MeshBasedCellPopulation.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 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 DIM>
class MeshBasedCellPopulation : public AbstractCentreBasedCellPopulation<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<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 & mMarkedSprings;
        archive & mUseAreaBasedDampingConstant;
        archive & mAreaBasedDampingConstantParameter;
        archive & mOutputVoronoiData;
        archive & mOutputCellPopulationVolumes;
        archive & mWriteVtkAsPoints;

        this->Validate();
    }

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

    MutableMesh<DIM, DIM>& mrMesh;

    VertexMesh<DIM, DIM>* mpVoronoiTessellation;

    bool mDeleteMesh;

    std::set<std::pair<CellPtr,CellPtr> > mMarkedSprings;

    out_stream mpVizElementsFile;

    out_stream mpVoronoiFile;

    out_stream mpCellPopulationVolumesFile;

    bool mUseAreaBasedDampingConstant;

    double mAreaBasedDampingConstantParameter;

    bool mOutputVoronoiData;

    bool mOutputCellPopulationVolumes;

    bool mWriteVtkAsPoints;

#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<DIM, DIM>& rMesh,
                    std::vector<CellPtr>& rCells,
                    const std::vector<unsigned> locationIndices=std::vector<unsigned>(),
                    bool deleteMesh=false,
                    bool validate=true);

    MeshBasedCellPopulation(MutableMesh<DIM, DIM>& rMesh);

    ~MeshBasedCellPopulation();

    MutableMesh<DIM, DIM>& rGetMesh();

    const MutableMesh<DIM, DIM>& rGetMesh() const;

    bool UseAreaBasedDampingConstant();

    void SetOutputVoronoiData(bool outputVoronoiData);

    unsigned AddNode(Node<DIM>* pNewNode);

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

    double GetDampingConstant(unsigned nodeIndex);

    void SetAreaBasedDampingConstant(bool useAreaBasedDampingConstant);

    virtual unsigned RemoveDeadCells();

    virtual CellPtr AddCell(CellPtr pNewCell, const c_vector<double,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<DIM>* GetNode(unsigned index);

    unsigned GetNumNodes();

    virtual void WriteVtkResultsToFile();

    void WriteVoronoiResultsToFile();

    void WriteCellPopulationVolumeResultsToFile();

    void WriteCellVolumeResultsToFile();

    void CreateVoronoiTessellation();

    VertexMesh<DIM, 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<DIM>* GetNodeA();

        Node<DIM>* GetNodeB();

        CellPtr GetCellA();

        CellPtr GetCellB();

        bool operator!=(const MeshBasedCellPopulation<DIM>::SpringIterator& rOther);

        SpringIterator& operator++();

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

    private:

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

        MeshBasedCellPopulation<DIM>& mrCellPopulation;

        typename MutableMesh<DIM, DIM>::EdgeIterator mEdgeIter;
    };

    SpringIterator SpringsBegin();

    SpringIterator SpringsEnd();

    void CheckCellPointers();

    std::pair<CellPtr,CellPtr> CreateCellPair(CellPtr pCell1, CellPtr pCell2);

    bool IsMarkedSpring(const std::pair<CellPtr,CellPtr>& rCellPair);

    void MarkSpring(std::pair<CellPtr,CellPtr>& rCellPair);

    void UnmarkSpring(std::pair<CellPtr,CellPtr>& rCellPair);

    double GetAreaBasedDampingConstantParameter();

    void SetAreaBasedDampingConstantParameter(double areaBasedDampingConstantParameter);

    bool GetOutputVoronoiData();

    bool GetOutputCellPopulationVolumes();

    void SetOutputCellPopulationVolumes(bool outputCellPopulationVolumes);

    void OutputCellPopulationParameters(out_stream& rParamsFile);

    void SetWriteVtkAsPoints(bool writeVtkAsPoints);

    bool GetWriteVtkAsPoints();

    std::set<unsigned> GetNeighbouringNodeIndices(unsigned index);
};
#undef COVERAGE_IGNORE // Avoid prototypes being treated as code by gcov

#include "SerializationExportWrapper.hpp"
EXPORT_TEMPLATE_CLASS_SAME_DIMS(MeshBasedCellPopulation)

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

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

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

#endif /*MESHBASEDCELLPOPULATION_HPP_*/