AbstractCardiacCell.hpp

/*

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This file is part of Chaste.

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 * Redistributions of source code must retain the above copyright notice,
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 * Redistributions in binary form must reproduce the above copyright notice,
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   contributors may be used to endorse or promote products derived from this
   software without specific prior written permission.

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AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
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ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE
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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);

    void SetParameter(unsigned parameterIndex, 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_*/