AbstractCardiacCell.hpp

/*
 
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*/
 
#ifndef ABSTRACTCARDIACCELL_HPP_
#define ABSTRACTCARDIACCELL_HPP_
 
#include "ChasteSerialization.hpp"
#include "ChasteSerializationVersion.hpp"
#include "ClassIsAbstract.hpp"
#include <boost/serialization/base_object.hpp>
#include <boost/shared_ptr.hpp>
#include <boost/serialization/shared_ptr.hpp>
 
 
// This is only needed to prevent compilation errors on PETSc 2.2/Boost 1.33.1 combo
#include "UblasVectorInclude.hpp"
 
#include "AbstractCardiacCellInterface.hpp"
#include "AbstractOdeSystem.hpp"
#include "AbstractIvpOdeSolver.hpp"
#include "AbstractStimulusFunction.hpp"
 
#include <vector>
 
typedef enum _CellModelState
{
    STATE_UNSET = 0,
    FAST_VARS_ONLY,
    ALL_VARS
} CellModelState;
 
class AbstractCardiacCell : public AbstractCardiacCellInterface, public AbstractOdeSystem
{
private:
    friend class boost::serialization::access;
    template<class Archive>
    void serialize(Archive & archive, const unsigned int version)
    {
        // This calls serialize on the base class.
        archive & boost::serialization::base_object<AbstractOdeSystem>(*this);
 
        if (version > 0)
        {
            archive & boost::serialization::base_object<AbstractCardiacCellInterface>(*this);
        }
        archive & mDt;
 
        // For version 2 and above these move into AbstractCardiacCellInterface
        // (AbstractCardiacCellInterface serialization moved to 1 at the same time as this moved to 2).
        if (version <= 1)
        {
            archive & this->mSetVoltageDerivativeToZero;
            if (version > 0)
            {
                // Note that when loading a version 0 archive, this will be initialised to
                // false by our constructor.  So we should get a consistent (wrong) answer
                // with previous versions of Chaste when in tissue.
                archive & this->mIsUsedInTissue;
                archive & this->mHasDefaultStimulusFromCellML;
            }
        }
 
        if (version == 0)
        {
            CheckForArchiveFix();
        }
 
        // Paranoia check
        assert(this->mParameters.size() == this->rGetParameterNames().size());
    }
 
    void CheckForArchiveFix();
 
protected:
    double mDt;
 
public:
    AbstractCardiacCell(boost::shared_ptr<AbstractIvpOdeSolver> pOdeSolver,
                        unsigned numberOfStateVariables,
                        unsigned voltageIndex,
                        boost::shared_ptr<AbstractStimulusFunction> pIntracellularStimulus);
 
    virtual ~AbstractCardiacCell();
 
    void Init();
 
    void SetTimestep(double dt);
 
    virtual void SolveAndUpdateState(double tStart, double tEnd);
 
    virtual OdeSolution Compute(double tStart, double tEnd, double tSamp=0.0);
 
    virtual void ComputeExceptVoltage(double tStart, double tEnd);
 
    void SetVoltage(double voltage);
 
    double GetVoltage();
 
 
    unsigned GetNumberOfStateVariables() const;
 
    unsigned GetNumberOfParameters() const;
 
    std::vector<double> GetStdVecStateVariables();
 
    const std::vector<std::string>& rGetStateVariableNames() const;
 
 
    void SetStateVariables(const std::vector<double>& rVariables);
 
    void SetStateVariable(unsigned index, double newValue);
 
    void SetStateVariable(const std::string& rName, double newValue);
 
    double GetAnyVariable(const std::string& rName, double time=0.0);
 
    double GetParameter(const std::string& rParameterName);
 
    double GetParameter(unsigned parameterIndex);
 
    void SetParameter(const std::string& rParameterName, double value);
 
    //  METHODS NEEDED BY FAST CARDIAC CELLS
 
    virtual void SetState(CellModelState state);
 
    virtual void SetSlowValues(const std::vector<double> &rSlowValues);
 
    virtual void GetSlowValues(std::vector<double>& rSlowValues);
 
    virtual bool IsFastOnly();
 
    virtual void AdjustOutOfRangeSlowValues(std::vector<double>& rSlowValues);
 
    virtual unsigned GetNumSlowValues();
};
 
CLASS_IS_ABSTRACT(AbstractCardiacCell)
BOOST_CLASS_VERSION(AbstractCardiacCell, 2)
 
#endif /*ABSTRACTCARDIACCELL_HPP_*/