CaBasedCellPopulation.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 CABASEDCELLPOPULATION_HPP_
#define CABASEDCELLPOPULATION_HPP_

#include <vector>
#include <set>
#include <string>

#include "UblasVectorInclude.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"

#include "AbstractOnLatticeCellPopulation.hpp"
#include "TetrahedralMesh.hpp"
#include "AbstractCaUpdateRule.hpp"

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

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

private:

    TetrahedralMesh<DIM, DIM>& mrMesh;

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

    std::vector<bool> mIsEmptySite;

    bool mOnlyUseNearestNeighboursForDivision;

    bool mUseVonNeumannNeighbourhoods;

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

    friend class boost::serialization::access;
    template<class Archive>
    void serialize(Archive & archive, const unsigned int version)
    {
        archive & boost::serialization::base_object<AbstractOnLatticeCellPopulation<DIM> >(*this);
        archive & mUpdateRuleCollection;
        archive & mIsEmptySite;
        archive & mOnlyUseNearestNeighboursForDivision;
        archive & mUseVonNeumannNeighbourhoods;
    }

    void Validate();

    void WriteVtkResultsToFile();

public:

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

    CaBasedCellPopulation(TetrahedralMesh<DIM, DIM>& rMesh);

    ~CaBasedCellPopulation();

    TetrahedralMesh<DIM, DIM>& rGetMesh();

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

    void UpdateCellLocations(double dt);

    void SetOnlyUseNearestNeighboursForDivision(bool onlyUseNearestNeighboursForDivision);

    bool GetOnlyUseNearestNeighboursForDivision();

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

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

    void SetUseVonNeumannNeighbourhoods(bool useVonNeumannNeighbourhoods);

    bool GetUseVonNeumannNeighbourhoods();

    std::vector<bool>& rGetEmptySites();

    bool IsEmptySite(unsigned index);

    std::set<unsigned> GetEmptySiteIndices();

    unsigned GetNumNodes();

    virtual Node<DIM>* GetNode(unsigned index);

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

    std::vector<unsigned> GetNeighbouringNodeIndicesVector(unsigned nodeIndex);

    std::set<unsigned> GetFreeNeighbouringNodeIndices(unsigned nodeIndex);

    std::vector<unsigned> GetMaximumDegreeInEachDirection(unsigned nodeIndex);

    std::set<unsigned> GetNthDegreeNeighbouringNodeIndices(unsigned nodeIndex, unsigned degree);

    unsigned RemoveDeadCells();

    void Update(bool hasHadBirthsOrDeaths=true);

    void WriteCellVolumeResultsToFile();

    void GenerateCellResults(unsigned locationIndex,
                             std::vector<unsigned>& rCellProliferativeTypeCounter,
                             std::vector<unsigned>& rCellCyclePhaseCounter);

    virtual void GenerateCellResultsAndWriteToFiles();

    bool IsCellAssociatedWithADeletedLocation(CellPtr pCell);

    void MoveCell(CellPtr pCell, unsigned newLocationIndex);

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

    void OutputCellPopulationParameters(out_stream& rParamsFile);

    double GetWidth(const unsigned& rDimension);

    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(CaBasedCellPopulation)

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

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

#endif /*CABASEDCELLPOPULATION_HPP_*/