""" freesurfer-stats, a Python Library to Read FreeSurfer's Cortical Parcellation Anatomical Statistics Copyright (C) 2019 Fabian Peter Hammerle This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or any later version. This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. You should have received a copy of the GNU General Public License along with this program. If not, see . """ import datetime import os import pathlib import numpy import pandas.util.testing import pytest from conftest import SUBJECTS_DIR from freesurfer_stats import CorticalParcellationStats # pylint: disable=too-many-arguments @pytest.mark.parametrize( ('path', 'headers', 'hemisphere', 'whole_brain_measurements', 'structural_measurements_length', 'structural_measurements_subset'), [(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_mm^2': 98553, 'mean_thickness_mm': 2.50462, 'brain_segmentation_volume_mm^3': 1327432.000000, 'brain_segmentation_volume_without_ventricles_mm^3': 1316285.000000, 'brain_segmentation_volume_without_ventricles_from_surf_mm^3': 1315572.548920, 'total_cortical_gray_matter_volume_mm^3': 553998.311189, 'supratentorial_volume_mm^3': 1172669.548920, 'supratentorial_volume_without_ventricles_mm^3': 1164180.548920, 'estimated_total_intracranial_volume_mm^3': 1670487.274486}, 3, [{'structure_name': 'caudalanteriorcingulate', 'number_of_vertices': 2061, 'surface_area_mm^2': 1472, 'gray_matter_volume_mm^3': 4258, 'average_thickness_mm': 2.653, 'thickness_stddev_mm': 0.644, 'integrated_rectified_mean_curvature_mm^-1': 0.135, 'integrated_rectified_gaussian_curvature_mm^-2': 0.020, 'folding_index': 27, 'intrinsic_curvature_index': 1.6}, {'structure_name': 'caudalmiddlefrontal', 'number_of_vertices': 4451, 'surface_area_mm^2': 3039, 'gray_matter_volume_mm^3': 8239, 'average_thickness_mm': 2.456, 'thickness_stddev_mm': 0.486, 'integrated_rectified_mean_curvature_mm^-1': 0.116, 'integrated_rectified_gaussian_curvature_mm^-2': 0.020, 'folding_index': 42, 'intrinsic_curvature_index': 3.7}, {'structure_name': 'insula', 'number_of_vertices': 3439, 'surface_area_mm^2': 2304, 'gray_matter_volume_mm^3': 7594, 'average_thickness_mm': 3.193, 'thickness_stddev_mm': 0.620, 'integrated_rectified_mean_curvature_mm^-1': 0.116, 'integrated_rectified_gaussian_curvature_mm^-2': 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_mm^2': 121260, 'mean_thickness_mm': 2.4817, 'brain_segmentation_volume_mm^3': 1327432.000000, 'brain_segmentation_volume_without_ventricles_mm^3': 1316285.000000, 'brain_segmentation_volume_without_ventricles_from_surf_mm^3': 1315572.548920, 'total_cortical_gray_matter_volume_mm^3': 553998.311189, 'supratentorial_volume_mm^3': 1172669.548920, 'supratentorial_volume_without_ventricles_mm^3': 1164180.548920, 'estimated_total_intracranial_volume_mm^3': 1670487.274486}, 2, [{'structure_name': 'bankssts', 'number_of_vertices': 1344, 'surface_area_mm^2': 825, 'gray_matter_volume_mm^3': 2171, 'average_thickness_mm': 2.436, 'thickness_stddev_mm': 0.381, 'integrated_rectified_mean_curvature_mm^-1': 0.115, 'integrated_rectified_gaussian_curvature_mm^-2': 0.028, 'folding_index': 19, 'intrinsic_curvature_index': 1.7}, {'structure_name': 'transversetemporal', 'number_of_vertices': 651, 'surface_area_mm^2': 545, 'gray_matter_volume_mm^3': 1061, 'average_thickness_mm': 2.251, 'thickness_stddev_mm': 0.317, 'integrated_rectified_mean_curvature_mm^-1': 0.110, 'integrated_rectified_gaussian_curvature_mm^-2': 0.021, 'folding_index': 3, 'intrinsic_curvature_index': 0.6}]), (os.path.join( SUBJECTS_DIR, 'soichi', 'stats', 'rh.aparc.stats'), {'CreationTime': datetime.datetime(2020, 5, 4, 22, 20, 26, tzinfo=datetime.timezone.utc), 'AnnotationFileTimeStamp': datetime.datetime(2020, 5, 4, 21, 58, 13), 'AnnotationFile': '../label/rh.aparc.annot', 'SUBJECTS_DIR': '/N/dc2/scratch/hayashis/bigred3-workflows' '/5eb0689676c10ead933d673c/5eb068b076c10e7b013d673f', 'anatomy_type': 'surface', 'cmdline': 'mris_anatomical_stats -th3 -mgz -cortex ../label/rh.cortex.label ' '-f ../stats/rh.aparc.stats -b -a ../label/rh.aparc.annot -c ' '../label/aparc.annot.ctab output rh white', 'cvs_version': '7.0.0', 'generating_program': 'mris_anatomical_stats', 'hemi': 'rh', 'hostname': 'nid00762', 'machine': 'x86_64', 'mrisurf.c-cvs_version': '7.0.0', 'subjectname': 'output', 'sysname': 'Linux', 'user': 'hayashis', 'BrainVolStatsFixed': 'NotNeeded because voxelvolume=1mm3'}, 'right', {'white_surface_total_area_mm^2': 83579.2, 'mean_thickness_mm': 2.35815, 'brain_segmentation_volume_mm^3': 1169408.0, 'brain_segmentation_volume_without_ventricles_mm^3': 1157593.0, 'brain_segmentation_volume_without_ventricles_from_surf_mm^3': 1157593.0, 'total_cortical_gray_matter_volume_mm^3': 454587.696158, 'supratentorial_volume_mm^3': 1023873.0, 'supratentorial_volume_without_ventricles_mm^3': 1012058.0, 'estimated_total_intracranial_volume_mm^3': 1420434.160521}, 34, [{'structure_name': 'bankssts', 'number_of_vertices': 1094, 'surface_area_mm^2': 757, 'gray_matter_volume_mm^3': 1725, 'average_thickness_mm': 2.215, 'thickness_stddev_mm': 0.544, 'integrated_rectified_mean_curvature_mm^-1': 0.109, 'integrated_rectified_gaussian_curvature_mm^-2': 0.025, 'folding_index': 9, 'intrinsic_curvature_index': 1.1}, {'structure_name': 'caudalanteriorcingulate', 'number_of_vertices': 1137, 'surface_area_mm^2': 780, 'gray_matter_volume_mm^3': 2327, 'average_thickness_mm': 2.842, 'thickness_stddev_mm': 0.667, 'integrated_rectified_mean_curvature_mm^-1': 0.116, 'integrated_rectified_gaussian_curvature_mm^-2': 0.021, 'folding_index': 11, 'intrinsic_curvature_index': 1.0}, {'structure_name': 'caudalmiddlefrontal', 'number_of_vertices': 3126, 'surface_area_mm^2': 2218, 'gray_matter_volume_mm^3': 5978, 'average_thickness_mm': 2.447, 'thickness_stddev_mm': 0.605, 'integrated_rectified_mean_curvature_mm^-1': 0.122, 'integrated_rectified_gaussian_curvature_mm^-2': 0.024, 'folding_index': 28, 'intrinsic_curvature_index': 3.1}])], ) def test_read(path, headers, hemisphere, whole_brain_measurements, structural_measurements_length, structural_measurements_subset): stats = CorticalParcellationStats.read(path) assert headers == stats.headers assert hemisphere == stats.hemisphere pandas.util.testing.assert_frame_equal( left=pandas.DataFrame([whole_brain_measurements]), right=stats.whole_brain_measurements, check_like=True, # ignore the order of index & columns check_dtype=True, check_names=True, ) assert list(stats.structural_measurements.columns) == [ 'structure_name', 'number_of_vertices', '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', 'intrinsic_curvature_index', ] assert len(stats.structural_measurements) == structural_measurements_length pandas.util.testing.assert_frame_equal( left=pandas.DataFrame(structural_measurements_subset), right=stats.structural_measurements.iloc[:3], check_like=True, # ignore the order of index & columns check_dtype=True, check_names=True, ) @pytest.mark.parametrize( ('path', 'structural_measurements_length'), [(os.path.join(SUBJECTS_DIR, 'soichi', 'stats', 'lh.BA_exvivo.stats'), 14), (os.path.join(SUBJECTS_DIR, 'soichi', 'stats', 'lh.BA_exvivo.thresh.stats'), 14), (os.path.join(SUBJECTS_DIR, 'soichi', 'stats', 'lh.aparc.DKTatlas.stats'), 31), (os.path.join(SUBJECTS_DIR, 'soichi', 'stats', 'lh.aparc.a2009s.stats'), 74), (os.path.join(SUBJECTS_DIR, 'soichi', 'stats', 'lh.aparc.pial.stats'), 34), (os.path.join(SUBJECTS_DIR, 'soichi', 'stats', 'lh.aparc.stats'), 34), (os.path.join(SUBJECTS_DIR, 'soichi', 'stats', 'rh.BA_exvivo.stats'), 14), (os.path.join(SUBJECTS_DIR, 'soichi', 'stats', 'rh.BA_exvivo.thresh.stats'), 14), (os.path.join(SUBJECTS_DIR, 'soichi', 'stats', 'rh.aparc.DKTatlas.stats'), 31), (os.path.join(SUBJECTS_DIR, 'soichi', 'stats', 'rh.aparc.a2009s.stats'), 74), (os.path.join(SUBJECTS_DIR, 'soichi', 'stats', 'rh.aparc.pial.stats'), 34), (os.path.join(SUBJECTS_DIR, 'soichi', 'stats', 'rh.aparc.stats'), 34)], ) def test_read_structural_measurements_length(path, structural_measurements_length): # simple test to verify no exception gets raised, see test_read for comprehensive test stats = CorticalParcellationStats.read(path) assert len(stats.structural_measurements) == structural_measurements_length @pytest.mark.parametrize( ("line", "expected_column_name", "expected_value"), [ ( "Measure Cortex, CortexVol Total cortical gray matter volume, 553998.311189, mm^3", "total_cortical_gray_matter_volume_mm^3", 553998.311189, ) ], ) def test__parse_whole_brain_measurements_line( line, expected_column_name, expected_value ): # pylint: disable=protected-access column_name, value = CorticalParcellationStats._parse_whole_brain_measurements_line( line, ) assert column_name == expected_column_name assert numpy.allclose(value, [expected_value]) @pytest.mark.parametrize( "line", ["Measure Cortex, CortexVol Total cortical gray matter volume, 553998.311189",], ) def test__parse_whole_brain_measurements_line_parse_error(line): # pylint: disable=protected-access with pytest.raises(ValueError): CorticalParcellationStats._parse_whole_brain_measurements_line(line) @pytest.mark.parametrize( "path_str", [os.path.join(SUBJECTS_DIR, "fabian", "stats", "lh.aparc.DKTatlas.stats.short"),], ) def test_read_pathlib(path_str: str): stats_str = CorticalParcellationStats.read(path_str) stats_pathlib = CorticalParcellationStats.read(pathlib.Path(path_str)) assert stats_str.headers == stats_pathlib.headers @pytest.mark.parametrize( "url", [ "https://raw.githubusercontent.com/fphammerle/freesurfer-stats" "/master/tests/subjects/fabian/stats/rh.aparc.stats" ], ) def test_read_https(url: str): stats = CorticalParcellationStats.read(url) assert stats.headers["generating_program"] == "mris_anatomical_stats"