AbstractPurkinjeCellFactory.cpp

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#include "AbstractPurkinjeCellFactory.hpp"
#include "PurkinjeVentricularJunctionStimulus.hpp"
#include "MultiStimulus.hpp"
#include "HeartConfig.hpp"
#include "Warnings.hpp"

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
AbstractPurkinjeCellFactory<ELEMENT_DIM,SPACE_DIM>::AbstractPurkinjeCellFactory()
    : AbstractCardiacCellFactory<ELEMENT_DIM,SPACE_DIM>(),
      mpMixedDimensionMesh(NULL)
{
}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void AbstractPurkinjeCellFactory<ELEMENT_DIM,SPACE_DIM>::ReadJunctionsFile()
{
    std::string pvj_file_name;
    bool file_specified = true;

    try
    {
        // HeartConfig::Instance()->GetMeshName() will throw an exception if no mesh name is defined
        pvj_file_name = HeartConfig::Instance()->GetMeshName() + ".pvj";
    }
    catch(Exception&)
    {
        file_specified = false;
    }

    FileFinder junction_file(pvj_file_name, RelativeTo::AbsoluteOrCwd);
    if (!file_specified || !junction_file.Exists() )
    {
        // In this case we expect the user to specify PVJ programmatically, so return immediately.
        WARNING("No Purkinje-Ventricular junction (.pvj) file found. Junctions must be specified manually.");
        return;
    }

    std::ifstream junction_stream(junction_file.GetAbsolutePath().c_str());

    if (!junction_stream.good())
    {   // file couldn't be opened
        EXCEPTION("Couldn't open data file: " << junction_file.GetAbsolutePath());
    }

    // Reads in file defining nodes and resistance (separated by space)
    while (junction_stream.good())
    {
        std::string this_line;
        getline(junction_stream, this_line);

        if (this_line=="" || this_line=="\r")
        {
            if (junction_stream.eof())
            {   // If the blank line is the last line carry on OK.
                break;
            }
            else
            {
                EXCEPTION("No data found on line in file: " << junction_file.GetAbsolutePath());
            }
        }
        std::stringstream line(this_line);

        unsigned node_id;
        line >> node_id;
        double resistance;
        line >> resistance;

        if (mpMixedDimensionMesh->rGetNodePermutation().size() != 0) //Do we have a permuted mesh?
        {
            unsigned mapped_node_id = mpMixedDimensionMesh->rGetNodePermutation()[node_id];

            mJunctionMap[mapped_node_id] = resistance;
        }
        else
        {
            mJunctionMap[node_id] = resistance;
        }
    }
}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void AbstractPurkinjeCellFactory<ELEMENT_DIM,SPACE_DIM>::CreateJunction(const Node<SPACE_DIM>* pNode,
                                                                        AbstractCardiacCellInterface* pPurkinjeCell,
                                                                        AbstractCardiacCellInterface* pCardiacCell,
                                                                        double resistance)
{
    // Figure out the effective resistance for this mesh, in kOhm.cm^3
    if (pNode) // Should always be provided apart from low-level tests!
    {
        assert(mpMixedDimensionMesh);
        typedef typename MixedDimensionMesh<ELEMENT_DIM,SPACE_DIM>::CableRangeAtNode CableRangeAtNode;
        CableRangeAtNode cable_range = mpMixedDimensionMesh->GetCablesAtNode(pNode);
        double total_cross_sectional_area = 0.0;
        for (typename MixedDimensionMesh<ELEMENT_DIM,SPACE_DIM>::NodeCableIterator iter=cable_range.first;
             iter != cable_range.second;
             ++iter)
        {
            Element<1u,SPACE_DIM>* p_cable = iter->second;
            double cable_radius = p_cable->GetAttribute();
            total_cross_sectional_area += M_PI*cable_radius*cable_radius;
        }
        resistance *= total_cross_sectional_area / HeartConfig::Instance()->GetPurkinjeSurfaceAreaToVolumeRatio();
    }
    // Create the junction stimuli, and associate them with the cells
    boost::shared_ptr<PurkinjeVentricularJunctionStimulus> p_pvj_ventricular_stim(new PurkinjeVentricularJunctionStimulus(resistance));
    boost::shared_ptr<PurkinjeVentricularJunctionStimulus> p_pvj_purkinje_stim(new PurkinjeVentricularJunctionStimulus(resistance));
    p_pvj_purkinje_stim->SetAppliedToPurkinjeCellModel();
    p_pvj_ventricular_stim->SetVentricularCellModel(pCardiacCell);
    p_pvj_ventricular_stim->SetPurkinjeCellModel(pPurkinjeCell);
    p_pvj_purkinje_stim->SetVentricularCellModel(pCardiacCell);
    p_pvj_purkinje_stim->SetPurkinjeCellModel(pPurkinjeCell);

    // Create new combined stimuli which add the junction stimuli to those already in the cells
    boost::shared_ptr<MultiStimulus> p_multi_stim_ventricular(new MultiStimulus);
    p_multi_stim_ventricular->AddStimulus(p_pvj_ventricular_stim);
    p_multi_stim_ventricular->AddStimulus(pCardiacCell->GetStimulusFunction());
    pCardiacCell->SetStimulusFunction(p_multi_stim_ventricular);

    boost::shared_ptr<MultiStimulus> p_multi_stim_purkinje(new MultiStimulus);
    p_multi_stim_purkinje->AddStimulus(p_pvj_purkinje_stim);
    p_multi_stim_purkinje->AddStimulus(pPurkinjeCell->GetStimulusFunction());
    pPurkinjeCell->SetStimulusFunction(p_multi_stim_purkinje);
}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void AbstractPurkinjeCellFactory<ELEMENT_DIM,SPACE_DIM>::SetMesh(AbstractTetrahedralMesh<ELEMENT_DIM,SPACE_DIM>* pMesh)
{
    mpMixedDimensionMesh = dynamic_cast<MixedDimensionMesh<ELEMENT_DIM,SPACE_DIM>*>(pMesh);
    if (mpMixedDimensionMesh == NULL)
    {
        EXCEPTION("AbstractPurkinjeCellFactory must take a MixedDimensionMesh");
    }
    mLocalPurkinjeNodes.clear();
    for (typename MixedDimensionMesh<ELEMENT_DIM,SPACE_DIM>::CableElementIterator iter = mpMixedDimensionMesh->GetCableElementIteratorBegin();
          iter != mpMixedDimensionMesh->GetCableElementIteratorEnd();
          ++iter)
    {
        mLocalPurkinjeNodes.insert((*iter)->GetNodeGlobalIndex(0u));
        mLocalPurkinjeNodes.insert((*iter)->GetNodeGlobalIndex(1u));
    }
    AbstractCardiacCellFactory<ELEMENT_DIM,SPACE_DIM>::SetMesh(pMesh);

    ReadJunctionsFile();
}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
AbstractCardiacCellInterface*  AbstractPurkinjeCellFactory<ELEMENT_DIM,SPACE_DIM>::CreatePurkinjeCellForNode(
        Node<SPACE_DIM>* pNode,
        AbstractCardiacCellInterface* pCardiacCell)
{
    unsigned node_index = pNode->GetIndex();
    if (mLocalPurkinjeNodes.count(node_index)>0)
    {
        return CreatePurkinjeCellForTissueNode(pNode, pCardiacCell);
    }
    else
    {
        return new FakeBathCell(this->mpSolver, this->mpZeroStimulus);
    }
}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
MixedDimensionMesh<ELEMENT_DIM,SPACE_DIM>* AbstractPurkinjeCellFactory<ELEMENT_DIM,SPACE_DIM>::GetMixedDimensionMesh()
{
    if (mpMixedDimensionMesh == NULL)
    {
        EXCEPTION("The mixed dimension mesh object has not been set in the cell factory");
    }
    return mpMixedDimensionMesh;
}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void AbstractPurkinjeCellFactory<ELEMENT_DIM,SPACE_DIM>::CreateJunctionFromFile(const Node<SPACE_DIM>* pNode,
                                                                                AbstractCardiacCellInterface* pPurkinjeCell,
                                                                                AbstractCardiacCellInterface* pCardiacCell)
{
    std::map<unsigned, double>::iterator iter = mJunctionMap.find(pNode->GetIndex());
    if (iter != mJunctionMap.end())
    {
        CreateJunction(pNode, pPurkinjeCell, pCardiacCell, iter->second);
    }
}

// Explicit instantiation
template class AbstractPurkinjeCellFactory<1,1>;
template class AbstractPurkinjeCellFactory<2,2>;
template class AbstractPurkinjeCellFactory<3,3>;
template class AbstractPurkinjeCellFactory<1,2>;
template class AbstractPurkinjeCellFactory<1,3>;