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FiffEvoked

Namespace: FIFFLIB  ·  Library: FIFF Library

Python equivalent

mne.Evoked in MNE-Python.

#include <fiff/fiff_evoked.h>

class FIFFLIB::FiffEvoked

Single averaged evoked response: time axis, data, baseline, channel info and averaging metadata.

Holds one FIFFB_EVOKED block: times, data, first / last sample indices, baseline, kind, nave, comment and the FiffInfo describing the channels. Use FiffEvokedSet for recordings that contain multiple averaging conditions.

Public Methods​

FiffEvoked()​

Constructs a fiff evoked data.

FiffEvoked(p_IODevice, setno, t_baseline, proj, p_aspect_kind)​

Constructs fiff evoked data, by reading from a IO device.

Parameters:

  • p_IODevice : QIODevice & IO device to read from the evoked data set.

  • setno : QVariant The set to pick. Dataset ID number (int) or comment/name (str). Optional if there isonly one data set in file.

  • t_baseline : QPair< float, float > The time interval to apply rescaling / baseline correction. If None do not apply it. If baseline is (a, b). the interval is between "a (s)" and "b (s)". If a is None the beginning of the data is used and if b is None then b is set to the end of the interval. If baseline is equal ot (None, None) all the time interval is used. If None, no correction is applied.

  • proj : bool Apply SSP projection vectors (optional, default = true).

  • p_aspect_kind : fiff_int_t Either "FIFFV_ASPECT_AVERAGE" or "FIFFV_ASPECT_STD_ERR". The type of data to read. Only used if "setno" is a str.

FiffEvoked(p_FiffEvoked)​

Copy constructor.

Parameters:

  • p_FiffEvoked : const FiffEvoked & Fiff evoked data which should be copied.

~FiffEvoked()​

Destroys the FiffEvoked.

ch_names()​

Returns list of channel names stored in fiff info -> this is to stay consistent with python.

Returns:

  • QStringList — List of channel names.

clear()​

Initializes fiff evoked data.

aspectKindToString()​

Provides the python Evoked string formatted aspect_kind, which is stored in kind: "average" <-> FIFFV_ASPECT_AVERAGE, "standard_error" <-> FIFFV_ASPECT_STD_ERR or "unknown".

Returns:

  • QString — string formatted aspect_kind.

isEmpty()​

Returns whether FiffEvoked is empty.

Returns:

  • bool — true if is empty, false otherwise.

pick_channels(include, exclude)​

fiff_pick_channels_evoked

Pick desired channels from evoked-response data

Parameters:

  • include : const QStringList &

    • Channels to include (if empty, include all available).

  • exclude : const QStringList &

    • Channels to exclude (if empty, do not exclude any).

Returns:

setInfo(p_info, proj)​

Set a new fiff measurement info.

Parameters:

  • p_info : const FiffInfo & Info to set.

  • proj : bool Apply SSP projection vectors (optional, default = true).

operator+=(newData)​

Inputs a new data set and recalculates the average.

This function also iterates the nave parameter by one.

Parameters:

  • newData : const Eigen::MatrixXd & the new data set which is to be added to the current average.

Returns:

applyBaselineCorrection(p_baseline)​

Applies baseline correction to the evoked data.

Parameters:

  • p_baseline : QPair< float, float > & time definition of the baseline in seconds [from, to].

Static Methods​

read(p_IODevice, p_FiffEvoked, setno, t_baseline, proj, p_aspect_kind)​

fiff_read_evoked

Wrapper for the FiffEvokedDataSet::read_evoked static function

Read one evoked data set

Parameters:

  • p_IODevice : QIODevice & An fiff IO device like a fiff QFile or QTCPSocket.

  • p_FiffEvoked : FiffEvoked & The read evoked data.

  • setno : QVariant the set to pick. Dataset ID number (int) or comment/name (str). Optional if there isonly one data set in file.

  • t_baseline : QPair< float, float > The time interval to apply rescaling / baseline correction. If None do not apply it. If baseline is (a, b). the interval is between "a (s)" and "b (s)". If a is None the beginning of the data is used and if b is None then b is set to the end of the interval. If baseline is equal ot (None, None) all the time interval is used. If None, no correction is applied.

  • proj : bool Apply SSP projection vectors (optional, default = true).

  • p_aspect_kind : fiff_int_t Either "FIFFV_ASPECT_AVERAGE" or "FIFFV_ASPECT_STD_ERR". The type of data to read. Only used if "setno" is a str.

Returns:

  • bool — true if successful, false otherwise.

Example​

Source: src/examples/ex_read_evoked/main.cpp

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

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

//=============================================================================================================
// 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 Evoked Example");
    parser.addHelpOption();

    QCommandLineOption evokedFileOption("ave", "Path to the evoked/average <file>.", "file", QCoreApplication::applicationDirPath() + "/../resources/data/MNE-sample-data/MEG/sample/sample_audvis-ave.fif");
    QCommandLineOption evokedIdxOption("aveIdx", "The average <index> to choose from the average file.", "index", "2");
    QCommandLineOption useCTFCompOption("useCTFComp", "Use the CTF compensator, if available.");

    parser.addOption(evokedFileOption);
    parser.addOption(evokedIdxOption);

    parser.process(a);

    //generate FiffEvoked object
    QFile t_sampleFile(parser.value(evokedFileOption));
    FiffEvoked p_FiffEvoked(t_sampleFile,QVariant(parser.value(evokedIdxOption)));

    //Select the head coordinate system
    bool use_ctf_head = parser.isSet(useCTFCompOption);
    FiffCoordTrans meg_trans;

    if(use_ctf_head) {
        if(p_FiffEvoked.info.ctf_head_t.isEmpty())
           std::cout << "\nNo CTF head transformation available" << std::endl;
        else {
            meg_trans = p_FiffEvoked.info.dev_ctf_t;
            FiffCoordTrans eeg_trans(meg_trans);
            eeg_trans.invert_transform();
            std::cout << "Employing the CTF/4D head coordinate system\n" << std::endl;
        }
    }
    else {
        meg_trans = p_FiffEvoked.info.dev_head_t;
        FiffCoordTrans eeg_trans;
        std::cout << "Employing the Neuromag head coordinate system\n" << std::endl;
    }

    //Transform coil and electrode locations to the desired coordinate frame
    //ToDo: MATLAB root fct fiff_transform_meg_chs and fiff_transform_eeg_chs needs to be implemented

    //Create the coil definitions
    //ToDo: MATLAB root fct mne_add_coil_defs needs to be implemented

    //N.B. If a nonstandard (in MNE sense) coil def file is used, do
    //ToDo: MATLAB root fct mne_load_coil_def, mne_add_coil_defs needs to be implemented

    return a.exec();
}

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

Authors of this file​