def test_stats_table_to_numpy_raises_on_invalied_type_count():
stats_file = os.path.join(TEST_DATA_DIR, 'subject1', 'stats', 'aseg.stats')
stats = bl.stat(stats_file)
types = [np.string_, np.string_] # wrong number of types!
with pytest.raises(ValueError) as exc_info:
numpy_data = st.stats_table_to_numpy(stats, types)
assert 'Length of type_list' in str(exc_info.value)
assert 'must match number of' in str(exc_info.value)
def test_measures_to_numpy():
stats_file = os.path.join(TEST_DATA_DIR, 'subject1', 'stats', 'aseg.stats')
stats = bl.stat(stats_file)
numpy_measures, measure_names = st.measures_to_numpy(stats['measures'])
assert numpy_measures.shape == (22, )
assert numpy_measures.shape[0] == len(stats['measures'])
assert measure_names[0] == ('BrainSeg', 'BrainSegVol')
assert numpy_measures[0] == pytest.approx(1243340.0, 0.01)
assert np.dtype(numpy_measures[0]) == np.float_
def test_header_line_raises_on_both_missing():
stats_file = os.path.join(TEST_DATA_DIR, 'subject1', 'stats',
'lh.aparc.DKTatlas.stats')
stats = bl.stat(stats_file)
del stats['table_meta_data']['column_info_']
del stats['table_meta_data']['ColHeaders']
with pytest.raises(ValueError) as exc_info:
hdr_string = st._header_line(stats['table_meta_data'])
assert 'Could not determine header line' in str(exc_info.value)
def test_header_line():
stats_file = os.path.join(TEST_DATA_DIR, 'subject1', 'stats',
'lh.aparc.DKTatlas.stats')
stats = bl.stat(stats_file)
hdr_string = st._header_line(stats['table_meta_data'])
assert hdr_string == '\t'.join([
'StructName', 'NumVert', 'SurfArea', 'GrayVol', 'ThickAvg', 'ThickStd',
'MeanCurv', 'GausCurv', 'FoldInd', 'CurvInd'
])
def test_sorted_header_indices():
stats_file = os.path.join(TEST_DATA_DIR, 'subject1', 'stats',
'lh.aparc.DKTatlas.stats')
stats = bl.stat(stats_file)
header_indices = st._sorted_header_indices(stats['table_meta_data'])
assert len(header_indices) == 10
assert header_indices[0] == '1'
assert header_indices[5] == '6'
assert header_indices[9] == '10'
def test_stats_table_to_numpy_aseg_stats():
stats_file = os.path.join(TEST_DATA_DIR, 'subject1', 'stats', 'aseg.stats')
stats = bl.stat(stats_file)
types = st.typelist_for_aseg_stats()
numpy_data = st.stats_table_to_numpy(stats, types)
assert len(numpy_data) == 10 # 10 columns
assert 'Index' in numpy_data
assert 'SegId' in numpy_data
for column_name in numpy_data:
assert len(numpy_data[column_name]) == 45 # 45 rows
def test_stats_table_to_numpy_aparc_dktatlas_stats():
stats_file = os.path.join(TEST_DATA_DIR, 'subject1', 'stats',
'lh.aparc.DKTatlas.stats')
stats = bl.stat(stats_file)
types = st.typelist_for_aparc_atlas_stats()
numpy_data = st.stats_table_to_numpy(stats, types)
assert len(numpy_data) == 10 # 10 columns
assert 'StructName' in numpy_data
assert 'NumVert' in numpy_data
for column_name in numpy_data:
assert len(numpy_data[column_name]) == 31
def test_header_line_missing_column_info_warns():
stats_file = os.path.join(TEST_DATA_DIR, 'subject1', 'stats',
'lh.aparc.DKTatlas.stats')
stats = bl.stat(stats_file)
del stats['table_meta_data']['column_info_']
with pytest.warns(UserWarning,
match='Stats data is missing some header data'):
hdr_string = st._header_line(stats['table_meta_data'])
assert hdr_string == '\t'.join([
'StructName', 'NumVert', 'SurfArea', 'GrayVol', 'ThickAvg', 'ThickStd',
'MeanCurv', 'GausCurv', 'FoldInd', 'CurvInd'
])
def test_measures_to_numpy_subset():
stats_file = os.path.join(TEST_DATA_DIR, 'subject1', 'stats', 'aseg.stats')
stats = bl.stat(stats_file)
requested_measures = [('BrainSeg', 'BrainSegVol'),
('SurfaceHoles', 'SurfaceHoles')]
numpy_measures, measure_names = st.measures_to_numpy(
stats['measures'], requested_measures=requested_measures)
assert numpy_measures.shape == (2, )
assert numpy_measures.shape[0] == len(requested_measures)
assert measure_names[0] == ('BrainSeg', 'BrainSegVol')
assert measure_names[1] == ('SurfaceHoles', 'SurfaceHoles')
assert numpy_measures[0] == pytest.approx(1243340.0, 0.01)
assert numpy_measures[1] == pytest.approx(29, 0.01)
def test_header_line_does_not_raise_on_broken_col_headers():
stats_file = os.path.join(TEST_DATA_DIR, 'subject1', 'stats',
'lh.aparc.DKTatlas.stats')
stats = bl.stat(stats_file)
stats['table_meta_data'][
'ColHeaders'] = 1 # ruin data: cannot split an int
with pytest.warns(UserWarning,
match='Stats data is missing some header data'):
hdr_string = st._header_line(stats['table_meta_data'])
assert hdr_string == '\t'.join([
'StructName', 'NumVert', 'SurfArea', 'GrayVol', 'ThickAvg', 'ThickStd',
'MeanCurv', 'GausCurv', 'FoldInd', 'CurvInd'
])
def test_header_line_inconsistent_warns():
stats_file = os.path.join(TEST_DATA_DIR, 'subject1', 'stats',
'lh.aparc.DKTatlas.stats')
stats = bl.stat(stats_file)
stats['table_meta_data'][
'ColHeaders'] = 'StructName NumVertBROKEN SurfArea GrayVol ThickAvg ThickStd MeanCurv GausCurv FoldInd CurvInd' # mess with data, add 'BROKEN' to 2nd header column
with pytest.warns(
UserWarning,
match=
'Stats data regarding table header is inconsistent between ColHeaders and TableCol->ColHeader entries'
):
hdr_string = st._header_line(stats['table_meta_data'])
assert hdr_string == '\t'.join([
'StructName', 'NumVert', 'SurfArea', 'GrayVol', 'ThickAvg', 'ThickStd',
'MeanCurv', 'GausCurv', 'FoldInd', 'CurvInd'
])
