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# Authors: The MNE-Python contributors.
# License: BSD-3-Clause
# Copyright the MNE-Python contributors.
import numpy as np
from .._fiff.pick import _picks_to_idx
from ..evoked import Evoked
from ..utils import _ensure_int, _validate_type, verbose
def _temp_proj(ref_2, ref_1, raw_data, n_proj=6):
# Orthonormalize gradiometer and magnetometer data by a QR decomposition
ref_1_orth = np.linalg.qr(ref_1.T)[0]
ref_2_orth = np.linalg.qr(ref_2.T)[0]
# Calculate cross-correlation
cross_corr = np.dot(ref_1_orth.T, ref_2_orth)
# Channel weights for common temporal subspace by SVD of cross-correlation
ref_1_ch_weights, _, _ = np.linalg.svd(cross_corr)
# Get temporal signals from channel weights
proj_mat = ref_1_orth @ ref_1_ch_weights
# Project out common subspace
filtered_data = raw_data
proj_vec = proj_mat[:, :n_proj]
weights = filtered_data @ proj_vec
filtered_data -= weights @ proj_vec.T
@verbose
def cortical_signal_suppression(
evoked, picks=None, mag_picks=None, grad_picks=None, n_proj=6, *, verbose=None
):
"""Apply cortical signal suppression (CSS) to evoked data.
Parameters
----------
evoked : instance of Evoked
The evoked object to use for CSS. Must contain magnetometer,
gradiometer, and EEG channels.
%(picks_good_data)s
mag_picks : array-like of int
Array of the first set of channel indices that will be used to find
the common temporal subspace. If None (default), all magnetometers will
be used.
grad_picks : array-like of int
Array of the second set of channel indices that will be used to find
the common temporal subspace. If None (default), all gradiometers will
be used.
n_proj : int
The number of projection vectors.
%(verbose)s
Returns
-------
evoked_subcortical : instance of Evoked
The evoked object with contributions from the ``mag_picks`` and ``grad_picks``
channels removed from the ``picks`` channels.
Notes
-----
This method removes the common signal subspace between two sets of
channels (``mag_picks`` and ``grad_picks``) from a set of channels
(``picks``) via a temporal projection using ``n_proj`` number of
projection vectors. In the reference publication :footcite:`Samuelsson2019`,
the joint subspace between magnetometers and gradiometers is used to
suppress the cortical signal in the EEG data. In principle, other
combinations of sensor types (or channels) could be used to suppress
signals from other sources.
References
----------
.. footbibliography::
"""
_validate_type(evoked, Evoked, "evoked")
n_proj = _ensure_int(n_proj, "n_proj")
picks = _picks_to_idx(evoked.info, picks, none="data", exclude="bads")
mag_picks = _picks_to_idx(evoked.info, mag_picks, none="mag", exclude="bads")
grad_picks = _picks_to_idx(evoked.info, grad_picks, none="grad", exclude="bads")
evoked_subcortical = evoked.copy()
# Get data
all_data = evoked.data
mag_data = all_data[mag_picks]
grad_data = all_data[grad_picks]
# Process data with temporal projection algorithm
data = all_data[picks]
_temp_proj(mag_data, grad_data, data, n_proj=n_proj)
evoked_subcortical.data[picks, :] = data
return evoked_subcortical
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