#ifndef __DefOrgViewerAdapterBaseTemplated_h
#define __DefOrgViewerAdapterBaseTemplated_h

#include "itkImageFileReader.h"
#include "itkImageFileWriter.h"

#include "vtkUnstructuredGrid.h"
#include "vtkCellArray.h"
#include "vtkProperty.h"

#include <iostream>

#include "itkImage.h"
#include "itkImageFileReader.h"
#include "vtkImageImport.h"
#include "itkVTKImageExport.h"
#include "DefOrgViewerAdapterBaseTemplated.h"
#include "DefOrgViewerAdapterBase.h"
#include "itkTriangleCell.h"
#include "itkQuadrilateralCell.h"
#include "itkDefaultDynamicMeshTraits.h"
#include "itkMesh.h"

#include <vtksys/SystemTools.hxx>
#include <vtksys/CommandLineArguments.hxx>
namespace mial{

#define N_DIMS 3
template<class MESHTYPE> class VistVTKCellsClass;
/*!Provide convience templated helper methods for derived classes*/
template <class ITKPIXELTYPE, class MESHDATATYPE>
class DefOrgViewerAdapterBaseTemplated:public DefOrgViewerAdapterBase{
public:

	//Constructor
	DefOrgViewerAdapterBaseTemplated(int maxNumImages):DefOrgViewerAdapterBase(maxNumImages){};

	//convenient typedefs for derived base classes
	typedef ITKPIXELTYPE									PixelType;
	typedef MESHDATATYPE									DataType;
	typedef typename itk::Image< PixelType, N_DIMS >		ImageType;
	typedef typename ImageType::Pointer						ImageTypePointer;
	typedef typename itk::ImageFileReader< ImageType >		ImageFileReader;
	typedef typename ImageFileReader::Pointer				ImageFileReaderPointer;
	typedef typename itk::VTKImageExport< ImageType >		itkImageExportType;
	typedef typename itkImageExportType::Pointer			itkImageExportTypePointer;
	typedef typename itk::SceneSpatialObject<N_DIMS>::Pointer		itkScenePointer;

	typedef typename itk::DefaultDynamicMeshTraits<
		DataType, N_DIMS, N_DIMS >							MeshTrait;
	typedef  typename itk::Mesh< DataType, N_DIMS, MeshTrait >		MeshType;
	typedef typename MeshType::CellTraits				MeshTypeCellTraits;
	typedef  typename MeshType::Pointer								MeshTypePointer;

	// typedefs for itk->vtk mesh conversion:
	typedef typename itk::TriangleCell< typename itk::CellInterface<MESHDATATYPE, MeshTypeCellTraits > > 
		 TriangleCell;
	typedef typename itk::CellInterfaceVisitorImplementation<
		DataType, MeshTypeCellTraits, TriangleCell, VistVTKCellsClass<typename DefOrgViewerAdapterBaseTemplated::MeshType> >
		 TriangleVisitor;
	typedef typename itk::QuadrilateralCell< typename itk::CellInterface<MESHDATATYPE, MeshTypeCellTraits > > QuadrilateralCell;
	typedef typename itk::CellInterfaceVisitorImplementation<
		DataType, MeshTypeCellTraits, QuadrilateralCell, VistVTKCellsClass<typename DefOrgViewerAdapterBaseTemplated::MeshType> > 
		QuadrilateralVisitor;
	
	virtual void SetupOrganism()=0;
	virtual void UpdateOrganism()=0;
	virtual void PopulateVtkImage()=0;
	virtual void PopulateVtkImageHelper(ImageTypePointer itkImage, vtkImageImport* vtkImporter);
	virtual void PopulateVtkUnstructuredGrid(vtkUnstructuredGrid* vtkGrid )=0;
	virtual void PopulateItkScene()=0;
	
protected:
	/*!Connect vtk and itk pipelines for image volumes*/
	virtual void ConnectPipelines( itkImageExportTypePointer exporter, vtkImageImport* importer);
	/*!Convert itk mesh into vtk unstructured grid.  Currently not used because SOViewer is used instead*/
	virtual void MeshToUnstructuredGrid( MeshTypePointer mesh, vtkUnstructuredGrid* vgrid);	

	ImageFileReaderPointer			m_InputImageReader;	
private:
	std::vector<itkImageExportTypePointer> m_itkImageExportPointerHolder;
};

/*!Internal class for MeshToUnstructuredGrid.  Do not use*/
template <class MESHTYPE>
class VistVTKCellsClass
{
	vtkCellArray* m_Cells;
	int* m_LastCell;
	int* m_TypeArray;
	public:
		// typedef the itk cells we are interested in
		typedef itk::CellInterface<
		typename MESHTYPE::PixelType, 
		typename MESHTYPE::CellTraits >  CellInterfaceType;

		typedef itk::TriangleCell<CellInterfaceType>      floatTriangleCell;
		typedef itk::QuadrilateralCell<CellInterfaceType> floatQuadrilateralCell;

		// Set the vtkCellArray that will be constructed
		void SetCellArray(vtkCellArray* a) 
		{
			m_Cells = a;
		}
		// Set the cell counter pointer
		void SetCellCounter(int* i)
		{
			m_LastCell = i;
		}
		// Set the type array for storing the vtk cell types
		void SetTypeArray(int* i)
		{
			m_TypeArray = i;
		}
		// Visit a triangle and create the VTK_TRIANGLE cell 
		void Visit(unsigned long, floatTriangleCell* t)
		{
			m_Cells->InsertNextCell(3,  (vtkIdType*)t->PointIdsBegin());
			m_TypeArray[*m_LastCell] = VTK_TRIANGLE;
			(*m_LastCell)++;
		}
		// Visit a triangle and create the VTK_QUAD cell 
		void Visit(unsigned long, floatQuadrilateralCell* t)
		{
			m_Cells->InsertNextCell(4,  (vtkIdType*)t->PointIdsBegin());
			m_TypeArray[*m_LastCell] = VTK_QUAD;
			(*m_LastCell)++;
		}
};

}
#endif