PottsBasedCellPopulation.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 POTTSBASEDCELLPOPULATION_HPP_
#define POTTSBASEDCELLPOPULATION_HPP_

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

    PottsMesh<DIM>& mrMesh;

    VertexMesh<DIM,DIM>* mpElementTessellation;

    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();

    virtual void GenerateCellResultsAndWriteToFiles();

    double GetWidth(const unsigned& rDimension);

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

    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();
};

#include "SerializationExportWrapper.hpp"
EXPORT_TEMPLATE_CLASS_SAME_DIMS(PottsBasedCellPopulation)

// No archiving yet so untested
#define COVERAGE_IGNORE
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 ...
#undef COVERAGE_IGNORE

#endif /*POTTSBASEDCELLPOPULATION_HPP_*/