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added test case for soichi/stats/rh.aparc.stats (freesurfer 7)
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@fphammerle
fphammerle committed May 6, 2020
1 parent 7a3b034 commit 3da1896
Showing 1 changed file with 72 additions and 5 deletions.
77 changes: 72 additions & 5 deletions tests/test_cortical_parcellation_stats.py
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Original file line number Diff line number Diff line change
Expand Up @@ -24,10 +24,12 @@
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'),
'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',
Expand Down Expand Up @@ -56,6 +58,7 @@
'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,
Expand Down Expand Up @@ -115,6 +118,7 @@
'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,
Expand All @@ -134,9 +138,71 @@
'integrated_rectified_mean_curvature_mm^-1': 0.110,
'integrated_rectified_gaussian_curvature_mm^-2': 0.021,
'folding_index': 3,
'intrinsic_curvature_index': 0.6}])],
'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'},
'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):
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
Expand All @@ -159,9 +225,10 @@ def test_read(path, headers, hemisphere, whole_brain_measurements, structural_me
'folding_index',
'intrinsic_curvature_index',
]
assert len(stats.structural_measurements) == structural_measurements_length
pandas.util.testing.assert_frame_equal(
left=pandas.DataFrame(structural_measurements),
right=stats.structural_measurements,
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,
Expand Down

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