freesurfer-stats/tests/test_cortical_parcellation_stats.py

import datetime
import os

import pandas.util.testing
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')},
      [{'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': (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')},
      [{'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}])],
)
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 list(stats.structure_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',
    ]
    pandas.util.testing.assert_frame_equal(
        left=pandas.DataFrame(structure_measurements),
        right=stats.structure_measurements,
        check_like=True,  # ignore the order of index & columns
        check_dtype=True,
        check_names=True,
    )