HeartConfigRelatedCellFactory.cpp

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#include "HeartConfigRelatedCellFactory.hpp"

#include <sstream>
#include "HeartGeometryInformation.hpp"
#include "ChasteNodesList.hpp"
#include "HeartFileFinder.hpp"
#include "CellMLToSharedLibraryConverter.hpp"
#include "AbstractCardiacCellInterface.hpp"
#include "Warnings.hpp"
// This is needed to prevent the chaste_libs=0 build failing
// on tests that use a dynamically loaded CVODE model
#include "AbstractCvodeCell.hpp"

template<unsigned SPACE_DIM>
HeartConfigRelatedCellFactory<SPACE_DIM>::HeartConfigRelatedCellFactory()
    : AbstractCardiacCellFactory<SPACE_DIM>(),
      mDefaultIonicModel(HeartConfig::Instance()->GetDefaultIonicModel())
{
    // Read and store possible region definitions
    HeartConfig::Instance()->GetIonicModelRegions(mIonicModelRegions,
                                                  mIonicModelsDefined);

    // Read and store Stimuli
    HeartConfig::Instance()->GetStimuli(mStimuliApplied, mStimulatedAreas);

    // if no stimuli provided in XML, need electrodes instead
    if (mStimuliApplied.size()==0  &&  (HeartConfig::Instance()->IsElectrodesPresent() == false) )
    {
         EXCEPTION("Simulation needs a stimulus (either <Stimuli> or <Electrodes>).");
    }

    // Read and store Cell Heterogeneities
    HeartConfig::Instance()->GetCellHeterogeneities(mCellHeterogeneityAreas,
                                                    mScaleFactorGks,
                                                    mScaleFactorIto,
                                                    mScaleFactorGkr,
                                                    &mParameterSettings);

    // Do we need to convert any CellML files?
    PreconvertCellmlFiles();
}

template<unsigned SPACE_DIM>
void HeartConfigRelatedCellFactory<SPACE_DIM>::PreconvertCellmlFiles()
{
    if (mDefaultIonicModel.Dynamic().present())
    {
        LoadDynamicModel(mDefaultIonicModel, true);
    }
    for (unsigned i=0; i<mIonicModelsDefined.size(); i++)
    {
        if (mIonicModelsDefined[i].Dynamic().present())
        {
            LoadDynamicModel(mIonicModelsDefined[i], true);
        }
    }
}

template<unsigned SPACE_DIM>
DynamicCellModelLoaderPtr HeartConfigRelatedCellFactory<SPACE_DIM>::LoadDynamicModel(
        const cp::ionic_model_selection_type& rModel,
        bool isCollective)
{
    assert(rModel.Dynamic().present());
    HeartFileFinder file_finder(rModel.Dynamic()->Path());
    CellMLToSharedLibraryConverter converter;
    return converter.Convert(file_finder, isCollective);
}

template<unsigned SPACE_DIM>
HeartConfigRelatedCellFactory<SPACE_DIM>::~HeartConfigRelatedCellFactory()
{
}

template<unsigned SPACE_DIM>
AbstractCardiacCellInterface* HeartConfigRelatedCellFactory<SPACE_DIM>::CreateCellWithIntracellularStimulus(
        boost::shared_ptr<AbstractStimulusFunction> intracellularStimulus,
        unsigned nodeIndex)
{
    cp::ionic_model_selection_type ionic_model = mDefaultIonicModel;

    for (unsigned ionic_model_region_index = 0;
         ionic_model_region_index < mIonicModelRegions.size();
         ++ionic_model_region_index)
    {
        if (mIonicModelRegions[ionic_model_region_index]->DoesContain(this->GetMesh()->GetNode(nodeIndex)->GetPoint()))
        {
            ionic_model = mIonicModelsDefined[ionic_model_region_index];
            break;
        }
    }

    AbstractCardiacCellInterface* p_cell = NULL;

    if (ionic_model.Dynamic().present())
    {
#ifndef CHASTE_CAN_CHECKPOINT_DLLS
        if (HeartConfig::Instance()->GetCheckpointSimulation())
        {
            EXCEPTION("Checkpointing is not compatible with dynamically loaded cell models on Mac OS X.");
        }
#endif // CHASTE_CAN_CHECKPOINT_DLLS
        // Load model from shared library
        DynamicCellModelLoaderPtr p_loader = LoadDynamicModel(ionic_model, false);
        p_cell = p_loader->CreateCell(this->mpSolver, intracellularStimulus);
    }
    else
    {
        assert(ionic_model.Hardcoded().present());
        switch(ionic_model.Hardcoded().get())
        {
            case(cp::ionic_models_available_type::LuoRudyI):
            {
                p_cell = new CellLuoRudy1991FromCellML(this->mpSolver, intracellularStimulus);
                break;
            }

            case(cp::ionic_models_available_type::LuoRudyIBackwardEuler):
            {
                p_cell = new CellLuoRudy1991FromCellMLBackwardEuler(this->mpSolver, intracellularStimulus);
                break;
            }

            case(cp::ionic_models_available_type::Fox2002):
            {
                p_cell = new CellFoxModel2002FromCellML(this->mpSolver, intracellularStimulus);
                break;
            }

            case(cp::ionic_models_available_type::Fox2002BackwardEuler):
            {
                p_cell = new CellFoxModel2002FromCellMLBackwardEuler(this->mpSolver, intracellularStimulus);
                break;
            }

            case(cp::ionic_models_available_type::DifrancescoNoble):
            {
                p_cell = new CellDiFrancescoNoble1985FromCellML(this->mpSolver, intracellularStimulus);
                break;
            }

            case(cp::ionic_models_available_type::MahajanShiferaw):
            {
                p_cell = new CellMahajan2008FromCellML(this->mpSolver, intracellularStimulus);
                break;
            }

            case(cp::ionic_models_available_type::MahajanShiferawBackwardEuler):
            {
                p_cell = new CellMahajan2008FromCellMLBackwardEuler(this->mpSolver, intracellularStimulus);
                break;
            }

            case(cp::ionic_models_available_type::tenTusscher2006):
            {
                p_cell = new CellTenTusscher2006EpiFromCellML(this->mpSolver, intracellularStimulus);
                break;
            }

            case(cp::ionic_models_available_type::tenTusscher2006BackwardEuler):
            {
                p_cell = new CellTenTusscher2006EpiFromCellMLBackwardEuler(this->mpSolver, intracellularStimulus);
                break;
            }

            case(cp::ionic_models_available_type::Maleckar):
            {
                p_cell = new CellMaleckar2008FromCellML(this->mpSolver, intracellularStimulus);
                break;
            }

            case(cp::ionic_models_available_type::HodgkinHuxley):
            {
                p_cell = new CellHodgkinHuxley1952FromCellML(this->mpSolver, intracellularStimulus);
                break;
            }

            case(cp::ionic_models_available_type::FaberRudy2000):
            {
                p_cell = new CellFaberRudy2000FromCellML(this->mpSolver, intracellularStimulus);
                break;
            }

            case(cp::ionic_models_available_type::FaberRudy2000Optimised):
            {
                p_cell = new CellFaberRudy2000FromCellMLOpt(this->mpSolver, intracellularStimulus);
                break;
            }

            default:
            {
               //If the ionic model is not in the current enumeration then the XML parser will have picked it up before now!
               NEVER_REACHED;
            }
        }
    }

    // Set parameters
    try
    {
        SetCellParameters(p_cell, nodeIndex);
    }
    catch (const Exception& e)
    {
        delete p_cell;
        throw e;
    }
    // Generate lookup tables if present
    p_cell->GetLookupTableCollection();

    return p_cell;
}

template<unsigned SPACE_DIM>
void HeartConfigRelatedCellFactory<SPACE_DIM>::SetCellParameters(AbstractCardiacCellInterface* pCell,
                                                                 unsigned nodeIndex)
{
    // Special case for backwards-compatibility: scale factors
    for (unsigned ht_index = 0;
         ht_index < mCellHeterogeneityAreas.size();
         ++ht_index)
    {
        if (mCellHeterogeneityAreas[ht_index]->DoesContain(this->GetMesh()->GetNode(nodeIndex)->GetPoint()))
        {
            try
            {
                pCell->SetParameter("ScaleFactorGks", mScaleFactorGks[ht_index]);
                pCell->SetParameter("ScaleFactorGkr", mScaleFactorGkr[ht_index]);
                pCell->SetParameter("ScaleFactorIto", mScaleFactorIto[ht_index]);
            }
            catch (const Exception&)
            {
                // Just ignore missing parameter errors in this case
            }
        }
    }

    if (HeartConfig::Instance()->HasDrugDose())
    {
        double drug_dose = HeartConfig::Instance()->GetDrugDose();
        std::map<std::string, std::pair<double, double> > ic50_values = HeartConfig::Instance()->GetIc50Values();
        for (std::map<std::string, std::pair<double, double> >::iterator it = ic50_values.begin();
             it != ic50_values.end();
             ++it)
        {
            const std::string param_name = it->first + "_conductance";
            if (dynamic_cast<AbstractUntemplatedParameterisedSystem*>(pCell)->HasParameter(param_name))
            {
                const double original_conductance = pCell->GetParameter(param_name);
                const double ic50 = it->second.first;
                const double hill = it->second.second;
                const double new_conductance = original_conductance/(1.0 + pow(drug_dose/ic50, hill));
                pCell->SetParameter(param_name, new_conductance);
            }
            else
            {
                WARNING("Cannot apply drug to cell at node " << nodeIndex << " as it has no parameter named '" << param_name << "'.");
            }
        }
    }

    // SetParameter elements go next so they override the old ScaleFactor* elements.
    for (unsigned ht_index = 0;
         ht_index < mCellHeterogeneityAreas.size();
         ++ht_index)
    {
        if (mCellHeterogeneityAreas[ht_index]->DoesContain(this->GetMesh()->GetNode(nodeIndex)->GetPoint()))
        {
            for (std::map<std::string, double>::iterator param_it = mParameterSettings[ht_index].begin();
                 param_it != mParameterSettings[ht_index].end();
                 ++param_it)
            {
                pCell->SetParameter(param_it->first, param_it->second);
            }
        }
    }
}

template<unsigned SPACE_DIM>
void HeartConfigRelatedCellFactory<SPACE_DIM>::SetCellIntracellularStimulus(AbstractCardiacCellInterface* pCell,
                                                                            unsigned nodeIndex)
{
    boost::shared_ptr<MultiStimulus> node_specific_stimulus(new MultiStimulus());
    // Check which of the defined stimuli contain the current node
    for (unsigned stimulus_index = 0;
         stimulus_index < mStimuliApplied.size();
         ++stimulus_index)
    {
        if (mStimulatedAreas[stimulus_index]->DoesContain(this->GetMesh()->GetNode(nodeIndex)->GetPoint()))
        {
            node_specific_stimulus->AddStimulus(mStimuliApplied[stimulus_index]);
        }
    }
    pCell->SetIntracellularStimulusFunction(node_specific_stimulus);
}

template<unsigned SPACE_DIM>
AbstractCardiacCellInterface* HeartConfigRelatedCellFactory<SPACE_DIM>::CreateCardiacCellForTissueNode(Node<SPACE_DIM>* pNode)
{
    boost::shared_ptr<MultiStimulus> node_specific_stimulus(new MultiStimulus());

    // Check which of the defined stimuli contain the current node
    for (unsigned stimulus_index = 0;
         stimulus_index < mStimuliApplied.size();
         ++stimulus_index)
    {
        if (mStimulatedAreas[stimulus_index]->DoesContain(pNode->GetPoint()))
        {
            node_specific_stimulus->AddStimulus(mStimuliApplied[stimulus_index]);
        }
    }

    unsigned node_index = pNode->GetIndex();
    return CreateCellWithIntracellularStimulus(node_specific_stimulus, node_index);
}

// LCOV_EXCL_START
template<unsigned SPACE_DIM>
void HeartConfigRelatedCellFactory<SPACE_DIM>::FillInCellularTransmuralAreas()
{
    NEVER_REACHED;
}
// LCOV_EXCL_STOP

template<>
void HeartConfigRelatedCellFactory<3u>::FillInCellularTransmuralAreas()
{
    std::string mesh_file_name = HeartConfig::Instance()->GetMeshName();
    //files containing list of nodes on each surface
    std::string epi_surface = mesh_file_name + ".epi";
    std::string lv_surface = mesh_file_name + ".lv";
    std::string rv_surface = mesh_file_name + ".rv";


    //create the HeartGeometryInformation object
    //HeartGeometryInformation<3u> info(mesh, epi_surface, lv_surface, rv_surface, true);
    HeartGeometryInformation<3u> info(*(this->GetMesh()), epi_surface, lv_surface, rv_surface, true);

    //We need the fractions of epi and endo layer supplied by the user
    double epi_fraction = HeartConfig::Instance()->GetEpiLayerFraction();
    double endo_fraction = HeartConfig::Instance()->GetEndoLayerFraction();

    //given the fraction of each layer, compute the distance map and fill in the vector
    info.DetermineLayerForEachNode(epi_fraction,endo_fraction);
    //get the big heterogeneity vector
    std::vector<unsigned> heterogeneity_node_list;
    for (unsigned index=0; index<this->GetMesh()->GetNumNodes(); index++)
    {
        heterogeneity_node_list.push_back(info.rGetLayerForEachNode()[index]);
    }

    std::vector<Node<3u>*> epi_nodes;
    std::vector<Node<3u>*> mid_nodes;
    std::vector<Node<3u>*> endo_nodes;

    //create the list of (pointer to object) nodes in each layer from the heterogeneities vector that was just filled in
    for (unsigned node_index = 0; node_index < this->GetMesh()->GetNumNodes(); node_index++)
    {
        if (this->GetMesh()->GetDistributedVectorFactory()->IsGlobalIndexLocal(node_index) )
        {
            switch (heterogeneity_node_list[node_index])
            {
                //epi
                case 2u:
                {
                    epi_nodes.push_back(this->GetMesh()->GetNode(node_index));
                    break;
                }
                //mid
                case 1u:
                {
                    mid_nodes.push_back(this->GetMesh()->GetNode(node_index));
                    break;
                }
                //endo
                case 0u:
                {
                    endo_nodes.push_back(this->GetMesh()->GetNode(node_index));
                    break;
                }
                default:
                NEVER_REACHED;
            }
        }
    }
    //assert((endo_nodes.size()+epi_nodes.size()+mid_nodes.size())==this->GetMesh()->GetNumNodes());

    // now the 3 list of pointer to nodes need to be pushed into the mCellHeterogeneityAreas vector,
    // IN THE ORDER PRESCRIBED BY THE USER IN THE XML FILE!
    // This is because the corresponding scale factors are already read in that order.

    //these three unsigned tell us in which order the user supplied each layer in the XML file
    unsigned user_supplied_epi_index = HeartConfig::Instance()->GetEpiLayerIndex();
    unsigned user_supplied_mid_index = HeartConfig::Instance()->GetMidLayerIndex();
    unsigned user_supplied_endo_index = HeartConfig::Instance()->GetEndoLayerIndex();

    //these three should have been set to 0, 1 and 2 by HeartConfig::GetCellHeterogeneities
    assert(user_supplied_epi_index<3);
    assert(user_supplied_mid_index<3);
    assert(user_supplied_endo_index<3);

    //pute them in a vector
    std::vector<unsigned> user_supplied_indices;
    user_supplied_indices.push_back(user_supplied_epi_index);
    user_supplied_indices.push_back(user_supplied_mid_index);
    user_supplied_indices.push_back(user_supplied_endo_index);

    //figure out who goes first

    //loop three times
    for (unsigned layer_index=0; layer_index<3; layer_index++)
    {
        unsigned counter = 0;
        //find the corresponding index
        for (unsigned supplied_index = 0; supplied_index<user_supplied_indices.size(); supplied_index++)
        {
            if (user_supplied_indices[supplied_index] == layer_index)
            {
                break;
            }
            counter++;
        }

        //create the node lists based on the calculations above
        if (counter==0)
        {
            mCellHeterogeneityAreas.push_back(boost::shared_ptr<AbstractChasteRegion<3u> >(new ChasteNodesList<3u>(epi_nodes)) );
        }
        if (counter==1)
        {
            mCellHeterogeneityAreas.push_back(boost::shared_ptr<AbstractChasteRegion<3u> >(new ChasteNodesList<3u>(mid_nodes)) );
        }
        if (counter==2)
        {
            mCellHeterogeneityAreas.push_back(boost::shared_ptr<AbstractChasteRegion<3u> >(new ChasteNodesList<3u>(endo_nodes)) );
        }
        assert(counter<3);
    }
    assert(mCellHeterogeneityAreas.size()==3);
}

// Explicit instantiation
template class HeartConfigRelatedCellFactory<1u>;
template class HeartConfigRelatedCellFactory<2u>;
template class HeartConfigRelatedCellFactory<3u>;