From e075840d77f751ceae5a293a61f1ec101a9456eb Mon Sep 17 00:00:00 2001
From: Alessandro Felder <alessandrofelder@users.noreply.github.com>
Date: Tue, 27 Feb 2024 13:26:14 +0000
Subject: [PATCH] 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 <1willgraham@gmail.com>
---
 pyproject.toml                              |  1 +
 tests/tests/test_brainreg/test_transform.py | 60 +++++++++++++++++++++
 2 files changed, 61 insertions(+)
 create mode 100644 tests/tests/test_brainreg/test_transform.py

diff --git a/pyproject.toml b/pyproject.toml
index 3b647cb..bc46b48 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -57,6 +57,7 @@ dev = [
     "pyqt5",
     "pytest-cov",
     "pytest-qt",
+    "pytest-mock",
     "pytest",
     "qtpy",
     "ruff",
diff --git a/tests/tests/test_brainreg/test_transform.py b/tests/tests/test_brainreg/test_transform.py
new file mode 100644
index 0000000..b99f203
--- /dev/null
+++ b/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