def test_find_emptyroom_ties(tmpdir):
"""Test that we receive a warning on a date tie."""
data_path = testing.data_path()
raw_fname = op.join(data_path, 'MEG', 'sample',
'sample_audvis_trunc_raw.fif')
bids_root = str(tmpdir)
bids_path.update(root=bids_root)
session = '20010101'
er_dir_path = BIDSPath(subject='emptyroom', session=session,
datatype='meg', root=bids_root)
er_dir = er_dir_path.mkdir().directory
meas_date = (datetime
.strptime(session, '%Y%m%d')
.replace(tzinfo=timezone.utc))
raw = _read_raw_fif(raw_fname)
er_raw_fname = op.join(data_path, 'MEG', 'sample', 'ernoise_raw.fif')
raw.copy().crop(0, 10).save(er_raw_fname, overwrite=True)
er_raw = _read_raw_fif(er_raw_fname)
raw.set_meas_date(meas_date)
er_raw.set_meas_date(meas_date)
write_raw_bids(raw, bids_path, overwrite=True)
er_bids_path = BIDSPath(subject='emptyroom', session=session)
er_basename_1 = er_bids_path.basename
er_basename_2 = BIDSPath(subject='emptyroom', session=session,
task='noise').basename
er_raw.save(op.join(er_dir, f'{er_basename_1}_meg.fif'))
er_raw.save(op.join(er_dir, f'{er_basename_2}_meg.fif'))
with pytest.warns(RuntimeWarning, match='Found more than one'):
bids_path.find_empty_room()
def test_find_emptyroom_no_meas_date(tmpdir):
"""Test that we warn if measurement date can be read or inferred."""
data_path = testing.data_path()
raw_fname = op.join(data_path, 'MEG', 'sample',
'sample_audvis_trunc_raw.fif')
bids_root = str(tmpdir)
bids_path.update(root=bids_root)
er_session = 'mysession'
er_meas_date = None
er_dir_path = BIDSPath(subject='emptyroom', session=er_session,
datatype='meg', root=bids_root)
er_dir = er_dir_path.mkdir().directory
er_bids_path = BIDSPath(subject='emptyroom', session=er_session,
task='noise', check=False)
er_basename = er_bids_path.basename
raw = _read_raw_fif(raw_fname)
er_raw_fname = op.join(data_path, 'MEG', 'sample', 'ernoise_raw.fif')
raw.copy().crop(0, 10).save(er_raw_fname, overwrite=True)
er_raw = _read_raw_fif(er_raw_fname)
er_raw.set_meas_date(er_meas_date)
er_raw.save(op.join(er_dir, f'{er_basename}_meg.fif'), overwrite=True)
# Write raw file data using mne-bids, and remove participants.tsv
# as it's incomplete (doesn't contain the emptyroom subject we wrote
# manually using MNE's Raw.save() above)
raw = _read_raw_fif(raw_fname)
write_raw_bids(raw, bids_path, overwrite=True)
os.remove(op.join(bids_root, 'participants.tsv'))
with pytest.warns(RuntimeWarning, match='Could not retrieve .* date'):
bids_path.find_empty_room()
def test_find_empty_room(return_bids_test_dir):
"""Test reading of empty room data."""
data_path = testing.data_path()
raw_fname = op.join(data_path, 'MEG', 'sample',
'sample_audvis_trunc_raw.fif')
bids_root = _TempDir()
tmp_dir = _TempDir()
raw = _read_raw_fif(raw_fname)
bids_path = BIDSPath(subject='01',
session='01',
task='audiovisual',
run='01',
root=bids_root,
suffix='meg')
write_raw_bids(raw, bids_path, overwrite=True)
# No empty-room data present.
er_basename = bids_path.find_empty_room()
assert er_basename is None
# Now create data resembling an empty-room recording.
# The testing data has no "noise" recording, so save the actual data
# as named as if it were noise. We first need to write the FIFF file
# before reading it back in.
er_raw_fname = op.join(tmp_dir, 'ernoise_raw.fif')
raw.copy().crop(0, 10).save(er_raw_fname, overwrite=True)
er_raw = _read_raw_fif(er_raw_fname)
if not isinstance(er_raw.info['meas_date'], datetime):
# mne < v0.20
er_date = datetime.fromtimestamp(er_raw.info['meas_date'][0])
else:
er_date = er_raw.info['meas_date']
er_date = er_date.strftime('%Y%m%d')
er_bids_path = BIDSPath(subject='emptyroom',
task='noise',
session=er_date,
suffix='meg',
root=bids_root)
write_raw_bids(er_raw, er_bids_path, overwrite=True)
recovered_er_bids_path = bids_path.find_empty_room()
assert er_bids_path == recovered_er_bids_path
# assert that we get best emptyroom if there are multiple available
sh.rmtree(op.join(bids_root, 'sub-emptyroom'))
dates = ['20021204', '20021201', '20021001']
for date in dates:
er_bids_path.update(session=date)
er_meas_date = datetime.strptime(date, '%Y%m%d')
er_meas_date = er_meas_date.replace(tzinfo=timezone.utc)
if check_version('mne', '0.20'):
er_raw.set_meas_date(er_meas_date)
else:
er_raw.info['meas_date'] = (er_meas_date.timestamp(), 0)
write_raw_bids(er_raw, er_bids_path)
best_er_basename = bids_path.find_empty_room()
assert best_er_basename.session == '20021204'
with pytest.raises(ValueError,
match='The root of the "bids_path" must be set'):
bids_path.copy().update(root=None).find_empty_room()
# assert that we get error if meas_date is not available.
raw = read_raw_bids(bids_path=bids_path)
if check_version('mne', '0.20'):
raw.set_meas_date(None)
else:
raw.info['meas_date'] = None
raw.annotations.orig_time = None
anonymize_info(raw.info)
write_raw_bids(raw, bids_path, overwrite=True)
with pytest.raises(ValueError,
match='The provided recording does not '
'have a measurement date set'):
bids_path.find_empty_room()
def test_find_empty_room(return_bids_test_dir, tmpdir):
"""Test reading of empty room data."""
data_path = testing.data_path()
raw_fname = op.join(data_path, 'MEG', 'sample',
'sample_audvis_trunc_raw.fif')
bids_root = tmpdir.mkdir("bids")
tmp_dir = tmpdir.mkdir("tmp")
raw = _read_raw_fif(raw_fname)
bids_path = BIDSPath(subject='01',
session='01',
task='audiovisual',
run='01',
root=bids_root,
suffix='meg')
write_raw_bids(raw, bids_path, overwrite=True)
# No empty-room data present.
er_basename = bids_path.find_empty_room()
assert er_basename is None
# Now create data resembling an empty-room recording.
# The testing data has no "noise" recording, so save the actual data
# as named as if it were noise. We first need to write the FIFF file
# before reading it back in.
er_raw_fname = op.join(tmp_dir, 'ernoise_raw.fif')
raw.copy().crop(0, 10).save(er_raw_fname, overwrite=True)
er_raw = _read_raw_fif(er_raw_fname)
if not isinstance(er_raw.info['meas_date'], datetime): # pragma: no cover
# mne < v0.20
er_date = datetime.fromtimestamp(er_raw.info['meas_date'][0])
else:
er_date = er_raw.info['meas_date']
er_date = er_date.strftime('%Y%m%d')
er_bids_path = BIDSPath(subject='emptyroom',
task='noise',
session=er_date,
suffix='meg',
root=bids_root)
write_raw_bids(er_raw, er_bids_path, overwrite=True)
recovered_er_bids_path = bids_path.find_empty_room()
assert er_bids_path == recovered_er_bids_path
# assert that we get best emptyroom if there are multiple available
sh.rmtree(op.join(bids_root, 'sub-emptyroom'))
dates = ['20021204', '20021201', '20021001']
for date in dates:
er_bids_path.update(session=date)
er_meas_date = datetime.strptime(date, '%Y%m%d')
er_meas_date = er_meas_date.replace(tzinfo=timezone.utc)
er_raw.set_meas_date(er_meas_date)
write_raw_bids(er_raw, er_bids_path)
best_er_basename = bids_path.find_empty_room()
assert best_er_basename.session == '20021204'
with pytest.raises(ValueError,
match='The root of the "bids_path" must be set'):
bids_path.copy().update(root=None).find_empty_room()
# assert that we get an error if meas_date is not available.
raw = read_raw_bids(bids_path=bids_path)
raw.set_meas_date(None)
anonymize_info(raw.info)
write_raw_bids(raw, bids_path, overwrite=True)
with pytest.raises(ValueError,
match='The provided recording does not '
'have a measurement date set'):
bids_path.find_empty_room()
# test that the `AssociatedEmptyRoom` key in MEG sidecar is respected
bids_root = tmpdir.mkdir('associated-empty-room')
raw = _read_raw_fif(raw_fname)
meas_date = datetime(year=2020, month=1, day=10, tzinfo=timezone.utc)
er_date = datetime(year=2010, month=1, day=1, tzinfo=timezone.utc)
raw.set_meas_date(meas_date)
er_raw_matching_date = er_raw.copy().set_meas_date(meas_date)
er_raw_associated = er_raw.copy().set_meas_date(er_date)
# First write empty-room data
# We write two empty-room recordings: one with a date matching exactly the
# experimental measurement date, and one dated approx. 10 years earlier
# We will want to enforce using the older recording via
# `AssociatedEmptyRoom` (without AssociatedEmptyRoom, find_empty_room()
# would return the recording with the matching date instead)
er_matching_date_bids_path = BIDSPath(subject='emptyroom',
session='20200110',
task='noise',
root=bids_root,
datatype='meg',
suffix='meg',
extension='.fif')
write_raw_bids(er_raw_matching_date, bids_path=er_matching_date_bids_path)
er_associated_bids_path = (er_matching_date_bids_path.copy().update(
session='20100101'))
write_raw_bids(er_raw_associated, bids_path=er_associated_bids_path)
# Now we write experimental data and associate it with the earlier
# empty-room recording
bids_path = (er_matching_date_bids_path.copy().update(subject='01',
session=None,
task='task'))
write_raw_bids(raw,
bids_path=bids_path,
empty_room=er_associated_bids_path)
# Retrieve empty-room BIDSPath
assert bids_path.find_empty_room() == er_associated_bids_path
# Should only work for MEG
with pytest.raises(ValueError, match='only supported for MEG'):
bids_path.copy().update(datatype='eeg').find_empty_room()
# Don't create `AssociatedEmptyRoom` entry in sidecar – we should now
# retrieve the empty-room recording closer in time
write_raw_bids(raw, bids_path=bids_path, empty_room=None, overwrite=True)
assert bids_path.find_empty_room() == er_matching_date_bids_path
