AbstractCellPopulation.hpp

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*/
 
#ifndef ABSTRACTCELLPOPULATION_HPP_
#define ABSTRACTCELLPOPULATION_HPP_
 
#include "Cell.hpp"
#include "OutputFileHandler.hpp"
 
#include <list>
#include <map>
#include <vector>
#include <boost/shared_ptr.hpp>
 
#include "ChasteSerialization.hpp"
#include "ClassIsAbstract.hpp"
 
#include <boost/serialization/vector.hpp>
#include <boost/serialization/list.hpp>
#include <boost/serialization/map.hpp>
#include <boost/serialization/set.hpp>
#include <boost/serialization/shared_ptr.hpp>
 
 
#include "AbstractMesh.hpp"
#include "TetrahedralMesh.hpp"
#include "CellPropertyRegistry.hpp"
#include "Identifiable.hpp"
#include "AbstractCellPopulationEventWriter.hpp"
#include "AbstractCellPopulationCountWriter.hpp"
#include "AbstractCellPopulationWriter.hpp"
#include "AbstractCellWriter.hpp"
 
// Forward declaration prevents circular include chain
template<unsigned ELEMENT_DIM, unsigned SPACE_DIM> class AbstractCellBasedSimulation;
#ifdef DOXYGEN_CHASTE_ISSUE_199 // See https://github.com/Chaste/Chaste/issues/199
template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
#else
template<unsigned ELEMENT_DIM, unsigned SPACE_DIM = ELEMENT_DIM>
#endif
class AbstractCellPopulation : public Identifiable
{
private:
 
    friend class boost::serialization::access;
 
    template<class Archive>
    void serialize(Archive & archive, const unsigned int version)
    {
        archive & mCells;
        archive & mLocationCellMap;
        archive & mCellLocationMap;
        archive & mpCellPropertyRegistry;
        archive & mOutputResultsForChasteVisualizer;
        archive & mCellWriters;
        archive & mCellPopulationWriters;
        archive & mCellPopulationCountWriters;
    }
 
    void OpenRoundRobinWritersFilesForAppend(OutputFileHandler& rOutputFileHandler);
 
    void CloseRoundRobinWritersFiles();
 
protected:
 
    std::map<unsigned, std::set<CellPtr> > mLocationCellMap;
 
    std::map<Cell*, unsigned> mCellLocationMap;
 
    AbstractMesh<ELEMENT_DIM, SPACE_DIM>& mrMesh;
 
    std::list<CellPtr> mCells;
 
    c_vector<double, SPACE_DIM> mCentroid;
 
    out_stream mpVtkMetaFile;
 
    boost::shared_ptr<CellPropertyRegistry> mpCellPropertyRegistry;
 
    bool mOutputResultsForChasteVisualizer;
 
    std::vector<boost::shared_ptr<AbstractCellWriter<ELEMENT_DIM, SPACE_DIM> > > mCellWriters;
 
    std::vector<boost::shared_ptr<AbstractCellPopulationWriter<ELEMENT_DIM, SPACE_DIM> > > mCellPopulationWriters;
 
    std::vector<boost::shared_ptr<AbstractCellPopulationCountWriter<ELEMENT_DIM, SPACE_DIM> > > mCellPopulationCountWriters;
 
    std::vector<boost::shared_ptr<AbstractCellPopulationEventWriter<ELEMENT_DIM, SPACE_DIM> > > mCellPopulationEventWriters;
 
    std::vector<std::string> mDivisionsInformation;
 
    std::vector<std::string> mRemovalsInformation;
 
    virtual void Validate()=0;
 
    virtual void WriteVtkResultsToFile(const std::string& rDirectory)=0;
 
    AbstractCellPopulation(AbstractMesh<ELEMENT_DIM, SPACE_DIM>& rMesh);
 
    virtual void AcceptCellWritersAcrossPopulation();
 
public:
 
    AbstractCellPopulation( AbstractMesh<ELEMENT_DIM, SPACE_DIM>& rMesh,
                            std::vector<CellPtr>& rCells,
                            const std::vector<unsigned> locationIndices=std::vector<unsigned>());
 
    virtual ~AbstractCellPopulation();
 
    void InitialiseCells();
 
    void SetDataOnAllCells(const std::string& rDataName, double dataValue);
 
    AbstractMesh<ELEMENT_DIM, SPACE_DIM>& rGetMesh();
 
    virtual TetrahedralMesh<ELEMENT_DIM, SPACE_DIM>* GetTetrahedralMeshForPdeModifier()=0;
 
    virtual bool IsPdeNodeAssociatedWithNonApoptoticCell(unsigned pdeNodeIndex);
 
    virtual double GetCellDataItemAtPdeNode(unsigned pdeNodeIndex,
                                            std::string& rVariableName,
                                            bool dirichletBoundaryConditionApplies=false,
                                            double dirichletBoundaryValue=0.0)=0;
 
    std::list<CellPtr>& rGetCells();
 
    virtual unsigned GetNumNodes()=0;
 
    virtual c_vector<double, SPACE_DIM> GetLocationOfCellCentre(CellPtr pCell)=0;
 
    virtual Node<SPACE_DIM>* GetNode(unsigned index)=0;
 
    virtual void SetNode(unsigned nodeIndex, ChastePoint<SPACE_DIM>& rNewLocation)=0;
 
    virtual bool IsCellAssociatedWithADeletedLocation(CellPtr pCell)=0;
 
    virtual void WriteDataToVisualizerSetupFile(out_stream& pVizSetupFile);
 
    virtual CellPtr AddCell(CellPtr pNewCell, CellPtr pParentCell=CellPtr())=0;
 
    virtual double GetDefaultTimeStep()=0;
 
    class Iterator; // Forward declaration; see below
 
    virtual unsigned RemoveDeadCells()=0;
 
    virtual void Update(bool hasHadBirthsOrDeaths=true)=0;
 
    std::vector<unsigned> GetCellMutationStateCount();
 
    std::vector<unsigned> GetCellProliferativeTypeCount();
 
    std::vector<unsigned> GetCellCyclePhaseCount();
 
    unsigned GetNumRealCells();
 
    unsigned GetNumAllCells();
 
    void SetCellAncestorsToLocationIndices();
 
    std::set<unsigned> GetCellAncestors();
 
    virtual CellPtr GetCellUsingLocationIndex(unsigned index);
 
    std::set<CellPtr> GetCellsUsingLocationIndex(unsigned index);
 
    virtual bool IsCellAttachedToLocationIndex(unsigned index);
 
    void SetCellUsingLocationIndex(unsigned index, CellPtr pCell);
 
    virtual void AddCellUsingLocationIndex(unsigned index, CellPtr pCell);
 
    virtual void RemoveCellUsingLocationIndex(unsigned index, CellPtr pCell);
 
    void MoveCellInLocationMap(CellPtr pCell, unsigned old_index, unsigned new_index);
 
    unsigned GetLocationIndexUsingCell(CellPtr pCell);
 
    boost::shared_ptr<CellPropertyRegistry> GetCellPropertyRegistry();
 
    void SetDefaultCellMutationStateAndProliferativeTypeOrdering();
 
    virtual double GetWidth(const unsigned& rDimension)=0;
 
    virtual double GetVolumeOfCell(CellPtr pCell)=0;
 
    virtual std::set<unsigned> GetNeighbouringNodeIndices(unsigned index)=0;
 
    virtual std::set<unsigned> GetNeighbouringLocationIndices(CellPtr pCell)=0;
 
    virtual std::set<std::pair<unsigned, unsigned>> GetNeighbouringEdgeIndices(CellPtr pCell, unsigned pEdgeIndex);
 
    c_vector<double, SPACE_DIM> GetCentroidOfCellPopulation();
 
    virtual void UpdateCellProcessLocation();
 
    virtual void OpenWritersFiles(OutputFileHandler& rOutputFileHandler);
 
    virtual void CloseWritersFiles();
 
    virtual void WriteResultsToFiles(const std::string& rDirectory);
 
    virtual void AcceptPopulationWriter(boost::shared_ptr<AbstractCellPopulationWriter<ELEMENT_DIM, SPACE_DIM> > pPopulationWriter)=0;
 
    virtual void AcceptPopulationCountWriter(boost::shared_ptr<AbstractCellPopulationCountWriter<ELEMENT_DIM, SPACE_DIM> > pPopulationCountWriter)=0;
 
    virtual void AcceptPopulationEventWriter(boost::shared_ptr<AbstractCellPopulationEventWriter<ELEMENT_DIM, SPACE_DIM> > pPopulationEventWriter)=0;
 
    virtual void AcceptCellWriter(boost::shared_ptr<AbstractCellWriter<ELEMENT_DIM, SPACE_DIM> > pCellWriter, CellPtr pCell) = 0;
 
    std::vector<std::string> GetDivisionsInformation();
 
    void AddDivisionInformation(std::string divisionInformation);
 
    void ClearDivisionsInformation();
 
    std::vector<std::string> GetRemovalsInformation();
 
    void AddRemovalInformation(std::string removalInformation);
 
    void ClearRemovalsInformation();
 
    void GenerateRemovalInformation(CellPtr pCell, std::string killerInfo);
 
    void KillCell(CellPtr pCell, std::string killerInfo);
 
    void StartApoptosisOnCell(CellPtr pCell, std::string killerInfo);
 
    void OutputCellPopulationInfo(out_stream& rParamsFile);
 
    virtual void OutputCellPopulationParameters(out_stream& rParamsFile)=0;
 
    virtual void SimulationSetupHook(AbstractCellBasedSimulation<ELEMENT_DIM, SPACE_DIM>* pSimulation);
 
    bool GetOutputResultsForChasteVisualizer();
 
    template<template <unsigned, unsigned> class T>
    void AddPopulationWriter()
    {
        mCellPopulationWriters.push_back(boost::shared_ptr< T<ELEMENT_DIM, SPACE_DIM> >(new T<ELEMENT_DIM, SPACE_DIM> ));
    }
 
    template<template <unsigned, unsigned> class T>
    void AddCellWriter()
    {
        mCellWriters.push_back(boost::shared_ptr< T<ELEMENT_DIM, SPACE_DIM> >(new T<ELEMENT_DIM, SPACE_DIM> ));
    }
 
    template<template <unsigned, unsigned> class T>
    void AddCellPopulationCountWriter()
    {
        mCellPopulationCountWriters.push_back(boost::shared_ptr< T<ELEMENT_DIM, SPACE_DIM> >(new T<ELEMENT_DIM, SPACE_DIM> ));
    }
 
    template<template <unsigned, unsigned> class T>
    void AddCellPopulationEventWriter()
    {
        mCellPopulationEventWriters.push_back(boost::shared_ptr< T<ELEMENT_DIM, SPACE_DIM> >(new T<ELEMENT_DIM, SPACE_DIM> ));
    }
 
    void AddPopulationWriter(boost::shared_ptr<AbstractCellPopulationWriter<ELEMENT_DIM, SPACE_DIM> > pPopulationWriter)
    {
        mCellPopulationWriters.push_back(pPopulationWriter);
    }
 
    void AddCellWriter(boost::shared_ptr<AbstractCellWriter<ELEMENT_DIM, SPACE_DIM> > pCellWriter)
    {
        mCellWriters.push_back(pCellWriter);
    }
 
    void AddCellPopulationCountWriter(boost::shared_ptr<AbstractCellPopulationCountWriter<ELEMENT_DIM, SPACE_DIM> > pCellPopulationCountWriter)
    {
        mCellPopulationCountWriters.push_back(pCellPopulationCountWriter);
    }
 
    void AddCellPopulationEventWriter(boost::shared_ptr<AbstractCellPopulationEventWriter<ELEMENT_DIM, SPACE_DIM> > pCellPopulationEventWriter)
    {
        mCellPopulationEventWriters.push_back(pCellPopulationEventWriter);
    }
 
    template<template <unsigned, unsigned> class T>
    bool HasWriter() const
    {
        typedef AbstractCellPopulationWriter<ELEMENT_DIM, SPACE_DIM> population_writer_t;
        for (boost::shared_ptr<population_writer_t> p_pop_writer : mCellPopulationWriters)
        {
            if (dynamic_cast<T<ELEMENT_DIM, SPACE_DIM>* >(p_pop_writer.get()))
            {
                return true;
            }
        }
        typedef AbstractCellWriter<ELEMENT_DIM, SPACE_DIM> cell_writer_t;
        for (boost::shared_ptr<cell_writer_t> p_cell_writer : mCellWriters)
        {
            if (dynamic_cast<T<ELEMENT_DIM, SPACE_DIM>* >(p_cell_writer.get()))
            {
                return true;
            }
        }
        typedef AbstractCellPopulationCountWriter<ELEMENT_DIM, SPACE_DIM> count_writer_t;
        for (boost::shared_ptr<count_writer_t> p_count_writer : mCellPopulationCountWriters)
        {
            if (dynamic_cast<T<ELEMENT_DIM, SPACE_DIM>* >(p_count_writer.get()))
            {
                return true;
            }
        }
        typedef AbstractCellPopulationEventWriter<ELEMENT_DIM, SPACE_DIM> event_writer_t;
        for (boost::shared_ptr<event_writer_t> p_event_writer : mCellPopulationEventWriters)
        {
            if (dynamic_cast<T<ELEMENT_DIM, SPACE_DIM>* >(p_event_writer.get()))
            {
                return true;
            }
        }
        return false;
    }
 
    void SetOutputResultsForChasteVisualizer(bool outputResultsForChasteVisualizer);
 
    c_vector<double,SPACE_DIM> GetSizeOfCellPopulation();
 
    virtual bool IsRoomToDivide(CellPtr pCell);
 
    std::pair<unsigned,unsigned> CreateOrderedPair(unsigned index1, unsigned index2);
 
    class Iterator
    {
    public:
 
        inline CellPtr operator*();
 
        inline CellPtr operator->();
 
        inline bool operator!=(const typename AbstractCellPopulation<ELEMENT_DIM, SPACE_DIM>::Iterator& rOther);
 
        inline Iterator& operator++();
 
        Iterator(AbstractCellPopulation& rCellPopulation, std::list<CellPtr>::iterator cellIter);
 
        virtual ~Iterator()
        {}
 
    private:
 
        virtual inline bool IsRealCell();
 
        inline bool IsAtEnd();
 
        AbstractCellPopulation& mrCellPopulation;
 
        std::list<CellPtr>::iterator mCellIter;
    };
 
    Iterator Begin();
 
    Iterator End();
};
 
TEMPLATED_CLASS_IS_ABSTRACT_1_UNSIGNED(AbstractCellPopulation)
 
 
//         Iterator class implementation - most methods are inlined         //
 
template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
CellPtr AbstractCellPopulation<ELEMENT_DIM, SPACE_DIM>::Iterator::operator*()
{
    assert(!IsAtEnd());
    return *mCellIter;
}
 
template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
CellPtr AbstractCellPopulation<ELEMENT_DIM, SPACE_DIM>::Iterator::operator->()
{
    assert(!IsAtEnd());
    return *mCellIter;
}
 
template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
bool AbstractCellPopulation<ELEMENT_DIM, SPACE_DIM>::Iterator::operator!=(const typename AbstractCellPopulation<ELEMENT_DIM, SPACE_DIM>::Iterator& rOther)
{
    return mCellIter != rOther.mCellIter;
}
 
template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
typename AbstractCellPopulation<ELEMENT_DIM, SPACE_DIM>::Iterator& AbstractCellPopulation<ELEMENT_DIM, SPACE_DIM>::Iterator::operator++()
{
    do
    {
        ++mCellIter;
    }
    while (!IsAtEnd() && !IsRealCell());
 
    return (*this);
}
 
template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
bool AbstractCellPopulation<ELEMENT_DIM, SPACE_DIM>::Iterator::IsRealCell()
{
    return !( mrCellPopulation.IsCellAssociatedWithADeletedLocation(*mCellIter) || (*this)->IsDead() );
}
 
template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
bool AbstractCellPopulation<ELEMENT_DIM, SPACE_DIM>::Iterator::IsAtEnd()
{
    return mCellIter == mrCellPopulation.rGetCells().end();
}
 
template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
AbstractCellPopulation<ELEMENT_DIM, SPACE_DIM>::Iterator::Iterator(AbstractCellPopulation& rCellPopulation, std::list<CellPtr>::iterator cellIter)
    : mrCellPopulation(rCellPopulation),
      mCellIter(cellIter)
{
    // The cell population can now return empty if it only has ghost nodes
    if (mrCellPopulation.rGetCells().empty())
    {
        mCellIter = mrCellPopulation.rGetCells().end();
    }
    else
    {
        // Make sure we start at a real cell
        if (mCellIter == mrCellPopulation.rGetCells().begin() && !IsRealCell())
        {
            ++(*this);
        }
    }
}
 
template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
typename AbstractCellPopulation<ELEMENT_DIM, SPACE_DIM>::Iterator AbstractCellPopulation<ELEMENT_DIM, SPACE_DIM>::Begin()
{
    return Iterator(*this, this->mCells.begin());
}
 
template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
typename AbstractCellPopulation<ELEMENT_DIM, SPACE_DIM>::Iterator AbstractCellPopulation<ELEMENT_DIM, SPACE_DIM>::End()
{
    return Iterator(*this, this->mCells.end());
}
 
#endif /*ABSTRACTCELLPOPULATION_HPP_*/