VesselNetwork.hpp

/*

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#ifndef VESSELNETWORK_HPP_
#define VESSELNETWORK_HPP_

#include <vector>
#include <set>
#include <map>
#include "Vessel.hpp"
#include "VesselSegment.hpp"
#include "VesselNode.hpp"
#include "UblasIncludes.hpp"
#include "UnitCollection.hpp"
#include "AbstractVesselNetworkComponent.hpp"

template<unsigned DIM>
class VesselNetwork : public boost::enable_shared_from_this<VesselNetwork<DIM> >, public AbstractVesselNetworkComponent<DIM>
{

private:

    std::vector<boost::shared_ptr<Vessel<DIM> > > mVessels;

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

    bool mSegmentsUpToDate;

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

    bool mNodesUpToDate;

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

    bool mVesselNodesUpToDate;

public:

    VesselNetwork();

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

    virtual ~VesselNetwork();

    void AddVessel(boost::shared_ptr<Vessel<DIM> > pVessel);

    void AddVessels(std::vector<boost::shared_ptr<Vessel<DIM> > > vessels);

    void CopySegmentFlowProperties(unsigned index=0);

    std::vector<boost::shared_ptr<Vessel<DIM> > > CopyVessels();

    std::vector<boost::shared_ptr<Vessel<DIM> > > CopyVessels(std::vector<boost::shared_ptr<Vessel<DIM> > > vessels);

    virtual boost::shared_ptr<VesselNode<DIM> > DivideVessel(boost::shared_ptr<Vessel<DIM> > pVessel,
                                                     const DimensionalChastePoint<DIM>& rLocation);

    virtual void ExtendVessel(boost::shared_ptr<Vessel<DIM> > pVessel, boost::shared_ptr<VesselNode<DIM> > pEndNode,
                      boost::shared_ptr<VesselNode<DIM> > pNewNode);

    virtual boost::shared_ptr<Vessel<DIM> > FormSprout(const DimensionalChastePoint<DIM>& sproutBaseLocation,
                                               const DimensionalChastePoint<DIM>& sproutTipLocation);

    units::quantity<unit::length> GetDistanceToNearestNode(const DimensionalChastePoint<DIM>& rLocation);

    boost::shared_ptr<VesselNode<DIM> > GetNearestNode(const DimensionalChastePoint<DIM>& rLocation);

    boost::shared_ptr<VesselNode<DIM> > GetNearestNode(boost::shared_ptr<VesselNode<DIM> > pInputNode);

    std::pair<boost::shared_ptr<VesselSegment<DIM> >, units::quantity<unit::length> > GetNearestSegment(boost::shared_ptr<VesselSegment<DIM> > pSegment);

    std::pair<boost::shared_ptr<VesselSegment<DIM> >, units::quantity<unit::length> > GetNearestSegment(boost::shared_ptr<VesselNode<DIM> > pNode,
                                                                                                        bool sameVessel = true);

    std::pair<boost::shared_ptr<VesselSegment<DIM> >, units::quantity<unit::length> > GetNearestSegment(const DimensionalChastePoint<DIM>& rLocation);

    boost::shared_ptr<Vessel<DIM> > GetNearestVessel(const DimensionalChastePoint<DIM>& rLocation);

    unsigned GetNodeIndex(boost::shared_ptr<VesselNode<DIM> > pNode);

    unsigned NumberOfNodesNearLocation(const DimensionalChastePoint<DIM>&  rLocation, double tolerance = 0.0);

    std::pair<DimensionalChastePoint<DIM>, DimensionalChastePoint<DIM> > GetExtents(bool useRadii = false);

    boost::shared_ptr<VesselNode<DIM> > GetNode(unsigned index);

    std::vector<boost::shared_ptr<VesselNode<DIM> > > GetNodes();

    unsigned GetNumberOfNodes();

    unsigned GetNumberOfVesselNodes();

    unsigned GetNumberOfVessels();

    unsigned GetMaxBranchesOnNode();

    std::map<std::string, double> GetOutputData();

    std::vector<boost::shared_ptr<VesselNode<DIM> > > GetVesselEndNodes();

    unsigned GetVesselIndex(boost::shared_ptr<Vessel<DIM> > pVessel);

    unsigned GetVesselSegmentIndex(boost::shared_ptr<VesselSegment<DIM> > pVesselSegment);

    std::vector<boost::shared_ptr<VesselSegment<DIM> > > GetVesselSegments();

    boost::shared_ptr<Vessel<DIM> > GetVessel(unsigned index);

    std::vector<boost::shared_ptr<Vessel<DIM> > > GetVessels();

    bool NodeIsInNetwork(boost::shared_ptr<VesselNode<DIM> > pSourceNode);

    void MergeShortVessels(units::quantity<unit::length> cutoff = 10.0 * 1.e-6 * unit::metres);

    void MergeCoincidentNodes(double tolerance = 0.0);

    void MergeCoincidentNodes(std::vector<boost::shared_ptr<Vessel<DIM> > > pVessels, double tolerance = 0.0);

    void MergeCoincidentNodes(std::vector<boost::shared_ptr<VesselNode<DIM> > > nodes, double tolerance = 0.0);

    void RemoveVessel(boost::shared_ptr<Vessel<DIM> > pVessel, bool deleteVessel = false);

    void RemoveShortVessels(units::quantity<unit::length> cutoff = 10.0* 1.e-6 * unit::metres, bool endsOnly = true);

    void SetNodeRadii(units::quantity<unit::length> radius);

    void SetNodeRadiiFromSegments();

    void SetSegmentProperties(boost::shared_ptr<VesselSegment<DIM> > prototype);

    void SetSegmentRadii(units::quantity<unit::length> radius);

    void SetSegmentViscosity(units::quantity<unit::dynamic_viscosity> viscosity);

    void Translate(DimensionalChastePoint<DIM> rTranslationVector);

    void Translate(DimensionalChastePoint<DIM> rTranslationVector, std::vector<boost::shared_ptr<Vessel<DIM> > > vessels);

    void UpdateNodes();

    void UpdateSegments();

    void UpdateVesselNodes();

    void UpdateVesselIds();

    void UpdateAll(bool merge=false);

    bool VesselCrossesLineSegment(const DimensionalChastePoint<DIM>& rCoord1, const DimensionalChastePoint<DIM>& rCoord2, double tolerance = 1e-6);

    void Write(const std::string& rFileName);

};

#endif /* VESSELNETWORK_HPP_ */