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tests/tests/test_brainreg/test_transform.py

@@ -1,8 +1,13 @@
-from brainglobe_utils.brainreg.transform import transform_points_from_downsampled_to_atlas_space
-import numpy as np
 from pathlib import Path
+
+import numpy as np
 from bg_atlasapi import BrainGlobeAtlas
 
+from brainglobe_utils.brainreg.transform import (
+    transform_points_from_downsampled_to_atlas_space,
+)
+
+
 def test_transform_points_from_downsampled_to_atlas_space(mocker):
     """
     Test case for transforming points from downsampled space to atlas space.
@@ -14,26 +19,34 @@ def test_transform_points_from_downsampled_to_atlas_space(mocker):
     Returns:
         None
     """
-    mock_deformation_field = np.ones((132, 80, 114)) # shape of allen 100 reference, has unit mm
+    mock_deformation_field = np.ones(
+        (132, 80, 114)
+    )  # shape of allen 100 reference, has unit mm
     mocker.patch(
-        "brainglobe_utils.brainreg.transform.tifffile.imread", side_effect=lambda x: mock_deformation_field
+        "brainglobe_utils.brainreg.transform.tifffile.imread",
+        side_effect=lambda x: mock_deformation_field,
     )
-    downsampled_points=np.array([[1,1,1], [2,2,2]])
-    transformed_points, points_out_of_bounds = transform_points_from_downsampled_to_atlas_space(
-        downsampled_points=downsampled_points,
-        atlas=BrainGlobeAtlas("allen_mouse_100um"),
-        deformation_field_paths=[
-            Path.home()/"dummy_x_deformation.tif",
-            Path.home()/"dummy_y_deformation.tif",
-            Path.home()/"dummy_z_deformation.tif"
-        ]
+    downsampled_points = np.array([[1, 1, 1], [2, 2, 2]])
+    transformed_points, points_out_of_bounds = (
+        transform_points_from_downsampled_to_atlas_space(
+            downsampled_points=downsampled_points,
+            atlas=BrainGlobeAtlas("allen_mouse_100um"),
+            deformation_field_paths=[
+                Path.home() / "dummy_x_deformation.tif",
+                Path.home() / "dummy_y_deformation.tif",
+                Path.home() / "dummy_z_deformation.tif",
+            ],
+        )
     )
-    # because we mock the deformation field as all ones, 
+    # because we mock the deformation field as all ones,
     # all coordinates should be mapped to [1,1,1]*1mm/100um = [10,10,10]
-    assert np.all(transformed_points == np.ones_like(transformed_points)*10)
+    assert np.all(transformed_points == np.ones_like(transformed_points) * 10)
     assert not points_out_of_bounds, str(points_out_of_bounds)
-
-def test_transform_points_from_downsampled_to_atlas_space_out_of_bounds(mocker):
+
+
+def test_transform_points_from_downsampled_to_atlas_space_out_of_bounds(
+    mocker,
+):
     """
     Test case for transforming points from downsampled space to atlas space when points are out of bounds.
     Points are out of bounds when they cause an index error on the deformation field.
@@ -44,21 +57,24 @@ def test_transform_points_from_downsampled_to_atlas_space_out_of_bounds(mocker):
     Returns:
         None
     """
-    mock_deformation_field = np.ones((4,4,4))
+    mock_deformation_field = np.ones((4, 4, 4))
     mocker.patch(
-        "brainglobe_utils.brainreg.transform.tifffile.imread", side_effect=lambda x: mock_deformation_field
+        "brainglobe_utils.brainreg.transform.tifffile.imread",
+        side_effect=lambda x: mock_deformation_field,
     )
-    downsampled_points=np.array([[5,5,5]])
-    transformed_points, points_out_of_bounds = transform_points_from_downsampled_to_atlas_space(
-        downsampled_points=downsampled_points,
-        atlas=BrainGlobeAtlas("allen_mouse_100um"),
-        deformation_field_paths=[
-            Path.home()/"dummy_x_deformation.tif",
-            Path.home()/"dummy_y_deformation.tif",
-            Path.home()/"dummy_z_deformation.tif"
-        ]
+    downsampled_points = np.array([[5, 5, 5]])
+    transformed_points, points_out_of_bounds = (
+        transform_points_from_downsampled_to_atlas_space(
+            downsampled_points=downsampled_points,
+            atlas=BrainGlobeAtlas("allen_mouse_100um"),
+            deformation_field_paths=[
+                Path.home() / "dummy_x_deformation.tif",
+                Path.home() / "dummy_y_deformation.tif",
+                Path.home() / "dummy_z_deformation.tif",
+            ],
+        )
     )
 
-    assert len(transformed_points)==0
-    assert len(points_out_of_bounds)==1
-    assert points_out_of_bounds[0]==[5,5,5]
+    assert len(transformed_points) == 0
+    assert len(points_out_of_bounds) == 1
+    assert points_out_of_bounds[0] == [5, 5, 5]