def test_raw_to_bids(tmpdir):
"""Test mne_bids raw_to_bids."""
output_path = str(tmpdir)
data_path = testing.data_path()
raw_fname = op.join(data_path, 'MEG', 'sample',
'sample_audvis_trunc_raw.fif')
# Check that help is printed
check_usage(mne_bids_raw_to_bids)
# Should work
with ArgvSetter(
('--subject_id', subject_id, '--task', task, '--raw', raw_fname,
'--bids_root', output_path, '--line_freq', 60)):
mne_bids_raw_to_bids.run()
# Test EDF files as well
edf_data_path = op.join(base_path, 'edf', 'tests', 'data')
edf_fname = op.join(edf_data_path, 'test.edf')
with ArgvSetter(
('--subject_id', subject_id, '--task', task, '--raw', edf_fname,
'--bids_root', output_path, '--line_freq', 60)):
mne_bids_raw_to_bids.run()
# Too few input args
with pytest.raises(SystemExit):
with ArgvSetter(('--subject_id', subject_id)):
mne_bids_cp.run()
def test_raw_to_bids():
"""Test mne_bids raw_to_bids."""
output_path = _TempDir()
data_path = testing.data_path()
raw_fname = op.join(data_path, 'MEG', 'sample',
'sample_audvis_trunc_raw.fif')
# check_usage(mne_bids_raw_to_bids)
with ArgvSetter(('--subject_id', subject_id, '--task', task, '--raw',
raw_fname, '--output_path', output_path)):
mne_bids_raw_to_bids.run()
def test_mark_bad_chanels_single_file(tmpdir):
"""Test mne_bids mark_channels."""
# Check that help is printed
check_usage(mne_bids_mark_channels)
# Create test dataset.
output_path = str(tmpdir)
data_path = testing.data_path()
raw_fname = op.join(data_path, 'MEG', 'sample',
'sample_audvis_trunc_raw.fif')
old_bads = mne.io.read_raw_fif(raw_fname).info['bads']
bids_path = BIDSPath(subject=subject_id,
task=task,
root=output_path,
datatype=datatype)
with ArgvSetter(
('--subject_id', subject_id, '--task', task, '--raw', raw_fname,
'--bids_root', output_path, '--line_freq', 60)):
mne_bids_raw_to_bids.run()
# Update the dataset.
ch_names = ['MEG 0112', 'MEG 0131']
descriptions = ['Really bad!', 'Even worse.']
args = [
'--subject_id', subject_id, '--task', task, '--bids_root', output_path,
'--type', datatype
]
for ch_name, description in zip(ch_names, descriptions):
args.extend(['--ch_name', ch_name])
args.extend(['--description', description])
args = tuple(args)
with ArgvSetter(args):
mne_bids_mark_channels.run()
# Check the data was properly written
with pytest.warns(RuntimeWarning, match='The unit for chann*'):
raw = read_raw_bids(bids_path=bids_path, verbose=False)
assert set(old_bads + ch_names) == set(raw.info['bads'])
# Test resetting bad channels.
args = ('--subject_id', subject_id, '--task', task, '--bids_root',
output_path, '--type', datatype, '--status', 'good', '--ch_name',
'')
with ArgvSetter(args):
mne_bids_mark_channels.run()
print('Finished running the reset...')
# Check the data was properly written
with pytest.warns(RuntimeWarning, match='The unit for chann*'):
raw = read_raw_bids(bids_path=bids_path)
assert raw.info['bads'] == []
def test_raw_to_bids(tmpdir):
"""Test mne_bids raw_to_bids."""
output_path = str(tmpdir)
data_path = testing.data_path()
raw_fname = op.join(data_path, 'MEG', 'sample',
'sample_audvis_trunc_raw.fif')
# Check that help is printed
check_usage(mne_bids_raw_to_bids)
# Should work
with ArgvSetter(('--subject_id', subject_id, '--task', task, '--raw',
raw_fname, '--output_path', output_path)):
mne_bids_raw_to_bids.run()
# Too few input args
with pytest.raises(SystemExit):
with ArgvSetter(('--subject_id', subject_id)):
mne_bids_cp.run()
def test_mark_bad_chanels_multiple_files(tmp_path):
"""Test mne_bids mark_channels."""
# Check that help is printed
check_usage(mne_bids_mark_channels)
# Create test dataset.
output_path = str(tmp_path)
data_path = testing.data_path()
raw_fname = op.join(data_path, 'MEG', 'sample',
'sample_audvis_trunc_raw.fif')
old_bads = mne.io.read_raw_fif(raw_fname).info['bads']
bids_path = BIDSPath(task=task, root=output_path, datatype=datatype)
subjects = ['01', '02', '03']
for subject in subjects:
with ArgvSetter(('--subject_id', subject, '--task', task,
'--raw', raw_fname, '--bids_root', output_path,
'--line_freq', 60)):
mne_bids_raw_to_bids.run()
# Update the dataset.
ch_names = ['MEG 0112', 'MEG 0131']
descriptions = ['Really bad!', 'Even worse.']
args = ['--task', task, '--bids_root', output_path, '--type', datatype]
for ch_name, description in zip(ch_names, descriptions):
args.extend(['--ch_name', ch_name])
args.extend(['--description', description])
args = tuple(args)
with ArgvSetter(args):
mne_bids_mark_channels.run()
# Check the data was properly written
for subject in subjects:
with pytest.warns(RuntimeWarning, match='The unit for chann*'):
raw = read_raw_bids(bids_path=bids_path.copy()
.update(subject=subject))
assert set(old_bads + ch_names) == set(raw.info['bads'])
