test: Access MRS NIfTI extension

Author: effigies

tests/conftest.py

@@ -10,28 +10,37 @@
 from .data import load_data
 
 
+def get_submod_or_env(dir_name: str, env_var: str) -> Path:
+    """Get submodule data path or override from environment variable.
+
+    Signals to skip tests if submodule is not checked out and no variable is set.
+    """
+    ret = os.getenv(env_var)
+    if not ret:
+        data_path = load_data(dir_name)
+        if not any(data_path.iterdir()):
+            pytest.skip(f'{dir_name} submodule is not checked out')
+        return data_path
+    return Path(ret)
+
+
 @pytest.fixture(scope='session')
 def examples() -> Path:
     """Get bids-examples from submodule, allow environment variable override."""
-    ret = os.getenv('BIDS_EXAMPLES')
-    if not ret:
-        examples = load_data('bids-examples')
-        if not any(examples.iterdir()):
-            pytest.skip('bids-examples submodule is not checked out')
-        return examples
-    return Path(ret)
+    return get_submod_or_env('bids-examples', 'BIDS_EXAMPLES')
 
 
 @pytest.fixture(scope='session')
 def gitignore_test() -> Path:
     """Get bids-examples from submodule, allow environment variable override."""
-    ret = os.getenv('GITIGNORE_TEST_DIR')
-    if not ret:
-        test_data = load_data('gitignore-test')
-        if not any(test_data.iterdir()):
-            pytest.skip('gitignore-test submodule is not checked out')
-        return test_data
-    return Path(ret)
+    return get_submod_or_env('gitignore-test', 'GITIGNORE_TEST_DIR')
+
+
+@pytest.fixture(scope='session')
+def mrs_data() -> Path:
+    """Get MRS data from submodule, allow environment variable override."""
+    mrs_nifti_standard = get_submod_or_env('mrs_nifti_standard', 'MRS_NIFTI_STANDARD')
+    return mrs_nifti_standard / 'example_data' / 'examples'
 
 
 @pytest.fixture(scope='session')

tests/test_context.py

@@ -206,3 +206,32 @@ def test_load_tsv_gz(synthetic_dataset: FileTree) -> None:
 
     assert tuple(tsvgz_file.keys()) == headers
     # Will need an additional test for the content
+
+
+def test_nifti_mrs_header(
+    mrs_data: Path,
+    schema: Namespace,
+    memfs: fsspec.AbstractFileSystem,
+    tmp_path: Path,
+) -> None:
+    example_01 = mrs_data / 'example_01.nii.gz'
+    memfs.pipe(
+        {
+            '/dataset_description.json': json.dumps(
+                {'Name': 'MRS Test Dataset', 'BIDSVersion': '1.10.1'}
+            ).encode(),
+            '/sub-01/mrs/sub-01_acq-press_mrs.nii.gz': example_01.read_bytes(),
+        }
+    )
+    memfs.get('memory:///', str(tmp_path), recursive=True)
+    dataset = FileTree.read_from_filesystem(tmp_path)
+    sub01 = dataset / 'sub-01'
+    mrs = dataset / 'sub-01' / 'mrs' / 'sub-01_acq-press_mrs.nii.gz'
+
+    ds = context.Dataset(dataset, schema)
+    subject = Subject(context.Sessions(sub01))
+    mrs_context = context.Context(mrs, ds, subject)
+
+    assert mrs_context.nifti_header is not None
+    assert isinstance(mrs_context.nifti_header.mrs, Namespace)
+    assert mrs_context.nifti_header.mrs.ResonantNucleus == ['1H']