add two simple additional validation functions (#261)

* add two simple additional validation functions

* add tests for reference/annotation comparison

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

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

* improve error message

Co-authored-by: Vasco Schiavo <115561717+VascoSch92@users.noreply.github.com>

* make linter happy

* adapt test accordingly

* revert to assertion error

for consistency with other validation functions.

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

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

* add tests for additional reference validation

* fix test failure due to typo

* document tests

* Apply suggestions from code review

Co-authored-by: Will Graham <32364977+willGraham01@users.noreply.github.com>

---------

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: Vasco Schiavo <115561717+VascoSch92@users.noreply.github.com>
Co-authored-by: Will Graham <32364977+willGraham01@users.noreply.github.com>

brainglobe_atlasapi/atlas_generation/validate_atlases.py

@@ -111,9 +111,36 @@ def validate_checksum(atlas: BrainGlobeAtlas):
     pass
 
 
-def check_additional_references(atlas: BrainGlobeAtlas):
-    # check additional references are different, but have same dimensions
-    pass
+def validate_image_dimensions(atlas: BrainGlobeAtlas):
+    """
+    Check that annotation and reference image have the same dimensions.
+    """
+    assert atlas.annotation.shape == atlas.reference.shape, (
+        "Annotation and reference image have different dimensions. \n"
+        f"Annotation image has dimension: {atlas.annotation.shape}, "
+        f"while reference image has dimension {atlas.reference.shape}."
+    )
+    return True
+
+
+def validate_additional_references(atlas: BrainGlobeAtlas):
+    """
+    Check that additional references are different, but have same dimensions.
+    """
+    for (
+        additional_reference_name
+    ) in atlas.additional_references.references_list:
+        additional_reference = atlas.additional_references[
+            additional_reference_name
+        ]
+        assert additional_reference.shape == atlas.reference.shape, (
+            f"Additional reference {additional_reference} "
+            "has unexpected dimension."
+        )
+        assert not np.all(
+            additional_reference == atlas.reference
+        ), "Additional reference is not different to main reference."
+    return True
 
 
 def catch_missing_mesh_files(atlas: BrainGlobeAtlas):
@@ -211,7 +238,8 @@ def validate_atlas(atlas_name, version, validation_functions):
         validate_mesh_matches_image_extents,
         open_for_visual_check,
         validate_checksum,
-        check_additional_references,
+        validate_image_dimensions,
+        validate_additional_references,
         catch_missing_mesh_files,
         catch_missing_structures,
     ]

tests/atlasgen/test_validation.py

@@ -2,16 +2,20 @@
 
 import numpy as np
 import pytest
+import tifffile
 
 from brainglobe_atlasapi import BrainGlobeAtlas
 from brainglobe_atlasapi.atlas_generation.validate_atlases import (
     _assert_close,
     catch_missing_mesh_files,
     catch_missing_structures,
+    validate_additional_references,
     validate_atlas_files,
+    validate_image_dimensions,
     validate_mesh_matches_image_extents,
 )
 from brainglobe_atlasapi.config import get_brainglobe_dir
+from brainglobe_atlasapi.core import AdditionalRefDict
 
 
 @pytest.fixture
@@ -36,6 +40,27 @@ def atlas_with_bad_reference_file():
     os.rename(bad_name, good_name)
 
 
+@pytest.fixture
+def atlas_with_bad_reference_tiff_content():
+    """A fixture providing an invalid version of Allen Mouse atlas for testing.
+    The atlas will have a misnamed template file that won't be found by the API
+    This fixture cleans up the invalid atlas after the test has run.
+    """
+    BrainGlobeAtlas("allen_mouse_100um")  # ensure atlas is locally downloaded
+    actual_name = (
+        get_brainglobe_dir() / "allen_mouse_100um_v1.2/reference.tiff"
+    )
+    backup_name = (
+        get_brainglobe_dir() / "allen_mouse_100um_v1.2/reference_backup.tiff"
+    )
+    os.rename(actual_name, backup_name)
+    too_small_reference = np.ones((3, 3, 3), dtype=np.uint16)
+    tifffile.imwrite(actual_name, too_small_reference)
+    yield BrainGlobeAtlas("allen_mouse_100um")
+    os.remove(actual_name)
+    os.rename(backup_name, actual_name)
+
+
 @pytest.fixture
 def atlas_with_missing_structure():
     atlas = BrainGlobeAtlas("osten_mouse_100um")
@@ -47,6 +72,54 @@ def atlas_with_missing_structure():
     return modified_atlas
 
 
+@pytest.fixture
+def atlas_with_valid_additional_reference():
+    """A fixture providing a testing-only version of the Allen Mouse atlas.
+    The instance of the atlas returned has an additional reference
+    consisting of an array of 1, of the correct size.
+    This fixture cleans up the invalid atlas after the test has run.
+    """
+    allen_100 = BrainGlobeAtlas(
+        "allen_mouse_100um"
+    )  # ensure atlas is locally downloaded
+    additional_reference_name = (
+        get_brainglobe_dir()
+        / "allen_mouse_100um_v1.2/mock_additional_reference.tiff"
+    )
+    additional_reference = np.ones(allen_100.reference.shape, dtype=np.uint16)
+    allen_100.additional_references = AdditionalRefDict(
+        ["mock_additional_reference"],
+        data_path=get_brainglobe_dir() / "allen_mouse_100um_v1.2",
+    )
+    tifffile.imwrite(additional_reference_name, additional_reference)
+    yield allen_100
+    os.remove(additional_reference_name)
+
+
+@pytest.fixture
+def atlas_with_reference_matching_additional_reference():
+    """A fixture providing an invalid version of Allen Mouse atlas for testing.
+    It provides the atlas, with an additional reference containing
+    the same data as the main reference image.
+    This fixture cleans up the invalid atlas after the test has run.
+    """
+    allen_100 = BrainGlobeAtlas(
+        "allen_mouse_100um"
+    )  # ensure atlas is locally downloaded
+    additional_reference_name = (
+        get_brainglobe_dir()
+        / "allen_mouse_100um_v1.2/mock_additional_reference.tiff"
+    )
+    additional_reference = allen_100.reference
+    allen_100.additional_references = AdditionalRefDict(
+        ["mock_additional_reference"],
+        data_path=get_brainglobe_dir() / "allen_mouse_100um_v1.2",
+    )
+    tifffile.imwrite(additional_reference_name, additional_reference)
+    yield allen_100
+    os.remove(additional_reference_name)
+
+
 def test_validate_mesh_matches_image_extents(atlas):
     assert validate_mesh_matches_image_extents(atlas)
 
@@ -121,3 +194,42 @@ def test_catch_missing_structures(atlas_with_missing_structure):
         "but are not accessible through the atlas.",
     ):
         catch_missing_structures(atlas_with_missing_structure)
+
+
+def test_atlas_image_dimensions_match(atlas):
+    """Check the atlas passes the annotation-reference dimension validation"""
+    assert validate_image_dimensions(atlas)
+
+
+def test_atlas_image_dimensions_match_negative(
+    atlas_with_bad_reference_tiff_content,
+):
+    """Checks that an atlas with different annotation and reference
+    dimensions is flagged by the validation."""
+    with pytest.raises(
+        AssertionError,
+        match=r"Annotation and reference image have different dimensions.*",
+    ):
+        validate_image_dimensions(atlas_with_bad_reference_tiff_content)
+
+
+def test_atlas_additional_reference_different(
+    atlas_with_valid_additional_reference,
+):
+    """Checks that an atlas with a reasonably sized additional reference
+    passes its validation."""
+    validate_additional_references(atlas_with_valid_additional_reference)
+
+
+def test_atlas_additional_reference_same(
+    atlas_with_reference_matching_additional_reference,
+):
+    """Checks that an atlas with a rduplicate additional reference
+    fails the validation for this case."""
+    with pytest.raises(
+        AssertionError,
+        match=r"Additional reference is not different to main reference.",
+    ):
+        validate_additional_references(
+            atlas_with_reference_matching_additional_reference
+        )