import datetime import os import pytest from conftest import SUBJECTS_DIR, assert_approx_equal from freesurfer_stats import CorticalParcellationStats @pytest.mark.parametrize( ('path', 'headers', 'hemisphere', 'whole_brain_measurements', 'structure_measurements'), [(os.path.join(SUBJECTS_DIR, 'fabian', 'stats', 'lh.aparc.DKTatlas.stats.short'), {'CreationTime': datetime.datetime(2019, 5, 9, 21, 5, 54, tzinfo=datetime.timezone.utc), 'generating_program': 'mris_anatomical_stats', 'cvs_version': 'Id: mris_anatomical_stats.c,v 1.79 2016/03/14 15:15:34 greve Exp', 'mrisurf.c-cvs_version': 'Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp', 'cmdline': 'mris_anatomical_stats -th3 -mgz -cortex ../label/lh.cortex.label' ' -f ../stats/lh.aparc.DKTatlas.stats -b -a ../label/lh.aparc.DKTatlas.annot' ' -c ../label/aparc.annot.DKTatlas.ctab fabian lh white', 'sysname': 'Linux', 'hostname': 'another-hostname', 'machine': 'x86_64', 'user': 'some-username', 'SUBJECTS_DIR': '/home/some-username/freesurfer-subjects', 'anatomy_type': 'surface', 'subjectname': 'fabian', 'hemi': 'lh', 'AnnotationFile': '../label/lh.aparc.DKTatlas.annot', 'AnnotationFileTimeStamp': datetime.datetime(2019, 5, 9, 23, 5, 40)}, 'left', {'White Surface Total Area': (98553, 'mm^2'), 'Mean Thickness': (2.50462, 'mm'), 'Brain Segmentation Volume': (1327432.000000, 'mm^3'), 'Brain Segmentation Volume Without Ventricles': (1316285.000000, 'mm^3'), 'Brain Segmentation Volume Without Ventricles from Surf': (1315572.548920, 'mm^3'), 'Total cortical gray matter volume': (553998.311189, 'mm^3'), 'Supratentorial volume': (1172669.548920, 'mm^3'), 'Supratentorial volume Without Ventricles': (1164180.548920, 'mm^3'), 'Estimated Total Intracranial Volume': (1670487.274486, 'mm^3')}, {'caudalanteriorcingulate': { 'Structure Name': 'caudalanteriorcingulate', 'Number of Vertices': 2061, 'Surface Area': 1472.0, 'Gray Matter Volume': 4258.0, 'Average Thickness': 2.653, 'Thickness StdDev': 0.644, 'Integrated Rectified Mean Curvature': 0.135, 'Integrated Rectified Gaussian Curvature': 0.020, 'Folding Index': 27, 'Intrinsic Curvature Index': 1.6}, 'caudalmiddlefrontal': { 'Structure Name': 'caudalmiddlefrontal', 'Number of Vertices': 4451, 'Surface Area': 3039.0, 'Gray Matter Volume': 8239.0, 'Average Thickness': 2.456, 'Thickness StdDev': 0.486, 'Integrated Rectified Mean Curvature': 0.116, 'Integrated Rectified Gaussian Curvature': 0.020, 'Folding Index': 42, 'Intrinsic Curvature Index': 3.7}, 'insula': { 'Structure Name': 'insula', 'Number of Vertices': 3439, 'Surface Area': 2304.0, 'Gray Matter Volume': 7594.0, 'Average Thickness': 3.193, 'Thickness StdDev': 0.620, 'Integrated Rectified Mean Curvature': 0.116, 'Integrated Rectified Gaussian Curvature': 0.027, 'Folding Index': 33, 'Intrinsic Curvature Index': 3.5}}), (os.path.join( SUBJECTS_DIR, 'fabian', 'stats', 'rh.aparc.pial.stats.short'), {'CreationTime': datetime.datetime(2019, 5, 9, 21, 3, 42, tzinfo=datetime.timezone.utc), 'generating_program': 'mris_anatomical_stats', 'cvs_version': 'Id: mris_anatomical_stats.c,v 1.79 2016/03/14 15:15:34 greve Exp', 'mrisurf.c-cvs_version': 'Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp', 'cmdline': 'mris_anatomical_stats -th3 -mgz -cortex ../label/rh.cortex.label' ' -f ../stats/rh.aparc.pial.stats -b -a ../label/rh.aparc.annot' ' -c ../label/aparc.annot.ctab fabian rh pial', 'sysname': 'Linux', 'hostname': 'some-hostname', 'machine': 'x86_64', 'user': 'some-username', 'SUBJECTS_DIR': '/home/some-username/freesurfer-subjects', 'anatomy_type': 'surface', 'subjectname': 'fabian', 'hemi': 'rh', 'AnnotationFile': '../label/rh.aparc.annot', 'AnnotationFileTimeStamp': datetime.datetime(2019, 5, 9, 22, 27, 28)}, 'right', {'Pial Surface Total Area': (121260, 'mm^2'), 'Mean Thickness': (2.4817, 'mm'), 'Brain Segmentation Volume': (1327432.000000, 'mm^3'), 'Brain Segmentation Volume Without Ventricles': (1316285.000000, 'mm^3'), 'Brain Segmentation Volume Without Ventricles from Surf': (1315572.548920, 'mm^3'), 'Total cortical gray matter volume': (553998.311189, 'mm^3'), 'Supratentorial volume': (1172669.548920, 'mm^3'), 'Supratentorial volume Without Ventricles': (1164180.548920, 'mm^3'), 'Estimated Total Intracranial Volume': (1670487.274486, 'mm^3')}, {'bankssts': { 'Structure Name': 'bankssts', 'Number of Vertices': 1344, 'Surface Area': 825.0, 'Gray Matter Volume': 2171.0, 'Average Thickness': 2.436, 'Thickness StdDev': 0.381, 'Integrated Rectified Mean Curvature': 0.115, 'Integrated Rectified Gaussian Curvature': 0.028, 'Folding Index': 19, 'Intrinsic Curvature Index': 1.7}, 'transversetemporal': { 'Structure Name': 'transversetemporal', 'Number of Vertices': 651, 'Surface Area': 545.0, 'Gray Matter Volume': 1061.0, 'Average Thickness': 2.251, 'Thickness StdDev': 0.317, 'Integrated Rectified Mean Curvature': 0.110, 'Integrated Rectified Gaussian Curvature': 0.021, 'Folding Index': 3, 'Intrinsic Curvature Index': 0.6}})], ) def test_read(path, headers, hemisphere, whole_brain_measurements, structure_measurements): stats = CorticalParcellationStats.read(path) assert headers == stats.headers assert hemisphere == stats.hemisphere assert_approx_equal(whole_brain_measurements, stats.whole_brain_measurements) assert stats.structure_measurement_units == { 'Structure Name': None, 'Number of Vertices': None, 'Surface Area': 'mm^2', 'Gray Matter Volume': 'mm^3', 'Average Thickness': 'mm', 'Thickness StdDev': 'mm', 'Integrated Rectified Mean Curvature': 'mm^-1', 'Integrated Rectified Gaussian Curvature': 'mm^-2', 'Folding Index': None, 'Intrinsic Curvature Index': None, } assert_approx_equal(structure_measurements, stats.structure_measurements)