def write_mnefiff(data, filename):
"""Export data to MNE using FIFF format.
Parameters
----------
data : instance of ChanTime
data with only one trial
filename : path to file
file to export to (include '.mat')
Notes
-----
It cannot store data larger than 2 GB.
The data is assumed to have only EEG electrodes.
It overwrites a file if it exists.
"""
from mne import create_info, set_log_level
from mne.io import RawArray
set_log_level(WARNING)
TRIAL = 0
info = create_info(list(data.axis['chan'][TRIAL]), data.s_freq, ['eeg', ] *
data.number_of('chan')[TRIAL])
UNITS = 1e-6 # mne wants data in uV
fiff = RawArray(data.data[0] * UNITS, info)
if data.attr['chan']:
fiff.set_channel_positions(data.attr['chan'].return_xyz(),
data.attr['chan'].return_label())
fiff.save(filename, overwrite=True)
def test_warn(capsys, tmp_path, monkeypatch):
"""Test the smart warn() function."""
with pytest.warns(RuntimeWarning, match='foo'):
warn('foo')
captured = capsys.readouterr()
assert captured.out == '' # gh-5592
assert captured.err == '' # this is because pytest.warns took it already
# test ignore_namespaces
bad_name = tmp_path / 'bad.fif'
raw = RawArray(np.zeros((1, 1)), create_info(1, 1000., 'eeg'))
with pytest.warns(RuntimeWarning, match='filename') as ws:
raw.save(bad_name)
assert len(ws) == 1
assert 'test_logging.py' in ws[0].filename # this file (it's in tests/)
def warn_wrap(msg):
warn(msg, ignore_namespaces=())
monkeypatch.setattr(check, 'warn', warn_wrap)
with pytest.warns(RuntimeWarning, match='filename') as ws:
raw.save(bad_name, overwrite=True)
assert len(ws) == 1
assert 'test_logging.py' not in ws[0].filename # this file
assert '_logging.py' in ws[0].filename # where `mne.utils.warn` lives
def test_date_none(tmpdir):
"""Test that DATE_NONE is used properly."""
# Regression test for gh-5908
n_chans = 139
n_samps = 20
data = np.random.random_sample((n_chans, n_samps))
ch_names = ['E{}'.format(x) for x in range(n_chans)]
ch_types = ['eeg'] * n_chans
info = create_info(ch_names=ch_names, ch_types=ch_types, sfreq=2048)
assert info['meas_date'] is None
raw = RawArray(data=data, info=info)
fname = op.join(str(tmpdir), 'test-raw.fif')
raw.save(fname)
raw_read = read_raw_fif(fname, preload=True)
assert raw_read.info['meas_date'] is None
def test_date_none(tmpdir):
"""Test that DATE_NONE is used properly."""
# Regression test for gh-5908
n_chans = 139
n_samps = 20
data = np.random.random_sample((n_chans, n_samps))
ch_names = ['E{}'.format(x) for x in range(n_chans)]
ch_types = ['eeg'] * n_chans
info = create_info(ch_names=ch_names, ch_types=ch_types, sfreq=2048)
assert info['meas_date'] is None
raw = RawArray(data=data, info=info)
fname = op.join(str(tmpdir), 'test-raw.fif')
raw.save(fname)
raw_read = read_raw_fif(fname, preload=True)
assert raw_read.info['meas_date'] is None
def test_annotations():
"""Test annotation class."""
raw = read_raw_fif(fif_fname)
assert raw.annotations is None
assert_raises(IOError, read_annotations, fif_fname)
onset = np.array(range(10))
duration = np.ones(10)
description = np.repeat('test', 10)
dt = datetime.utcnow()
meas_date = raw.info['meas_date']
# Test time shifts.
for orig_time in [None, dt, meas_date[0], meas_date]:
annot = Annotations(onset, duration, description, orig_time)
assert_raises(ValueError, Annotations, onset, duration, description[:9])
assert_raises(ValueError, Annotations, [onset, 1], duration, description)
assert_raises(ValueError, Annotations, onset, [duration, 1], description)
# Test combining annotations with concatenate_raws
raw2 = raw.copy()
orig_time = (meas_date[0] + meas_date[1] * 0.000001 +
raw2.first_samp / raw2.info['sfreq'])
annot = Annotations(onset, duration, description, orig_time)
assert_true(' segments' in repr(annot))
raw2.annotations = annot
assert_array_equal(raw2.annotations.onset, onset)
concatenate_raws([raw, raw2])
raw.annotations.delete(-1) # remove boundary annotations
raw.annotations.delete(-1)
assert_array_almost_equal(onset + 20., raw.annotations.onset, decimal=2)
assert_array_equal(annot.duration, raw.annotations.duration)
assert_array_equal(raw.annotations.description, np.repeat('test', 10))
# Test combining with RawArray and orig_times
data = np.random.randn(2, 1000) * 10e-12
sfreq = 100.
info = create_info(ch_names=['MEG1', 'MEG2'], ch_types=['grad'] * 2,
sfreq=sfreq)
info['meas_date'] = 0
raws = []
for i, fs in enumerate([12300, 100, 12]):
raw = RawArray(data.copy(), info, first_samp=fs)
ants = Annotations([1., 2.], [.5, .5], 'x', fs / sfreq)
raw.annotations = ants
raws.append(raw)
raw = RawArray(data.copy(), info)
raw.annotations = Annotations([1.], [.5], 'x', None)
raws.append(raw)
raw = concatenate_raws(raws)
boundary_idx = np.where(raw.annotations.description == 'BAD boundary')[0]
assert_equal(len(boundary_idx), 3)
raw.annotations.delete(boundary_idx)
boundary_idx = np.where(raw.annotations.description == 'EDGE boundary')[0]
assert_equal(len(boundary_idx), 3)
raw.annotations.delete(boundary_idx)
assert_array_equal(raw.annotations.onset, [1., 2., 11., 12., 21., 22.,
31.])
raw.annotations.delete(2)
assert_array_equal(raw.annotations.onset, [1., 2., 12., 21., 22., 31.])
raw.annotations.append(5, 1.5, 'y')
assert_array_equal(raw.annotations.onset, [1., 2., 12., 21., 22., 31., 5])
assert_array_equal(raw.annotations.duration, [.5, .5, .5, .5, .5, .5, 1.5])
assert_array_equal(raw.annotations.description, ['x', 'x', 'x', 'x', 'x',
'x', 'y'])
# Test concatenating annotations with and without orig_time.
raw = read_raw_fif(fif_fname)
last_time = raw.last_samp / raw.info['sfreq']
raw2 = raw.copy()
raw.annotations = Annotations([45.], [3], 'test', raw.info['meas_date'])
raw2.annotations = Annotations([2.], [3], 'BAD', None)
raw = concatenate_raws([raw, raw2])
raw.annotations.delete(-1) # remove boundary annotations
raw.annotations.delete(-1)
assert_array_almost_equal(raw.annotations.onset, [45., 2. + last_time],
decimal=2)
# Test IO
tempdir = _TempDir()
fname = op.join(tempdir, 'test-annot.fif')
raw.annotations.save(fname)
annot_read = read_annotations(fname)
for attr in ('onset', 'duration', 'orig_time'):
assert_allclose(getattr(annot_read, attr),
getattr(raw.annotations, attr))
assert_array_equal(annot_read.description, raw.annotations.description)
annot = Annotations((), (), ())
annot.save(fname)
assert_raises(IOError, read_annotations, fif_fname) # none in old raw
annot = read_annotations(fname)
assert isinstance(annot, Annotations)
assert len(annot) == 0
# Test that empty annotations can be saved with an object
fname = op.join(tempdir, 'test_raw.fif')
raw.annotations = annot
raw.save(fname)
raw_read = read_raw_fif(fname)
assert isinstance(raw_read.annotations, Annotations)
assert len(raw_read.annotations) == 0
raw.annotations = None
raw.save(fname, overwrite=True)
raw_read = read_raw_fif(fname)
assert raw_read.annotations is None
