AbstractCellPopulation.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 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"

template<unsigned 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 & mCellPopulationContainsMesh;
        archive & mpCellPropertyRegistry;
        archive & mDampingConstantNormal;
        archive & mDampingConstantMutant;
        archive & mOutputCellIdData;
        archive & mOutputCellMutationStates;
        archive & mOutputCellAncestors;
        archive & mOutputCellProliferativeTypes;
        archive & mOutputCellVariables;
        archive & mOutputCellCyclePhases;
        archive & mOutputCellAges;
        archive & mOutputCellVolumes;
    }

protected:

    std::list<CellPtr> mCells;

    std::map<unsigned, CellPtr> mLocationCellMap;

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

    std::vector<unsigned> mCellProliferativeTypeCount;

    std::vector<unsigned> mCellCyclePhaseCount;

    out_stream mpVizNodesFile;

    out_stream mpVizCellProliferativeTypesFile;

    out_stream mpCellMutationStatesFile;

    out_stream mpVizCellAncestorsFile;

    out_stream mpCellProliferativeTypesFile;

    out_stream mpCellCyclePhasesFile;

    out_stream mpCellVariablesFile;

    out_stream mpCellAgesFile;

    out_stream mpCellIdFile;

    out_stream mpVizBoundaryNodesFile;

    std::string mDirPath;

    out_stream mpVtkMetaFile;

    bool mCellPopulationContainsMesh;

    boost::shared_ptr<CellPropertyRegistry> mpCellPropertyRegistry;

    double mDampingConstantNormal;

    double mDampingConstantMutant;

    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()
    {
    }

public:

    AbstractCellPopulation(std::vector<CellPtr>& rCells,
                           const std::vector<unsigned> locationIndices=std::vector<unsigned>());

    virtual ~AbstractCellPopulation();

    void InitialiseCells();

    std::list<CellPtr>& rGetCells();

    bool IsMeshBasedCellPopulation();

    virtual unsigned GetNumNodes()=0;

    virtual c_vector<double, DIM> GetLocationOfCellCentre(CellPtr pCell)=0;

    virtual Node<DIM>* GetNode(unsigned index)=0;

    virtual unsigned AddNode(Node<DIM>* pNewNode)=0;

    virtual void SetNode(unsigned nodeIndex, ChastePoint<DIM>& rNewLocation)=0;

    virtual bool IsCellAssociatedWithADeletedLocation(CellPtr pCell)=0;

    virtual void UpdateNodeLocations(const std::vector< c_vector<double, DIM> >& rNodeForces, double dt)=0;

    virtual double GetDampingConstant(unsigned nodeIndex)=0;

    virtual CellPtr AddCell(CellPtr pNewCell, const c_vector<double,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);

    unsigned GetLocationIndexUsingCell(CellPtr pCell);

    boost::shared_ptr<CellPropertyRegistry> GetCellPropertyRegistry();

    void SetDefaultMutationStateOrdering();

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

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

    virtual void WriteResultsToFiles();

    virtual void WriteTimeAndNodeResultsToFiles();

    virtual void GenerateCellResultsAndWriteToFiles()=0;

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

    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;

    double GetDampingConstantNormal();
    double GetDampingConstantMutant();

    bool GetOutputCellIdData();

    bool GetOutputCellMutationStates();

    bool GetOutputCellAncestors();

    bool GetOutputCellProliferativeTypes();

    bool GetOutputCellVariables();

    bool GetOutputCellCyclePhases();

    bool GetOutputCellAges();

    bool GetOutputCellVolumes();

    void SetDampingConstantNormal(double dampingConstantNormal);

    void SetDampingConstantMutant(double dampingConstantMutant);

    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);

    virtual void SetOutputCellVolumes(bool outputCellVolumes);

    class Iterator
    {
    public:

        inline CellPtr operator*();

        inline CellPtr operator->();

        inline bool operator!=(const AbstractCellPopulation<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 DIM>
CellPtr AbstractCellPopulation<DIM>::Iterator::operator*()
{
    assert(!IsAtEnd());
    return *mCellIter;
}

template<unsigned DIM>
CellPtr AbstractCellPopulation<DIM>::Iterator::operator->()
{
    assert(!IsAtEnd());
    return *mCellIter;
}

template<unsigned DIM>
bool AbstractCellPopulation<DIM>::Iterator::operator!=(const AbstractCellPopulation<DIM>::Iterator& rOther)
{
    return mCellIter != rOther.mCellIter;
}

template<unsigned DIM>
typename AbstractCellPopulation<DIM>::Iterator& AbstractCellPopulation<DIM>::Iterator::operator++()
{
    do
    {
        ++mCellIter;
    }
    while (!IsAtEnd() && !IsRealCell());

    return (*this);
}

template<unsigned DIM>
bool AbstractCellPopulation<DIM>::Iterator::IsRealCell()
{
    return !( mrCellPopulation.IsCellAssociatedWithADeletedLocation(*mCellIter) || (*this)->IsDead() );
}

template<unsigned DIM>
bool AbstractCellPopulation<DIM>::Iterator::IsAtEnd()
{
    return mCellIter == mrCellPopulation.rGetCells().end();
}

template<unsigned DIM>
AbstractCellPopulation<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 DIM>
typename AbstractCellPopulation<DIM>::Iterator AbstractCellPopulation<DIM>::Begin()
{
    return Iterator(*this, this->mCells.begin());
}

template<unsigned DIM>
typename AbstractCellPopulation<DIM>::Iterator AbstractCellPopulation<DIM>::End()
{
    return Iterator(*this, this->mCells.end());
}


#endif /*ABSTRACTCELLPOPULATION_HPP_*/

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