AbstractTissue.hpp

/*

Copyright (C) University of Oxford, 2005-2010

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 ABSTRACTTISSUE_HPP_
#define ABSTRACTTISSUE_HPP_

#include "TissueCell.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 "CellMutationStateRegistry.hpp"
// Needed here to avoid serialization errors (on Boost<1.37)
#include "WildTypeCellMutationState.hpp"
#include "LabelledCellMutationState.hpp"
#include "ApcOneHitCellMutationState.hpp"
#include "ApcTwoHitCellMutationState.hpp"
#include "BetaCateninOneHitCellMutationState.hpp"

template<unsigned DIM>
class AbstractTissue
{
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 & mTissueContainsMesh;
        archive & mpMutationStateRegistry;
    }

protected:

    std::list<TissueCell> mCells;

    std::map<unsigned, TissueCell*> mLocationCellMap;

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

    std::vector<unsigned> mCellProliferativeTypeCount;

    std::vector<unsigned> mCellCyclePhaseCount;

    out_stream mpVizNodesFile;

    out_stream mpVizCellProliferativeTypesFile;

    out_stream mpCellMutationStatesFile;

    out_stream mpCellAncestorsFile;

    out_stream mpCellProliferativeTypesFile;

    out_stream mpCellCyclePhasesFile;

    out_stream mpCellVariablesFile;

    out_stream mpCellAgesFile;

    out_stream mpCellIdFile;

    out_stream mpBoundaryNodesFile;

    bool mTissueContainsMesh;

    boost::shared_ptr<CellMutationStateRegistry> mpMutationStateRegistry;

    virtual void Validate()=0;

protected:
    AbstractTissue()
    {
    }

public:

    AbstractTissue(std::vector<TissueCell>& rCells,
                   const std::vector<unsigned> locationIndices=std::vector<unsigned>());

    virtual ~AbstractTissue()
    {}

    void InitialiseCells();

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

    bool HasMesh();

    virtual unsigned GetNumNodes()=0;

    virtual c_vector<double, DIM> GetLocationOfCellCentre(TissueCell& rCell)=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(TissueCell& rCell)=0;

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

    virtual double GetDampingConstant(unsigned nodeIndex)=0;

    virtual TissueCell* AddCell(TissueCell& rNewCell, const c_vector<double,DIM>& rCellDivisionVector, TissueCell* pParentCell=NULL)=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();

    TissueCell& rGetCellUsingLocationIndex(unsigned index);

    unsigned GetLocationIndexUsingCell(TissueCell& rCell);

    boost::shared_ptr<CellMutationStateRegistry> GetMutationRegistry();

    void SetDefaultMutationStateOrdering();

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

    virtual void WriteResultsToFiles();

    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();

    class Iterator
    {
    public:

        inline TissueCell& operator*();

        inline TissueCell* operator->();

        inline bool operator!=(const AbstractTissue<DIM>::Iterator& rOther);

        inline Iterator& operator++();

        Iterator(AbstractTissue& rTissue, std::list<TissueCell>::iterator cellIter);

        virtual ~Iterator()
        {}

    private:

        virtual inline bool IsRealCell();

        inline bool IsAtEnd();

        AbstractTissue& mrTissue;

        std::list<TissueCell>::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(AbstractTissue);

//         Iterator class implementation - most methods are inlined         //

template<unsigned DIM>
TissueCell& AbstractTissue<DIM>::Iterator::operator*()
{
    assert(!IsAtEnd());
    return *mCellIter;
}

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

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

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

    return (*this);
}

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

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

template<unsigned DIM>
AbstractTissue<DIM>::Iterator::Iterator(AbstractTissue& rTissue, std::list<TissueCell>::iterator cellIter)
    : mrTissue(rTissue),
      mCellIter(cellIter)
{
    // The tissue can now return empty if it only has ghost nodes
    if (mrTissue.rGetCells().size() == 0)
    {
        mCellIter = mrTissue.rGetCells().end();
    }
    else
    {
        // Make sure we start at a real cell
        if (mCellIter == mrTissue.rGetCells().begin() && !IsRealCell())
        {
            ++(*this);
        }
    }
}

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

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


#endif /*ABSTRACTTISSUE_HPP_*/