def test_read_stats_file_lh_aparc_DKTatlas():
stats_file = os.path.join(TEST_DATA_DIR, 'subject1', 'stats',
'lh.aparc.DKTatlas.stats')
stats = st.stat(stats_file)
assert len(stats) == 5
assert len(stats['ignored_lines']) == 18
assert len(stats['measures']) == 10
assert len(stats['table_data']) == 31
assert len(stats['table_meta_data']) == 3
assert len(stats['table_column_headers']) == 10
assert 'ColHeaders' in stats['table_meta_data']
assert 'NTableCols' in stats['table_meta_data']
assert 'column_info_' in stats['table_meta_data']
assert len(stats['table_meta_data']['column_info_']) == 10
def test_read_stats_file_rh_aparc_DKTatlas():
stats_file = os.path.join(TEST_DATA_DIR, 'subject1', 'stats',
'rh.aparc.DKTatlas.stats')
stats = st.stat(stats_file)
assert len(stats) == 5
assert len(stats['ignored_lines']) == 18
assert len(stats['measures']) == 10
assert len(stats['table_data']) == 31
assert len(stats['table_meta_data']) == 3
assert len(stats['table_column_headers']) == 10
assert stats['table_column_headers'] == [
'StructName', 'NumVert', 'SurfArea', 'GrayVol', 'ThickAvg', 'ThickStd',
'MeanCurv', 'GausCurv', 'FoldInd', 'CurvInd'
]
assert 'ColHeaders' in stats['table_meta_data']
assert 'NTableCols' in stats['table_meta_data']
assert 'column_info_' in stats['table_meta_data']
assert len(stats['table_meta_data']['column_info_']) == 10
def test_read_stats_file_aseg():
stats_file = os.path.join(TEST_DATA_DIR, 'subject1', 'stats', 'aseg.stats')
stats = st.stat(stats_file)
assert len(stats) == 5
assert 'measures' in stats
assert 'table_data' in stats
assert 'table_meta_data' in stats
assert 'ignored_lines' in stats
assert 'table_column_headers' in stats
# check ignored lines
ignored_lines = stats['ignored_lines']
assert len(ignored_lines) == 25
# check measures
measures = stats['measures']
assert len(measures) == 22
expected_measures = [
'BrainSeg', 'BrainSegNotVent', 'BrainSegNotVentSurf',
'VentricleChoroidVol', 'lhCortex', 'rhCortex', 'Cortex',
'lhCerebralWhiteMatter', 'rhCerebralWhiteMatter',
'CerebralWhiteMatter', 'SubCortGray', 'TotalGray', 'SupraTentorial',
'SupraTentorialNotVent', 'SupraTentorialNotVentVox', 'Mask',
'BrainSegVol-to-eTIV', 'MaskVol-to-eTIV', 'lhSurfaceHoles',
'rhSurfaceHoles', 'SurfaceHoles', 'EstimatedTotalIntraCranialVol'
]
for measure_data_list in measures:
assert len(measure_data_list) == 5
measure_name = measure_data_list[0]
assert measure_name in expected_measures
# fully test a single measure
assert measures[0][0] == 'BrainSeg'
assert measures[0][1] == 'BrainSegVol'
assert measures[0][2] == 'Brain Segmentation Volume'
assert measures[0][3] == '1243340.000000'
assert measures[0][4] == 'mm^3'
# check table_data
table_data = stats['table_data']
assert len(table_data) == 45
for index, row in enumerate(table_data):
assert len(row) == 10
assert int(
row[0]
) == index + 1 # first element should be the row index, and it starts at 1 (and lines should be in the order in which they appear in the file)
# fully test a row
row10 = table_data[9]
assert row10[0] == "10"
assert row10[1] == "15"
assert row10[2] == "2099"
assert row10[3] == "2209.1"
assert row10[4] == "4th-Ventricle"
assert row10[5] == "25.1806"
assert row10[6] == "10.7109"
assert row10[7] == "8.0000"
assert row10[8] == "74.0000"
assert row10[9] == "66.0000"
# check table meta data
table_meta_data = stats['table_meta_data']
assert table_meta_data['NRows'] == "45"
assert table_meta_data['NTableCols'] == "10"
assert 'column_info_' in table_meta_data
assert len(table_meta_data['column_info_']) == 10
# fully test a single column info
second_column_header = table_meta_data['column_info_']['2']
assert len(second_column_header) == 3
for expected_key in ['ColHeader', 'FieldName', 'Units']:
assert expected_key in second_column_header.keys()
assert second_column_header['ColHeader'] == "SegId"
assert second_column_header['FieldName'] == "Segmentation Id"
assert second_column_header['Units'] == "NA"