def test_source_space_from_label(tmp_path, pass_ids):
"""Test generating a source space from volume label."""
aseg_short = 'aseg.mgz'
atlas_ids, _ = read_freesurfer_lut()
volume_label = 'Left-Cerebellum-Cortex'
# Test pos as dict
pos = dict()
with pytest.raises(ValueError, match='mri must be None if pos is a dict'):
setup_volume_source_space(
'sample', pos=pos, volume_label=volume_label, mri=aseg_short,
subjects_dir=subjects_dir)
# Test T1.mgz provided
with pytest.raises(RuntimeError, match=r'Must use a \*aseg.mgz file'):
setup_volume_source_space(
'sample', mri='T1.mgz', volume_label=volume_label,
subjects_dir=subjects_dir)
# Test invalid volume label
mri = aseg_short
with pytest.raises(ValueError, match="'Left-Cerebral' not found.*Did you"):
setup_volume_source_space(
'sample', volume_label='Left-Cerebral', mri=mri,
subjects_dir=subjects_dir)
# These should be equivalent
if pass_ids:
use_volume_label = {volume_label: atlas_ids[volume_label]}
else:
use_volume_label = volume_label
# ensure it works even when not provided (detect that it should be aseg)
src = setup_volume_source_space(
'sample', volume_label=use_volume_label, add_interpolator=False,
subjects_dir=subjects_dir)
assert_equal(volume_label, src[0]['seg_name'])
assert src[0]['nuse'] == 404 # for our given pos and label
# test reading and writing
out_name = tmp_path / 'temp-src.fif'
write_source_spaces(out_name, src)
src_from_file = read_source_spaces(out_name)
_compare_source_spaces(src, src_from_file, mode='approx')
def test_read_freesurfer_lut(fname):
"""Test reading volume label names."""
atlas_ids, colors = read_freesurfer_lut(fname)
assert list(atlas_ids).count('Brain-Stem') == 1
assert len(colors) == len(atlas_ids) == 1266
label_names, label_colors = get_volume_labels_from_aseg(aseg_fname,
return_colors=True)
assert isinstance(label_names, list)
assert isinstance(label_colors, list)
assert label_names.count('Brain-Stem') == 1
for c in label_colors:
assert isinstance(c, np.ndarray)
assert c.shape == (4, )
assert len(label_names) == len(label_colors) == 46
with pytest.raises(ValueError, match='must be False'):
get_volume_labels_from_aseg(aseg_fname,
return_colors=True,
atlas_ids=atlas_ids)
label_names_2 = get_volume_labels_from_aseg(aseg_fname,
atlas_ids=atlas_ids)
assert label_names == label_names_2