HeartConfigRelatedCellFactory.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 "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>
DynamicCellModelLoader* 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>
AbstractCardiacCell* 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;
        }
    }
    
    AbstractCardiacCell* 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 Boost<1.37.");
        }
#endif // CHASTE_CAN_CHECKPOINT_DLLS
        // Load model from shared library
        DynamicCellModelLoader* p_loader = LoadDynamicModel(ionic_model, false);
        AbstractCardiacCellInterface* p_loaded_cell = p_loader->CreateCell(this->mpSolver, intracellularStimulus);
        p_cell = dynamic_cast<AbstractCardiacCell*>(p_loaded_cell);
        if (!p_cell)
        {
            delete p_loaded_cell;
            EXCEPTION("CVODE cannot be used as a cell model solver in tissue simulations: do not use the --cvode flag.");
        }
    }
    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::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::tenTusscher2006):
            {
                p_cell = new CellTenTusscher2006EpiFromCellML(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(AbstractCardiacCell* 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& e)
            {
                // 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 (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
            {
                std::stringstream msg;
                msg << "Cannot apply drug to cell at node " << nodeIndex << " as it has no parameter named '" << param_name << "'.";
                WARNING(msg.str());
            }
        }
    }
        
    // 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)
            {
                unsigned param_index = pCell->GetParameterIndex(param_it->first);
                pCell->SetParameter(param_index, param_it->second);
            }
        }
    }
}


template<unsigned SPACE_DIM>
void HeartConfigRelatedCellFactory<SPACE_DIM>::SetCellIntracellularStimulus(AbstractCardiacCell* 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>
AbstractCardiacCell* HeartConfigRelatedCellFactory<SPACE_DIM>::CreateCardiacCellForTissueNode(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]);
        }
    }

    return CreateCellWithIntracellularStimulus(node_specific_stimulus, nodeIndex);
}

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

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>;

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