AbstractCardiacCellInterface.hpp

/*

Copyright (c) 2005-2012, University of Oxford.
All rights reserved.

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.

Redistribution and use in source and binary forms, with or without
modification, are permitted provided that the following conditions are met:
 * Redistributions of source code must retain the above copyright notice,
   this list of conditions and the following disclaimer.
 * Redistributions in binary form must reproduce the above copyright notice,
   this list of conditions and the following disclaimer in the documentation
   and/or other materials provided with the distribution.
 * Neither the name of the University of Oxford nor the names of its
   contributors may be used to endorse or promote products derived from this
   software without specific prior written permission.

THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE
LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE
GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION)
HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT
OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

*/

#ifndef ABSTRACTCARDIACCELLINTERFACE_HPP_
#define ABSTRACTCARDIACCELLINTERFACE_HPP_

#include <boost/shared_ptr.hpp>

#include "ChasteSerialization.hpp"
#include "ChasteSerializationVersion.hpp"
#include "ClassIsAbstract.hpp"

#include "AbstractIvpOdeSolver.hpp"
#include "AbstractStimulusFunction.hpp"
#include "OdeSolution.hpp"
#include "AbstractLookupTableCollection.hpp"

class AbstractCardiacCellInterface
{
public:
    AbstractCardiacCellInterface(boost::shared_ptr<AbstractIvpOdeSolver> pOdeSolver,
                                 unsigned voltageIndex,
                                 boost::shared_ptr<AbstractStimulusFunction> pIntracellularStimulus);

    virtual ~AbstractCardiacCellInterface();

    virtual void SetTimestep(double dt)=0;

    virtual unsigned GetNumberOfStateVariables() const=0;

    virtual unsigned GetNumberOfParameters() const=0;

    virtual std::vector<double> GetStdVecStateVariables()=0;

    virtual const std::vector<std::string>& rGetStateVariableNames() const=0;


    virtual void SetStateVariables(const std::vector<double>& rVariables)=0;

    virtual void SetStateVariable(unsigned index, double newValue)=0;

    virtual void SetStateVariable(const std::string& rName, double newValue)=0;

    virtual double GetAnyVariable(const std::string& rName, double time)=0;

    virtual double GetParameter(const std::string& rParameterName)=0;

    virtual double GetParameter(unsigned parameterIndex)=0;

    virtual void SetParameter(const std::string& rParameterName, double value)=0;

    virtual void SetParameter(unsigned parameterIdx, double value)=0;


    virtual void SolveAndUpdateState(double tStart, double tEnd)=0;

    virtual OdeSolution Compute(double tStart, double tEnd, double tSamp=0.0)=0;

    virtual void ComputeExceptVoltage(double tStart, double tEnd)=0;

    virtual double GetIIonic(const std::vector<double>* pStateVariables=NULL)=0;

    virtual void SetVoltage(double voltage)=0;

    virtual double GetVoltage()=0;

    unsigned GetVoltageIndex();

    void SetStimulusFunction(boost::shared_ptr<AbstractStimulusFunction> pStimulus);

    double GetStimulus(double time);

    void SetIntracellularStimulusFunction(boost::shared_ptr<AbstractStimulusFunction> pStimulus);

    double GetIntracellularStimulus(double time);

    double GetIntracellularAreaStimulus(double time);

    void SetUsedInTissueSimulation(bool tissue=true);

    virtual void UseCellMLDefaultStimulus();

    bool HasCellMLDefaultStimulus();

    virtual AbstractLookupTableCollection* GetLookupTableCollection()
    {
        return NULL;
    }

    boost::shared_ptr<AbstractStimulusFunction> GetStimulusFunction();

    const boost::shared_ptr<AbstractStimulusFunction> GetStimulusFunction() const;

    const boost::shared_ptr<AbstractIvpOdeSolver> GetSolver() const;

    virtual void SetVoltageDerivativeToZero(bool clamp=true);

    void SetFixedVoltage(double voltage);

    virtual void SetStretch(double stretch)
    {
    }

    virtual double GetIntracellularCalciumConcentration();

protected:
    unsigned mVoltageIndex;

    boost::shared_ptr<AbstractIvpOdeSolver> mpOdeSolver;

    boost::shared_ptr<AbstractStimulusFunction> mpIntracellularStimulus;

    bool mSetVoltageDerivativeToZero;

    bool mIsUsedInTissue;

    bool mHasDefaultStimulusFromCellML;

    double mFixedVoltage;

private:
    friend class boost::serialization::access;
    template<class Archive>
    void serialize(Archive & archive, const unsigned int version)
    {
        // For version 0 these were archived by AbstractCardiacCell, now
        // we have AbstractCvodeCells too, so doing it here.
        if (version > 0)
        {
            archive & mSetVoltageDerivativeToZero;
            archive & mIsUsedInTissue;
            archive & mHasDefaultStimulusFromCellML;
            // archive & mFixedVoltage; - this doesn't need archiving as it is reset every PDE time step if used.
        }
        // archive & mVoltageIndex; - always set by constructor - called by concrete class
        // archive & mpOdeSolver; - always set by constructor - called by concrete class
        // archive & mpIntracellularStimulus; - always set by constructor - called by concrete class
    }
};

CLASS_IS_ABSTRACT(AbstractCardiacCellInterface)
BOOST_CLASS_VERSION(AbstractCardiacCellInterface, 1)

#endif /*ABSTRACTCARDIACCELLINTERFACE_HPP_*/