DiscreteContinuumMesh.hpp

/*

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#ifndef DISCRETECONTINUUMMESH_HPP_
#define DISCRETECONTINUUMMESH_HPP_

#include <vector>
#include "SmartPointers.hpp"
#include "ChastePoint.hpp"
#include "TetrahedralMesh.hpp"
#define _BACKWARD_BACKWARD_WARNING_H 1 //Cut out the vtk deprecated warning
#include <vtkSmartPointer.h>
#include <vtkUnstructuredGrid.h>
#include <vtkCellLocator.h>
#include "Part.hpp"
#include "Cell.hpp"
#include "Element.hpp"
#include "DimensionalChastePoint.hpp"
#include "DiscreteContinuumMeshGenerator.hpp"
#include "VesselSegment.hpp"
#include "VesselNetwork.hpp"
#include "AbstractCellPopulation.hpp"
#include "UnitCollection.hpp"

// Forward declaration
template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
class DiscreteContinuumMeshGenerator;

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM = ELEMENT_DIM>
class DiscreteContinuumMesh : public TetrahedralMesh<ELEMENT_DIM, SPACE_DIM>
{
    friend class DiscreteContinuumMeshGenerator<ELEMENT_DIM, SPACE_DIM>;

    std::vector<unsigned> mAttributes;

    units::quantity<unit::length> mReferenceLength;

    vtkSmartPointer<vtkUnstructuredGrid> mpVtkMesh;

    vtkSmartPointer<vtkCellLocator> mpVtkCellLocator;

    bool mVtkRepresentationUpToDate;

    std::vector<std::vector<unsigned> > mPointElementMap;

    std::vector<std::vector<boost::shared_ptr<VesselSegment<SPACE_DIM> > > > mSegmentElementMap;

    std::vector<std::vector<CellPtr > > mCellElementMap;

    boost::shared_ptr<VesselNetwork<SPACE_DIM> > mpNetwork;

    AbstractCellPopulation<SPACE_DIM>* mpCellPopulation;

    units::quantity<unit::length> mCellPopulationReferenceLength;

public:

    DiscreteContinuumMesh();

    ~DiscreteContinuumMesh();

    static boost::shared_ptr<DiscreteContinuumMesh<ELEMENT_DIM, SPACE_DIM> > Create();

    std::vector<std::vector<unsigned> > GetConnectivity();

    std::vector<c_vector<double, SPACE_DIM> > GetNodeLocations();

    std::vector<c_vector<double, SPACE_DIM> > GetElementCentroids();

    std::vector<DimensionalChastePoint<SPACE_DIM> > GetNodeLocationsAsPoints();

    std::vector<unsigned> GetElementRegionMarkers();

    units::quantity<unit::length> GetReferenceLengthScale();

    std::vector<std::vector<unsigned> > GetPointElementMap(std::vector<DimensionalChastePoint<SPACE_DIM> > points);

    const std::vector<std::vector<CellPtr> >& GetElementCellMap(bool update = true);

    std::vector<std::vector<boost::shared_ptr<VesselSegment<SPACE_DIM> > > > GetElementSegmentMap(bool update = true,
                                                                                                  bool useVesselSurface = false);

    vtkSmartPointer<vtkUnstructuredGrid> GetAsVtkUnstructuredGrid();

    void SetAttributes(std::vector<unsigned> attributes);

    void SetCellPopulation(AbstractCellPopulation<SPACE_DIM>& rCellPopulation, units::quantity<unit::length> cellLengthScale);

    void SetVesselNetwork(boost::shared_ptr<VesselNetwork<SPACE_DIM> > pNetwork);

    void ImportDiscreteContinuumMeshFromTetgen(tetgen::tetgenio& mesherOutput, unsigned numberOfElements, int *elementList,
                          unsigned numberOfFaces, int *faceList, int *edgeMarkerList);

};

#endif /* DISCRETECONTINUUMMESH_HPP_*/