MeshBasedCellPopulation.hpp

/*

Copyright (c) 2005-2012, University of Oxford.
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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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*/

#ifndef MESHBASEDCELLPOPULATION_HPP_
#define MESHBASEDCELLPOPULATION_HPP_

#include <map>
#include "AbstractCentreBasedCellPopulation.hpp"
#include "MutableMesh.hpp"
#include "VertexMesh.hpp"
#include "TrianglesMeshReader.hpp"

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


template<unsigned ELEMENT_DIM, unsigned SPACE_DIM=ELEMENT_DIM>
class MeshBasedCellPopulation : public AbstractCentreBasedCellPopulation<ELEMENT_DIM, SPACE_DIM>
{
    friend class TestMeshBasedCellPopulation;
private:
    friend class boost::serialization::access;
    template<class Archive>
    void serialize(Archive & archive, const unsigned int version)
    {
        archive & boost::serialization::base_object<AbstractCentreBasedCellPopulation<ELEMENT_DIM, SPACE_DIM> >(*this);

        /*
         * In its current form the code does not allow the direct serialization
         * of the VertexMesh class, so instead we delete mpVoronoiTessellation.
         */
        delete mpVoronoiTessellation;
        mpVoronoiTessellation = NULL;

        archive & mSpringRestLengths;
        archive & mUseAreaBasedDampingConstant;
        archive & mAreaBasedDampingConstantParameter;
        archive & mOutputVoronoiData;
        archive & mOutputCellPopulationVolumes;
        archive & mWriteVtkAsPoints;
        archive & mHasVariableRestLength;


        this->Validate();
    }

protected:
#define COVERAGE_IGNORE // Avoid prototypes being treated as code by gcov

    VertexMesh<ELEMENT_DIM, SPACE_DIM>* mpVoronoiTessellation;

    MutableMesh<ELEMENT_DIM, SPACE_DIM>* mpMutableMesh;

    bool mDeleteMesh;

    std::map<std::pair<unsigned,unsigned>, double> mSpringRestLengths;

    out_stream mpVizElementsFile;

    out_stream mpVoronoiFile;

    out_stream mpCellPopulationVolumesFile;

    bool mUseAreaBasedDampingConstant;

    double mAreaBasedDampingConstantParameter;

    bool mOutputVoronoiData;

    bool mOutputCellPopulationVolumes;

    bool mWriteVtkAsPoints;

    bool mHasVariableRestLength;

    std::set< std::pair<Node<SPACE_DIM>*, Node<SPACE_DIM>* > > mNodePairs;

#undef COVERAGE_IGNORE // Avoid prototypes being treated as code by gcov

    virtual void UpdateGhostNodesAfterReMesh(NodeMap& rMap);

    virtual void Validate();

public:
#define COVERAGE_IGNORE // Avoid prototypes being treated as code by gcov

    MeshBasedCellPopulation(MutableMesh<ELEMENT_DIM, SPACE_DIM>& rMesh,
                    std::vector<CellPtr>& rCells,
                    const std::vector<unsigned> locationIndices=std::vector<unsigned>(),
                    bool deleteMesh=false,
                    bool validate=true);

    MeshBasedCellPopulation(MutableMesh<ELEMENT_DIM, SPACE_DIM>& rMesh);

    virtual ~MeshBasedCellPopulation();

    MutableMesh<ELEMENT_DIM, SPACE_DIM>& rGetMesh();

    const MutableMesh<ELEMENT_DIM, SPACE_DIM>& rGetMesh() const;

    bool UseAreaBasedDampingConstant();

    void SetOutputVoronoiData(bool outputVoronoiData);

    unsigned AddNode(Node<SPACE_DIM>* pNewNode);

    void SetNode(unsigned nodeIndex, ChastePoint<SPACE_DIM>& rNewLocation);

    double GetDampingConstant(unsigned nodeIndex);

    void SetAreaBasedDampingConstant(bool useAreaBasedDampingConstant);

    virtual unsigned RemoveDeadCells();

    virtual CellPtr AddCell(CellPtr pNewCell, const c_vector<double,SPACE_DIM>& rCellDivisionVector, CellPtr pParentCell);

    void CreateOutputFiles(const std::string& rDirectory, bool cleanOutputDirectory);

    void CloseOutputFiles();

    void WriteResultsToFiles();

    virtual void Update(bool hasHadBirthsOrDeaths=true);

    void TessellateIfNeeded();

    Node<SPACE_DIM>* GetNode(unsigned index);

    unsigned GetNumNodes();

    virtual void WriteVtkResultsToFile();

    void WriteVoronoiResultsToFile();

    void WriteCellPopulationVolumeResultsToFile();

    void WriteCellVolumeResultsToFile();

    double GetVolumeOfCell(CellPtr pCell);

    void CreateVoronoiTessellation();

    VertexMesh<ELEMENT_DIM, SPACE_DIM>* GetVoronoiTessellation();

    double GetVolumeOfVoronoiElement(unsigned index);

    double GetSurfaceAreaOfVoronoiElement(unsigned index);

    double GetVoronoiEdgeLength(unsigned index1, unsigned index2);

    double GetWidth(const unsigned& rDimension);

    class SpringIterator
    {
    public:

        Node<SPACE_DIM>* GetNodeA();

        Node<SPACE_DIM>* GetNodeB();

        CellPtr GetCellA();

        CellPtr GetCellB();

        bool operator!=(const MeshBasedCellPopulation<ELEMENT_DIM, SPACE_DIM>::SpringIterator& rOther);

        SpringIterator& operator++();

        SpringIterator(MeshBasedCellPopulation<ELEMENT_DIM, SPACE_DIM>& rCellPopulation, typename MutableMesh<ELEMENT_DIM, SPACE_DIM>::EdgeIterator edgeIter);

    private:

        std::set<std::set<unsigned> > mSpringsVisited;

        MeshBasedCellPopulation<ELEMENT_DIM, SPACE_DIM>& mrCellPopulation;

        typename MutableMesh<ELEMENT_DIM, SPACE_DIM>::EdgeIterator mEdgeIter;
    };

    SpringIterator SpringsBegin();

    SpringIterator SpringsEnd();

    void CheckCellPointers();

    double GetAreaBasedDampingConstantParameter();

    void SetAreaBasedDampingConstantParameter(double areaBasedDampingConstantParameter);

    bool GetOutputVoronoiData();

    bool GetOutputCellPopulationVolumes();

    void SetOutputCellPopulationVolumes(bool outputCellPopulationVolumes);

    std::set< std::pair<Node<SPACE_DIM>*, Node<SPACE_DIM>* > >& rGetNodePairs();

    void OutputCellPopulationParameters(out_stream& rParamsFile);

    void SetWriteVtkAsPoints(bool writeVtkAsPoints);

    bool GetWriteVtkAsPoints();

    std::set<unsigned> GetNeighbouringNodeIndices(unsigned index);

    void CalculateRestLengths();

    double GetRestLength(unsigned indexA, unsigned indexB);
};
#undef COVERAGE_IGNORE // Avoid prototypes being treated as code by gcov

#include "SerializationExportWrapper.hpp"
EXPORT_TEMPLATE_CLASS_ALL_DIMS(MeshBasedCellPopulation)

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

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

    // Invoke inplace constructor to initialise instance
    ::new(t)MeshBasedCellPopulation<ELEMENT_DIM, SPACE_DIM>(*p_mesh);
}
}
} // namespace ...

#endif /*MESHBASEDCELLPOPULATION_HPP_*/