/*=============================================================================

Julio Lajara
CSCI-4968 Open Source Software Practice
Project 2: ITK Image Segmentation

Purpose: Use ITK libraries to perform image segmentation on a brain data set
         in order to isolate the ventricles in the image.

Compiler: MS Visual Studio 2005

=============================================================================*/

/*=============================================================================
		IMPORTED LIBRARIES
=============================================================================*/

//Image Reading/Writing Libraries
#include "itkImageFileReader.h" 
#include "itkImageFileWriter.h"

//Image Segmentation and Processing Libraries
#include "itkConnectedThresholdImageFilter.h"
#include "itkCurvatureFlowImageFilter.h"
#include "itkCastImageFilter.h"

#include <sstream>

using std::stringstream;

/*=============================================================================
		MAIN SEGMENTATION APPLICATION
=============================================================================*/

int main(int argc, char* argv[])
{
	if(argc != 8)
	{
		using std::cerr;

		cerr << "Usage: " << argv[0] << " [input file] [output file] [lowerThreshold (int)] "
			 << "[upperThreshold (int)] [seedIndex-x (float)] [seedIndex-y (float)] [seedIndex-z (float)]\n\n";

		return EXIT_FAILURE;
	}

	stringstream strToDigBuf;									//String to digit conversion buffer

	typedef float PixelTypef;									//Float Image Pixel Type
	typedef unsigned short PixelTypei;							//Integer Image Pixel Type

	const unsigned int Dim3D = 3;								//3D Image Dimensions
	const unsigned int Dim2D = 2;								//2D Image Dimensions

	typedef itk::Image< PixelTypef, Dim3D > ImageType3D;		//3D Float Image
	typedef itk::Image< PixelTypef, Dim2D > ImageType2D;        //2D Float Image

	typedef itk::Image< PixelTypei, Dim3D > ImageType3Di;		//3D Integer Image
	typedef itk::Image< PixelTypei, Dim2D > ImageType2Di;       //2D Interger Image

	typedef itk::ImageFileReader< ImageType3D > ReaderType3D;	//3D Image Reader
	typedef itk::ImageFileWriter< ImageType3Di > WriterType3Di; //3Di Image Writer

	ReaderType3D::Pointer reader3D = ReaderType3D::New();       //Create 3D Image Reader
	WriterType3Di::Pointer writer3Di = WriterType3Di::New();    //Create 3D Image Writer

	typedef itk::CurvatureFlowImageFilter< ImageType3D, ImageType3D > CurvatureFlowImageFilterType3D; //Image Processing Filter
	typedef itk::ConnectedThresholdImageFilter< ImageType3D, ImageType3D > ConnectedFilterType3D;	  //Region Growing Filter
	typedef itk::CastImageFilter< ImageType3D, ImageType3Di > CastFilterType3D;					      //Pixel Type Cast Filter

	CurvatureFlowImageFilterType3D::Pointer smoothing3D = CurvatureFlowImageFilterType3D::New();      //Create Processing Filter

	ConnectedFilterType3D::Pointer connectedThreshold3D = ConnectedFilterType3D::New();               //Create Growing Filter

	CastFilterType3D::Pointer castFilter3D = CastFilterType3D::New();								  //Create Pixel Type Cast Filter

	reader3D->SetFileName( argv[1] );								//Set read input file name
	writer3Di->SetFileName( argv[2] );								//Set write output file name

	smoothing3D->SetInput( reader3D->GetOutput() );					//Send image reader output into smoothing filter
	connectedThreshold3D->SetInput( smoothing3D->GetOutput() );		//Send smoothing filter output into growing filter
	castFilter3D->SetInput( connectedThreshold3D->GetOutput() );	//Send growing filter output into pixel cast filter
	writer3Di->SetInput( castFilter3D->GetOutput() );				//Send pixel cast filter output into image writer

	smoothing3D->SetNumberOfIterations( 10 );						//Smoothing Iterations for higher smoothness
	smoothing3D->SetTimeStep( 0.0625 );								//Delta Time step

	int lowerThreshold, upperThreshold;								//Intensity threshold range

	strToDigBuf << argv[3] << " " << argv[4];						//Buffer intensity threshold range

	strToDigBuf >> lowerThreshold >> upperThreshold;				//Convert intensity threshold range

	connectedThreshold3D->SetLower( lowerThreshold );				//Set growing filter lower threshold value
	connectedThreshold3D->SetUpper( upperThreshold );				//Set growing filter upper threshold value

	connectedThreshold3D->SetReplaceValue( 255 );					//Set threshold intensity value to highest possible

	float seedIndexX, seedIndexY, seedIndexZ;						//Seed Index components

	strToDigBuf.clear();											//Reset buffer for reuse
	strToDigBuf.str("");

	strToDigBuf << argv[5] << " " << argv[6] << " " << argv[7];		//Buffer seed index components

	strToDigBuf >> seedIndexX >> seedIndexY >> seedIndexZ;			//Convert seed index components

	itk::Index<3> seedIndex3D = {seedIndexX, seedIndexY, 
								 seedIndexZ};						//Create the starting seed point index

	connectedThreshold3D->SetSeed( seedIndex3D );					//Set seed point index

	try
	{	
		writer3Di->Update();										//Begin processing of pipeline
	}
	catch( itk::ExceptionObject & err )								//Catch error processing pipeline
	{
		using std::cerr;

		cerr << "Exception Thrown: " << err << "\n\n";
		return EXIT_FAILURE;
	}

	return 0;
}