NodeBasedCellPopulation.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 NODEBASEDCELLPOPULATION_HPP_
#define NODEBASEDCELLPOPULATION_HPP_

#include "AbstractCentreBasedCellPopulation.hpp"
#include "NodesOnlyMesh.hpp"
#include "BoxCollection.hpp"

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

template<unsigned DIM>
class NodeBasedCellPopulation : public AbstractCentreBasedCellPopulation<DIM>
{
    friend class TestNodeBasedCellPopulation;
    friend class TestBoxCollection;

private:

    NodesOnlyMesh<DIM>* mpNodesOnlyMesh;

    c_vector<double, DIM> mMinSpatialPositions;

    c_vector<double, DIM> mMaxSpatialPositions;

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

    std::map<unsigned, std::set<unsigned> > mNodeNeighbours;

    bool mDeleteMesh;

    double mMechanicsCutOffLength;

    bool mUseVariableRadii;

    friend class boost::serialization::access;
    template<class Archive>
    void serialize(Archive & archive, const unsigned int version)
    {
        archive & boost::serialization::base_object<AbstractCentreBasedCellPopulation<DIM> >(*this);
        archive & mMechanicsCutOffLength;
        archive & mUseVariableRadii;

        this->Validate();
    }

    unsigned AddNode(Node<DIM>* pNewNode);


protected:

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

    virtual void UpdateParticlesAfterReMesh(NodeMap& rMap);

    virtual void Validate();

private:

    void SplitUpIntoBoxes(double cutOffLength, c_vector<double, 2*DIM> domainSize);

    void FindMaxAndMin();

    void WriteCellVolumeResultsToFile();

    void WriteVtkResultsToFile();

public:

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

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

    NodeBasedCellPopulation(NodesOnlyMesh<DIM>& rMesh);

    virtual ~NodeBasedCellPopulation();

    NodesOnlyMesh<DIM>& rGetMesh();

    const NodesOnlyMesh<DIM>& rGetMesh() const;

    unsigned GetNumNodes();

    Node<DIM>* GetNode(unsigned index);

    unsigned RemoveDeadCells();

    void Clear();

    void Update(bool hasHadBirthsOrDeaths=true);

    BoxCollection<DIM>* GetBoxCollection();

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

    void OutputCellPopulationParameters(out_stream& rParamsFile);

    double GetMechanicsCutOffLength();

    void SetMechanicsCutOffLength(double mechanicsCutOffLength);

    bool GetUseVariableRadii();

    void SetUseVariableRadii(bool useVariableRadii=true);

    double GetWidth(const unsigned& rDimension);

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

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

    double GetVolumeOfCell(CellPtr pCell);
};

#include "SerializationExportWrapper.hpp"
EXPORT_TEMPLATE_CLASS_SAME_DIMS(NodeBasedCellPopulation)

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

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

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

#endif /*NODEBASEDCELLPOPULATION_HPP_*/