def process(self, trials, metadata=None):
# expecting trials in b01c format with tf layout for 01-axes
assert trials.shape[2] == 1
from mne.time_frequency import cwt_morlet
tfr_trials = []
for trial in trials:
# print trial.shape
trial = trial[:,0,:] # get rid of 1-axis
trial = trial.T # put channels first
tfr = cwt_morlet(trial,
sfreq=self.sfreq,
freqs=self.freqs,
use_fft=self.use_fft,
n_cycles=self.n_cycles,
zero_mean=self.zero_mean)
tfr = abs(tfr) ** 2
# tfr format: channels x freqs x samples
# desired output format: samples x freqs x channels
tfr = np.swapaxes(tfr, 0, 2)
# print tfr.shape
tfr_trials.append(tfr)
tfr_trials = np.asarray(tfr_trials)
# print tfr_trials.shape
return tfr_trials
def single_epoch_tf_source(epochs, inv, src, label):
"""Calculates single trail power
Parameter
---------
epochs : ???
The subject number to use.
inv = inverse_operator
...
src : source space
...
label : label
...
"""
snr = 1.0
lambda2 = 1.0 / snr ** 2
method = "dSPM" # use dSPM method (could also be MNE or sLORETA)
frequencies = np.arange(8, 13, 1)
stcs = apply_inverse_epochs(epochs, inv, lambda2=lambda2, method=method,
label=None, pick_ori=None)
time_series = [stc.extract_label_time_course(labels=label, src=src,
mode="pca_flip")[0]
for stc in stcs]
ts_signed = []
for j in range(len(time_series)):
tmp = time_series[j]
tmp *= np.sign(tmp[np.argmax(np.abs(tmp))])
ts_signed.append(tmp)
tfr = cwt_morlet(np.asarray(ts_signed), epochs.info["sfreq"], frequencies,
use_fft=True, n_cycles=4)
return tfr
def single_trial_tf(epochs, frequencies, n_cycles=4.):
"""
Parameters
----------
epochs : Epochs object
The epochs to calculate TF analysis on.
frequencies : numpy array
n_cycles : int
The number of cycles for the Morlet wavelets.
Returns
-------
results : numpy array
"""
results = []
for j in range(len(epochs)):
tfr = cwt_morlet(epochs.get_data()[j],
sfreq=epochs.info["sfreq"],
freqs=frequencies,
use_fft=True,
n_cycles=n_cycles,
# decim=2,
zero_mean=False)
results.append(tfr)
return results
def single_trial_tf(epochs, frequencies, n_cycles):
"""Something here.
Parameters
----------
epochs : Epochs object
The epochs to calculate TF analysis on.
n_cycles : int or numpy array
The number of cycles for the Morlet wavelets.
Returns
-------
results : numpy array
"""
results = []
for j in range(len(epochs)):
tfr = cwt_morlet(epochs.get_data()[j],
sfreq=epochs.info["sfreq"],
freqs=frequencies,
use_fft=True,
n_cycles=n_cycles,
zero_mean=False)
results.append(tfr)
return results
def process(self, trials, metadata=None):
# expecting trials in b01c format with tf layout for 01-axes
assert trials.shape[2] == 1
from mne.time_frequency import cwt_morlet
tfr_trials = []
for trial in trials:
# print trial.shape
trial = trial[:, 0, :] # get rid of 1-axis
trial = trial.T # put channels first
tfr = cwt_morlet(trial,
sfreq=self.sfreq,
freqs=self.freqs,
use_fft=self.use_fft,
n_cycles=self.n_cycles,
zero_mean=self.zero_mean)
tfr = abs(tfr)**2
# tfr format: channels x freqs x samples
# desired output format: samples x freqs x channels
tfr = np.swapaxes(tfr, 0, 2)
# print tfr.shape
tfr_trials.append(tfr)
tfr_trials = np.asarray(tfr_trials)
# print tfr_trials.shape
return tfr_trials
def tft_transofrm(source,freqs):
# average : bool - averaging of output data in sliding windows
# average_w_width sliding window width
# average_w_step sliding window step
sfreq = 1000
res = np.zeros((source.shape[0],source.shape[1],len(freqs),source.shape[2]),dtype=np.float32)
for i in xrange(source.shape[0]):
res[i,:,:,:] = np.absolute(cwt_morlet(source[i,:,:], sfreq, freqs, use_fft=True, n_cycles=7.0, zero_mean=True, decim=1)).astype('float32',casting='same_kind')
return res
def _extract_phase_and_amp(data_phase, data_amp, sfreq, freqs_phase,
freqs_amp, scale=True):
"""Extract the phase and amplitude of two signals for PAC viz.
data should be shape (n_epochs, n_times)"""
from sklearn.preprocessing import scale
# Morlet transform to get complex representation
band_ph = cwt_morlet(data_phase, sfreq, freqs_phase)
band_amp = cwt_morlet(data_amp, sfreq, freqs_amp)
# Calculate the phase/amplitude of relevant signals across epochs
band_ph_stacked = np.hstack(np.real(band_ph))
angle_ph = np.hstack(np.angle(band_ph))
amp = np.hstack(np.abs(band_amp) ** 2)
# Scale the amplitude for viz so low freqs don't dominate highs
if scale is True:
amp = scale(amp, axis=1)
return angle_ph, band_ph_stacked, amp
def extract_amplitude(inst, freqs, n_cycles=7, normalize=False):
"""Extract the time-varying amplitude for a frequency band.
If multiple freqs are given, the amplitude is calculated at each frequency
and then averaged across frequencies.
Parameters
----------
inst : instance of Raw
The data to have amplitude extracted
freqs : array of ints/floats, shape (n_freqs)
The frequencies to use. If multiple frequency bands given, amplitude
will be extracted at each and then averaged between frequencies. The
structure of each band is fmin, fmax.
n_cycles : int
The number of cycles to include in the filter length for the wavelet.
normalize : bool
Normalize the power of each band by its mean before combining.
Returns
-------
inst : mne instance, same type as input 'inst'
The MNE instance with channels replaced with their time-varying
amplitude for the supplied frequency range.
"""
# Data checks
freqs = np.atleast_1d(freqs)
picks = range(len(inst.ch_names))
if inst.preload is False:
raise ValueError('Data must be preloaded.')
# Filter for HFB and extract amplitude
bands = np.zeros([len(picks), inst.n_times])
for ifreq in tqdm(freqs):
with warnings.catch_warnings():
warnings.simplefilter("ignore")
# Extract power for this frequency + modify in place to save mem
band = np.abs(cwt_morlet(inst._data, inst.info['sfreq'], [ifreq]))
band = band[:, 0, :]
if normalize is True:
# Scale frequency band so that the ratios of all are the same
band /= band.mean()
bands += np.abs(band)
# Convert into an average
bands /= len(freqs)
inst = inst.copy()
inst._data = bands
return inst
def extract_amplitude(inst, freqs, n_cycles=7, normalize=False):
"""Extract the time-varying amplitude for a frequency band.
If multiple freqs are given, the amplitude is calculated at each frequency
and then averaged across frequencies.
Parameters
----------
inst : instance of Raw
The data to have amplitude extracted
freqs : array of ints/floats, shape (n_freqs)
The frequencies to use. If multiple frequency bands given, amplitude
will be extracted at each and then averaged between frequencies. The
structure of each band is fmin, fmax.
n_cycles : int
The number of cycles to include in the filter length for the wavelet.
normalize : bool
Normalize the power of each band by its mean before combining.
Returns
-------
inst : mne instance, same type as input 'inst'
The MNE instance with channels replaced with their time-varying
amplitude for the supplied frequency range.
"""
# Data checks
freqs = np.atleast_1d(freqs)
picks = range(len(inst.ch_names))
if inst.preload is False:
raise ValueError('Data must be preloaded.')
# Filter for HFB and extract amplitude
bands = np.zeros([len(picks), inst.n_times])
for ifreq in tqdm(freqs):
with warnings.catch_warnings():
warnings.simplefilter("ignore")
# Extract power for this frequency + modify in place to save mem
band = np.abs(cwt_morlet(inst._data, inst.info['sfreq'], [ifreq]))
band = band[:, 0, :]
if normalize is True:
# Scale frequency band so that the ratios of all are the same
band /= band.mean()
bands += np.abs(band)
# Convert into an average
bands /= len(freqs)
inst = inst.copy()
inst._data = bands
return inst
def _extract_phase_and_amp(data_phase,
data_amp,
sfreq,
freqs_phase,
freqs_amp,
scale=True):
"""Extract the phase and amplitude of two signals for PAC viz.
data should be shape (n_epochs, n_times)"""
from sklearn.preprocessing import scale
# Morlet transform to get complex representation
band_ph = cwt_morlet(data_phase, sfreq, freqs_phase)
band_amp = cwt_morlet(data_amp, sfreq, freqs_amp)
# Calculate the phase/amplitude of relevant signals across epochs
band_ph_stacked = np.hstack(np.real(band_ph))
angle_ph = np.hstack(np.angle(band_ph))
amp = np.hstack(np.abs(band_amp)**2)
# Scale the amplitude for viz so low freqs don't dominate highs
if scale is True:
amp = scale(amp, axis=1)
return angle_ph, band_ph_stacked, amp
def single_epoch_tf_source(epochs, inv, src, label):
"""Calculates single trail power
Parameter
---------
epochs : ???
The subject number to use.
inv = inverse_operator
...
src : source space
...
label : label
...
"""
snr = 1.0
lambda2 = 1.0 / snr**2
method = "dSPM" # use dSPM method (could also be MNE or sLORETA)
frequencies = np.arange(8, 13, 1)
stcs = apply_inverse_epochs(epochs,
inv,
lambda2=lambda2,
method=method,
label=None,
pick_ori=None)
time_series = [
stc.extract_label_time_course(labels=label, src=src,
mode="pca_flip")[0] for stc in stcs
]
ts_signed = []
for j in range(len(time_series)):
tmp = time_series[j]
tmp *= np.sign(tmp[np.argmax(np.abs(tmp))])
ts_signed.append(tmp)
tfr = cwt_morlet(np.asarray(ts_signed),
epochs.info["sfreq"],
frequencies,
use_fft=True,
n_cycles=4)
return tfr
import numpy as np
import sys
from mne.time_frequency import cwt_morlet
from my_settings import *
subject = sys.argv[1]
sfreq = 500
frequencies = np.arange(4, 90, 2)
n_cycles = frequencies / 3.
for condition in conditions:
ts = np.load(source_folder + "ave_ts/%s_%s_ts-epo.npy" % (subject,
condition))
tfr_all = np.empty(
[ts.shape[0], ts.shape[1], frequencies.shape[0], ts.shape[2]],
dtype="complex128")
for j, t in enumerate(ts):
tfr = cwt_morlet(t,
sfreq=sfreq,
freqs=frequencies,
use_fft=True,
n_cycles=n_cycles)
tfr_all[j] = tfr
np.save(source_folder + "source_TF/%s_%s_tfr-extract.npy" % (subject,
condition),
tfr_all)
def tfr_morlet(data,
sfreq,
freqs,
kind='amplitude',
n_cycles=3.,
use_fft=True,
decimate=1,
average=False):
"""Calculate the time-frequency representation of a signal.
Parameters
----------
data : array, shape (n_signals, n_times) | (n_epochs, n_signals, n_times)
The data to calculate the TFR.
sfreq : float | int
The sampling frequency of the data
freqs : array, shape (n_frequencies)
The frequencies to calculate for the TFR.
kind : string, 'filter', 'amplitude'
What kind of TFR to output. If "filter", then the output will be a
band pass filter of the signal. If "amplitude", the output will be
the amplitude at each frequency band.
n_cycles : int | array, shape (n_frequencies)
The number of cycles for each frequency to include.
use_fft : bool
Whether to use an FFT to calculate the wavelet transform
decimate : int
The amount to decimate the output. If 1, no decimation will be done.
average : bool
Whether to average across the first dimension before returning results.
Returns
-------
tfr : array, shape ([n_epochs], n_channels, n_frequencies, n_times)
The time-frequency data calculated from inputs. If `average=True`, the
output will be averaged across the first dimension (epochs).
"""
# Loop through our data
if average is True:
if data.ndim < 3:
raise ValueError('If averaging, data should have at least 3 dims')
n_ep, n_sig, n_times = data.shape[-3:]
n_freqs = len(freqs)
tfr = np.zeros([n_sig, n_freqs, int(np.round(n_times / decimate))])
else:
tfr = []
for i_data in tqdm(data):
# Calculate the wavelet transform for each iteration and stack
i_data = np.atleast_2d(i_data)
with warnings.catch_warnings():
warnings.simplefilter("ignore")
this_tfr = cwt_morlet(i_data,
sfreq,
freqs,
n_cycles=n_cycles,
use_fft=use_fft)
if kind == 'filter':
# In this case, we'll just take the real values
this_tfr = np.real(this_tfr)
if decimate != 1:
warn('Decimating band-passed data may cause artifacts.')
elif kind == 'amplitude':
# Now take the absolute value so it's only amplitude
this_tfr = np.abs(this_tfr)
else:
raise ValueError('kind must be one of "filter" | "amplitude"')
this_tfr = this_tfr[..., ::decimate]
if average is True:
tfr += this_tfr
else:
tfr.append(this_tfr)
if average is True:
tfr /= n_ep
else:
tfr = np.asarray(tfr)
return tfr.squeeze()
def tfr_morlet(data, sfreq, freqs, kind='amplitude', n_cycles=3.,
use_fft=True, decimate=1, average=False):
"""Calculate the time-frequency representation of a signal.
Parameters
----------
data : array, shape (n_signals, n_times) | (n_epochs, n_signals, n_times)
The data to calculate the TFR.
sfreq : float | int
The sampling frequency of the data
freqs : array, shape (n_frequencies)
The frequencies to calculate for the TFR.
kind : string, 'filter', 'amplitude'
What kind of TFR to output. If "filter", then the output will be a
band pass filter of the signal. If "amplitude", the output will be
the amplitude at each frequency band.
n_cycles : int | array, shape (n_frequencies)
The number of cycles for each frequency to include.
use_fft : bool
Whether to use an FFT to calculate the wavelet transform
decimate : int
The amount to decimate the output. If 1, no decimation will be done.
average : bool
Whether to average across the first dimension before returning results.
Returns
-------
tfr : array, shape ([n_epochs], n_channels, n_frequencies, n_times)
The time-frequency data calculated from inputs. If `average=True`, the
output will be averaged across the first dimension (epochs).
"""
# Loop through our data
if average is True:
if data.ndim < 3:
raise ValueError('If averaging, data should have at least 3 dims')
n_ep, n_sig, n_times = data.shape[-3:]
n_freqs = len(freqs)
tfr = np.zeros([n_sig, n_freqs, int(np.round(n_times / decimate))])
else:
tfr = []
for i_data in tqdm(data):
# Calculate the wavelet transform for each iteration and stack
i_data = np.atleast_2d(i_data)
with warnings.catch_warnings():
warnings.simplefilter("ignore")
this_tfr = cwt_morlet(i_data, sfreq,
freqs, n_cycles=n_cycles,
use_fft=use_fft)
if kind == 'filter':
# In this case, we'll just take the real values
this_tfr = np.real(this_tfr)
if decimate != 1:
warn('Decimating band-passed data may cause artifacts.')
elif kind == 'amplitude':
# Now take the absolute value so it's only amplitude
this_tfr = np.abs(this_tfr)
else:
raise ValueError('kind must be one of "filter" | "amplitude"')
this_tfr = this_tfr[..., ::decimate]
if average is True:
tfr += this_tfr
else:
tfr.append(this_tfr)
if average is True:
tfr /= n_ep
else:
tfr = np.asarray(tfr)
return tfr.squeeze()
method,
pick_ori=None)
for label in labels_sel:
label_ts = []
for j in range(len(stcs)):
ts = mne.extract_label_time_course(stcs[j],
labels=label,
src=src,
mode="pca_flip")
ts = np.squeeze(ts)
ts *= np.sign(ts[np.argmax(np.abs(ts))])
label_ts.append(ts)
label_ts = np.asarray(label_ts)
tfr = cwt_morlet(label_ts, epochs.info["sfreq"], freqs,
use_fft=True, n_cycles=n_cycle)
np.save(tf_folder + "%s_%s_%s_%s_%s_sf-tfr" % (subject,
condition[:3],
condition[4:],
label.name, method),
tfr)
np.save(tf_folder + "%s_%s_%s_%s_%s_sf-ts" % (subject,
condition[:3],
condition[4:],
label.name, method),
label_ts)
del stcs
del tfr
initOSCServer(ip=ip, port=6400, mode=1)
# and now set it into action
startOSCServer()
# get measurement info guessed by MNE-Python
ch_names = ['EEG-%i' % i for i in np.arange(n_eeg)]
raw_info = mne.create_info(ch_names, sfreq)
with FieldTripClient(info=raw_info, host='localhost', port=1972,
tmax=150, wait_max=10) as rt_client:
tstart = time.time()
told = tstart
for ii in range(100):
epoch = rt_client.get_data_as_epoch(n_samples=n_samples, picks=picks)
filt = band_pass_filter(epoch.get_data(), sfreq, fmin, fmax)
# compute band power features
bp = np.log10(np.abs(cwt_morlet(filt[0], sfreq, [(fmin + fmax) / 2.])))
if told - tstart < baseline:
bp_base.append(bp[:, 0, n_samples/2].mean())
else:
bp_sample = bp[:, 0, n_samples/2].mean()
bp_ratio = (np.mean(bp_base) - bp_sample) / np.mean(bp_base)
sendOSCMsg("/nmx/bandpower/", [bp_ratio])
print "%i - sending /nmx/bandpower/%i" %(ii, bp_ratio)
tcurrent = time.time()
time.sleep(.5)
told = tcurrent
startOSCServer()
# get measurement info guessed by MNE-Python
ch_names = ['EEG-%i' % i for i in np.arange(n_eeg)]
raw_info = mne.create_info(ch_names, sfreq)
with FieldTripClient(info=raw_info,
host='localhost',
port=1972,
tmax=150,
wait_max=10) as rt_client:
tstart = time.time()
told = tstart
for ii in range(100):
epoch = rt_client.get_data_as_epoch(n_samples=n_samples, picks=picks)
filt = band_pass_filter(epoch.get_data(), sfreq, fmin, fmax)
# compute band power features
bp = np.log10(np.abs(cwt_morlet(filt[0], sfreq, [(fmin + fmax) / 2.])))
if told - tstart < baseline:
bp_base.append(bp[:, 0, n_samples / 2].mean())
else:
bp_sample = bp[:, 0, n_samples / 2].mean()
bp_ratio = (np.mean(bp_base) - bp_sample) / np.mean(bp_base)
sendOSCMsg("/nmx/bandpower/", [bp_ratio])
print "%i - sending /nmx/bandpower/%i" % (ii, bp_ratio)
tcurrent = time.time()
time.sleep(.5)
told = tcurrent
subject = 1
epochs = mne.read_epochs(data_folder + "sub_%s-epo.fif" % subject)
freqs = np.arange(4, 90, 3)
n_cycles = freqs / 3.
data_target = epochs["Happiness"].get_data()
data_nontarget = epochs["non-target"].get_data()
tfr_target = []
tfr_nontarget = []
for j in range(len(data_target)):
tfr_target.append(cwt_morlet(data_target[j, :, :],
sfreq=125,
freqs=freqs,
n_cycles=n_cycles))
for j in range(len(data_nontarget)):
tfr_nontarget.append(cwt_morlet(data_nontarget[j, :, :],
sfreq=125,
freqs=freqs,
n_cycles=n_cycles))
# Convert to numpy arrays
tfr_target = np.asarray(tfr_target)
tfr_nontarget = np.asarray(tfr_nontarget)
# Take power of signal
pow_target = np.abs(tfr_target)**2
pow_nontarget = np.abs(tfr_nontarget)**2