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/shared_ptr.hpp>

#include "Node.hpp"
#include "CellPropertyRegistry.hpp"
#include "Identifiable.hpp"

// Needed here to avoid serialization errors (on Boost<1.37)
#include "WildTypeCellMutationState.hpp"
#include "ApcOneHitCellMutationState.hpp"
#include "ApcTwoHitCellMutationState.hpp"
#include "BetaCateninOneHitCellMutationState.hpp"
#include "ApoptoticCellProperty.hpp"
#include "CellLabel.hpp"
#include "CellData.hpp"
#include "AbstractMesh.hpp"

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 & mCellProliferativeTypeCount;
        archive & mCellCyclePhaseCount;
        archive & mpCellPropertyRegistry;
        archive & mOutputCellIdData;
        archive & mOutputCellMutationStates;
        archive & mOutputCellAncestors;
        archive & mOutputCellProliferativeTypes;
        archive & mOutputCellVariables;
        archive & mOutputCellCyclePhases;
        archive & mOutputCellAges;
        archive & mOutputCellVolumes;
    }

protected:

    std::map<unsigned, std::set<CellPtr> > mLocationCellMap;

    std::map<Cell*, unsigned> mCellLocationMap;

    AbstractMesh<ELEMENT_DIM, SPACE_DIM>& mrMesh;

    std::list<CellPtr> mCells;

    std::vector<unsigned> mCellProliferativeTypeCount;

    std::vector<unsigned> mCellCyclePhaseCount;

    c_vector<double, SPACE_DIM> mCentroid;

    out_stream mpVizNodesFile;

    out_stream mpVizCellProliferativeTypesFile;

    out_stream mpVizCellProliferativePhasesFile;

    out_stream mpCellMutationStatesFile;

    out_stream mpVizCellAncestorsFile;

    out_stream mpCellProliferativeTypesFile;

    out_stream mpCellCyclePhasesFile;

    out_stream mpCellVariablesFile;

    out_stream mpCellAgesFile;

    out_stream mpCellIdFile;

    out_stream mpCellVolumesFile;

    out_stream mpVizBoundaryNodesFile;

    std::string mDirPath;

    out_stream mpVtkMetaFile;

    boost::shared_ptr<CellPropertyRegistry> mpCellPropertyRegistry;

    bool mOutputCellIdData;

    bool mOutputCellMutationStates;

    bool mOutputCellAncestors;

    bool mOutputCellProliferativeTypes;

    bool mOutputCellVariables;

    bool mOutputCellCyclePhases;

    bool mOutputCellAges;

    bool mOutputCellVolumes;

    virtual void Validate()=0;

    virtual void WriteVtkResultsToFile()=0;

    AbstractCellPopulation(AbstractMesh<ELEMENT_DIM, SPACE_DIM>& rMesh);

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& dataName, double dataValue);

    AbstractMesh<ELEMENT_DIM, SPACE_DIM>& rGetMesh();

    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 CellPtr AddCell(CellPtr pNewCell, const c_vector<double,SPACE_DIM>& rCellDivisionVector, CellPtr pParentCell=CellPtr())=0;

    class Iterator; // Forward declaration; see below

    virtual unsigned RemoveDeadCells()=0;

    virtual void Update(bool hasHadBirthsOrDeaths=true)=0;

    std::vector<unsigned> GetCellMutationStateCount();

     const std::vector<unsigned>& rGetCellProliferativeTypeCount() const;

    const std::vector<unsigned>& rGetCellCyclePhaseCount() const;

    unsigned GetNumRealCells();

    void SetCellAncestorsToLocationIndices();

    void WriteCellIdDataToFile();

    std::set<unsigned> GetCellAncestors();

    CellPtr GetCellUsingLocationIndex(unsigned index);

    std::set<CellPtr> GetCellsUsingLocationIndex(unsigned index);

    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 SetDefaultMutationStateOrdering();

    virtual double GetWidth(const unsigned& rDimension)=0;

    virtual double GetVolumeOfCell(CellPtr pCell)=0;

    virtual std::set<unsigned> GetNeighbouringNodeIndices(unsigned index)=0;

    c_vector<double, SPACE_DIM> GetCentroidOfCellPopulation();

    virtual void CreateOutputFiles(const std::string& rDirectory,
                                   bool cleanOutputDirectory);

    virtual void WriteResultsToFiles();

    virtual void WriteTimeAndNodeResultsToFiles();

    virtual void GenerateCellResultsAndWriteToFiles()=0;

    virtual void GenerateCellResults(CellPtr pCell,
                             std::vector<unsigned>& rCellProliferativeTypeCounter,
                             std::vector<unsigned>& rCellCyclePhaseCounter);

    virtual void WriteCellVolumeResultsToFile()=0;

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

    virtual void CloseOutputFiles();

    void OutputCellPopulationInfo(out_stream& rParamsFile);

    virtual void OutputCellPopulationParameters(out_stream& rParamsFile)=0;

    bool GetOutputCellIdData();

    bool GetOutputCellMutationStates();

    bool GetOutputCellAncestors();

    bool GetOutputCellProliferativeTypes();

    bool GetOutputCellVariables();

    bool GetOutputCellCyclePhases();

    bool GetOutputCellAges();

    bool GetOutputCellVolumes();

    void SetOutputCellIdData(bool outputCellIdData);

    void SetOutputCellMutationStates(bool outputCellMutationStates);

    void SetOutputCellAncestors(bool outputCellAncestors);

    void SetOutputCellProliferativeTypes(bool outputCellProliferativeTypes);

    void SetOutputCellVariables(bool outputCellVariables);

    void SetOutputCellCyclePhases(bool outputCellCyclePhases);

    void SetOutputCellAges(bool outputCellAges);

    void SetOutputCellVolumes(bool outputCellVolumes);

    c_vector<double,SPACE_DIM> GetSizeOfCellPopulation();

    class Iterator
    {
    public:

        inline CellPtr operator*();

        inline CellPtr operator->();

        inline bool operator!=(const 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();

};

enum cell_colours
{
    STEM_COLOUR, // 0
    TRANSIT_COLOUR, // 1
    DIFFERENTIATED_COLOUR, // 2
    EARLY_CANCER_COLOUR, // 3
    LATE_CANCER_COLOUR, // 4
    LABELLED_COLOUR, // 5
    APOPTOSIS_COLOUR, // 6
    INVISIBLE_COLOUR // visualizer treats '7' as invisible
};

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 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_*/