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

  Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de
  l'Image). All rights reserved. See Doc/License.txt or
  http://www.creatis.insa-lyon.fr/Public/Gdcm/License.html 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.
                                                                             
=========================================================================*/

/**
 -------------------------------------------------------------------
 * @file   clitkGuerreroVentilationGenericFilter.cxx
 * @author Joël Schaerer
 * @date   20 April 2009

 * @brief  
 -------------------------------------------------------------------*/

#include "clitkGuerreroVentilationGenericFilter.h"
#include <itkBinaryGuerreroFilter.h>
#include <itkImageDuplicator.h>
#include <itkExtractImageFilter.h>

//--------------------------------------------------------------------
clitk::GuerreroVentilationGenericFilter::GuerreroVentilationGenericFilter() 
  :ImageToImageGenericFilter<Self>("GuerreroVentilationGenericFilter") {
  blood_mass_factor=1.;
  InitializeImageType<2>();
  InitializeImageType<3>();
}
//--------------------------------------------------------------------

//--------------------------------------------------------------------
template<unsigned int Dim>
void clitk::GuerreroVentilationGenericFilter::InitializeImageType() {      
  ADD_IMAGE_TYPE(Dim, short);
}
//--------------------------------------------------------------------


//--------------------------------------------------------------------
template<class ImageType>
void clitk::GuerreroVentilationGenericFilter::UpdateWithInputImageType() {

    // Input should be 2
    assert(mInputFilenames.size() == 2);

    // Reading input
    typedef ImageType InputImageType;
    typename InputImageType::Pointer input = this->template GetInput<InputImageType>(0);
    typename InputImageType::Pointer ref = this->template GetInput<InputImageType>(1);

    typedef itk::Image<float,InputImageType::ImageDimension> OutputImageType;
    //    typename ImageType::Pointer input = clitk::readImage<ImageType>(mInputFilenames[0], mIOVerbose);
    //typename ImageType::Pointer ref = clitk::readImage<ImageType>(mInputFilenames[1], mIOVerbose);

    typedef itk::BinaryGuerreroFilter<ImageType,ImageType,OutputImageType> GFilterType;
    typename GFilterType::Pointer filter = GFilterType::New();
    filter->SetInput1(ref);
    filter->SetInput2(input);
    filter->SetBloodCorrectionFactor(blood_mass_factor);
    filter->SetUseCorrectFormula(use_correct_formula);
    filter->Update();

    this->SetNextOutput<OutputImageType>(filter->GetOutput());
    //clitk::writeImage<OutputImageType>(filter->GetOutput(), mOutputFilename, mIOVerbose);
    //std::cout << "Warning: removed " << filter->GetFunctor().aberant_voxels << " aberant voxels from the ventilation image"
        //<< std::endl;
}