rename class freesurfer.FreesurferHippocampalVolumeFile -> freesurfer.HippocampalSubfieldsVolumeFile

examples/barplot.py

@@ -4,7 +4,7 @@ from matplotlib import pyplot
 import pandas
 import seaborn
 
-from freesurfer_volume_reader.freesurfer import FreesurferHippocampalVolumeFile
+from freesurfer_volume_reader.freesurfer import HippocampalSubfieldsVolumeFile
 from freesurfer_volume_reader import read_hippocampal_volume_file_dataframe
 
 
@@ -18,7 +18,7 @@ def main():
     argparser.add_argument('--subjects-dir', dest='subjects_dir_path', required=True)
     args = argparser.parse_args()
     volume_frame = pandas.concat(read_hippocampal_volume_file_dataframe(p)
-                                 for p in FreesurferHippocampalVolumeFile.find(args.subjects_dir_path))
+                                 for p in HippocampalSubfieldsVolumeFile.find(args.subjects_dir_path))
     volume_frame = volume_frame[volume_frame['subject'] == args.subject]
     volume_frame['subfield_segmentation_mode'] = volume_frame.apply(
         lambda row: ' & '.join(filter(None, ('T1' if row['T1_input'] else None,

freesurfer_volume_reader/__init__.py

@@ -11,7 +11,7 @@ import typing
 
 import pandas
 
-from freesurfer_volume_reader.freesurfer import FreesurferHippocampalVolumeFile
+from freesurfer_volume_reader.freesurfer import HippocampalSubfieldsVolumeFile
 
 VOLUME_FILENAME_HEMISPHERE_MAP = {'l': 'left', 'r': 'right'}
 
@@ -33,7 +33,7 @@ def read_hippocampal_volumes_mm3(volume_file_path: str) -> dict:
 
 def parse_hippocampal_volume_file_path(volume_file_path: str) -> dict:
     subject_dir_path = os.path.dirname(os.path.dirname(os.path.abspath(volume_file_path)))
-    filename_match = FreesurferHippocampalVolumeFile.FILENAME_REGEX.match(
+    filename_match = HippocampalSubfieldsVolumeFile.FILENAME_REGEX.match(
         os.path.basename(volume_file_path))
     assert filename_match, volume_file_path
     filename_groups = filename_match.groupdict()
@@ -61,7 +61,7 @@ def main():
     argparser = argparse.ArgumentParser(description=__doc__)
     argparser.add_argument('--filename-regex', type=re.compile,
                            default=remove_group_names_from_regex(
-                               FreesurferHippocampalVolumeFile.FILENAME_PATTERN),
+                               HippocampalSubfieldsVolumeFile.FILENAME_PATTERN),
                            help='default: %(default)s')
     argparser.add_argument('--output-format', choices=['csv'], default='csv',
                            help='default: %(default)s')
@@ -73,7 +73,7 @@ def main():
                            help='default: $SUBJECTS_DIR ({})'.format(subjects_dir_path))
     args = argparser.parse_args()
     volume_file_paths = [p for d in args.root_dir_paths
-                         for p in FreesurferHippocampalVolumeFile.find(
+                         for p in HippocampalSubfieldsVolumeFile.find(
                              root_dir_path=d, filename_regex=args.filename_regex)]
     volume_frames = []
     for volume_file_path in volume_file_paths:

freesurfer_volume_reader/freesurfer.py

@@ -4,7 +4,7 @@ import typing
 
 
 # pylint: disable=too-few-public-methods
-class FreesurferHippocampalVolumeFile:
+class HippocampalSubfieldsVolumeFile:
 
     # https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfields
     FILENAME_PATTERN = r'^(?P<h>[lr])h\.hippoSfVolumes' \

tests/freesurfer_test.py

@@ -3,7 +3,7 @@ import re
 
 import pytest
 
-from freesurfer_volume_reader.freesurfer import FreesurferHippocampalVolumeFile
+from freesurfer_volume_reader.freesurfer import HippocampalSubfieldsVolumeFile
 
 SUBJECTS_DIR = os.path.join(os.path.dirname(__file__), 'subjects')
 
@@ -22,7 +22,7 @@ SUBJECTS_DIR = os.path.join(os.path.dirname(__file__), 'subjects')
 ])
 def test_find_hippocampal_volume_files(root_dir_path, expected_file_paths):
     assert expected_file_paths == set(
-        FreesurferHippocampalVolumeFile.find(root_dir_path=root_dir_path))
+        HippocampalSubfieldsVolumeFile.find(root_dir_path=root_dir_path))
 
 
 @pytest.mark.parametrize(('root_dir_path', 'filename_pattern', 'expected_file_paths'), [
@@ -36,5 +36,5 @@ def test_find_hippocampal_volume_files(root_dir_path, expected_file_paths):
 ])
 def test_find_hippocampal_volume_files_pattern(root_dir_path, filename_pattern,
                                                expected_file_paths):
-    assert expected_file_paths == set(FreesurferHippocampalVolumeFile.find(
+    assert expected_file_paths == set(HippocampalSubfieldsVolumeFile.find(
         root_dir_path=root_dir_path, filename_regex=re.compile(filename_pattern)))