def test_sim_peak_oscillation():
sig_ap = sim_powerlaw(N_SECONDS, FS)
sig = sim_peak_oscillation(sig_ap, FS, FREQ1, bw=5, height=10)
check_sim_output(sig)
# Ensure the peak is at or close (+/- 5hz) to FREQ1
_, powers_ap = compute_spectrum(sig_ap, FS)
_, powers = compute_spectrum(sig, FS)
assert abs(np.argmax(powers - powers_ap) - FREQ1) < 5
def ft(subset, **ft_kwargs):
"""
Decomposition in time over both summed and non summed neurons
returns: freqs, powers_summed, powers_chans (2d array n_chans x n_freqs)
"""
if not isinstance(subset, np.ndarray):
subset = np.array(subset)
summed_neurons = subset.sum(axis= 1) # summing data for ft decomp.
freqs, powers_summed = compute_spectrum(summed_neurons, **ft_kwargs) #powers_sum is an array
freqs, powers_chans = compute_spectrum(subset.T, **ft_kwargs) #returns a matrix! #TODO make sure transpose
return freqs, powers_summed, powers_chans
def plot_power_spectrum_neurodsp(dt, rate_conn, rate_noconn, analysis):
fs = 1 / dt
# Plot the results for L23
freq_mean_L23_conn, P_mean_L23_conn = spectral.compute_spectrum(
rate_conn[0, :, 0], fs, method='mean')
freq_mean_L23_noconn, P_mean_L23_noconn = spectral.compute_spectrum(
rate_noconn[0, :, 0], fs, method='mean')
plt.figure()
plt.loglog(freq_mean_L23_conn,
P_mean_L23_conn,
label='Coupled',
linewidth=2,
color='g')
plt.loglog(freq_mean_L23_noconn,
P_mean_L23_noconn,
label='Uncoupled',
linewidth=2,
color='k')
plt.xlim([1, 100])
plt.ylim([10**-4, 10**-2])
plt.ylabel('Power')
plt.xlabel('Frequency (Hz)')
plt.legend()
# Plot the results for L56
freq_mean_L56_conn, P_mean_L56_conn = spectral.compute_spectrum(
rate_conn[2, :, 0], fs, method='mean')
freq_mean_L56_noconn, P_mean_L56_noconn = spectral.compute_spectrum(
rate_noconn[2, :, 0], fs, method='mean')
plt.figure()
plt.loglog(freq_mean_L56_conn,
P_mean_L56_conn,
label='Coupled',
linewidth=2,
color='#FF7F50')
plt.loglog(freq_mean_L56_noconn,
P_mean_L56_noconn,
label='Uncoupled',
linewidth=2,
color='k')
plt.xlim([1, 100])
plt.ylim([10**-5, 10**-0])
plt.ylabel('Power')
plt.xlabel('Frequency (Hz)')
plt.legend()
def calc_spectral_psd(data, srate, method_type="median"):
# (f, psd) = spectral.compute_spectrum(sig = data, fs = srate, method = method_type, nperseg = srate*2)
(f, psd) = spectral.compute_spectrum(sig=data,
fs=srate,
avg_type=method_type,
nperseg=srate * 2)
return (f, psd)
def getMeanFreqPSD(eeg_data, fs=eeg_fs):
freq_mean, psd_mean = compute_spectrum(eeg_data,
fs,
method='welch',
avg_type='mean',
nperseg=fs * 2)
return freq_mean, psd_mean
def get_spectrum(self, samples):
spectrums = []
for i in range(self.NDIMS):
freqs, spectre = spectral.compute_spectrum(samples[i, :],
self.SAMPLE_RATE)
spectrums.append(spectre)
return freqs, np.asarray(spectrums)
def test_data(sim_sig):
# Load data
sig_1d = sim_sig['sig']
fs = sim_sig['fs']
f_range = sim_sig['f_range']
# Duplicate sig to create 2d/3d arrays
sig_2d = np.array([sig_1d] * 2)
sig_3d = np.array([sig_2d] * 2)
sig_4d = np.array([sig_3d] * 2)
# FFT
freqs, powers_1d = compute_spectrum(sig_1d, fs, f_range=f_range)
# Create a (2, 100) array
powers_2d = np.array([powers_1d for dim1 in range(2)])
# Create a (2, 2, 100) array
powers_3d = np.array([[powers_1d for dim1 in range(2)] for dim2 in range(2)])
# Create a (2, 2, 2, 100) array
powers_4d = np.array([[[powers_1d for dim1 in range(2)] for dim2 in range(2)] \
for dim3 in range(2)])
yield {'sig_1d': sig_1d, 'sig_2d': sig_2d, 'sig_3d': sig_3d, 'sig_4d': sig_4d,
'fs': fs, 'f_range': f_range, 'freqs': freqs, 'powers_1d': powers_1d,
'powers_2d': powers_2d, 'powers_3d': powers_3d, 'powers_4d': powers_4d}
def test_sim_knee():
# Build the signal and run a smoke test
sig = sim_knee(N_SECONDS, FS, EXP1, EXP2, KNEE)
check_sim_output(sig)
# Check against the power spectrum when you take the Fourier transform
sig_len = int(FS * N_SECONDS)
freqs = np.linspace(0, FS / 2, num=sig_len // 2, endpoint=True)
# Ignore the DC component to avoid division by zero in the Lorentzian
freqs = freqs[1:]
true_psd = np.array(
[1 / (freq**-EXP1 * (freq**(-EXP2 - EXP1) + KNEE)) for freq in freqs])
# Only look at the frequencies (ignoring DC component) up to the nyquist rate
sig_hat = np.fft.fft(sig)[1:sig_len // 2]
numerical_psd = np.abs(sig_hat)**2
np.allclose(true_psd, numerical_psd, atol=EPS)
# Accuracy test for a single exponent
sig = sim_knee(n_seconds=N_SECONDS, fs=FS, chi1=0, chi2=EXP2, knee=KNEE)
freqs, powers = compute_spectrum(sig, FS, f_range=(1, 200))
def _estimate_single_knee(xs, offset, knee, exponent):
return np.zeros_like(xs) + offset - np.log10(xs**exponent + knee)
ap_params, _ = curve_fit(_estimate_single_knee, freqs, np.log10(powers))
_, _, EXP2_hat = ap_params[:]
assert -round(EXP2_hat) == EXP2
def get_fft(data, fs):
sp = np.abs(np.fft.fft(data))
freq = np.fft.fftfreq(len(data))*fs
# This breaks the data up into two-second windows (nperseg=fs*2) and applies a hanning window
# to the time-series windows (window='hann'). It then FFTs each hanning'd window, and then
# averages all those FFTs (method='mean') mean of spectrogram (Welch)
freq_mean, P_mean = spectral.compute_spectrum(data, fs, method='mean', window='hann', nperseg=fs*2)
return freq, sp, freq_mean, P_mean
def ft_on_data(subset, fs, nperseg, noverlap):
"""
Decomposition in time
"""
summed_neurons = subset.sum(axis= 1) # summing data for ft decomp.
freqs, powers = compute_spectrum(summed_neurons, fs = fs, nperseg = nperseg, noverlap = noverlap) #making these parameters now
return freqs, powers
def test_compute_irasa(tsig_comb):
# Estimate periodic and aperiodic components with IRASA
f_range = [1, 30]
freqs, psd_ap, psd_pe = compute_irasa(tsig_comb, FS, f_range, noverlap=int(2*FS))
assert len(freqs) == len(psd_ap) == len(psd_pe)
# Compute r-squared for the full model, comparing to a standard power spectrum
_, powers = trim_spectrum(*compute_spectrum(tsig_comb, FS, nperseg=int(4*FS)), f_range)
r_sq = np.corrcoef(np.array([powers, psd_ap+psd_pe]))[0][1]
assert r_sq > .95
def get_spectrum(
self, samples
): #Recibe DESDE Data_Manager las muestras tomadas y guardadas en el BUFFER tras ser filtradas
spectrums = []
# Trata la señal almacenada en cada fila de la muestra, proveniente de cada sensor
for i in range(self.constants.NDIMS):
# Calcula la frecuencia y el espectro de potencia de la muestra y la añade al vector de espectros
freqs, spectre = spectral.compute_spectrum(
samples[i, :], self.constants.SAMPLE_RATE
) #Analiza las muestras a la frecuencia de muestreo
spectrums.append(spectre)
return freqs, np.asarray(
spectrums) #Devuelve la frecuencia y una matriz de espectros
def plot_spectra(self, result_index, f_range=(1, 100), figsize=(8, 8)):
if self.results[result_index].sig_pe is None or self.results[
result_index].sig_ap is None:
self.decompose()
# Compute spectra
freqs, powers = compute_spectrum(self.sig, self.fs, f_range=f_range)
freqs_pe, powers_pe = compute_spectrum(
self.results[result_index].sig_pe, self.fs, f_range=f_range)
freqs_ap, powers_ap = compute_spectrum(
self.results[result_index].sig_ap, self.fs, f_range=f_range)
# Plot
_, ax = plt.subplots(figsize=figsize)
plot_power_spectra(freqs, [powers, powers_pe, powers_ap],
title="Reconstructed Components",
labels=['Orig', 'PE Recon', 'AP Recon'],
ax=ax,
alpha=[0.7, 0.7, 0.7],
lw=3)
def build_all(sig, fs, n_build=np.inf, sleep=0.05, label='viz', save=False):
"""Build all plots together."""
size = 750
step = 2
start = 2000
sig_yielder = yield_sig(sig, start=start, size=size, step=step)
for ind in range(n_build):
clear_output(wait=True)
fig, axes = make_axes()
spect_sig = sig[start + step * ind - 2000:start + step * ind + 2000]
freqs, powers = trim_spectrum(*compute_spectrum(spect_sig, fs=fs),
[1, 50])
plot_timeseries(next(sig_yielder), ax=axes[0])
plot_spectra(freqs, powers, log_freqs=True, ax=axes[1])
animate_plot(fig, save, ind, label=label, sleep=sleep)
}
###################################################################################################
# Simulate an oscillation over an aperiodic component
signal = sim.sim_combined(n_seconds, fs, components)
###################################################################################################
# Plot the simulated data, in the time domain
plot_time_series(times, signal)
###################################################################################################
# Plot the simulated data, in the frequency domain
freqs, psd = spectral.compute_spectrum(signal, fs)
plot_power_spectra(freqs, psd)
###################################################################################################
#
# We can switch out any components that we want, for example trading the stationary oscillation
# for a bursting oscillation, also with an aperiodic component.
#
# We can also control the relative proportions of each component, by using a parameter called
# `component_variances` that specifies the variance of each component.
#
###################################################################################################
# Define the components of the combined signal to simulate
components = {
# Plot a segment of the extracted time series data plot_time_series(times, sig) ################################################################################################### # Calculate Power Spectra # ----------------------- # # Next lets check the data in the frequency domain, calculating a power spectrum # with the median welch's procedure from NeuroDSP. # ################################################################################################### # Calculate the power spectrum, using a median welch & extract a frequency range of interest freqs, powers = compute_spectrum(sig, fs, method='welch', avg_type='median') freqs, powers = trim_spectrum(freqs, powers, [3, 30]) ################################################################################################### # Check where the peak power is peak_cf = freqs[np.argmax(powers)] print(peak_cf) ################################################################################################### # Plot the power spectra, and note the peak power plot_power_spectra(freqs, powers) plt.plot(freqs[np.argmax(powers)], np.max(powers), '.r', ms=12) ###################################################################################################
# Set the exponent for brown noise, which is -2 exponent = -2 # Simulate powerlaw activity br_noise = sim_powerlaw(n_seconds, fs, exponent) ################################################################################################### # Plot the simulated data, in the time domain plot_time_series(times, br_noise, title='Brown Noise') ################################################################################################### # Plot the simulated data, in the frequency domain freqs, psd = compute_spectrum(br_noise, fs) plot_power_spectra(freqs, psd) ################################################################################################### # Simulate Filtered 1/f Activity # ------------------------------ # # The power law simulation function is also integrated with a filter. This can be useful # for filtering out some low frequencies, as is often done with neural signals, # to remove the very slow drifts that we see in the pure 1/f simulations. # # To filter a simulated power law signal, simply pass in a filter range, and the filter will # be applied to the simulated data before being returned. # # Here we will apply a high-pass filter. We can see that the resulting signal has much less # low-frequency drift than the first one.
#
# However, in physiological data, we may be interested in visualizing the distribution of
# power values around the mean at each frequency, as estimated in sequential slices of
# short-time Fourier transform (STFT), since it may reveal non-stationarities in the data
# or particular frequencies that are not like the rest. Here, we simply bin the log-power
# values across time, in a histogram, to observe the noise distribution at each frequency.
#
###################################################################################################
# Calculate the spectral histogram
freqs, bins, spect_hist = compute_spectral_hist(sig, fs, nbins=50, f_range=(0, 80),
cut_pct=(0.1, 99.9))
# Calculate a power spectrum, with median Welch
freq_med, psd_med = compute_spectrum(sig, fs, method='welch',
avg_type='median', nperseg=fs*2)
# Plot the spectral histogram
plot_spectral_hist(freqs, bins, spect_hist, freq_med, psd_med)
###################################################################################################
#
# Notice in the plot that not only is theta power higher overall (shifted up),
# it also has lower variance around its mean.
#
###################################################################################################
# Spectral Coefficient of Variation (SCV)
# ---------------------------------------
#
# Next, let's look at computing the spectral coefficient of variation, with
# Simulate brown noise n_seconds = 10 fs = 1000 exponent = -2 times = create_times(n_seconds, fs) br_noise = sim.sim_powerlaw(n_seconds, fs, exponent) ################################################################################################### # Plot the simulated data, in the time domain plot_time_series(times, br_noise) ################################################################################################### # Plot the simulated data, in the frequency domain freqs, psd = spectral.compute_spectrum(br_noise, fs) plot_power_spectra(freqs, psd) ################################################################################################### # # Simulate filtered brown noise # ----------------------------- # # However, brown noise has a lot of power in very slow frequnecies, # whereas these slow frequencies are often not present or filtered out # in neural signals. Therefore, we may desire our brown noise to be # high-pass filtered. See that the resulting signal has much less # low-frequency drift. # # Note this might not be ideal because it creates an "oscillation" at # the cutoff frequency.
def main(argv):
# defining basepaths
basepath = '/Users/rdgao/Documents/data/CRCNS/fcx1/'
rec_dirs = [
f for f in np.sort(os.listdir(basepath)) if os.path.isdir(basepath + f)
]
result_basepath = '/Users/rdgao/Documents/code/research/field-echos/results/fcx1/wakesleep/'
if 'do_psds' in argv:
print('Computing PSDs...')
for cur_rec in range(len(rec_dirs)):
print(rec_dirs[cur_rec])
# compute PSDs
psd_path = result_basepath + rec_dirs[cur_rec] + '/psd_spikes/'
# load data
ephys_data = io.loadmat(basepath + rec_dirs[cur_rec] + '/' +
rec_dirs[cur_rec] + '_ephys.mat',
squeeze_me=True)
behav_data = pd.read_csv(basepath + rec_dirs[cur_rec] + '/' +
rec_dirs[cur_rec] + '_wakesleep.csv',
index_col=0)
elec_region = np.unique(ephys_data['elec_regions'])[0]
elec_shank_map = ephys_data['elec_shank_map']
# some organization of spike meta datafile
# NOTE that all this had to be done because I was an idiot and
# organized the spikeinfo table and spikes in some dumb way
# make spike info into df and access based on cell, and add end time
df_spkinfo = pd.DataFrame(ephys_data['spike_info'],
columns=ephys_data['spike_info_cols'])
df_spkinfo.insert(
len(df_spkinfo.columns) - 1, 'spike_start_ind',
np.concatenate(
([0], df_spkinfo['num_spikes_cumsum'].iloc[:-1].values)))
df_spkinfo.rename(columns={'num_spikes_cumsum': 'spike_end_ind'},
inplace=True)
# this is now a list of N arrays, where N is the number of cells
# now we can aggregate arbitrarily based on cell index
spikes_list = utils.spikes_as_list(ephys_data['spiketrain'],
df_spkinfo)
# pooling across populations from the same shanks
df_spkinfo_pooled = df_spkinfo.copy()
for g_i, g in df_spkinfo.groupby(['shank', 'cell_EI_type']):
# super python magic that collapses all the spikes of the same pop on the same shank into one array
spikes_list.append(
np.sort(
np.hstack(
[spikes_list[c_i] for c_i, cell in g.iterrows()])))
# update spike info dataframe
df_pop = pd.DataFrame({
'shank': g['shank'].head(1),
'cell_EI_type': g['cell_EI_type'].head(1),
'num_spikes': g['num_spikes'].sum(),
'cell_id': 0
})
df_spkinfo_pooled = df_spkinfo_pooled.append(df_pop,
ignore_index=True)
# pooling across entire recording
for g_i, g in df_spkinfo.groupby(['cell_EI_type']):
spikes_list.append(
np.sort(
np.hstack(
[spikes_list[c_i] for c_i, cell in g.iterrows()])))
df_pop = pd.DataFrame({
'shank': 0,
'cell_id': 0,
'cell_EI_type': g['cell_EI_type'].head(1),
'num_spikes': g['num_spikes'].sum()
})
df_spkinfo_pooled = df_spkinfo_pooled.append(df_pop,
ignore_index=True)
# save spikeinfo table to recording folder
utils.makedir(psd_path, timestamp=False)
df_spkinfo_pooled.to_csv(psd_path + '/spike_info.csv')
##### ------------- #####
# compute PSDs across conditions and populations
# individual cells
dt = 0.005
fs = 1 / dt
# name, nperseg, noverlap, f_range, outlier_pct
p_configs = [['2sec', int(2 * fs),
int(2 * fs * 4 / 5)],
['5sec', int(5 * fs),
int(5 * fs * 4 / 5)]]
behav_sub = behav_data[behav_data['Label'].isin(['Wake', 'Sleep'
])].reset_index()
behav_info = np.array(behav_sub)
num_block, num_cell = len(behav_sub), len(spikes_list)
for p_cfg in p_configs:
print(p_cfg)
saveout_path = psd_path + p_cfg[0]
nperseg, noverlap = p_cfg[1:]
psd_mean = np.zeros(
(num_block, num_cell, int(p_cfg[1] / 2 + 1)))
psd_med = np.zeros(
(num_block, num_cell, int(p_cfg[1] / 2 + 1)))
for cell, spikes in enumerate(spikes_list):
print(cell, end='|')
for block, cur_eps in behav_sub.iterrows():
spikes_eps = spikes[np.logical_and(
spikes >= cur_eps['Start'],
spikes < cur_eps['End'])]
t_spk, spikes_binned = utils.bin_spiketrain(
spikes_eps, dt, cur_eps[['Start', 'End']])
f_axis, psd_mean[block,
cell, :] = spectral.compute_spectrum(
spikes_binned,
fs,
method='welch',
avg_type='mean',
nperseg=nperseg,
noverlap=noverlap)
f_axis, psd_med[block,
cell, :] = spectral.compute_spectrum(
spikes_binned,
fs,
method='welch',
avg_type='median',
nperseg=nperseg,
noverlap=noverlap)
# save PSDs and spike_info dataframe
save_dict = {}
for name in [
'psd_mean', 'psd_med', 'nperseg', 'noverlap', 'fs',
'behav_info', 'elec_region', 'elec_shank_map', 'f_axis'
]:
save_dict[name] = eval(name)
utils.makedir(saveout_path, timestamp=False)
np.savez(file=saveout_path + '/psds.npz', **save_dict)
if 'do_fooof' in argv:
fooof_settings = [['fixed', 2, (.5, 80)], ['fixed', 1, (.5, 5)],
['fixed', 1, (10, 20)], ['fixed', 1, (30, 80)]]
for cur_rec in range(len(rec_dirs)):
print(rec_dirs[cur_rec])
psd_path = result_basepath + rec_dirs[cur_rec] + '/psd_spikes/'
df_spkinfo_pooled = pd.read_csv(psd_path + '/spike_info.csv',
index_col=0)
# grab only the aggregate cells
df_pops = df_spkinfo_pooled[df_spkinfo_pooled['cell_id'] == 0]
df_pops.to_csv(psd_path + '/pop_spike_info.csv')
for psd_win in ['2sec/', '5sec/']:
psd_folder = psd_path + psd_win
psd_data = np.load(psd_folder + 'psds.npz')
for psd_mode in ['psd_mean']:
psd_spikes = psd_data[psd_mode][:, df_pops.index.values, :]
if np.any(np.isinf(np.log(psd_spikes[:, :, 0]))):
# if any PSDs are 0s, set it to ones
print('Null PSDs found.')
zero_inds = np.where(
np.isinf(np.log(psd_spikes[:, :, 0])))
psd_spikes[zero_inds] = 1.
fg_all = []
for f_s in fooof_settings:
fg = FOOOFGroup(aperiodic_mode=f_s[0],
max_n_peaks=f_s[1],
peak_width_limits=(5, 20))
fgs = fit_fooof_group_3d(fg,
psd_data['f_axis'],
psd_spikes,
freq_range=f_s[2])
fg_all = combine_fooofs(fgs)
fooof_savepath = utils.makedir(psd_folder,
'/fooof/' + psd_mode +
'/',
timestamp=False)
fg_all.save('fg_%s_%ipks_%i-%iHz' %
(f_s[0], f_s[1], f_s[2][0], f_s[2][1]),
fooof_savepath,
save_results=True,
save_settings=True)
print('Done.')
def compute_irasa(sig,
fs,
f_range=None,
hset=None,
thresh=None,
**spectrum_kwargs):
"""Separate aperiodic and periodic components using IRASA.
Parameters
----------
sig : 1d array
Time series.
fs : float
The sampling frequency of sig.
f_range : tuple, optional
Frequency range to restrict the analysis to.
hset : 1d array, optional
Resampling factors used in IRASA calculation.
If not provided, defaults to values from 1.1 to 1.9 with an increment of 0.05.
thresh : float, optional
A relative threshold to apply when separating out periodic components.
The threshold is defined in terms of standard deviations of the original spectrum.
spectrum_kwargs : dict
Optional keywords arguments that are passed to `compute_spectrum`.
Returns
-------
freqs : 1d array
Frequency vector.
psd_aperiodic : 1d array
The aperiodic component of the power spectrum.
psd_periodic : 1d array
The periodic component of the power spectrum.
Notes
-----
Irregular-Resampling Auto-Spectral Analysis (IRASA) is an algorithm ([1]_) that aims to
separate 1/f and periodic components by resampling time series and computing power spectra,
averaging away any activity that is frequency specific to isolate the aperiodic component.
References
----------
.. [1] Wen, H., & Liu, Z. (2016). Separating Fractal and Oscillatory Components in
the Power Spectrum of Neurophysiological Signal. Brain Topography, 29(1), 13–26.
DOI: https://doi.org/10.1007/s10548-015-0448-0
"""
# Check & get the resampling factors, with rounding to avoid floating point precision errors
hset = np.arange(1.1, 1.95, 0.05) if hset is None else hset
hset = np.round(hset, 4)
# The `nperseg` input needs to be set to lock in the size of the FFT's
if 'nperseg' not in spectrum_kwargs:
spectrum_kwargs['nperseg'] = int(4 * fs)
# Calculate the original spectrum across the whole signal
freqs, psd = compute_spectrum(sig, fs, **spectrum_kwargs)
# Do the IRASA resampling procedure
psds = np.zeros((len(hset), *psd.shape))
for ind, h_val in enumerate(hset):
# Get the up-sampling / down-sampling (h, 1/h) factors as integers
rat = fractions.Fraction(str(h_val))
up, dn = rat.numerator, rat.denominator
# Resample signal
sig_up = signal.resample_poly(sig, up, dn, axis=-1)
sig_dn = signal.resample_poly(sig, dn, up, axis=-1)
# Calculate the power spectrum, using the same params as original
freqs_up, psd_up = compute_spectrum(sig_up, h_val * fs,
**spectrum_kwargs)
freqs_dn, psd_dn = compute_spectrum(sig_dn, fs / h_val,
**spectrum_kwargs)
# Calculate the geometric mean of h and 1/h
psds[ind, :] = np.sqrt(psd_up * psd_dn)
# Take the median resampled spectra, as an estimate of the aperiodic component
psd_aperiodic = np.median(psds, axis=0)
# Subtract aperiodic from original, to get the periodic component
psd_periodic = psd - psd_aperiodic
# Apply a relative threshold for tuning which activity is labeled as periodic
if thresh is not None:
sub_thresh = np.where(
psd_periodic - psd_aperiodic < thresh * np.std(psd))[0]
psd_periodic[sub_thresh] = 0
psd_aperiodic[sub_thresh] = psd[sub_thresh]
# Restrict spectrum to requested range
if f_range:
psds = np.array([psd_aperiodic, psd_periodic])
freqs, (psd_aperiodic,
psd_periodic) = trim_spectrum(freqs, psds, f_range)
return freqs, psd_aperiodic, psd_periodic
# Plot the simulated data, in the time domain plot_time_series(times, [osc_sine, osc_shape], ['rdsym='+str(.5), 'rdsym='+str(.3)]) ################################################################################################### # # We can also compare these signals in the frequency. # # Notice that the asymmetric oscillation has strong harmonics resulting from the # non-sinusoidal nature of the oscillation. # ################################################################################################### # Plot the simulated data, in the frequency domain freqs_sine, psd_sine = compute_spectrum(osc_sine, fs) freqs_shape, psd_shape = compute_spectrum(osc_shape, fs) plot_power_spectra([freqs_sine, freqs_shape], [psd_sine, psd_shape]) ################################################################################################### # Simulate a Bursty Oscillation # ----------------------------- # # Sometimes we want to study oscillations that come and go, so it can be useful to simulate # oscillations with this property. # # You can simulate bursty oscillations with :func:`~neurodsp.sim.periodic.sim_bursty_oscillation`. # # To control the bursitness of the simulated signal, you can control the probability # that a burst will start or stop with each new cycle.
def main(argv):
# defining basepaths
basepath = '/Users/rdgao/Documents/data/CRCNS/fcx1/'
rec_dirs = [f for f in np.sort(os.listdir(basepath)) if os.path.isdir(basepath+f)]
result_basepath = '/Users/rdgao/Documents/code/research/field-echos/results/fcx1/wakesleep/'
if 'do_psds' in argv:
print('Computing PSDs...')
for cur_rec in range(len(rec_dirs))[21:]:
print(rec_dirs[cur_rec])
# compute PSDs
psd_path = result_basepath + rec_dirs[cur_rec] + '/psd/'
# load data
ephys_data = io.loadmat(basepath+rec_dirs[cur_rec]+'/'+rec_dirs[cur_rec]+'_ephys.mat', squeeze_me=True)
behav_data = pd.read_csv(basepath+rec_dirs[cur_rec]+'/'+rec_dirs[cur_rec]+'_wakesleep.csv', index_col=0)
# get some params
nchan,nsamp = ephys_data['lfp'].shape
fs = ephys_data['fs']
ephys_data['t_lfp'] = np.arange(0,nsamp)/fs
elec_region = np.unique(ephys_data['elec_regions'])[0]
# get subset of behavior that marks wake and sleep
behav_sub = behav_data[behav_data['Label'].isin(['Wake', 'Sleep'])]
# name, nperseg, noverlap, f_range, outlier_pct
p_configs = [['1sec', int(fs), int(fs/2), [0., 200.], 5],
['5sec', int(fs*5), int(fs*4), [0., 200.], 5]]
for p_cfg in p_configs:
# parameter def
print(p_cfg)
saveout_path = psd_path+ p_cfg[0]
nperseg, noverlap, f_range, outlier_pct = p_cfg[1:]
psd_mean, psd_med, = [], []
for ind, cur_eps in behav_sub.iterrows():
# find indices of LFP that correspond to behavior
lfp_inds = np.where(np.logical_and(ephys_data['t_lfp']>=cur_eps['Start'],ephys_data['t_lfp']<cur_eps['End']))[0]
# compute mean and median welchPSD
p_squished = spectral.compute_spectrum(ephys_data['lfp'][:,lfp_inds], ephys_data['fs'], method='welch',avg_type='mean', nperseg=nperseg, noverlap=noverlap, f_range=f_range, outlier_pct=outlier_pct)
f_axis, cur_psd_mean = p_squished[0,:], p_squished[1::2,:] # work-around for ndsp currently squishing together the outputs
p_squished = spectral.compute_spectrum(ephys_data['lfp'][:,lfp_inds], ephys_data['fs'], method='welch',avg_type='median', nperseg=nperseg, noverlap=noverlap, f_range=f_range, outlier_pct=outlier_pct)
f_axis, cur_psd_med = p_squished[0,:], p_squished[1::2,:]
# append to list
psd_mean.append(cur_psd_mean)
psd_med.append(cur_psd_med)
# collect, stack, and save out
psd_mean, psd_med, behav_info = np.array(psd_mean), np.array(psd_med), np.array(behav_sub)
save_dict = {}
for name in ['psd_mean', 'psd_med','nperseg','noverlap','fs','outlier_pct', 'behav_info', 'elec_region', 'f_axis']:
save_dict[name] = eval(name)
utils.makedir(saveout_path, timestamp=False)
np.savez(file=saveout_path+'/psds.npz', **save_dict)
if 'do_fooof' in argv:
fooof_settings = [['knee', 4, (0.1,200)],
['fixed', 4, (0.1,200)],
['fixed', 2, (0.1,10)],
['fixed', 2, (30,55)]]
for cur_rec in range(len(rec_dirs)):
print(rec_dirs[cur_rec])
psd_path = result_basepath + rec_dirs[cur_rec] + '/psd/'
for psd_win in ['1sec/', '5sec/']:
psd_folder = psd_path+psd_win
psd_data = np.load(psd_folder+'psds.npz')
for psd_mode in ['psd_mean', 'psd_med']:
for f_s in fooof_settings:
fg = FOOOFGroup(aperiodic_mode=f_s[0], max_n_peaks=f_s[1])
fgs = fit_fooof_group_3d(fg, psd_data['f_axis'], psd_data[psd_mode], freq_range=f_s[2])
fg_all = combine_fooofs(fgs)
fooof_savepath = utils.makedir(psd_folder, '/fooof/'+psd_mode+'/', timestamp=False)
fg_all.save('fg_%s_%ipks_%i-%iHz'%(f_s[0],f_s[1],f_s[2][0],f_s[2][1]), fooof_savepath, save_results=True, save_settings=True)
n_windows = len(window_starts_ep)
for i in tqdm(range(n_windows)):
end_ind = ((window_starts_ep[i] + large_win_samps) if i <
(n_windows - 1) else -1)
first_elec = nwb.acquisition["ElectricalSeries"].data[
window_starts_ep[i]:end_ind, 0]
if np.sum(np.isnan(first_elec)) == 0:
dat = (nwb.acquisition["ElectricalSeries"].data[
window_starts_ep[i]:end_ind, :].T)
# Compute power using Welch's method
f_welch, spg = compute_spectrum(
dat,
fs,
method="welch",
avg_type="median",
nperseg=win_n_samps,
f_range=freq_range,
)
# Interpolate power to integer frequencies
f = interpolate.interp1d(f_welch, spg)
spg_new = f(freqs)
# Project power to ROI of interest
spg_proj = project_power(spg_new, proj_mats[part_ind],
good_rois[selected_roi])
# Append result to final list
if pows_sbj is None:
pows_sbj = spg_proj[np.newaxis, :].copy()
def compute_irasa(sig, fs=None, f_range=(1, 30), hset=None, **spectrum_kwargs):
"""Separate the aperiodic and periodic components using the IRASA method.
Parameters
----------
sig : 1d array
Time series.
fs : float
The sampling frequency of sig.
f_range : tuple or None
Frequency range.
hset : 1d array
Resampling factors used in IRASA calculation.
If not provided, defaults to values from 1.1 to 1.9 with an increment of 0.05.
spectrum_kwargs : dict
Optional keywords arguments that are passed to `compute_spectrum`.
Returns
-------
freqs : 1d array
Frequency vector.
psd_aperiodic : 1d array
The aperiodic component of the power spectrum.
psd_periodic : 1d array
The periodic component of the power spectrum.
Notes
-----
Irregular-Resampling Auto-Spectral Analysis (IRASA) is described in Wen & Liu (2016).
Briefly, it aims to separate 1/f and periodic components by resampling time series, and
computing power spectra, effectively averaging away any activity that is frequency specific.
References
----------
Wen, H., & Liu, Z. (2016). Separating Fractal and Oscillatory Components in the Power Spectrum
of Neurophysiological Signal. Brain Topography, 29(1), 13–26. DOI: 10.1007/s10548-015-0448-0
"""
# Check & get the resampling factors, with rounding to avoid floating point precision errors
hset = np.arange(1.1, 1.95, 0.05) if not hset else hset
hset = np.round(hset, 4)
# The `nperseg` input needs to be set to lock in the size of the FFT's
if 'nperseg' not in spectrum_kwargs:
spectrum_kwargs['nperseg'] = int(4 * fs)
# Calculate the original spectrum across the whole signal
freqs, psd = compute_spectrum(sig, fs, **spectrum_kwargs)
# Do the IRASA resampling procedure
psds = np.zeros((len(hset), *psd.shape))
for ind, h_val in enumerate(hset):
# Get the up-sampling / down-sampling (h, 1/h) factors as integers
rat = fractions.Fraction(str(h_val))
up, dn = rat.numerator, rat.denominator
# Resample signal
sig_up = signal.resample_poly(sig, up, dn, axis=-1)
sig_dn = signal.resample_poly(sig, dn, up, axis=-1)
# Calculate the power spectrum using the same params as original
freqs_up, psd_up = compute_spectrum(sig_up, h_val * fs,
**spectrum_kwargs)
freqs_dn, psd_dn = compute_spectrum(sig_dn, fs / h_val,
**spectrum_kwargs)
# Geometric mean of h and 1/h
psds[ind, :] = np.sqrt(psd_up * psd_dn)
# Now we take the median resampled spectra, as an estimate of the aperiodic component
psd_aperiodic = np.median(psds, axis=0)
# Subtract aperiodic from original, to get the periodic component
psd_periodic = psd - psd_aperiodic
# Restrict spectrum to requested range
if f_range:
psds = np.array([psd_aperiodic, psd_periodic])
freqs, (psd_aperiodic,
psd_periodic) = trim_spectrum(freqs, psds, f_range)
return freqs, psd_aperiodic, psd_periodic
# Simulate a time series
sig = sim_combined(n_seconds, fs, components, comp_vars)
###################################################################################################
# Bandstop filter the signal to remove line noise frequencies
sig_filt = filter_signal(sig,
fs,
'bandstop', (57, 63),
n_seconds=2,
remove_edges=False)
###################################################################################################
# Compute a power spectrum of the simulated signal
freqs, powers_pre = trim_spectrum(*compute_spectrum(sig, fs), [3, 75])
freqs, powers_post = trim_spectrum(*compute_spectrum(sig_filt, fs), [3, 75])
###################################################################################################
# Plot the spectrum of the data, pre and post bandstop filtering
plot_spectra(freqs, [powers_pre, powers_post],
log_powers=True,
labels=['Pre-Filter', 'Post-Filter'])
###################################################################################################
#
# In the above, we can see that the the bandstop filter removes power in the filtered range,
# leaving a "dip" in the power spectrum. This dip causes issues with subsequent fitting.
#
fontsize=16.0)
return ax
gridsize = (3, 2)
fig = plt.figure(figsize=(20, 20))
ax1 = plt.subplot2grid(gridsize, (0, 0), colspan=2, rowspan=1)
ax2 = plt.subplot2grid(gridsize, (1, 0))
ax3 = plt.subplot2grid(gridsize, (1, 1))
ax4 = plt.subplot2grid(gridsize, (2, 0))
ax5 = plt.subplot2grid(gridsize, (2, 1))
qq = 0
######## ax2: PSD Welch
freq_mean, psd_mean = spectral.compute_spectrum(sig, fs, method='welch', avg_type='mean', nperseg=fs*2)
ax2.loglog(freq_mean[:118],psd_mean[:118])
add_titlebox(ax2, 'PSD Welch up to 118 Hz', 1)
######## ax5: stats
# Initialize FOOOF model
fm = FOOOF(peak_width_limits=bw_lims, background_mode='knee', max_n_peaks=max_n_peaks)
# fit model
fm.fit(freq_mean, psd_mean, freq_range)
# Central frequency, Amplitude, Bandwidth
peak_params = fm.peak_params_
#offset, knee, slope
def refit(fm, sig, fs, f_range, imf_kwargs=None, power_thresh=.2, energy_thresh=0., refit_ap=False):
"""Refit a power spectrum using EMD based parameter estimation.
Parameters
----------
fm : fooof.FOOOF
FOOOF object containing results from fitting.
sig : 1d array
Voltage time series.
fs : float
Sampling rate, in Hz.
f_range : tuple of [float, float]
Frequency range to restrict power spectrum to.
imf_kwargs : optional, default: None
Optional keyword arguments for compute_emd. Includes:
- max_imfs
- sift_thresh
- env_step_size
- max_iters
- energy_thresh
- stop_method
- sd_thresh
- rilling_thresh
power_thresh : float, optional, default: .2
IMF power threshold as the mean power above the initial aperiodic fit.
energy_thresh : float, optional, default: 0.
Normalized HHT energy threshold to define oscillatory frequencies. This aids the removal of
harmonic peaks if present.
refit_ap : bool, optional, default: None
Refits the aperiodic component when True. When False, the aperiodic component is defined
from the intial specparam fit.
Returns
-------
fm : fooof.FOOOF
Updated FOOOF fit.
imf : 2d array
Intrinsic modes functions.
pe_mask : 1d array
Booleans to mark imfs above aperiodic fit.
"""
fm_refit = fm.copy()
if imf_kwargs is None:
imf_kwargs = {'sd_thresh': .1}
# Compute modes
imf = compute_emd(sig, **imf_kwargs)
# Convert spectra of mode timeseries
_, powers_imf = compute_spectrum(imf, fs, f_range=f_range)
freqs = fm_refit.freqs
powers = fm_refit.power_spectrum
powers_imf = np.log10(powers_imf)
# Initial aperiodic fit
powers_ap = fm_refit._ap_fit
# Select superthreshold modes
pe_mask = select_modes(powers_imf, powers_ap, power_thresh=power_thresh)
# Refit periodic
if not pe_mask.any():
warnings.warn('No IMFs are above the intial aperiodic fit. '
'Returning the inital spectral fit.')
return fm_refit, imf, pe_mask
if energy_thresh > 0:
# Limit frequency ranges to fit using HHT
freqs_min, freqs_max = limit_freqs_hht(imf[pe_mask], freqs, fs,
energy_thresh=energy_thresh)
if freqs_min is None and freqs_max is None:
warnings.warn('No superthreshold energy in HHT. '
'Returning the inital spectral fit.')
return fm_refit, imf, np.zeros(len(pe_mask), dtype=bool)
limits = (freqs_min, freqs_max)
gauss_params = fit_gaussians(freqs, powers, powers_imf, powers_ap, pe_mask, limits)
else:
gauss_params = fit_gaussians(freqs, powers, powers_imf, powers_ap, pe_mask)
if gauss_params is not None:
fm_refit.peak_params_ = fm_refit._create_peak_params(gauss_params)
fm_refit._peak_fit = gen_periodic(freqs, gauss_params.flatten())
else:
fm_refit.peak_params_ = None
fm_refit._peak_fit = np.zeros_like(freqs)
# Refit aperiodic
if refit_ap:
ap_params, ap_fit = refit_aperiodic(freqs, powers, fm_refit._peak_fit)
fm_refit._ap_fit = ap_fit
fm_refit.aperiodic_params_ = ap_params
# Update attibutes
fm_refit.gaussian_params_ = gauss_params
fm_refit.fooofed_spectrum_ = fm_refit._peak_fit + fm_refit._ap_fit
fm_refit._calc_r_squared()
fm_refit._calc_error()
return fm_refit, imf, pe_mask
# Setting for the simulation exponent = -2 # Simulate powerlaw activity, specifically brown noise times = create_times(n_seconds, fs) br_noise = sim.sim_powerlaw(n_seconds, fs, exponent) ################################################################################################### # Plot the simulated data, in the time domain plot_time_series(times, br_noise) ################################################################################################### # Plot the simulated data, in the frequency domain freqs, psd = spectral.compute_spectrum(br_noise, fs) plot_power_spectra(freqs, psd) ################################################################################################### # # Simulate Filtered 1/f Activity # ------------------------------ # # The powerlaw simulation function is also integrated with a filter. This can be useful # if one wants to filter out the slow frequencies, as is often done with neural signals, # to remove the very slow drifts that we see in the pure 1/f simulations. # # To filter a simulated powerlaw signal, simply pass in a filter range, and the filter will # be applied to the simulated data before being returned. Here we will apply a high-pass filter. # # We can see that the resulting signal has much less low-frequency drift than the first one.
},
'sim_powerlaw': {
'exponent': exp
}
}
# Define the frequency range of interest for the analysis
f_range = (1, 40)
# Create the simulate time series
sig = sim_combined(n_seconds, fs, components)
###################################################################################################
# Compute the power spectrum of the simulated signal
freqs, psd = compute_spectrum(sig, fs, nperseg=4 * fs)
# Trim the power spectrum to the frequency range of interest
freqs, psd = trim_spectrum(freqs, psd, f_range)
# Plot the computed power spectrum
plot_power_spectra(freqs, psd, title="Original Spectrum")
###################################################################################################
#
# In the above spectrum, we can see a pattern of power across all frequencies, which reflects
# the 1/f activity, as well as a peak at 10 Hz, which represents the simulated oscillation.
#
###################################################################################################
# IRASA