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

  Program:   Insight Segmentation & Registration Toolkit
  Module:    VectorCurvatureAnisotropicDiffusionImageFilter.cxx
  Language:  C++
  Date:      $Date$
  Version:   $Revision$

  Copyright (c) Insight Software Consortium. All rights reserved.
  See ITKCopyright.txt or http://www.itk.org/HTML/Copyright.htm for details.

     This software is distributed WITHOUT ANY WARRANTY; without even 
     the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
     PURPOSE.  See the above copyright notices for more information.

=========================================================================*/
#if defined(_MSC_VER)
#pragma warning ( disable : 4786 )
#endif

#ifdef __BORLANDC__
#define ITK_LEAN_AND_MEAN
#endif

//  Software Guide : BeginLatex
//
//  The \doxygen{VectorCurvatureAnisotropicDiffusionImageFilter} performs
//  anisotropic diffusion on a vector image using a modified curvature
//  diffusion equation (MCDE).  The MCDE is the same described in
//  \ref{sec:CurvatureAnisotropicDiffusionImageFilter}.
//
//  Typically in vector-valued diffusion, vector components are diffused
//  independently of one another using a conductance term that is linked across
//  the components. 
//
//  This filter is designed to process images of \doxygen{Vector} type.  The
//  code relies on various typedefs and overloaded operators defined in
//  Vector. It is perfectly reasonable, however, to apply this
//  filter to images of other, user-defined types as long as the appropriate
//  typedefs and operator overloads are in place.  As a general rule, follow
//  the example of the Vector class in defining your data types.
//
//  \index{itk::Vector\-Curvature\-Anisotropic\-Diffusion\-Image\-Filter}
//
//  Software Guide : EndLatex 


#include "itkImage.h"
#include "itkImageFileReader.h"
#include "itkImageFileWriter.h"
#include "itkRescaleIntensityImageFilter.h"
#include "itkGradientRecursiveGaussianImageFilter.h"
#include "itkVectorIndexSelectionCastImageFilter.h"


//  Software Guide : BeginLatex
//
//  The first step required to use this filter is to include its header file.
//
//  \index{itk::Vector\-Curvature\-Anisotropic\-Diffusion\-Image\-Filter!header}
//
//  Software Guide : EndLatex 

// Software Guide : BeginCodeSnippet
#include "itkVectorCurvatureAnisotropicDiffusionImageFilter.h"
// Software Guide : EndCodeSnippet


int main( int argc, char * argv[] )
{
  if( argc < 6 ) 
    { 
    std::cerr << "Usage: " << std::endl;
    std::cerr << argv[0] << "  inputImageFile  outputGradientImageFile ";
    std::cerr << "outputSmoothedGradientImageFile ";
    std::cerr << "numberOfIterations  timeStep  " << std::endl;
    return EXIT_FAILURE;
    }

  
  //  Software Guide : BeginLatex
  //
  //  Types should be selected based on required pixel type for the input and
  //  output images.  The image types are defined using the pixel type and
  //  the dimension.
  //
  //  Software Guide : EndLatex 

  // Software Guide : BeginCodeSnippet
  typedef    float    InputPixelType;
  typedef itk::CovariantVector<float,2>    VectorPixelType;
  typedef itk::Image< InputPixelType,  2 >   InputImageType;
  typedef itk::Image< VectorPixelType, 2 >   VectorImageType;
  // Software Guide : EndCodeSnippet


  typedef itk::ImageFileReader< InputImageType >  ReaderType;
  ReaderType::Pointer reader = ReaderType::New();
  reader->SetFileName( argv[1] );


  //  Software Guide : BeginLatex
  //
  //  The filter type is now instantiated using both the input image and the
  //  output image types. The filter object is created by the \code{New()}
  //  method.
  //
  //  \index{itk::Vector\-Curvature\-Anisotropic\-Diffusion\-Image\-Filter!instantiation}
  //  \index{itk::Vector\-Curvature\-Anisotropic\-Diffusion\-Image\-Filter!New()}
  //  \index{itk::Vector\-Curvature\-Anisotropic\-Diffusion\-Image\-Filter!Pointer}
  //
  //  Software Guide : EndLatex 

  // Software Guide : BeginCodeSnippet
  typedef itk::VectorCurvatureAnisotropicDiffusionImageFilter<
                       VectorImageType, VectorImageType >  FilterType;
  FilterType::Pointer filter = FilterType::New();
  // Software Guide : EndCodeSnippet


  typedef itk::GradientRecursiveGaussianImageFilter< 
                       InputImageType, VectorImageType >   GradientFilterType;

  GradientFilterType::Pointer gradient = GradientFilterType::New();


  //  Software Guide : BeginLatex
  //
  //  The input image can be obtained from the output of another filter. Here,
  //  an image reader is used as source and its data is passed through a
  //  gradient filter in order to generate an image of vectors.
  //
  //  Software Guide : EndLatex 

  // Software Guide : BeginCodeSnippet
  gradient->SetInput( reader->GetOutput() );
  filter->SetInput( gradient->GetOutput() );
  // Software Guide : EndCodeSnippet

  const unsigned int numberOfIterations = atoi( argv[4] );
  const double       timeStep = atof( argv[5] );


  //  Software Guide : BeginLatex
  //
  //  This filter requires two parameters, the number of iterations to be
  //  performed and the time step used in the computation of the level set
  //  evolution. These parameters are set using the methods
  //  \code{SetNumberOfIterations()} and \code{SetTimeStep()} respectively.
  //  The filter can be executed by invoking \code{Update()}.
  //
  //  \index{itk::Vector\-Curvature\-Anisotropic\-Diffusion\-Image\-Filter!Update()}
  //  \index{itk::Vector\-Curvature\-Anisotropic\-Diffusion\-Image\-Filter!SetTimeStep()}
  //  \index{itk::Vector\-Curvature\-Anisotropic\-Diffusion\-Image\-Filter!SetNumberOfIterations()}
  //  \index{SetTimeStep()!itk::Vector\-Curvature\-Anisotropic\-Diffusion\-Image\-Filter}
  //  \index{SetNumberOfIterations()!itk::Vector\-Curvature\-Anisotropic\-Diffusion\-Image\-Filter}
  //
  //  Software Guide : EndLatex 

  // Software Guide : BeginCodeSnippet
  filter->SetNumberOfIterations( numberOfIterations );
  filter->SetTimeStep( timeStep );
  filter->SetConductanceParameter(1.0);
  filter->Update();
  // Software Guide : EndCodeSnippet


  //  Software Guide : BeginLatex
  //
  //  Typical values for the time step are $0.125$ in $2D$ images and
  //  $0.0625$ in $3D$ images. The number of iterations can be usually around
  //  $5$, more iterations will result in further smoothing and will increase
  //  linearly the computing time.
  //
  //  Software Guide : EndLatex 


  //
  //  If the output of this filter has been connected to other filters down the
  //  pipeline, updating any of the downstream filters would have triggered the
  //  execution of this one. For example, a writer filter could have been used
  //  after the curvature flow filter.
  //
  typedef    float    OutputPixelType;
  typedef itk::Image< OutputPixelType,  2 >   OutputImageType;
  typedef itk::VectorIndexSelectionCastImageFilter< 
                  VectorImageType, OutputImageType > ComponentFilterType;
  ComponentFilterType::Pointer component = ComponentFilterType::New();

  // Select the component to extract.
  component->SetIndex( 0 );

  typedef unsigned char WritePixelType;
  typedef itk::Image< WritePixelType, 2 > WriteImageType;
  typedef itk::RescaleIntensityImageFilter< 
               OutputImageType, WriteImageType > RescaleFilterType;
  RescaleFilterType::Pointer rescaler = RescaleFilterType::New();
  rescaler->SetOutputMinimum(   0 );
  rescaler->SetOutputMaximum( 255 );
  
  typedef itk::ImageFileWriter< WriteImageType >  WriterType;
  WriterType::Pointer writer = WriterType::New();
  rescaler->SetInput( component->GetOutput() );
  writer->SetInput( rescaler->GetOutput() );

  // Save the component of the original gradient
  component->SetInput( gradient->GetOutput() );
  writer->SetFileName( argv[2] );
  writer->Update();


  // Save the component of the smoothed gradient
  component->SetInput( filter->GetOutput() );
  writer->SetFileName( argv[3] );
  writer->Update();


  //  Software Guide : BeginLatex
  //  
  // \begin{figure} \center
  // \includegraphics[width=0.44\textwidth]{VectorCurvatureAnisotropicDiffusionImageFilterInput.eps}
  // \includegraphics[width=0.44\textwidth]{VectorCurvatureAnisotropicDiffusionImageFilterOutput.eps}
  // \itkcaption[VectorCurvatureAnisotropicDiffusionImageFilter output]{Effect
  // of the VectorCurvatureAnisotropicDiffusionImageFilter on the $X$ component
  // of the gradient from a MRIproton density brain image.}
  // \label{fig:VectorCurvatureAnisotropicDiffusionImageFilterInputOutput}
  // \end{figure}
  //
  //  Figure~\ref{fig:VectorCurvatureAnisotropicDiffusionImageFilterInputOutput}
  //  illustrates the effect of this filter on a MRI proton density image of
  //  the brain. The images show the $X$ component of the gradient before
  //  (left) and after (right) the application of the filter. In this example
  //  the filter was run with a time step of 0.25, and 5 iterations.
  //
  //  Software Guide : EndLatex 

  return EXIT_SUCCESS;
}