add tests for transforming to atlas space function

pyproject.toml

@@ -57,6 +57,7 @@ dev = [
     "pyqt5",
     "pytest-cov",
     "pytest-qt",
+    "pytest-mock",
     "pytest",
     "qtpy",
     "ruff",

tests/tests/test_brainreg/test_transform.py

@@ -0,0 +1,85 @@
+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.
+    This is a basic test case that covers a deformation field that maps
+    everything to [1, 1, 1].
+
+    Args:
+        mocker: The mocker object used to patch the reading of deformation
+                field tiffs.
+
+    Returns:
+        None
+    """
+    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,
+    )
+    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,
+    # 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 not points_out_of_bounds, str(points_out_of_bounds)
+
+
+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.
+
+    Args:
+        mocker: The mocker object to patch the reading of deformation
+                field tiffs
+
+    Returns:
+        None
+    """
+    mock_deformation_field = np.ones((4, 4, 4))
+    mocker.patch(
+        "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",
+            ],
+        )
+    )
+
+    assert len(transformed_points) == 0
+    assert len(points_out_of_bounds) == 1
+    assert points_out_of_bounds[0] == [5, 5, 5]