Fixed pre-commit

brainglobe_registration/registration_widget.py

@@ -9,14 +9,16 @@
 """
 
 from pathlib import Path
+from typing import Optional
 
 import dask.array as da
+import napari.layers
 import numpy as np
+import numpy.typing as npt
 from bg_atlasapi import BrainGlobeAtlas
 from bg_atlasapi.list_atlases import get_downloaded_atlases
 from brainglobe_utils.qtpy.collapsible_widget import CollapsibleWidgetContainer
 from dask_image.ndinterp import affine_transform as dask_affine_transform
-from scipy.ndimage.interpolation import affine_transform
 from napari.qt.threading import thread_worker
 from napari.utils.notifications import show_error
 from napari.viewer import Viewer
@@ -54,11 +56,11 @@ def __init__(self, napari_viewer: Viewer):
         self.setContentsMargins(10, 10, 10, 10)
 
         self._viewer = napari_viewer
-        self._atlas: BrainGlobeAtlas = None
-        self._atlas_data_layer = None
-        self._atlas_annotations_layer = None
-        self._moving_image = None
-        self._moving_image_data_backup = None
+        self._atlas: Optional[BrainGlobeAtlas] = None
+        self._atlas_data_layer: Optional[napari.layers.Image] = None
+        self._atlas_annotations_layer: Optional[napari.layers.Labels] = None
+        self._moving_image: Optional[napari.layers.Image] = None
+        self._moving_image_data_backup: Optional[npt.NDArray] = None
 
         self.transform_params: dict[str, dict] = {
             "rigid": {},
@@ -196,11 +198,19 @@ def _on_atlas_dropdown_index_changed(self, index):
         self._atlas = BrainGlobeAtlas(atlas_name)
         atlas_dask_array = da.from_array(
             self._atlas.reference,
-            chunks=(1, self._atlas.reference.shape[1], self._atlas.reference.shape[2]),
+            chunks=(
+                1,
+                self._atlas.reference.shape[1],
+                self._atlas.reference.shape[2],
+            ),
         )
         dask_annotations = da.from_array(
             self._atlas.annotation,
-            chunks=(1, self._atlas.annotation.shape[1], self._atlas.annotation.shape[2]),
+            chunks=(
+                1,
+                self._atlas.annotation.shape[1],
+                self._atlas.annotation.shape[2],
+            ),
         )
 
         self._atlas_data_layer = self._viewer.add_image(
@@ -229,15 +239,17 @@ def _on_sample_dropdown_index_changed(self, index):
     def _on_adjust_moving_image(self, x: int, y: int, rotate: float):
         if not self._moving_image:
             show_error(
-                "No moving image selected. Please select a moving image before adjusting"
+                "No moving image selected. "
+                "Please select a moving image before adjusting"
             )
             return
         adjust_napari_image_layer(self._moving_image, x, y, rotate)
 
     def _on_adjust_moving_image_reset_button_click(self):
         if not self._moving_image:
             show_error(
-                "No moving image selected. Please select a moving image before adjusting"
+                "No moving image selected. "
+                "Please select a moving image before adjusting"
             )
             return
         adjust_napari_image_layer(self._moving_image, 0, 0, 0)
@@ -388,7 +400,11 @@ def _on_scale_moving_image(self, x: float, y: float):
         )
 
     def _on_adjust_atlas_rotation(self, pitch: float, yaw: float, roll: float):
-        if not self._atlas:
+        if not (
+            self._atlas
+            and self._atlas_data_layer
+            and self._atlas_annotations_layer
+        ):
             show_error(
                 "No atlas selected. Please select an atlas before rotating"
             )

brainglobe_registration/utils/utils.py

@@ -1,5 +1,5 @@
 from pathlib import Path
-from typing import List, Tuple, Dict
+from typing import Dict, List, Tuple
 
 import napari
 import numpy as np

tests/test_registration_widget.py

@@ -1,11 +1,7 @@
 import pytest
-from pytransform3d.rotations import active_matrix_from_angle
-import numpy as np
 
 from brainglobe_registration.registration_widget import RegistrationWidget
 
-from brainglobe_registration.utils.utils import calculate_rotated_bounding_box
-
 
 @pytest.fixture()
 def registration_widget(make_napari_viewer_with_images):
@@ -153,11 +149,10 @@ def test_scale_moving_image(
     "pitch, yaw, roll, expected_shape",
     [
         (0, 0, 0, (132, 80, 114)),
-        (45, 0, 0, (150, 150,  114)),
+        (45, 0, 0, (150, 150, 114)),
         (0, 45, 0, (174, 80, 174)),
         (0, 0, 45, (132, 137, 137)),
     ],
-
 )
 def test_on_adjust_atlas_rotation(
     registration_widget_with_example_atlas,
@@ -169,18 +164,14 @@ def test_on_adjust_atlas_rotation(
     reg_widget = registration_widget_with_example_atlas
     atlas_shape = reg_widget._atlas.reference.shape
 
-    reg_widget._on_adjust_atlas_rotation(
-        pitch, yaw, roll
-    )
+    reg_widget._on_adjust_atlas_rotation(pitch, yaw, roll)
 
     assert reg_widget._atlas_data_layer.data.shape == expected_shape
     assert reg_widget._atlas_annotations_layer.data.shape == expected_shape
     assert reg_widget._atlas.reference.shape == atlas_shape
 
 
-def test_on_adjust_atlas_rotation_no_atlas(
-    registration_widget, mocker
-):
+def test_on_adjust_atlas_rotation_no_atlas(registration_widget, mocker):
     mocked_show_error = mocker.patch(
         "brainglobe_registration.registration_widget.show_error"
     )
@@ -190,9 +181,7 @@ def test_on_adjust_atlas_rotation_no_atlas(
     )
 
 
-def test_on_atlas_reset(
-    registration_widget_with_example_atlas
-):
+def test_on_atlas_reset(registration_widget_with_example_atlas):
     reg_widget = registration_widget_with_example_atlas
     atlas_shape = reg_widget._atlas.reference.shape
     reg_widget._on_adjust_atlas_rotation(10, 10, 10)
@@ -204,9 +193,7 @@ def test_on_atlas_reset(
     assert reg_widget._atlas_annotations_layer.data.shape == atlas_shape
 
 
-def test_on_atlas_reset_no_atlas(
-    registration_widget, mocker
-):
+def test_on_atlas_reset_no_atlas(registration_widget, mocker):
     mocked_show_error = mocker.patch(
         "brainglobe_registration.registration_widget.show_error"
     )

tests/test_utils.py

@@ -7,10 +7,10 @@
 
 from brainglobe_registration.utils.utils import (
     adjust_napari_image_layer,
+    calculate_rotated_bounding_box,
     find_layer_index,
     get_image_layer_names,
     open_parameter_file,
-    calculate_rotated_bounding_box,
 )
 
 
@@ -101,7 +101,7 @@ def test_get_image_layer_names(make_napari_viewer_with_images):
     [
         (0, 0, (50, 100, 200)),
         (0, 90, (50, 200, 100)),
-        (0, 180,  (50, 100, 200)),
+        (0, 180, (50, 100, 200)),
         (0, 45, (50, 212, 212)),
         (1, 0, (50, 100, 200)),
         (1, 90, (200, 100, 50)),
@@ -111,12 +111,14 @@ def test_get_image_layer_names(make_napari_viewer_with_images):
         (2, 90, (100, 50, 200)),
         (2, 180, (50, 100, 200)),
         (2, 45, (106, 106, 200)),
-    ]
+    ],
 )
 def test_calculate_rotated_bounding_box(basis, rotation, expected_bounds):
     image_shape = (50, 100, 200)
     rotation_matrix = np.eye(4)
-    rotation_matrix[:-1, :-1] = active_matrix_from_angle(basis, np.deg2rad(rotation))
+    rotation_matrix[:-1, :-1] = active_matrix_from_angle(
+        basis, np.deg2rad(rotation)
+    )
 
     result_shape = calculate_rotated_bounding_box(image_shape, rotation_matrix)