mne.decoding.LinearModel¶

class mne.decoding.LinearModel(model=None)[source]¶

Compute and store patterns from linear models.

The linear model coefficients (filters) are used to extract discriminant neural sources from the measured data. This class computes the corresponding patterns of these linear filters to make them more interpretable [R38].

Parameters:	model : object | None A linear model from scikit-learn with a fit method that updates a coef_ attribute. If None the model will be LogisticRegression.

See also

CSP, mne.preprocessing.ICA, mne.preprocessing.Xdawn

Notes

New in version 0.10.

References

[R38]

(1, 2) Haufe, S., Meinecke, F., Gorgen, K., Dahne, S., Haynes, J.-D., Blankertz, B., & Biebmann, F. (2014). On the interpretation of weight vectors of linear models in multivariate neuroimaging. NeuroImage, 87, 96-110.

Attributes

filters_	(ndarray) If fit, the filters used to decompose the data.
patterns_	(ndarray) If fit, the patterns used to restore M/EEG signals.

Methods

__hash__() <==> hash(x)
fit(X, y)	Estimate the coefficients of the linear model.
fit_transform(X, y)	Fit the data and transform it using the linear model.
get_params([deep])	Get parameters for this estimator.
plot_filters(*args, **kwargs)	Warning DEPRECATED: plot_filters is deprecated and will be removed in 0.15, use EvokedArray instead.
plot_patterns(*args, **kwargs)	Warning DEPRECATED: plot_filters is deprecated and will be removed in 0.15, use EvokedArray instead.
predict(X)	Compute predictions of y from X.
score(X, y)	Score the linear model computed on the given test data.
set_params(**params)	Set the parameters of this estimator.
transform(X)	Transform the data using the linear model.

__hash__() <==> hash(x)¶

fit(X, y)[source]¶

Estimate the coefficients of the linear model.

Save the coefficients in the attribute filters_ and computes the attribute patterns_.

Parameters:	X : array, shape (n_samples, n_features) The training input samples to estimate the linear coefficients. y : array, shape (n_samples,) The target values.
Returns:	self : instance of LinearModel Returns the modified instance.

fit_transform(X, y)[source]¶

Fit the data and transform it using the linear model.

Parameters:	X : array, shape (n_samples, n_features) The training input samples to estimate the linear coefficients. y : array, shape (n_samples,) The target values.
Returns:	y_pred : array, shape (n_samples,) The predicted targets.

get_params(deep=True)[source]¶

Get parameters for this estimator.

Parameters:	deep : boolean, optional If True, will return the parameters for this estimator and contained subobjects that are estimators.
Returns:	params : mapping of string to any Parameter names mapped to their values.

plot_filters(*args, **kwargs)[source]¶

Warning

DEPRECATED: plot_filters is deprecated and will be removed in 0.15, use EvokedArray instead.

Plot topographic filters of the linear model.

The filters are used to extract discriminant neural sources from the measured data (a.k.a. the backward model).

Parameters:

info : instance of Info Info dictionary of the epochs used to fit the linear model. If not possible, consider using create_info. times : float | array of floats | None. The time point(s) to plot. If None, the number of axes determines the amount of time point(s). If axes is also None, 10 topographies will be shown with a regular time spacing between the first and last time instant. ch_type : ‘mag’ | ‘grad’ | ‘planar1’ | ‘planar2’ | ‘eeg’ | None The channel type to plot. For ‘grad’, the gradiometers are collected in pairs and the RMS for each pair is plotted. If None, then first available channel type from order given above is used. Defaults to None. layout : None | Layout Layout instance specifying sensor positions (does not need to be specified for Neuromag data). If possible, the correct layout file is inferred from the data; if no appropriate layout file was found the layout is automatically generated from the sensor locations. vmin : float | callable The value specfying the lower bound of the color range. If None, and vmax is None, -vmax is used. Else np.min(data). If callable, the output equals vmin(data). vmax : float | callable The value specfying the upper bound of the color range. If None, the maximum absolute value is used. If vmin is None, but vmax is not, defaults to np.min(data). If callable, the output equals vmax(data). cmap : matplotlib colormap | (colormap, bool) | ‘interactive’ | None Colormap to use. If tuple, the first value indicates the colormap to use and the second value is a boolean defining interactivity. In interactive mode the colors are adjustable by clicking and dragging the colorbar with left and right mouse button. Left mouse button moves the scale up and down and right mouse button adjusts the range. Hitting space bar resets the range. Up and down arrows can be used to change the colormap. If None, ‘Reds’ is used for all positive data, otherwise defaults to ‘RdBu_r’. If ‘interactive’, translates to (None, True). Defaults to ‘RdBu_r’. Warning Interactive mode works smoothly only for a small amount of topomaps. sensors : bool | str Add markers for sensor locations to the plot. Accepts matplotlib plot format string (e.g., ‘r+’ for red plusses). If True, a circle will be used (via .add_artist). Defaults to True. colorbar : bool Plot a colorbar. scale : dict | float | None Scale the data for plotting. If None, defaults to 1e6 for eeg, 1e13 for grad and 1e15 for mag. scale_time : float | None Scale the time labels. Defaults to 1e3. unit : dict | str | None The unit of the channel type used for colorbar label. If scale is None the unit is automatically determined. res : int The resolution of the topomap image (n pixels along each side). size : float Side length per topomap in inches. cbar_fmt : str String format for colorbar values. name_format : str String format for topomap values. Defaults to “%03f ms” proj : bool | ‘interactive’ If true SSP projections are applied before display. If ‘interactive’, a check box for reversible selection of SSP projection vectors will be show. show : bool Show figure if True. show_names : bool | callable If True, show channel names on top of the map. If a callable is passed, channel names will be formatted using the callable; e.g., to delete the prefix ‘MEG ‘ from all channel names, pass the function lambda x: x.replace(‘MEG ‘, ”). If mask is not None, only significant sensors will be shown. title : str | None Title. If None (default), no title is displayed. mask : ndarray of bool, shape (n_channels, n_times) | None The channels to be marked as significant at a given time point. Indices set to True will be considered. Defaults to None. mask_params : dict | None Additional plotting parameters for plotting significant sensors. Default (None) equals: dict(marker='o', markerfacecolor='w', markeredgecolor='k', linewidth=0, markersize=4) outlines : ‘head’ | ‘skirt’ | dict | None The outlines to be drawn. If ‘head’, the default head scheme will be drawn. If ‘skirt’ the head scheme will be drawn, but sensors are allowed to be plotted outside of the head circle. If dict, each key refers to a tuple of x and y positions, the values in ‘mask_pos’ will serve as image mask, and the ‘autoshrink’ (bool) field will trigger automated shrinking of the positions due to points outside the outline. Alternatively, a matplotlib patch object can be passed for advanced masking options, either directly or as a function that returns patches (required for multi-axis plots). If None, nothing will be drawn. Defaults to ‘head’. contours : int | False | None The number of contour lines to draw. If 0, no contours will be drawn. image_interp : str The image interpolation to be used. All matplotlib options are accepted. average : float | None The time window around a given time to be used for averaging (seconds). For example, 0.01 would translate into window that starts 5 ms before and ends 5 ms after a given time point. Defaults to None, which means no averaging. head_pos : dict | None If None (default), the sensors are positioned such that they span the head circle. If dict, can have entries ‘center’ (tuple) and ‘scale’ (tuple) for what the center and scale of the head should be relative to the electrode locations.

Returns:

fig : instance of matplotlib.figure.Figure The figure.

plot_patterns(*args, **kwargs)[source]¶

Warning

DEPRECATED: plot_filters is deprecated and will be removed in 0.15, use EvokedArray instead.

Plot topographic patterns of the linear model.

The patterns explain how the measured data was generated from the neural sources (a.k.a. the forward model).

Parameters:

info : instance of Info Info dictionary of the epochs used to fit the linear model. If not possible, consider using create_info. times : float | array of floats | None. The time point(s) to plot. If None, the number of axes determines the amount of time point(s). If axes is also None, 10 topographies will be shown with a regular time spacing between the first and last time instant. ch_type : ‘mag’ | ‘grad’ | ‘planar1’ | ‘planar2’ | ‘eeg’ | None The channel type to plot. For ‘grad’, the gradiometers are collected in pairs and the RMS for each pair is plotted. If None, then first available channel type from order given above is used. Defaults to None. layout : None | Layout Layout instance specifying sensor positions (does not need to be specified for Neuromag data). If possible, the correct layout file is inferred from the data; if no appropriate layout file was found the layout is automatically generated from the sensor locations. vmin : float | callable The value specfying the lower bound of the color range. If None, and vmax is None, -vmax is used. Else np.min(data). If callable, the output equals vmin(data). vmax : float | callable The value specfying the upper bound of the color range. If None, the maximum absolute value is used. If vmin is None, but vmax is not, defaults to np.min(data). If callable, the output equals vmax(data). cmap : matplotlib colormap | (colormap, bool) | ‘interactive’ | None Colormap to use. If tuple, the first value indicates the colormap to use and the second value is a boolean defining interactivity. In interactive mode the colors are adjustable by clicking and dragging the colorbar with left and right mouse button. Left mouse button moves the scale up and down and right mouse button adjusts the range. Hitting space bar resets the range. Up and down arrows can be used to change the colormap. If None, ‘Reds’ is used for all positive data, otherwise defaults to ‘RdBu_r’. If ‘interactive’, translates to (None, True). Defaults to ‘RdBu_r’. Warning Interactive mode works smoothly only for a small amount of topomaps. sensors : bool | str Add markers for sensor locations to the plot. Accepts matplotlib plot format string (e.g., ‘r+’ for red plusses). If True, a circle will be used (via .add_artist). Defaults to True. colorbar : bool Plot a colorbar. scale : dict | float | None Scale the data for plotting. If None, defaults to 1e6 for eeg, 1e13 for grad and 1e15 for mag. scale_time : float | None Scale the time labels. Defaults to 1e3. unit : dict | str | None The unit of the channel type used for colorbar label. If scale is None the unit is automatically determined. res : int The resolution of the topomap image (n pixels along each side). size : float Side length per topomap in inches. cbar_fmt : str String format for colorbar values. name_format : str String format for topomap values. Defaults to “%03f ms” proj : bool | ‘interactive’ If true SSP projections are applied before display. If ‘interactive’, a check box for reversible selection of SSP projection vectors will be show. show : bool Show figure if True. show_names : bool | callable If True, show channel names on top of the map. If a callable is passed, channel names will be formatted using the callable; e.g., to delete the prefix ‘MEG ‘ from all channel names, pass the function lambda x: x.replace(‘MEG ‘, ”). If mask is not None, only significant sensors will be shown. title : str | None Title. If None (default), no title is displayed. mask : ndarray of bool, shape (n_channels, n_times) | None The channels to be marked as significant at a given time point. Indices set to True will be considered. Defaults to None. mask_params : dict | None Additional plotting parameters for plotting significant sensors. Default (None) equals: dict(marker='o', markerfacecolor='w', markeredgecolor='k', linewidth=0, markersize=4) outlines : ‘head’ | ‘skirt’ | dict | None The outlines to be drawn. If ‘head’, the default head scheme will be drawn. If ‘skirt’ the head scheme will be drawn, but sensors are allowed to be plotted outside of the head circle. If dict, each key refers to a tuple of x and y positions, the values in ‘mask_pos’ will serve as image mask, and the ‘autoshrink’ (bool) field will trigger automated shrinking of the positions due to points outside the outline. Alternatively, a matplotlib patch object can be passed for advanced masking options, either directly or as a function that returns patches (required for multi-axis plots). If None, nothing will be drawn. Defaults to ‘head’. contours : int | False | None The number of contour lines to draw. If 0, no contours will be drawn. image_interp : str The image interpolation to be used. All matplotlib options are accepted. average : float | None The time window around a given time to be used for averaging (seconds). For example, 0.01 would translate into window that starts 5 ms before and ends 5 ms after a given time point. Defaults to None, which means no averaging. head_pos : dict | None If None (default), the sensors are positioned such that they span the head circle. If dict, can have entries ‘center’ (tuple) and ‘scale’ (tuple) for what the center and scale of the head should be relative to the electrode locations.

Returns:

fig : instance of matplotlib.figure.Figure The figure.

predict(X)[source]¶

Compute predictions of y from X.

Parameters:	X : array, shape (n_samples, n_features) The data used to compute the predictions.
Returns:	y_pred : array, shape (n_samples,) The predictions.

score(X, y)[source]¶

Score the linear model computed on the given test data.

Parameters:	X : array, shape (n_samples, n_features) The data to transform. y : array, shape (n_samples,) The target values.
Returns:	score : float Score of the linear model

set_params(**params)[source]¶

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. Returns ——- self

transform(X)[source]¶

Transform the data using the linear model.

Parameters:	X : array, shape (n_samples, n_features) The data to transform.
Returns:	y_pred : array, shape (n_samples,) The predicted targets.