C:/cmcintos/defOrgs/source/geometrical/Geom_MeshSpatialObject.h

#if !defined(_GEOM_MESHSPATIALOBJECT)
#define _GEOM_MESHSPATIALOBJECT

#include "Geometric.h"
#include <itkMeshSpatialObject.h>
#include <itkSpatialObjectReader.h>
#include <itkSpatialObjectWriter.h>
#include <itkSpatialObjectToImageFilter.h>
#include <itkDefaultDynamicMeshTraits.h>
#include "itkLineCell.h"
#include "itkTriangleCell.h"
#include "itkImage.h"
#include <itkBinaryMask3DMeshSource.h>
#include <itkMinimumMaximumImageFilter.h>
#include "vnl/vnl_cross.h"
#include "itkImageRegionConstIterator.h"
#include "itkImageRegionIterator.h"
#include "itkTriangleMeshToBinaryImageFilter.h"

namespace mial{


        template < class dType, int nDims, class MType = vnl_matrix<dType>, class VType = vnl_vector<dType> >
        class Geom_MeshSpatialObject
                : public Geometric< dType, nDims, MType, VType >
        {
                /****************************************************
                MEMBERS
                *****************************************************/
        public:

                //Smartpointer
                typedef Geom_MeshSpatialObject Self;
                typedef itk::SmartPointer<Self>  Pointer;
                typedef itk::SmartPointer<const Self>  ConstPointer;
                typedef itk::WeakPointer<const Self>  ConstWeakPointer;
                itkNewMacro(Self);


                typedef MType MatrixType;
                typedef VType VectorType;

                typedef itk::DefaultDynamicMeshTraits< dType, nDims, nDims >    MeshTrait;
                typedef itk::Mesh< dType, nDims, MeshTrait >                    MeshType;
                typedef typename MeshType::PointType                            PointType;
                typedef typename itk::MeshSpatialObject< MeshType >             MeshSpatialObjectType;
                typedef typename MeshSpatialObjectType::Pointer                 MeshSpatialObjectPointerType;

                typename MeshSpatialObjectType::Pointer                         theMeshSpatialObject;
                typename MeshType::Pointer                                      theMesh;
                //Note you need to overwrite this whenever you overwrite the spatialobjects mesh

                typedef typename MeshType::CellType                             CellType;
                typedef typename CellType::CoordRepType                         CoordRepType;
                //typedef itk::LineCell< CellType >                             LineType;
                typedef itk::TriangleCell<CellType>                             TriangleType;
                typedef typename CellType::CellAutoPointer                      CellAutoPointer;
                typedef typename MeshType::CellsContainer::ConstIterator        CellIterator;

                typedef itk::GroupSpatialObject< nDims >                        GroupType;
                typedef itk::SpatialObjectReader<nDims,dType,MeshTrait>         ReaderType;
                typedef itk::SpatialObjectWriter< nDims, dType, MeshTrait >     WriterType;
                typename WriterType::Pointer                                    writer;

                typedef typename Geometric< dType, nDims >::BinaryImageType     BinaryImageType;
                typedef typename BinaryImageType::Pointer                       BinaryImageTypePointer;

                /*****************************************************
                METHODS
                ******************************************************/
        public:

                virtual MatrixType getMatrixNodePositions();

                virtual void writeNodesToFile(std::string fileName);

                virtual void readNodesFromFile(std::string fileName);
                virtual bool readTopologyFromFile(std::string fileName);

                virtual bool setMatrixNodePositions(MatrixType,int *);

                virtual bool setMatrixNodePositions(MatrixType);

                virtual void writeObjectToFile(std::string fileName);


                //TODO Fix to use correct type
                virtual typename itk::Image< unsigned char, nDims>::Pointer generateBinaryImageFromTopology( typename BinaryImageType::SizeType size);

                virtual void generateTopologyFromBinaryImage( BinaryImageTypePointer binaryInputImage );

                
                // TODO fill in code for adding/removing nodes
                virtual bool removeNode(int nodeNumber){return false;};
                virtual bool addNodes(MatrixType node,VectorType classes);
                virtual bool addConnection(int,int);
                virtual MatrixType getMatrixConnections(){/* TODO fill in implmentation.*/ return this->mConnections;};

                virtual bool isInside(VectorType p);
        private:
                virtual void updateMatrixNodePositions();
                virtual void updateMeshNodePositions();
                virtual void updateMatrixConnections();
                virtual bool intersectWithLine( VectorType L, VectorType P, TriangleType* tri);

                dType m_IsInsidePrecision;
        
        protected:

                Geom_MeshSpatialObject(dType p=0.001);

        };
}//end mial
#include "Geom_MeshSpatialObject.cxx"
#endif

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