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@@ -24,10 +24,12 @@ import pytest
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from conftest import SUBJECTS_DIR
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from freesurfer_stats import CorticalParcellationStats
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+# pylint: disable=too-many-arguments
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@pytest.mark.parametrize(
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('path', 'headers', 'hemisphere',
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- 'whole_brain_measurements', 'structural_measurements'),
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+ 'whole_brain_measurements', 'structural_measurements_length',
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+ 'structural_measurements_subset'),
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[(os.path.join(SUBJECTS_DIR, 'fabian', 'stats', 'lh.aparc.DKTatlas.stats.short'),
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{'CreationTime': datetime.datetime(2019, 5, 9, 21, 5, 54, tzinfo=datetime.timezone.utc),
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'generating_program': 'mris_anatomical_stats',
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@@ -56,6 +58,7 @@ from freesurfer_stats import CorticalParcellationStats
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'supratentorial_volume_mm^3': 1172669.548920,
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'supratentorial_volume_without_ventricles_mm^3': 1164180.548920,
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'estimated_total_intracranial_volume_mm^3': 1670487.274486},
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+ 3,
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[{'structure_name': 'caudalanteriorcingulate',
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'number_of_vertices': 2061,
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'surface_area_mm^2': 1472,
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@@ -115,6 +118,7 @@ from freesurfer_stats import CorticalParcellationStats
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'supratentorial_volume_mm^3': 1172669.548920,
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'supratentorial_volume_without_ventricles_mm^3': 1164180.548920,
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'estimated_total_intracranial_volume_mm^3': 1670487.274486},
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+ 2,
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[{'structure_name': 'bankssts',
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'number_of_vertices': 1344,
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'surface_area_mm^2': 825,
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@@ -134,9 +138,71 @@ from freesurfer_stats import CorticalParcellationStats
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'integrated_rectified_mean_curvature_mm^-1': 0.110,
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'integrated_rectified_gaussian_curvature_mm^-2': 0.021,
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'folding_index': 3,
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- 'intrinsic_curvature_index': 0.6}])],
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+ 'intrinsic_curvature_index': 0.6}]),
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+ (os.path.join(
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+ SUBJECTS_DIR, 'soichi', 'stats', 'rh.aparc.stats'),
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+ {'CreationTime': datetime.datetime(2020, 5, 4, 22, 20, 26, tzinfo=datetime.timezone.utc),
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+ 'AnnotationFileTimeStamp': datetime.datetime(2020, 5, 4, 21, 58, 13),
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+ 'AnnotationFile': '../label/rh.aparc.annot',
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+ 'SUBJECTS_DIR': '/N/dc2/scratch/hayashis/bigred3-workflows'
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+ '/5eb0689676c10ead933d673c/5eb068b076c10e7b013d673f',
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+ 'anatomy_type': 'surface',
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+ 'cmdline': 'mris_anatomical_stats -th3 -mgz -cortex ../label/rh.cortex.label '
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+ '-f ../stats/rh.aparc.stats -b -a ../label/rh.aparc.annot -c '
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+ '../label/aparc.annot.ctab output rh white',
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+ 'cvs_version': '7.0.0',
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+ 'generating_program': 'mris_anatomical_stats',
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+ 'hemi': 'rh',
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+ 'hostname': 'nid00762',
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+ 'machine': 'x86_64',
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+ 'mrisurf.c-cvs_version': '7.0.0',
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+ 'subjectname': 'output',
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+ 'sysname': 'Linux',
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+ 'user': 'hayashis'},
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+ 'right',
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+ {'white_surface_total_area_mm^2': 83579.2,
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+ 'mean_thickness_mm': 2.35815,
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+ 'brain_segmentation_volume_mm^3': 1169408.0,
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+ 'brain_segmentation_volume_without_ventricles_mm^3': 1157593.0,
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+ 'brain_segmentation_volume_without_ventricles_from_surf_mm^3': 1157593.0,
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+ 'total_cortical_gray_matter_volume_mm^3': 454587.696158,
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+ 'supratentorial_volume_mm^3': 1023873.0,
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+ 'supratentorial_volume_without_ventricles_mm^3': 1012058.0,
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+ 'estimated_total_intracranial_volume_mm^3': 1420434.160521},
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+ 34,
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+ [{'structure_name': 'bankssts',
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+ 'number_of_vertices': 1094,
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+ 'surface_area_mm^2': 757,
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+ 'gray_matter_volume_mm^3': 1725,
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+ 'average_thickness_mm': 2.215,
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+ 'thickness_stddev_mm': 0.544,
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+ 'integrated_rectified_mean_curvature_mm^-1': 0.109,
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+ 'integrated_rectified_gaussian_curvature_mm^-2': 0.025,
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+ 'folding_index': 9,
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+ 'intrinsic_curvature_index': 1.1},
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+ {'structure_name': 'caudalanteriorcingulate',
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+ 'number_of_vertices': 1137,
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+ 'surface_area_mm^2': 780,
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+ 'gray_matter_volume_mm^3': 2327,
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+ 'average_thickness_mm': 2.842,
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+ 'thickness_stddev_mm': 0.667,
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+ 'integrated_rectified_mean_curvature_mm^-1': 0.116,
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+ 'integrated_rectified_gaussian_curvature_mm^-2': 0.021,
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+ 'folding_index': 11,
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+ 'intrinsic_curvature_index': 1.0},
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+ {'structure_name': 'caudalmiddlefrontal',
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+ 'number_of_vertices': 3126,
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+ 'surface_area_mm^2': 2218,
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+ 'gray_matter_volume_mm^3': 5978,
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+ 'average_thickness_mm': 2.447,
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+ 'thickness_stddev_mm': 0.605,
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+ 'integrated_rectified_mean_curvature_mm^-1': 0.122,
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+ 'integrated_rectified_gaussian_curvature_mm^-2': 0.024,
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+ 'folding_index': 28,
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+ 'intrinsic_curvature_index': 3.1}])],
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)
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-def test_read(path, headers, hemisphere, whole_brain_measurements, structural_measurements):
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+def test_read(path, headers, hemisphere, whole_brain_measurements, structural_measurements_length,
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+ structural_measurements_subset):
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stats = CorticalParcellationStats.read(path)
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assert headers == stats.headers
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assert hemisphere == stats.hemisphere
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@@ -159,9 +225,10 @@ def test_read(path, headers, hemisphere, whole_brain_measurements, structural_me
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'folding_index',
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'intrinsic_curvature_index',
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]
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+ assert len(stats.structural_measurements) == structural_measurements_length
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pandas.util.testing.assert_frame_equal(
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- left=pandas.DataFrame(structural_measurements),
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- right=stats.structural_measurements,
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+ left=pandas.DataFrame(structural_measurements_subset),
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+ right=stats.structural_measurements.iloc[:3],
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check_like=True, # ignore the order of index & columns
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check_dtype=True,
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check_names=True,
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