/*=========================================================================
  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://oncora1.lyon.fnclcc.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 CLITKSEGMENTATIONUTILS_H
#define CLITKSEGMENTATIONUTILS_H

#include "clitkCommon.h"
#include "clitkAutoCropFilter.h"
#include "clitkLabelizeParameters.h"
#include <itkBoundingBox.h>

namespace clitk {

  //--------------------------------------------------------------------
  template<class ImageType>
  void ComputeBBFromImageRegion(typename ImageType::Pointer image, 
                                typename ImageType::RegionType region,
                                typename itk::BoundingBox<unsigned long, 
                                ImageType::ImageDimension>::Pointer bb);
  
  //--------------------------------------------------------------------
  template<int Dimension>
  void ComputeBBIntersection(typename itk::BoundingBox<unsigned long, Dimension>::Pointer bbo, 
                             typename itk::BoundingBox<unsigned long, Dimension>::Pointer bbi1, 
                             typename itk::BoundingBox<unsigned long, Dimension>::Pointer bbi2);

  //--------------------------------------------------------------------
  template<class ImageType>
  void ComputeRegionFromBB(typename ImageType::Pointer image, 
                           const typename itk::BoundingBox<unsigned long, 
                           ImageType::ImageDimension>::Pointer bb, 
                           typename ImageType::RegionType & region);
  //--------------------------------------------------------------------
  template<class TInternalImageType, class TMaskInternalImageType>
  typename TInternalImageType::Pointer
  SetBackground(typename TInternalImageType::ConstPointer input,
                typename TMaskInternalImageType::ConstPointer mask, 
                typename TMaskInternalImageType::PixelType maskBG, 
                typename TInternalImageType::PixelType outValue);
  //--------------------------------------------------------------------

    
  //--------------------------------------------------------------------
  template<class TInternalImageType, class TMaskInternalImageType>
  typename TInternalImageType::Pointer
  SetBackground(typename TInternalImageType::Pointer input, 
                typename TMaskInternalImageType::Pointer mask, 
                typename TMaskInternalImageType::PixelType maskBG, 
                typename TInternalImageType::PixelType outValue) {
    return SetBackground<TInternalImageType, TMaskInternalImageType>
      (static_cast<typename TInternalImageType::ConstPointer>(input),  
       static_cast<typename TMaskInternalImageType::ConstPointer>(mask), 
       maskBG, outValue);
  }
  //--------------------------------------------------------------------


  //--------------------------------------------------------------------
  template<class ImageType>
  int GetNumberOfConnectedComponentLabels(typename ImageType::Pointer input, 
                                          typename ImageType::PixelType BG, 
                                          bool isFullyConnected);
  //--------------------------------------------------------------------


  //-------------------------------------------------------------------- 
  template<class TImageType>
  typename TImageType::Pointer
  Labelize(typename TImageType::Pointer input, 
           typename TImageType::PixelType BG, 
           bool isFullyConnected, 
           int minimalComponentSize);
  //--------------------------------------------------------------------


  //--------------------------------------------------------------------
  template<class ImageType>
  typename ImageType::Pointer
  RemoveLabels(typename ImageType::Pointer input, 
               typename ImageType::PixelType BG, 
               std::vector<typename ImageType::PixelType> & labelsToRemove);
  //--------------------------------------------------------------------


  //--------------------------------------------------------------------
  template<class ImageType>
    typename ImageType::Pointer
    AutoCrop(typename ImageType::Pointer input, 
	     typename ImageType::PixelType BG) {
      typedef clitk::AutoCropFilter<ImageType> AutoCropFilterType;
      typename AutoCropFilterType::Pointer autoCropFilter = AutoCropFilterType::New();
      autoCropFilter->SetInput(input);
      autoCropFilter->Update();   
      return autoCropFilter->GetOutput();
  }

  //--------------------------------------------------------------------


  //--------------------------------------------------------------------
  template<class TImageType>
  typename TImageType::Pointer
  KeepLabels(typename TImageType::Pointer input,
             typename TImageType::PixelType BG, 
             typename TImageType::PixelType FG,  
             typename TImageType::PixelType firstKeep, 
             typename TImageType::PixelType lastKeep, 
             bool useLastKeep);
  //--------------------------------------------------------------------


  //--------------------------------------------------------------------
  template<class TImageType>
  typename TImageType::Pointer
  LabelizeAndSelectLabels(typename TImageType::Pointer input,
                          typename TImageType::PixelType BG, 
                          typename TImageType::PixelType FG, 
                          bool isFullyConnected,
                          int minimalComponentSize,
                          LabelizeParameters<typename TImageType::PixelType> * param);

  //--------------------------------------------------------------------
  template<class ImageType>
  typename ImageType::Pointer
  EnlargeImageLike(typename ImageType::Pointer input,
                   typename ImageType::Pointer like, 
                   typename ImageType::PixelType BG);

}

#include "clitkSegmentationUtils.txx"

#endif