//  Software Guide : BeginLatex
//
//  The following code is an implementation of a small Insight
//  program. It tests including header files and linking with ITK
//  libraries.
//
//  Software Guide : EndLatex 

// Software Guide : BeginCodeSnippet
#include "itkImage.h"
#include <iostream>
#include "itkImageFileReader.h"
#include "itkImageFileWriter.h"
#include "itkConnectedThresholdImageFilter.h"

int main()
{
  typedef short      PixelType;
  const   unsigned int        Dimension = 3;
  typedef itk::Image< PixelType, Dimension >    ImageType;
  typedef itk::ImageFileReader< ImageType >  ReaderType;
  typedef itk::ImageFileWriter< ImageType >  WriterType;
  typedef itk::ConnectedThresholdImageFilter< ImageType, ImageType > ConnectedFilterType;
  ConnectedFilterType::Pointer connectedThreshold = ConnectedFilterType::New();

  itk::Index<3> index = {{ 100, 119, 69 }};

  ReaderType::Pointer reader = ReaderType::New();
  WriterType::Pointer writer = WriterType::New();

  reader->SetFileName( "Normal066-T2.mhd" );
  writer->SetFileName( "Segment066.mhd" );

  connectedThreshold->SetInput( reader->GetOutput() );
  writer->SetInput( connectedThreshold->GetOutput() );

  connectedThreshold->SetLower( 2000 );
  connectedThreshold->SetUpper( 2300 );

  connectedThreshold->SetReplaceValue( 255 );

  connectedThreshold->SetSeed( index );

  try 
    { 
    writer->Update(); 
    } 
  catch( itk::ExceptionObject & excep ) 
    { 
    std::cerr << "ExceptionObject caught !" << std::endl; 
    std::cerr << excep << std::endl; 
    return EXIT_FAILURE;
    }

  return 0;
}
// Software Guide : EndCodeSnippet

//  Software Guide : BeginLatex
//
//  This code instantiates a $3D$ image\footnote{Also known as a
//  \emph{volume}.} whose pixels are represented with type \code{unsigned
//  short}. The image is then constructed and assigned to a
//  \doxygen{SmartPointer}. Although later in the text we will discuss
//  \code{SmartPointer}'s in detail, for now think of it as a handle on an
//  instance of an object (see section \ref{sec:SmartPointers} for more
//  information).  The \doxygen{Image} class will be described in
//  Section~\ref{sec:ImageSection}.
//
//  Software Guide : EndLatex