crosscorrelation.cpp

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//=============================================================================================================
 
//=============================================================================================================
// INCLUDES
//=============================================================================================================
 
#include "crosscorrelation.h"
#include "../network/networknode.h"
#include "../network/networkedge.h"
#include "../network/network.h"
 
#include <math/spectral.h>
 
//=============================================================================================================
// QT INCLUDES
//=============================================================================================================
 
#include <QDebug>
#include <QtConcurrent>
 
//=============================================================================================================
// EIGEN INCLUDES
//=============================================================================================================
 
#include <unsupported/Eigen/FFT>
 
//=============================================================================================================
// USED NAMESPACES
//=============================================================================================================
 
using namespace CONNECTIVITYLIB;
using namespace Eigen;
using namespace UTILSLIB;
 
//=============================================================================================================
// DEFINE GLOBAL METHODS
//=============================================================================================================
 
//=============================================================================================================
// DEFINE MEMBER METHODS
//=============================================================================================================
 
CrossCorrelation::CrossCorrelation()
{
}
 
//=============================================================================================================
 
Network CrossCorrelation::calculate(ConnectivitySettings& connectivitySettings)
{
//    QElapsedTimer timer;
//    qint64 iTime = 0;
//    timer.start();
 
    #ifdef EIGEN_FFTW_DEFAULT
        fftw_make_planner_thread_safe();
    #endif
 
    Network finalNetwork("XCOR");
 
    if(connectivitySettings.isEmpty()) {
        qDebug() << "CrossCorrelation::calculate - Input data is empty";
        return finalNetwork;
    }
 
    if(AbstractMetric::m_bStorageModeIsActive == false) {
        connectivitySettings.clearIntermediateData();
    }
 
    finalNetwork.setSamplingFrequency(connectivitySettings.getSamplingFrequency());
 
    //Create nodes
    int rows = connectivitySettings.at(0).matData.rows();
    RowVectorXf rowVert = RowVectorXf::Zero(3);
 
    for(int i = 0; i < rows; ++i) {
        rowVert = RowVectorXf::Zero(3);
 
        if(connectivitySettings.getNodePositions().rows() != 0 && i < connectivitySettings.getNodePositions().rows()) {
            rowVert(0) = connectivitySettings.getNodePositions().row(i)(0);
            rowVert(1) = connectivitySettings.getNodePositions().row(i)(1);
            rowVert(2) = connectivitySettings.getNodePositions().row(i)(2);
        }
 
        finalNetwork.append(NetworkNode::SPtr(new NetworkNode(i, rowVert)));
    }
 
    // Generate tapers
    int iSignalLength = connectivitySettings.at(0).matData.cols();
    int iNfft = connectivitySettings.getFFTSize();
 
    QPair<MatrixXd, VectorXd> tapers = Spectral::generateTapers(iSignalLength, connectivitySettings.getWindowType());
 
    // Compute the cross correlation in parallel
    QMutex mutex;
    MatrixXd matDist;
 
    std::function<void(ConnectivitySettings::IntermediateTrialData&)> computeLambda = [&](ConnectivitySettings::IntermediateTrialData& inputData) {
        compute(inputData,
                matDist,
                mutex,
                iNfft,
                tapers);
    };
 
//    iTime = timer.elapsed();
//    qWarning() << "Preparation" << iTime;
//    timer.restart();
 
    // Calculate connectivity matrix over epochs and average afterwards
    QFuture<void> resultMat = QtConcurrent::map(connectivitySettings.getTrialData(),
                                                computeLambda);
    resultMat.waitForFinished();
 
    matDist /= connectivitySettings.size();
 
//    iTime = timer.elapsed();
//    qWarning() << "ComputeSpectraPSDCSD" << iTime;
//    timer.restart();
 
    //Add edges to network
    MatrixXd matWeight(1,1);
    QSharedPointer<NetworkEdge> pEdge;
    int j;
 
    for(int i = 0; i < matDist.rows(); ++i) {
        for(j = i; j < matDist.cols(); ++j) {
            matWeight << matDist(i,j);
 
            pEdge = QSharedPointer<NetworkEdge>(new NetworkEdge(i, j, matWeight));
 
            finalNetwork.getNodeAt(i)->append(pEdge);
            finalNetwork.getNodeAt(j)->append(pEdge);
            finalNetwork.append(pEdge);
        }
    }
 
//    iTime = timer.elapsed();
//    qWarning() << "Compute" << iTime;
//    timer.restart();
 
    return finalNetwork;
}
 
//=============================================================================================================
 
void CrossCorrelation::compute(ConnectivitySettings::IntermediateTrialData& inputData,
                               MatrixXd& matDist,
                               QMutex& mutex,
                               int iNfft,
                               const QPair<MatrixXd, VectorXd>& tapers)
{
//    QElapsedTimer timer;
//    qint64 iTime = 0;
//    timer.start();
 
    // Calculate tapered spectra if not available already
    RowVectorXd vecInputFFT, rowData;
    RowVectorXcd vecResultFreq;
 
    FFT<double> fft;
    fft.SetFlag(fft.HalfSpectrum);
 
    int i, j;
    int iNRows = inputData.matData.rows();
 
    // Calculate tapered spectra if not available already
    // This code was copied and changed modified Utils/Spectra since we do not want to call the function due to time loss.
    if(inputData.vecTapSpectra.isEmpty()) {
        int iNFreqs = int(floor(iNfft / 2.0)) + 1;
        MatrixXcd matTapSpectrum(tapers.first.rows(), iNFreqs);
 
        for (i = 0; i < iNRows; ++i) {
            // Substract mean
            rowData.array() = inputData.matData.row(i).array() - inputData.matData.row(i).mean();
 
            // Calculate tapered spectra
            for(j = 0; j < tapers.first.rows(); j++) {
                // Zero padd if necessary. The zero padding in Eigen's FFT is only working for column vectors.
                if (rowData.cols() < iNfft) {
                    vecInputFFT.setZero(iNfft);
                    vecInputFFT.block(0,0,1,rowData.cols()) = rowData.cwiseProduct(tapers.first.row(j));;
                } else {
                    vecInputFFT = rowData.cwiseProduct(tapers.first.row(j));
                }
 
                // FFT for freq domain returning the half spectrum and multiply taper weights
                fft.fwd(vecResultFreq, vecInputFFT, iNfft);
                matTapSpectrum.row(j) = vecResultFreq * tapers.second(j);
            }
 
            inputData.vecTapSpectra.append(matTapSpectrum);
        }
    }
 
//    iTime = timer.elapsed();
//    qDebug() << QThread::currentThreadId() << "CrossCorrelation::compute timer - Tapered spectra:" << iTime;
//    timer.restart();
 
    // Perform multiplication and transform back to time domain to find max XCOR coefficient
    // Note that the result in time domain is mirrored around the center of the data (compared to Matlab)
    MatrixXd matDistTrial = MatrixXd::Zero(iNRows, iNRows);
    RowVectorXcd vecResultXCor;
    int idx = 0;
    double denom = tapers.second.sum();
 
    for(i = 0; i < inputData.vecTapSpectra.size(); ++i) {
        vecResultFreq = inputData.vecTapSpectra.at(i).colwise().sum() / denom;
 
        for(j = i; j < inputData.vecTapSpectra.size(); ++j) {
            vecResultXCor = vecResultFreq.cwiseProduct(inputData.vecTapSpectra.at(j).colwise().sum() / denom);
 
            fft.inv(vecInputFFT, vecResultXCor, iNfft);
 
            vecInputFFT.maxCoeff(&idx);
 
            matDistTrial(i,j) = vecInputFFT(idx);
        }
    }
 
//    iTime = timer.elapsed();
//    qDebug() << QThread::currentThreadId() << "CrossCorrelation::compute timer - Multiplication and inv FFT:" << iTime;
//    timer.restart();
 
    // Sum up weights
    mutex.lock();
 
    if(matDist.rows() != matDistTrial.rows() || matDist.cols() != matDistTrial.cols()) {
        matDist.resize(matDistTrial.rows(), matDistTrial.cols());
        matDist.setZero();
    }
 
    matDist += matDistTrial;
 
    mutex.unlock();
 
//    iTime = timer.elapsed();
//    qDebug() << QThread::currentThreadId() << "CrossCorrelation::compute timer - Summing up matDist:" << iTime;
//    timer.restart();
 
    if(!m_bStorageModeIsActive) {
        inputData.vecTapSpectra.clear();
    }
}