add tests for transforming to atlas space function (#38)

* add tests for transforming to atlas space function

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

* Ruff is not smart enough to break strings

* parametrise test

---------

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: willGraham01 <[email protected]>

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 +1,60 @@
+from pathlib import Path
+
+import numpy as np
+import pytest
+from bg_atlasapi import BrainGlobeAtlas
+
+from brainglobe_utils.brainreg.transform import (
+ transform_points_from_downsampled_to_atlas_space,
+)
+
+
+@pytest.mark.parametrize(
+ (
+ "mock_deformation_field",
+ "expected_transformed_points",
+ "expected_points_out_of_bounds",
+ ),
+ [
+ (np.ones((132, 80, 114)), [[10, 10, 10], [10, 10, 10]], []),
+ (np.ones((4, 4, 4)), np.atleast_3d([]), [[5, 5, 5], [6, 6, 6]]),
+ ],
+)
+def test_transform_points_from_downsampled_to_atlas_space(
+ mocker,
+ mock_deformation_field,
+ expected_transformed_points,
+ expected_points_out_of_bounds,
+):
+ """
+ Test case for transforming points from downsampled space to atlas space.
+ * check that deformation field of ones maps to 1,1,1*resolution
+ * check that too small deformation field maps points to out-of-bounds
+
+ Args:
+ mocker: The mocker object used to patch the reading of deformation
+ field tiffs.
+
+ Returns:
+ None
+ """
+ mocker.patch(
+ "brainglobe_utils.brainreg.transform.tifffile.imread",
+ side_effect=lambda x: mock_deformation_field,
+ )
+ downsampled_points = np.array([[5, 5, 5], [6, 6, 6]])
+ 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 == expected_transformed_points)
+ assert points_out_of_bounds == expected_points_out_of_bounds