#include <iostream>

#include "itkVectorGradientAnisotropicDiffusionImageFilter.h"
#include "itkVectorGradientMagnitudeImageFilter.h"
#include "itkWatershedImageFilter.h"

#include "itkImageFileReader.h"
#include "itkImageFileWriter.h"
#include "itkVectorCastImageFilter.h"
#include "itkUnaryFunctorImageFilter.h"
#include "itkScalarToRGBPixelFunctor.h"


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

  typedef itk::RGBPixel<unsigned char>   RGBPixelType;
  typedef itk::Image<RGBPixelType, 3>    RGBImageType;
  typedef itk::Vector<float, 3>          VectorPixelType;
  typedef itk::Image<VectorPixelType, 3> VectorImageType;
  typedef itk::Image<unsigned long, 3>   LabeledImageType;
  typedef itk::Image<float, 3>           ScalarImageType;

  typedef itk::ImageFileReader<RGBImageType> FileReaderType;
  typedef itk::VectorCastImageFilter<RGBImageType, VectorImageType> 
    CastFilterType;
  typedef itk::VectorGradientAnisotropicDiffusionImageFilter<VectorImageType,
    VectorImageType>  DiffusionFilterType;
  typedef itk::VectorGradientMagnitudeImageFilter<VectorImageType>
    GradientMagnitudeFilterType; 
  typedef itk::WatershedImageFilter<ScalarImageType> WatershedFilterType;

  typedef itk::ImageFileWriter<RGBImageType> FileWriterType;

  FileReaderType::Pointer reader = FileReaderType::New();
  reader->SetFileName("Normal107-T2.mha");
  
  CastFilterType::Pointer caster = CastFilterType::New();
  

  DiffusionFilterType::Pointer diffusion = DiffusionFilterType::New();
  diffusion->SetNumberOfIterations(5.0);
  diffusion->SetConductanceParameter(9.0);
  diffusion->SetTimeStep(0.0625);


  GradientMagnitudeFilterType::Pointer 
    gradient = GradientMagnitudeFilterType::New();
  gradient->SetUsePrincipleComponents(false);


  WatershedFilterType::Pointer watershed = WatershedFilterType::New();
  watershed->SetLevel(0.2);
  watershed->SetThreshold(0.01);


  typedef itk::Functor::ScalarToRGBPixelFunctor<unsigned long>
    ColorMapFunctorType;
  typedef itk::UnaryFunctorImageFilter<LabeledImageType,
    RGBImageType, ColorMapFunctorType> ColorMapFilterType;
  ColorMapFilterType::Pointer colormapper = ColorMapFilterType::New();


  caster->SetInput(reader->GetOutput());
  diffusion->SetInput(caster->GetOutput());
  gradient->SetInput(diffusion->GetOutput());
  watershed->SetInput(gradient->GetOutput());
  colormapper->SetInput(watershed->GetOutput());


  FileWriterType::Pointer writer = FileWriterType::New();
  writer->SetFileName("Normal107-T2.mhd");
  writer->SetInput(colormapper->GetOutput());
  writer->Update();
    
  return 0;
}