"""
.. _ex-css:

=================================================================
Cortical Signal Suppression (CSS) for removal of cortical signals
=================================================================

This script shows an example of how to use CSS
:footcite:`Samuelsson2019` . CSS suppresses the cortical contribution
to the signal subspace in EEG data using MEG data, facilitating
detection of subcortical signals. We will illustrate how it works by
simulating one cortical and one subcortical oscillation at different
frequencies; 40 Hz and 239 Hz for cortical and subcortical activity,
respectively, then process it with CSS and look at the power spectral
density of the raw and processed data.

"""
# Author: John G Samuelsson <johnsam@mit.edu>
# License: BSD-3-Clause
# Copyright the MNE-Python contributors.

import matplotlib.pyplot as plt
import numpy as np

import mne
from mne.datasets import sample
from mne.simulation import simulate_evoked, simulate_sparse_stc

###############################################################################
# Load sample subject data
data_path = sample.data_path()
subjects_dir = data_path / "subjects"
meg_path = data_path / "MEG" / "sample"
fwd_fname = meg_path / "sample_audvis-meg-eeg-oct-6-fwd.fif"
ave_fname = meg_path / "sample_audvis-no-filter-ave.fif"
cov_fname = meg_path / "sample_audvis-cov.fif"
trans_fname = meg_path / "sample_audvis_raw-trans.fif"
bem_fname = subjects_dir / "sample" / "bem" / "/sample-5120-bem-sol.fif"

raw = mne.io.read_raw_fif(meg_path / "sample_audvis_raw.fif")
fwd = mne.read_forward_solution(fwd_fname)
fwd = mne.convert_forward_solution(fwd, force_fixed=True, surf_ori=True)
fwd = mne.pick_types_forward(fwd, meg=True, eeg=True, exclude=raw.info["bads"])
cov = mne.read_cov(cov_fname)

###############################################################################
# Find patches (labels) to activate
all_labels = mne.read_labels_from_annot(subject="sample", subjects_dir=subjects_dir)
labels = []
for select_label in ["parahippocampal-lh", "postcentral-rh"]:
    labels.append([lab for lab in all_labels if lab.name in select_label][0])
hiplab, postcenlab = labels

###############################################################################
# Simulate one cortical dipole (40 Hz) and one subcortical (239 Hz)


def cortical_waveform(times):
    """Create a cortical waveform."""
    return 10e-9 * np.cos(times * 2 * np.pi * 40)


def subcortical_waveform(times):
    """Create a subcortical waveform."""
    return 10e-9 * np.cos(times * 2 * np.pi * 239)


times = np.linspace(0, 0.5, int(0.5 * raw.info["sfreq"]))
stc = simulate_sparse_stc(
    fwd["src"],
    n_dipoles=2,
    times=times,
    location="center",
    subjects_dir=subjects_dir,
    labels=[postcenlab, hiplab],
    data_fun=cortical_waveform,
)
stc.data[np.where(np.isin(stc.vertices[0], hiplab.vertices))[0], :] = (
    subcortical_waveform(times)
)
evoked = simulate_evoked(fwd, stc, raw.info, cov, nave=15)

###############################################################################
# Process with CSS and plot PSD of EEG data before and after processing
evoked_subcortical = mne.preprocessing.cortical_signal_suppression(evoked, n_proj=6)
chs = mne.pick_types(evoked.info, meg=False, eeg=True)

psd = np.mean(np.abs(np.fft.rfft(evoked.data)) ** 2, axis=0)
psd_proc = np.mean(np.abs(np.fft.rfft(evoked_subcortical.data)) ** 2, axis=0)
freq = np.arange(
    0, stop=int(evoked.info["sfreq"] / 2), step=evoked.info["sfreq"] / (2 * len(psd))
)

fig, ax = plt.subplots()
ax.plot(freq, psd, label="raw")
ax.plot(freq, psd_proc, label="processed")
ax.text(0.2, 0.7, "cortical", transform=ax.transAxes)
ax.text(0.8, 0.25, "subcortical", transform=ax.transAxes)
ax.set(ylabel="EEG Power spectral density", xlabel="Frequency (Hz)")
ax.legend()

###############################################################################
# References
# ^^^^^^^^^^
#
# .. footbibliography::
