/*=========================================================================
  Program:   vv                     http://www.creatis.insa-lyon.fr/rio/vv

  Authors belong to: 
  - University of LYON              http://www.universite-lyon.fr/
  - Léon Bérard cancer center       http://www.centreleonberard.fr
  - CREATIS CNRS laboratory         http://www.creatis.insa-lyon.fr

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

  It is distributed under dual licence

  - BSD        See included LICENSE.txt file
  - CeCILL-B   http://www.cecill.info/licences/Licence_CeCILL-B_V1-en.html
  ===========================================================================**/

#ifndef CLITKAUTOCROPFILTER_TXX
#define CLITKAUTOCROPFILTER_TXX

// clitk
#include "clitkCommon.h"

// itk
#include "itkAutoCropLabelMapFilter.h"
#include "itkStatisticsLabelObject.h"
#include "itkLabelImageToLabelMapFilter.h"
#include "itkLabelMapToLabelImageFilter.h"
#include "itkRegionOfInterestImageFilter.h"
#include "itkExtractImageFilter.h"

namespace clitk {

  //--------------------------------------------------------------------
  template <class ImageType>
  AutoCropFilter<ImageType>::
  AutoCropFilter():itk::ImageToImageFilter<ImageType, ImageType>() {
    this->SetNumberOfRequiredInputs(1);
    m_BackgroundValue  = 0;
    UseBorderOff();
  }
  //--------------------------------------------------------------------


  //--------------------------------------------------------------------
  template <class ImageType>
  void 
  AutoCropFilter<ImageType>::
  SetInput(const ImageType * image) {
    // Process object is not const-correct so the const casting is required.
    this->SetNthInput(0, const_cast<ImageType *>( image ));
  }
  //--------------------------------------------------------------------
  

  //--------------------------------------------------------------------
  template <class ImageType>
  void 
  AutoCropFilter<ImageType>::  
  SetBackgroundValue(ImagePixelType p) {
    m_BackgroundValue = p;
  }
  //--------------------------------------------------------------------


  //--------------------------------------------------------------------
  template <class ImageType>
  void 
  AutoCropFilter<ImageType>::
  GenerateOutputInformation() {    

    // Superclass
    // do not call the superclass' implementation of this method since
    // this filter allows the input the output to be of different dimensions
    // Superclass::GenerateOutputInformation();

    // Get input pointers
    ImageConstPointer input = dynamic_cast<const ImageType*>(itk::ProcessObject::GetInput(0));
    
    // Get output pointer
    ImagePointer output = this->GetOutput(0);
  
    // Convert to LabelMap
    static const unsigned int Dim = ImageType::ImageDimension;
    //    typedef unsigned long LabelType; // unsigned long needed (!!??)
    typedef itk::StatisticsLabelObject< LabelType, Dim > LabelObjectType;
    typedef itk::LabelMap< LabelObjectType > LabelMapType;
    typedef itk::LabelImageToLabelMapFilter<ImageType, LabelMapType> ImageToMapFilterType;
    typename ImageToMapFilterType::Pointer imageToLabelFilter = ImageToMapFilterType::New();  
    imageToLabelFilter->SetBackgroundValue(m_BackgroundValue);
    imageToLabelFilter->SetInput(input);
    
    // AutoCrop
    typedef itk::AutoCropLabelMapFilter<LabelMapType> AutoCropFilterType;
    typename AutoCropFilterType::Pointer autoCropFilter = AutoCropFilterType::New();
    autoCropFilter->SetInput(imageToLabelFilter->GetOutput());
    //    autoCropFilter->ReleaseDataFlagOff(); 
    if (GetUseBorder()) {
      DD("Crop UseBorder : not correctly implemented do not use (use PadLabelMapFilter)");
      // http://www.itk.org/Doxygen/html/classitk_1_1AutoCropLabelMapFilter.html#a54f49fdff8d9f2d2313134109d510285
      exit(0); 
      typename ImageType::SizeType s;
      for(uint i=0; i<ImageType::ImageDimension; i++) s[i] = 1;
      autoCropFilter->SetCropBorder(s);
    }
    autoCropFilter->ReleaseDataFlagOn(); 

    // Convert to LabelImage
    typedef itk::LabelMapToLabelImageFilter<LabelMapType, ImageType> MapToImageFilterType;
    typename MapToImageFilterType::Pointer labelToImageFilter = MapToImageFilterType::New();       
    labelToImageFilter->SetInput(autoCropFilter->GetOutput());

    // Go ! (needed)
    labelToImageFilter->Update();
    m_labeImage = labelToImageFilter->GetOutput();

    // Update the output size
    m_Region = m_labeImage->GetLargestPossibleRegion();
    // Sometimes the index is 9223372036854775807 ???
    if (m_Region.GetIndex()[0] > 99999) {
      std::cerr << "Warning !! BUG int clitkAutoCropFilter ?" << std::endl;
      typename ImageType::IndexType index; 
      index.Fill(0);
      m_Region.SetIndex(index);
    }

    // Set the region to output
    output->SetLargestPossibleRegion(m_Region);
    output->SetRequestedRegion(m_Region);
    output->SetBufferedRegion(m_Region);
    output->SetRegions(m_Region);
  }
  //--------------------------------------------------------------------
   
  //--------------------------------------------------------------------
  template <class ImageType>
  void 
  AutoCropFilter<ImageType>::
  GenerateData() {
    // Get input pointers
    ImageConstPointer input = dynamic_cast<const ImageType*>(itk::ProcessObject::GetInput(0));
  
    // Extract the region with RegionOfInterestImageFilter or ExtractImageFilter ? 
    // The second is when reducing the nb of dimension (index always zero)
    // The first keep index. 
    // OLD : typedef itk::ExtractImageFilter<ImageType, ImageType> CropFilterType;
    // OLD : cropFilter->SetExtractionRegion(m_Region);

    typedef itk::RegionOfInterestImageFilter<ImageType, ImageType> CropFilterType;
    m_labeImage->SetRequestedRegion(m_labeImage->GetLargestPossibleRegion());
    typename CropFilterType::Pointer cropFilter = CropFilterType::New();
    cropFilter->SetInput(m_labeImage);
    cropFilter->SetReleaseDataFlag(this->GetReleaseDataFlag());
    cropFilter->SetRegionOfInterest(m_Region);

    // Go ! 
    cropFilter->Update();

    // Get (graft) output (SetNthOutput does not fit here because of Origin).
    this->GraftOutput(cropFilter->GetOutput());
  }
  //--------------------------------------------------------------------
   
}//end clitk
 
#endif //#define CLITKAUTOCROPFILTER