#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{

	//! Derived geometric class based on a spatial object.
	/*!
	A derived class of the Geometrical ABC, this class provides
	the framework with the functionality of ITK mesh spatial objects.
	Creating a deformable organism is made easy with this class, as it
	can import any triangulated mesh spatial object contained in a
	meta file. It can also convert triangulated BYU surfaces to meta
	format, and import those. The primary restriction of this class is
	that it must be a triangulated mesh and, as such, parts of this
	classes functionality are currently restricted to 3D.
	Specifically, its ability to generate binary images from mesh
	objects. This class is also designed specifically to complement
	the Phys_LevelSet class. This class is currently classified as
	unstable, since it is constantly evolving to meet the changing
	needs of our framework.
	\param dType The data type used for numerical storage.
	\param nDims The number of dimensions.
	\param MType The matrix type used for internal matrix storage. Defaults to vnl_matrix<dType>. Only vnl is supported at this time.
	\param VType The vector type used for internal vector storage. Defaults to vnl_vector<dType>. Only vnl is supported at this time.
	*/
	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:
		//! The default constructor
		/*!
		\param p The precision used to check if a point lies inside the object for conversion to a binary image.
		*/
		Geom_MeshSpatialObject(dType p=0.001);

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