FilterElectrogram.cpp

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///////////////////////////////////////////////////////////////////////////////
//
// File FilterElectrogram.cpp
//
// For more information, please see: http://www.nektar.info
//
// The MIT License
//
// Copyright (c) 2006 Division of Applied Mathematics, Brown University (USA),
// Department of Aeronautics, Imperial College London (UK), and Scientific
// Computing and Imaging Institute, University of Utah (USA).
//
// License for the specific language governing rights and limitations under
// Permission is hereby granted, free of charge, to any person obtaining a
// copy of this software and associated documentation files (the "Software"),
// to deal in the Software without restriction, including without limitation
// the rights to use, copy, modify, merge, publish, distribute, sublicense,
// and/or sell copies of the Software, and to permit persons to whom the
// Software is furnished to do so, subject to the following conditions:
//
// The above copyright notice and this permission notice shall be included
// in all copies or substantial portions of the Software.
//
// THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS
// OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
// FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
// THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
// LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
// FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
// DEALINGS IN THE SOFTWARE.
//
// Description: Outputs virtual electrograms at specific locations.
//
///////////////////////////////////////////////////////////////////////////////

#include <LibUtilities/Memory/NekMemoryManager.hpp>
#include <iomanip>
#include <CardiacEPSolver/Filters/FilterElectrogram.h>

using namespace std;

namespace Nektar
{
std::string FilterElectrogram::className =
        SolverUtils::GetFilterFactory().RegisterCreatorFunction(
                "Electrogram",
                FilterElectrogram::create);

/**
 *
 */
FilterElectrogram::FilterElectrogram(
        const LibUtilities::SessionReaderSharedPtr &pSession,
        const ParamMap &pParams)
    : Filter(pSession)
{
    ParamMap::const_iterator it;

    // OutputFile
    it = pParams.find("OutputFile");
    if (it == pParams.end())
    {
        m_outputFile = m_session->GetSessionName();
    }
    else
    {
        ASSERTL0(it->second.length() > 0, "Missing parameter 'OutputFile'.");
        m_outputFile = it->second;
    }
    if (!(m_outputFile.length() >= 4
          && m_outputFile.substr(m_outputFile.length() - 4) == ".ecg"))
    {
        m_outputFile += ".ecg";
    }

    // OutputFrequency
    it = pParams.find("OutputFrequency");
    if (it == pParams.end())
    {
        m_outputFrequency = 1;
    }
    else
    {
        LibUtilities::Equation equ(m_session, it->second);
        m_outputFrequency = floor(equ.Evaluate());
    }

    // Points
    it = pParams.find("Points");
    ASSERTL0(it != pParams.end(), "Missing parameter 'Points'.");
    m_electrogramStream.str(it->second);
    m_index = 0;
}


/**
 *
 */
FilterElectrogram::~FilterElectrogram()
{

}


/**
 *
 */
void FilterElectrogram::v_Initialise(
        const Array<OneD, const MultiRegions::ExpListSharedPtr> &pFields,
        const NekDouble &time)
{
    ASSERTL0(!m_electrogramStream.fail(),
             "No history points in stream.");

    m_index = 0;
    Array<OneD, NekDouble>  gloCoord(3,0.0);
    LibUtilities::CommSharedPtr vComm = pFields[0]->GetComm();

    // Read electrogram points
    // Always use dim = 3 to allow electrode to be above surface
    const int dim = 3;
    int i = 0;

    while (!m_electrogramStream.fail())
    {
        m_electrogramStream >> gloCoord[0] >> gloCoord[1] >> gloCoord[2];
        if (!m_electrogramStream.fail())
        {
            SpatialDomains::PointGeomSharedPtr vert
                = MemoryManager<SpatialDomains::PointGeom>
                ::AllocateSharedPtr(dim, i, gloCoord[0],
                                    gloCoord[1], gloCoord[2]);

            m_electrogramPoints.push_back(vert);
            ++i;
        }
    }

    if (vComm->GetRank() == 0)
    {
        // Open output stream
        m_outputStream.open(m_outputFile.c_str());
        m_outputStream << "# Electrogram data for variables (:";

        for (i = 0; i < pFields.num_elements(); ++i)
        {
            m_outputStream << m_session->GetVariable(i) <<",";
        }

        m_outputStream << ") at points:" << endl;

        for (i = 0; i < m_electrogramPoints.size(); ++i)
        {
            m_electrogramPoints[i]->GetCoords(  gloCoord[0],
                                            gloCoord[1],
                                            gloCoord[2]);

            m_outputStream << "# \t" << i;
            m_outputStream.width(8);
            m_outputStream << gloCoord[0];
            m_outputStream.width(8);
            m_outputStream << gloCoord[1];
            m_outputStream.width(8);
            m_outputStream << gloCoord[2];
            m_outputStream << endl;
        }
    }

    // Compute the distance function for each electrogram point
    const unsigned int nq   = pFields[0]->GetNpoints();
    const unsigned int npts = m_electrogramPoints.size();
    NekDouble px, py, pz;
    m_grad_R_x = Array<OneD, Array<OneD, NekDouble> >(npts);
    m_grad_R_y = Array<OneD, Array<OneD, NekDouble> >(npts);
    m_grad_R_z = Array<OneD, Array<OneD, NekDouble> >(npts);

    Array<OneD, NekDouble> x(nq);
    Array<OneD, NekDouble> y(nq);
    Array<OneD, NekDouble> z(nq);

    Array<OneD, NekDouble> oneOverR(nq);
    for (unsigned int i = 0; i < npts; ++i)
    {
        m_grad_R_x[i] = Array<OneD, NekDouble>(nq);
        m_grad_R_y[i] = Array<OneD, NekDouble>(nq);
        m_grad_R_z[i] = Array<OneD, NekDouble>(nq);

        // Compute 1/R
        m_electrogramPoints[i]->GetCoords(px,py,pz);

        pFields[0]->GetCoords(x,y,z);

        Vmath::Sadd   (nq, -px, x, 1, x, 1);
        Vmath::Sadd   (nq, -py, y, 1, y, 1);
        Vmath::Sadd   (nq, -pz, z, 1, z, 1);
        Vmath::Vvtvvtp(nq, x, 1, x, 1, y, 1, y, 1, oneOverR, 1);
        Vmath::Vvtvp  (nq, z, 1, z, 1, oneOverR, 1, oneOverR, 1);
        Vmath::Vsqrt  (nq, oneOverR, 1, oneOverR, 1);
        Vmath::Sdiv   (nq, 1.0, oneOverR, 1, oneOverR, 1);

        // Compute grad 1/R
        pFields[0]->PhysDeriv(oneOverR, m_grad_R_x[i], m_grad_R_y[i],
                                        m_grad_R_z[i]);
    }

    // Compute electrogram point for initial condition
    v_Update(pFields, time);
}


/**
 *
 */
void FilterElectrogram::v_Update(
        const Array<OneD, const MultiRegions::ExpListSharedPtr> &pFields,
        const NekDouble &time)
{
    // Only output every m_outputFrequency.
    if ((m_index++) % m_outputFrequency)
    {
        return;
    }

    const unsigned int nq = pFields[0]->GetNpoints();
    const unsigned int npoints = m_electrogramPoints.size();
    LibUtilities::CommSharedPtr vComm = pFields[0]->GetComm();

    unsigned int i = 0;
    Array<OneD, NekDouble> e(npoints);

    // Compute grad V
    Array<OneD, NekDouble> grad_V_x(nq), grad_V_y(nq), grad_V_z(nq);
    pFields[0]->PhysDeriv(pFields[0]->GetPhys(),
                          grad_V_x, grad_V_y, grad_V_z);

    for (i = 0; i < npoints; ++i)
    {
        // Multiply together
        Array<OneD, NekDouble> output(nq);
        Vmath::Vvtvvtp(nq, m_grad_R_x[i], 1, grad_V_x, 1, m_grad_R_y[i], 1,
                           grad_V_y,      1, output,   1);
        Vmath::Vvtvp  (nq, m_grad_R_z[i], 1, grad_V_z, 1, output, 1,
                           output,        1);

        e[i] = pFields[0]->Integral(output);
    }

    // Exchange history data
    // This could be improved to reduce communication but works for now
    vComm->AllReduce(e, LibUtilities::ReduceSum);

    // Only the root process writes out electrogram data
    if (vComm->GetRank() == 0)
    {
        m_outputStream.width(8);
        m_outputStream << setprecision(6) << time;

        // Write data values point by point
        for (i = 0; i < m_electrogramPoints.size(); ++i)
        {
            m_outputStream.width(25);
            m_outputStream << setprecision(16) << e[i];
        }
        m_outputStream << endl;
    }
}


/**
 *
 */
void FilterElectrogram::v_Finalise(
        const Array<OneD, const MultiRegions::ExpListSharedPtr> &pFields,
        const NekDouble &time)
{
    if (pFields[0]->GetComm()->GetRank() == 0)
    {
        m_outputStream.close();
    }
}


/**
 *
 */
bool FilterElectrogram::v_IsTimeDependent()
{
    return true;
}
}