MeshBasedTissue.hpp

/*

Copyright (C) University of Oxford, 2005-2009

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 MESHBASEDTISSUE_HPP_
#define MESHBASEDTISSUE_HPP_

#include "AbstractCellCentreBasedTissue.hpp"
#include "MutableMesh.hpp"
#include "VoronoiTessellation.hpp"
#include "Exception.hpp"
#include "MeshArchiveInfo.hpp"

#include <boost/serialization/access.hpp>
#include <boost/serialization/base_object.hpp>
#include <boost/serialization/set.hpp>
#include <boost/serialization/vector.hpp>


template<unsigned DIM>
class MeshBasedTissue : public AbstractCellCentreBasedTissue<DIM>
{
    friend class TestMeshBasedTissue;

protected:
#define COVERAGE_IGNORE //Avoid prototypes being treated as code by gcov

    MutableMesh<DIM, DIM>& mrMesh;

    VoronoiTessellation<DIM>* mpVoronoiTessellation;

    bool mDeleteMesh;

    std::set<std::set<TissueCell*> > mMarkedSprings;

    bool mWriteVoronoiData;

    bool mFollowLoggedCell;

    bool mWriteTissueAreas;

    out_stream mpElementFile;

    out_stream mpVoronoiFile;

    out_stream mpTissueAreasFile;

    std::set<TissueCell*> CreateCellPair(TissueCell&, TissueCell&);

    bool mUseAreaBasedDampingConstant;
#undef COVERAGE_IGNORE //Avoid prototypes being treated as code by gcov

    friend class boost::serialization::access;
    template<class Archive>
    void serialize(Archive & archive, const unsigned int version)
    {
        archive & boost::serialization::base_object<AbstractCellCentreBasedTissue<DIM> >(*this);

        // The Voronoi stuff can't be archived yet
        //archive & mpVoronoiTessellation
        delete mpVoronoiTessellation;
        mpVoronoiTessellation = NULL;

        archive & mMarkedSprings;
        archive & mWriteVoronoiData;
        archive & mFollowLoggedCell;
        archive & mWriteTissueAreas;
        archive & mUseAreaBasedDampingConstant;

        // In its present form, a call to MeshBasedTissue::Validate() here
        // would result in a seg fault in the situation where we are actually loading
        // a MeshBasedTissueWithGhostNodes. Commenting out this call breaks no tests.

        // Validate();
    }

    virtual void UpdateGhostNodesAfterReMesh(NodeMap& rMap);

    virtual void Validate();

public:
#define COVERAGE_IGNORE //Avoid prototypes being treated as code by gcov

    MeshBasedTissue(MutableMesh<DIM, DIM>& rMesh,
                    const std::vector<TissueCell>& rCells,
                    const std::vector<unsigned> locationIndices=std::vector<unsigned>(),
                    bool deleteMesh=false,
                    bool validate=true);

    MeshBasedTissue(MutableMesh<DIM, DIM>& rMesh);

    ~MeshBasedTissue();

    MutableMesh<DIM, DIM>& rGetMesh();

    const MutableMesh<DIM, DIM>& rGetMesh() const;

    bool GetWriteVoronoiData();

    bool GetWriteTissueAreas();

    bool UseAreaBasedDampingConstant();

    void SetWriteVoronoiData(bool writeVoronoiData, bool followLoggedCell);

    unsigned AddNode(Node<DIM> *pNewNode);

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

    virtual bool IsGhostNode(unsigned index);

    double GetDampingConstant(unsigned nodeIndex);

    void SetWriteTissueAreas(bool writeTissueAreas);

    void SetAreaBasedDampingConstant(bool useAreaBasedDampingConstant);

    virtual unsigned RemoveDeadCells();

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

    void WriteMeshToFile(const std::string &rArchiveDirectory, const std::string &rMeshFileName);

    void CreateOutputFiles(const std::string &rDirectory,
                           bool rCleanOutputDirectory,
                           bool outputCellMutationStates,
                           bool outputCellTypes,
                           bool outputCellVariables,
                           bool outputCellCyclePhases,
                           bool outputCellAncestors);
    void CloseOutputFiles(bool outputCellMutationStates,
                          bool outputCellTypes,
                          bool outputCellVariables,
                          bool outputCellCyclePhases,
                          bool outputCellAncestors);

    void WriteResultsToFiles(bool outputCellMutationStates,
                             bool outputCellTypes,
                             bool outputCellVariables,
                             bool outputCellCyclePhases,
                             bool outputCellAncestors);

    virtual void Update();

    Node<DIM>* GetNode(unsigned index);

    unsigned GetNumNodes();

    void SetBottomCellAncestors();

    void WriteVoronoiResultsToFile();

    void WriteTissueAreaResultsToFile();

    void CreateVoronoiTessellation();

    VoronoiTessellation<DIM>& rGetVoronoiTessellation();

    class SpringIterator
    {
    public:

        Node<DIM>* GetNodeA();

        Node<DIM>* GetNodeB();

        TissueCell& rGetCellA();

        TissueCell& rGetCellB();

        bool operator!=(const SpringIterator& other);

        SpringIterator& operator++();

        SpringIterator(MeshBasedTissue& rTissue, typename MutableMesh<DIM,DIM>::EdgeIterator edgeIter);

    private:

        std::set<std::set<unsigned> > mSpringsVisited;

        MeshBasedTissue& mrTissue;

        typename MutableMesh<DIM, DIM>::EdgeIterator mEdgeIter;
    };

    SpringIterator SpringsBegin();

    SpringIterator SpringsEnd();

    void CheckTissueCellPointers();

    bool IsMarkedSpring(TissueCell&, TissueCell&);

    void MarkSpring(TissueCell&, TissueCell&);

    void UnmarkSpring(TissueCell&, TissueCell&);

};
#undef COVERAGE_IGNORE //Avoid prototypes being treated as code by gcov


#include "TemplatedExport.hpp"
EXPORT_TEMPLATE_CLASS_SAME_DIMS(MeshBasedTissue)

namespace boost
{
namespace serialization
{
template<class Archive, unsigned DIM>
inline void save_construct_data(
    Archive & ar, const MeshBasedTissue<DIM> * t, const BOOST_PFTO unsigned int file_version)
{
    // Save data required to construct instance
    const MutableMesh<DIM,DIM>* p_mesh = &(t->rGetMesh());
    ar & p_mesh;
}

template<class Archive, unsigned DIM>
inline void load_construct_data(
    Archive & ar, MeshBasedTissue<DIM> * t, const unsigned int file_version)
{
    // Retrieve data from archive required to construct new instance
    assert(MeshArchiveInfo::meshPathname.length() > 0);
    MutableMesh<DIM,DIM>* p_mesh;
    ar >> p_mesh;

    // Re-initialise the mesh
    p_mesh->Clear();
    TrianglesMeshReader<DIM,DIM> mesh_reader(MeshArchiveInfo::meshPathname);
    p_mesh->ConstructFromMeshReader(mesh_reader);

    // Needed for cylindrical meshes at present; should be safe in any case.
    NodeMap map(p_mesh->GetNumNodes());
    p_mesh->ReMesh(map);

    // Invoke inplace constructor to initialise instance
    ::new(t)MeshBasedTissue<DIM>(*p_mesh);
}
}
} // namespace ...

#endif /*MESHBASEDTISSUE_HPP_*/

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