refactor: rename read_hippocampal_volumes -> read_hippocampal_volumes_mm3

freesurfer_volume_reader/__init__.py

@@ -23,13 +23,14 @@ def find_hippocampal_volume_files(root_dir_path: str,
             yield os.path.join(dirpath, filename)
 
 
-def read_hippocampal_volumes(volume_file_path: str) -> dict:
+def read_hippocampal_volumes_mm3(volume_file_path: str) -> dict:
     subfield_volumes = {}
     with open(volume_file_path, 'r') as volume_file:
         for line in volume_file.read().rstrip().split('\n'):
+            # https://github.com/freesurfer/freesurfer/blob/release_6_0_0/HippoSF/src/segmentSubjectT1T2_autoEstimateAlveusML.m#L8
             # https://github.com/freesurfer/freesurfer/blob/release_6_0_0/HippoSF/src/segmentSubjectT1T2_autoEstimateAlveusML.m#L1946
-            subfield_name, subfield_volume_str = line.split(' ')
-            subfield_volumes[subfield_name] = float(subfield_volume_str)
+            subfield_name, subfield_volume_mm3_str = line.split(' ')
+            subfield_volumes[subfield_name] = float(subfield_volume_mm3_str)
     return subfield_volumes
 
 
@@ -49,7 +50,7 @@ def parse_hippocampal_volume_file_path(volume_file_path: str) -> dict:
 
 def read_hippocampal_volume_file_dataframe(volume_file_path: str) -> pandas.DataFrame:
     volumes_frame = pandas.DataFrame(
-        read_hippocampal_volumes(volume_file_path).items(),
+        read_hippocampal_volumes_mm3(volume_file_path).items(),
         columns=['subfield', 'volume'])
     for key, value in parse_hippocampal_volume_file_path(volume_file_path).items():
         volumes_frame[key] = value

tests/hippocampus_test.py

@@ -60,14 +60,14 @@ def test_find_hippocampal_volume_files_pattern(root_dir_path, filename_pattern,
       'HATA': 91.234567,
       'Whole_hippocampus': 1234.567899}),
 ])
-def test_read_hippocampal_volumes(volume_file_path, expected_volumes):
-    assert expected_volumes == freesurfer_volume_reader.read_hippocampal_volumes(
+def test_read_hippocampal_volumes_mm3(volume_file_path, expected_volumes):
+    assert expected_volumes == freesurfer_volume_reader.read_hippocampal_volumes_mm3(
         volume_file_path)
 
 
-def test_read_hippocampal_volumes_not_found():
+def test_read_hippocampal_volumes_mm3_not_found():
     with pytest.raises(FileNotFoundError):
-        freesurfer_volume_reader.read_hippocampal_volumes(
+        freesurfer_volume_reader.read_hippocampal_volumes_mm3(
             os.path.join(SUBJECTS_DIR, 'non-existing', 'lh.hippoSfVolumes-T1.v10.txt'))