def test_cov_estimation_on_raw():
"""Test estimation from raw (typically empty room)"""
tempdir = _TempDir()
raw = Raw(raw_fname, preload=False)
cov_mne = read_cov(erm_cov_fname)
cov = compute_raw_covariance(raw, tstep=None)
assert_equal(cov.ch_names, cov_mne.ch_names)
assert_equal(cov.nfree, cov_mne.nfree)
assert_snr(cov.data, cov_mne.data, 1e4)
cov = compute_raw_covariance(raw) # tstep=0.2 (default)
assert_equal(cov.nfree, cov_mne.nfree - 119) # cutoff some samples
assert_snr(cov.data, cov_mne.data, 1e2)
# test IO when computation done in Python
cov.save(op.join(tempdir, 'test-cov.fif')) # test saving
cov_read = read_cov(op.join(tempdir, 'test-cov.fif'))
assert_true(cov_read.ch_names == cov.ch_names)
assert_true(cov_read.nfree == cov.nfree)
assert_array_almost_equal(cov.data, cov_read.data)
# test with a subset of channels
picks = pick_channels(raw.ch_names, include=raw.ch_names[:5])
cov = compute_raw_covariance(raw, picks=picks, tstep=None)
assert_true(cov_mne.ch_names[:5] == cov.ch_names)
assert_snr(cov.data, cov_mne.data[picks][:, picks], 1e4)
cov = compute_raw_covariance(raw, picks=picks)
assert_snr(cov.data, cov_mne.data[picks][:, picks], 90) # cutoff samps
# make sure we get a warning with too short a segment
raw_2 = raw.crop(0, 1)
with warnings.catch_warnings(record=True) as w:
warnings.simplefilter('always')
cov = compute_raw_covariance(raw_2)
assert_true(any('Too few samples' in str(ww.message) for ww in w))
def test_cov_estimation_on_raw_segment():
"""Test estimation from raw on continuous recordings (typically empty room)
"""
tempdir = _TempDir()
raw = Raw(raw_fname, preload=False)
cov = compute_raw_covariance(raw)
cov_mne = read_cov(erm_cov_fname)
assert_true(cov_mne.ch_names == cov.ch_names)
assert_true(linalg.norm(cov.data - cov_mne.data, ord='fro') /
linalg.norm(cov.data, ord='fro') < 1e-4)
# test IO when computation done in Python
cov.save(op.join(tempdir, 'test-cov.fif')) # test saving
cov_read = read_cov(op.join(tempdir, 'test-cov.fif'))
assert_true(cov_read.ch_names == cov.ch_names)
assert_true(cov_read.nfree == cov.nfree)
assert_array_almost_equal(cov.data, cov_read.data)
# test with a subset of channels
picks = pick_channels(raw.ch_names, include=raw.ch_names[:5])
cov = compute_raw_covariance(raw, picks=picks)
assert_true(cov_mne.ch_names[:5] == cov.ch_names)
assert_true(linalg.norm(cov.data - cov_mne.data[picks][:, picks],
ord='fro') / linalg.norm(cov.data, ord='fro') < 1e-4)
# make sure we get a warning with too short a segment
raw_2 = raw.crop(0, 1)
with warnings.catch_warnings(record=True) as w:
warnings.simplefilter('always')
cov = compute_raw_covariance(raw_2)
assert_true(len(w) == 1)
def test_compute_whitener(proj, pca):
"""Test properties of compute_whitener."""
raw = read_raw_fif(raw_fname).crop(0, 3).load_data()
raw.pick_types(eeg=True, exclude=())
if proj:
raw.apply_proj()
else:
raw.del_proj()
with pytest.warns(RuntimeWarning, match='Too few samples'):
cov = compute_raw_covariance(raw)
W, _, C = compute_whitener(cov, raw.info, pca=pca, return_colorer=True,
verbose='error')
n_channels = len(raw.ch_names)
n_reduced = len(raw.ch_names)
rank = n_channels - len(raw.info['projs'])
n_reduced = rank if pca is True else n_channels
assert W.shape == C.shape[::-1] == (n_reduced, n_channels)
# round-trip mults
round_trip = np.dot(W, C)
if pca is True:
assert_allclose(round_trip, np.eye(n_reduced), atol=1e-7)
elif pca == 'white':
# Our first few rows/cols are zeroed out in the white space
assert_allclose(round_trip[-rank:, -rank:],
np.eye(rank), atol=1e-7)
else:
assert pca is False
assert_allclose(round_trip, np.eye(n_channels), atol=0.05)
def test_compute_whitener(proj, pca):
"""Test properties of compute_whitener."""
raw = read_raw_fif(raw_fname).crop(0, 3).load_data()
raw.pick_types(eeg=True, exclude=())
if proj:
raw.apply_proj()
else:
raw.del_proj()
with pytest.warns(RuntimeWarning, match='Too few samples'):
cov = compute_raw_covariance(raw)
W, _, C = compute_whitener(cov,
raw.info,
pca=pca,
return_colorer=True,
verbose='error')
n_channels = len(raw.ch_names)
n_reduced = len(raw.ch_names)
rank = n_channels - len(raw.info['projs'])
n_reduced = rank if pca is True else n_channels
assert W.shape == C.shape[::-1] == (n_reduced, n_channels)
# round-trip mults
round_trip = np.dot(W, C)
if pca is True:
assert_allclose(round_trip, np.eye(n_reduced), atol=1e-7)
elif pca == 'white':
# Our first few rows/cols are zeroed out in the white space
assert_allclose(round_trip[-rank:, -rank:], np.eye(rank), atol=1e-7)
else:
assert pca is False
assert_allclose(round_trip, np.eye(n_channels), atol=0.05)
def compute_noise_cov(subject, hcp_path, noise_cov_fname=''):
if noise_cov_fname == '':
noise_cov_fname = meg.NOISE_COV.format(cond='empty_room')
if op.isfile(noise_cov_fname):
noise_cov = mne.read_cov(noise_cov_fname)
return noise_cov
utils.make_dir(utils.get_parent_fol(noise_cov_fname))
raw_noise = hcp.read_raw(subject=subject,
hcp_path=hcp_path,
data_type='noise_empty_room')
raw_noise.load_data()
# apply ref channel correction and drop ref channels
preproc.apply_ref_correction(raw_noise)
raw_noise.filter(0.50,
None,
method='iir',
iir_params=dict(order=4, ftype='butter'),
n_jobs=1)
raw_noise.filter(None,
60,
method='iir',
iir_params=dict(order=4, ftype='butter'),
n_jobs=1)
##############################################################################
# Note that using the empty room noise covariance will inflate the SNR of the
# evkoked and renders comparisons to `baseline` rather uninformative.
noise_cov = mne.compute_raw_covariance(raw_noise, method='empirical')
noise_cov.save(noise_cov_fname)
return noise_cov
def test_lcmv_raw():
"""Test LCMV with raw data
"""
raw, _, _, _, noise_cov, label, forward, _, _, _ =\
_get_data(all_forward=False, epochs=False, data_cov=False)
tmin, tmax = 0, 20
start, stop = raw.time_as_index([tmin, tmax])
# use only the left-temporal MEG channels for LCMV
left_temporal_channels = mne.read_selection('Left-temporal')
picks = mne.pick_types(raw.info, meg=True, exclude='bads',
selection=left_temporal_channels)
data_cov = mne.compute_raw_covariance(raw, tmin=tmin, tmax=tmax)
stc = lcmv_raw(raw, forward, noise_cov, data_cov, reg=0.01, label=label,
start=start, stop=stop, picks=picks)
assert_array_almost_equal(np.array([tmin, tmax]),
np.array([stc.times[0], stc.times[-1]]),
decimal=2)
# make sure we get an stc with vertices only in the lh
vertno = [forward['src'][0]['vertno'], forward['src'][1]['vertno']]
assert_true(len(stc.vertices[0]) == len(np.intersect1d(vertno[0],
label.vertices)))
assert_true(len(stc.vertices[1]) == 0)
def compute_cov_from_empty_room(subject, session):
deriv_path = config.get_subject_deriv_path(subject=subject,
session=session,
kind=config.get_kind())
bids_basename = BIDSPath(subject=subject,
session=session,
task=config.get_task(),
acquisition=config.acq,
run=None,
recording=config.rec,
space=config.space,
prefix=deriv_path,
check=False)
raw_er_fname = bids_basename.copy().update(kind=config.get_kind(),
task='noise',
processing='filt',
extension='.fif')
cov_fname = bids_basename.copy().update(kind='cov', extension='.fif')
extra_params = dict()
if not config.use_maxwell_filter and config.allow_maxshield:
extra_params['allow_maxshield'] = config.allow_maxshield
msg = (f'Computing regularized covariance based on empty-room recording. '
f'Input: {raw_er_fname}, Output: {cov_fname}')
logger.info(
gen_log_message(message=msg, step=11, subject=subject,
session=session))
raw_er = mne.io.read_raw_fif(raw_er_fname, preload=True, **extra_params)
cov = mne.compute_raw_covariance(raw_er, method='shrunk', rank='info')
cov.save(cov_fname)
def test_lcmv_raw():
"""Test LCMV with raw data."""
raw, _, _, _, noise_cov, label, forward, _, _, _ =\
_get_data(all_forward=False, epochs=False, data_cov=False)
tmin, tmax = 0, 20
start, stop = raw.time_as_index([tmin, tmax])
# use only the left-temporal MEG channels for LCMV
data_cov = mne.compute_raw_covariance(raw, tmin=tmin, tmax=tmax)
filters = make_lcmv(raw.info,
forward,
data_cov,
reg=0.01,
noise_cov=noise_cov,
label=label)
stc = apply_lcmv_raw(raw,
filters,
start=start,
stop=stop,
max_ori_out='signed')
assert_array_almost_equal(np.array([tmin, tmax]),
np.array([stc.times[0], stc.times[-1]]),
decimal=2)
# make sure we get an stc with vertices only in the lh
vertno = [forward['src'][0]['vertno'], forward['src'][1]['vertno']]
assert len(stc.vertices[0]) == len(
np.intersect1d(vertno[0], label.vertices))
assert len(stc.vertices[1]) == 0
def compute_cov_from_empty_room(cfg, subject, session):
bids_path = BIDSPath(subject=subject,
session=session,
task=cfg.task,
acquisition=cfg.acq,
run=None,
recording=cfg.rec,
space=cfg.space,
extension='.fif',
datatype=cfg.datatype,
root=cfg.deriv_root,
check=False)
raw_er_fname = bids_path.copy().update(processing='filt',
task='noise',
suffix='raw')
cov_fname = bids_path.copy().update(suffix='cov')
msg = (f'Computing regularized covariance based on empty-room recording. '
f'Input: {raw_er_fname}, Output: {cov_fname}')
logger.info(
**gen_log_kwargs(message=msg, subject=subject, session=session))
raw_er = mne.io.read_raw_fif(raw_er_fname, preload=True)
cov = mne.compute_raw_covariance(raw_er, method='shrunk', rank='info')
cov.save(cov_fname)
def test_XdawnTransformer():
"""Test _XdawnTransformer."""
# Get data
raw, events, picks = _get_data()
epochs = Epochs(raw, events, event_id, tmin, tmax, picks=picks,
preload=True, baseline=None, verbose=False,
add_eeg_ref=False)
X = epochs._data
y = epochs.events[:, -1]
# Fit
xdt = _XdawnTransformer()
xdt.fit(X, y)
assert_raises(ValueError, xdt.fit, X, y[1:])
assert_raises(ValueError, xdt.fit, 'foo')
# Provide covariance object
signal_cov = compute_raw_covariance(raw, picks=picks)
xdt = _XdawnTransformer(signal_cov=signal_cov)
xdt.fit(X, y)
# Provide ndarray
signal_cov = np.eye(len(picks))
xdt = _XdawnTransformer(signal_cov=signal_cov)
xdt.fit(X, y)
# Provide ndarray of bad shape
signal_cov = np.eye(len(picks) - 1)
xdt = _XdawnTransformer(signal_cov=signal_cov)
assert_raises(ValueError, xdt.fit, X, y)
# Provide another type
signal_cov = 42
xdt = _XdawnTransformer(signal_cov=signal_cov)
assert_raises(ValueError, xdt.fit, X, y)
# Fit with y as None
xdt = _XdawnTransformer()
xdt.fit(X)
# Compare xdawn and _XdawnTransformer
xd = Xdawn(correct_overlap=False)
xd.fit(epochs)
xdt = _XdawnTransformer()
xdt.fit(X, y)
assert_array_almost_equal(xd.filters_['cond2'][:, :2],
xdt.filters_.reshape(2, 2, 8)[0].T)
# Transform testing
xdt.transform(X[1:, ...]) # different number of epochs
xdt.transform(X[:, :, 1:]) # different number of time
assert_raises(ValueError, xdt.transform, X[:, 1:, :])
Xt = xdt.transform(X)
assert_raises(ValueError, xdt.transform, 42)
# Inverse transform testing
Xinv = xdt.inverse_transform(Xt)
assert_equal(Xinv.shape, X.shape)
xdt.inverse_transform(Xt[1:, ...])
xdt.inverse_transform(Xt[:, :, 1:])
# should raise an error if not correct number of components
assert_raises(ValueError, xdt.inverse_transform, Xt[:, 1:, :])
assert_raises(ValueError, xdt.inverse_transform, 42)
def test_XdawnTransformer():
"""Test _XdawnTransformer."""
# Get data
raw, events, picks = _get_data()
raw.del_proj()
epochs = Epochs(raw, events, event_id, tmin, tmax, picks=picks,
preload=True, baseline=None, verbose=False)
X = epochs._data
y = epochs.events[:, -1]
# Fit
xdt = _XdawnTransformer()
xdt.fit(X, y)
pytest.raises(ValueError, xdt.fit, X, y[1:])
pytest.raises(ValueError, xdt.fit, 'foo')
# Provide covariance object
signal_cov = compute_raw_covariance(raw, picks=picks)
xdt = _XdawnTransformer(signal_cov=signal_cov)
xdt.fit(X, y)
# Provide ndarray
signal_cov = np.eye(len(picks))
xdt = _XdawnTransformer(signal_cov=signal_cov)
xdt.fit(X, y)
# Provide ndarray of bad shape
signal_cov = np.eye(len(picks) - 1)
xdt = _XdawnTransformer(signal_cov=signal_cov)
pytest.raises(ValueError, xdt.fit, X, y)
# Provide another type
signal_cov = 42
xdt = _XdawnTransformer(signal_cov=signal_cov)
pytest.raises(ValueError, xdt.fit, X, y)
# Fit with y as None
xdt = _XdawnTransformer()
xdt.fit(X)
# Compare xdawn and _XdawnTransformer
xd = Xdawn(correct_overlap=False)
xd.fit(epochs)
xdt = _XdawnTransformer()
xdt.fit(X, y)
assert_array_almost_equal(xd.filters_['cond2'][:, :2],
xdt.filters_.reshape(2, 2, 8)[0].T)
# Transform testing
xdt.transform(X[1:, ...]) # different number of epochs
xdt.transform(X[:, :, 1:]) # different number of time
pytest.raises(ValueError, xdt.transform, X[:, 1:, :])
Xt = xdt.transform(X)
pytest.raises(ValueError, xdt.transform, 42)
# Inverse transform testing
Xinv = xdt.inverse_transform(Xt)
assert Xinv.shape == X.shape
xdt.inverse_transform(Xt[1:, ...])
xdt.inverse_transform(Xt[:, :, 1:])
# should raise an error if not correct number of components
pytest.raises(ValueError, xdt.inverse_transform, Xt[:, 1:, :])
pytest.raises(ValueError, xdt.inverse_transform, 42)
def test_sss_proj():
"""Test `meg` proj option."""
raw = read_raw_fif(raw_fname)
raw.crop(0, 1.0).load_data().pick_types(exclude=())
raw.pick_channels(raw.ch_names[:51]).del_proj()
with pytest.raises(ValueError, match='can only be used with Maxfiltered'):
compute_proj_raw(raw, meg='combined')
raw_sss = maxwell_filter(raw, int_order=5, ext_order=2)
sss_rank = 21 # really low due to channel picking
assert len(raw_sss.info['projs']) == 0
for meg, n_proj, want_rank in (('separate', 6, sss_rank),
('combined', 3, sss_rank - 3)):
proj = compute_proj_raw(raw_sss, n_grad=3, n_mag=3, meg=meg,
verbose='error')
this_raw = raw_sss.copy().add_proj(proj).apply_proj()
assert len(this_raw.info['projs']) == n_proj
sss_proj_rank = _compute_rank_int(this_raw)
cov = compute_raw_covariance(this_raw, verbose='error')
W, ch_names, rank = compute_whitener(cov, this_raw.info,
return_rank=True)
assert ch_names == this_raw.ch_names
assert want_rank == sss_proj_rank == rank # proper reduction
if meg == 'combined':
assert this_raw.info['projs'][0]['data']['col_names'] == ch_names
else:
mag_names = ch_names[2::3]
assert this_raw.info['projs'][3]['data']['col_names'] == mag_names
def compute_noise_cov(cov_fname, raw):
import os.path as op
from mne import compute_raw_covariance, pick_types, write_cov
from nipype.utils.filemanip import split_filename as split_f
from neuropype_ephy.preproc import create_reject_dict
print '***** COMPUTE RAW COV *****' + cov_fname
if not op.isfile(cov_fname):
data_path, basename, ext = split_f(raw.info['filename'])
fname = op.join(data_path, '%s-cov.fif' % basename)
reject = create_reject_dict(raw.info)
# reject = dict(mag=4e-12, grad=4000e-13, eog=250e-6)
picks = pick_types(raw.info, meg=True, ref_meg=False, exclude='bads')
noise_cov = compute_raw_covariance(raw, picks=picks, reject=reject)
write_cov(fname, noise_cov)
else:
print '*** NOISE cov file %s exists!!!' % cov_fname
return cov_fname
def test_sss_proj():
"""Test `meg` proj option."""
raw = read_raw_fif(raw_fname)
raw.crop(0, 1.0).load_data().pick_types(meg=True, exclude=())
raw.pick_channels(raw.ch_names[:51]).del_proj()
raw_sss = maxwell_filter(raw, int_order=5, ext_order=2)
sss_rank = 21 # really low due to channel picking
assert len(raw_sss.info['projs']) == 0
for meg, n_proj, want_rank in (('separate', 6, sss_rank), ('combined', 3,
sss_rank - 3)):
proj = compute_proj_raw(raw_sss,
n_grad=3,
n_mag=3,
meg=meg,
verbose='error')
this_raw = raw_sss.copy().add_proj(proj).apply_proj()
assert len(this_raw.info['projs']) == n_proj
sss_proj_rank = _compute_rank_int(this_raw)
cov = compute_raw_covariance(this_raw, verbose='error')
W, ch_names, rank = compute_whitener(cov,
this_raw.info,
return_rank=True)
assert ch_names == this_raw.ch_names
assert want_rank == sss_proj_rank == rank # proper reduction
if meg == 'combined':
assert this_raw.info['projs'][0]['data']['col_names'] == ch_names
else:
mag_names = ch_names[2::3]
assert this_raw.info['projs'][3]['data']['col_names'] == mag_names
def get_epochs_and_cov(X, y, window=100):
"""return epochs from array."""
raw_train = toMNE(X, y)
picks = range(len(getChannelNames()))
events = list()
events_id = dict()
for j, eid in enumerate(getEventNames()):
tmp = find_events(raw_train, stim_channel=eid, verbose=False)
tmp[:, -1] = j + 1
events.append(tmp)
events_id[eid] = j + 1
# concatenate and sort events
events = np.concatenate(events, axis=0)
order_ev = np.argsort(events[:, 0])
events = events[order_ev]
# epochs = Epochs(raw_train, events, events_id,
# tmin=-(window / 500.0) + 1 / 500.0 + 0.150,
# tmax=0.150, proj=False, picks=picks, baseline=None,
# preload=True, add_eeg_ref=False, verbose=False)
epochs = Epochs(raw_train, events, events_id,
tmin=-(window / 128.0) + 1 / 128.0 + 0.150,
tmax=0.150, proj=False, picks=picks, baseline=None,
preload=True, add_eeg_ref=False, verbose=False)
cov_signal = compute_raw_covariance(raw_train, verbose=False)
# pdb.set_trace()
return epochs, cov_signal
def test_maxwell_filter_additional():
"""Test processing of Maxwell filtered data"""
# TODO: Future tests integrate with mne/io/tests/test_proc_history
# Load testing data (raw, SSS std origin, SSS non-standard origin)
data_path = op.join(testing.data_path(download=False))
file_name = 'test_move_anon'
raw_fname = op.join(data_path, 'SSS', file_name + '_raw.fif')
with warnings.catch_warnings(record=True): # maxshield
# Use 2.0 seconds of data to get stable cov. estimate
raw = Raw(raw_fname, preload=False, proj=False,
allow_maxshield=True).crop(0., 2., False)
# Get MEG channels, compute Maxwell filtered data
raw.load_data()
raw.pick_types(meg=True, eeg=False)
int_order, ext_order = 8, 3
raw_sss = maxwell.maxwell_filter(raw, int_order=int_order,
ext_order=ext_order)
# Test io on processed data
tempdir = _TempDir()
test_outname = op.join(tempdir, 'test_raw_sss.fif')
raw_sss.save(test_outname)
raw_sss_loaded = Raw(test_outname, preload=True, proj=False,
allow_maxshield=True)
# Some numerical imprecision since save uses 'single' fmt
assert_allclose(raw_sss_loaded._data[:, :], raw_sss._data[:, :],
rtol=1e-6, atol=1e-20)
# Test rank of covariance matrices for raw and SSS processed data
cov_raw = compute_raw_covariance(raw)
cov_sss = compute_raw_covariance(raw_sss)
scalings = None
cov_raw_rank = _estimate_rank_meeg_cov(cov_raw['data'], raw.info, scalings)
cov_sss_rank = _estimate_rank_meeg_cov(cov_sss['data'], raw_sss.info,
scalings)
assert_equal(cov_raw_rank, raw.info['nchan'])
assert_equal(cov_sss_rank, maxwell.get_num_moments(int_order, 0))
def test_add_noise():
"""Test noise addition."""
if check_version('numpy', '1.17'):
rng = np.random.default_rng(0)
else:
rng = np.random.RandomState(0)
raw = read_raw_fif(raw_fname)
raw.del_proj()
picks = pick_types(raw.info, meg=True, eeg=True, exclude=())
cov = compute_raw_covariance(raw, picks=picks)
with pytest.raises(RuntimeError, match='to be loaded'):
add_noise(raw, cov)
raw.crop(0, 1).load_data()
with pytest.raises(TypeError, match='Raw, Epochs, or Evoked'):
add_noise(0., cov)
with pytest.raises(TypeError, match='Covariance'):
add_noise(raw, 0.)
# test a no-op (data preserved)
orig_data = raw[:][0]
zero_cov = cov.copy()
zero_cov['data'].fill(0)
add_noise(raw, zero_cov)
new_data = raw[:][0]
assert_allclose(orig_data, new_data, atol=1e-30)
# set to zero to make comparisons easier
raw._data[:] = 0.
epochs = EpochsArray(np.zeros((1, len(raw.ch_names), 100)),
raw.info.copy())
epochs.info['bads'] = []
evoked = epochs.average(picks=np.arange(len(raw.ch_names)))
for inst in (raw, epochs, evoked):
with catch_logging() as log:
add_noise(inst, cov, random_state=rng, verbose=True)
log = log.getvalue()
want = ('to {0}/{1} channels ({0}'
.format(len(cov['names']), len(raw.ch_names)))
assert want in log
if inst is evoked:
inst = EpochsArray(inst.data[np.newaxis], inst.info)
if inst is raw:
cov_new = compute_raw_covariance(inst, picks=picks)
else:
cov_new = compute_covariance(inst)
assert cov['names'] == cov_new['names']
r = np.corrcoef(cov['data'].ravel(), cov_new['data'].ravel())[0, 1]
assert r > 0.99
def test_xdawn_fit():
"""Test Xdawn fit."""
# Get data
raw, events, picks = _get_data()
raw.del_proj()
epochs = Epochs(raw,
events,
event_id,
tmin,
tmax,
picks=picks,
preload=True,
baseline=None,
verbose=False)
# =========== Basic Fit test =================
# Test base xdawn
xd = Xdawn(n_components=2, correct_overlap='auto')
xd.fit(epochs)
# With these parameters, the overlap correction must be False
assert not xd.correct_overlap_
# No overlap correction should give averaged evoked
evoked = epochs['cond2'].average()
assert_array_equal(evoked.data, xd.evokeds_['cond2'].data)
assert_allclose(np.linalg.norm(xd.filters_['cond2'], axis=1), 1)
# ========== with signal cov provided ====================
# Provide covariance object
signal_cov = compute_raw_covariance(raw, picks=picks)
xd = Xdawn(n_components=2, correct_overlap=False, signal_cov=signal_cov)
xd.fit(epochs)
# Provide ndarray
signal_cov = np.eye(len(picks))
xd = Xdawn(n_components=2, correct_overlap=False, signal_cov=signal_cov)
xd.fit(epochs)
# Provide ndarray of bad shape
signal_cov = np.eye(len(picks) - 1)
xd = Xdawn(n_components=2, correct_overlap=False, signal_cov=signal_cov)
pytest.raises(ValueError, xd.fit, epochs)
# Provide another type
signal_cov = 42
xd = Xdawn(n_components=2, correct_overlap=False, signal_cov=signal_cov)
pytest.raises(ValueError, xd.fit, epochs)
# Fit with baseline correction and overlap correction should throw an
# error
# XXX This is a buggy test, the epochs here don't overlap
epochs = Epochs(raw,
events,
event_id,
tmin,
tmax,
picks=picks,
preload=True,
baseline=(None, 0),
verbose=False)
xd = Xdawn(n_components=2, correct_overlap=True)
pytest.raises(ValueError, xd.fit, epochs)
def test_maxwell_filter_additional():
"""Test processing of Maxwell filtered data"""
# TODO: Future tests integrate with mne/io/tests/test_proc_history
# Load testing data (raw, SSS std origin, SSS non-standard origin)
data_path = op.join(testing.data_path(download=False))
file_name = 'test_move_anon'
raw_fname = op.join(data_path, 'SSS', file_name + '_raw.fif')
with warnings.catch_warnings(record=True): # maxshield
# Use 2.0 seconds of data to get stable cov. estimate
raw = Raw(raw_fname, allow_maxshield=True).crop(0., 2., False)
# Get MEG channels, compute Maxwell filtered data
raw.load_data()
raw.pick_types(meg=True, eeg=False)
int_order = 8
raw_sss = maxwell_filter(raw,
origin=mf_head_origin,
regularize=None,
bad_condition='ignore')
# Test io on processed data
tempdir = _TempDir()
test_outname = op.join(tempdir, 'test_raw_sss.fif')
raw_sss.save(test_outname)
raw_sss_loaded = Raw(test_outname, preload=True)
# Some numerical imprecision since save uses 'single' fmt
assert_allclose(raw_sss_loaded[:][0], raw_sss[:][0], rtol=1e-6, atol=1e-20)
# Test rank of covariance matrices for raw and SSS processed data
cov_raw = compute_raw_covariance(raw)
cov_sss = compute_raw_covariance(raw_sss)
scalings = None
cov_raw_rank = _estimate_rank_meeg_cov(cov_raw['data'], raw.info, scalings)
cov_sss_rank = _estimate_rank_meeg_cov(cov_sss['data'], raw_sss.info,
scalings)
assert_equal(cov_raw_rank, raw.info['nchan'])
assert_equal(cov_sss_rank, _get_n_moments(int_order))
def test_add_noise():
"""Test noise addition."""
rng = np.random.RandomState(0)
data_path = testing.data_path()
raw = read_raw_fif(data_path + '/MEG/sample/sample_audvis_trunc_raw.fif')
raw.del_proj()
picks = pick_types(raw.info, eeg=True, exclude=())
cov = compute_raw_covariance(raw, picks=picks)
with pytest.raises(RuntimeError, match='to be loaded'):
add_noise(raw, cov)
raw.crop(0, 1).load_data()
with pytest.raises(TypeError, match='Raw, Epochs, or Evoked'):
add_noise(0., cov)
with pytest.raises(TypeError, match='Covariance'):
add_noise(raw, 0.)
# test a no-op (data preserved)
orig_data = raw[:][0]
zero_cov = cov.copy()
zero_cov['data'].fill(0)
add_noise(raw, zero_cov)
new_data = raw[:][0]
assert_allclose(orig_data, new_data, atol=1e-30)
# set to zero to make comparisons easier
raw._data[:] = 0.
epochs = EpochsArray(np.zeros((1, len(raw.ch_names), 100)),
raw.info.copy())
epochs.info['bads'] = []
evoked = epochs.average(picks=np.arange(len(raw.ch_names)))
for inst in (raw, epochs, evoked):
with catch_logging() as log:
add_noise(inst, cov, random_state=rng, verbose=True)
log = log.getvalue()
want = ('to {0}/{1} channels ({0}'
.format(len(cov['names']), len(raw.ch_names)))
assert want in log
if inst is evoked:
inst = EpochsArray(inst.data[np.newaxis], inst.info)
if inst is raw:
cov_new = compute_raw_covariance(inst, picks=picks,
verbose='error') # samples
else:
cov_new = compute_covariance(inst, verbose='error') # avg ref
assert cov['names'] == cov_new['names']
r = np.corrcoef(cov['data'].ravel(), cov_new['data'].ravel())[0, 1]
assert r > 0.99
def compute_cov(cov_object, reject=None, tmax=0, method='shrunk'):
if isinstance(cov_object, mne.epochs._BaseEpochs):
cov = mne.compute_covariance(cov_object, tmax=tmax, method=method)
elif isinstance(cov_object, mne.io.base._BaseRaw):
if reject is None:
reject, picks = compute_reject_picks(cov_object)
cov = mne.compute_raw_covariance(cov_object,
reject=reject,
picks=picks)
return cov
def test_maxwell_filter_additional():
"""Test processing of Maxwell filtered data."""
# TODO: Future tests integrate with mne/io/tests/test_proc_history
# Load testing data (raw, SSS std origin, SSS non-standard origin)
data_path = op.join(testing.data_path(download=False))
file_name = 'test_move_anon'
raw_fname = op.join(data_path, 'SSS', file_name + '_raw.fif')
# Use 2.0 seconds of data to get stable cov. estimate
raw = read_crop(raw_fname, (0., 2.))
# Get MEG channels, compute Maxwell filtered data
raw.load_data()
raw.pick_types(meg=True, eeg=False)
int_order = 8
raw_sss = maxwell_filter(raw, origin=mf_head_origin, regularize=None,
bad_condition='ignore')
# Test io on processed data
tempdir = _TempDir()
test_outname = op.join(tempdir, 'test_raw_sss.fif')
raw_sss.save(test_outname)
raw_sss_loaded = read_crop(test_outname).load_data()
# Some numerical imprecision since save uses 'single' fmt
assert_allclose(raw_sss_loaded[:][0], raw_sss[:][0],
rtol=1e-6, atol=1e-20)
# Test rank of covariance matrices for raw and SSS processed data
cov_raw = compute_raw_covariance(raw)
cov_sss = compute_raw_covariance(raw_sss)
scalings = None
cov_raw_rank = _estimate_rank_meeg_cov(cov_raw['data'], raw.info, scalings)
cov_sss_rank = _estimate_rank_meeg_cov(cov_sss['data'], raw_sss.info,
scalings)
assert_equal(cov_raw_rank, raw.info['nchan'])
assert_equal(cov_sss_rank, _get_n_moments(int_order))
def test_maxwell_filter_additional(tmpdir):
"""Test processing of Maxwell filtered data."""
# TODO: Future tests integrate with mne/io/tests/test_proc_history
# Load testing data (raw, SSS std origin, SSS non-standard origin)
data_path = op.join(testing.data_path(download=False))
file_name = 'test_move_anon'
raw_fname = op.join(data_path, 'SSS', file_name + '_raw.fif')
# Use 2.0 seconds of data to get stable cov. estimate
raw = read_crop(raw_fname, (0., 2.))
# Get MEG channels, compute Maxwell filtered data
raw.load_data()
raw.pick_types(meg=True, eeg=False)
int_order = 8
raw_sss = maxwell_filter(raw, origin=mf_head_origin, regularize=None,
bad_condition='ignore')
# Test io on processed data
tempdir = str(tmpdir)
test_outname = op.join(tempdir, 'test_raw_sss.fif')
raw_sss.save(test_outname)
raw_sss_loaded = read_crop(test_outname).load_data()
# Some numerical imprecision since save uses 'single' fmt
assert_allclose(raw_sss_loaded[:][0], raw_sss[:][0],
rtol=1e-6, atol=1e-20)
# Test rank of covariance matrices for raw and SSS processed data
cov_raw = compute_raw_covariance(raw)
cov_sss = compute_raw_covariance(raw_sss)
scalings = None
cov_raw_rank = _compute_rank_int(
cov_raw, scalings=scalings, info=raw.info, proj=False)
cov_sss_rank = _compute_rank_int(
cov_sss, scalings=scalings, info=raw_sss.info, proj=False)
assert cov_raw_rank == raw.info['nchan']
assert cov_sss_rank == _get_n_moments(int_order)
def test_cov_estimation_on_raw_reg():
"""Test estimation from raw with regularization."""
raw = read_raw_fif(raw_fname, preload=True)
raw.info['sfreq'] /= 10.
raw = RawArray(raw._data[:, ::10].copy(), raw.info) # decimate for speed
cov_mne = read_cov(erm_cov_fname)
with pytest.warns(RuntimeWarning, match='Too few samples'):
# "diagonal_fixed" is much faster. Use long epochs for speed.
cov = compute_raw_covariance(raw, tstep=5., method='diagonal_fixed')
assert_snr(cov.data, cov_mne.data, 5)
def test_cov_estimation_on_raw():
"""Test estimation from raw (typically empty room)"""
tempdir = _TempDir()
raw = Raw(raw_fname, preload=True)
cov_mne = read_cov(erm_cov_fname)
# The pure-string uses the more efficient numpy-based method, the
# the list gets triaged to compute_covariance (should be equivalent
# but use more memory)
for method in ('empirical', ['empirical']):
cov = compute_raw_covariance(raw, tstep=None, method=method)
assert_equal(cov.ch_names, cov_mne.ch_names)
assert_equal(cov.nfree, cov_mne.nfree)
assert_snr(cov.data, cov_mne.data, 1e4)
cov = compute_raw_covariance(raw, method=method) # tstep=0.2 (default)
assert_equal(cov.nfree, cov_mne.nfree - 119) # cutoff some samples
assert_snr(cov.data, cov_mne.data, 1e2)
# test IO when computation done in Python
cov.save(op.join(tempdir, 'test-cov.fif')) # test saving
cov_read = read_cov(op.join(tempdir, 'test-cov.fif'))
assert_true(cov_read.ch_names == cov.ch_names)
assert_true(cov_read.nfree == cov.nfree)
assert_array_almost_equal(cov.data, cov_read.data)
# test with a subset of channels
picks = pick_channels(raw.ch_names, include=raw.ch_names[:5])
raw_pick = raw.pick_channels([raw.ch_names[pick] for pick in picks],
copy=True)
raw_pick.info.normalize_proj()
cov = compute_raw_covariance(raw_pick, picks=picks, tstep=None,
method=method)
assert_true(cov_mne.ch_names[:5] == cov.ch_names)
assert_snr(cov.data, cov_mne.data[picks][:, picks], 1e4)
cov = compute_raw_covariance(raw_pick, picks=picks, method=method)
assert_snr(cov.data, cov_mne.data[picks][:, picks], 90) # cutoff samps
# make sure we get a warning with too short a segment
raw_2 = Raw(raw_fname).crop(0, 1)
with warnings.catch_warnings(record=True) as w:
warnings.simplefilter('always')
cov = compute_raw_covariance(raw_2, method=method)
assert_true(any('Too few samples' in str(ww.message) for ww in w))
def test_cov_estimation_on_raw_reg():
"""Test estimation from raw with regularization."""
raw = read_raw_fif(raw_fname, preload=True)
raw.info['sfreq'] /= 10.
raw = RawArray(raw._data[:, ::10].copy(), raw.info) # decimate for speed
cov_mne = read_cov(erm_cov_fname)
with pytest.warns(RuntimeWarning, match='Too few samples'):
# XXX don't use "shrunk" here, for some reason it makes Travis 2.7
# hang... "diagonal_fixed" is much faster. Use long epochs for speed.
cov = compute_raw_covariance(raw, tstep=5., method='diagonal_fixed')
assert_snr(cov.data, cov_mne.data, 5)
def test_maxwell_filter_additional():
"""Test processing of Maxwell filtered data"""
# TODO: Future tests integrate with mne/io/tests/test_proc_history
# Load testing data (raw, SSS std origin, SSS non-standard origin)
data_path = op.join(testing.data_path(download=False))
file_name = "test_move_anon"
raw_fname = op.join(data_path, "SSS", file_name + "_raw.fif")
with warnings.catch_warnings(record=True): # maxshield
# Use 2.0 seconds of data to get stable cov. estimate
raw = Raw(raw_fname, allow_maxshield=True).crop(0.0, 2.0, False)
# Get MEG channels, compute Maxwell filtered data
raw.load_data()
raw.pick_types(meg=True, eeg=False)
int_order = 8
raw_sss = maxwell_filter(raw, origin=mf_head_origin, regularize=None, bad_condition="ignore")
# Test io on processed data
tempdir = _TempDir()
test_outname = op.join(tempdir, "test_raw_sss.fif")
raw_sss.save(test_outname)
raw_sss_loaded = Raw(test_outname, preload=True)
# Some numerical imprecision since save uses 'single' fmt
assert_allclose(raw_sss_loaded[:][0], raw_sss[:][0], rtol=1e-6, atol=1e-20)
# Test rank of covariance matrices for raw and SSS processed data
cov_raw = compute_raw_covariance(raw)
cov_sss = compute_raw_covariance(raw_sss)
scalings = None
cov_raw_rank = _estimate_rank_meeg_cov(cov_raw["data"], raw.info, scalings)
cov_sss_rank = _estimate_rank_meeg_cov(cov_sss["data"], raw_sss.info, scalings)
assert_equal(cov_raw_rank, raw.info["nchan"])
assert_equal(cov_sss_rank, _get_n_moments(int_order))
def test_cov_estimation_on_raw_reg():
"""Test estimation from raw with regularization."""
raw = read_raw_fif(raw_fname, preload=True, add_eeg_ref=False)
raw.info["sfreq"] /= 10.0
raw = RawArray(raw._data[:, ::10].copy(), raw.info) # decimate for speed
cov_mne = read_cov(erm_cov_fname)
with warnings.catch_warnings(record=True): # too few samples
warnings.simplefilter("always")
# XXX don't use "shrunk" here, for some reason it makes Travis 2.7
# hang... "diagonal_fixed" is much faster. Use long epochs for speed.
cov = compute_raw_covariance(raw, tstep=5.0, method="diagonal_fixed")
assert_snr(cov.data, cov_mne.data, 5)
def test_make_fixed_length_events():
"""Test making events of a fixed length."""
raw = read_raw_fif(raw_fname)
events = make_fixed_length_events(raw, id=1)
assert events.shape[1] == 3
events_zero = make_fixed_length_events(raw, 1, first_samp=False)
assert_equal(events_zero[0, 0], 0)
assert_array_equal(events_zero[:, 0], events[:, 0] - raw.first_samp)
# With limits
tmin, tmax = raw.times[[0, -1]]
duration = tmax - tmin
events = make_fixed_length_events(raw, 1, tmin, tmax, duration)
assert_equal(events.shape[0], 1)
# With bad limits (no resulting events)
pytest.raises(ValueError, make_fixed_length_events, raw, 1,
tmin, tmax - 1e-3, duration)
# not raw, bad id or duration
pytest.raises(TypeError, make_fixed_length_events, raw, 2.3)
pytest.raises(TypeError, make_fixed_length_events, 'not raw', 2)
pytest.raises(TypeError, make_fixed_length_events, raw, 23, tmin, tmax,
'abc')
# Let's try some ugly sample rate/sample count combos
data = np.random.RandomState(0).randn(1, 27768)
# This breaks unless np.round() is used in make_fixed_length_events
info = create_info(1, 155.4499969482422)
raw = RawArray(data, info)
events = make_fixed_length_events(raw, 1, duration=raw.times[-1])
assert events[0, 0] == 0
assert len(events) == 1
# Without use_rounding=True this breaks
raw = RawArray(data[:, :21216], info)
events = make_fixed_length_events(raw, 1, duration=raw.times[-1])
assert events[0, 0] == 0
assert len(events) == 1
# Make sure it gets used properly by compute_raw_covariance
cov = compute_raw_covariance(raw, tstep=None)
expected = np.cov(data[:, :21216])
np.testing.assert_allclose(cov['data'], expected, atol=1e-12)
# overlaps
events = make_fixed_length_events(raw, 1, duration=1)
assert len(events) == 136
events_ol = make_fixed_length_events(raw, 1, duration=1, overlap=0.5)
assert len(events_ol) == 271
events_ol_2 = make_fixed_length_events(raw, 1, duration=1, overlap=0.9)
assert len(events_ol_2) == 1355
assert_array_equal(events_ol_2[:, 0], np.unique(events_ol_2[:, 0]))
with pytest.raises(ValueError, match='overlap must be'):
make_fixed_length_events(raw, 1, duration=1, overlap=1.1)
def test_make_fixed_length_events():
"""Test making events of a fixed length."""
raw = read_raw_fif(raw_fname)
events = make_fixed_length_events(raw, id=1)
assert events.shape[1] == 3
events_zero = make_fixed_length_events(raw, 1, first_samp=False)
assert_equal(events_zero[0, 0], 0)
assert_array_equal(events_zero[:, 0], events[:, 0] - raw.first_samp)
# With limits
tmin, tmax = raw.times[[0, -1]]
duration = tmax - tmin
events = make_fixed_length_events(raw, 1, tmin, tmax, duration)
assert_equal(events.shape[0], 1)
# With bad limits (no resulting events)
pytest.raises(ValueError, make_fixed_length_events, raw, 1, tmin,
tmax - 1e-3, duration)
# not raw, bad id or duration
pytest.raises(TypeError, make_fixed_length_events, raw, 2.3)
pytest.raises(TypeError, make_fixed_length_events, 'not raw', 2)
pytest.raises(TypeError, make_fixed_length_events, raw, 23, tmin, tmax,
'abc')
# Let's try some ugly sample rate/sample count combos
data = np.random.RandomState(0).randn(1, 27768)
# This breaks unless np.round() is used in make_fixed_length_events
info = create_info(1, 155.4499969482422)
raw = RawArray(data, info)
events = make_fixed_length_events(raw, 1, duration=raw.times[-1])
assert events[0, 0] == 0
assert len(events) == 1
# Without use_rounding=True this breaks
raw = RawArray(data[:, :21216], info)
events = make_fixed_length_events(raw, 1, duration=raw.times[-1])
assert events[0, 0] == 0
assert len(events) == 1
# Make sure it gets used properly by compute_raw_covariance
cov = compute_raw_covariance(raw, tstep=None)
expected = np.cov(data[:, :21216])
np.testing.assert_allclose(cov['data'], expected, atol=1e-12)
# overlaps
events = make_fixed_length_events(raw, 1, duration=1)
assert len(events) == 136
events_ol = make_fixed_length_events(raw, 1, duration=1, overlap=0.5)
assert len(events_ol) == 271
events_ol_2 = make_fixed_length_events(raw, 1, duration=1, overlap=0.9)
assert len(events_ol_2) == 1355
assert_array_equal(events_ol_2[:, 0], np.unique(events_ol_2[:, 0]))
with pytest.raises(ValueError, match='overlap must be'):
make_fixed_length_events(raw, 1, duration=1, overlap=1.1)
def test_cov_estimation_on_raw_reg():
"""Test estimation from raw with regularization."""
raw = read_raw_fif(raw_fname, preload=True)
raw.info['sfreq'] /= 10.
raw = RawArray(raw._data[:, ::10].copy(), raw.info) # decimate for speed
cov_mne = read_cov(erm_cov_fname)
with warnings.catch_warnings(record=True): # too few samples
warnings.simplefilter('always')
# XXX don't use "shrunk" here, for some reason it makes Travis 2.7
# hang... "diagonal_fixed" is much faster. Use long epochs for speed.
cov = compute_raw_covariance(raw, tstep=5., method='diagonal_fixed')
assert_snr(cov.data, cov_mne.data, 5)
def test_cov_estimation_on_raw(method, tmpdir):
"""Test estimation from raw (typically empty room)."""
tempdir = str(tmpdir)
raw = read_raw_fif(raw_fname, preload=True)
cov_mne = read_cov(erm_cov_fname)
# The pure-string uses the more efficient numpy-based method, the
# the list gets triaged to compute_covariance (should be equivalent
# but use more memory)
with pytest.warns(None): # can warn about EEG ref
cov = compute_raw_covariance(raw,
tstep=None,
method=method,
rank='full')
assert_equal(cov.ch_names, cov_mne.ch_names)
assert_equal(cov.nfree, cov_mne.nfree)
assert_snr(cov.data, cov_mne.data, 1e4)
# tstep=0.2 (default)
with pytest.warns(None): # can warn about EEG ref
cov = compute_raw_covariance(raw, method=method, rank='full')
assert_equal(cov.nfree, cov_mne.nfree - 119) # cutoff some samples
assert_snr(cov.data, cov_mne.data, 1e2)
# test IO when computation done in Python
cov.save(op.join(tempdir, 'test-cov.fif')) # test saving
cov_read = read_cov(op.join(tempdir, 'test-cov.fif'))
assert cov_read.ch_names == cov.ch_names
assert cov_read.nfree == cov.nfree
assert_array_almost_equal(cov.data, cov_read.data)
# test with a subset of channels
raw_pick = raw.copy().pick_channels(raw.ch_names[:5])
raw_pick.info.normalize_proj()
cov = compute_raw_covariance(raw_pick,
tstep=None,
method=method,
rank='full')
assert cov_mne.ch_names[:5] == cov.ch_names
assert_snr(cov.data, cov_mne.data[:5, :5], 1e4)
cov = compute_raw_covariance(raw_pick, method=method, rank='full')
assert_snr(cov.data, cov_mne.data[:5, :5], 90) # cutoff samps
# make sure we get a warning with too short a segment
raw_2 = read_raw_fif(raw_fname).crop(0, 1)
with pytest.warns(RuntimeWarning, match='Too few samples'):
cov = compute_raw_covariance(raw_2, method=method)
# no epochs found due to rejection
pytest.raises(ValueError,
compute_raw_covariance,
raw,
tstep=None,
method='empirical',
reject=dict(eog=200e-6))
# but this should work
cov = compute_raw_covariance(raw.copy().crop(0, 10.),
tstep=None,
method=method,
reject=dict(eog=1000e-6),
verbose='error')
def test_bad_proj():
"""Test dealing with bad projection application."""
raw = read_raw_fif(raw_fname, preload=True)
events = read_events(event_fname)
picks = pick_types(raw.info,
meg=True,
stim=False,
ecg=False,
eog=False,
exclude='bads')
picks = picks[2:9:3]
_check_warnings(raw, events, picks)
# still bad
raw.pick_channels([raw.ch_names[ii] for ii in picks])
_check_warnings(raw, events)
# "fixed"
raw.info.normalize_proj() # avoid projection warnings
_check_warnings(raw, events, count=0)
# eeg avg ref is okay
raw = read_raw_fif(raw_fname, preload=True).pick_types(meg=False, eeg=True)
raw.set_eeg_reference(projection=True)
_check_warnings(raw, events, count=0)
raw.info['bads'] = raw.ch_names[:10]
_check_warnings(raw, events, count=0)
raw = read_raw_fif(raw_fname)
pytest.raises(ValueError, raw.del_proj, 'foo')
n_proj = len(raw.info['projs'])
raw.del_proj(0)
assert_equal(len(raw.info['projs']), n_proj - 1)
raw.del_proj()
assert_equal(len(raw.info['projs']), 0)
# Ensure we deal with newer-style Neuromag projs properly, were getting:
#
# Projection vector "PCA-v2" has magnitude 1.00 (should be unity),
# applying projector with 101/306 of the original channels available
# may be dangerous.
raw = read_raw_fif(raw_fname).crop(0, 1)
raw.info['bads'] = ['MEG 0111']
meg_picks = mne.pick_types(raw.info, meg=True, exclude=())
ch_names = [raw.ch_names[pick] for pick in meg_picks]
for p in raw.info['projs'][:-1]:
data = np.zeros((1, len(ch_names)))
idx = [ch_names.index(ch_name) for ch_name in p['data']['col_names']]
data[:, idx] = p['data']['data']
p['data'].update(ncol=len(meg_picks), col_names=ch_names, data=data)
with warnings.catch_warnings(record=True) as w:
mne.cov.regularize(mne.compute_raw_covariance(raw, verbose='error'),
raw.info)
assert_equal(len(w), 0)
def _compute_cov(subject):
fname = subject + '_EC.set'
raw = mne.io.read_raw_eeglab(op.join(out_path, fname))
raw.annotations.duration[raw.annotations.description == 'boundary'] = 0.0
raw.annotations.description[raw.annotations.description ==
'boundary'] = "edge"
raw = _interpolate_missing(raw, ref_info)
for fmin, fmax, band in freqs:
raw_f = raw.copy().filter(fmin, fmax)
cov_f = mne.compute_raw_covariance(raw_f, method="oas")
cov_f.save(f"./derivatives/{subject}-{band}-cov.fif")
def createInv(subj):
# subjdir = os.environ['SUBJECTS_DIR']
file_path = '/m/nbe/scratch/restmeg/data/camcan/cc700/mri/pipeline/release004/BIDSsep/megraw/sub-' + subj + '/meg/'
raw = mne.io.fiff.Raw(file_path + 'rest_raw.fif')
fname_trans = file_path + 'rest_raw-trans.fif'
src = mne.read_source_spaces(
'/m/nbe/scratch/restmeg/data/camcan/subjects/' + subj + '/bem/' +
subj + '-oct-6-src.fif')
bem_sol = mne.read_bem_solution(subj + '-5120-5120-5120-bem-sol.fif')
fwd = mne.make_forward_solution(raw.info, fname_trans, src, bem_sol)
cov = mne.compute_raw_covariance(raw)
inv = mne.minimum_norm.make_inverse_operator(raw.info, fwd, cov, loose=0.2)
mne.minimum_norm.write_inverse_operator(subj + '-inv.fif', inv)
def test_explicit_bads_pick():
"""Test when bads channels are explicitly passed + default picks=None."""
raw = read_raw_fif(raw_fname, preload=True)
raw.pick_types(eeg=True, meg=True, ref_meg=True)
# Covariance
# Default picks=None
raw.info['bads'] = list()
noise_cov_1 = compute_raw_covariance(raw, picks=None)
rank = compute_rank(noise_cov_1, info=raw.info)
assert rank == dict(meg=303, eeg=60)
assert raw.info['bads'] == []
raw.info['bads'] = ['EEG 002', 'EEG 012', 'EEG 015', 'MEG 0122']
noise_cov = compute_raw_covariance(raw, picks=None)
rank = compute_rank(noise_cov, info=raw.info)
assert rank == dict(meg=302, eeg=57)
assert raw.info['bads'] == ['EEG 002', 'EEG 012', 'EEG 015', 'MEG 0122']
# Explicit picks
picks = pick_types(raw.info, meg=True, eeg=True, exclude=[])
noise_cov_2 = compute_raw_covariance(raw, picks=picks)
rank = compute_rank(noise_cov_2, info=raw.info)
assert rank == dict(meg=303, eeg=60)
assert raw.info['bads'] == ['EEG 002', 'EEG 012', 'EEG 015', 'MEG 0122']
assert_array_equal(noise_cov_1['data'], noise_cov_2['data'])
assert noise_cov_1['names'] == noise_cov_2['names']
# Raw
raw.info['bads'] = list()
rank = compute_rank(raw)
assert rank == dict(meg=303, eeg=60)
raw.info['bads'] = ['EEG 002', 'EEG 012', 'EEG 015', 'MEG 0122']
rank = compute_rank(raw)
assert rank == dict(meg=302, eeg=57)
def test_cov_estimation_on_raw():
"""Test estimation from raw (typically empty room)"""
tempdir = _TempDir()
raw = Raw(raw_fname, preload=True)
cov_mne = read_cov(erm_cov_fname)
cov = compute_raw_covariance(raw, tstep=None)
assert_equal(cov.ch_names, cov_mne.ch_names)
assert_equal(cov.nfree, cov_mne.nfree)
assert_snr(cov.data, cov_mne.data, 1e4)
cov = compute_raw_covariance(raw) # tstep=0.2 (default)
assert_equal(cov.nfree, cov_mne.nfree - 119) # cutoff some samples
assert_snr(cov.data, cov_mne.data, 1e2)
# test IO when computation done in Python
cov.save(op.join(tempdir, 'test-cov.fif')) # test saving
cov_read = read_cov(op.join(tempdir, 'test-cov.fif'))
assert_true(cov_read.ch_names == cov.ch_names)
assert_true(cov_read.nfree == cov.nfree)
assert_array_almost_equal(cov.data, cov_read.data)
# test with a subset of channels
picks = pick_channels(raw.ch_names, include=raw.ch_names[:5])
raw.pick_channels([raw.ch_names[pick] for pick in picks])
raw.info.normalize_proj()
cov = compute_raw_covariance(raw, picks=picks, tstep=None)
assert_true(cov_mne.ch_names[:5] == cov.ch_names)
assert_snr(cov.data, cov_mne.data[picks][:, picks], 1e4)
cov = compute_raw_covariance(raw, picks=picks)
assert_snr(cov.data, cov_mne.data[picks][:, picks], 90) # cutoff samps
# make sure we get a warning with too short a segment
raw_2 = Raw(raw_fname).crop(0, 1)
with warnings.catch_warnings(record=True) as w:
warnings.simplefilter('always')
cov = compute_raw_covariance(raw_2)
assert_true(any('Too few samples' in str(ww.message) for ww in w))
def spatial_filter(raw, epochs):
print('spatial filtering using xDawn')
picks = pick_types(raw.info,
meg=False,
eeg=True,
stim=False,
eog=False,
exclude='bads')
signal_cov = compute_raw_covariance(raw, picks=picks)
xd = Xdawn(n_components=2, signal_cov=signal_cov)
print('fiting xDawn')
xd.fit(epochs)
print('epoch denoising started')
epochs_denoised = xd.apply(epochs)
print('epoch_denoise complete')
return epochs_denoised
def test_bad_proj():
"""Test dealing with bad projection application."""
raw = read_raw_fif(raw_fname, preload=True)
events = read_events(event_fname)
picks = pick_types(raw.info, meg=True, stim=False, ecg=False,
eog=False, exclude='bads')
picks = picks[2:9:3]
_check_warnings(raw, events, picks)
# still bad
raw.pick_channels([raw.ch_names[ii] for ii in picks])
_check_warnings(raw, events)
# "fixed"
raw.info.normalize_proj() # avoid projection warnings
_check_warnings(raw, events, count=0)
# eeg avg ref is okay
raw = read_raw_fif(raw_fname, preload=True).pick_types(meg=False, eeg=True)
raw.set_eeg_reference()
_check_warnings(raw, events, count=0)
raw.info['bads'] = raw.ch_names[:10]
_check_warnings(raw, events, count=0)
raw = read_raw_fif(raw_fname)
assert_raises(ValueError, raw.del_proj, 'foo')
n_proj = len(raw.info['projs'])
raw.del_proj(0)
assert_equal(len(raw.info['projs']), n_proj - 1)
raw.del_proj()
assert_equal(len(raw.info['projs']), 0)
# Ensure we deal with newer-style Neuromag projs properly, were getting:
#
# Projection vector "PCA-v2" has magnitude 1.00 (should be unity),
# applying projector with 101/306 of the original channels available
# may be dangerous.
raw = read_raw_fif(raw_fname).crop(0, 1)
raw.info['bads'] = ['MEG 0111']
meg_picks = mne.pick_types(raw.info, meg=True, exclude=())
ch_names = [raw.ch_names[pick] for pick in meg_picks]
for p in raw.info['projs'][:-1]:
data = np.zeros((1, len(ch_names)))
idx = [ch_names.index(ch_name) for ch_name in p['data']['col_names']]
data[:, idx] = p['data']['data']
p['data'].update(ncol=len(meg_picks), col_names=ch_names, data=data)
with warnings.catch_warnings(record=True) as w:
mne.cov.regularize(mne.compute_raw_covariance(raw, verbose='error'),
raw.info)
assert_equal(len(w), 0)
def test_xdawn_fit():
"""Test Xdawn fit."""
# Get data
raw, events, picks = _get_data()
epochs = Epochs(raw, events, event_id, tmin, tmax, picks=picks,
preload=True, baseline=None, verbose=False,
add_eeg_ref=False)
# =========== Basic Fit test =================
# Test base xdawn
xd = Xdawn(n_components=2, correct_overlap='auto')
xd.fit(epochs)
# With these parameters, the overlap correction must be False
assert_equal(xd.correct_overlap_, False)
# No overlap correction should give averaged evoked
evoked = epochs['cond2'].average()
assert_array_equal(evoked.data, xd.evokeds_['cond2'].data)
# ========== with signal cov provided ====================
# Provide covariance object
signal_cov = compute_raw_covariance(raw, picks=picks)
xd = Xdawn(n_components=2, correct_overlap=False,
signal_cov=signal_cov)
xd.fit(epochs)
# Provide ndarray
signal_cov = np.eye(len(picks))
xd = Xdawn(n_components=2, correct_overlap=False,
signal_cov=signal_cov)
xd.fit(epochs)
# Provide ndarray of bad shape
signal_cov = np.eye(len(picks) - 1)
xd = Xdawn(n_components=2, correct_overlap=False,
signal_cov=signal_cov)
assert_raises(ValueError, xd.fit, epochs)
# Provide another type
signal_cov = 42
xd = Xdawn(n_components=2, correct_overlap=False,
signal_cov=signal_cov)
assert_raises(ValueError, xd.fit, epochs)
# Fit with baseline correction and overlap correction should throw an
# error
# XXX This is a buggy test, the epochs here don't overlap
epochs = Epochs(raw, events, event_id, tmin, tmax, picks=picks,
preload=True, baseline=(None, 0), verbose=False,
add_eeg_ref=False)
xd = Xdawn(n_components=2, correct_overlap=True)
assert_raises(ValueError, xd.fit, epochs)
def test_xdawn_fit():
"""Test Xdawn fit."""
# get data
raw, events, picks = _get_data()
epochs = Epochs(raw, events, event_id, tmin, tmax, picks=picks,
preload=True, baseline=None, verbose=False)
# =========== Basic Fit test =================
# test base xdawn
xd = Xdawn(n_components=2, correct_overlap='auto',
signal_cov=None, reg=None)
xd.fit(epochs)
# with this parameters, the overlapp correction must be False
assert_equal(xd.correct_overlap, False)
# no overlapp correction should give averaged evoked
evoked = epochs['cond2'].average()
assert_array_equal(evoked.data, xd.evokeds_['cond2'].data)
# ========== with signal cov provided ====================
# provide covariance object
signal_cov = compute_raw_covariance(raw, picks=picks)
xd = Xdawn(n_components=2, correct_overlap=False,
signal_cov=signal_cov, reg=None)
xd.fit(epochs)
# provide ndarray
signal_cov = np.eye(len(picks))
xd = Xdawn(n_components=2, correct_overlap=False,
signal_cov=signal_cov, reg=None)
xd.fit(epochs)
# provide ndarray of bad shape
signal_cov = np.eye(len(picks) - 1)
xd = Xdawn(n_components=2, correct_overlap=False,
signal_cov=signal_cov, reg=None)
assert_raises(ValueError, xd.fit, epochs)
# provide another type
signal_cov = 42
xd = Xdawn(n_components=2, correct_overlap=False,
signal_cov=signal_cov, reg=None)
assert_raises(ValueError, xd.fit, epochs)
# fit with baseline correction and ovverlapp correction should throw an
# error
epochs = Epochs(raw, events, event_id, tmin, tmax, picks=picks,
preload=True, baseline=(None, 0), verbose=False)
xd = Xdawn(n_components=2, correct_overlap=True)
assert_raises(ValueError, xd.fit, epochs)
def compute_noise_cov(cov_fname, raw):
"""Compute noise covariance data from a continuous segment of raw data.
Employ empty room data (collected without the subject) to calculate
the full noise covariance matrix. This is recommended for analyzing ongoing
spontaneous activity.
Parameters
----------
cov_fname : str
noise covariance file name
raw : Raw
the raw data
Returns
-------
cov_fname : str
noise covariance file name in which is saved the noise covariance
matrix
"""
import os.path as op
from mne import compute_raw_covariance, pick_types, write_cov
from nipype.utils.filemanip import split_filename as split_f
from ephypype.preproc import create_reject_dict
print(('***** COMPUTE RAW COV *****' + cov_fname))
if not op.isfile(cov_fname):
data_path, basename, ext = split_f(raw.info['filename'])
fname = op.join(data_path, '%s-cov.fif' % basename)
reject = create_reject_dict(raw.info)
picks = pick_types(raw.info, meg=True, ref_meg=False, exclude='bads')
noise_cov = compute_raw_covariance(raw, picks=picks, reject=reject)
write_cov(fname, noise_cov)
else:
print(('*** NOISE cov file %s exists!!!' % cov_fname))
return cov_fname
def compute_noise_cov(fname_template, raw_filename):
"""
Compute noise covariance data from a continuous segment of raw data.
Employ empty room data (collected without the subject) to calculate
the full noise covariance matrix.
This is recommended for analyzing ongoing spontaneous activity.
Inputs
cov_fname : str
noise covariance file name template
raw_filename : str
raw filename
Output
cov_fname : str
noise covariance file name in which is saved the noise covariance
matrix
"""
# Check if cov matrix exists
cov_fname = _get_cov_fname(fname_template)
if not op.isfile(cov_fname):
er_raw, cov_fname = _get_er_data(fname_template)
if not op.isfile(cov_fname) and er_raw:
reject = _create_reject_dict(er_raw.info)
picks = pick_types(er_raw.info,
meg=True,
ref_meg=False,
exclude='bads')
noise_cov = compute_raw_covariance(er_raw,
picks=picks,
reject=reject)
write_cov(cov_fname, noise_cov)
elif op.isfile(cov_fname):
print(('*** NOISE cov file {} exists!!!'.format(cov_fname)))
elif not er_raw:
cov_fname = compute_cov_identity(raw_filename)
else:
print(('*** NOISE cov file {} exists!!!'.format(cov_fname)))
return cov_fname
def test_cov_estimation_on_raw():
"""Test estimation from raw (typically empty room)."""
tempdir = _TempDir()
raw = read_raw_fif(raw_fname, preload=True)
cov_mne = read_cov(erm_cov_fname)
# The pure-string uses the more efficient numpy-based method, the
# the list gets triaged to compute_covariance (should be equivalent
# but use more memory)
for method in (None, ['empirical']): # None is cast to 'empirical'
cov = compute_raw_covariance(raw, tstep=None, method=method)
assert_equal(cov.ch_names, cov_mne.ch_names)
assert_equal(cov.nfree, cov_mne.nfree)
assert_snr(cov.data, cov_mne.data, 1e4)
cov = compute_raw_covariance(raw, method=method) # tstep=0.2 (default)
assert_equal(cov.nfree, cov_mne.nfree - 119) # cutoff some samples
assert_snr(cov.data, cov_mne.data, 1e2)
# test IO when computation done in Python
cov.save(op.join(tempdir, 'test-cov.fif')) # test saving
cov_read = read_cov(op.join(tempdir, 'test-cov.fif'))
assert_true(cov_read.ch_names == cov.ch_names)
assert_true(cov_read.nfree == cov.nfree)
assert_array_almost_equal(cov.data, cov_read.data)
# test with a subset of channels
raw_pick = raw.copy().pick_channels(raw.ch_names[:5])
raw_pick.info.normalize_proj()
cov = compute_raw_covariance(raw_pick, tstep=None, method=method)
assert_true(cov_mne.ch_names[:5] == cov.ch_names)
assert_snr(cov.data, cov_mne.data[:5, :5], 1e4)
cov = compute_raw_covariance(raw_pick, method=method)
assert_snr(cov.data, cov_mne.data[:5, :5], 90) # cutoff samps
# make sure we get a warning with too short a segment
raw_2 = read_raw_fif(raw_fname).crop(0, 1)
with warnings.catch_warnings(record=True) as w:
warnings.simplefilter('always')
cov = compute_raw_covariance(raw_2, method=method)
assert_true(any('Too few samples' in str(ww.message) for ww in w))
# no epochs found due to rejection
assert_raises(ValueError,
compute_raw_covariance,
raw,
tstep=None,
method='empirical',
reject=dict(eog=200e-6))
# but this should work
cov = compute_raw_covariance(raw.copy().crop(0, 10.),
tstep=None,
method=method,
reject=dict(eog=1000e-6))
def test_cov_estimation_on_raw(method, tmpdir):
"""Test estimation from raw (typically empty room)."""
tempdir = str(tmpdir)
raw = read_raw_fif(raw_fname, preload=True)
cov_mne = read_cov(erm_cov_fname)
# The pure-string uses the more efficient numpy-based method, the
# the list gets triaged to compute_covariance (should be equivalent
# but use more memory)
with pytest.warns(None): # can warn about EEG ref
cov = compute_raw_covariance(raw, tstep=None, method=method,
rank='full')
assert_equal(cov.ch_names, cov_mne.ch_names)
assert_equal(cov.nfree, cov_mne.nfree)
assert_snr(cov.data, cov_mne.data, 1e4)
# tstep=0.2 (default)
with pytest.warns(None): # can warn about EEG ref
cov = compute_raw_covariance(raw, method=method, rank='full')
assert_equal(cov.nfree, cov_mne.nfree - 119) # cutoff some samples
assert_snr(cov.data, cov_mne.data, 1e2)
# test IO when computation done in Python
cov.save(op.join(tempdir, 'test-cov.fif')) # test saving
cov_read = read_cov(op.join(tempdir, 'test-cov.fif'))
assert cov_read.ch_names == cov.ch_names
assert cov_read.nfree == cov.nfree
assert_array_almost_equal(cov.data, cov_read.data)
# test with a subset of channels
raw_pick = raw.copy().pick_channels(raw.ch_names[:5])
raw_pick.info.normalize_proj()
cov = compute_raw_covariance(raw_pick, tstep=None, method=method,
rank='full')
assert cov_mne.ch_names[:5] == cov.ch_names
assert_snr(cov.data, cov_mne.data[:5, :5], 1e4)
cov = compute_raw_covariance(raw_pick, method=method, rank='full')
assert_snr(cov.data, cov_mne.data[:5, :5], 90) # cutoff samps
# make sure we get a warning with too short a segment
raw_2 = read_raw_fif(raw_fname).crop(0, 1)
with pytest.warns(RuntimeWarning, match='Too few samples'):
cov = compute_raw_covariance(raw_2, method=method)
# no epochs found due to rejection
pytest.raises(ValueError, compute_raw_covariance, raw, tstep=None,
method='empirical', reject=dict(eog=200e-6))
# but this should work
cov = compute_raw_covariance(raw.copy().crop(0, 10.),
tstep=None, method=method,
reject=dict(eog=1000e-6),
verbose='error')
def test_xdawntransformer_fit():
"""Test Xdawn fit."""
# get data
raw, events, picks = _get_data()
epochs = Epochs(raw, events, event_id, tmin, tmax, picks=picks,
preload=True, baseline=None, verbose=False)
X = epochs._data
y = epochs.events[:, -1]
# =========== Basic Fit test =================
# test base xdawn
xd = XdawnTransformer()
xd.fit(X, y)
# ========== with signal cov provided ====================
# provide covariance object
signal_cov = compute_raw_covariance(raw, picks=picks)
xd = XdawnTransformer(signal_cov=signal_cov)
xd.fit(X, y)
# provide ndarray
signal_cov = np.eye(len(picks))
xd = XdawnTransformer(signal_cov=signal_cov)
xd.fit(X, y)
# provide ndarray of bad shape
signal_cov = np.eye(len(picks) - 1)
xd = XdawnTransformer(signal_cov=signal_cov)
assert_raises(ValueError, xd.fit, X, y)
# provide another type
signal_cov = 42
xd = XdawnTransformer(signal_cov=signal_cov)
assert_raises(ValueError, xd.fit, X, y)
# fit with y as None results in error
xd = XdawnTransformer()
assert_raises(ValueError, xd.fit, X, None)
# compare xdawn and XdawnTransformer
xd = Xdawn()
xd.fit(epochs)
xdt = XdawnTransformer()
xdt.fit(X, y)
assert_array_equal(xdt.filters_['cond2'], xd.filters_['cond2'])
def get_epochs_and_cov(raw_data, picks, window=500):
events = list()
events_id = dict()
for j, eid in enumerate(getEventNames()):
tmp = find_events(raw_data, stim_channel=eid, verbose=False)
tmp[:, -1] = j + 1
events.append(tmp)
events_id[eid] = j + 1
events = np.concatenate(events, axis=0)
order_ev = np.argsort(events[:, 0])
events = events[order_ev]
epochs = Epochs(raw_data, events, events_id,
tmin=-(window / 500.0) + 1 / 500.0 + 0.150,
tmax=0.150, proj=False, picks=picks, baseline=None,
preload=True, add_eeg_ref=False, verbose=False)
cov_signal = compute_raw_covariance(raw_data, verbose=False)
return epochs, cov_signal
def get_epochs(raw, events, event_id):
event_id_ = dict(normal=event_id)
tmin = -0.3
tmax = 0.8
picks = mne.pick_types(raw.info,
meg=False,
eeg=True,
eog=True,
exclude='bads')
baseline = (tmin, 0) # means from the first instant to t = 0
epochs = mne.Epochs(raw,
events,
event_id_,
tmin,
tmax,
proj=True,
picks=picks,
baseline=baseline,
preload=True)
epochs.decimate(9)
tmax = (events[0, 0] - 10000) / raw.info['sfreq']
return epochs, mne.compute_raw_covariance(raw,
tmin=0,
tmax=tmax,
tstep=1,
reject=None,
flat=None,
picks=picks,
method='shrunk',
method_params=None,
cv=3,
scalings=None,
n_jobs=1,
return_estimators=False,
reject_by_annotation=True,
rank=None,
verbose=None)
def test_apply_inverse_cov(method, pick_ori):
"""Test MNE with precomputed inverse operator on cov."""
raw = read_raw_fif(fname_raw, preload=True)
# use 10 sec of data
raw.crop(0, 10)
raw.filter(1, None)
label_lh = read_label(fname_label % 'Aud-lh')
# test with a free ori inverse
inverse_operator = read_inverse_operator(fname_inv)
data_cov = compute_raw_covariance(raw, tstep=None)
with pytest.raises(ValueError, match='has not been prepared'):
apply_inverse_cov(data_cov, raw.info, inverse_operator,
lambda2=lambda2, prepared=True)
this_inv_op = prepare_inverse_operator(inverse_operator, nave=1,
lambda2=lambda2, method=method)
raw_ori = 'normal' if pick_ori == 'normal' else 'vector'
stc_raw = apply_inverse_raw(
raw, this_inv_op, lambda2, method, label=label_lh, nave=1,
pick_ori=raw_ori, prepared=True)
stc_cov = apply_inverse_cov(
data_cov, raw.info, this_inv_op, method=method, pick_ori=pick_ori,
label=label_lh, prepared=True, lambda2=lambda2)
n_sources = np.prod(stc_cov.data.shape[:-1])
raw_data = stc_raw.data.reshape(n_sources, -1)
exp_res = np.diag(np.cov(raw_data, ddof=1)).copy()
exp_res *= 1 if raw_ori == pick_ori else 3.
# There seems to be some precision penalty when combining orientations,
# but it's probably acceptable
rtol = 5e-4 if pick_ori is None else 1e-12
assert_allclose(exp_res, stc_cov.data.ravel(), rtol=rtol)
with pytest.raises(ValueError, match='Invalid value'):
apply_inverse_cov(
data_cov, raw.info, this_inv_op, method=method, pick_ori='vector')
def test_cov_estimation_on_raw():
"""Test estimation from raw (typically empty room)."""
tempdir = _TempDir()
raw = read_raw_fif(raw_fname, preload=True)
cov_mne = read_cov(erm_cov_fname)
# The pure-string uses the more efficient numpy-based method, the
# the list gets triaged to compute_covariance (should be equivalent
# but use more memory)
for method in (None, ['empirical']): # None is cast to 'empirical'
cov = compute_raw_covariance(raw, tstep=None, method=method)
assert_equal(cov.ch_names, cov_mne.ch_names)
assert_equal(cov.nfree, cov_mne.nfree)
assert_snr(cov.data, cov_mne.data, 1e4)
cov = compute_raw_covariance(raw, method=method) # tstep=0.2 (default)
assert_equal(cov.nfree, cov_mne.nfree - 119) # cutoff some samples
assert_snr(cov.data, cov_mne.data, 1e2)
# test IO when computation done in Python
cov.save(op.join(tempdir, 'test-cov.fif')) # test saving
cov_read = read_cov(op.join(tempdir, 'test-cov.fif'))
assert_true(cov_read.ch_names == cov.ch_names)
assert_true(cov_read.nfree == cov.nfree)
assert_array_almost_equal(cov.data, cov_read.data)
# test with a subset of channels
raw_pick = raw.copy().pick_channels(raw.ch_names[:5])
raw_pick.info.normalize_proj()
cov = compute_raw_covariance(raw_pick, tstep=None, method=method)
assert_true(cov_mne.ch_names[:5] == cov.ch_names)
assert_snr(cov.data, cov_mne.data[:5, :5], 1e4)
cov = compute_raw_covariance(raw_pick, method=method)
assert_snr(cov.data, cov_mne.data[:5, :5], 90) # cutoff samps
# make sure we get a warning with too short a segment
raw_2 = read_raw_fif(raw_fname).crop(0, 1)
with warnings.catch_warnings(record=True) as w:
warnings.simplefilter('always')
cov = compute_raw_covariance(raw_2, method=method)
assert_true(any('Too few samples' in str(ww.message) for ww in w))
# no epochs found due to rejection
assert_raises(ValueError, compute_raw_covariance, raw, tstep=None,
method='empirical', reject=dict(eog=200e-6))
# but this should work
cov = compute_raw_covariance(raw.copy().crop(0, 10.),
tstep=None, method=method,
reject=dict(eog=1000e-6))
def test_lcmv_raw():
"""Test LCMV with raw data."""
raw, _, _, _, noise_cov, label, forward, _, _, _ =\
_get_data(all_forward=False, epochs=False, data_cov=False)
tmin, tmax = 0, 20
start, stop = raw.time_as_index([tmin, tmax])
# use only the left-temporal MEG channels for LCMV
data_cov = mne.compute_raw_covariance(raw, tmin=tmin, tmax=tmax)
stc = lcmv_raw(raw, forward, noise_cov, data_cov, reg=0.01,
label=label, start=start, stop=stop,
max_ori_out='signed')
assert_array_almost_equal(np.array([tmin, tmax]),
np.array([stc.times[0], stc.times[-1]]),
decimal=2)
# make sure we get an stc with vertices only in the lh
vertno = [forward['src'][0]['vertno'], forward['src'][1]['vertno']]
assert_true(len(stc.vertices[0]) == len(np.intersect1d(vertno[0],
label.vertices)))
assert_true(len(stc.vertices[1]) == 0)
# field is called "MNE_LOGGING_LEVEL".
mne.set_config('MNE_LOGGING_LEVEL', 'INFO')
print(mne.get_config(key='MNE_LOGGING_LEVEL'))
###############################################################################
# The default value is now set to INFO. This level will now be used by default
# every time we call a function in MNE. We can set the global logging level for
# only this session by calling :func:`mne.set_log_level` function.
mne.set_log_level('WARNING')
print(mne.get_config(key='MNE_LOGGING_LEVEL'))
###############################################################################
# Notice how the value in the config file was not changed. Logging level of
# WARNING only applies for this session. Let's see what logging level of
# WARNING prints for :func:`mne.compute_raw_covariance`.
cov_raw = mne.compute_raw_covariance(raw)
###############################################################################
# Nothing. This means that no warnings were emitted during the computation. If
# you look at the documentation of :func:`mne.compute_raw_covariance`, you
# notice the ``verbose`` keyword. Setting this parameter does not touch the
# configurations, but sets the logging level for just this one function call.
# Let's see what happens with logging level of INFO.
cov = mne.compute_raw_covariance(raw, verbose=True)
###############################################################################
# As you see there is some info about what the function is doing. The logging
# level can be set to 'DEBUG', 'INFO', 'WARNING', 'ERROR' or 'CRITICAL'. It can
# also be set to an integer or a boolean value. The correspondence to string
# values can be seen in the table below. ``verbose=None`` uses the default
# value from the configuration file.
def test_rank():
"""Test cov rank estimation."""
# Test that our rank estimation works properly on a simple case
evoked = read_evokeds(ave_fname, condition=0, baseline=(None, 0),
proj=False)
cov = read_cov(cov_fname)
ch_names = [ch for ch in evoked.info['ch_names'] if '053' not in ch and
ch.startswith('EEG')]
cov = prepare_noise_cov(cov, evoked.info, ch_names, None)
assert_equal(cov['eig'][0], 0.) # avg projector should set this to zero
assert_true((cov['eig'][1:] > 0).all()) # all else should be > 0
# Now do some more comprehensive tests
raw_sample = read_raw_fif(raw_fname)
raw_sss = read_raw_fif(hp_fif_fname)
raw_sss.add_proj(compute_proj_raw(raw_sss))
cov_sample = compute_raw_covariance(raw_sample)
cov_sample_proj = compute_raw_covariance(
raw_sample.copy().apply_proj())
cov_sss = compute_raw_covariance(raw_sss)
cov_sss_proj = compute_raw_covariance(
raw_sss.copy().apply_proj())
picks_all_sample = pick_types(raw_sample.info, meg=True, eeg=True)
picks_all_sss = pick_types(raw_sss.info, meg=True, eeg=True)
info_sample = pick_info(raw_sample.info, picks_all_sample)
picks_stack_sample = [('eeg', pick_types(info_sample, meg=False,
eeg=True))]
picks_stack_sample += [('meg', pick_types(info_sample, meg=True))]
picks_stack_sample += [('all',
pick_types(info_sample, meg=True, eeg=True))]
info_sss = pick_info(raw_sss.info, picks_all_sss)
picks_stack_somato = [('eeg', pick_types(info_sss, meg=False, eeg=True))]
picks_stack_somato += [('meg', pick_types(info_sss, meg=True))]
picks_stack_somato += [('all',
pick_types(info_sss, meg=True, eeg=True))]
iter_tests = list(itt.product(
[(cov_sample, picks_stack_sample, info_sample),
(cov_sample_proj, picks_stack_sample, info_sample),
(cov_sss, picks_stack_somato, info_sss),
(cov_sss_proj, picks_stack_somato, info_sss)], # sss
[dict(mag=1e15, grad=1e13, eeg=1e6)]
))
for (cov, picks_list, this_info), scalings in iter_tests:
for ch_type, picks in picks_list:
this_very_info = pick_info(this_info, picks)
# compute subset of projs
this_projs = [c['active'] and
len(set(c['data']['col_names'])
.intersection(set(this_very_info['ch_names']))) >
0 for c in cov['projs']]
n_projs = sum(this_projs)
# count channel types
ch_types = [channel_type(this_very_info, idx)
for idx in range(len(picks))]
n_eeg, n_mag, n_grad = [ch_types.count(k) for k in
['eeg', 'mag', 'grad']]
n_meg = n_mag + n_grad
if ch_type in ('all', 'eeg'):
n_projs_eeg = 1
else:
n_projs_eeg = 0
# check sss
if len(this_very_info['proc_history']) > 0:
mf = this_very_info['proc_history'][0]['max_info']
n_free = _get_sss_rank(mf)
if 'mag' not in ch_types and 'grad' not in ch_types:
n_free = 0
# - n_projs XXX clarify
expected_rank = n_free + n_eeg
if n_projs > 0 and ch_type in ('all', 'eeg'):
expected_rank -= n_projs_eeg
else:
expected_rank = n_meg + n_eeg - n_projs
C = cov['data'][np.ix_(picks, picks)]
est_rank = _estimate_rank_meeg_cov(C, this_very_info,
scalings=scalings)
assert_equal(expected_rank, est_rank)
# alignement and the sphere location.
sphere = mne.make_sphere_model(r0=(0., 0., 0.), head_radius=None)
mne.viz.plot_alignment(raw.info, subject='sample',
meg='helmet', bem=sphere, dig=True,
surfaces=['brain'])
del raw, epochs
###############################################################################
# To do a dipole fit, let's use the covariance provided by the empty room
# recording.
raw_erm = read_raw_ctf(erm_path).apply_gradient_compensation(0)
raw_erm = mne.preprocessing.maxwell_filter(raw_erm, coord_frame='meg',
**mf_kwargs)
cov = mne.compute_raw_covariance(raw_erm)
del raw_erm
dip, residual = fit_dipole(evoked, cov, sphere)
###############################################################################
# Compare the actual position with the estimated one.
expected_pos = np.array([18., 0., 49.])
diff = np.sqrt(np.sum((dip.pos[0] * 1000 - expected_pos) ** 2))
print('Actual pos: %s mm' % np.array_str(expected_pos, precision=1))
print('Estimated pos: %s mm' % np.array_str(dip.pos[0] * 1000, precision=1))
print('Difference: %0.1f mm' % diff)
print('Amplitude: %0.1f nAm' % (1e9 * dip.amplitude[0]))
print('GOF: %0.1f %%' % dip.gof[0])
##############################################################################
# Compute and apply inverse to PSD estimated using multitaper + Welch.
# Group into frequency bands, then normalize each source point and sensor
# independently. This makes the value of each sensor point and source location
# in each frequency band the percentage of the PSD accounted for by that band.
freq_bands = dict(
delta=(2, 4), theta=(5, 7), alpha=(8, 12), beta=(15, 29), gamma=(30, 45))
topos = dict(vv=dict(), opm=dict())
stcs = dict(vv=dict(), opm=dict())
snr = 3.
lambda2 = 1. / snr ** 2
for kind in kinds:
noise_cov = mne.compute_raw_covariance(raw_erms[kind])
inverse_operator = mne.minimum_norm.make_inverse_operator(
raws[kind].info, forward=fwd[kind], noise_cov=noise_cov, verbose=True)
stc_psd, sensor_psd = mne.minimum_norm.compute_source_psd(
raws[kind], inverse_operator, lambda2=lambda2,
n_fft=n_fft, dB=False, return_sensor=True, verbose=True)
topo_norm = sensor_psd.data.sum(axis=1, keepdims=True)
stc_norm = stc_psd.sum() # same operation on MNE object, sum across freqs
# Normalize each source point by the total power across freqs
for band, limits in freq_bands.items():
data = sensor_psd.copy().crop(*limits).data.sum(axis=1, keepdims=True)
topos[kind][band] = mne.EvokedArray(
100 * data / topo_norm, sensor_psd.info)
stcs[kind][band] = \
100 * stc_psd.copy().crop(*limits).sum() / stc_norm.data
def test_rank():
"""Test cov rank estimation"""
raw_sample = Raw(raw_fname)
raw_sss = Raw(hp_fif_fname)
raw_sss.add_proj(compute_proj_raw(raw_sss))
cov_sample = compute_raw_covariance(raw_sample)
cov_sample_proj = compute_raw_covariance(
raw_sample.copy().apply_proj())
cov_sss = compute_raw_covariance(raw_sss)
cov_sss_proj = compute_raw_covariance(
raw_sss.copy().apply_proj())
picks_all_sample = pick_types(raw_sample.info, meg=True, eeg=True)
picks_all_sss = pick_types(raw_sss.info, meg=True, eeg=True)
info_sample = pick_info(raw_sample.info, picks_all_sample)
picks_stack_sample = [('eeg', pick_types(info_sample, meg=False,
eeg=True))]
picks_stack_sample += [('meg', pick_types(info_sample, meg=True))]
picks_stack_sample += [('all',
pick_types(info_sample, meg=True, eeg=True))]
info_sss = pick_info(raw_sss.info, picks_all_sss)
picks_stack_somato = [('eeg', pick_types(info_sss, meg=False, eeg=True))]
picks_stack_somato += [('meg', pick_types(info_sss, meg=True))]
picks_stack_somato += [('all',
pick_types(info_sss, meg=True, eeg=True))]
iter_tests = list(itt.product(
[(cov_sample, picks_stack_sample, info_sample),
(cov_sample_proj, picks_stack_sample, info_sample),
(cov_sss, picks_stack_somato, info_sss),
(cov_sss_proj, picks_stack_somato, info_sss)], # sss
[dict(mag=1e15, grad=1e13, eeg=1e6)]
))
for (cov, picks_list, this_info), scalings in iter_tests:
for ch_type, picks in picks_list:
this_very_info = pick_info(this_info, picks)
# compute subset of projs
this_projs = [c['active'] and
len(set(c['data']['col_names'])
.intersection(set(this_very_info['ch_names']))) >
0 for c in cov['projs']]
n_projs = sum(this_projs)
# count channel types
ch_types = [channel_type(this_very_info, idx)
for idx in range(len(picks))]
n_eeg, n_mag, n_grad = [ch_types.count(k) for k in
['eeg', 'mag', 'grad']]
n_meg = n_mag + n_grad
if ch_type in ('all', 'eeg'):
n_projs_eeg = 1
else:
n_projs_eeg = 0
# check sss
if 'proc_history' in this_very_info:
mf = this_very_info['proc_history'][0]['max_info']
n_free = _get_sss_rank(mf)
if 'mag' not in ch_types and 'grad' not in ch_types:
n_free = 0
# - n_projs XXX clarify
expected_rank = n_free + n_eeg
if n_projs > 0 and ch_type in ('all', 'eeg'):
expected_rank -= n_projs_eeg
else:
expected_rank = n_meg + n_eeg - n_projs
C = cov['data'][np.ix_(picks, picks)]
est_rank = _estimate_rank_meeg_cov(C, this_very_info,
scalings=scalings)
assert_equal(expected_rank, est_rank)
# as the end of the recording, see :func:`mne.compute_raw_covariance`).
#
# Keep in mind that you want to match your empty room dataset to your
# actual MEG data, processing-wise. Ensure that filters
# are all the same and if you use ICA, apply it to your empty-room and subject
# data equivalently. In this case we did not filter the data and
# we don't use ICA. However, we do have bad channels and projections in
# the MEG data, and, hence, we want to make sure they get stored in the
# covariance object.
raw_empty_room.info['bads'] = [
bb for bb in raw.info['bads'] if 'EEG' not in bb]
raw_empty_room.add_proj(
[pp.copy() for pp in raw.info['projs'] if 'EEG' not in pp['desc']])
noise_cov = mne.compute_raw_covariance(
raw_empty_room, tmin=0, tmax=None)
###############################################################################
# Now that you have the covariance matrix in an MNE-Python object you can
# save it to a file with :func:`mne.write_cov`. Later you can read it back
# using :func:`mne.read_cov`.
#
# You can also use the pre-stimulus baseline to estimate the noise covariance.
# First we have to construct the epochs. When computing the covariance, you
# should use baseline correction when constructing the epochs. Otherwise the
# covariance matrix will be inaccurate. In MNE this is done by default, but
# just to be sure, we define it here manually.
events = mne.find_events(raw)
epochs = mne.Epochs(raw, events, event_id=1, tmin=-0.2, tmax=0.5,
baseline=(-0.2, 0.0), decim=3, # we'll decimate for speed
verbose='error') # and ignore the warning about aliasing
evoked_std.plot_topomap(times=times, title='Standard')
evoked_dev.plot_topomap(times=times, title='Deviant')
###############################################################################
# We can see the MMN effect more clearly by looking at the difference between
# the two conditions. P50 and N100 are no longer visible, but MMN/P200 and
# P300 are emphasised.
evoked_difference = combine_evoked([evoked_dev, evoked_std], weights=[1, -1])
evoked_difference.plot(window_title='Difference', gfp=True)
###############################################################################
# Source estimation.
# We compute the noise covariance matrix from the empty room measurement
# and use it for the other runs.
reject = dict(mag=4e-12)
cov = mne.compute_raw_covariance(raw_erm, reject=reject)
cov.plot(raw_erm.info)
del raw_erm
###############################################################################
# The transformation is read from a file. More information about coregistering
# the data, see :ref:`ch_interactive_analysis` or
# :func:`mne.gui.coregistration`.
trans_fname = op.join(data_path, 'MEG', 'bst_auditory',
'bst_auditory-trans.fif')
trans = mne.read_trans(trans_fname)
###############################################################################
# To save time and memory, the forward solution is read from a file. Set
# ``use_precomputed=False`` in the beginning of this script to build the
# forward solution from scratch. The head surfaces for constructing a BEM
data_type='noise_empty_room')
raw_noise.load_data()
# apply ref channel correction and drop ref channels
preproc.apply_ref_correction(raw_noise)
# Note: MNE complains on Python 2.7
raw_noise.filter(0.50, None, method='iir',
iir_params=dict(order=4, ftype='butter'), n_jobs=1)
raw_noise.filter(None, 60, method='iir',
iir_params=dict(order=4, ftype='butter'), n_jobs=1)
##############################################################################
# Note that using the empty room noise covariance will inflate the SNR of the
# evkoked and renders comparisons to `baseline` rather uninformative.
noise_cov = mne.compute_raw_covariance(raw_noise, method='empirical')
##############################################################################
# Now we assemble the inverse operator, project the data and show the results
# on the `fsaverage` surface, the freesurfer average brain.
inv_op = mne.minimum_norm.make_inverse_operator(
evoked.info, fwd, noise_cov=noise_cov)
stc = mne.minimum_norm.apply_inverse( # these data have a pretty high SNR and
evoked, inv_op, method='MNE', lambda2=1./9.**2) # 9 is a lovely number.
stc = stc.to_original_src(
src_outputs['src_fsaverage'], subjects_dir=subjects_dir)
