phaselagindex.cpp

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//=============================================================================================================
 
//=============================================================================================================
// INCLUDES
//=============================================================================================================
 
#include "phaselagindex.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
//=============================================================================================================
 
PhaseLagIndex::PhaseLagIndex()
{
}
 
//*******************************************************************************************************
 
Network PhaseLagIndex::calculate(ConnectivitySettings& connectivitySettings)
{
    //    QElapsedTimer timer;
    //    qint64 iTime = 0;
    //    timer.start();
 
    Network finalNetwork("PLI");
 
    if (connectivitySettings.isEmpty()) {
        qDebug() << "PhaseLagIndex::calculate - Input data is empty";
        return finalNetwork;
    }
 
    if (AbstractMetric::m_bStorageModeIsActive == false) {
        connectivitySettings.clearIntermediateData();
    }
 
    finalNetwork.setSamplingFrequency(connectivitySettings.getSamplingFrequency());
 
#ifdef EIGEN_FFTW_DEFAULT
    fftw_make_planner_thread_safe();
#endif
 
    //Create nodes
    int iNRows = connectivitySettings.at(0).matData.rows();
    RowVectorXf rowVert = RowVectorXf::Zero(3);
 
    for (int i = 0; i < iNRows; ++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)));
    }
 
    // Check that iNfft >= signal length
    int iSignalLength = connectivitySettings.at(0).matData.cols();
    int iNfft = connectivitySettings.getFFTSize();
 
    // Generate tapers
    QPair<MatrixXd, VectorXd> tapers = Spectral::generateTapers(iSignalLength, connectivitySettings.getWindowType());
 
    // Initialize
    int iNFreqs = int(floor(iNfft / 2.0)) + 1;
 
    // Check if start and bin amount need to be reset to full spectrum
    if (m_iNumberBinStart == -1 ||
        m_iNumberBinAmount == -1 ||
        m_iNumberBinStart > iNFreqs ||
        m_iNumberBinAmount > iNFreqs ||
        m_iNumberBinAmount + m_iNumberBinStart > iNFreqs) {
        qDebug() << "PhaseLagIndex::calculate - Resetting to full spectrum";
        AbstractMetric::m_iNumberBinStart = 0;
        AbstractMetric::m_iNumberBinAmount = iNFreqs;
    }
 
    // Pass information about the FFT length. Use iNFreqs because we only use the half spectrum
    finalNetwork.setFFTSize(iNFreqs);
    finalNetwork.setUsedFreqBins(AbstractMetric::m_iNumberBinAmount);
 
    QMutex mutex;
 
    std::function<void(ConnectivitySettings::IntermediateTrialData&)> computeLambda = [&](ConnectivitySettings::IntermediateTrialData& inputData) {
        compute(inputData,
                connectivitySettings.getIntermediateSumData().vecPairCsdSum,
                connectivitySettings.getIntermediateSumData().vecPairCsdImagSignSum,
                mutex,
                iNRows,
                iNFreqs,
                iNfft,
                tapers);
    };
 
    //    iTime = timer.elapsed();
    //    qWarning() << "Preparation" << iTime;
    //    timer.restart();
 
    // Compute DSWPLV in parallel for all trials
    QFuture<void> result = QtConcurrent::map(connectivitySettings.getTrialData(),
                                             computeLambda);
    result.waitForFinished();
 
    //    iTime = timer.elapsed();
    //    qWarning() << "ComputeSpectraPSDCSD" << iTime;
    //    timer.restart();
 
    // Compute PLI
    computePLI(connectivitySettings,
               finalNetwork);
 
    //    iTime = timer.elapsed();
    //    qWarning() << "Compute" << iTime;
    //    timer.restart();
 
    return finalNetwork;
}
 
//=============================================================================================================
 
void PhaseLagIndex::compute(ConnectivitySettings::IntermediateTrialData& inputData,
                            QVector<QPair<int, MatrixXcd>>& vecPairCsdSum,
                            QVector<QPair<int, MatrixXd>>& vecPairCsdImagSignSum,
                            QMutex& mutex,
                            int iNRows,
                            int iNFreqs,
                            int iNfft,
                            const QPair<MatrixXd, VectorXd>& tapers)
{
    if (inputData.vecPairCsdImagSign.size() == iNRows) {
        //qDebug() << "PhaseLagIndex::compute - vecPairCsdImagSign was already computed for this trial.";
        return;
    }
 
    int i;
 
    // 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()) {
        RowVectorXd vecInputFFT, rowData;
        RowVectorXcd vecTmpFreq;
 
        MatrixXcd matTapSpectrum(tapers.first.rows(), iNFreqs);
 
        FFT<double> fft;
        fft.SetFlag(fft.HalfSpectrum);
 
        for (i = 0; i < iNRows; ++i) {
            // Substract mean
            rowData.array() = inputData.matData.row(i).array() - inputData.matData.row(i).mean();
 
            // Calculate tapered spectra
            for (int 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(vecTmpFreq, vecInputFFT, iNfft);
                matTapSpectrum.row(j) = vecTmpFreq * tapers.second(j);
            }
 
            inputData.vecTapSpectra.append(matTapSpectrum);
        }
    }
 
    // Compute CSD
    if (inputData.vecPairCsd.isEmpty()) {
        MatrixXcd matCsd = MatrixXcd(iNRows, m_iNumberBinAmount);
 
        double denomCSD = sqrt(tapers.second.cwiseAbs2().sum()) * sqrt(tapers.second.cwiseAbs2().sum()) / 2.0;
 
        bool bNfftEven = false;
        if (iNfft % 2 == 0) {
            bNfftEven = true;
        }
 
        for (i = 0; i < iNRows; ++i) {
            for (int j = i; j < iNRows; ++j) {
                // Compute CSD (average over tapers if necessary)
                matCsd.row(j) = inputData.vecTapSpectra.at(i).block(0, m_iNumberBinStart, inputData.vecTapSpectra.at(i).rows(), m_iNumberBinAmount).cwiseProduct(inputData.vecTapSpectra.at(j).block(0, m_iNumberBinStart, inputData.vecTapSpectra.at(j).rows(), m_iNumberBinAmount).conjugate()).colwise().sum() / denomCSD;
 
                // Divide first and last element by 2 due to half spectrum
                if (m_iNumberBinStart == 0) {
                    matCsd.row(j)(0) /= 2.0;
                }
 
                if (bNfftEven && m_iNumberBinStart + m_iNumberBinAmount >= iNFreqs) {
                    matCsd.row(j).tail(1) /= 2.0;
                }
            }
 
            inputData.vecPairCsd.append(QPair<int, MatrixXcd>(i, matCsd));
            inputData.vecPairCsdImagSign.append(QPair<int, MatrixXd>(i, matCsd.imag().cwiseSign()));
        }
 
        mutex.lock();
 
        if (vecPairCsdSum.isEmpty()) {
            vecPairCsdSum = inputData.vecPairCsd;
            vecPairCsdImagSignSum = inputData.vecPairCsdImagSign;
        } else {
            for (int j = 0; j < vecPairCsdSum.size(); ++j) {
                vecPairCsdSum[j].second += inputData.vecPairCsd.at(j).second;
                vecPairCsdImagSignSum[j].second += inputData.vecPairCsdImagSign.at(j).second;
            }
        }
 
        mutex.unlock();
    } else {
        if (inputData.vecPairCsdImagSign.isEmpty()) {
            for (i = 0; i < inputData.vecPairCsd.size(); ++i) {
                inputData.vecPairCsdImagSign.append(QPair<int, MatrixXd>(i, inputData.vecPairCsd.at(i).second.imag().cwiseSign()));
            }
 
            mutex.lock();
 
            if (vecPairCsdImagSignSum.isEmpty()) {
                vecPairCsdImagSignSum = inputData.vecPairCsdImagSign;
            } else {
                for (int j = 0; j < vecPairCsdImagSignSum.size(); ++j) {
                    vecPairCsdImagSignSum[j].second += inputData.vecPairCsdImagSign.at(j).second;
                }
            }
 
            mutex.unlock();
        }
    }
 
    if (!m_bStorageModeIsActive) {
        inputData.vecPairCsd.clear();
        inputData.vecTapSpectra.clear();
        inputData.vecPairCsdImagSign.clear();
    }
}
 
//=============================================================================================================
 
void PhaseLagIndex::computePLI(ConnectivitySettings& connectivitySettings,
                               Network& finalNetwork)
{
    // Compute final PLI and create Network
    MatrixXd matNom;
    MatrixXd matWeight;
    QSharedPointer<NetworkEdge> pEdge;
    int j;
 
    for (int i = 0; i < connectivitySettings.getIntermediateSumData().vecPairCsdImagSignSum.size(); ++i) {
        matNom = connectivitySettings.getIntermediateSumData().vecPairCsdImagSignSum.at(i).second.cwiseAbs() / connectivitySettings.size();
 
        for (j = i; j < matNom.rows(); ++j) {
            matWeight = matNom.row(j).transpose();
 
            pEdge = QSharedPointer<NetworkEdge>(new NetworkEdge(i, j, matWeight));
 
            finalNetwork.getNodeAt(i)->append(pEdge);
            finalNetwork.getNodeAt(j)->append(pEdge);
            finalNetwork.append(pEdge);
        }
    }
}