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"""
.. _ex-ssd-spatial-filters:
================================================================
Compute spatial filters with Spatio-Spectral Decomposition (SSD)
================================================================
In this example, we will compute spatial filters for retaining
oscillatory brain activity and down-weighting 1/f background signals
as proposed by :footcite:`NikulinEtAl2011`.
The idea is to learn spatial filters that separate oscillatory dynamics
from surrounding non-oscillatory noise based on the covariance in the
frequency band of interest and the noise covariance based on surrounding
frequencies.
"""
# Author: Denis A. Engemann <denis.engemann@gmail.com>
# Victoria Peterson <victoriapeterson09@gmail.com>
# License: BSD-3-Clause
# Copyright the MNE-Python contributors.
# %%
import matplotlib.pyplot as plt
import mne
from mne import Epochs
from mne.datasets.fieldtrip_cmc import data_path
from mne.decoding import SSD
# %%
# Define parameters
fname = data_path() / "SubjectCMC.ds"
# Prepare data
raw = mne.io.read_raw_ctf(fname)
raw.crop(tmin=50.0, tmax=110.0).load_data() # crop for memory purposes
raw.resample(sfreq=250)
raw.pick_types(meg=True, ref_meg=False)
freqs_sig = 9, 12
freqs_noise = 8, 13
ssd = SSD(
info=raw.info,
reg="oas",
sort_by_spectral_ratio=False, # False for purpose of example.
filt_params_signal=dict(
l_freq=freqs_sig[0],
h_freq=freqs_sig[1],
l_trans_bandwidth=1,
h_trans_bandwidth=1,
),
filt_params_noise=dict(
l_freq=freqs_noise[0],
h_freq=freqs_noise[1],
l_trans_bandwidth=1,
h_trans_bandwidth=1,
),
)
ssd.fit(X=raw.get_data())
# %%
# Let's investigate spatial filter with the max power ratio.
# We will first inspect the topographies.
# According to Nikulin et al. (2011), this is done by either inverting the filters
# (W^{-1}) or by multiplying the noise cov with the filters Eq. (22) (C_n W)^t.
# We rely on the inversion approach here.
pattern = mne.EvokedArray(data=ssd.patterns_[:4].T, info=ssd.info)
pattern.plot_topomap(units=dict(mag="A.U."), time_format="")
# The topographies suggest that we picked up a parietal alpha generator.
# Transform
ssd_sources = ssd.transform(X=raw.get_data())
# Get psd of SSD-filtered signals.
psd, freqs = mne.time_frequency.psd_array_welch(
ssd_sources, sfreq=raw.info["sfreq"], n_fft=4096
)
# Get spec_ratio information (already sorted).
# Note that this is not necessary if sort_by_spectral_ratio=True (default).
spec_ratio, sorter = ssd.get_spectral_ratio(ssd_sources)
# Plot spectral ratio (see Eq. 24 in Nikulin et al., 2011).
fig, ax = plt.subplots(1)
ax.plot(spec_ratio, color="black")
ax.plot(spec_ratio[sorter], color="orange", label="sorted eigenvalues")
ax.set_xlabel("Eigenvalue Index")
ax.set_ylabel(r"Spectral Ratio $\frac{P_f}{P_{sf}}$")
ax.legend()
ax.axhline(1, linestyle="--")
# We can see that the initial sorting based on the eigenvalues
# was already quite good. However, when using few components only
# the sorting might make a difference.
# %%
# Let's also look at the power spectrum of that source and compare it
# to the power spectrum of the source with lowest SNR.
below50 = freqs < 50
# for highlighting the freq. band of interest
bandfilt = (freqs_sig[0] <= freqs) & (freqs <= freqs_sig[1])
fig, ax = plt.subplots(1)
ax.loglog(freqs[below50], psd[0, below50], label="max SNR")
ax.loglog(freqs[below50], psd[-1, below50], label="min SNR")
ax.loglog(freqs[below50], psd[:, below50].mean(axis=0), label="mean")
ax.fill_between(freqs[bandfilt], 0, 10000, color="green", alpha=0.15)
ax.set_xlabel("log(frequency)")
ax.set_ylabel("log(power)")
ax.legend()
# We can clearly see that the selected component enjoys an SNR that is
# way above the average power spectrum.
# %%
# Epoched data
# ------------
# Although we suggest using this method before epoching, there might be some
# situations in which data can only be treated by chunks.
# Build epochs as sliding windows over the continuous raw file.
events = mne.make_fixed_length_events(raw, id=1, duration=5.0, overlap=0.0)
# Epoch length is 5 seconds.
epochs = Epochs(raw, events, tmin=0.0, tmax=5, baseline=None, preload=True)
ssd_epochs = SSD(
info=epochs.info,
reg="oas",
filt_params_signal=dict(
l_freq=freqs_sig[0],
h_freq=freqs_sig[1],
l_trans_bandwidth=1,
h_trans_bandwidth=1,
),
filt_params_noise=dict(
l_freq=freqs_noise[0],
h_freq=freqs_noise[1],
l_trans_bandwidth=1,
h_trans_bandwidth=1,
),
)
ssd_epochs.fit(X=epochs.get_data(copy=False))
# Plot topographies.
pattern_epochs = mne.EvokedArray(data=ssd_epochs.patterns_[:4].T, info=ssd_epochs.info)
pattern_epochs.plot_topomap(units=dict(mag="A.U."), time_format="")
# %%
# References
# ----------
#
# .. footbibliography::
|
