro-sam.sample_data_image_series
+    #   python_name: micro_sam.sample_data:sample_data_image_series
+    #   title: Load image series sample data from micro-sam plugin
     - id: micro-sam.sample_data_wholeslide
       python_name: micro_sam.sample_data:sample_data_wholeslide
       title: Load WholeSlide sample data from micro-sam plugin
@@ -47,9 +51,9 @@ contributions:
       title: Set cache directory
 
   sample_data:
-    - command: micro-sam.sample_data_image_series
-      display_name: Image series example data
-      key: micro-sam-image-series
+    # - command: micro-sam.sample_data_image_series
+    #   display_name: Image series example data
+    #   key: micro-sam-image-series
     - command: micro-sam.sample_data_wholeslide
       display_name: WholeSlide example data
       key: micro-sam-wholeslide

micro_sam/sam_annotator/image_series_annotator.py

@@ -191,6 +191,9 @@ def next_image(*args):
         # Save the current segmentation.
         _save_segmentation(images[next_image_id], next_image_id, segmentation)
 
+        # Clear the segmentation already to avoid lagging removal.
+        viewer.layers["committed_objects"].data = np.zeros_like(viewer.layers["committed_objects"].data)
+
         # Load the next image.
         next_image_id += 1
         if next_image_id == len(images):