#include "itkImage.h"
#include "itkImageFileReader.h"
#include "itkRecursiveGaussianImageFilter.h"
#include "itkRescaleIntensityImageFilter.h"
#include "itkRegionOfInterestImageFilter.h"
#include "itkImageFileWriter.h"
#include "itkCommand.h"

#include "itkDirectFourierReconstructionImageToImageFilter.h"

typedef double InternalPixelType;
typedef short int OutputPixelType;

typedef itk::Image< OutputPixelType, 3 > OutputImageType;
typedef itk::DirectFourierReconstructionImageToImageFilter< InternalPixelType, InternalPixelType > ReconstructionFilterType;
typedef ReconstructionFilterType::OutputImageType InternalImageType;

typedef itk::RecursiveGaussianImageFilter< InternalImageType, InternalImageType > SmootherType;
typedef itk::RescaleIntensityImageFilter< InternalImageType, OutputImageType > RescalerType;
typedef itk::RegionOfInterestImageFilter< OutputImageType, OutputImageType > ROIFilterType;
typedef itk::ImageFileReader< InternalImageType > ReaderType;
typedef itk::ImageFileWriter< OutputImageType > WriterType;



class CommandProgressUpdate : public itk::Command
{
	public:
		typedef CommandProgressUpdate Self;
		typedef itk::Command Superclass;
		
		typedef itk::SmartPointer< Self > Pointer;
		
		itkNewMacro( Self );
		
	protected:
		CommandProgressUpdate() {}; // purposely not implemented
	
		typedef const ReconstructionFilterType * ReconstructionFilterPointer;
	
		void Execute(itk::Object * caller, const itk::EventObject & event )
		{
			Execute( ( const itk::Object * )caller, event);
		}
		
		void Execute( const itk::Object * caller, const itk::EventObject & event )
		{
			ReconstructionFilterPointer reconstructor = dynamic_cast< ReconstructionFilterPointer >( caller );
			
			if ( ! itk::ProgressEvent().CheckEvent( &event ) )
			{
				return;
			}
			
			std::cout << (int)( 100 * reconstructor->GetProgress() ) << "%" << std::endl;
		}
};




int main (int argc, char * argv[] )
{

	if ( argc != 18)
	{
		std::cerr << "Wrong number of input arguments" << std::endl;
		std::cerr << "Usage : " << std::endl << "\t";
		std::cerr << argv[0] << " input output r_dir z_dir alpha_dir nz ng fc nb alpha_range x y z sx sy sz sigma" << std::endl;
		return 1;
	}

	ReaderType::Pointer reader = ReaderType::New();
	reader->SetFileName( argv[1] );
	
	
	SmootherType::Pointer smoother = SmootherType::New();
	smoother->SetInput( reader->GetOutput() );
	smoother->SetSigma( atof( argv[17] ) );
	smoother->SetDirection( atoi( argv[3] ) );
	
	
	
	
	ReconstructionFilterType::Pointer reconstruct = ReconstructionFilterType::New();
	if ( atof( argv[17] ) == 0 ) reconstruct->SetInput( reader->GetOutput() );
	else reconstruct->SetInput( smoother->GetOutput() );
	reconstruct->SetRDirection( atoi( argv[3] ) );
	reconstruct->SetZDirection( atoi( argv[4] ) );
	reconstruct->SetAlphaDirection( atoi( argv[5] ) );
	reconstruct->SetZeroPadding( atoi( argv[6] ) );
	reconstruct->SetOverSampling( atoi( argv[7] ) );
	reconstruct->SetCutoff( atof( argv[8] ) );
	reconstruct->SetRadialSplineOrder( atoi( argv[9] ) );
	reconstruct->SetAlphaRange( atoi( argv[10] ) );

	CommandProgressUpdate::Pointer observer = CommandProgressUpdate::New();
	reconstruct->AddObserver( itk::ProgressEvent(), observer );	
	
	
	
	RescalerType::Pointer rescaler = RescalerType::New();
	rescaler->SetInput( reconstruct->GetOutput() );
	rescaler->SetOutputMinimum( itk::NumericTraits< OutputPixelType >::min() );
	rescaler->SetOutputMaximum( itk::NumericTraits< OutputPixelType >::max() );
	
	
	
	ROIFilterType::Pointer ROIFilter = ROIFilterType::New();
	ROIFilter->SetInput( rescaler->GetOutput() );
	
	ROIFilterType::IndexType start;
	ROIFilterType::SizeType size;
	
	start[0] = atoi( argv[11] );
	start[1] = atoi( argv[12] );
	start[2] = atoi( argv[13] );
	
	size[0] = atoi( argv[14] );
	size[1] = atoi( argv[15] );
	size[2] = atoi( argv[16] );

	ROIFilterType::RegionType requestedRegion; 	
	requestedRegion.SetIndex( start );
	requestedRegion.SetSize( size );
	
	ROIFilter->SetRegionOfInterest( requestedRegion );
	
	
	
	
	WriterType::Pointer writer = WriterType::New();
	writer->SetFileName( argv[2] );
	writer->SetInput( ROIFilter->GetOutput() );

	
	
	
	
	
	try 
	{
		writer->Update();	
	} 
	catch ( itk::ExceptionObject err )
	{
		std::cerr << "An error occurred somewhere:" << std::endl;
		std::cerr << err << std::endl;
		return 2;
	}

	std::cout << "Done" << std::endl;
	
	std::cout << reconstruct << std::endl;

	return 0;

} // main