RegularGrid.hpp

/*

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 */

#ifndef REGULARGRID_HPP_
#define REGULARGRID_HPP_

#include <vector>
#define _BACKWARD_BACKWARD_WARNING_H 1 //Cut out the vtk deprecated warning for now (gcc4.3)
#include <vtkImageData.h>
#include <vtkSmartPointer.h>
#include "UblasIncludes.hpp"
#include "SmartPointers.hpp"
#include "VesselNetwork.hpp"
#include "VesselSegment.hpp"
#include "VesselNode.hpp"
#include "AbstractCellPopulation.hpp"
#include "CaBasedCellPopulation.hpp"
#include "Part.hpp"
#include "UnitCollection.hpp"
#include "DimensionalChastePoint.hpp"

template<unsigned DIM>
class RegularGrid
{
    units::quantity<unit::length> mSpacing;

    std::vector<unsigned> mExtents;

    DimensionalChastePoint<DIM> mOrigin;

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

    AbstractCellPopulation<DIM>* mpCellPopulation;

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

    std::vector<std::vector<CellPtr> > mPointCellMap;

    std::vector<std::vector<boost::shared_ptr<VesselNode<DIM> > > > mPointNodeMap;

    std::vector<std::vector<boost::shared_ptr<VesselSegment<DIM> > > > mPointSegmentMap;

    std::vector<double> mPointSolution;

    vtkSmartPointer<vtkImageData> mpVtkGrid;

    bool mVtkGridIsSetUp;

    std::vector<std::vector<unsigned> > mNeighbourData;

    bool mHasCellPopulation;

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

public:

    RegularGrid();

    static boost::shared_ptr<RegularGrid<DIM> > Create();

    ~RegularGrid();

    void CalculateNeighbourData();

    void GenerateFromPart(boost::shared_ptr<Part<DIM> > pPart, units::quantity<unit::length> gridSize);

    unsigned Get1dGridIndex(unsigned xIndex, unsigned yIndex, unsigned zIndex);

    unsigned GetNearestGridIndex(const DimensionalChastePoint<DIM>& rLocation);

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

    std::vector<unsigned> GetExtents();

    DimensionalChastePoint<DIM> GetLocation(unsigned xIndex, unsigned yIndex, unsigned zIndex);

    DimensionalChastePoint<DIM> GetLocationOf1dIndex(unsigned gridIndex);

    std::vector<DimensionalChastePoint<DIM> > GetLocations();

    unsigned GetNumberOfPoints();

    DimensionalChastePoint<DIM> GetOrigin();

    std::vector<std::vector<unsigned> > GetPointPointMap(std::vector<DimensionalChastePoint<DIM> > inputPoints);

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

    const std::vector<std::vector<boost::shared_ptr<VesselNode<DIM> > > >& GetPointNodeMap(bool update = true);

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

    bool IsSegmentAtLatticeSite(unsigned index, bool update);

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

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

    vtkSmartPointer<vtkImageData> GetVtkGrid();

    std::vector<double> InterpolateGridValues(std::vector<DimensionalChastePoint<DIM> > locations,
                                              std::vector<double> values, bool useVtk = false);

    bool IsLocationInPointVolume(DimensionalChastePoint<DIM> point, unsigned gridIndex);

    bool IsOnBoundary(unsigned gridIndex);

    bool IsOnBoundary(unsigned xIndex, unsigned yIndex, unsigned zIndex);

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

    void SetExtents(std::vector<unsigned> extents);

    void SetOrigin(DimensionalChastePoint<DIM> origin);

    void SetPointValues(std::vector<double> pointSolution);

    void SetSpacing(units::quantity<unit::length> spacing);

    void SetUpVtkGrid();

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

    void Write(boost::shared_ptr<OutputFileHandler> pFileHandler);
};

#endif /* REGULARGRID_HPP_*/