ElectrodesStimulusFactory.cpp

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#include "ElectrodesStimulusFactory.hpp"
#include "DistributedTetrahedralMesh.hpp"
#include "IsNan.hpp"
#include "HeartConfig.hpp"
#include "GaussianQuadratureRule.hpp"
#include "RegularStimulus.hpp"

template<unsigned DIM>
ElectrodesStimulusFactory<DIM>::ElectrodesStimulusFactory(std::vector<std::pair<AbstractChasteRegion<DIM>*, AbstractChasteRegion<DIM>*> >& rElectrodePairs,
                                                          std::vector<double>& rStimulusMagnitudes,
                                                          std::vector<double>& rDurations,
                                                          std::vector<double>& rPeriods,
                                                          std::vector<double>& rStarts,
                                                          std::vector<double>& rEnds)
    : mrElectrodePairs(rElectrodePairs),
      mrMagnitudes(rStimulusMagnitudes),
      mrDurations(rDurations),
      mrPeriods(rPeriods),
      mrStarts(rStarts),
      mrEnds(rEnds),
      mGroundSecondElectrode(false)
{
    if ((rElectrodePairs.size() != rStimulusMagnitudes.size()) ||
        (rElectrodePairs.size() != rDurations.size()) ||
        (rElectrodePairs.size() != rPeriods.size()) ||
        (rElectrodePairs.size() != rStarts.size()) ||
        (rElectrodePairs.size() != rEnds.size()))
    {
        EXCEPTION ("Vector of electrode pairs and vector of stimulation paremeters must have the same size");
    }

    mMagnitudesElectrode1 = mrMagnitudes;
    mMagnitudesElectrode2 = mrMagnitudes;
}

template<unsigned DIM>
ElectrodesStimulusFactory<DIM>::~ElectrodesStimulusFactory()
{
}

template<unsigned DIM>
void ElectrodesStimulusFactory<DIM>::CheckForElectrodesIntersection()
{
    std::vector<unsigned> nodes_in_all_electrodes;
    for (unsigned global_node_index = 0; global_node_index < this->mpMesh->GetNumNodes(); global_node_index++)
    {
        if (this->mpMesh->GetDistributedVectorFactory()->IsGlobalIndexLocal(global_node_index))
        {
            for (unsigned pair_index = 0; pair_index <mrElectrodePairs.size(); pair_index++)
            {
                if (mrElectrodePairs[pair_index].first->DoesContain( this->mpMesh->GetNode(global_node_index)->GetPoint()))
                {
                    nodes_in_all_electrodes.push_back( this->mpMesh->GetNode(global_node_index)->GetIndex() );
                }
                if (mrElectrodePairs[pair_index].second->DoesContain( this->mpMesh->GetNode(global_node_index)->GetPoint()))
                {
                    nodes_in_all_electrodes.push_back( this->mpMesh->GetNode(global_node_index)->GetIndex() );
                }
            }
        }
    }
    PetscTools::Barrier();
    for (unsigned node_index = 0; node_index < nodes_in_all_electrodes.size(); node_index++)
    {
        unsigned number_of_hits = 0;
        for (unsigned node_to_check = 0; node_to_check < nodes_in_all_electrodes.size(); node_to_check++)
        {
            if (nodes_in_all_electrodes[node_index] == nodes_in_all_electrodes[node_to_check] )
            {
                number_of_hits++;
            }
        }
        if (number_of_hits>1)
        {
            EXCEPTION("Two or more electrodes intersect with each other");
        }
    }
}

template<unsigned DIM>
void ElectrodesStimulusFactory<DIM>::GroundSecondElectrode(bool grounded)
{
    mGroundSecondElectrode = grounded;
}

template<unsigned DIM>
void ElectrodesStimulusFactory<DIM>::SetCompatibleExtracellularStimulus()
{
    assert(this->mpMesh!=NULL);
    try
    {
        CheckForElectrodesIntersection();
    }
    catch (Exception &e)
    {
        PetscTools::ReplicateException(true); //Electrodes intersect
        throw e;
    }
    PetscTools::ReplicateException(false);

    for (unsigned pair_index = 0; pair_index < mrElectrodePairs.size(); pair_index++)
    {

        if (!mGroundSecondElectrode)//no grounding of second electrode
        {
            //compute the two fluxes for this pair
            double flux_electrode_1  = ComputeElectrodeTotalFlux(mrElectrodePairs[pair_index].first, mMagnitudesElectrode1[pair_index]);
            double flux_electrode_2  = ComputeElectrodeTotalFlux(mrElectrodePairs[pair_index].second, mMagnitudesElectrode2[pair_index]);

            //Scale the magnitude of the second electrode for this pair
            mMagnitudesElectrode2[pair_index] = -mMagnitudesElectrode1[pair_index]*flux_electrode_1/flux_electrode_2;

            // Paranoia.
            assert( flux_electrode_2 != 0.0);
            assert( ! std::isnan(mMagnitudesElectrode2[pair_index]));

        }
        else//second electrode is grounded
        {
            this->mGroundedRegions.push_back( mrElectrodePairs[pair_index].second );
        }
    }
}

template<unsigned DIM>
boost::shared_ptr<AbstractStimulusFunction> ElectrodesStimulusFactory<DIM>::CreateStimulusForNode(Node<DIM>* pNode)
{
    boost::shared_ptr<RegularStimulus> p_stimulus;
    for (unsigned pair_index = 0; pair_index < mrElectrodePairs.size(); pair_index++)
    {
        if (mrElectrodePairs[pair_index].first->DoesContain(pNode->GetPoint()) )
        {
            p_stimulus.reset( new RegularStimulus(mMagnitudesElectrode1[pair_index], mrDurations[pair_index], mrPeriods[pair_index], mrStarts[pair_index], mrEnds[pair_index]));

        }
        else if (mrElectrodePairs[pair_index].second->DoesContain(pNode->GetPoint()) )
        {
            p_stimulus.reset ( new RegularStimulus(mMagnitudesElectrode2[pair_index], mrDurations[pair_index], mrPeriods[pair_index], mrStarts[pair_index], mrEnds[pair_index]));

        }
        else//no stimulus here
        {
            p_stimulus.reset ( new RegularStimulus(0.0, mrDurations[pair_index], mrPeriods[pair_index], mrStarts[pair_index], mrEnds[pair_index]));
        }
    }
    return p_stimulus;
}

template<unsigned DIM>
double ElectrodesStimulusFactory<DIM>::ComputeElectrodeTotalFlux(AbstractChasteRegion<DIM>* pRegion, double stimulusMagnitude)
{
    GaussianQuadratureRule<DIM>* pQuadRule = new GaussianQuadratureRule<DIM>(2);

    //the basis functions
    c_vector<double, DIM+1> phi;

    double total_electrode_flux = 0.0;
    double ret;

    for (typename AbstractTetrahedralMesh<DIM,DIM>::NodeIterator node_iter=this->mpMesh->GetNodeIteratorBegin();
         node_iter != this->mpMesh->GetNodeIteratorEnd();
         ++node_iter)
    {
        if (pRegion->DoesContain((*node_iter).GetPoint()))
        {
            unsigned node_index = node_iter->GetIndex();
            assert(node_index < this->mpMesh->GetNumNodes());
            double contribution_of_this_node = 0.0;
            // Loop over the elements where this node is contained
            for (std::set<unsigned>::iterator iter = this->mpMesh->GetNode(node_index)->rGetContainingElementIndices().begin();
                 iter != this->mpMesh->GetNode(node_index)->rGetContainingElementIndices().end();
                 ++iter)
            {
                Element<DIM,DIM>* p_element = this->mpMesh->GetElement(*iter);

                /*Determine jacobian for this element*/
                c_matrix<double, DIM, DIM> jacobian;
                c_matrix<double, DIM, DIM> inverse_jacobian;//unused here, but needed for the function below
                double jacobian_determinant;
                this->mpMesh->GetInverseJacobianForElement(p_element->GetIndex(), jacobian, jacobian_determinant, inverse_jacobian);

                double contribution_of_this_element = 0.0;//...to this node
                 // loop over Gauss points
                for (unsigned quad_index=0; quad_index < pQuadRule->GetNumQuadPoints(); quad_index++)
                {
                    const ChastePoint<DIM>& quad_point = pQuadRule->rGetQuadPoint(quad_index);
                    BasisFunction::ComputeBasisFunctions(quad_point, phi);

                    double interpolated_stimulus = 0.0;
                    //loop over nodes in this element
                    for (unsigned node_index_in_element = 0; node_index_in_element < p_element->GetNumNodes(); node_index_in_element++)
                    {
                        //const Node<DIM>* p_node = p_element->GetNode(node_index_in_element);
                        assert(p_element->GetNumNodes() == DIM+1);
                        interpolated_stimulus += stimulusMagnitude*phi(node_index_in_element);
                        contribution_of_this_element += interpolated_stimulus * phi(node_index_in_element) * jacobian_determinant * pQuadRule->GetWeight(quad_index);
                    }

                }/*end of loop over gauss points*/
                contribution_of_this_node += contribution_of_this_element;

            }/*end of loop over elements where the node is contained*/
            total_electrode_flux += contribution_of_this_node;
        }/* end of if that checks if node is in the electrode*/
    }/* end of loop over nodes in the mesh*/
#ifndef NDEBUG
    int mpi_ret = MPI_Allreduce(&total_electrode_flux, &ret, 1, MPI_DOUBLE, MPI_SUM, PETSC_COMM_WORLD);
    assert(mpi_ret == MPI_SUCCESS);
#else
    MPI_Allreduce(&total_electrode_flux, &ret, 1, MPI_DOUBLE, MPI_SUM, PETSC_COMM_WORLD);
#endif

    //clear up memory
    delete pQuadRule;

    assert(ret < DBL_MAX);
    return ret;
}

// Explicit instantiation
template class ElectrodesStimulusFactory<1>;
template class ElectrodesStimulusFactory<2>;
template class ElectrodesStimulusFactory<3>;