Fix amg for the image series annotator (#398)

* Fix amg for the image series annotator

* Skip widget test on windows

* Bump version

Author: constantinpape

README.md

@@ -58,6 +58,10 @@ Compared to these we support more applications (2d, 3d and tracking), and provid
 
 ## Release Overview
 
+**New in version 0.4.1**
+
+- Bugfix for the image series annotator. Before the automatic segmentation did not work correctly.
+
 **New in version 0.4.0**
 
 - Significantly improved model finetuning

micro_sam/__version__.py

@@ -1 +1 @@
-__version__ = "0.4.0"
+__version__ = "0.4.1"

micro_sam/sam_annotator/image_series_annotator.py

@@ -14,6 +14,7 @@
 from .. import util
 from ..precompute_state import _precompute_state_for_files
 from .annotator_2d import annotator_2d
+from ._state import AnnotatorState
 
 
 def image_series_annotator(
@@ -92,6 +93,8 @@ def next_image(*args):
         print("Loading next image from:", image_files[next_image_id])
         image = imageio.imread(image_files[next_image_id])
         image_embedding_path = None if embedding_paths is None else embedding_paths[next_image_id]
+        # Reset the state.
+        AnnotatorState().reset_state()
         annotator_2d(image, embedding_path=image_embedding_path, v=v, return_viewer=True, predictor=predictor, **kwargs)
 
     v.window.add_dock_widget(next_image)

test/test_sam_annotator/test_widgets.py

@@ -1,8 +1,10 @@
 import json
 import os
+import platform
 
 from mobile_sam.predictor import SamPredictor as MobileSamPredictor
 from segment_anything.predictor import SamPredictor
+import pytest
 import torch
 import zarr
 
@@ -15,6 +17,7 @@
 # you don't need to import it, as long as napari is installed
 # in your testing environment.
 # tmp_path is a regular pytest fixture.
+@pytest.mark.skipif(platform.system() == "Windows", reason="Gui test is not working on windows.")
 def test_embedding_widget(make_napari_viewer, tmp_path):
     """Test embedding widget for micro-sam napari plugin."""
     # setup