ex_interpolation

Example of using the interpolation library and geometryInfo library.

Libraries: Inverse, 3D Visualization, MNE Core, FIFF I/O, Utilities

Options

Option	Description
--subjectPath	Selected subject path <subjectPath>.
--surfType	FsSurface type <type>.
--annotType	FsAnnotation type <type>.
--hemi	Selected hemisphere <hemi>.
--subject	Selected subject <subject>.
--ave	Path to the evoked/average <file>.

Build and run

cmake --build build/developer-dynamic --target ex_interpolation
./out/Release/examples/ex_interpolation --help

The default inputs come from the MNE sample dataset.

Used in the API reference

• GeometryInfo
• Interpolation

Source

src/examples/ex_interpolation/main.cpp

//=============================================================================================================
/**
 * SPDX-License-Identifier: BSD-3-Clause
 * Copyright (c) 2017-2026 MNE-CPP Authors
 *
 * @file     main.cpp
 * @author   Gabriel Motta <gabrielbenmotta@gmail.com>;
 *           Christoph Dinh <christoph.dinh@mne-cpp.org>;
 *           Lars Debor <Lars.Debor@tu-ilmenau.de>;
 *           Blerta Hamzallari <blerta.hamzallari@tu-ilmenau.de>;
 *           Felix Griesau <Felix.Griesau@tu-ilmenau.de>;
 *           Lorenz Esch <lorenz.esch@tu-ilmenau.de>;
 *           Simon Heinke <Simon.Heinke@tu-ilmenau.de>
 * @since    0.1.0
 * @date     May, 2017
 * @brief    Example of using the interpolation library and geometryInfo library
 */

//=============================================================================================================
// INCLUDES
//=============================================================================================================

#include <inv/inv_source_estimate.h>
#include <mne/mne_bem.h>

#include <iostream>

#include <disp3D/helpers/geometryinfo.h>
#include <disp3D/helpers/interpolation.h>
#include <fiff/fiff_constants.h>

#include <utils/generics/mne_logger.h>

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

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

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

using namespace MNELIB;
using namespace FIFFLIB;
using namespace DISP3DLIB;
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[])
{
#ifdef STATICBUILD
// Q_INIT_RESOURCE(mne_disp3d);
#endif

    qInstallMessageHandler(UTILSLIB::MNELogger::customLogWriter);
    QCoreApplication a(argc, argv);

    // Command Line Parser
    QCommandLineParser parser;
    parser.setApplicationDescription("ex_interpolation");
    parser.addHelpOption();

    QCommandLineOption subjectPathOption("subjectPath", "Selected subject path <subjectPath>.", "subjectPath", QCoreApplication::applicationDirPath() + "/../resources/data/MNE-sample-data/subjects");
    QCommandLineOption surfOption("surfType", "FsSurface type <type>.", "type", "pial");
    QCommandLineOption annotOption("annotType", "FsAnnotation type <type>.", "type", "aparc.a2009s");
    QCommandLineOption hemiOption("hemi", "Selected hemisphere <hemi>.", "hemi", "2");
    QCommandLineOption subjectOption("subject", "Selected subject <subject>.", "subject", "sample");
    QCommandLineOption sampleEvokedFileOption("ave", "Path to the evoked/average <file>.", "file", QCoreApplication::applicationDirPath() + "/../resources/data/MNE-sample-data/MEG/sample/sample_audvis-ave.fif");

    parser.addOption(surfOption);
    parser.addOption(annotOption);
    parser.addOption(hemiOption);
    parser.addOption(subjectOption);
    parser.addOption(subjectPathOption);
    parser.addOption(sampleEvokedFileOption);

    parser.process(a);

    //acquire sensor positions
    QFile t_fileEvoked(parser.value(sampleEvokedFileOption));

    // Load data
    fiff_int_t setno = 0;
    QPair<float, float> baseline(-1.0f, -1.0f);
    FiffEvoked evoked(t_fileEvoked, setno, baseline);
    if (evoked.isEmpty()) {
        return 1;
    }

    // Build sensor position matrices
    int nEeg = 0, nMeg = 0;
    for (const FiffChInfo& info : evoked.info.chs) {
        if (info.kind == FIFFV_EEG_CH && info.unit == FIFF_UNIT_V)
            ++nEeg;
        if (info.kind == FIFFV_MEG_CH && info.unit == FIFF_UNIT_T)
            ++nMeg;
    }
    MatrixX3f eegSensors(nEeg, 3);
    MatrixX3f megSensors(nMeg, 3);
    int iEeg = 0, iMeg = 0;
    for (const FiffChInfo& info : evoked.info.chs) {
        if (info.kind == FIFFV_EEG_CH && info.unit == FIFF_UNIT_V) {
            eegSensors.row(iEeg++) = info.chpos.r0.transpose();
        }
        if (info.kind == FIFFV_MEG_CH && info.unit == FIFF_UNIT_T) {
            megSensors.row(iMeg++) = info.chpos.r0.transpose();
        }
    }

    //acquire surface data
    QFile t_filesensorSurfaceVV(QCoreApplication::applicationDirPath() + "/../resources/data/MNE-sample-data/subjects/sample/bem/sample-5120-5120-5120-bem.fif");
    MNEBem t_sensorSurfaceVV(t_filesensorSurfaceVV);

    //projecting with MEG
    qint64 startTimeProjecting = QDateTime::currentMSecsSinceEpoch();
    VectorXi mappedSubSet = GeometryInfo::projectSensors(t_sensorSurfaceVV[0].rr, megSensors);
    std::cout << "Projecting duration: " << QDateTime::currentMSecsSinceEpoch() - startTimeProjecting << " ms " << std::endl;

    //SCDC with cancel distance 0.03
    qint64 startTimeScdc = QDateTime::currentMSecsSinceEpoch();
    QSharedPointer<MatrixXd> distanceMatrix = GeometryInfo::scdc(t_sensorSurfaceVV[0].rr, t_sensorSurfaceVV[0].neighbor_vert, mappedSubSet, 0.2);
    std::cout << "SCDC duration: " << QDateTime::currentMSecsSinceEpoch() - startTimeScdc << " ms " << std::endl;

    //filter out bad MEG channels
    GeometryInfo::filterBadChannels(distanceMatrix, evoked.info, FIFFV_MEG_CH);

    //weight matrix
    qint64 startTimeWMat = QDateTime::currentMSecsSinceEpoch();
    QSharedPointer<SparseMatrix<float>> interpolationMatrix = Interpolation::createInterpolationMat(mappedSubSet,
                                                                                                    distanceMatrix,
                                                                                                    Interpolation::linear,
                                                                                                    FLOAT_INFINITY);
    std::cout << "Weight matrix duration: " << QDateTime::currentMSecsSinceEpoch() - startTimeWMat << " ms " << std::endl;

    //realtime interpolation (1 iteration)
    VectorXd signal = VectorXd::Random(megSensors.rows());
    qint64 startTimeRTI = QDateTime::currentMSecsSinceEpoch();
    Interpolation::interpolateSignal(*interpolationMatrix, signal.cast<float>());
    std::cout << "Real time interpol. : " << QDateTime::currentMSecsSinceEpoch() - startTimeRTI << " ms " << std::endl;

    return 0;
}