alexandrebarachant/pyRiemann

"""
============================================
Embedding ERP MEG data in 2D Euclidean space
============================================

Riemannian embeddings via Laplacian Eigenmaps (LE) and Locally Linear
Embedding (LLE) of a set of ERP data. Embedding via Laplacian Eigenmaps is
referred to as Spectral Embedding (SE).

Locally Linear Embedding (LLE) assumes that the local neighborhood of a
point on the manifold can be well approximated by  the affine subspace
spanned by the k-nearest neighbors of the point and finds a low-dimensional
embedding of the data based on these affine approximations.

Laplacian Eigenmaps (LE) are based on computing the low dimensional
representation that best preserves locality instead of local linearity in LLE
[1]_.
"""
# Authors:  Pedro Rodrigues <pedro.rodrigues01@gmail.com>,
#           Gabriel Wagner vom Berg <gabriel@bccn-berlin.de>
# License: BSD (3-clause)

import matplotlib.pyplot as plt
import mne
from mne import io
from mne.datasets import sample
from sklearn.model_selection import train_test_split

from pyriemann.estimation import XdawnCovariances
from pyriemann.utils.viz import plot_embedding

print(__doc__)


###############################################################################
# Set parameters and read data
# ----------------------------

data_path = str(sample.data_path())
raw_fname = data_path + '/MEG/sample/sample_audvis_filt-0-40_raw.fif'
event_fname = data_path + '/MEG/sample/sample_audvis_filt-0-40_raw-eve.fif'
tmin, tmax = -0., 1
event_id = dict(aud_l=1, aud_r=2, vis_l=3, vis_r=4)

# Setup for reading the raw data
raw = io.Raw(raw_fname, preload=True, verbose=False)
raw.filter(2, None, method='iir')  # replace baselining with high-pass
events = mne.read_events(event_fname)

raw.info['bads'] = ['MEG 2443']  # set bad channels
picks = mne.pick_types(raw.info, meg=True, eeg=False, stim=False, eog=False,
                       exclude='bads')

# Read epochs
epochs = mne.Epochs(raw, events, event_id, tmin, tmax, proj=False,
                    picks=picks, baseline=None, preload=True, verbose=False)

X = epochs.get_data(copy=False)
y = epochs.events[:, -1]

###############################################################################
# Embedding of Xdawn covariance matrices
# --------------------------------------

nfilter = 4
xdwn = XdawnCovariances(estimator='scm', nfilter=nfilter)
split = train_test_split(X, y, train_size=0.25, random_state=42)
Xtrain, Xtest, ytrain, ytest = split
covs = xdwn.fit(Xtrain, ytrain).transform(Xtest)

###############################################################################
# Laplacian Eigenmaps (LE), also called Spectral Embedding (SE)
# -------------------------------------------------------------

plot_embedding(covs, ytest, metric='riemann', embd_type='Spectral',
               normalize=True)
plt.show()

###############################################################################
# Locally Linear Embedding (LLE)
# ------------------------------

plot_embedding(covs, ytest, metric='riemann', embd_type='LocallyLinear',
               normalize=False)
plt.show()


###############################################################################
# References
# ----------
# .. [1] `Clustering and dimensionality reduction on Riemannian manifolds
#    <https://ieeexplore.ieee.org/document/4587422>`_
#    A. Goh and R Vidal, in 2008 IEEE Conference on Computer Vision and Pattern
#    Recognition.