/*=========================================================================
  Program:   Insight Segmentation & Registration Toolkit
  Module:    $RCSfile: OtsuThresholdImageFilter.cxx,v $
  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
//
// This example illustrates how to use the \doxygen{OtsuThresholdImageFilter}.
//
// Software Guide : EndLatex 

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

#include "itkImage.h"
#include "itkImageFileReader.h"
#include "itkImageFileWriter.h"

#include "itkPluginFilterWatcher.h"

#include "OtsuThresholdImageFilterCLP.h"

// Use an anonymous namespace to keep class types and function names
// from colliding when module is used as shared object module.  Every
// thing should be in an anonymous namespace except for the module
// entry point, e.g. main()
//
namespace {

} // end of anonymous namespace


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

  PARSE_ARGS;

  //  Software Guide : BeginLatex
  //
  //  The next step is to decide which pixel types to use for the input and output
  //  images.
  //
  //  Software Guide : EndLatex 

  // Software Guide : BeginCodeSnippet
  typedef  short  InputPixelType;
  typedef  short  OutputPixelType;
  // Software Guide : EndCodeSnippet


  //  Software Guide : BeginLatex
  //
  //  The input and output image types are now defined using their respective
  //  pixel types and dimensions.
  //
  //  Software Guide : EndLatex 

  // Software Guide : BeginCodeSnippet
  typedef itk::Image< InputPixelType,  3 >   InputImageType;
  typedef itk::Image< OutputPixelType, 3 >   OutputImageType;
  // Software Guide : EndCodeSnippet


  //  Software Guide : BeginLatex
  //
  //  The filter type can be instantiated using the input and output image
  //  types defined above.
  //
  //  Software Guide : EndLatex 

  // Software Guide : BeginCodeSnippet
  typedef itk::OtsuThresholdImageFilter<
               InputImageType, OutputImageType >  FilterType;
  // Software Guide : EndCodeSnippet


  //  Software Guide : BeginLatex
  //
  //  An \doxygen{ImageFileReader} class is also instantiated in order to read
  //  image data from a file. (See Section \ref{sec:IO} on page 
  //  \pageref{sec:IO} for more information about reading
  //  and writing data.) 
  //
  //  Software Guide : EndLatex 

  // Software Guide : BeginCodeSnippet
  typedef itk::ImageFileReader< InputImageType >  ReaderType;
  // Software Guide : EndCodeSnippet


  //  Software Guide : BeginLatex
  //  
  // An \doxygen{ImageFileWriter} is instantiated in order to write the output
  // image to a file.
  //
  //  Software Guide : EndLatex 


  // Software Guide : BeginCodeSnippet
  typedef itk::ImageFileWriter< OutputImageType >  WriterType;
  // Software Guide : EndCodeSnippet


  //  Software Guide : BeginLatex
  //
  //  Both the filter and the reader are created by invoking their \code{New()}
  //  methods and assigning the result to \doxygen{SmartPointer}s.
  //
  //  Software Guide : EndLatex 

  // Software Guide : BeginCodeSnippet
  ReaderType::Pointer reader = ReaderType::New();
  FilterType::Pointer filter = FilterType::New();
  itk::PluginFilterWatcher watcher(filter, "Otsu Threshold Image Filter",
                                   CLPProcessInformation);

  // Software Guide : EndCodeSnippet

  WriterType::Pointer writer = WriterType::New();
  writer->SetInput( filter->GetOutput() );
  writer->SetUseCompression(1);
  reader->SetFileName( inputVolume.c_str() );


  //  Software Guide : BeginLatex
  //  
  //  The image obtained with the reader is passed as input to the
  //  OtsuThresholdImageFilter.
  //
  //  \index{itk::Otsu\-Threshold\-Image\-Filter!SetInput()}
  //  \index{itk::FileImageReader!GetOutput()}
  //
  //  Software Guide : EndLatex 

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


  //  Software Guide : BeginLatex
  //  
  //  The method \code{SetOutsideValue()} defines the intensity value to be
  //  assigned to those pixels whose intensities are outside the range defined
  //  by the lower and upper thresholds. The method \code{SetInsideValue()}
  //  defines the intensity value to be assigned to pixels with intensities
  //  falling inside the threshold range.
  //  
  //  \index{itk::Otsu\-Threshold\-Image\-Filter!SetOutsideValue()}
  //  \index{itk::Otsu\-Threshold\-Image\-Filter!SetInsideValue()}
  //  \index{SetOutsideValue()!itk::Otsu\-Threshold\-Image\-Filter}
  //  \index{SetInsideValue()!itk::Otsu\-Threshold\-Image\-Filter}
  //
  //  Software Guide : EndLatex 

  // Software Guide : BeginCodeSnippet
  filter->SetOutsideValue( outsideValue );
  filter->SetInsideValue(  insideValue  );
  // Software Guide : EndCodeSnippet


  //  Software Guide : BeginLatex
  //  
  //  The method \code{SetNumberOfHistogramBins()} defines the number of bins
  //  to be used for computing the histogram. This histogram will be used
  //  internally in order to compute the Otsu threshold.
  //
  //  Software Guide : EndLatex 

  // Software Guide : BeginCodeSnippet
  filter->SetNumberOfHistogramBins( numberOfBins );
  // Software Guide : EndCodeSnippet


  //  Software Guide : BeginLatex
  //  
  //  The execution of the filter is triggered by invoking the \code{Update()}
  //  method.   If the filter's output has been passed as input to subsequent
  //  filters, the \code{Update()} call on any posterior filters in the
  //  pipeline will indirectly trigger the update of this filter.
  //
  //  Software Guide : EndLatex 

  // Software Guide : BeginCodeSnippet
  filter->Update();
  // Software Guide : EndCodeSnippet



  //  Software Guide : BeginLatex
  //  
  //  We print out here the Threshold value that was computed internally by the
  //  filter. For this we invoke the \code{GetThreshold} method.
  //
  //  Software Guide : EndLatex 

  // Software Guide : BeginCodeSnippet
  int threshold = filter->GetThreshold();
  std::cout << "Threshold = " << threshold << std::endl;
  // Software Guide : EndCodeSnippet



  //  Software Guide : BeginLatex
  //  
  // \begin{figure}
  // \center
  // \includegraphics[width=0.44\textwidth]{BrainProtonDensitySlice.eps}
  // \includegraphics[width=0.44\textwidth]{OtsuThresholdImageFilterOutput.eps}
  // \itkcaption[OtsuThresholdImageFilter output]{Effect of the OtsuThresholdImageFilter on a slice from a MRI
  // proton density image  of the brain.}
  // \label{fig:OtsuThresholdImageFilterInputOutput}
  // \end{figure}
  //
  //  Figure \ref{fig:OtsuThresholdImageFilterInputOutput} illustrates the
  //  effect of this filter on a MRI proton density image of the brain. This
  //  figure shows the limitations of this filter for performing segmentation
  //  by itself. These limitations are particularly noticeable in noisy images
  //  and in images lacking spatial uniformity as is the case with MRI due to
  //  field bias.
  //
  //  \relatedClasses
  //  \begin{itemize}
  //  \item \doxygen{ThresholdImageFilter}
  //  \end{itemize}
  //
  //  Software Guide : EndLatex 

  writer->SetFileName( outputVolume.c_str() );
  writer->Update();

  return EXIT_SUCCESS;
}

