mne.decoding.SSD

class mne.decoding.SSD(info, filt_params_signal, filt_params_noise, reg=None, n_components=None, picks=None, sort_by_spectral_ratio=True, return_filtered=False, n_fft=None, cov_method_params=None, rank=None)

Signal decomposition using the Spatio-Spectral Decomposition (SSD).

SSD seeks to maximize the power at a frequency band of interest while simultaneously minimizing it at the flanking (surrounding) frequency bins (considered noise). It extremizes the covariance matrices associated with signal and noise [1].

SSD can either be used as a dimensionality reduction method or a ‘denoised’ low rank factorization method [2].

Parameters:

infomne.Info

The mne.Info object with information about the sensors and methods of measurement. Must match the input data.

filt_params_signaldict

Filtering for the frequencies of interest.

filt_params_noisedict

Filtering for the frequencies of non-interest.

regfloat | str | None (default)

Which covariance estimator to use. If not None (same as ‘empirical’), allow regularization for covariance estimation. If float, shrinkage is used (0 <= shrinkage <= 1). For str options, reg will be passed to method mne.compute_covariance().

n_componentsint | None (default None)

The number of components to extract from the signal. If None, the number of components equal to the rank of the data are returned (see rank).

picksarray of int | None (default None)

The indices of good channels.

sort_by_spectral_ratiobool (default True)

If set to True, the components are sorted according to the spectral ratio. See Eq. (24) in [1].

return_filteredbool (default False)

If return_filtered is True, data is bandpassed and projected onto the SSD components.

n_fftint (default None)

If sort_by_spectral_ratio is set to True, then the SSD sources will be sorted according to their spectral ratio which is calculated based on mne.time_frequency.psd_array_welch(). The n_fft parameter sets the length of FFT used. See mne.time_frequency.psd_array_welch() for more information.

cov_method_paramsdict | None (default None)

As in mne.decoding.SPoC The default is None.

rankNone | dict | ‘info’ | ‘full’

As in mne.decoding.SPoC This controls the rank computation that can be read from the measurement info or estimated from the data, which determines the maximum possible number of components. See Notes of mne.compute_rank() for details. We recommend to use ‘full’ when working with epoched data.

References

[1] (1,2,3)

Vadim V Nikulin, Guido Nolte, and Gabriel Curio. A novel method for reliable and fast extraction of neuronal EEG/MEG oscillations on the basis of spatio-spectral decomposition. NeuroImage, 55(4):1528–1535, 2011. doi:10.1016/j.neuroimage.2011.01.057.

[2] (1,2)

Stefan Haufe, Sven Dähne, and Vadim V Nikulin. Dimensionality reduction for the analysis of brain oscillations. NeuroImage, 101:583–597, 2014. doi:https://doi.org/10.1016/j.neuroimage.2014.06.073.

Attributes:

filters_array, shape (n_channels, n_components)

The spatial filters to be multiplied with the signal.

patterns_array, shape (n_components, n_channels)

The patterns for reconstructing the signal from the filtered data.

Methods

apply(X)	Remove selected components from the signal.
fit(X[, y])	Estimate the SSD decomposition on raw or epoched data.
fit_transform(X[, y])	Fit to data, then transform it.
get_params([deep])	Get parameters for this estimator.
get_spectral_ratio(ssd_sources)	Get the spectal signal-to-noise ratio for each spatial filter.
inverse_transform()	Not implemented yet.
set_params(**params)	Set the parameters of this estimator.
transform(X)	Estimate epochs sources given the SSD filters.

apply(X)

Remove selected components from the signal.

This procedure will reconstruct M/EEG signals from which the dynamics described by the excluded components is subtracted (denoised by low-rank factorization). See [2] for more information.

Note

Unlike in other classes with an apply method, only NumPy arrays are supported (not instances of MNE objects).

Parameters:

Xarray, shape ([n_epochs, ]n_channels, n_times)

The input data from which to estimate the SSD. Either 2D array obtained from continuous data or 3D array obtained from epoched data.

Returns:

Xarray, shape ([n_epochs, ]n_channels, n_times)

The processed data.

fit(X, y=None)

Estimate the SSD decomposition on raw or epoched data.

Parameters:

Xarray, shape ([n_epochs, ]n_channels, n_times)

The input data from which to estimate the SSD. Either 2D array obtained from continuous data or 3D array obtained from epoched data.

yNone | array, shape (n_samples,)

Used for scikit-learn compatibility.

Returns:

selfinstance of SSD

Returns the modified instance.

Examples using fit:

Compute Spectro-Spatial Decomposition (SSD) spatial filters

Compute Spectro-Spatial Decomposition (SSD) spatial filters

fit_transform(X, y=None, **fit_params)

Fit to data, then transform it.

Fits transformer to X and y with optional parameters fit_params, and returns a transformed version of X.

Parameters:

Xarray, shape (n_samples, n_features)

Training set.

yarray, shape (n_samples,)

Target values or class labels.

**fit_paramsdict

Additional fitting parameters passed to the fit method..

Returns:

X_newarray, shape (n_samples, n_features_new)

Transformed array.

get_params(deep=True)

Get parameters for this estimator.

Parameters:

deepbool, optional

If True, will return the parameters for this estimator and contained subobjects that are estimators.

Returns:

paramsdict

Parameter names mapped to their values.

get_spectral_ratio(ssd_sources)

Get the spectal signal-to-noise ratio for each spatial filter.

Spectral ratio measure for best n_components selection See [1], Eq. (24).

Parameters:

ssd_sourcesarray

Data projected to SSD space.

Returns:

spec_ratioarray, shape (n_channels)

Array with the sprectal ratio value for each component.

sorter_specarray, shape (n_channels)

Array of indices for sorting spec_ratio.

References

Examples using get_spectral_ratio:

Compute Spectro-Spatial Decomposition (SSD) spatial filters

Compute Spectro-Spatial Decomposition (SSD) spatial filters

inverse_transform()

Not implemented yet.

set_params(**params)

Set the parameters of this estimator.

The method works on simple estimators as well as on nested objects (such as pipelines). The latter have parameters of the form <component>__<parameter> so that it’s possible to update each component of a nested object.

Parameters:

**paramsdict

Parameters.

Returns:

instinstance

The object.

transform(X)

Estimate epochs sources given the SSD filters.

Parameters:

Xarray, shape ([n_epochs, ]n_channels, n_times)

The input data from which to estimate the SSD. Either 2D array obtained from continuous data or 3D array obtained from epoched data.

Returns:

X_ssdarray, shape ([n_epochs, ]n_components, n_times)

The processed data.

Examples using transform:

Compute Spectro-Spatial Decomposition (SSD) spatial filters

Compute Spectro-Spatial Decomposition (SSD) spatial filters

Examples using mne.decoding.SSD

Compute Spectro-Spatial Decomposition (SSD) spatial filters

Compute Spectro-Spatial Decomposition (SSD) spatial filters