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 <boost/foreach.hpp>

#include "AbstractMesh.hpp"
#include "TetrahedralMesh.hpp"
#include "CellPropertyRegistry.hpp"
#include "Identifiable.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;

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM=ELEMENT_DIM>
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;

    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;

    c_vector<double, SPACE_DIM> GetCentroidOfCellPopulation();

    virtual void UpdateCellProcessLocation();

    virtual void OpenWritersFiles(OutputFileHandler& rOutputFileHandler);

    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 AcceptCellWriter(boost::shared_ptr<AbstractCellWriter<ELEMENT_DIM, SPACE_DIM> > pCellWriter, CellPtr pCell)=0;

    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> ));
    }

    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);
    }

    template<template <unsigned, unsigned> class T>
    bool HasWriter() const
    {
        typedef AbstractCellPopulationWriter<ELEMENT_DIM, SPACE_DIM> population_writer_t;
        BOOST_FOREACH(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;
        BOOST_FOREACH(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;
        BOOST_FOREACH(boost::shared_ptr<count_writer_t> p_count_writer, mCellPopulationCountWriters)
        {
            if (dynamic_cast<T<ELEMENT_DIM, SPACE_DIM>* >(p_count_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_*/