FiffEpochs

Namespace: FIFFLIB · Library: FIFF Library

Python equivalent

mne.Epochs in MNE-Python.

#include <fiff/fiff_epochs.h>

class FiffEpochs

Free / static helpers that turn a FiffRawData plus an event list into fixed-length epochs.

Stateless — operates on the FiffRawData and event arguments directly. Used by the source-reconstruction pipeline and by the offline averaging tooling when building epochs for an FiffEvokedSet.

Static Methods

makeFixedLengthEpochs(matData, dSFreq, dDuration, dOverlap, bDropLast)

Create fixed-length epochs from continuous data.

Segments the data matrix into non-overlapping (or overlapping) epochs of the specified duration.

Parameters:

matData : const Eigen::MatrixXd & Continuous data (n_channels × n_times).
dSFreq : double Sampling frequency in Hz.
dDuration : double Epoch duration in seconds.
dOverlap : double Overlap between epochs in seconds (default 0.0).
bDropLast : bool Drop the last epoch if it's shorter than duration (default true).

Returns:

QList< FiffEpochData > — List of epoch data structures.

concatenateEpochs(epochSets)

Concatenate multiple epoch sets into a single list.

Parameters:

epochSets : const QList< QList< FiffEpochData > > & List of epoch sets to concatenate.

Returns:

QList< FiffEpochData > — Combined list of all epochs.

averageEpochs(epochs, dSFreq, comment)

Compute the average (evoked response) across epochs.

All epochs must have the same dimensions. Returns a FiffEvoked with data, nave, times, and aspect_kind populated.

Parameters:

epochs : const QList< FiffEpochData > & List of epochs.
dSFreq : double Sampling frequency in Hz (used to compute times vector).
comment : const QString & Comment string for the evoked (default "Average").

Returns:

FiffEvoked — FiffEvoked with averaged data and metadata.

toMatrixList(epochs)

Extract data matrices from epoch structures.

Convenience method to get a list of data matrices from epoch structures, suitable for use with CSP, SPoC, SSD, etc.

Parameters:

epochs : const QList< FiffEpochData > & List of epoch data.

Returns:

QList< Eigen::MatrixXd > — List of data matrices (n_channels × n_times).

Example

Source: src/examples/ex_read_epochs/main.cpp

#include <iostream>
#include <vector>
#include <math.h>

//=============================================================================================================
// MNE INCLUDES
//=============================================================================================================

#include <fiff/fiff.h>
#include <mne/mne.h>

#include <mne/mne_epoch_data_list.h>

#include <utils/generics/mne_logger.h>

//=============================================================================================================
// QT INCLUDES
//=============================================================================================================

#include <QtCore/QCoreApplication>
#include <QCommandLineParser>
#include <QFile>

//=============================================================================================================
// USED NAMESPACES
//=============================================================================================================

using namespace FIFFLIB;
using namespace MNELIB;
using namespace UTILSLIB;
using namespace Eigen;

//=============================================================================================================
// MAIN
//=============================================================================================================

//=============================================================================================================
/**
 * The function main marks the entry point of the program.
 * By default, main has the storage class extern.
 *
 * @param[in] argc (argument count) is an integer that indicates how many arguments were entered on the command line when the program was started.
 * @param[in] argv (argument vector) is an array of pointers to arrays of character objects. The array objects are null-terminated strings, representing the arguments that were entered on the command line when the program was started.
 * @return the value that was set to exit() (which is 0 if exit() is called via quit()).
 */
int main(int argc, char *argv[])
{
    qInstallMessageHandler(MNELogger::customLogWriter);
    QCoreApplication a(argc, argv);

    // Command Line Parser
    QCommandLineParser parser;
    parser.setApplicationDescription("Read Epochs Example");
    parser.addHelpOption();

    QCommandLineOption inputOption("fileIn", "The input file <in>.", "in", QCoreApplication::applicationDirPath() + "/../resources/data/MNE-sample-data/MEG/sample/sample_audvis_raw.fif");
    QCommandLineOption eventsFileOption("eve", "Path to the event <file>.", "file", QCoreApplication::applicationDirPath() + "/../resources/data/MNE-sample-data/MEG/sample/sample_audvis_raw-eve.fif");
    QCommandLineOption evokedIdxOption("aveIdx", "The average <index> to choose from the average file.", "index", "3");
    QCommandLineOption pickAllOption("pickAll", "Pick all channels.", "pickAll", "true");
    QCommandLineOption keepCompOption("keepComp", "Keep compensators.", "keepComp", "false");
    QCommandLineOption destCompsOption("destComps", "<Destination> of the compensator which is to be calculated.", "destination", "0");

    parser.addOption(inputOption);
    parser.addOption(eventsFileOption);
    parser.addOption(evokedIdxOption);
    parser.addOption(pickAllOption);
    parser.addOption(keepCompOption);
    parser.addOption(destCompsOption);

    parser.process(a);

    //Load data
    QString t_fileRawName = parser.value(inputOption);
    QFile t_fileRaw(t_fileRawName);

    qint32 event = parser.value(evokedIdxOption).toInt();
    QString t_sEventName = parser.value(eventsFileOption);
    float fTMin = -1.5f;
    float fTMax = 1.5f;

    bool keep_comp = false;
    if(parser.value(keepCompOption) == "false" || parser.value(keepCompOption) == "0") {
        keep_comp = false;
    } else if(parser.value(keepCompOption) == "true" || parser.value(keepCompOption) == "1") {
        keep_comp = true;
    }

    fiff_int_t dest_comp = parser.value(destCompsOption).toInt();

    bool pick_all = false;
    if(parser.value(pickAllOption) == "false" || parser.value(pickAllOption) == "0") {
        pick_all = false;
    } else if(parser.value(pickAllOption) == "true" || parser.value(pickAllOption) == "1") {
        pick_all = true;
    }

    // Setup for reading the raw data
    FiffRawData raw(t_fileRaw);
    MNE::setup_compensators(raw, dest_comp, keep_comp);

    RowVectorXi picks;
    if (pick_all) {
        // Pick all
        picks.resize(raw.info.nchan);

        for(qint32 k = 0; k < raw.info.nchan; ++k) {
            picks(k) = k;
        }
    } else {
        QStringList include;
        include << "STI 014";
        bool want_meg   = true;
        bool want_eeg   = false;
        bool want_stim  = false;

        picks = raw.info.pick_types(want_meg,
                                    want_eeg,
                                    want_stim,
                                    include,
                                    raw.info.bads);
    }

    // Read the events
    MatrixXi events;    
    MNE::read_events(t_sEventName,
                     t_fileRawName,
                     events);

    // Read the epochs and reject epochs with EOG higher than 300e-06
    QMap<QString,double> mapReject;
    mapReject.insert("eog", 300e-06);

    MNEEpochDataList data = MNEEpochDataList::readEpochs(raw,
                                                         events,
                                                         fTMin,
                                                         fTMax,
                                                         event,
                                                         mapReject,
                                                         QStringList(),
                                                         picks);

    return a.exec();
}

//=============================================================================================================
// STATIC DEFINITIONS
//=============================================================================================================

Authors of this file

Christoph Dinh <christoph.dinh@mne-cpp.org>

Static Methods​

makeFixedLengthEpochs(matData, dSFreq, dDuration, dOverlap, bDropLast)​

concatenateEpochs(epochSets)​

averageEpochs(epochs, dSFreq, comment)​

toMatrixList(epochs)​

Example​

Authors of this file​

Static Methods

makeFixedLengthEpochs(matData, dSFreq, dDuration, dOverlap, bDropLast)

concatenateEpochs(epochSets)

averageEpochs(epochs, dSFreq, comment)

toMatrixList(epochs)

Example

Authors of this file