HeartConfigRelatedCellFactory.hpp

/*

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*/

#ifndef HEARTCONFIGRELATEDCELLFACTORY_HPP_
#define HEARTCONFIGRELATEDCELLFACTORY_HPP_

#include <vector>
#include <map>
#include <boost/shared_ptr.hpp>

#include "AbstractCardiacCellFactory.hpp"
#include "HeartConfig.hpp"

#include "AbstractStimulusFunction.hpp"
#include "MultiStimulus.hpp" // Included here for archiving - see below.
#include "SimpleStimulus.hpp"

#include "ChasteCuboid.hpp"
#include "AbstractChasteRegion.hpp"

#include "DynamicCellModelLoader.hpp"

/*
 * Even though these classes are only used in the .cpp file, they need to be
 * included here for serialization to work - the archiving code needs to see
 * the CHASTE_CLASS_EXPORT incantations.
 */
#include "DiFrancescoNoble1985.hpp"
#include "FaberRudy2000.hpp"
#include "FaberRudy2000Opt.hpp"
#include "FoxModel2002.hpp"
#include "FoxModel2002BackwardEuler.hpp"
#include "HodgkinHuxley1952.hpp"
#include "LuoRudy1991.hpp"
#include "LuoRudy1991BackwardEuler.hpp"
#include "Mahajan2008.hpp"
#include "Mahajan2008BackwardEuler.hpp"
#include "Maleckar2008.hpp"
#include "TenTusscher2006Epi.hpp"
#include "TenTusscher2006EpiBackwardEuler.hpp"

/*
 * The following cell models aren't used by this class, but do exist in Chaste.
 * So users of the source code could see issues with archiving if they aren't included.
 */
#include "FoxModel2002Opt.hpp"
#include "LuoRudy1991Opt.hpp"
#include "Mahajan2008Opt.hpp"
#include "Maleckar2008Opt.hpp"
#include "NobleVargheseKohlNoble1998a.hpp"
#include "NobleVargheseKohlNoble1998aOpt.hpp"
#include "NobleVargheseKohlNoble1998aBackwardEuler.hpp"
#include "Shannon2004.hpp"
#include "TenTusscher2006EpiOpt.hpp"

template<unsigned SPACE_DIM>
class HeartConfigRelatedCellFactory : public AbstractCardiacCellFactory<SPACE_DIM>
{
private:
    cp::ionic_model_selection_type mDefaultIonicModel;
    std::vector<boost::shared_ptr<AbstractChasteRegion<SPACE_DIM> > > mIonicModelRegions;
    std::vector<cp::ionic_model_selection_type> mIonicModelsDefined;

    std::vector<boost::shared_ptr<AbstractChasteRegion<SPACE_DIM> > > mStimulatedAreas;
    std::vector<boost::shared_ptr<AbstractStimulusFunction> > mStimuliApplied;

    std::vector<boost::shared_ptr<AbstractChasteRegion<SPACE_DIM> > > mCellHeterogeneityAreas;
    std::vector<double> mScaleFactorGks;
    std::vector<double> mScaleFactorIto;
    std::vector<double> mScaleFactorGkr;

    std::vector<std::map<std::string, double> > mParameterSettings;

    void PreconvertCellmlFiles();

    DynamicCellModelLoaderPtr LoadDynamicModel(const cp::ionic_model_selection_type& rModel,
                                               bool isCollective);

public:
    HeartConfigRelatedCellFactory();

    ~HeartConfigRelatedCellFactory();

    AbstractCardiacCellInterface* CreateCellWithIntracellularStimulus(
            boost::shared_ptr<AbstractStimulusFunction> intracellularStimulus,
            unsigned nodeIndex);

    AbstractCardiacCellInterface* CreateCardiacCellForTissueNode(Node<SPACE_DIM>* pNode);

    void FillInCellularTransmuralAreas();

    void SetCellParameters(AbstractCardiacCellInterface* pCell, unsigned nodeIndex);

    void SetCellIntracellularStimulus(AbstractCardiacCellInterface* pCell, unsigned nodeIndex);
};


#endif /*HEARTCONFIGRELATEDCELLFACTORY_HPP_*/