def test_dig_io(tmp_path):
"""Test passing different coordinate frames give proper warnings."""
bids_root = tmp_path / 'bids1'
raw = _load_raw()
for datatype in ('eeg', 'ieeg'):
os.makedirs(op.join(bids_root, 'sub-01', 'ses-01', datatype))
# test no coordinate frame in dig or in bids_path.space
montage = raw.get_montage()
montage.apply_trans(mne.transforms.Transform('head', 'unknown'))
for datatype in ('eeg', 'ieeg'):
bids_path = _bids_path.copy().update(root=bids_root,
datatype=datatype,
space=None)
with pytest.warns(RuntimeWarning,
match='Coordinate frame could not be inferred'):
_write_dig_bids(bids_path, raw, montage, acpc_aligned=True)
# test coordinate frame-BIDSPath.space mismatch
raw = _load_raw()
montage = raw.get_montage()
print(montage.get_positions()['coord_frame'])
bids_path = _bids_path.copy().update(root=bids_root,
datatype='eeg',
space='fsaverage')
with pytest.raises(ValueError,
match='Coordinates in the raw object '
'or montage are in the CapTrak '
'coordinate frame but '
'BIDSPath.space is fsaverage'):
_write_dig_bids(bids_path, raw, montage)
# test MEG space conflict fif (ElektaNeuromag) != CTF
bids_path = _bids_path.copy().update(root=bids_root,
datatype='meg',
space='CTF')
with pytest.raises(ValueError, match='conflicts'):
write_raw_bids(raw, bids_path)
def test_dig_pixels(tmp_path):
"""Test dig stored correctly for the Pixels coordinate frame."""
bids_root = tmp_path / 'bids1'
# test coordinates in pixels
bids_path = _bids_path.copy().update(root=bids_root,
datatype='ieeg',
space='Pixels')
os.makedirs(op.join(bids_root, 'sub-01', 'ses-01', bids_path.datatype),
exist_ok=True)
raw_test = raw.copy()
raw_test.pick_types(eeg=True)
raw_test.del_proj()
raw_test.set_channel_types({ch: 'ecog' for ch in raw_test.ch_names})
mnt = raw_test.get_montage()
# fake transform to pixel coordinates
mnt.apply_trans(mne.transforms.Transform('head', 'unknown'))
_write_dig_bids(bids_path, raw_test, mnt)
electrodes_path = bids_path.copy().update(task=None,
run=None,
suffix='electrodes',
extension='.tsv')
coordsystem_path = bids_path.copy().update(task=None,
run=None,
suffix='coordsystem',
extension='.json')
with pytest.warns(RuntimeWarning,
match='not an MNE-Python coordinate frame'):
_read_dig_bids(electrodes_path, coordsystem_path, bids_path.datatype,
raw_test)
mnt2 = raw_test.get_montage()
assert mnt2.get_positions()['coord_frame'] == 'unknown'
assert_almost_equal(
np.array(list(mnt.get_positions()['ch_pos'].values())),
np.array(list(mnt2.get_positions()['ch_pos'].values())))
def test_dig_template(tmp_path):
"""Test that eeg and ieeg dig are stored properly."""
bids_root = tmp_path / 'bids1'
for datatype in ('eeg', 'ieeg'):
(bids_root / 'sub-01' / 'ses-01' / datatype).mkdir(parents=True)
raw_test = raw.copy().pick_types(eeg=True)
for datatype in ('eeg', 'ieeg'):
bids_path = _bids_path.copy().update(root=bids_root, datatype=datatype)
for coord_frame in BIDS_STANDARD_TEMPLATE_COORDINATE_SYSTEMS:
bids_path.update(space=coord_frame)
mnt = montage.copy()
pos = mnt.get_positions()
mne_coord_frame = BIDS_TO_MNE_FRAMES.get(coord_frame, None)
if mne_coord_frame is None:
mnt.apply_trans(mne.transforms.Transform('head', 'unknown'))
else:
mnt.apply_trans(
mne.transforms.Transform('head', mne_coord_frame))
_write_dig_bids(bids_path, raw_test, mnt, acpc_aligned=True)
electrodes_path = bids_path.copy().update(task=None,
run=None,
suffix='electrodes',
extension='.tsv')
coordsystem_path = bids_path.copy().update(task=None,
run=None,
suffix='coordsystem',
extension='.json')
if mne_coord_frame is None:
with pytest.warns(RuntimeWarning,
match='not an MNE-Python coordinate frame'):
_read_dig_bids(electrodes_path, coordsystem_path, datatype,
raw_test)
else:
if coord_frame == 'MNI305': # saved to fsaverage, same
electrodes_path.update(space='fsaverage')
coordsystem_path.update(space='fsaverage')
_read_dig_bids(electrodes_path, coordsystem_path, datatype,
raw_test)
mnt2 = raw_test.get_montage()
pos2 = mnt2.get_positions()
np.testing.assert_array_almost_equal(
np.array(list(pos['ch_pos'].values())),
np.array(list(pos2['ch_pos'].values())))
if mne_coord_frame is None:
assert pos2['coord_frame'] == 'unknown'
else:
assert pos2['coord_frame'] == mne_coord_frame
# test MEG
raw_test = raw.copy()
for coord_frame in BIDS_STANDARD_TEMPLATE_COORDINATE_SYSTEMS:
bids_path = _bids_path.copy().update(root=bids_root,
datatype='meg',
space=coord_frame)
write_raw_bids(raw_test, bids_path)
raw_test2 = read_raw_bids(bids_path)
for ch, ch2 in zip(raw.info['chs'], raw_test2.info['chs']):
np.testing.assert_array_equal(ch['loc'], ch2['loc'])
assert ch['coord_frame'] == ch2['coord_frame']