PottsBasedCellPopulation.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 POTTSBASEDCELLPOPULATION_HPP_
#define POTTSBASEDCELLPOPULATION_HPP_

#include "AbstractOnLatticeCellPopulation.hpp"
#include "PottsMesh.hpp"
#include "VertexMesh.hpp"
#include "AbstractPottsUpdateRule.hpp"
#include "MutableMesh.hpp"

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

// Needed here to avoid serialization errors (on Boost<1.37)
#include "WildTypeCellMutationState.hpp"

template<unsigned DIM>
class AbstractPottsUpdateRule; // Circular definition

template<unsigned DIM>
class PottsBasedCellPopulation : public AbstractOnLatticeCellPopulation<DIM>
{
    friend class TestPottsBasedCellPopulation;

private:

    VertexMesh<DIM,DIM>* mpElementTessellation;

    PottsMesh<DIM>* mpPottsMesh;

    MutableMesh<DIM,DIM>* mpMutableMesh;

    out_stream mpVizElementsFile;

    std::vector<boost::shared_ptr<AbstractPottsUpdateRule<DIM> > > mUpdateRuleCollection;

    double mTemperature;

    unsigned mNumSweepsPerTimestep;

    friend class boost::serialization::access;
    template<class Archive>
    void serialize(Archive & archive, const unsigned int version)
    {
#define COVERAGE_IGNORE
        archive & boost::serialization::base_object<AbstractOnLatticeCellPopulation<DIM> >(*this);

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

        archive & mUpdateRuleCollection;
        archive & mTemperature;
        archive & mNumSweepsPerTimestep;

#undef COVERAGE_IGNORE
    }

    void Validate();

    void WriteVtkResultsToFile();

public:

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

    PottsBasedCellPopulation(PottsMesh<DIM>& rMesh);

    virtual ~PottsBasedCellPopulation();

    PottsMesh<DIM>& rGetMesh();

    const PottsMesh<DIM>& rGetMesh() const;

    PottsElement<DIM>* GetElement(unsigned elementIndex);

    unsigned GetNumElements();

    Node<DIM>* GetNode(unsigned index);

    unsigned GetNumNodes();

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

    PottsElement<DIM>* GetElementCorrespondingToCell(CellPtr pCell);

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

    unsigned RemoveDeadCells();

    void UpdateCellLocations(double dt);

    bool IsCellAssociatedWithADeletedLocation(CellPtr pCell);

    void Update(bool hasHadBirthsOrDeaths=true);

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

    void CloseOutputFiles();

    void WriteResultsToFiles();

    void WriteCellVolumeResultsToFile();

    double GetVolumeOfCell(CellPtr pCell);

    virtual void GenerateCellResultsAndWriteToFiles();

    double GetWidth(const unsigned& rDimension);

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

    void RemoveAllUpdateRules();

    const std::vector<boost::shared_ptr<AbstractPottsUpdateRule<DIM> > >& rGetUpdateRuleCollection() const;

    void OutputCellPopulationParameters(out_stream& rParamsFile);

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

    void SetTemperature(double temperature);

    double GetTemperature();

    void SetNumSweepsPerTimestep(unsigned numSweepsPerTimestep);

    unsigned GetNumSweepsPerTimestep();

    void CreateElementTessellation();

    VertexMesh<DIM,DIM>* GetElementTessellation();

    void CreateMutableMesh();

    MutableMesh<DIM,DIM>* GetMutableMesh();
};

#include "SerializationExportWrapper.hpp"
EXPORT_TEMPLATE_CLASS_SAME_DIMS(PottsBasedCellPopulation)

namespace boost
{
namespace serialization
{
template<class Archive, unsigned DIM>
inline void save_construct_data(
    Archive & ar, const PottsBasedCellPopulation<DIM> * t, const BOOST_PFTO 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, PottsBasedCellPopulation<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)PottsBasedCellPopulation<DIM>(*p_mesh);
}
}
} // namespace ...

#endif /*POTTSBASEDCELLPOPULATION_HPP_*/