freesurfer-stats/tests/test_cortical_parcellation_stats.py

"""
freesurfer-stats, a Python Library to Read FreeSurfer's Cortical Parcellation Anatomical Statistics
Copyright (C) 2019 Fabian Peter Hammerle <fabian@hammerle.me>

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 <https://www.gnu.org/licenses/>.
"""
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"