CaBasedCellPopulation.hpp

/*

Copyright (c) 2005-2016, 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 CABASEDCELLPOPULATION_HPP_
#define CABASEDCELLPOPULATION_HPP_

#include "AbstractOnLatticeCellPopulation.hpp"
#include "PottsMesh.hpp"
#include "VertexMesh.hpp"
#include "AbstractCaUpdateRule.hpp"
#include "AbstractCaSwitchingUpdateRule.hpp"
#include "AbstractCaBasedDivisionRule.hpp"


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

template<unsigned DIM> class AbstractCaBasedDivisionRule; // Circular definition thing.

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

template<unsigned DIM>
class CaBasedCellPopulation : public AbstractOnLatticeCellPopulation<DIM>
{
    friend class TestCaBasedCellPopulation;

private:

    unsigned mLatticeCarryingCapacity;

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

    std::vector<boost::shared_ptr<AbstractCaSwitchingUpdateRule<DIM> > > mSwitchingUpdateRuleCollection;

    std::vector<unsigned> mAvailableSpaces;

    boost::shared_ptr<AbstractCaBasedDivisionRule<DIM> > mpCaBasedDivisionRule;

    void SetEmptySites(const std::set<unsigned>& rEmptySiteIndices);

    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);
        archive & mLatticeCarryingCapacity;
        archive & mUpdateRuleCollection;
        archive & mAvailableSpaces;
        archive & mpCaBasedDivisionRule;
#undef COVERAGE_IGNORE
    }

    void Validate();

    virtual void WriteVtkResultsToFile(const std::string& rDirectory);

public:

    CaBasedCellPopulation(PottsMesh<DIM>& rMesh,
                                  std::vector<CellPtr>& rCells,
                                  const std::vector<unsigned> locationIndices,
                                  unsigned latticeCarryingCapacity=1u,
                                  bool deleteMesh=false,
                                  bool validate=false);

    CaBasedCellPopulation(PottsMesh<DIM>& rMesh);

    virtual ~CaBasedCellPopulation();

    std::vector<unsigned>& rGetAvailableSpaces();

    virtual bool IsSiteAvailable(unsigned index, CellPtr pCell);

    PottsMesh<DIM>& rGetMesh();

    const PottsMesh<DIM>& rGetMesh() const;

    Node<DIM>* GetNode(unsigned index);

    unsigned GetNumNodes();

    std::set<unsigned> GetNeighbouringLocationIndices(CellPtr pCell);

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

    void AddCellUsingLocationIndex(unsigned index, CellPtr pCell);

    void RemoveCellUsingLocationIndex(unsigned index, CellPtr pCell);

     Node<DIM>* GetNodeCorrespondingToCell(CellPtr pCell);

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

     double virtual EvaluateDivisionPropensity(unsigned currentNodeIndex,
                                        unsigned targetNodeIndex,
                                        CellPtr pCell);
    unsigned RemoveDeadCells();

    virtual void OpenWritersFiles(OutputFileHandler& rOutputFileHandler);

    void UpdateCellLocations(double dt);

    bool IsCellAssociatedWithADeletedLocation(CellPtr pCell);

    void Update(bool hasHadBirthsOrDeaths=true);

    virtual void AcceptPopulationWriter(boost::shared_ptr<AbstractCellPopulationWriter<DIM, DIM> > pPopulationWriter);

    virtual void AcceptPopulationCountWriter(boost::shared_ptr<AbstractCellPopulationCountWriter<DIM, DIM> > pPopulationCountWriter);

    virtual void AcceptCellWriter(boost::shared_ptr<AbstractCellWriter<DIM, DIM> > pCellWriter, CellPtr pCell);

    double GetVolumeOfCell(CellPtr pCell);

    double GetWidth(const unsigned& rDimension);

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

    void RemoveAllUpdateRules();

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

    void AddSwitchingUpdateRule(boost::shared_ptr<AbstractCaSwitchingUpdateRule<DIM> > pUpdateRule);

    void RemoveAllSwitchingUpdateRules();

    const std::vector<boost::shared_ptr<AbstractCaSwitchingUpdateRule<DIM> > >& rGetSwitchingUpdateRuleCollection() const;

    void OutputCellPopulationParameters(out_stream& rParamsFile);

    bool IsRoomToDivide(CellPtr pCell);


    boost::shared_ptr<AbstractCaBasedDivisionRule<DIM> > GetCaBasedDivisionRule();

    void SetCaBasedDivisionRule(boost::shared_ptr<AbstractCaBasedDivisionRule<DIM> > pCaBasedDivisionRule);


};

#include "SerializationExportWrapper.hpp"
EXPORT_TEMPLATE_CLASS_SAME_DIMS(CaBasedCellPopulation)

// 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 CaBasedCellPopulation<DIM> * t, const 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, CaBasedCellPopulation<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)CaBasedCellPopulation<DIM>(*p_mesh);
}
}
} // namespace ...
#undef COVERAGE_IGNORE

#endif /*CABASEDCELLPOPULATION_HPP_*/