/*=========================================================================
  Program:   Insight Segmentation & Registration Toolkit
  Module:    OtsuMultipleThresholdImageFilter.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 : BeginCommandLineArgs
//    INPUTS: {BrainProtonDensitySlice.png}
//    OtsuMultipleThresholdsOutput png 4
//  Software Guide : EndCommandLineArgs

// Software Guide : BeginLatex
// This example illustrates how to use the \doxygen{OtsuMultipleThresholdsCalculator}.
// Software Guide : EndLatex 

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

#include "itkImage.h"
#include "itkImageFileReader.h"
#include "itkImageFileWriter.h"
#include "itkScalarImageToHistogramGenerator.h"
#include "itkBinaryThresholdImageFilter.h"
#include "itkNumericTraits.h"

#include <stdio.h>
int main( int argc, char * argv[] )
{
  if( argc < 5 )
    {
    std::cerr << "Usage: " << argv[0];
    std::cerr << " inputImageFile outputImageFileBase ";  
    std::cerr << "  outputImageFileExtension numberOfThresholdsToCalculate "  << std::endl;  
    return EXIT_FAILURE;
    }
  
  //Convenience typedefs
  typedef  unsigned short  InputPixelType;
  typedef  unsigned char   OutputPixelType;
  
  typedef itk::Image< InputPixelType,  2 >   InputImageType;
  typedef itk::Image< OutputPixelType, 2 >   OutputImageType;
  
  // Software Guide : BeginLatex
  //
  // OtsuMultipleThresholdsCalculator calculates thresholds for a given
  // histogram so as to maximize the between-class variance. We use
  // ScalarImageToHistogramGenerator to generate histograms. The histogram type
  // defined by the generator is then used for instantiating the type of the
  // Otsu threshold calculator. 
  // 
  // Software Guide : EndLatex

  // Software Guide : BeginCodeSnippet
  typedef itk::Statistics::ScalarImageToHistogramGenerator< 
  InputImageType > 
    ScalarImageToHistogramGeneratorType;

  typedef ScalarImageToHistogramGeneratorType::HistogramType    HistogramType;

  typedef itk::OtsuMultipleThresholdsCalculator< HistogramType >   CalculatorType;
  // Software Guide : EndCodeSnippet

  typedef itk::ImageFileReader< InputImageType >  ReaderType;
  typedef itk::ImageFileWriter< OutputImageType >  WriterType;


  // Software Guide : BeginLatex
  // 
  // Once thresholds are computed we will use BinaryThresholdImageFilter to 
  // segment the input image into segments.
  //
  // Software Guide : EndLatex

  // Software Guide : BeginCodeSnippet
  typedef itk::BinaryThresholdImageFilter< 
  InputImageType, OutputImageType >  FilterType;
  // Software Guide : EndCodeSnippet
  
  //Create using static New() method

  // Software Guide : BeginCodeSnippet
  ScalarImageToHistogramGeneratorType::Pointer scalarImageToHistogramGenerator = 
    ScalarImageToHistogramGeneratorType::New();

  CalculatorType::Pointer calculator = CalculatorType::New();
  FilterType::Pointer filter = FilterType::New();
  // Software Guide : EndCodeSnippet

  ReaderType::Pointer reader = ReaderType::New();
  WriterType::Pointer writer = WriterType::New();
  
  //Set Properties

  // Software Guide : BeginCodeSnippet
  scalarImageToHistogramGenerator->SetNumberOfBins( 128 );
  calculator->SetNumberOfThresholds( atoi( argv[4] ) );
  // Software Guide : EndCodeSnippet

  const OutputPixelType outsideValue = 0;
  const OutputPixelType insideValue = 255;

  filter->SetOutsideValue( outsideValue );
  filter->SetInsideValue(  insideValue  );

  //Connect Pipeline
  reader->SetFileName( argv[1] );

  // Software Guide : BeginLatex
  // The pipeline will look as follows:
  // Software Guide : EndLatex
  // Software Guide : BeginCodeSnippet
  scalarImageToHistogramGenerator->SetInput( reader->GetOutput() );
  calculator->SetInputHistogram( scalarImageToHistogramGenerator->GetOutput() );
  filter->SetInput( reader->GetOutput() );
  writer->SetInput( filter->GetOutput() );
  // Software Guide : EndCodeSnippet
  
  
  //Invoke pipeline
  try
    { 
    reader->Update();
    }
  catch( itk::ExceptionObject & excp )
    {
    std::cerr << "Exception thrown while reading image" << excp << std::endl;
    }
  scalarImageToHistogramGenerator->Compute();
  
  try
    { 
    calculator->Update();
    }
  catch( itk::ExceptionObject & excp )
    {
    std::cerr << "Exception thrown " << excp << std::endl;
    }

  // Software Guide : BeginLatex
  // Thresholds are obtained using the \code{GetOutput} method
  // \index{itk::OtsuMultipleThresholdsCalculator!GetOutput()}
  // Software Guide : EndLatex
  //Get Thresholds
  // Software Guide : BeginCodeSnippet
  const CalculatorType::OutputType &thresholdVector = calculator->GetOutput(); 
  CalculatorType::OutputType::const_iterator itNum = thresholdVector.begin();
  // Software Guide : EndCodeSnippet

  //Threshold into separate segments and write out as binary images
  std::string outputFileBase = argv[2];
  std::string outputFile;
  
  InputPixelType lowerThreshold = 0;
  InputPixelType upperThreshold;

  std::string format = argv[2];
    
  char outputFilename[1000];
  outputFile = outputFileBase + "%03d.";
  outputFile += argv[3];   // filename extension

  
  // Software Guide : BeginCodeSnippet
  for(; itNum < thresholdVector.end(); itNum++) 
    {
    std::cout << "OtsuThreshold["
              << (int)(itNum - thresholdVector.begin())
              << "] = " 
              << static_cast<itk::NumericTraits<CalculatorType::MeasurementType>::PrintType>(*itNum) 
              << std::endl;  
    // Software Guide : EndCodeSnippet
    
    upperThreshold = static_cast<InputPixelType>(*itNum);
    
    filter->SetLowerThreshold( lowerThreshold );
    filter->SetUpperThreshold( upperThreshold );

    lowerThreshold = upperThreshold;

    sprintf (outputFilename, outputFile.c_str(), (itNum - thresholdVector.begin()));
    writer->SetFileName( outputFilename );
    

    try
      { 
      writer->Update(); 
      }
    catch( itk::ExceptionObject & excp )
      {
      std::cerr << "Exception thrown " << excp << std::endl;
      }
    // Software Guide : BeginCodeSnippet
    }
  // Software Guide : EndCodeSnippet

  // Also write out the image thresholded between the upper threshold and
  // the max intensity.
  upperThreshold = itk::NumericTraits<InputPixelType>::max();
  filter->SetLowerThreshold( lowerThreshold );
  filter->SetUpperThreshold( upperThreshold );
  
  sprintf (outputFilename, outputFile.c_str(), (thresholdVector.size() ));
  writer->SetFileName( outputFilename );
    
  try
    { 
    writer->Update(); 
    }
  catch( itk::ExceptionObject & excp )
    {
    std::cerr << "Exception thrown " << excp << std::endl;
    }


  return EXIT_SUCCESS;
}