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"