/*=========================================================================
 *
 *  Copyright Insight Software Consortium
 *
 *  Licensed under the Apache License, Version 2.0 (the "License");
 *  you may not use this file except in compliance with the License.
 *  You may obtain a copy of the License at
 *
 *         http://www.apache.org/licenses/LICENSE-2.0.txt
 *
 *  Unless required by applicable law or agreed to in writing, software
 *  distributed under the License is distributed on an "AS IS" BASIS,
 *  WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 *  See the License for the specific language governing permissions and
 *  limitations under the License.
 *
 *=========================================================================*/
#ifndef itkVarianceImageFilter_hxx
#define itkVarianceImageFilter_hxx
#include "itkVarianceImageFilter.h"

#include "itkConstNeighborhoodIterator.h"
#include "itkNeighborhoodInnerProduct.h"
#include "itkImageRegionIterator.h"
#include "itkNeighborhoodAlgorithm.h"
#include "itkOffset.h"
#include "itkProgressReporter.h"

namespace itk
{
template< typename TInputImage, typename TOutputImage >
VarianceImageFilter< TInputImage, TOutputImage >
::VarianceImageFilter()
{}

template< typename TInputImage, typename TOutputImage >
void
VarianceImageFilter< TInputImage, TOutputImage >
::ThreadedGenerateData(const OutputImageRegionType & outputRegionForThread,
                       ThreadIdType threadId)
{
  unsigned int i;

  ZeroFluxNeumannBoundaryCondition< InputImageType > nbc;

  ConstNeighborhoodIterator< InputImageType > bit;
  ImageRegionIterator< OutputImageType >      it;

  // Allocate output
  typename OutputImageType::Pointer output = this->GetOutput();
  typename  InputImageType::ConstPointer input  = this->GetInput();

  // Find the data-set boundary "faces"
  typename NeighborhoodAlgorithm::ImageBoundaryFacesCalculator< InputImageType >::FaceListType faceList;
  NeighborhoodAlgorithm::ImageBoundaryFacesCalculator< InputImageType > bC;
  faceList = bC( input, outputRegionForThread, this->GetRadius() );

  typename NeighborhoodAlgorithm::ImageBoundaryFacesCalculator< InputImageType >::FaceListType::iterator fit;

  // support progress methods/callbacks
  ProgressReporter progress( this, threadId, outputRegionForThread.GetNumberOfPixels() );

  InputRealType sum;
  InputRealType sumOfSquares;

  // Process each of the boundary faces.  These are N-d regions which border
  // the edge of the buffer.
  for ( fit = faceList.begin(); fit != faceList.end(); ++fit )
    {
    bit = ConstNeighborhoodIterator< InputImageType >(this->GetRadius(),
                                                      input, *fit);
    unsigned int neighborhoodSize = bit.Size();
    it = ImageRegionIterator< OutputImageType >(output, *fit);
    bit.OverrideBoundaryCondition(&nbc);
    bit.GoToBegin();

    while ( !bit.IsAtEnd() )
      {
      sum = NumericTraits< InputRealType >::ZeroValue();
      sumOfSquares = NumericTraits< InputRealType >::ZeroValue();

      for ( i = 0; i < neighborhoodSize; ++i )
        {
        sum += static_cast< InputRealType >( bit.GetPixel(i) );
        sumOfSquares += vnl_math_sqr( static_cast< InputRealType >( bit.GetPixel(i) ) );
        }

      // get the variance value
      const double num = static_cast< double >( neighborhoodSize );
      OutputPixelType var = ( sumOfSquares - ( vnl_math_sqr( sum ) / num ) ) / ( num - 1.0 );

      it.Set( var );

      ++bit;
      ++it;
      progress.CompletedPixel();
      }
    }
}
} // end namespace itk

#endif
