/*=========================================================================
  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 CLITKCONNECTEDCOMPONENTLABELINGSGENERICFILTER_TXX
#define CLITKCONNECTEDCOMPONENTLABELINGSGENERICFILTER_TXX

// clitk
#include "clitkImageCommon.h"

// itk
#include "itkConnectedComponentImageFilter.h"
#include "itkRelabelComponentImageFilter.h"
  
//--------------------------------------------------------------------
template<class ArgsInfoType>
clitk::ConnectedComponentLabelingGenericFilter<ArgsInfoType>::ConnectedComponentLabelingGenericFilter():
  ImageToImageGenericFilter<Self>("ConnectedComponentLabeling") 
{
  //  InitializeImageType<2>();
  InitializeImageType<3>();
  //InitializeImageType<4>();
}
//--------------------------------------------------------------------


//--------------------------------------------------------------------
template<class ArgsInfoType>
template<unsigned int Dim>
void clitk::ConnectedComponentLabelingGenericFilter<ArgsInfoType>::InitializeImageType() 
{  
  ADD_IMAGE_TYPE(Dim, uchar);
  ADD_IMAGE_TYPE(Dim, short);
  // ADD_IMAGE_TYPE(Dim, int);
  // ADD_IMAGE_TYPE(Dim, float);
}
//--------------------------------------------------------------------
  

//--------------------------------------------------------------------
template<class ArgsInfoType>
void clitk::ConnectedComponentLabelingGenericFilter<ArgsInfoType>::SetArgsInfo(const ArgsInfoType & a) 
{
  mArgsInfo=a;
  SetIOVerbose(mArgsInfo.verbose_flag);
  if (mArgsInfo.imagetypes_flag) this->PrintAvailableImageTypes();
  if (mArgsInfo.input_given)   AddInputFilename(mArgsInfo.input_arg);
  if (mArgsInfo.output_given)  SetOutputFilename(mArgsInfo.output_arg);
}
//--------------------------------------------------------------------


//--------------------------------------------------------------------
// Update with the number of dimensions and the pixeltype
//--------------------------------------------------------------------
template<class ArgsInfoType>
template<class ImageType>
void clitk::ConnectedComponentLabelingGenericFilter<ArgsInfoType>::UpdateWithInputImageType() 
{ 
  DD("UpdateWithInputImageType");

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

  // Output image type
  typedef itk::Image<int, ImageType::ImageDimension> OutputImageType;

  // Create CCL filter
  DD("CCL");
  typedef itk::ConnectedComponentImageFilter<ImageType, OutputImageType> ConnectFilterType;
  typename ConnectFilterType::Pointer connectFilter = ConnectFilterType::New();
  connectFilter->SetInput(input);
  connectFilter->SetBackgroundValue(mArgsInfo.inputBG_arg);
  connectFilter->SetFullyConnected(mArgsInfo.full_flag);

  // TODO SetBackgroud to zero forr relabel ?


  // Sort by size and remove too small area.
  typedef itk::RelabelComponentImageFilter<OutputImageType, OutputImageType> RelabelFilterType;
  typename RelabelFilterType::Pointer relabelFilter = RelabelFilterType::New();
  //  relabelFilter->InPlaceOn();
  relabelFilter->SetInput(connectFilter->GetOutput());
  relabelFilter->SetMinimumObjectSize(mArgsInfo.minSize_arg);
  relabelFilter->Update();

  DD(mArgsInfo.inputBG_arg);
  DD(mArgsInfo.full_flag);
  DD(mArgsInfo.minSize_arg);
  
  // Set information
  const std::vector<typename RelabelFilterType::ObjectSizeType> & a = relabelFilter->GetSizeOfObjectsInPixels();
  m_SizeOfObjectsInPixels.resize(a.size());
  for(unsigned int i=0; i<a.size(); i++) m_SizeOfObjectsInPixels[i] = a[i];
  m_SizeOfObjectsInPhysicalUnits = relabelFilter->GetSizeOfObjectsInPhysicalUnits();
  m_OriginalNumberOfObjects = relabelFilter->GetOriginalNumberOfObjects();
  DD(m_OriginalNumberOfObjects);
  DD(m_SizeOfObjectsInPhysicalUnits.size());

  // Write/Save results
  typename OutputImageType::Pointer output = relabelFilter->GetOutput();
  this->template SetNextOutput<OutputImageType>(output); 
}
//--------------------------------------------------------------------

#endif //#define CLITKCONNECTEDCOMPONENTLABELINGSGENERICFILTER_TXX