# desired baseline length, and 0 for tmax_plot.
# Note, if using baseline data, the averaged evoked response in the baseline
# period should be flat.
noise_covs = []
for (l_freq, h_freq) in freq_bins:
raw_band = raw_noise.copy()
raw_band.filter(l_freq, h_freq, picks=epochs.picks, method='iir', n_jobs=1)
epochs_band = mne.Epochs(raw_band, epochs_noise.events, event_id,
tmin=tmin_plot, tmax=tmax_plot, baseline=None,
picks=epochs.picks, proj=True)
noise_cov = compute_covariance(epochs_band)
noise_cov = mne.cov.regularize(noise_cov, epochs_band.info, mag=noise_reg,
grad=noise_reg, eeg=noise_reg, proj=True)
noise_covs.append(noise_cov)
del raw_band # to save memory
# Computing LCMV solutions for time-frequency windows in a label in source
# space for faster computation, use label=None for full solution
stcs = tf_lcmv(epochs, forward, noise_covs, tmin, tmax, tstep, win_lengths,
freq_bins=freq_bins, subtract_evoked=subtract_evoked,
reg=data_reg, label=label)
# Plotting source spectrogram for source with maximum activity.
# Note that tmin and tmax are set to display a time range that is smaller than
# the one for which beamforming estimates were calculated. This ensures that
# all time bins shown are a result of smoothing across an identical number of
# time windows.
plot_source_spectrogram(stcs, freq_bins, tmin=tmin_plot, tmax=tmax_plot,
source_index=None, colorbar=True)
tmax=tmax,
picks=epochs.picks,
proj=True)
noise_cov = compute_covariance(epochs_band)
noise_cov = mne.cov.regularize(noise_cov,
epochs_band.info,
mag=noise_reg,
grad=noise_reg,
eeg=noise_reg,
proj=True)
noise_covs.append(noise_cov)
del raw_band # to save memory
# Computing LCMV solutions for time-frequency windows in a label in source
# space for faster computation, use label=None for full solution
stcs = tf_lcmv(epochs,
forward,
noise_covs,
tmin,
tmax,
tstep,
win_lengths,
freq_bins=freq_bins,
subtract_evoked=subtract_evoked,
reg=data_reg,
label=label)
# Plotting source spectrogram for source with maximum activity
plot_source_spectrogram(stcs, freq_bins, source_index=None, colorbar=True)
def test_tf_lcmv():
"""Test TF beamforming based on LCMV
"""
fname_raw = op.join(data_path, 'MEG', 'sample',
'sample_audvis_filt-0-40_raw.fif')
label = mne.read_label(fname_label)
events = mne.read_events(fname_event)
raw = mne.io.Raw(fname_raw, preload=True)
forward = mne.read_forward_solution(fname_fwd)
event_id, tmin, tmax = 1, -0.2, 0.2
# Setup for reading the raw data
raw.info['bads'] = ['MEG 2443', 'EEG 053'] # 2 bads channels
# Set up pick list: MEG - bad channels
left_temporal_channels = mne.read_selection('Left-temporal')
picks = mne.pick_types(raw.info,
meg=True,
eeg=False,
stim=True,
eog=True,
exclude='bads',
selection=left_temporal_channels)
# Read epochs
epochs = mne.Epochs(raw,
events,
event_id,
tmin,
tmax,
proj=True,
picks=picks,
baseline=None,
preload=False,
reject=dict(grad=4000e-13, mag=4e-12, eog=150e-6))
epochs.drop_bad_epochs()
freq_bins = [(4, 12), (15, 40)]
time_windows = [(-0.1, 0.1), (0.0, 0.2)]
win_lengths = [0.2, 0.2]
tstep = 0.1
reg = 0.05
source_power = []
noise_covs = []
for (l_freq, h_freq), win_length in zip(freq_bins, win_lengths):
raw_band = raw.copy()
raw_band.filter(l_freq, h_freq, method='iir', n_jobs=1, picks=picks)
epochs_band = mne.Epochs(raw_band,
epochs.events,
epochs.event_id,
tmin=tmin,
tmax=tmax,
baseline=None,
proj=True)
with warnings.catch_warnings(record=True): # not enough samples
noise_cov = compute_covariance(epochs_band,
tmin=tmin,
tmax=tmin + win_length)
noise_cov = mne.cov.regularize(noise_cov,
epochs_band.info,
mag=reg,
grad=reg,
eeg=reg,
proj=True)
noise_covs.append(noise_cov)
del raw_band # to save memory
# Manually calculating source power in on frequency band and several
# time windows to compare to tf_lcmv results and test overlapping
if (l_freq, h_freq) == freq_bins[0]:
for time_window in time_windows:
with warnings.catch_warnings(record=True):
data_cov = compute_covariance(epochs_band,
tmin=time_window[0],
tmax=time_window[1])
stc_source_power = _lcmv_source_power(epochs.info,
forward,
noise_cov,
data_cov,
reg=reg,
label=label)
source_power.append(stc_source_power.data)
stcs = tf_lcmv(epochs,
forward,
noise_covs,
tmin,
tmax,
tstep,
win_lengths,
freq_bins,
reg=reg,
label=label)
assert_true(len(stcs) == len(freq_bins))
assert_true(stcs[0].shape[1] == 4)
# Averaging all time windows that overlap the time period 0 to 100 ms
source_power = np.mean(source_power, axis=0)
# Selecting the first frequency bin in tf_lcmv results
stc = stcs[0]
# Comparing tf_lcmv results with _lcmv_source_power results
assert_array_almost_equal(stc.data[:, 2], source_power[:, 0])
# Test if using unsupported max-power orientation is detected
assert_raises(ValueError,
tf_lcmv,
epochs,
forward,
noise_covs,
tmin,
tmax,
tstep,
win_lengths,
freq_bins=freq_bins,
pick_ori='max-power')
# Test if incorrect number of noise CSDs is detected
# Test if incorrect number of noise covariances is detected
assert_raises(ValueError, tf_lcmv, epochs, forward, [noise_covs[0]], tmin,
tmax, tstep, win_lengths, freq_bins)
# Test if freq_bins and win_lengths incompatibility is detected
assert_raises(ValueError,
tf_lcmv,
epochs,
forward,
noise_covs,
tmin,
tmax,
tstep,
win_lengths=[0, 1, 2],
freq_bins=freq_bins)
# Test if time step exceeding window lengths is detected
assert_raises(ValueError,
tf_lcmv,
epochs,
forward,
noise_covs,
tmin,
tmax,
tstep=0.15,
win_lengths=[0.2, 0.1],
freq_bins=freq_bins)
# Test correct detection of preloaded epochs objects that do not contain
# the underlying raw object
epochs_preloaded = mne.Epochs(raw,
events,
event_id,
tmin,
tmax,
proj=True,
baseline=(None, 0),
preload=True)
assert_raises(ValueError, tf_lcmv, epochs_preloaded, forward, noise_covs,
tmin, tmax, tstep, win_lengths, freq_bins)
with warnings.catch_warnings(record=True): # not enough samples
# Pass only one epoch to test if subtracting evoked
# responses yields zeros
stcs = tf_lcmv(epochs[0],
forward,
noise_covs,
tmin,
tmax,
tstep,
win_lengths,
freq_bins,
subtract_evoked=True,
reg=reg,
label=label)
assert_array_almost_equal(stcs[0].data, np.zeros_like(stcs[0].data))
def test_tf_lcmv():
"""Test TF beamforming based on LCMV
"""
fname_raw = op.join(data_path, 'MEG', 'sample',
'sample_audvis_filt-0-40_raw.fif')
label = mne.read_label(fname_label)
events = mne.read_events(fname_event)
raw = mne.fiff.Raw(fname_raw, preload=True)
forward = mne.read_forward_solution(fname_fwd)
event_id, tmin, tmax = 1, -0.2, 0.2
# Setup for reading the raw data
raw.info['bads'] = ['MEG 2443', 'EEG 053'] # 2 bads channels
# Set up pick list: MEG - bad channels
left_temporal_channels = mne.read_selection('Left-temporal')
picks = mne.fiff.pick_types(raw.info, meg=True, eeg=False,
stim=True, eog=True, exclude='bads',
selection=left_temporal_channels)
# Read epochs
epochs = mne.Epochs(raw, events, event_id, tmin, tmax, proj=True,
picks=picks, baseline=(None, 0),
preload=False,
reject=dict(grad=4000e-13, mag=4e-12, eog=150e-6))
epochs.drop_bad_epochs()
freq_bins = [(4, 12), (15, 40)]
time_windows = [(-0.1, 0.1), (0.0, 0.2)]
win_lengths = [0.2, 0.2]
tstep = 0.1
reg = 0.05
source_power = []
noise_covs = []
for (l_freq, h_freq), win_length in zip(freq_bins, win_lengths):
raw_band = raw.copy()
raw_band.filter(l_freq, h_freq, method='iir', n_jobs=1, picks=picks)
epochs_band = mne.Epochs(raw_band, epochs.events, epochs.event_id,
tmin=tmin, tmax=tmax, proj=True)
with warnings.catch_warnings(record=True): # not enough samples
noise_cov = compute_covariance(epochs_band, tmin=tmin, tmax=tmin +
win_length)
noise_cov = mne.cov.regularize(noise_cov, epochs_band.info, mag=reg,
grad=reg, eeg=reg, proj=True)
noise_covs.append(noise_cov)
del raw_band # to save memory
# Manually calculating source power in on frequency band and several
# time windows to compare to tf_lcmv results and test overlapping
if (l_freq, h_freq) == freq_bins[0]:
for time_window in time_windows:
with warnings.catch_warnings(record=True):
data_cov = compute_covariance(epochs_band,
tmin=time_window[0],
tmax=time_window[1])
stc_source_power = _lcmv_source_power(epochs.info, forward,
noise_cov, data_cov,
reg=reg, label=label)
source_power.append(stc_source_power.data)
stcs = tf_lcmv(epochs, forward, noise_covs, tmin, tmax, tstep, win_lengths,
freq_bins, reg=reg, label=label)
assert_true(len(stcs) == len(freq_bins))
assert_true(stcs[0].shape[1] == 4)
# Averaging all time windows that overlap the time period 0 to 100 ms
source_power = np.mean(source_power, axis=0)
# Selecting the first frequency bin in tf_lcmv results
stc = stcs[0]
# Comparing tf_lcmv results with _lcmv_source_power results
assert_array_almost_equal(stc.data[:, 2], source_power[:, 0])
# Test if using unsupported max-power orientation is detected
assert_raises(ValueError, tf_lcmv, epochs, forward, noise_covs, tmin, tmax,
tstep, win_lengths, freq_bins=freq_bins,
pick_ori='max-power')
# Test if incorrect number of noise CSDs is detected
# Test if incorrect number of noise covariances is detected
assert_raises(ValueError, tf_lcmv, epochs, forward, [noise_covs[0]], tmin,
tmax, tstep, win_lengths, freq_bins)
# Test if freq_bins and win_lengths incompatibility is detected
assert_raises(ValueError, tf_lcmv, epochs, forward, noise_covs, tmin, tmax,
tstep, win_lengths=[0, 1, 2], freq_bins=freq_bins)
# Test if time step exceeding window lengths is detected
assert_raises(ValueError, tf_lcmv, epochs, forward, noise_covs, tmin, tmax,
tstep=0.15, win_lengths=[0.2, 0.1], freq_bins=freq_bins)
# Test correct detection of preloaded epochs objects that do not contain
# the underlying raw object
epochs_preloaded = mne.Epochs(raw, events, event_id, tmin, tmax, proj=True,
baseline=(None, 0), preload=True)
assert_raises(ValueError, tf_lcmv, epochs_preloaded, forward, noise_covs,
tmin, tmax, tstep, win_lengths, freq_bins)
with warnings.catch_warnings(record=True): # not enough samples
# Pass only one epoch to test if subtracting evoked
# responses yields zeros
stcs = tf_lcmv(epochs[0], forward, noise_covs, tmin, tmax, tstep,
win_lengths, freq_bins, subtract_evoked=True, reg=reg,
label=label)
assert_array_almost_equal(stcs[0].data, np.zeros_like(stcs[0].data))
def test_tf_lcmv():
"""Test TF beamforming based on LCMV."""
label = mne.read_label(fname_label)
events = mne.read_events(fname_event)
raw = mne.io.read_raw_fif(fname_raw, preload=True)
forward = mne.read_forward_solution(fname_fwd)
event_id, tmin, tmax = 1, -0.2, 0.2
# Setup for reading the raw data
raw.info['bads'] = ['MEG 2443', 'EEG 053'] # 2 bads channels
# Set up pick list: MEG - bad channels
left_temporal_channels = mne.read_selection('Left-temporal')
picks = mne.pick_types(raw.info, selection=left_temporal_channels)
picks = picks[::4] # decimate for speed
raw.pick_channels([raw.ch_names[ii] for ii in picks])
raw.info.normalize_proj() # avoid projection warnings
del picks
# Read epochs
epochs = mne.Epochs(raw,
events,
event_id,
tmin,
tmax,
proj=True,
baseline=None,
preload=False,
reject=reject)
epochs.load_data()
freq_bins = [(4, 12), (15, 40)]
time_windows = [(-0.1, 0.1), (0.0, 0.2)]
win_lengths = [0.2, 0.2]
tstep = 0.1
reg = 0.05
source_power = []
noise_covs = []
for (l_freq, h_freq), win_length in zip(freq_bins, win_lengths):
raw_band = raw.copy()
raw_band.filter(l_freq,
h_freq,
method='iir',
n_jobs=1,
iir_params=dict(output='ba'))
epochs_band = mne.Epochs(raw_band,
epochs.events,
epochs.event_id,
tmin=tmin,
tmax=tmax,
baseline=None,
proj=True)
with warnings.catch_warnings(record=True): # not enough samples
noise_cov = mne.compute_covariance(epochs_band,
tmin=tmin,
tmax=tmin + win_length)
noise_cov = mne.cov.regularize(noise_cov,
epochs_band.info,
mag=reg,
grad=reg,
eeg=reg,
proj=True)
noise_covs.append(noise_cov)
del raw_band # to save memory
# Manually calculating source power in on frequency band and several
# time windows to compare to tf_lcmv results and test overlapping
if (l_freq, h_freq) == freq_bins[0]:
for time_window in time_windows:
with warnings.catch_warnings(record=True): # bad samples
data_cov = mne.compute_covariance(epochs_band,
tmin=time_window[0],
tmax=time_window[1])
with warnings.catch_warnings(record=True): # bad proj
stc_source_power = _lcmv_source_power(
epochs.info,
forward,
noise_cov,
data_cov,
reg=reg,
label=label,
weight_norm='unit-noise-gain')
source_power.append(stc_source_power.data)
pytest.raises(ValueError,
tf_lcmv,
epochs,
forward,
noise_covs,
tmin,
tmax,
tstep,
win_lengths,
freq_bins,
reg=reg,
label=label)
stcs = tf_lcmv(epochs,
forward,
noise_covs,
tmin,
tmax,
tstep,
win_lengths,
freq_bins,
reg=reg,
label=label,
raw=raw)
assert (len(stcs) == len(freq_bins))
assert (stcs[0].shape[1] == 4)
# Averaging all time windows that overlap the time period 0 to 100 ms
source_power = np.mean(source_power, axis=0)
# Selecting the first frequency bin in tf_lcmv results
stc = stcs[0]
# Comparing tf_lcmv results with _lcmv_source_power results
assert_array_almost_equal(stc.data[:, 2], source_power[:, 0])
# Test if using unsupported max-power orientation is detected
pytest.raises(ValueError,
tf_lcmv,
epochs,
forward,
noise_covs,
tmin,
tmax,
tstep,
win_lengths,
freq_bins=freq_bins,
pick_ori='max-power')
# Test if incorrect number of noise CSDs is detected
# Test if incorrect number of noise covariances is detected
pytest.raises(ValueError, tf_lcmv, epochs, forward, [noise_covs[0]], tmin,
tmax, tstep, win_lengths, freq_bins)
# Test if freq_bins and win_lengths incompatibility is detected
pytest.raises(ValueError,
tf_lcmv,
epochs,
forward,
noise_covs,
tmin,
tmax,
tstep,
win_lengths=[0, 1, 2],
freq_bins=freq_bins)
# Test if time step exceeding window lengths is detected
pytest.raises(ValueError,
tf_lcmv,
epochs,
forward,
noise_covs,
tmin,
tmax,
tstep=0.15,
win_lengths=[0.2, 0.1],
freq_bins=freq_bins)
# Test if missing of noise covariance matrix is detected when more than
# one channel type is present in the data
pytest.raises(ValueError,
tf_lcmv,
epochs,
forward,
noise_covs=None,
tmin=tmin,
tmax=tmax,
tstep=tstep,
win_lengths=win_lengths,
freq_bins=freq_bins)
# Test if unsupported weight normalization specification is detected
pytest.raises(ValueError,
tf_lcmv,
epochs,
forward,
noise_covs,
tmin,
tmax,
tstep,
win_lengths,
freq_bins,
weight_norm='nai')
# Test unsupported pick_ori (vector not supported here)
with pytest.raises(ValueError, match='pick_ori must be one of'):
tf_lcmv(epochs,
forward,
noise_covs,
tmin,
tmax,
tstep,
win_lengths,
freq_bins,
pick_ori='vector')
# Test correct detection of preloaded epochs objects that do not contain
# the underlying raw object
epochs_preloaded = mne.Epochs(raw,
events,
event_id,
tmin,
tmax,
proj=True,
baseline=(None, 0),
preload=True)
epochs_preloaded._raw = None
with warnings.catch_warnings(record=True): # not enough samples
pytest.raises(ValueError, tf_lcmv, epochs_preloaded, forward,
noise_covs, tmin, tmax, tstep, win_lengths, freq_bins)
with warnings.catch_warnings(record=True): # not enough samples
# Pass only one epoch to test if subtracting evoked
# responses yields zeros
stcs = tf_lcmv(epochs[0],
forward,
noise_covs,
tmin,
tmax,
tstep,
win_lengths,
freq_bins,
subtract_evoked=True,
reg=reg,
label=label,
raw=raw)
assert_array_almost_equal(stcs[0].data, np.zeros_like(stcs[0].data))
def test_tf_lcmv():
"""Test TF beamforming based on LCMV."""
label = mne.read_label(fname_label)
events = mne.read_events(fname_event)
raw = mne.io.read_raw_fif(fname_raw, preload=True)
forward = mne.read_forward_solution(fname_fwd)
event_id, tmin, tmax = 1, -0.2, 0.2
# Setup for reading the raw data
raw.info['bads'] = ['MEG 2443', 'EEG 053'] # 2 bads channels
# Set up pick list: MEG - bad channels
left_temporal_channels = mne.read_selection('Left-temporal')
picks = mne.pick_types(raw.info, selection=left_temporal_channels)
picks = picks[::2] # decimate for speed
raw.pick_channels([raw.ch_names[ii] for ii in picks])
raw.info.normalize_proj() # avoid projection warnings
del picks
# Read epochs
epochs = mne.Epochs(raw, events, event_id, tmin, tmax, proj=True,
baseline=None, preload=False, reject=reject)
epochs.load_data()
freq_bins = [(4, 12), (15, 40)]
time_windows = [(-0.1, 0.1), (0.0, 0.2)]
win_lengths = [0.2, 0.2]
tstep = 0.1
reg = 0.05
source_power = []
noise_covs = []
for (l_freq, h_freq), win_length in zip(freq_bins, win_lengths):
raw_band = raw.copy()
raw_band.filter(l_freq, h_freq, method='iir', n_jobs=1,
iir_params=dict(output='ba'))
epochs_band = mne.Epochs(
raw_band, epochs.events, epochs.event_id, tmin=tmin, tmax=tmax,
baseline=None, proj=True)
noise_cov = mne.compute_covariance(
epochs_band, tmin=tmin, tmax=tmin + win_length)
noise_cov = mne.cov.regularize(
noise_cov, epochs_band.info, mag=reg, grad=reg, eeg=reg,
proj=True)
noise_covs.append(noise_cov)
del raw_band # to save memory
# Manually calculating source power in on frequency band and several
# time windows to compare to tf_lcmv results and test overlapping
if (l_freq, h_freq) == freq_bins[0]:
for time_window in time_windows:
data_cov = mne.compute_covariance(
epochs_band, tmin=time_window[0], tmax=time_window[1])
stc_source_power = _lcmv_source_power(
epochs.info, forward, noise_cov, data_cov,
reg=reg, label=label, weight_norm='unit-noise-gain')
source_power.append(stc_source_power.data)
pytest.raises(ValueError, tf_lcmv, epochs, forward, noise_covs, tmin, tmax,
tstep, win_lengths, freq_bins, reg=reg, label=label)
stcs = tf_lcmv(epochs, forward, noise_covs, tmin, tmax, tstep,
win_lengths, freq_bins, reg=reg, label=label, raw=raw)
assert (len(stcs) == len(freq_bins))
assert (stcs[0].shape[1] == 4)
# Averaging all time windows that overlap the time period 0 to 100 ms
source_power = np.mean(source_power, axis=0)
# Selecting the first frequency bin in tf_lcmv results
stc = stcs[0]
# Comparing tf_lcmv results with _lcmv_source_power results
assert_array_almost_equal(stc.data[:, 2], source_power[:, 0])
# Test if using unsupported max-power orientation is detected
pytest.raises(ValueError, tf_lcmv, epochs, forward, noise_covs, tmin, tmax,
tstep, win_lengths, freq_bins=freq_bins,
pick_ori='max-power')
# Test if incorrect number of noise CSDs is detected
# Test if incorrect number of noise covariances is detected
pytest.raises(ValueError, tf_lcmv, epochs, forward, [noise_covs[0]], tmin,
tmax, tstep, win_lengths, freq_bins)
# Test if freq_bins and win_lengths incompatibility is detected
pytest.raises(ValueError, tf_lcmv, epochs, forward, noise_covs, tmin, tmax,
tstep, win_lengths=[0, 1, 2], freq_bins=freq_bins)
# Test if time step exceeding window lengths is detected
pytest.raises(ValueError, tf_lcmv, epochs, forward, noise_covs, tmin, tmax,
tstep=0.15, win_lengths=[0.2, 0.1], freq_bins=freq_bins)
# Test if missing of noise covariance matrix is detected when more than
# one channel type is present in the data
pytest.raises(ValueError, tf_lcmv, epochs, forward, noise_covs=None,
tmin=tmin, tmax=tmax, tstep=tstep, win_lengths=win_lengths,
freq_bins=freq_bins)
# Test if unsupported weight normalization specification is detected
pytest.raises(ValueError, tf_lcmv, epochs, forward, noise_covs, tmin, tmax,
tstep, win_lengths, freq_bins, weight_norm='nai')
# Test unsupported pick_ori (vector not supported here)
with pytest.raises(ValueError, match='pick_ori must be one of'):
tf_lcmv(epochs, forward, noise_covs, tmin, tmax, tstep, win_lengths,
freq_bins, pick_ori='vector')
# Test correct detection of preloaded epochs objects that do not contain
# the underlying raw object
epochs_preloaded = mne.Epochs(raw, events, event_id, tmin, tmax, proj=True,
baseline=(None, 0), preload=True)
epochs_preloaded._raw = None
pytest.raises(ValueError, tf_lcmv, epochs_preloaded, forward,
noise_covs, tmin, tmax, tstep, win_lengths, freq_bins)
# Pass only one epoch to test if subtracting evoked
# responses yields zeros
with pytest.warns(RuntimeWarning,
match='Too few samples .* estimate may be unreliable'):
stcs = tf_lcmv(epochs[0], forward, noise_covs, tmin, tmax, tstep,
win_lengths, freq_bins, subtract_evoked=True, reg=reg,
label=label, raw=raw)
assert_array_almost_equal(stcs[0].data, np.zeros_like(stcs[0].data))