def _get_mrk_meas_date(mrk):
"""Find the measurement date from a KIT marker file."""
info = get_kit_info(mrk, False)[0]
meas_date = info.get('meas_date', None)
if isinstance(meas_date, (tuple, list, np.ndarray)):
meas_date = meas_date[0]
if meas_date is not None:
meas_datetime = datetime.fromtimestamp(meas_date)
else:
meas_datetime = datetime.min
return meas_datetime
def test_unknown_format(tmp_path):
"""Test our warning about an unknown format."""
fname = tmp_path / op.basename(ricoh_path)
_, kit_info = get_kit_info(ricoh_path, allow_unknown_format=False)
n_before = kit_info['dirs'][KIT.DIR_INDEX_SYSTEM]['offset']
with open(fname, 'wb') as fout:
with open(ricoh_path, 'rb') as fin:
fout.write(fin.read(n_before))
version, revision = np.fromfile(fin, '<i4', 2)
assert version > 2 # good
version = 1 # bad
np.array([version, revision], '<i4').tofile(fout)
fout.write(fin.read())
with pytest.raises(ValueError, match='SQD file format V1R000 is not offi'):
read_raw_kit(fname)
# it's not actually an old file, so it actually raises an exception later
# about an unknown datatype
with pytest.raises(Exception):
with pytest.warns(RuntimeWarning, match='Force loading'):
read_raw_kit(fname, allow_unknown_format=True)
def test_kit(_bids_validate):
"""Test functionality of the write_raw_bids conversion for KIT data."""
output_path = _TempDir()
data_path = op.join(base_path, 'kit', 'tests', 'data')
raw_fname = op.join(data_path, 'test.sqd')
events_fname = op.join(data_path, 'test-eve.txt')
hpi_fname = op.join(data_path, 'test_mrk.sqd')
hpi_pre_fname = op.join(data_path, 'test_mrk_pre.sqd')
hpi_post_fname = op.join(data_path, 'test_mrk_post.sqd')
electrode_fname = op.join(data_path, 'test_elp.txt')
headshape_fname = op.join(data_path, 'test_hsp.txt')
event_id = dict(cond=1)
kit_bids_basename = bids_basename.replace('_acq-01', '')
raw = mne.io.read_raw_kit(raw_fname,
mrk=hpi_fname,
elp=electrode_fname,
hsp=headshape_fname)
write_raw_bids(raw,
kit_bids_basename,
output_path,
events_data=events_fname,
event_id=event_id,
overwrite=False)
_bids_validate(output_path)
assert op.exists(op.join(output_path, 'participants.tsv'))
read_raw_bids(kit_bids_basename + '_meg.sqd', output_path)
# test anonymize
output_path = _test_anonymize(raw, kit_bids_basename, events_fname,
event_id)
_bids_validate(output_path)
# ensure the channels file has no STI 014 channel:
channels_tsv = make_bids_basename(subject=subject_id,
session=session_id,
task=task,
run=run,
suffix='channels.tsv',
prefix=op.join(output_path, 'sub-01',
'ses-01', 'meg'))
data = _from_tsv(channels_tsv)
assert 'STI 014' not in data['name']
# ensure the marker file is produced in the right place
marker_fname = make_bids_basename(subject=subject_id,
session=session_id,
task=task,
run=run,
suffix='markers.sqd',
prefix=op.join(output_path, 'sub-01',
'ses-01', 'meg'))
assert op.exists(marker_fname)
# test attempts at writing invalid event data
event_data = np.loadtxt(events_fname)
# make the data the wrong number of dimensions
event_data_3d = np.atleast_3d(event_data)
other_output_path = _TempDir()
with pytest.raises(ValueError, match='two dimensions'):
write_raw_bids(raw,
bids_basename,
other_output_path,
events_data=event_data_3d,
event_id=event_id,
overwrite=True)
# remove 3rd column
event_data = event_data[:, :2]
with pytest.raises(ValueError, match='second dimension'):
write_raw_bids(raw,
bids_basename,
other_output_path,
events_data=event_data,
event_id=event_id,
overwrite=True)
# test correct naming of marker files
raw = mne.io.read_raw_kit(raw_fname,
mrk=[hpi_pre_fname, hpi_post_fname],
elp=electrode_fname,
hsp=headshape_fname)
write_raw_bids(raw,
kit_bids_basename.replace('sub-01', 'sub-%s' % subject_id2),
output_path,
events_data=events_fname,
event_id=event_id,
overwrite=False)
_bids_validate(output_path)
# ensure the marker files are renamed correctly
marker_fname = make_bids_basename(subject=subject_id2,
session=session_id,
task=task,
run=run,
suffix='markers.sqd',
acquisition='pre',
prefix=os.path.join(
output_path, 'sub-02', 'ses-01',
'meg'))
info = get_kit_info(marker_fname, False)[0]
assert info['meas_date'] == get_kit_info(hpi_pre_fname,
False)[0]['meas_date']
marker_fname = marker_fname.replace('acq-pre', 'acq-post')
info = get_kit_info(marker_fname, False)[0]
assert info['meas_date'] == get_kit_info(hpi_post_fname,
False)[0]['meas_date']
# check that providing markers in the wrong order raises an error
raw = mne.io.read_raw_kit(raw_fname,
mrk=[hpi_post_fname, hpi_pre_fname],
elp=electrode_fname,
hsp=headshape_fname)
with pytest.raises(ValueError, match='Markers'):
write_raw_bids(raw,
kit_bids_basename.replace('sub-01',
'sub-%s' % subject_id2),
output_path,
events_data=events_fname,
event_id=event_id,
overwrite=True)