Fixed key error for transforming annotation

brainglobe · Jan 2, 2025 · b10f636 · b10f636
1 parent b4ceda3
commit b10f636
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Showing 3 changed files with 13 additions and 3 deletions.
diff --git a/brainglobe_registration/elastix/register.py b/brainglobe_registration/elastix/register.py
@@ -73,7 +73,7 @@ def run_registration(
 
 
 def transform_annotation_image(
-    annotation_image: npt.NDArray,
+    annotation_image: npt.NDArray[np.uint32],
     transform_parameters: itk.ParameterObject,
 ) -> npt.NDArray[np.uint32]:
     """

diff --git a/brainglobe_registration/registration_widget.py b/brainglobe_registration/registration_widget.py
@@ -427,8 +427,17 @@ def _on_run_button_click(self):
 
         data_in_atlas_space = transform_image(moving_image, inverse_parameters)
 
-        registered_annotation_image = transform_annotation_image(
+        # Creating fresh array is necessary to avoid a crash on Windows
+        # Otherwise self._atlas_annotations_layer.data.dtype.type returns
+        # np.uintc which is not supported by ITK. After creating a new array
+        # annotations.dtype.type returns np.uint32 which is supported by ITK.
+        annotation = np.array(
             self._atlas_annotations_layer.data[current_atlas_slice, :, :],
+            dtype=np.uint32,
+        )
+
+        registered_annotation_image = transform_annotation_image(
+            annotation,
             parameters,
         )
 

diff --git a/tests/test_register.py b/tests/test_register.py
@@ -55,7 +55,8 @@ def atlas_reference(atlas, slice_number=SLICE_NUMBER):
 
 @pytest.fixture(scope="module")
 def atlas_annotation(atlas, slice_number=SLICE_NUMBER):
-    return atlas.annotation[slice_number, :, :]
+    # Need the astype call to avoid a crash on Windows
+    return atlas.annotation[slice_number, :, :].astype(np.uint32)
 
 
 @pytest.fixture(scope="module")