mne.MixedSourceEstimate

class mne.MixedSourceEstimate(data, vertices=None, tmin=None, tstep=None, subject=None, verbose=None)[source]

Container for mixed surface and volume source estimates.

Parameters
dataarray of shape (n_dipoles, n_times) | tuple, shape (2,)

The data in source space. The data can either be a single array or a tuple with two arrays: “kernel” shape (n_vertices, n_sensors) and “sens_data” shape (n_sensors, n_times). In this case, the source space data corresponds to np.dot(kernel, sens_data).

verticeslist of array

Vertex numbers corresponding to the data. The list contains arrays with one array per source space.

tminscalar

Time point of the first sample in data.

tstepscalar

Time step between successive samples in data.

subjectstr | None

The subject name. While not necessary, it is safer to set the subject parameter to avoid analysis errors.

verbosebool, str, int, or None

If not None, override default verbose level (see mne.verbose() and Logging documentation for more).

See also

SourceEstimate

A container for surface source estimates.

VectorSourceEstimate

A container for vector source estimates.

VolSourceEstimate

A container for volume source estimates.

VolVectorSourceEstimate

A container for Volume vector source estimates.

Notes

New in version 0.9.0.

Attributes
subjectstr | None

The subject name.

timesarray of shape (n_times,)

A timestamp for each sample.

verticeslist of array

Vertex numbers corresponding to the data. The list contains arrays with one array per source space.

dataarray of shape (n_dipoles, n_times)

Numpy array of source estimate data.

shapetuple

Shape of the data.

Methods

__add__(a)

Add source estimates.

__div__(a)

Divide source estimates.

__hash__(/)

Return hash(self).

__mul__(a)

Multiply source estimates.

__neg__()

Negate the source estimate.

__sub__(a)

Subtract source estimates.

bin(width[, tstart, tstop, func])

Return a source estimate object with data summarized over time bins.

copy()

Return copy of source estimate instance.

crop([tmin, tmax, include_tmax])

Restrict SourceEstimate to a time interval.

extract_label_time_course(labels, src[, …])

Extract label time courses for lists of labels.

get_peak([tmin, tmax, mode, vert_as_index, …])

Get location and latency of peak amplitude.

mean()

Make a summary stc file with mean over time points.

plot([subject, surface, hemi, colormap, …])

Plot SourceEstimate.

plot_surface(**kwargs)

Warning

DEPRECATED: stc_mixed.plot_surface(…) is deprecated and will be removed in 0.22, use stc_mixed.surface().plot(…)

resample(sfreq[, npad, window, n_jobs, verbose])

Resample data.

save(fname[, ftype, verbose])

Save the full source estimate to an HDF5 file.

sqrt()

Take the square root.

sum()

Make a summary stc file with sum over time points.

surface()

Return the cortical surface source estimate.

time_as_index(times[, use_rounding])

Convert time to indices.

to_data_frame([index, scalings, …])

Export data in tabular structure as a pandas DataFrame.

transform(func[, idx, tmin, tmax, copy])

Apply linear transform.

transform_data(func[, idx, tmin_idx, tmax_idx])

Get data after a linear (time) transform has been applied.

volume()

Return the volume surface source estimate.

__add__(a)[source]

Add source estimates.

__div__(a)[source]

Divide source estimates.

__mul__(a)[source]

Multiply source estimates.

__neg__()[source]

Negate the source estimate.

__sub__(a)[source]

Subtract source estimates.

bin(width, tstart=None, tstop=None, func=<function mean>)[source]

Return a source estimate object with data summarized over time bins.

Time bins of width seconds. This method is intended for visualization only. No filter is applied to the data before binning, making the method inappropriate as a tool for downsampling data.

Parameters
widthscalar

Width of the individual bins in seconds.

tstartscalar | None

Time point where the first bin starts. The default is the first time point of the stc.

tstopscalar | None

Last possible time point contained in a bin (if the last bin would be shorter than width it is dropped). The default is the last time point of the stc.

funccallable()

Function that is applied to summarize the data. Needs to accept a numpy.array as first input and an axis keyword argument.

Returns
stcSourceEstimate | VectorSourceEstimate

The binned source estimate.

copy()[source]

Return copy of source estimate instance.

Returns
stcinstance of SourceEstimate

A copy of the source estimate.

crop(tmin=None, tmax=None, include_tmax=True)[source]

Restrict SourceEstimate to a time interval.

Parameters
tminfloat | None

The first time point in seconds. If None the first present is used.

tmaxfloat | None

The last time point in seconds. If None the last present is used.

include_tmaxbool

If True (default), include tmax. If False, exclude tmax (similar to how Python indexing typically works).

New in version 0.19.

Returns
stcinstance of SourceEstimate

The cropped source estimate.

property data

Numpy array of source estimate data.

extract_label_time_course(labels, src, mode='auto', allow_empty=False, verbose=None)[source]

Extract label time courses for lists of labels.

This function will extract one time course for each label. The way the time courses are extracted depends on the mode parameter.

Parameters
labelsLabel | BiHemiLabel | list | tuple | str

If using a surface or mixed source space, this should be the Label’s for which to extract the time course. If working with whole-brain volume source estimates, this must be one of:

  • a string path to a FreeSurfer atlas for the subject (e.g., their ‘aparc.a2009s+aseg.mgz’) to extract time courses for all volumes in the atlas

  • a two-element list or tuple, the first element being a path to an atlas, and the second being a list or dict of volume_labels to extract (see mne.setup_volume_source_space() for details).

Changed in version 0.21.0: Support for volume source estimates.

srcinstance of SourceSpaces

The source spaces for the source time courses.

modestr

Extraction mode, see Notes.

allow_emptybool | str

False (default) will emit an error if there are labels that have no vertices in the source estimate. True and 'ignore' will return all-zero time courses for labels that do not have any vertices in the source estimate, and True will emit a warning while and “ignore” will just log a message.

Changed in version 0.21.0: Support for “ignore”.

verbosebool, str, int, or None

If not None, override default verbose level (see mne.verbose() and Logging documentation for more). Defaults to self.verbose.

Returns
label_tcarray | list (or generator) of array, shape (n_labels[, n_orient], n_times)

Extracted time course for each label and source estimate.

See also

extract_label_time_course

Extract time courses for multiple STCs.

Notes

Valid values for mode are:

  • 'max'

    Maximum value across vertices at each time point within each label.

  • 'mean'

    Average across vertices at each time point within each label. Ignores orientation of sources for standard source estimates, which varies across the cortical surface, which can lead to cancellation. Vector source estimates are always in XYZ / RAS orientation, and are thus already geometrically aligned.

  • 'mean_flip'

    Finds the dominant direction of source space normal vector orientations within each label, applies a sign-flip to time series at vertices whose orientation is more than 180° different from the dominant direction, and then averages across vertices at each time point within each label.

  • 'pca_flip'

    Applies singular value decomposition to the time courses within each label, and uses the first right-singular vector as the representative label time course. This signal is scaled so that its power matches the average (per-vertex) power within the label, and sign-flipped by multiplying by np.sign(u @ flip), where u is the first left-singular vector and flip is the same sign-flip vector used when mode='mean_flip'. This sign-flip ensures that extracting time courses from the same label in similar STCs does not result in 180° direction/phase changes.

  • 'auto' (default)

    Uses 'mean_flip' when a standard source estimate is applied, and 'mean' when a vector source estimate is supplied.

    New in version 0.21: Support for 'auto', vector, and volume source estimates.

The only modes that work for vector and volume source estimates are 'mean', 'max', and 'auto'.

get_peak(tmin=None, tmax=None, mode='abs', vert_as_index=False, time_as_index=False)[source]

Get location and latency of peak amplitude.

Parameters
tminfloat | None

The minimum point in time to be considered for peak getting.

tmaxfloat | None

The maximum point in time to be considered for peak getting.

mode{‘pos’, ‘neg’, ‘abs’}

How to deal with the sign of the data. If ‘pos’ only positive values will be considered. If ‘neg’ only negative values will be considered. If ‘abs’ absolute values will be considered. Defaults to ‘abs’.

vert_as_indexbool

Whether to return the vertex index (True) instead of of its ID (False, default).

time_as_indexbool

Whether to return the time index (True) instead of the latency (False, default).

Returns
posint

The vertex exhibiting the maximum response, either ID or index.

latencyfloat

The latency in seconds.

mean()[source]

Make a summary stc file with mean over time points.

Returns
stcSourceEstimate | VectorSourceEstimate

The modified stc.

plot(subject=None, surface='inflated', hemi='lh', colormap='auto', time_label='auto', smoothing_steps=10, transparent=True, alpha=1.0, time_viewer='auto', subjects_dir=None, figure=None, views='auto', colorbar=True, clim='auto', cortex='classic', size=800, background='black', foreground=None, initial_time=None, time_unit='s', backend='auto', spacing='oct6', title=None, show_traces='auto', src=None, volume_options=1.0, view_layout='vertical', add_data_kwargs=None, verbose=None)[source]

Plot SourceEstimate.

Parameters
subjectstr | None

The subject name corresponding to FreeSurfer environment variable SUBJECT. If None stc.subject will be used. If that is None, the environment will be used.

surfacestr

The type of surface (inflated, white etc.).

hemistr

Hemisphere id (ie ‘lh’, ‘rh’, ‘both’, or ‘split’). In the case of ‘both’, both hemispheres are shown in the same window. In the case of ‘split’ hemispheres are displayed side-by-side in different viewing panes.

colormapstr | np.ndarray of float, shape(n_colors, 3 | 4)

Name of colormap to use or a custom look up table. If array, must be (n x 3) or (n x 4) array for with RGB or RGBA values between 0 and 255. The default (‘auto’) uses ‘hot’ for one-sided data and ‘mne’ for two-sided data.

time_labelstr | callable() | None

Format of the time label (a format string, a function that maps floating point time values to strings, or None for no label). The default is 'auto', which will use time=%0.2f ms if there is more than one time point.

smoothing_stepsint

The amount of smoothing.

transparentbool | None

If True, use a linear transparency between fmin and fmid. None will choose automatically based on colormap type.

alphafloat

Alpha value to apply globally to the overlay. Has no effect with mpl backend.

time_viewerbool | str

Display time viewer GUI. Can also be ‘auto’, which will mean True for the PyVista backend and False otherwise.

Changed in version 0.20.0: “auto” mode added.

subjects_dirstr | None

The path to the freesurfer subjects reconstructions. It corresponds to Freesurfer environment variable SUBJECTS_DIR.

figureinstance of mayavi.core.api.Scene | instance of matplotlib.figure.Figure | list | int | None

If None, a new figure will be created. If multiple views or a split view is requested, this must be a list of the appropriate length. If int is provided it will be used to identify the Mayavi figure by it’s id or create a new figure with the given id. If an instance of matplotlib figure, mpl backend is used for plotting.

viewsstr | list

View to use. Can be any of:

['lateral', 'medial', 'rostral', 'caudal', 'dorsal', 'ventral',
 'frontal', 'parietal', 'axial', 'sagittal', 'coronal']

Three letter abbreviations (e.g., 'lat') are also supported. Using multiple views (list) is not supported for mpl backend.

When plotting a standard SourceEstimate (not volume, mixed, or vector) and using the PyVista backend, views='flat' is also supported to plot cortex as a flatmap.

Changed in version 0.21.0: Support for flatmaps.

colorbarbool

If True, display colorbar on scene.

climstr | dict

Colorbar properties specification. If ‘auto’, set clim automatically based on data percentiles. If dict, should contain:

kind‘value’ | ‘percent’

Flag to specify type of limits.

limslist | np.ndarray | tuple of float, 3 elements

Lower, middle, and upper bounds for colormap.

pos_limslist | np.ndarray | tuple of float, 3 elements

Lower, middle, and upper bound for colormap. Positive values will be mirrored directly across zero during colormap construction to obtain negative control points.

Note

Only one of lims or pos_lims should be provided. Only sequential colormaps should be used with lims, and only divergent colormaps should be used with pos_lims.

cortexstr or tuple

Specifies how binarized curvature values are rendered. Either the name of a preset PySurfer cortex colorscheme (one of ‘classic’, ‘bone’, ‘low_contrast’, or ‘high_contrast’), or the name of mayavi colormap, or a tuple with values (colormap, min, max, reverse) to fully specify the curvature colors. Has no effect with mpl backend.

sizefloat or tuple of float

The size of the window, in pixels. can be one number to specify a square window, or the (width, height) of a rectangular window. Has no effect with mpl backend.

backgroundmatplotlib color

Color of the background of the display window.

foregroundmatplotlib color | None

Color of the foreground of the display window. Has no effect with mpl backend. None will choose white or black based on the background color.

initial_timefloat | None

The time to display on the plot initially. None to display the first time sample (default).

time_unit‘s’ | ‘ms’

Whether time is represented in seconds (“s”, default) or milliseconds (“ms”).

backend‘auto’ | ‘mayavi’ | ‘matplotlib’

Which backend to use. If 'auto' (default), tries to plot with mayavi, but resorts to matplotlib if mayavi is not available.

New in version 0.15.0.

spacingstr

The spacing to use for the source space. Can be 'ico#' for a recursively subdivided icosahedron, 'oct#' for a recursively subdivided octahedron, or 'all' for all points. In general, you can speed up the plotting by selecting a sparser source space. Has no effect with mayavi backend. Defaults to ‘oct6’.

New in version 0.15.0.

titlestr | None

Title for the figure. If None, the subject name will be used.

New in version 0.17.0.

show_tracesbool | str | float

If True, enable interactive picking of a point on the surface of the brain and plot its time course. This feature is only available with the PyVista 3d backend, and requires time_viewer=True. Defaults to ‘auto’, which will use True if and only if time_viewer=True, the backend is PyVista, and there is more than one time point. If float (between zero and one), it specifies what proportion of the total window should be devoted to traces (True is equivalent to 0.25, i.e., it will occupy the bottom 1/4 of the figure).

New in version 0.20.0.

srcinstance of SourceSpaces | None

The source space corresponding to the source estimate. Only necessary if the STC is a volume or mixed source estimate.

volume_optionsfloat | dict | None

Options for volumetric source estimate plotting, with key/value pairs:

  • 'resolution'float | None

    Resolution (in mm) of volume rendering. Smaller (e.g., 1.) looks better at the cost of speed. None (default) uses the volume source space resolution, which is often something like 7 or 5 mm, without resampling.

  • 'blending'str

    Can be “mip” (default) for maximum intensity projection or “composite” for composite blending using alpha values.

  • 'alpha'float | None

    Alpha for the volumetric rendering. Defaults are 0.4 for vector source estimates and 1.0 for scalar source estimates.

  • 'surface_alpha'float | None

    Alpha for the surface enclosing the volume(s). None (default) will use half the volume alpha. Set to zero to avoid plotting the surface.

  • 'silhouette_alpha'float | None

    Alpha for a silhouette along the outside of the volume. None (default) will use 0.25 * surface_alpha.

  • 'silhouette_linewidth'float

    The line width to use for the silhouette. Default is 2.

A float input (default 1.) or None will be used for the 'resolution' entry.

view_layoutstr

Can be “vertical” (default) or “horizontal”. When using “horizontal” mode, the PyVista backend must be used and hemi cannot be “split”.

add_data_kwargsdict | None

Additional arguments to brain.add_data (e.g., dict(time_label_size=10)).

verbosebool, str, int, or None

If not None, override default verbose level (see mne.verbose() and Logging documentation for more).

Returns
figureinstance of surfer.Brain | matplotlib.figure.Figure

An instance of surfer.Brain from PySurfer or matplotlib figure.

Notes

Flatmaps are available by default for fsaverage but not for other subjects reconstructed by FreeSurfer. We recommend using mne.compute_source_morph() to morph source estimates to fsaverage for flatmap plotting. If you want to construct your own flatmap for a given subject, these links might help:

plot_surface(**kwargs)[source]

Warning

DEPRECATED: stc_mixed.plot_surface(…) is deprecated and will be removed in 0.22, use stc_mixed.surface().plot(…)

Plot surface source estimates with PySurfer.

Note: PySurfer currently needs the SUBJECTS_DIR environment variable, which will automatically be set by this function. Plotting multiple SourceEstimates with different values for subjects_dir will cause PySurfer to use the wrong FreeSurfer surfaces when using methods of the returned Brain object. It is therefore recommended to set the SUBJECTS_DIR environment variable or always use the same value for subjects_dir (within the same Python session).

Parameters
srcSourceSpaces

The source spaces to plot.

subjectstr | None

The subject name corresponding to FreeSurfer environment variable SUBJECT. If None stc.subject will be used. If that is None, the environment will be used.

surfacestr

The type of surface (inflated, white etc.).

hemistr, ‘lh’ | ‘rh’ | ‘split’ | ‘both’

The hemisphere to display. Using ‘both’ or ‘split’ requires PySurfer version 0.4 or above.

colormapstr | np.ndarray of float, shape(n_colors, 3 | 4)

Name of colormap to use. See plot_source_estimates.

time_labelstr

How to print info about the time instant visualized.

smoothing_stepsint

The amount of smoothing.

transparentbool | None

If True, use a linear transparency between fmin and fmid. None will choose automatically based on colormap type.

alphafloat

Alpha value to apply globally to the overlay.

time_viewerbool

Display time viewer GUI.

subjects_dirstr | None

The path to the freesurfer subjects reconstructions. It corresponds to Freesurfer environment variable SUBJECTS_DIR.

figureinstance of mayavi.mlab.Figure | None

If None, the last figure will be cleaned and a new figure will be created.

viewsstr | list

View to use. See surfer.Brain.

colorbarbool

If True, display colorbar on scene.

climstr | dict

Colorbar properties specification. See plot_source_estimates.

Returns
braininstance of surfer.Brain

A instance of surfer.Brain from PySurfer.

resample(sfreq, npad='auto', window='boxcar', n_jobs=1, verbose=None)[source]

Resample data.

Parameters
sfreqfloat

New sample rate to use.

npadint | str

Amount to pad the start and end of the data. Can also be “auto” to use a padding that will result in a power-of-two size (can be much faster).

windowstr | tuple

Window to use in resampling. See scipy.signal.resample().

n_jobsint

The number of jobs to run in parallel (default 1). Requires the joblib package.

verbosebool, str, int, or None

If not None, override default verbose level (see mne.verbose() and Logging documentation for more). Defaults to self.verbose.

Returns
stcinstance of SourceEstimate

The resampled source estimate.

Notes

For some data, it may be more accurate to use npad=0 to reduce artifacts. This is dataset dependent – check your data!

Note that the sample rate of the original data is inferred from tstep.

save(fname, ftype='h5', verbose=None)[source]

Save the full source estimate to an HDF5 file.

Parameters
fnamestr

The file name to write the source estimate to, should end in ‘-stc.h5’.

ftypestr

File format to use. Currently, the only allowed values is “h5”.

verbosebool, str, int, or None

If not None, override default verbose level (see mne.verbose() and Logging documentation for more). Defaults to self.verbose.

property sfreq

Sample rate of the data.

property shape

Shape of the data.

sqrt()[source]

Take the square root.

Returns
stcinstance of SourceEstimate

A copy of the SourceEstimate with sqrt(data).

sum()[source]

Make a summary stc file with sum over time points.

Returns
stcSourceEstimate | VectorSourceEstimate

The modified stc.

surface()[source]

Return the cortical surface source estimate.

Returns
stcinstance of SourceEstimate or VectorSourceEstimate

The surface source estimate.

Examples using surface:

time_as_index(times, use_rounding=False)[source]

Convert time to indices.

Parameters
timeslist-like | float | int

List of numbers or a number representing points in time.

use_roundingbool

If True, use rounding (instead of truncation) when converting times to indices. This can help avoid non-unique indices.

Returns
indexndarray

Indices corresponding to the times supplied.

property times

A timestamp for each sample.

property tmin

The first timestamp.

to_data_frame(index=None, scalings=None, long_format=False, time_format='ms')[source]

Export data in tabular structure as a pandas DataFrame.

Vertices are converted to columns in the DataFrame. By default, an additional column “time” is added, unless index='time' (in which case time values form the DataFrame’s index).

Parameters
index‘time’ | None

Kind of index to use for the DataFrame. If None, a sequential integer index (pandas.RangeIndex) will be used. If 'time', a pandas.Float64Index, pandas.Int64Index, or pandas.TimedeltaIndex will be used (depending on the value of time_format). Defaults to None.

scalingsdict | None

Scaling factor applied to the channels picked. If None, defaults to dict(eeg=1e6, mag=1e15, grad=1e13) — i.e., converts EEG to µV, magnetometers to fT, and gradiometers to fT/cm.

long_formatbool

If True, the DataFrame is returned in long format where each row is one observation of the signal at a unique combination of time point and vertex. Defaults to False.

time_formatstr | None

Desired time format. If None, no conversion is applied, and time values remain as float values in seconds. If 'ms', time values will be rounded to the nearest millisecond and converted to integers. If 'timedelta', time values will be converted to pandas.Timedelta values. Defaults to 'ms'.

New in version 0.20.

Returns
dfinstance of pandas.DataFrame

A dataframe suitable for usage with other statistical/plotting/analysis packages.

transform(func, idx=None, tmin=None, tmax=None, copy=False)[source]

Apply linear transform.

The transform is applied to each source time course independently.

Parameters
funccallable()

The transform to be applied, including parameters (see, e.g., functools.partial()). The first parameter of the function is the input data. The first two dimensions of the transformed data should be (i) vertices and (ii) time. See Notes for details.

idxarray | None

Indices of source time courses for which to compute transform. If None, all time courses are used.

tminfloat | int | None

First time point to include (ms). If None, self.tmin is used.

tmaxfloat | int | None

Last time point to include (ms). If None, self.tmax is used.

copybool

If True, return a new instance of SourceEstimate instead of modifying the input inplace.

Returns
stcsSourceEstimate | VectorSourceEstimate | list

The transformed stc or, in the case of transforms which yield N-dimensional output (where N > 2), a list of stcs. For a list, copy must be True.

Notes

Transforms which yield 3D output (e.g. time-frequency transforms) are valid, so long as the first two dimensions are vertices and time. In this case, the copy parameter must be True and a list of SourceEstimates, rather than a single instance of SourceEstimate, will be returned, one for each index of the 3rd dimension of the transformed data. In the case of transforms yielding 2D output (e.g. filtering), the user has the option of modifying the input inplace (copy = False) or returning a new instance of SourceEstimate (copy = True) with the transformed data.

Applying transforms can be significantly faster if the SourceEstimate object was created using “(kernel, sens_data)”, for the “data” parameter as the transform is applied in sensor space. Inverse methods, e.g., “apply_inverse_epochs”, or “apply_lcmv_epochs” do this automatically (if possible).

transform_data(func, idx=None, tmin_idx=None, tmax_idx=None)[source]

Get data after a linear (time) transform has been applied.

The transform is applied to each source time course independently.

Parameters
funccallable()

The transform to be applied, including parameters (see, e.g., functools.partial()). The first parameter of the function is the input data. The first return value is the transformed data, remaining outputs are ignored. The first dimension of the transformed data has to be the same as the first dimension of the input data.

idxarray | None

Indicices of source time courses for which to compute transform. If None, all time courses are used.

tmin_idxint | None

Index of first time point to include. If None, the index of the first time point is used.

tmax_idxint | None

Index of the first time point not to include. If None, time points up to (and including) the last time point are included.

Returns
data_tndarray

The transformed data.

Notes

Applying transforms can be significantly faster if the SourceEstimate object was created using “(kernel, sens_data)”, for the “data” parameter as the transform is applied in sensor space. Inverse methods, e.g., “apply_inverse_epochs”, or “apply_lcmv_epochs” do this automatically (if possible).

property tstep

The change in time between two consecutive samples (1 / sfreq).

volume()[source]

Return the volume surface source estimate.

Returns
stcinstance of VolSourceEstimate or VolVectorSourceEstimate

The volume source estimate.

Examples using volume: