ElectrodesStimulusFactory.cpp

/*

Copyright (C) University of Oxford, 2005-2011

University of Oxford means the Chancellor, Masters and Scholars of the
University of Oxford, having an administrative office at Wellington
Square, Oxford OX1 2JD, UK.

This file is part of Chaste.

Chaste is free software: you can redistribute it and/or modify it
under the terms of the GNU Lesser General Public License as published
by the Free Software Foundation, either version 2.1 of the License, or
(at your option) any later version.

Chaste is distributed in the hope that it will be useful, but WITHOUT
ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
FITNESS FOR A PARTICULAR PURPOSE.  See the GNU Lesser General Public
License for more details. The offer of Chaste under the terms of the
License is subject to the License being interpreted in accordance with
English Law and subject to any action against the University of Oxford
being under the jurisdiction of the English Courts.

You should have received a copy of the GNU Lesser General Public License
along with Chaste. If not, see <http://www.gnu.org/licenses/>.

*/

#include "ElectrodesStimulusFactory.hpp"
#include "DistributedTetrahedralMesh.hpp"
#include "IsNan.hpp"
#include "HeartConfig.hpp"
#include "GaussianQuadratureRule.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(unsigned nodeIndex)
{
    boost::shared_ptr<RegularStimulus> p_stimulus;
    for (unsigned pair_index = 0; pair_index < mrElectrodePairs.size(); pair_index++)
    {
        if (mrElectrodePairs[pair_index].first->DoesContain(this->mpMesh->GetNode(nodeIndex)->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(this->mpMesh->GetNode(nodeIndex)->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)
{
        //assume 2 gauss points
        GaussianQuadratureRule<DIM>* pQuadRule = new GaussianQuadratureRule<DIM>(2u);

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

        double total_electrode_flux = 0.0;
        double ret;

        for (typename AbstractTetrahedralMesh<DIM,DIM>::NodeIterator iter=this->mpMesh->GetNodeIteratorBegin();
             iter != this->mpMesh->GetNodeIteratorEnd();
             ++iter)
        {
            if ( pRegion->DoesContain( (*iter).GetPoint() ) )
            {
                unsigned node_index =     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>;