CaBasedCellPopulation.hpp

/*

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*/

#ifndef CABASEDCELLPOPULATION_HPP_
#define CABASEDCELLPOPULATION_HPP_

#include "AbstractOnLatticeCellPopulation.hpp"
#include "PottsMesh.hpp"
#include "VertexMesh.hpp"
#include "AbstractUpdateRule.hpp"
#include "AbstractCaBasedDivisionRule.hpp"

#include "ChasteSerialization.hpp"
#include <boost/serialization/base_object.hpp>
#include <boost/serialization/vector.hpp>

template<unsigned DIM> class AbstractCaBasedDivisionRule; // Circular definition thing.

template<unsigned DIM>
class CaBasedCellPopulation : public AbstractOnLatticeCellPopulation<DIM>
{
    friend class TestCaBasedCellPopulation;

private:

    unsigned mLatticeCarryingCapacity;

    std::vector<boost::shared_ptr<AbstractUpdateRule<DIM> > > mSwitchingUpdateRuleCollection;

    std::vector<unsigned> mAvailableSpaces;

    boost::shared_ptr<AbstractCaBasedDivisionRule<DIM> > mpCaBasedDivisionRule;

    void SetEmptySites(const std::set<unsigned>& rEmptySiteIndices);

    friend class boost::serialization::access;
    template<class Archive>
    void serialize(Archive & archive, const unsigned int version)
    {
        archive & boost::serialization::base_object<AbstractOnLatticeCellPopulation<DIM> >(*this);
        archive & mSwitchingUpdateRuleCollection;
        archive & mLatticeCarryingCapacity;
        archive & mAvailableSpaces;
        archive & mpCaBasedDivisionRule;
    }

    void Validate();

    virtual void WriteVtkResultsToFile(const std::string& rDirectory);

public:

    CaBasedCellPopulation(PottsMesh<DIM>& rMesh,
                                  std::vector<CellPtr>& rCells,
                                  const std::vector<unsigned> locationIndices,
                                  unsigned latticeCarryingCapacity=1u,
                                  bool deleteMesh=false,
                                  bool validate=false);

    CaBasedCellPopulation(PottsMesh<DIM>& rMesh);

    virtual ~CaBasedCellPopulation();

    std::vector<unsigned>& rGetAvailableSpaces();

    virtual bool IsSiteAvailable(unsigned index, CellPtr pCell);

    PottsMesh<DIM>& rGetMesh();

    const PottsMesh<DIM>& rGetMesh() const;

    virtual TetrahedralMesh<DIM, DIM>* GetTetrahedralMeshForPdeModifier();

    Node<DIM>* GetNode(unsigned index);

    unsigned GetNumNodes();

    std::set<unsigned> GetNeighbouringLocationIndices(CellPtr pCell);

    c_vector<double, DIM> GetLocationOfCellCentre(CellPtr pCell);

    void AddCellUsingLocationIndex(unsigned index, CellPtr pCell);

    void RemoveCellUsingLocationIndex(unsigned index, CellPtr pCell);

     Node<DIM>* GetNodeCorrespondingToCell(CellPtr pCell);

    CellPtr AddCell(CellPtr pNewCell, CellPtr pParentCell=CellPtr());

     double virtual EvaluateDivisionPropensity(unsigned currentNodeIndex,
                                               unsigned targetNodeIndex,
                                               CellPtr pCell);
    unsigned RemoveDeadCells();

    virtual void OpenWritersFiles(OutputFileHandler& rOutputFileHandler);

    void UpdateCellLocations(double dt);

    bool IsCellAssociatedWithADeletedLocation(CellPtr pCell);

    void Update(bool hasHadBirthsOrDeaths=true);

    virtual void AcceptPopulationWriter(boost::shared_ptr<AbstractCellPopulationWriter<DIM, DIM> > pPopulationWriter);

    virtual void AcceptPopulationCountWriter(boost::shared_ptr<AbstractCellPopulationCountWriter<DIM, DIM> > pPopulationCountWriter);

    virtual void AcceptCellWriter(boost::shared_ptr<AbstractCellWriter<DIM, DIM> > pCellWriter, CellPtr pCell);

    double GetVolumeOfCell(CellPtr pCell);

    double GetWidth(const unsigned& rDimension);

    void RemoveAllUpdateRules();

    void OutputCellPopulationParameters(out_stream& rParamsFile);

    bool IsRoomToDivide(CellPtr pCell);

    boost::shared_ptr<AbstractCaBasedDivisionRule<DIM> > GetCaBasedDivisionRule();

    void SetCaBasedDivisionRule(boost::shared_ptr<AbstractCaBasedDivisionRule<DIM> > pCaBasedDivisionRule);

    virtual void AddUpdateRule(boost::shared_ptr<AbstractUpdateRule<DIM> > pUpdateRule);

    virtual const std::vector<boost::shared_ptr<AbstractUpdateRule<DIM> > > GetUpdateRuleCollection() const;

    virtual double GetCellDataItemAtPdeNode(unsigned pdeNodeIndex,
                                            std::string& rVariableName,
                                            bool dirichletBoundaryConditionApplies=false,
                                            double dirichletBoundaryValue=0.0);

    virtual bool IsPdeNodeAssociatedWithNonApoptoticCell(unsigned pdeNodeIndex);
};

#include "SerializationExportWrapper.hpp"
EXPORT_TEMPLATE_CLASS_SAME_DIMS(CaBasedCellPopulation)


namespace boost
{
namespace serialization
{
template<class Archive, unsigned DIM>
inline void save_construct_data(
    Archive & ar, const CaBasedCellPopulation<DIM> * t, const unsigned int file_version)
{
    // Save data required to construct instance
    const PottsMesh<DIM>* p_mesh = &(t->rGetMesh());
    ar & p_mesh;
}

template<class Archive, unsigned DIM>
inline void load_construct_data(
    Archive & ar, CaBasedCellPopulation<DIM> * t, const unsigned int file_version)
{
    // Retrieve data from archive required to construct new instance
    PottsMesh<DIM>* p_mesh;
    ar >> p_mesh;

    // Invoke inplace constructor to initialise instance
    ::new(t)CaBasedCellPopulation<DIM>(*p_mesh);
}
}
} // namespace ...


#endif /*CABASEDCELLPOPULATION_HPP_*/