def test_csd_morlet():
"""Test computing cross-spectral density using Morlet wavelets."""
epochs = _generate_coherence_data()
sfreq = epochs.info['sfreq']
# Compute CSDs by a variety of methods
freqs = [10, 15, 22]
n_cycles = [20, 30, 44]
times = [(None, None), (1, 9)]
as_arrays = [False, True]
parameters = product(times, as_arrays)
for (tmin, tmax), as_array in parameters:
if as_array:
csd = csd_array_morlet(epochs.get_data(),
sfreq,
freqs,
t0=epochs.tmin,
n_cycles=n_cycles,
tmin=tmin,
tmax=tmax,
ch_names=epochs.ch_names)
else:
csd = csd_morlet(epochs,
frequencies=freqs,
n_cycles=n_cycles,
tmin=tmin,
tmax=tmax)
if tmin is None and tmax is None:
assert csd.tmin == 0 and csd.tmax == 9.98
else:
assert csd.tmin == tmin and csd.tmax == tmax
_test_csd_matrix(csd)
# CSD diagonals should contain PSD
tfr = tfr_morlet(epochs, freqs, n_cycles, return_itc=False)
power = np.mean(tfr.data, 2)
csd = csd_morlet(epochs, frequencies=freqs, n_cycles=n_cycles)
assert_allclose(csd._data[[0, 3, 5]] * sfreq, power)
# Test using plain convolution instead of FFT
csd = csd_morlet(epochs,
frequencies=freqs,
n_cycles=n_cycles,
use_fft=False)
assert_allclose(csd._data[[0, 3, 5]] * sfreq, power)
# Test baselining warning
with warnings.catch_warnings(record=True) as w:
warnings.simplefilter('always')
epochs_nobase = epochs.copy()
epochs_nobase.baseline = None
epochs_nobase.info['highpass'] = 0
csd = csd_morlet(epochs_nobase, frequencies=[10], decim=20)
assert len(w) == 1
def _gen_dics(active_win, baseline_win, epochs):
freqs = np.logspace(np.log10(12), np.log10(30), 9)
csd = csd_morlet(epochs, freqs, tmin=-1, tmax=1.5, decim=20)
csd_baseline = csd_morlet(epochs, freqs, tmin=baseline_win[0],
tmax=baseline_win[1], decim=20)
csd_ers = csd_morlet(epochs, freqs, tmin=active_win[0], tmax=active_win[1],
decim=20)
filters = make_dics(epochs.info, fwd, csd.mean(), pick_ori='max-power',
reduce_rank=True, real_filter=True)
stc_base, freqs = apply_dics_csd(csd_baseline.mean(), filters)
stc_act, freqs = apply_dics_csd(csd_ers.mean(), filters)
stc_act /= stc_base
return stc_act
def _simulate_data(fwd, idx): # Somewhere on the frontal lobe by default
"""Simulate an oscillator on the cortex."""
source_vertno = fwd['src'][0]['vertno'][idx]
sfreq = 50. # Hz.
times = np.arange(10 * sfreq) / sfreq # 10 seconds of data
signal = np.sin(20 * 2 * np.pi * times) # 20 Hz oscillator
signal[:len(times) // 2] *= 2 # Make signal louder at the beginning
signal *= 1e-9 # Scale to be in the ballpark of MEG data
# Construct a SourceEstimate object that describes the signal at the
# cortical level.
stc = mne.SourceEstimate(
signal[np.newaxis, :],
vertices=[[source_vertno], []],
tmin=0,
tstep=1 / sfreq,
subject='sample',
)
# Create an info object that holds information about the sensors
info = mne.create_info(fwd['info']['ch_names'], sfreq, ch_types='grad')
info.update(fwd['info']) # Merge in sensor position information
# heavily decimate sensors to make it much faster
info = mne.pick_info(info, np.arange(info['nchan'])[::5])
fwd = mne.pick_channels_forward(fwd, info['ch_names'])
# Run the simulated signal through the forward model, obtaining
# simulated sensor data.
raw = mne.apply_forward_raw(fwd, stc, info)
# Add a little noise
random = np.random.RandomState(42)
noise = random.randn(*raw._data.shape) * 1e-14
raw._data += noise
# Define a single epoch (weird baseline but shouldn't matter)
epochs = mne.Epochs(raw, [[0, 0, 1]],
event_id=1,
tmin=0,
tmax=raw.times[-1],
baseline=(0., 0.),
preload=True)
evoked = epochs.average()
# Compute the cross-spectral density matrix
csd = csd_morlet(epochs, frequencies=[10, 20], n_cycles=[5, 10], decim=10)
labels = mne.read_labels_from_annot('sample',
hemi='lh',
subjects_dir=subjects_dir)
label = [
label for label in labels if np.in1d(source_vertno, label.vertices)[0]
]
assert len(label) == 1
label = label[0]
vertices = np.intersect1d(label.vertices, fwd['src'][0]['vertno'])
source_ind = vertices.tolist().index(source_vertno)
assert vertices[source_ind] == source_vertno
return epochs, evoked, csd, source_vertno, label, vertices, source_ind
def test_csd_morlet():
"""Test computing cross-spectral density using Morlet wavelets."""
epochs = _generate_coherence_data()
sfreq = epochs.info['sfreq']
# Compute CSDs by a variety of methods
freqs = [10, 15, 22]
n_cycles = [20, 30, 44]
times = [(None, None), (1, 9)]
as_arrays = [False, True]
parameters = product(times, as_arrays)
for (tmin, tmax), as_array in parameters:
if as_array:
csd = csd_array_morlet(epochs.get_data(), sfreq, freqs,
t0=epochs.tmin, n_cycles=n_cycles,
tmin=tmin, tmax=tmax,
ch_names=epochs.ch_names)
else:
csd = csd_morlet(epochs, frequencies=freqs, n_cycles=n_cycles,
tmin=tmin, tmax=tmax)
if tmin is None and tmax is None:
assert csd.tmin == 0 and csd.tmax == 9.98
else:
assert csd.tmin == tmin and csd.tmax == tmax
_test_csd_matrix(csd)
# CSD diagonals should contain PSD
tfr = tfr_morlet(epochs, freqs, n_cycles, return_itc=False)
power = np.mean(tfr.data, 2)
csd = csd_morlet(epochs, frequencies=freqs, n_cycles=n_cycles)
assert_allclose(csd._data[[0, 3, 5]] * sfreq, power)
# Test using plain convolution instead of FFT
csd = csd_morlet(epochs, frequencies=freqs, n_cycles=n_cycles,
use_fft=False)
assert_allclose(csd._data[[0, 3, 5]] * sfreq, power)
# Test baselining warning
epochs_nobase = epochs.copy()
epochs_nobase.baseline = None
epochs_nobase.info['highpass'] = 0
with pytest.warns(RuntimeWarning, match='baseline'):
csd = csd_morlet(epochs_nobase, frequencies=[10], decim=20)
def _simulate_data(fwd_fixed, source_vertno1, source_vertno2):
"""Simulate two oscillators on the cortex."""
sfreq = 50. # Hz.
base_freq = 10
t_rand = 0.001
std = 0.1
times = np.arange(10. * sfreq) / sfreq # 10 seconds of data
n_times = len(times)
# Generate an oscillator with varying frequency and phase lag.
iflaw = base_freq / sfreq + t_rand * np.random.randn(n_times)
signal1 = np.exp(1j * 2.0 * np.pi * np.cumsum(iflaw))
signal1 *= np.conj(signal1[0])
signal1 = signal1.real
# Add some random fluctuations to the signal.
signal1 += std * np.random.randn(n_times)
signal1 *= 1e-7
# Make identical signal
signal2 = signal1.copy()
# Add random fluctuations
signal1 += 1e-8 * np.random.randn(len(times))
signal2 += 1e-8 * np.random.randn(len(times))
# Construct a SourceEstimate object
stc = mne.SourceEstimate(
np.vstack((signal1[np.newaxis, :], signal2[np.newaxis, :])),
vertices=[np.array([source_vertno1]), np.array([source_vertno2])],
tmin=0,
tstep=1 / sfreq,
subject='sample',
)
# Create an info object that holds information about the sensors
info = mne.create_info(fwd_fixed['info']['ch_names'], sfreq,
ch_types='grad')
info.update(fwd_fixed['info']) # Merge in sensor position information
# Simulated sensor data.
raw = mne.apply_forward_raw(fwd_fixed, stc, info)
# Add noise
noise = random.randn(*raw._data.shape) * 1e-14
raw._data += noise
# Define a single epoch
epochs = mne.Epochs(raw, np.array([[0, 0, 1]]), event_id=1, tmin=0,
tmax=raw.times[-1], preload=True, baseline=(0, 0))
# Compute the cross-spectral density matrix
csd = csd_morlet(epochs, frequencies=[10, 20])
return csd
def _simulate_data(fwd):
"""Simulate an oscillator on the cortex."""
source_vertno = 146374 # Somewhere on the frontal lobe
sfreq = 50. # Hz.
times = np.arange(10 * sfreq) / sfreq # 10 seconds of data
signal = np.sin(20 * 2 * np.pi * times) # 20 Hz oscillator
signal[:len(times) // 2] *= 2 # Make signal louder at the beginning
signal *= 1e-9 # Scale to be in the ballpark of MEG data
# Construct a SourceEstimate object that describes the signal at the
# cortical level.
stc = mne.SourceEstimate(
signal[np.newaxis, :],
vertices=[[source_vertno], []],
tmin=0,
tstep=1 / sfreq,
subject='sample',
)
# Create an info object that holds information about the sensors
info = mne.create_info(fwd['info']['ch_names'], sfreq, ch_types='grad')
info.update(fwd['info']) # Merge in sensor position information
# heavily decimate sensors to make it much faster
info = mne.pick_info(info, np.arange(info['nchan'])[::5])
fwd = mne.pick_channels_forward(fwd, info['ch_names'])
# Run the simulated signal through the forward model, obtaining
# simulated sensor data.
raw = mne.apply_forward_raw(fwd, stc, info)
# Add a little noise
random = np.random.RandomState(42)
noise = random.randn(*raw._data.shape) * 1e-14
raw._data += noise
# Define a single epoch
epochs = mne.Epochs(raw, [[0, 0, 1]],
event_id=1,
tmin=0,
tmax=raw.times[-1],
preload=True)
evoked = epochs.average()
# Compute the cross-spectral density matrix
csd = csd_morlet(epochs, frequencies=[10, 20], n_cycles=[5, 10], decim=10)
return epochs, evoked, csd, source_vertno
def _simulate_data(fwd):
"""Simulate an oscillator on the cortex."""
source_vertno = 146374 # Somewhere on the frontal lobe
sfreq = 50. # Hz.
times = np.arange(10 * sfreq) / sfreq # 10 seconds of data
signal = np.sin(20 * 2 * np.pi * times) # 20 Hz oscillator
signal[:len(times) // 2] *= 2 # Make signal louder at the beginning
signal *= 1e-9 # Scale to be in the ballpark of MEG data
# Construct a SourceEstimate object that describes the signal at the
# cortical level.
stc = mne.SourceEstimate(
signal[np.newaxis, :],
vertices=[[source_vertno], []],
tmin=0,
tstep=1 / sfreq,
subject='sample',
)
# Create an info object that holds information about the sensors
info = mne.create_info(fwd['info']['ch_names'], sfreq, ch_types='grad')
info.update(fwd['info']) # Merge in sensor position information
# heavily decimate sensors to make it much faster
info = mne.pick_info(info, np.arange(info['nchan'])[::5])
fwd = mne.pick_channels_forward(fwd, info['ch_names'])
# Run the simulated signal through the forward model, obtaining
# simulated sensor data.
raw = mne.apply_forward_raw(fwd, stc, info)
# Add a little noise
random = np.random.RandomState(42)
noise = random.randn(*raw._data.shape) * 1e-14
raw._data += noise
# Define a single epoch
epochs = mne.Epochs(raw, [[0, 0, 1]], event_id=1, tmin=0,
tmax=raw.times[-1], preload=True)
evoked = epochs.average()
# Compute the cross-spectral density matrix
csd = csd_morlet(epochs, frequencies=[10, 20], n_cycles=[5, 10], decim=10)
return epochs, evoked, csd, source_vertno
dir=proc_dir, sub=sub, run=run, wav=wav_name)
epo = mne.read_epochs(epo_name)
all_bads += epo.info["bads"]
epos.append(epo)
wav_epos.append(epo)
epo_names.append("{}_{}".format(run, wav_name))
epo_conds.append(mne.concatenate_epochs(wav_epos))
epo_cond_names.append(run)
for x in epos:
x.info["bads"] = all_bads
x.info["dev_head_t"] = epos[0].info["dev_head_t"]
epo = mne.concatenate_epochs(epos)
csd = csd_morlet(epo,
frequencies=freqs,
n_jobs=n_jobs,
n_cycles=c,
decim=3)
#csd = csd.mean()
fwd_name = "{dir}nc_{sub}_{sp}-fwd.fif".format(dir=proc_dir,
sub=sub,
sp=spacing)
fwd = mne.read_forward_solution(fwd_name)
filters = make_dics(epo.info,
fwd,
csd,
real_filter=True,
weight_norm="nai",
reduce_rank=False,
pick_ori="max-power")
del epo, csd, fwd
# Read in the simulated data
stc_signal = mne.read_source_estimate(
fname.stc_signal(noise=config.noise, vertex=config.vertex))
epochs = mne.read_epochs(
fname.simulated_epochs(noise=config.noise, vertex=config.vertex))
fwd = mne.read_forward_solution(fname.fwd)
# For pick_ori='normal', the fwd needs to be in surface orientation
fwd = mne.convert_forward_solution(fwd, surf_ori=True)
# The DICS beamformer currently only uses one sensor type
epochs_grad = epochs.copy().pick_types(meg='grad')
epochs_mag = epochs.copy().pick_types(meg='mag')
# Make CSD matrix
csd = csd_morlet(epochs, [config.signal_freq])
# Compute the settings grid
regs = [0.05, 0.1, 0.5]
sensor_types = ['grad', 'mag']
pick_oris = [None, 'normal', 'max-power']
inversions = ['single', 'matrix']
weight_norms = ['unit-noise-gain', 'nai', None]
normalize_fwds = [True, False]
real_filters = [True, False]
settings = list(
product(regs, sensor_types, pick_oris, inversions, weight_norms,
normalize_fwds, real_filters))
# Compute DICS beamformer with all possible settings
dists = []
epochs = mne.Epochs(raw, events, event_id=1, tmin=-1.5, tmax=2, picks=picks,
preload=True)
# Read forward operator
fwd = mne.read_forward_solution(fname_fwd)
###############################################################################
# We are interested in the beta band. Define a range of frequencies, using a
# log scale, from 12 to 30 Hz.
freqs = np.logspace(np.log10(12), np.log10(30), 9)
###############################################################################
# Computing the cross-spectral density matrix for the beta frequency band, for
# different time intervals. We use a decim value of 20 to speed up the
# computation in this example at the loss of accuracy.
csd = csd_morlet(epochs, freqs, tmin=-1, tmax=1.5, decim=20)
csd_baseline = csd_morlet(epochs, freqs, tmin=-1, tmax=0, decim=20)
# ERS activity starts at 0.5 seconds after stimulus onset
csd_ers = csd_morlet(epochs, freqs, tmin=0.5, tmax=1.5, decim=20)
###############################################################################
# Computing DICS spatial filters using the CSD that was computed on the entire
# timecourse.
filters = make_dics(epochs.info, fwd, csd.mean(), pick_ori='max-power')
###############################################################################
# Applying DICS spatial filters separately to the CSD computed using the
# baseline and the CSD computed during the ERS activity.
baseline_source_power, freqs = apply_dics_csd(csd_baseline.mean(), filters)
beta_source_power, freqs = apply_dics_csd(csd_ers.mean(), filters)
# other sources as much as possible.
#
# The :func:`mne.beamformer.make_dics` function has many switches that offer
# precise control
# over the way the filter weights are computed. Currently, there is no clear
# consensus regarding the best approach. This is why we will demonstrate two
# approaches here:
#
# 1. The approach as described in [2]_, which first normalizes the forward
# solution and computes a vector beamformer.
# 2. The scalar beamforming approach based on [3]_, which uses weight
# normalization instead of normalizing the forward solution.
# Estimate the cross-spectral density (CSD) matrix on the trial containing the
# signal.
csd_signal = csd_morlet(epochs['signal'], frequencies=[10])
# Compute the spatial filters for each vertex, using two approaches.
filters_approach1 = make_dics(info,
fwd,
csd_signal,
reg=0.05,
pick_ori='max-power',
normalize_fwd=True,
inversion='single',
weight_norm=None)
print(filters_approach1)
filters_approach2 = make_dics(info,
fwd,
csd_signal,
###############################################################################
# When computing the CSD with Morlet wavelets, you specify the exact
# frequencies at which to compute it. For each frequency, a corresponding
# wavelet will be constructed and convolved with the signal, resulting in a
# time-frequency decomposition.
#
# The CSD is constructed by computing the correlation between the
# time-frequency representations between all sensor-to-sensor pairs. The
# time-frequency decomposition originally has the same sampling rate as the
# signal, in our case ~600Hz. This means the decomposition is over-specified in
# time and we may not need to use all samples during our CSD computation, just
# enough to get a reliable correlation statistic. By specifying ``decim=10``,
# we use every 10th sample, which will greatly speed up the computation and
# will have a minimal effect on the CSD.
frequencies = [16, 17, 18, 19, 20]
csd_wav = csd_morlet(epochs, frequencies, decim=10, n_jobs=n_jobs)
###############################################################################
# The resulting :class:`mne.time_frequency.CrossSpectralDensity` objects have a
# plotting function we can use to compare the results of the different methods.
# We're plotting the mean CSD across frequencies.
csd_fft.mean().plot()
plt.suptitle('short-term Fourier transform')
csd_mt.mean().plot()
plt.suptitle('adaptive multitapers')
csd_wav.mean().plot()
plt.suptitle('Morlet wavelet transform')
# Read epochs
event_id, tmin, tmax = 1, -0.2, 0.5
events = mne.read_events(event_fname)
epochs = mne.Epochs(raw, events, event_id, tmin, tmax, proj=True,
picks=picks, baseline=(None, 0), preload=True,
reject=dict(grad=4000e-13, mag=4e-12))
evoked = epochs.average()
# Read forward operator
forward = mne.read_forward_solution(fname_fwd)
# Computing the data and noise cross-spectral density matrices
# The time-frequency window was chosen on the basis of spectrograms from
# example time_frequency/plot_time_frequency.py
# We use Morlet wavelets to estimate the CSD for two specific frequencies.
data_csds = csd_morlet(epochs, tmin=0.04, tmax=0.15, frequencies=[18, 27])
noise_csds = csd_morlet(epochs, tmin=-0.11, tmax=-0.001, frequencies=[18, 27])
# Compute DICS spatial filter and estimate source power
stc = dics_source_power(epochs.info, forward, noise_csds, data_csds)
# Plot the power maps at both frequencies
for i, freq in enumerate(data_csds.frequencies):
message = 'DICS source power at %0.1f Hz' % freq
brain = stc.plot(surface='inflated', hemi='rh', subjects_dir=subjects_dir,
time_label=message, figure=i)
brain.set_data_time_index(i)
brain.show_view('lateral')
# Uncomment line below to save images
# brain.save_image('DICS_source_power_freq_%d.png' % csd.freqs[0])
###############################################################################
# When computing the CSD with Morlet wavelets, you specify the exact
# frequencies at which to compute it. For each frequency, a corresponding
# wavelet will be constructed and convolved with the signal, resulting in a
# time-frequency decomposition.
#
# The CSD is constructed by computing the correlation between the
# time-frequency representations between all sensor-to-sensor pairs. The
# time-frequency decomposition originally has the same sampling rate as the
# signal, in our case ~600Hz. This means the decomposition is over-specified in
# time and we may not need to use all samples during our CSD computation, just
# enough to get a reliable correlation statistic. By specifying ``decim=10``,
# we use every 10th sample, which will greatly speed up the computation and
# will have a minimal effect on the CSD.
frequencies = [16, 17, 18, 19, 20]
csd_wav = csd_morlet(epochs, frequencies, decim=10, n_jobs=n_jobs)
###############################################################################
# The resulting :class:`mne.time_frequency.CrossSpectralDensity` objects have a
# plotting function we can use to compare the results of the different methods.
# We're plotting the mean CSD across frequencies.
csd_fft.mean().plot()
plt.suptitle('short-term Fourier transform')
csd_mt.mean().plot()
plt.suptitle('adaptive multitapers')
csd_wav.mean().plot()
plt.suptitle('Morlet wavelet transform')
rest = mne.read_epochs("{dir}nc_{sub}_1_ica-epo.fif".format(dir=meg_dir,
sub=meg))
ton = mne.read_epochs("{dir}nc_{sub}_2_ica-epo.fif".format(dir=meg_dir,
sub=meg))
# override head_position data to append sensor data (just for calculating CSD !)
rest.info['dev_head_t'] = ton.info['dev_head_t']
epo_bas = mne.concatenate_epochs([rest, ton])
epo_exp = mne.read_epochs("{dir}nc_{sub}_exp-epo.fif".format(dir=meg_dir,
sub=meg))
#separate positive and negative condition epochs
pos = epo_exp['positive']
neg = epo_exp['negative']
# calculate & save CSDs
csd_bas_gamma_high = csd_morlet(epo_bas,
frequencies=freqs["gamma_high"],
n_jobs=8,
n_cycles=cycles["gamma_high"],
decim=1)
csd_bas_gamma_high.save("{dir}nc_{meg}-csd_bas_gamma_high.h5".format(
dir=meg_dir, meg=meg))
csd_exp_gamma_high = csd_morlet(epo_exp,
frequencies=freqs["gamma_high"],
n_jobs=8,
n_cycles=cycles["gamma_high"],
decim=1)
csd_exp_gamma_high.save("{dir}nc_{meg}-csd_exp_gamma_high.h5".format(
dir=meg_dir, meg=meg))
csd_rest_gamma_high = csd_morlet(rest,
frequencies=freqs["gamma_high"],
n_jobs=8,
n_cycles=cycles["gamma_high"],
rest = mne.read_epochs("{dir}nc_{sub}_1_ica-epo.fif".format(dir=meg_dir,
sub=meg))
ton = mne.read_epochs("{dir}nc_{sub}_2_ica-epo.fif".format(dir=meg_dir,
sub=meg))
epo_exp = mne.read_epochs("{dir}nc_{sub}_exp-epo.fif".format(dir=meg_dir,
sub=meg))
neg = epo_exp['negative']
pos = epo_exp['positive']
# override head_position data to append sensor data (just for calculating CSD !)
rest.info['dev_head_t'] = ton.info['dev_head_t']
epo_bas = mne.concatenate_epochs([rest, ton])
# make and save CSDs for 1-90 Hz range
frequencies = np.linspace(1, 90, num=90)
csd_exp = csd_morlet(epo_exp,
frequencies=frequencies,
n_jobs=8,
n_cycles=7,
decim=1)
csd_exp.save("{dir}nc_{meg}-csd_exp_1-90.h5".format(dir=meg_dir, meg=meg))
csd_bas = csd_morlet(epo_bas,
frequencies=frequencies,
n_jobs=8,
n_cycles=7,
decim=1)
csd_bas.save("{dir}nc_{meg}-csd_bas_1-90.h5".format(dir=meg_dir, meg=meg))
csd_ton = csd_morlet(ton,
frequencies=frequencies,
n_jobs=8,
n_cycles=7,
decim=1)
csd_ton.save("{dir}nc_{meg}-csd_ton_1-90.h5".format(dir=meg_dir, meg=meg))
true_ori = fwd_disc_true['src'][0]['nn'][config.vertex] del info, fwd_disc_true, er_raw epochs = create_epochs(raw) ############################################################################### # Sensor level analysis ############################################################################### epochs_grad = epochs.copy().pick_types(meg='grad') epochs_mag = epochs.copy().pick_types(meg='mag') epochs_joint = epochs.copy().pick_types(meg=True) # Make CSD matrix csd = csd_morlet(epochs, [config.signal_freq], tmin=0, tmax=1) noise_csd = csd_morlet(epochs, [config.signal_freq], tmin=-1, tmax=0) # Compute evokeds evoked_grad = epochs_grad.average() evoked_mag = epochs_mag.average() evoked_joint = epochs_joint.average() ############################################################################### # Compute DICS beamformer results ############################################################################### # Read in forward solution fwd_disc_man = mne.read_forward_solution(fname.fwd_discrete_man) dists = []
# CSD over all conditions to calculate shared filters
for sub in subjs:
# read in the epo files
epo = mne.read_epochs("{}{}-analysis-epo.fif".format(proc_dir, sub))
# # calculate "big" alpha CSDs for common filters
# csd = csd_morlet(epo, frequencies=freqs, n_jobs=8, n_cycles=cycs, decim=1)
# csd.save("{}{}_alpha-csd.h5".format(proc_dir,sub))
#
# # calculate "small" alpha CSDs for each condition and time window
# for i, (tmin, tmax) in enumerate(zip(tmins,tmaxs)):
# epo_win = epo.copy()
# epo_win.crop(tmin=tmin, tmax=tmax)
# for cond in conds:
# csd_ct = csd_morlet(epo_win[cond], frequencies=freqs, n_jobs=8, n_cycles=cycs, decim=1)
# csd_ct.save("{}{}_alpha_{}_TW{}-csd.h5".format(proc_dir,sub,cond,i))
# calculate new "small" alpha CSDs for each condition and time window (before, after)
for (tmin, tmax, tw) in zip(new_tmins, new_tmaxs, new_tws):
epo_win = epo.copy()
epo_win.crop(tmin=tmin, tmax=tmax)
for cond in conds:
csd_ct = csd_morlet(epo_win[cond],
frequencies=freqs,
n_jobs=8,
n_cycles=cycs,
decim=1)
csd_ct.save("{}{}_alpha_{}_{}-csd.h5".format(
proc_dir, sub, cond, tw))
for wav_idx, wav_name in enumerate(wavs):
epo_name = "{dir}nc_{sub}_{run}_{wav}_hand-epo.fif".format(
dir=proc_dir, sub=sub, run=run, wav=wav_name)
epo = mne.read_epochs(epo_name)
all_bads += epo.info["bads"]
epos.append(epo)
wav_epos.append(epo)
epo_names.append("{}_{}".format(run,wav_name))
epo_conds.append(mne.concatenate_epochs(wav_epos))
epo_cond_names.append(run)
for x in epos:
x.info["bads"] = all_bads
x.info["dev_head_t"] = epos[0].info["dev_head_t"]
epo = mne.concatenate_epochs(epos)
csd = csd_morlet(epo, frequencies=freqs, n_jobs=n_jobs, n_cycles=cycles, decim=3)
csd = csd.mean()
fwd_name = "{dir}nc_{sub}_{sp}-fwd.fif".format(dir=proc_dir, sub=sub, sp=spacing)
fwd = mne.read_forward_solution(fwd_name)
filters = make_dics(epo.info, fwd, csd, real_filter=True)
del epo, csd, fwd
print("\n\n")
print("\n\n")
if not doTones:
epos = epo_conds
epo_names = epo_cond_names
for epo,epo_name in zip(epos,epo_names):
epo_csd = csd_morlet(epo, frequencies=freqs,
n_jobs=n_jobs, n_cycles=cycles, decim=3)
epo_csd = epo_csd.mean()
event_id, tmin, tmax = 1, -0.2, 0.5
events = mne.read_events(event_fname)
epochs = mne.Epochs(raw, events, event_id, tmin, tmax, proj=True,
picks=picks, baseline=(None, 0), preload=True,
reject=dict(grad=4000e-13, mag=4e-12))
evoked = epochs.average()
# Read forward operator
forward = mne.read_forward_solution(fname_fwd)
###############################################################################
# Computing the cross-spectral density matrix at 4 evenly spaced frequencies
# from 6 to 10 Hz. We use a decim value of 20 to speed up the computation in
# this example at the loss of accuracy.
#
# .. warning:: The use of several sensor types with the DICS beamformer is
# not heavily tested yet. Here we use verbose='error' to
# suppress a warning along these lines.
csd = csd_morlet(epochs, tmin=0, tmax=0.5, decim=20,
frequencies=np.linspace(6, 10, 4),
n_cycles=2.5) # short signals, must live with few cycles
# Compute DICS spatial filter and estimate source power.
filters = make_dics(epochs.info, forward, csd, reg=0.5, verbose='error')
print(filters)
stc, freqs = apply_dics_csd(csd, filters)
message = 'DICS source power in the 8-12 Hz frequency band'
brain = stc.plot(surface='inflated', hemi='rh', subjects_dir=subjects_dir,
time_label=message)
# Individual frequencies to estimate the CSD for
fmin = freq_bands[0][0]
fmax = freq_bands[-1][1]
frequencies = np.arange(fmin, fmax + 1, 2)
# Compute CSD matrices for each frequency and each condition.
for condition in conditions:
print('Condition:', condition)
# Remove the mean during the time interval for which we compute the CSD
epochs_baselined = epochs[condition].apply_baseline((csd_tmin, csd_tmax))
# Compute CSD for the desired time interval
csd = csd_morlet(epochs_baselined,
frequencies=frequencies,
tmin=csd_tmin,
tmax=csd_tmax,
decim=20,
n_jobs=n_jobs,
verbose=True)
# Save the CSD matrices
csd.save(fname.csd(condition=condition, subject=subject))
report.add_figs_to_section(csd.plot(show=False),
['CSD for %s' % condition],
section='Sensor-level')
# Also compute the CSD for the baseline period (use all epochs for this,
# regardless of condition). This way, we can compare the change in power caused
# by the presentation of the stimulus.
epochs = epochs.apply_baseline((-0.2, 0)) # Make sure data is zero-mean
csd_baseline = csd_morlet(epochs,
tmax,
proj=True,
picks=picks,
baseline=(None, 0),
preload=True,
reject=dict(grad=4000e-13, mag=4e-12))
evoked = epochs.average()
# Read forward operator
forward = mne.read_forward_solution(fname_fwd)
###############################################################################
# Computing the cross-spectral density matrix at 4 evenly spaced frequencies
# from 6 to 10 Hz. We use a decim value of 20 to speed up the computation in
# this example at the loss of accuracy.
csd = csd_morlet(epochs,
tmin=0,
tmax=0.5,
decim=20,
frequencies=np.linspace(6, 10, 4))
# Compute DICS spatial filter and estimate source power.
filters = make_dics(epochs.info, forward, csd, reg=0.5)
stc, freqs = apply_dics_csd(csd, filters)
message = 'DICS source power in the 8-12 Hz frequency band'
brain = stc.plot(surface='inflated',
hemi='rh',
subjects_dir=subjects_dir,
time_label=message)
# pass activity originating from the vertex, while dampening activity from
# other sources as much as possible.
#
# The :func:`make_dics` function has many switches that offer precise control
# over the way the filter weights are computed. Currently, there is no clear
# consensus regarding the best approach. This is why we will demonstrate two
# approaches here:
#
# 1. The approach as described in [2]_, which first normalizes the forward
# solution and computes a vector beamformer.
# 2. The scalar beamforming approach based on [3]_, which uses weight
# normalization instead of normalizing the forward solution.
# Estimate the cross-spectral density (CSD) matrix on the trial containing the
# signal.
csd_signal = csd_morlet(epochs['signal'], frequencies=[10])
# Compute the spatial filters for each vertex, using two approaches.
filters_approach1 = make_dics(
info, fwd, csd_signal, reg=0.05, pick_ori='max-power', normalize_fwd=True,
inversion='single', weight_norm=None)
filters_approach2 = make_dics(
info, fwd, csd_signal, reg=0.05, pick_ori='max-power', normalize_fwd=False,
inversion='matrix', weight_norm='unit-noise-gain')
# Compute the DICS power map by applying the spatial filters to the CSD matrix.
power_approach1, f = apply_dics_csd(csd_signal, filters_approach1)
power_approach2, f = apply_dics_csd(csd_signal, filters_approach2)
# Plot the DICS power maps for both approaches.
for approach, power in enumerate([power_approach1, power_approach2], 1):
def test_tf_dics(_load_forward, idx, mat_tol, vol_tol):
"""Test 5D time-frequency beamforming based on DICS."""
fwd_free, fwd_surf, fwd_fixed, _ = _load_forward
epochs, _, _, source_vertno, label, vertices, source_ind = \
_simulate_data(fwd_fixed, idx)
reg = 1 # Lots of regularization for our toy dataset
tmin = 0
tmax = 9
tstep = 4
win_lengths = [5, 5]
frequencies = [10, 20]
freq_bins = [(8, 12), (18, 22)]
with pytest.raises(RuntimeError, match='several sensor types'):
stcs = tf_dics(epochs,
fwd_surf,
None,
tmin,
tmax,
tstep,
win_lengths,
freq_bins=freq_bins,
frequencies=frequencies,
decim=10,
reg=reg,
label=label)
epochs.pick_types(meg='grad')
# Compute DICS for two time windows and two frequencies
for mode in ['fourier', 'multitaper', 'cwt_morlet']:
stcs = tf_dics(epochs,
fwd_surf,
None,
tmin,
tmax,
tstep,
win_lengths,
mode=mode,
freq_bins=freq_bins,
frequencies=frequencies,
decim=10,
reg=reg,
label=label)
# Did we find the true source at 20 Hz?
dist = _fwd_dist(stcs[1], fwd_surf, vertices, source_ind, tidx=0)
assert dist == 0
dist = _fwd_dist(stcs[1], fwd_surf, vertices, source_ind, tidx=1)
assert dist == 0
# 20 Hz power should decrease over time
assert stcs[1].data[source_ind, 0] > stcs[1].data[source_ind, 1]
# 20 Hz power should be more than 10 Hz power at the true source
assert stcs[1].data[source_ind, 0] > stcs[0].data[source_ind, 0]
# Manually compute source power and compare with the last tf_dics result.
source_power = []
time_windows = [(0, 5), (4, 9)]
for time_window in time_windows:
csd = csd_morlet(epochs,
frequencies=[frequencies[1]],
tmin=time_window[0],
tmax=time_window[1],
decim=10)
csd = csd.sum()
csd._data /= csd.n_fft
filters = make_dics(epochs.info, fwd_surf, csd, reg=reg, label=label)
stc_source_power, _ = apply_dics_csd(csd, filters)
source_power.append(stc_source_power.data)
# Comparing tf_dics results with dics_source_power results
assert_allclose(stcs[1].data, np.array(source_power).squeeze().T, atol=0)
# Test using noise csds. We're going to use identity matrices. That way,
# since we're using unit-noise-gain weight normalization, there should be
# no effect.
stcs = tf_dics(epochs,
fwd_surf,
None,
tmin,
tmax,
tstep,
win_lengths,
mode='cwt_morlet',
frequencies=frequencies,
decim=10,
reg=reg,
label=label,
normalize_fwd=False,
weight_norm='unit-noise-gain')
noise_csd = csd.copy()
inds = np.triu_indices(csd.n_channels)
# Using [:, :] syntax for in-place broadcasting
noise_csd._data[:, :] = 2 * np.eye(csd.n_channels)[inds][:, np.newaxis]
noise_csd.n_fft = 2 # Dividing by n_fft should yield an identity CSD
noise_csds = [noise_csd, noise_csd] # Two frequency bins
stcs_norm = tf_dics(epochs,
fwd_surf,
noise_csds,
tmin,
tmax,
tstep,
win_lengths,
mode='cwt_morlet',
frequencies=frequencies,
decim=10,
reg=reg,
label=label,
normalize_fwd=False,
weight_norm='unit-noise-gain')
assert_allclose(stcs_norm[0].data, stcs[0].data, atol=0)
assert_allclose(stcs_norm[1].data, stcs[1].data, atol=0)
# Test invalid parameter combinations
with pytest.raises(ValueError, match='fourier.*freq_bins" parameter'):
tf_dics(epochs,
fwd_surf,
None,
tmin,
tmax,
tstep,
win_lengths,
mode='fourier',
freq_bins=None)
with pytest.raises(ValueError, match='cwt_morlet.*frequencies" param'):
tf_dics(epochs,
fwd_surf,
None,
tmin,
tmax,
tstep,
win_lengths,
mode='cwt_morlet',
frequencies=None)
# Test if incorrect number of noise CSDs is detected
with pytest.raises(ValueError, match='One noise CSD object expected per'):
tf_dics(epochs,
fwd_surf, [noise_csds[0]],
tmin,
tmax,
tstep,
win_lengths,
freq_bins=freq_bins)
# Test if freq_bins and win_lengths incompatibility is detected
with pytest.raises(ValueError, match='One time window length expected'):
tf_dics(epochs,
fwd_surf,
None,
tmin,
tmax,
tstep,
win_lengths=[0, 1, 2],
freq_bins=freq_bins)
# Test if time step exceeding window lengths is detected
with pytest.raises(ValueError, match='Time step should not be larger'):
tf_dics(epochs,
fwd_surf,
None,
tmin,
tmax,
tstep=0.15,
win_lengths=[0.2, 0.1],
freq_bins=freq_bins)
# Test if incorrect number of n_ffts is detected
with pytest.raises(ValueError, match='When specifying number of FFT'):
tf_dics(epochs,
fwd_surf,
None,
tmin,
tmax,
tstep,
win_lengths,
freq_bins=freq_bins,
n_ffts=[1])
# Test if incorrect number of mt_bandwidths is detected
with pytest.raises(ValueError, match='When using multitaper mode and'):
tf_dics(epochs,
fwd_surf,
None,
tmin,
tmax,
tstep,
win_lengths=win_lengths,
freq_bins=freq_bins,
mode='multitaper',
mt_bandwidths=[20])
# Test if subtracting evoked responses yields NaN's, since we only have one
# epoch. Suppress division warnings.
assert len(epochs) == 1, len(epochs)
with np.errstate(invalid='ignore'):
stcs = tf_dics(epochs,
fwd_surf,
None,
tmin,
tmax,
tstep,
win_lengths,
mode='cwt_morlet',
frequencies=frequencies,
subtract_evoked=True,
reg=reg,
label=label,
decim=20)
assert np.all(np.isnan(stcs[0].data))
fname_fwd = op.join(data_path, 'derivatives', 'sub-{}'.format(subject),
'sub-{}_task-{}-fwd.fif'.format(subject, task))
subjects_dir = op.join(data_path, 'derivatives', 'freesurfer', 'subjects')
fwd = mne.read_forward_solution(fname_fwd)
###############################################################################
# We are interested in the beta band. Define a range of frequencies, using a
# log scale, from 12 to 30 Hz.
freqs = np.logspace(np.log10(12), np.log10(30), 9)
###############################################################################
# Computing the cross-spectral density matrix for the beta frequency band, for
# different time intervals. We use a decim value of 20 to speed up the
# computation in this example at the loss of accuracy.
csd = csd_morlet(epochs, freqs, tmin=-1, tmax=1.5, decim=20)
csd_baseline = csd_morlet(epochs, freqs, tmin=-1, tmax=0, decim=20)
# ERS activity starts at 0.5 seconds after stimulus onset
csd_ers = csd_morlet(epochs, freqs, tmin=0.5, tmax=1.5, decim=20)
###############################################################################
# To compute the source power for a frequency band, rather than each frequency
# separately, we average the CSD objects across frequencies.
csd = csd.mean()
csd_baseline = csd_baseline.mean()
csd_ers = csd_ers.mean()
###############################################################################
# Computing DICS spatial filters using the CSD that was computed on the entire
# timecourse.
filters = make_dics(epochs.info,
('sLORETA', [3, 5, 7]),
('eLORETA', [0.75, 1.25, 1.75]),
)):
# surfer_kwargs['clim']['lims'] = lims
stc1 = apply_inverse(evoked,
inverse_operator,
lambda2,
method=method,
pick_ori=None)
brain = stc1.plot(figure=mi, **surfer_kwargs)
brain.add_text(0.1, 0.9, method, 'title', font_size=20)
#%%
from mne.time_frequency import csd_morlet
from mne.beamformer import make_dics, apply_dics_csd
csd = csd_morlet(epochs, tmin=0, tmax=0.25, frequencies=np.linspace(2, 4))
# Compute DICS spatial filter and estimate source power.
filters = make_dics(epochs.info, fwd, csd, real_filter=True)
stc, freqs = apply_dics_csd(csd, filters)
message = 'DICS source power in the 8-12 Hz frequency band'
brain = stc.plot(surface='inflated',
hemi='rh',
subjects_dir=subjects_dir,
time_label=message,
time_viewer=True)
def test_tf_dics():
"""Test 5D time-frequency beamforming based on DICS."""
fwd_free, fwd_surf, fwd_fixed, fwd_vol, label = _load_forward()
epochs, evoked, _, source_vertno = _simulate_data(fwd_fixed)
vertices = np.intersect1d(label.vertices, fwd_free['src'][0]['vertno'])
source_ind = vertices.tolist().index(source_vertno)
reg = 1 # Lots of regularization for our toy dataset
tmin = 0
tmax = 9
tstep = 4
win_lengths = [5, 5]
frequencies = [10, 20]
freq_bins = [(8, 12), (18, 22)]
# Compute DICS for two time windows and two frequencies
for mode in ['fourier', 'multitaper', 'cwt_morlet']:
stcs = tf_dics(epochs, fwd_surf, None, tmin, tmax, tstep, win_lengths,
mode=mode, freq_bins=freq_bins, frequencies=frequencies,
decim=10, reg=reg, label=label)
# Did we find the true source at 20 Hz?
assert np.argmax(stcs[1].data[:, 0]) == source_ind
assert np.argmax(stcs[1].data[:, 1]) == source_ind
# 20 Hz power should decrease over time
assert stcs[1].data[source_ind, 0] > stcs[1].data[source_ind, 1]
# 20 Hz power should be more than 10 Hz power at the true source
assert stcs[1].data[source_ind, 0] > stcs[0].data[source_ind, 0]
# Manually compute source power and compare with the last tf_dics result.
source_power = []
time_windows = [(0, 5), (4, 9)]
for time_window in time_windows:
csd = csd_morlet(epochs, frequencies=[frequencies[1]],
tmin=time_window[0], tmax=time_window[1], decim=10)
csd = csd.sum()
csd._data /= csd.n_fft
filters = make_dics(epochs.info, fwd_surf, csd, reg=reg, label=label)
stc_source_power, _ = apply_dics_csd(csd, filters)
source_power.append(stc_source_power.data)
# Comparing tf_dics results with dics_source_power results
assert_allclose(stcs[1].data, np.array(source_power).squeeze().T, atol=0)
# Test using noise csds. We're going to use identity matrices. That way,
# since we're using unit-noise-gain weight normalization, there should be
# no effect.
stcs = tf_dics(epochs, fwd_surf, None, tmin, tmax, tstep, win_lengths,
mode='cwt_morlet', frequencies=frequencies, decim=10,
reg=reg, label=label, normalize_fwd=False,
weight_norm='unit-noise-gain')
noise_csd = csd.copy()
inds = np.triu_indices(csd.n_channels)
# Using [:, :] syntax for in-place broadcasting
noise_csd._data[:, :] = 2 * np.eye(csd.n_channels)[inds][:, np.newaxis]
noise_csd.n_fft = 2 # Dividing by n_fft should yield an identity CSD
noise_csds = [noise_csd, noise_csd] # Two frequency bins
stcs_norm = tf_dics(epochs, fwd_surf, noise_csds, tmin, tmax, tstep,
win_lengths, mode='cwt_morlet',
frequencies=frequencies, decim=10, reg=reg,
label=label, normalize_fwd=False,
weight_norm='unit-noise-gain')
assert_allclose(stcs_norm[0].data, stcs[0].data, atol=0)
assert_allclose(stcs_norm[1].data, stcs[1].data, atol=0)
# Test invalid parameter combinations
raises(ValueError, tf_dics, epochs, fwd_surf, None, tmin, tmax, tstep,
win_lengths, mode='fourier', freq_bins=None)
raises(ValueError, tf_dics, epochs, fwd_surf, None, tmin, tmax, tstep,
win_lengths, mode='cwt_morlet', frequencies=None)
# Test if incorrect number of noise CSDs is detected
raises(ValueError, tf_dics, epochs, fwd_surf, [noise_csds[0]], tmin, tmax,
tstep, win_lengths, freq_bins=freq_bins)
# Test if freq_bins and win_lengths incompatibility is detected
raises(ValueError, tf_dics, epochs, fwd_surf, None, tmin, tmax, tstep,
win_lengths=[0, 1, 2], freq_bins=freq_bins)
# Test if time step exceeding window lengths is detected
raises(ValueError, tf_dics, epochs, fwd_surf, None, tmin, tmax, tstep=0.15,
win_lengths=[0.2, 0.1], freq_bins=freq_bins)
# Test if incorrent number of n_ffts is detected
raises(ValueError, tf_dics, epochs, fwd_surf, None, tmin, tmax, tstep,
win_lengths, freq_bins=freq_bins, n_ffts=[1])
# Test if incorrect number of mt_bandwidths is detected
raises(ValueError, tf_dics, epochs, fwd_surf, None, tmin, tmax, tstep,
win_lengths=win_lengths, freq_bins=freq_bins, mode='multitaper',
mt_bandwidths=[20])
# Test if subtracting evoked responses yields NaN's, since we only have one
# epoch. Suppress division warnings.
with pytest.warns(RuntimeWarning, match='[invalid|empty]'):
stcs = tf_dics(epochs, fwd_surf, None, tmin, tmax, tstep, win_lengths,
mode='cwt_morlet', frequencies=frequencies,
subtract_evoked=True, reg=reg, label=label, decim=20)
assert np.all(np.isnan(stcs[0].data))
# the frequencies passed as lists (for CSD calculation)
# take some time to choose appropriate values for your analysis, esp. for cycle number: what are your goals? what is the window length? etc.
freqs_n = [3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]
cycs_n = [5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 9, 9, 9, 9, 9, 9, 9, 9, 11, 11, 11, 11, 11, 11, 11, 11, 11, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13]
freqs_g = [65, 67, 69, 71, 73, 75, 77, 79, 81, 83, 85, 87, 89, 91, 93, 95]
cycs_g = [15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15]
# fmins = [3, 8, 14, 22, 31]
# fmaxs = [7, 13, 21, 30, 46]
# for the Beamforming analysis, you need a CSD over all conditions to calculate shared filters
# for each subject, calc csd_all& csd_g_all
for sub in subjs:
epo = mne.read_epochs("{}{}_2-epo.fif".format(proc_dir,sub))
csd_n = csd_morlet(epo, frequencies=freqs_n, n_jobs=8, n_cycles=cycs_n, decim=1)
csd_n.save("{}{}-csd.h5".format(proc_dir,sub))
breakpoint()
csd_g = csd_morlet(epo, frequencies=freqs_g, n_jobs=8, n_cycles=cycs_g, decim=1)
csd_g.save("{}{}-gamma-csd.h5".format(proc_dir,sub))
# then, you need CSDs for the single conditions you want to pass through the filters and compare
# for each subject, calc csd & csd_g for each condition
for sub in subjs:
epo = mne.read_epochs("{}{}_2-epo.fif".format(proc_dir,sub))
for cond,c in conditions.items():
csd_n = csd_morlet(epo[c], frequencies=freqs_n, n_jobs=8, n_cycles=cycs_n, decim=1)
csd_n.save("{}{}_{}-csd.h5".format(proc_dir,sub,cond))
# Set picks
picks = mne.pick_types(raw.info, meg=True, eeg=False, eog=False,
stim=False, exclude='bads')
# Read epochs
event_id, tmin, tmax = 1, -0.2, 0.5
events = mne.read_events(event_fname)
epochs = mne.Epochs(raw, events, event_id, tmin, tmax, proj=True,
picks=picks, baseline=(None, 0), preload=True,
reject=dict(grad=4000e-13, mag=4e-12))
evoked = epochs.average()
# Read forward operator
forward = mne.read_forward_solution(fname_fwd)
###############################################################################
# Computing the cross-spectral density matrix at 4 evenly spaced frequencies
# from 6 to 10 Hz. We use a decim value of 20 to speed up the computation in
# this example at the loss of accuracy.
csd = csd_morlet(epochs, tmin=0, tmax=0.5, decim=20,
frequencies=np.linspace(6, 10, 4))
# Compute DICS spatial filter and estimate source power.
filters = make_dics(epochs.info, forward, csd, reg=0.5)
stc, freqs = apply_dics_csd(csd, filters)
message = 'DICS source power in the 8-12 Hz frequency band'
brain = stc.plot(surface='inflated', hemi='rh', subjects_dir=subjects_dir,
time_label=message)
size=400)
# Indicate the true locations of the source activity on the plot.
brain.add_foci(source_vert1, coords_as_verts=True, hemi='lh')
brain.add_foci(source_vert2, coords_as_verts=True, hemi='rh')
# Rotate the view and add a title.
mlab.view(0, 0, 550, [0, 0, 0])
mlab.title('MNE-dSPM inverse (RMS)', height=0.9)
###############################################################################
# Computing a cortical power map at 10 Hz. using a DICS beamformer:
# Estimate the cross-spectral density (CSD) matrix on the trial containing the
# signal.
csd_signal = csd_morlet(epochs['signal'], frequencies=[10])
# Compute the DICS powermap. For this simulated dataset, we need a lot of
# regularization for the beamformer to behave properly. For real recordings,
# this amount of regularization is probably too much.
filters = make_dics(epochs.info, fwd, csd_signal, reg=1, pick_ori='max-power')
power, f = apply_dics_csd(csd_signal, filters)
# Plot the DICS power map.
brain = power.plot('sample',
subjects_dir=subjects_dir,
hemi='both',
figure=2,
size=400)
# Indicate the true locations of the source activity on the plot.
# Create epochs
###############################################################################
title = 'Simulated evoked for two signal vertices'
epochs = create_epochs(raw2,
title=title,
fn_simulated_epochs=None,
fn_report_h5=fn_report_h5)
epochs_grad = epochs.copy().pick_types(meg='grad')
epochs_mag = epochs.copy().pick_types(meg='mag')
epochs_joint = epochs.copy().pick_types(meg=True)
# Make CSDs
csd = csd_morlet(epochs, [config.signal_freq, config.signal_freq2],
tmin=0,
tmax=1,
decim=5)
noise_csd = csd_morlet(epochs, [config.signal_freq, config.signal_freq2],
tmin=-1,
tmax=0,
decim=5)
###############################################################################
# Compute DICS beamformer results
###############################################################################
# Speed things up by restricting the forward solution to only the two
# relevant source points.
src_sel = np.sort(np.array([config.vertex, nb_vertex]))
fwd = _restrict_forward_to_src_sel(fwd_disc_man, src_sel)
picks=picks,
baseline=(None, 0),
preload=True,
reject=dict(grad=4000e-13))
evoked = epochs.average()
# Read forward operator
forward = mne.read_forward_solution(fname_fwd)
###############################################################################
# Computing the cross-spectral density matrix at 4 evenly spaced frequencies
# from 6 to 10 Hz. We use a decim value of 20 to speed up the computation in
# this example at the loss of accuracy.
csd = csd_morlet(epochs,
tmin=0,
tmax=0.5,
decim=20,
frequencies=np.linspace(6, 10, 4),
n_cycles=2.5) # short signals, must live with few cycles
# Compute DICS spatial filter and estimate source power.
filters = make_dics(epochs.info, forward, csd, reg=0.5)
print(filters)
stc, freqs = apply_dics_csd(csd, filters)
message = 'DICS source power in the 8-12 Hz frequency band'
brain = stc.plot(surface='inflated',
hemi='rh',
subjects_dir=subjects_dir,
time_label=message)
def test_tf_dics():
"""Test 5D time-frequency beamforming based on DICS."""
fwd_free, fwd_surf, fwd_fixed, fwd_vol, label = _load_forward()
epochs, evoked, _, source_vertno = _simulate_data(fwd_fixed)
vertices = np.intersect1d(label.vertices, fwd_free['src'][0]['vertno'])
source_ind = vertices.tolist().index(source_vertno)
reg = 1 # Lots of regularization for our toy dataset
tmin = 0
tmax = 9
tstep = 4
win_lengths = [5, 5]
frequencies = [10, 20]
freq_bins = [(8, 12), (18, 22)]
# Compute DICS for two time windows and two frequencies
for mode in ['fourier', 'multitaper', 'cwt_morlet']:
stcs = tf_dics(epochs, fwd_surf, None, tmin, tmax, tstep, win_lengths,
mode=mode, freq_bins=freq_bins, frequencies=frequencies,
decim=10, reg=reg, label=label)
# Did we find the true source at 20 Hz?
assert np.argmax(stcs[1].data[:, 0]) == source_ind
assert np.argmax(stcs[1].data[:, 1]) == source_ind
# 20 Hz power should decrease over time
assert stcs[1].data[source_ind, 0] > stcs[1].data[source_ind, 1]
# 20 Hz power should be more than 10 Hz power at the true source
assert stcs[1].data[source_ind, 0] > stcs[0].data[source_ind, 0]
# Manually compute source power and compare with the last tf_dics result.
source_power = []
time_windows = [(0, 5), (4, 9)]
for time_window in time_windows:
csd = csd_morlet(epochs, frequencies=[frequencies[1]],
tmin=time_window[0], tmax=time_window[1], decim=10)
csd = csd.sum()
csd._data /= csd.n_fft
filters = make_dics(epochs.info, fwd_surf, csd, reg=reg, label=label)
stc_source_power, _ = apply_dics_csd(csd, filters)
source_power.append(stc_source_power.data)
# Comparing tf_dics results with dics_source_power results
assert_allclose(stcs[1].data, np.array(source_power).squeeze().T, atol=0)
# Test using noise csds. We're going to use identity matrices. That way,
# since we're using unit-noise-gain weight normalization, there should be
# no effect.
stcs = tf_dics(epochs, fwd_surf, None, tmin, tmax, tstep, win_lengths,
mode='cwt_morlet', frequencies=frequencies, decim=10,
reg=reg, label=label, normalize_fwd=False,
weight_norm='unit-noise-gain')
noise_csd = csd.copy()
inds = np.triu_indices(csd.n_channels)
# Using [:, :] syntax for in-place broadcasting
noise_csd._data[:, :] = 2 * np.eye(csd.n_channels)[inds][:, np.newaxis]
noise_csd.n_fft = 2 # Dividing by n_fft should yield an identity CSD
noise_csds = [noise_csd, noise_csd] # Two frequency bins
stcs_norm = tf_dics(epochs, fwd_surf, noise_csds, tmin, tmax, tstep,
win_lengths, mode='cwt_morlet',
frequencies=frequencies, decim=10, reg=reg,
label=label, normalize_fwd=False,
weight_norm='unit-noise-gain')
assert_allclose(stcs_norm[0].data, stcs[0].data, atol=0)
assert_allclose(stcs_norm[1].data, stcs[1].data, atol=0)
# Test invalid parameter combinations
raises(ValueError, tf_dics, epochs, fwd_surf, None, tmin, tmax, tstep,
win_lengths, mode='fourier', freq_bins=None)
raises(ValueError, tf_dics, epochs, fwd_surf, None, tmin, tmax, tstep,
win_lengths, mode='cwt_morlet', frequencies=None)
# Test if incorrect number of noise CSDs is detected
raises(ValueError, tf_dics, epochs, fwd_surf, [noise_csds[0]], tmin, tmax,
tstep, win_lengths, freq_bins=freq_bins)
# Test if freq_bins and win_lengths incompatibility is detected
raises(ValueError, tf_dics, epochs, fwd_surf, None, tmin, tmax, tstep,
win_lengths=[0, 1, 2], freq_bins=freq_bins)
# Test if time step exceeding window lengths is detected
raises(ValueError, tf_dics, epochs, fwd_surf, None, tmin, tmax, tstep=0.15,
win_lengths=[0.2, 0.1], freq_bins=freq_bins)
# Test if incorrent number of n_ffts is detected
raises(ValueError, tf_dics, epochs, fwd_surf, None, tmin, tmax, tstep,
win_lengths, freq_bins=freq_bins, n_ffts=[1])
# Test if incorrect number of mt_bandwidths is detected
raises(ValueError, tf_dics, epochs, fwd_surf, None, tmin, tmax, tstep,
win_lengths=win_lengths, freq_bins=freq_bins, mode='multitaper',
mt_bandwidths=[20])
# Test if subtracting evoked responses yields NaN's, since we only have one
# epoch. Suppress division warnings.
with pytest.warns(RuntimeWarning, match='[invalid|empty]'):
stcs = tf_dics(epochs, fwd_surf, None, tmin, tmax, tstep, win_lengths,
mode='cwt_morlet', frequencies=frequencies,
subtract_evoked=True, reg=reg, label=label, decim=20)
assert np.all(np.isnan(stcs[0].data))
s=meg,
n1=len(neg['r1']),
n2=len(neg['r2']),
n3=len(neg['s1']),
n4=len(neg['s2']),
p1=len(pos['r1']),
p2=len(pos['r2']),
p3=len(pos['s1']),
p4=len(pos['s2'])))
# calculate CSD matrix for each all, base, exp, rest
## alternative with multitaper - template: csd = csd_multitaper(epo,fmin=7,fmax=14,bandwidth=1)
csd_all_alpha = csd_morlet(epo_all,
frequencies=freqs["alpha"],
n_jobs=8,
n_cycles=cycles["alpha"],
decim=1)
csd_all_alpha.save("{dir}nc_{meg}-csd_all_alpha.h5".format(dir=meg_dir,
meg=meg))
csd_all_theta = csd_morlet(epo_all,
frequencies=freqs["theta"],
n_jobs=8,
n_cycles=cycles["theta"],
decim=1)
csd_all_theta.save("{dir}nc_{meg}-csd_all_theta.h5".format(dir=meg_dir,
meg=meg))
csd_all_beta_low = csd_morlet(epo_all,
frequencies=freqs["beta_low"],
n_jobs=8,
n_cycles=cycles["beta_low"],