PseudoEcgCalculator.cpp

/*

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*/

#include "PseudoEcgCalculator.hpp"
#include "HeartRegionCodes.hpp"
#include "HeartConfig.hpp"
#include "PetscTools.hpp"
#include "Version.hpp"
#include <iostream>

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>
double PseudoEcgCalculator<ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM> ::GetIntegrand(ChastePoint<SPACE_DIM>& rX,
                                c_vector<double,PROBLEM_DIM>& rU,
                                c_matrix<double,PROBLEM_DIM,SPACE_DIM>& rGradU)
{
    c_vector<double,SPACE_DIM> r_vector = rX.rGetLocation()- mProbeElectrode.rGetLocation();
    double norm_r = norm_2(r_vector);
    if (norm_r <= DBL_EPSILON)
    {
        EXCEPTION("Probe is on a mesh Gauss point.");
    }
    c_vector<double,SPACE_DIM> grad_one_over_r = - (r_vector)*SmallPow( (1/norm_r) , 3);
    matrix_row<c_matrix<double, PROBLEM_DIM, SPACE_DIM> > grad_u_row(rGradU, 0);
    double integrand = inner_prod(grad_u_row, grad_one_over_r);

    return -mDiffusionCoefficient*integrand;
}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>
PseudoEcgCalculator<ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM>::PseudoEcgCalculator(AbstractTetrahedralMesh<ELEMENT_DIM,SPACE_DIM>& rMesh,
                                                                              const ChastePoint<SPACE_DIM>& rProbeElectrode,
                                                                              const FileFinder& rDirectory,
                                                                              std::string hdf5File,
                                                                              std::string variableName,
                                                                              unsigned timestepStride)
  : mrMesh(rMesh),
    mProbeElectrode(rProbeElectrode),
    mVariableName(variableName),
    mTimestepStride(timestepStride)
{
    mpDataReader = new Hdf5DataReader(rDirectory, hdf5File);
    mNumberOfNodes = mpDataReader->GetNumberOfRows();
    mNumTimeSteps = mpDataReader->GetVariableOverTime(mVariableName, 0u).size();
    mDiffusionCoefficient = 1.0;
    //check that the hdf file was generated by simulations from the same mesh
    assert(mNumberOfNodes == mrMesh.GetNumNodes());
}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>
bool PseudoEcgCalculator<ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM>::ShouldSkipThisElement(Element<ELEMENT_DIM,SPACE_DIM>& rElement)
{
    bool result = false; // Don't skip usually
    if (mVariableName=="V")
    {
        // If we are integrating voltage and this element is in the bath then skip it.
        result = HeartRegionCode::IsRegionBath(rElement.GetUnsignedAttribute());
    }
    return result;
}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>
PseudoEcgCalculator<ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM>::~PseudoEcgCalculator()
{
    delete mpDataReader;
}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>
void PseudoEcgCalculator<ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM>::SetDiffusionCoefficient(double diffusionCoefficient)
{
    assert(diffusionCoefficient>=0);
    mDiffusionCoefficient = diffusionCoefficient;
}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>
double PseudoEcgCalculator<ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM>::ComputePseudoEcgAtOneTimeStep (unsigned timeStep)
{
    Vec solution_at_one_time_step = PetscTools::CreateVec(mNumberOfNodes);
    mpDataReader->GetVariableOverNodes(solution_at_one_time_step, mVariableName , timeStep);

    double pseudo_ecg_at_one_timestep;
    try
    {
        pseudo_ecg_at_one_timestep = this->Calculate(mrMesh, solution_at_one_time_step);
    }
    catch (Exception &e)
    {
        PetscTools::Destroy(solution_at_one_time_step);
        throw e;
    }
    PetscTools::Destroy(solution_at_one_time_step);
    return pseudo_ecg_at_one_timestep;
}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>
void PseudoEcgCalculator<ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM>::WritePseudoEcg ()
{
    // Cache the time values so that we can plot a decent x-axis
    std::vector<double> time_points = mpDataReader->GetUnlimitedDimensionValues();

    std::stringstream stream;
    stream << "PseudoEcgFromElectrodeAt" << "_" << mProbeElectrode.GetWithDefault(0)
                          << "_" << mProbeElectrode.GetWithDefault(1)
                          << "_" << mProbeElectrode.GetWithDefault(2) << ".dat";
    OutputFileHandler output_file_handler(HeartConfig::Instance()->GetOutputDirectory() + "/output", false);
    out_stream p_file=out_stream(NULL);
    if (PetscTools::AmMaster())
    {
        p_file = output_file_handler.OpenOutputFile(stream.str());
        *p_file << "#Time(ms)\tPseudo-ECG\n";
    }
    for (unsigned time_step = 0; time_step < mNumTimeSteps; time_step+=mTimestepStride)
    {
        double pseudo_ecg_at_one_timestep = ComputePseudoEcgAtOneTimeStep(time_step);
        if (PetscTools::AmMaster())
        {
            *p_file << time_points[time_step] << "\t" <<pseudo_ecg_at_one_timestep << "\n";
        }
    }
    if (PetscTools::AmMaster())
    {
        //write provenance info
        std::string comment = "# " + ChasteBuildInfo::GetProvenanceString();
        *p_file << comment;
        p_file->close();
    }
}
// Explicit instantiation

template class PseudoEcgCalculator<1,1,1>;
template class PseudoEcgCalculator<1,2,1>;
template class PseudoEcgCalculator<1,3,1>;
template class PseudoEcgCalculator<2,2,1>;
//template class PseudoEcgCalculator<2,3,1>;
template class PseudoEcgCalculator<3,3,1>;