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

// clitk
#include "clitkCommon.h"
#include "clitkAutoCropFilter.h"
#include "clitkLabelizeParameters.h"

// itk
#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(const TInternalImageType * input,
                const TMaskInternalImageType * mask, 
                typename TMaskInternalImageType::PixelType maskBG, 
                typename TInternalImageType::PixelType outValue);
  //--------------------------------------------------------------------


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


  //-------------------------------------------------------------------- 
  template<class TImageType>
  typename TImageType::Pointer
  Labelize(const TImageType * 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->SetBackgroundValue(BG);
    autoCropFilter->Update();   
    return autoCropFilter->GetOutput();
  }
  //--------------------------------------------------------------------


  //--------------------------------------------------------------------
  template<class TImageType>
  typename TImageType::Pointer
  KeepLabels(const TImageType * 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
  ResizeImageLike(typename ImageType::Pointer input,
                  typename ImageType::Pointer like, 
                  typename ImageType::PixelType BG);


  //--------------------------------------------------------------------
  template<class MaskImageType>
  typename MaskImageType::Pointer
  SliceBySliceRelativePosition(const MaskImageType * input,
			       const MaskImageType * object,
			       int direction, 
			       double threshold, 
			       std::string orientation, 
                               bool uniqueConnectedComponent=false, 
                               double spacing=-1, 
			       bool notflag=false);

  //--------------------------------------------------------------------
  // In a binary image, search for the point belonging to the FG that
  // is the most exterma in the direction 'direction' (or in the
  // opposite if notFlag is given). if 'point' and 'distanceMax' are
  // given, do not consider points that are away from 'point' more
  // than 'distanceMax'
  template<class SliceType>
  typename SliceType::PointType 
  FindExtremaPointInAGivenDirection(const SliceType * input, 
                                    typename SliceType::PixelType bg, 
                                    int direction, 
                                    bool notFlag, 
                                    typename SliceType::PointType point,
                                    double distanceMax);

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

  //--------------------------------------------------------------------
  template<class ImageType>
  typename ImageType::Pointer
  CropImageAlongOneAxis(typename ImageType::Pointer image, 
                        int dim, double min, double max, 
                        bool autoCrop = false,
                        typename ImageType::PixelType BG=0);
  //--------------------------------------------------------------------
}

#include "clitkSegmentationUtils.txx"

#endif