HeartConfigRelatedCellFactory.hpp

/*

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/>.

*/

#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 "FoxModel2002BackwardEuler.hpp"
#include "HodgkinHuxley1952.hpp"
#include "LuoRudy1991.hpp"
#include "LuoRudy1991BackwardEuler.hpp"
#include "Mahajan2008.hpp"
#include "Maleckar2008.hpp"
#include "TenTusscher2006Epi.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 "FoxModel2002.hpp"
#include "FoxModel2002Opt.hpp"
#include "LuoRudy1991Opt.hpp"
#include "Mahajan2008Opt.hpp"
#include "Mahajan2008BackwardEuler.hpp"
#include "Maleckar2008Opt.hpp"
#include "NobleVargheseKohlNoble1998a.hpp"
#include "NobleVargheseKohlNoble1998aOpt.hpp"
#include "NobleVargheseKohlNoble1998aBackwardEuler.hpp"
#include "Shannon2004.hpp"
#include "TenTusscher2006EpiOpt.hpp"
#include "TenTusscher2006EpiBackwardEuler.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();

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

public:
    HeartConfigRelatedCellFactory();

    ~HeartConfigRelatedCellFactory();

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

    AbstractCardiacCell* CreateCardiacCellForTissueNode(unsigned nodeIndex);

    void FillInCellularTransmuralAreas();

    void SetCellParameters(AbstractCardiacCell* pCell, unsigned nodeIndex);

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


#endif /*HEARTCONFIGRELATEDCELLFACTORY_HPP_*/