import os import pytest from freesurfer_volume_reader.ashs import HippocampalSubfieldsVolumeFile from conftest import SUBJECTS_DIR @pytest.mark.parametrize(('volume_file_path', 'expected_attrs'), [ ('ashs/final/bert_left_heur_volumes.txt', {'subject': 'bert', 'hemisphere': 'left', 'correction': None}), ('ashs/final/bert_left_corr_nogray_volumes.txt', {'subject': 'bert', 'hemisphere': 'left', 'correction': 'nogray'}), ('ashs/final/bert_left_corr_usegray_volumes.txt', {'subject': 'bert', 'hemisphere': 'left', 'correction': 'usegray'}), ('ashs/final/bert_right_heur_volumes.txt', {'subject': 'bert', 'hemisphere': 'right', 'correction': None}), ('ashs/final/bert_right_corr_nogray_volumes.txt', {'subject': 'bert', 'hemisphere': 'right', 'correction': 'nogray'}), ('ashs/final/bert_right_corr_usegray_volumes.txt', {'subject': 'bert', 'hemisphere': 'right', 'correction': 'usegray'}), ('somewhere/else/bert_right_heur_volumes.txt', {'subject': 'bert', 'hemisphere': 'right', 'correction': None}), ('somewhere/else/bert_right_corr_nogray_volumes.txt', {'subject': 'bert', 'hemisphere': 'right', 'correction': 'nogray'}), ('bert_right_heur_volumes.txt', {'subject': 'bert', 'hemisphere': 'right', 'correction': None}), ('/foo/bar/alice_20190503_right_corr_nogray_volumes.txt', {'subject': 'alice_20190503', 'hemisphere': 'right', 'correction': 'nogray'}), ]) def test_hippocampal_subfields_volume_file_init(volume_file_path, expected_attrs): volume_file = HippocampalSubfieldsVolumeFile(path=volume_file_path) assert os.path.abspath(volume_file_path) == volume_file.absolute_path for attr, value in expected_attrs.items(): assert value == getattr(volume_file, attr) @pytest.mark.parametrize('volume_file_path', [ 'bert_middle_heur_volumes.txt', 'bert_right_hear_volumes.txt', 'bert_right_heur_volumes.nii', 'bert_left_lfseg_corr_usegray.nii.gz', ]) def test_hippocampal_subfields_volume_file_init_invalid(volume_file_path): with pytest.raises(Exception): HippocampalSubfieldsVolumeFile(path=volume_file_path) @pytest.mark.parametrize(('volume_file_path', 'expected_volumes'), [ (os.path.join(SUBJECTS_DIR, 'bert', 'final', 'bert_left_corr_nogray_volumes.txt'), {'CA1': 678.901, 'CA2+3': 123.456, 'DG': 901.234, 'ERC': 678.901, 'PHC': 2345.876, 'PRC': 2345.678, 'SUB': 457.789}), ]) def test_hippocampal_subfields_volume_file_read_volumes_mm3(volume_file_path, expected_volumes): volume_file = HippocampalSubfieldsVolumeFile(path=volume_file_path) assert expected_volumes == volume_file.read_volumes_mm3() def test_hippocampal_subfields_volume_file_read_volumes_mm3_not_found(): volume_file = HippocampalSubfieldsVolumeFile( path=os.path.join(SUBJECTS_DIR, 'nobert', 'final', 'bert_left_corr_nogray_volumes.txt')) with pytest.raises(FileNotFoundError): volume_file.read_volumes_mm3()