def test_time_frequency():
"""Test time frequency transform (PSD and phase lock)
"""
# Set parameters
event_id = 1
tmin = -0.2
tmax = 0.5
# Setup for reading the raw data
raw = fiff.Raw(raw_fname)
events = read_events(event_fname)
include = []
exclude = raw.info['bads'] + ['MEG 2443', 'EEG 053'] # bads + 2 more
# picks MEG gradiometers
picks = fiff.pick_types(raw.info, meg='grad', eeg=False,
stim=False, include=include, exclude=exclude)
picks = picks[:2]
epochs = Epochs(raw, events, event_id, tmin, tmax, picks=picks,
baseline=(None, 0))
data = epochs.get_data()
times = epochs.times
frequencies = np.arange(6, 20, 5) # define frequencies of interest
Fs = raw.info['sfreq'] # sampling in Hz
n_cycles = frequencies / float(4)
power, phase_lock = induced_power(data, Fs=Fs, frequencies=frequencies,
n_cycles=n_cycles, use_fft=True)
assert_true(power.shape == (len(picks), len(frequencies), len(times)))
assert_true(power.shape == phase_lock.shape)
assert_true(np.sum(phase_lock >= 1) == 0)
assert_true(np.sum(phase_lock <= 0) == 0)
power, phase_lock = induced_power(data, Fs=Fs, frequencies=frequencies,
n_cycles=2, use_fft=False)
assert_true(power.shape == (len(picks), len(frequencies), len(times)))
assert_true(power.shape == phase_lock.shape)
assert_true(np.sum(phase_lock >= 1) == 0)
assert_true(np.sum(phase_lock <= 0) == 0)
tfr = cwt_morlet(data[0], Fs, frequencies, use_fft=True, n_cycles=2)
assert_true(tfr.shape == (len(picks), len(frequencies), len(times)))
single_power = single_trial_power(data, Fs, frequencies, use_fft=False,
n_cycles=2)
assert_array_almost_equal(np.mean(single_power), power)
def test_time_frequency():
"""Test time frequency transform (PSD and phase lock)
"""
# Set parameters
event_id = 1
tmin = -0.2
tmax = 0.5
# Setup for reading the raw data
raw = io.Raw(raw_fname)
events = read_events(event_fname)
include = []
exclude = raw.info['bads'] + ['MEG 2443', 'EEG 053'] # bads + 2 more
# picks MEG gradiometers
picks = pick_types(raw.info, meg='grad', eeg=False,
stim=False, include=include, exclude=exclude)
picks = picks[:2]
epochs = Epochs(raw, events, event_id, tmin, tmax, picks=picks,
baseline=(None, 0))
data = epochs.get_data()
times = epochs.times
frequencies = np.arange(6, 20, 5) # define frequencies of interest
Fs = raw.info['sfreq'] # sampling in Hz
n_cycles = frequencies / float(4)
power, phase_lock = induced_power(data, Fs=Fs, frequencies=frequencies,
n_cycles=n_cycles, use_fft=True)
assert_true(power.shape == (len(picks), len(frequencies), len(times)))
assert_true(power.shape == phase_lock.shape)
assert_true(np.sum(phase_lock >= 1) == 0)
assert_true(np.sum(phase_lock <= 0) == 0)
power, phase_lock = induced_power(data, Fs=Fs, frequencies=frequencies,
n_cycles=2, use_fft=False)
assert_true(power.shape == (len(picks), len(frequencies), len(times)))
assert_true(power.shape == phase_lock.shape)
assert_true(np.sum(phase_lock >= 1) == 0)
assert_true(np.sum(phase_lock <= 0) == 0)
tfr = cwt_morlet(data[0], Fs, frequencies, use_fft=True, n_cycles=2)
assert_true(tfr.shape == (len(picks), len(frequencies), len(times)))
single_power = single_trial_power(data, Fs, frequencies, use_fft=False,
n_cycles=2)
assert_array_almost_equal(np.mean(single_power), power)
def normSignal(grid,frequencies = None,nc=None,dec=None,events=None):
"""Returns normalised power spectrums for events (using morlet wavelets) [n_epochs,n_channels,n_frequencies]
frequencies -- Morlet frequencies
nc -- Number of cycles (DEFAULT 12*np.arange(1,len(frequencies)+1) #Linear formula [Chan,Baker et al. JNS 2011])
Dec -- Decimation factor
Events - events to find power of"""
if frequencies is None:
frequencies = np.arange(1,101)
if nc is None:
nc = 0.12*np.arange(1,len(frequencies)+1) #Linear formula [Chan,Baker et al. JNS 2011]
print nc
if dec is None:
dec = 1
if events is None:
events=grid.event_matrix()
events = events[events['event.code']==5] #Use ISIs as baseline
#Pre allocate power matrix for efficiency
pows = np.zeros([len(events),len(grid.wc()),len(frequencies)])
for j,chan in enumerate(grid.wc()):
for i,(on,off) in enumerate(events[['pulse.on','pulse.off']].values):
logger.info( 'Normalising power on channel '+chan+' baseline event '+str(i+1)+'/'+str(len(events)))
data = grid.splice(grid.wd()[chan],times=[on,off])[None,None,:]
data = np.vstack([data,data]) #mne doesn't allow only 1 event so duplicate the same event (which will then be averaged)
p,phase=mtf.induced_power(data, Fs=grid.fs(), frequencies=frequencies, use_fft=False, n_cycles=nc, decim=dec, n_jobs=1,normFreqs=None)
pows[i,j,:]=p.mean(axis=2).squeeze() #Take average across time for each frequency
return pows
def morlet(grid,dec=None,frequencies=None,fs=None,events=None,nc=None,normFreqs=None):
#Performs a morlet wavelet analysis across events
if events is None:
events = grid.event_matrix()
if fs is None:
fs = grid.fs()
if dec is None:
dec = 1
if frequencies is None:
frequencies= np.arange(1,101,dec)
if nc is None:
nc = 0.12*np.arange(1,len(frequencies)+1)
print nc
sigs = grid.wd()
maxtimediff = (events['pulse.off']-events['pulse.on']).max()
maxtimepoints = round(maxtimediff*fs)+1
data = np.zeros([len(events),len(grid.wc()),maxtimepoints])
for k,chan in enumerate(grid.wc()):
for j,(on,off) in enumerate(events.values):
print 'Pre-processing Channel:'+chan + ' | Event '+str(j)+'/'+str(len(events.values))
d=grid.splice(sigs[chan], times=[on,off])
data[j,k,:len(d)] = d
pows,phase=mtf.induced_power(data, Fs=float(fs), frequencies=frequencies, use_fft=False, n_cycles=nc, decim=dec, n_jobs=1,normFreqs=normFreqs)
return pows,phase
def test_compute_epochs_csd():
"""Test computing cross-spectral density from epochs
"""
epochs, epochs_sin = _get_data()
# Check that wrong parameters are recognized
assert_raises(ValueError, compute_epochs_csd, epochs, mode="notamode")
assert_raises(ValueError, compute_epochs_csd, epochs, fmin=20, fmax=10)
assert_raises(ValueError, compute_epochs_csd, epochs, fmin=20, fmax=20.1)
assert_raises(ValueError, compute_epochs_csd, epochs, tmin=0.15, tmax=0.1)
assert_raises(ValueError, compute_epochs_csd, epochs, tmin=0, tmax=10)
assert_raises(ValueError, compute_epochs_csd, epochs, tmin=10, tmax=11)
data_csd_mt = compute_epochs_csd(epochs, mode="multitaper", fmin=8, fmax=12, tmin=0.04, tmax=0.15)
data_csd_fourier = compute_epochs_csd(epochs, mode="fourier", fmin=8, fmax=12, tmin=0.04, tmax=0.15)
# Check shape of the CSD matrix
n_chan = len(data_csd_mt.ch_names)
assert_equal(data_csd_mt.data.shape, (n_chan, n_chan))
assert_equal(data_csd_fourier.data.shape, (n_chan, n_chan))
# Check if the CSD matrix is hermitian
assert_array_equal(np.tril(data_csd_mt.data).T.conj(), np.triu(data_csd_mt.data))
assert_array_equal(np.tril(data_csd_fourier.data).T.conj(), np.triu(data_csd_fourier.data))
# Computing induced power for comparison
epochs.crop(tmin=0.04, tmax=0.15)
power, _ = induced_power(epochs.get_data(), epochs.info["sfreq"], [10], n_cycles=0.6)
power = np.mean(power, 2)
# Maximum PSD should occur for specific channel
max_ch_power = power.argmax()
max_ch_mt = data_csd_mt.data.diagonal().argmax()
max_ch_fourier = data_csd_fourier.data.diagonal().argmax()
assert_equal(max_ch_mt, max_ch_power)
assert_equal(max_ch_fourier, max_ch_power)
# Maximum CSD should occur for specific channel
ch_csd_mt = [np.abs(data_csd_mt.data[max_ch_power][i]) if i != max_ch_power else 0 for i in range(n_chan)]
max_ch_csd_mt = np.argmax(ch_csd_mt)
ch_csd_fourier = [np.abs(data_csd_fourier.data[max_ch_power][i]) if i != max_ch_power else 0 for i in range(n_chan)]
max_ch_csd_fourier = np.argmax(ch_csd_fourier)
assert_equal(max_ch_csd_mt, max_ch_csd_fourier)
# Check a list of CSD matrices is returned for multiple frequencies within
# a given range when fsum=False
csd_fsum = compute_epochs_csd(epochs, mode="fourier", fmin=8, fmax=20, fsum=True)
csds = compute_epochs_csd(epochs, mode="fourier", fmin=8, fmax=20, fsum=False)
freqs = [csd.frequencies[0] for csd in csds]
csd_sum = np.zeros_like(csd_fsum.data)
for csd in csds:
csd_sum += csd.data
assert len(csds) == 2
assert len(csd_fsum.frequencies) == 2
assert_array_equal(csd_fsum.frequencies, freqs)
assert_array_equal(csd_fsum.data, csd_sum)
def normSignal(grid, frequencies=None, nc=None, dec=None, events=None):
"""Returns normalised power spectrums for events (using morlet wavelets) [n_epochs,n_channels,n_frequencies]
frequencies -- Morlet frequencies
nc -- Number of cycles (DEFAULT 12*np.arange(1,len(frequencies)+1) #Linear formula [Chan,Baker et al. JNS 2011])
Dec -- Decimation factor
Events - events to find power of"""
if frequencies is None:
frequencies = np.arange(1, 101)
if nc is None:
nc = 0.12 * np.arange(
1,
len(frequencies) + 1) #Linear formula [Chan,Baker et al. JNS 2011]
print nc
if dec is None:
dec = 1
if events is None:
events = grid.event_matrix()
events = events[events['event.code'] == 5] #Use ISIs as baseline
#Pre allocate power matrix for efficiency
pows = np.zeros([len(events), len(grid.wc()), len(frequencies)])
for j, chan in enumerate(grid.wc()):
for i, (on, off) in enumerate(events[['pulse.on',
'pulse.off']].values):
logger.info('Normalising power on channel ' + chan +
' baseline event ' + str(i + 1) + '/' +
str(len(events)))
data = grid.splice(grid.wd()[chan], times=[on, off])[None, None, :]
data = np.vstack(
[data, data]
) #mne doesn't allow only 1 event so duplicate the same event (which will then be averaged)
p, phase = mtf.induced_power(data,
Fs=grid.fs(),
frequencies=frequencies,
use_fft=False,
n_cycles=nc,
decim=dec,
n_jobs=1,
normFreqs=None)
pows[i, j, :] = p.mean(
axis=2).squeeze() #Take average across time for each frequency
return pows
times = 1e3 * epochs.times # change unit to ms
evoked_data = evoked.data * 1e13 # change unit to fT / cm
# Take only one channel
data = data[:, 97:98, :]
evoked_data = evoked_data[97:98, :]
frequencies = np.arange(7, 30, 3) # define frequencies of interest
n_cycles = frequencies / float(7) # different number of cycle per frequency
Fs = raw.info['sfreq'] # sampling in Hz
decim = 3
power, phase_lock = induced_power(data,
Fs=Fs,
frequencies=frequencies,
n_cycles=n_cycles,
n_jobs=1,
use_fft=False,
decim=decim,
zero_mean=True)
# baseline corrections with ratio
power /= np.mean(power[:, :, times[::decim] < 0], axis=2)[:, :, None]
###############################################################################
# View time-frequency plots
import matplotlib.pyplot as plt
plt.clf()
plt.subplots_adjust(0.1, 0.08, 0.96, 0.94, 0.2, 0.63)
plt.subplot(3, 1, 1)
plt.plot(times, evoked_data.T)
def test_compute_epochs_csd():
"""Test computing cross-spectral density from epochs
"""
epochs, epochs_sin = _get_data()
# Check that wrong parameters are recognized
assert_raises(ValueError, compute_epochs_csd, epochs, mode='notamode')
assert_raises(ValueError, compute_epochs_csd, epochs, fmin=20, fmax=10)
assert_raises(ValueError, compute_epochs_csd, epochs, fmin=20, fmax=20.1)
assert_raises(ValueError, compute_epochs_csd, epochs, tmin=0.15, tmax=0.1)
assert_raises(ValueError, compute_epochs_csd, epochs, tmin=0, tmax=10)
assert_raises(ValueError, compute_epochs_csd, epochs, tmin=10, tmax=11)
data_csd_mt = compute_epochs_csd(epochs, mode='multitaper', fmin=8,
fmax=12, tmin=0.04, tmax=0.15)
data_csd_fourier = compute_epochs_csd(epochs, mode='fourier', fmin=8,
fmax=12, tmin=0.04, tmax=0.15)
# Check shape of the CSD matrix
n_chan = len(data_csd_mt.ch_names)
assert_equal(data_csd_mt.data.shape, (n_chan, n_chan))
assert_equal(data_csd_fourier.data.shape, (n_chan, n_chan))
# Check if the CSD matrix is hermitian
assert_array_equal(np.tril(data_csd_mt.data).T.conj(),
np.triu(data_csd_mt.data))
assert_array_equal(np.tril(data_csd_fourier.data).T.conj(),
np.triu(data_csd_fourier.data))
# Computing induced power for comparison
epochs.crop(tmin=0.04, tmax=0.15)
power, _ = induced_power(epochs.get_data(), epochs.info['sfreq'], [10],
n_cycles=0.6)
power = np.mean(power, 2)
# Maximum PSD should occur for specific channel
max_ch_power = power.argmax()
max_ch_mt = data_csd_mt.data.diagonal().argmax()
max_ch_fourier = data_csd_fourier.data.diagonal().argmax()
assert_equal(max_ch_mt, max_ch_power)
assert_equal(max_ch_fourier, max_ch_power)
# Maximum CSD should occur for specific channel
ch_csd_mt = [np.abs(data_csd_mt.data[max_ch_power][i])
if i != max_ch_power else 0 for i in range(n_chan)]
max_ch_csd_mt = np.argmax(ch_csd_mt)
ch_csd_fourier = [np.abs(data_csd_fourier.data[max_ch_power][i])
if i != max_ch_power else 0 for i in range(n_chan)]
max_ch_csd_fourier = np.argmax(ch_csd_fourier)
assert_equal(max_ch_csd_mt, max_ch_csd_fourier)
# Check a list of CSD matrices is returned for multiple frequencies within
# a given range when fsum=False
csd_fsum = compute_epochs_csd(epochs, mode='fourier', fmin=8, fmax=20,
fsum=True)
csds = compute_epochs_csd(epochs, mode='fourier', fmin=8, fmax=20,
fsum=False)
freqs = [csd.frequencies[0] for csd in csds]
csd_sum = np.zeros_like(csd_fsum.data)
for csd in csds:
csd_sum += csd.data
assert(len(csds) == 2)
assert(len(csd_fsum.frequencies) == 2)
assert_array_equal(csd_fsum.frequencies, freqs)
assert_array_equal(csd_fsum.data, csd_sum)
tmax=2.5,
baseline=(-0.5, 0.0),
reject=dict(eeg=200e-6))
# Calculate power, plv
Fs = raw.info['sfreq']
times = epochs.times
plv = np.zeros((len(conds), len(freqs), len(times)))
tfspec = np.zeros((len(conds), len(freqs), len(times)))
condorder = np.zeros(len(conds)) # To save the order in which they come
for condind, cond in enumerate(condstr):
dat = epochs[cond].get_data()[:, ch, :].mean(axis=1, keepdims=True)
powtemp, plvtemp = induced_power(dat,
Fs=Fs,
frequencies=freqs,
n_cycles=n_cycles,
zero_mean=True)
plv[condind, :, :] = plvtemp.squeeze()
tfspec[condind, :, :] = powtemp.squeeze()
# Save results to the RES directory
savedict = dict(tfspec=tfspec,
plv=plv,
times=times,
conds=conds,
freqs=freqs)
save_name = subj + '_plv_inducedpow_2Hz_100Hz.mat'
print 'Saving data for subject', subj
if (not os.path.isdir(respath)):
os.mkdir(respath)
epochs = mne.Epochs(raw, events, event_id, tmin, tmax, picks=picks,
baseline=(None, 0), reject=dict(grad=4000e-13, eog=150e-6))
data = epochs.get_data() # as 3D matrix
layout = mne.find_layout(epochs.info, 'meg')
###############################################################################
# Calculate power and phase locking value
frequencies = np.arange(7, 30, 3) # define frequencies of interest
n_cycles = frequencies / float(7) # different number of cycle per frequency
Fs = raw.info['sfreq'] # sampling in Hz
decim = 3
power, phase_lock = induced_power(data, Fs=Fs, frequencies=frequencies,
n_cycles=n_cycles, n_jobs=1, use_fft=False,
decim=decim, zero_mean=True)
###############################################################################
# Prepare topography plots, set baseline correction parameters
baseline = (None, 0) # set the baseline for induced power
mode = 'ratio' # set mode for baseline rescaling
###############################################################################
# Show topography of power.
title = 'Induced power - MNE sample data'
plot_topo_power(epochs, power, frequencies, layout, baseline=baseline,
mode=mode, decim=decim, vmin=0., vmax=14, title=title)
plt.show()
# get data #
OCP = epochs['OCP'].get_data()
CVC = epochs['CVC'].get_data()
# gather info for time freq
import numpy as np
n_cycles = 2 # number of cycles in Morlet wavelet
frequencies = np.arange(7, 30, 3) # frequencies of interest
Fs = raw.info['sfreq'] # sampling in Hz
#Compute induced power and phase-locking values:
from mne.time_frequency import induced_power
power, phase_lock = induced_power(OCP, Fs=Fs, frequencies=frequencies, n_cycles=2, n_jobs=1)
power2 = np.mean(power, axis=0) # average over sources
phase = np.mean(phase_lock, axis=0) # average over sources
times = epochs.times
# plot result #
plt.imshow(power2,extent=[times[0],times[-1],frequencies[0],frequencies[-1]],aspect='auto',origin='lower')
# plt.imshow(phase,extent=[times[0],times[-1],frequencies[0],frequencies[-1]],aspect='auto',origin='lower')
plt.xlabel('Time (s)')
plt.ylabel('Frequency (Hz)')
epochs = mne.Epochs(raw, events, event_id, tmin, tmax, picks=picks,
baseline=(None, 0), reject=dict(grad=4000e-13, eog=150e-6))
data = epochs.get_data() # as 3D matrix
evoked = epochs.average() # compute evoked fields
times = 1e3 * epochs.times # change unit to ms
evoked_data = evoked.data * 1e13 # change unit to fT / cm
# Take only one channel
data = data[:, 97:98, :]
evoked_data = evoked_data[97:98, :]
frequencies = np.arange(7, 30, 3) # define frequencies of interest
Fs = raw.info['sfreq'] # sampling in Hz
power, phase_lock = induced_power(data, Fs=Fs, frequencies=frequencies,
n_cycles=2, n_jobs=1, use_fft=False)
power /= np.mean(power[:, :, times < 0], axis=2)[:, :, None] # baseline ratio
###############################################################################
# View time-frequency plots
import pylab as pl
pl.clf()
pl.subplots_adjust(0.1, 0.08, 0.96, 0.94, 0.2, 0.63)
pl.subplot(3, 1, 1)
pl.plot(times, evoked_data.T)
pl.title('Evoked response (%s)' % evoked.ch_names[97])
pl.xlabel('time (ms)')
pl.ylabel('Magnetic Field (fT/cm)')
pl.xlim(times[0], times[-1])
pl.ylim(-150, 300)
epochs = mne.Epochs(raw, events, event_id, tmin, tmax, picks=picks,
baseline=(None, 0), reject=dict(grad=4000e-13, eog=150e-6))
data = epochs.get_data() # as 3D matrix
evoked = epochs.average() # compute evoked fields
times = 1e3 * epochs.times # change unit to ms
evoked_data = evoked.data * 1e13 # change unit to fT / cm
# Take only one channel
data = data[:, 97:98, :]
evoked_data = evoked_data[97:98, :]
frequencies = np.arange(7, 30, 3) # define frequencies of interest
Fs = raw.info['sfreq'] # sampling in Hz
power, phase_lock = induced_power(data, Fs=Fs, frequencies=frequencies,
n_cycles=2, n_jobs=1, use_fft=False)
power /= np.mean(power[:, :, times < 0], axis=2)[:, :, None] # baseline ratio
###############################################################################
# View time-frequency plots
import pylab as pl
pl.clf()
pl.subplots_adjust(0.1, 0.08, 0.96, 0.94, 0.2, 0.63)
pl.subplot(3, 1, 1)
pl.plot(times, evoked_data.T)
pl.title('Evoked response (%s)' % raw.info['ch_names'][picks[0]])
pl.xlabel('time (ms)')
pl.ylabel('Magnetic Field (fT/cm)')
pl.xlim(times[0], times[-1])
pl.ylim(-150, 300)
epo=mne.read_epochs(pin+'/'+fraw_LLon)
freqs = np.arange(6, 200, 3) # define frequencies of interest
n_cycles = freqs / 6. # different number of cycle per frequency
power, itc = tfr_morlet(epo, freqs=freqs, n_cycles=n_cycles, use_fft=False,
return_itc=True, decim=3, n_jobs=4)
power.plot_topo(baseline=(-0.2, 0), mode='logratio', title='Average power')
#power.plot([189], baseline=(-0.2, 0), mode='logratio')
#
from mne.time_frequency import induced_power
power, phase_lock = induced_power(epo, Fs=Fs, frequencies=frequencies, n_cycles=2, n_jobs=1)
from mne.time_frequency import tfr_stockwell
power, itc = tfr_stockwell(epo, fmin=6 ,fmax=100,return_itc=True,decim=2,n_jobs=4)
from mne.time_frequency import induced_power
power, phase_lock = induced_power(epochs_data, Fs=Fs, frequencies=frequencies, n_cycles=2, n_jobs=1)
# x(t)=cos(2*pi*5*t)+cos(2*pi*10*t)+cos(2*pi*20*t)+cos(2*pi*50*t)