""" 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"