itkRegularizedIVIMLocalVariationImageFilter.txx

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

The Medical Imaging Interaction Toolkit (MITK)

Copyright (c) German Cancer Research Center,
Division of Medical and Biological Informatics.
All rights reserved.

This software is distributed WITHOUT ANY WARRANTY; without
even the implied warranty of MERCHANTABILITY or FITNESS FOR
A PARTICULAR PURPOSE.

See LICENSE.txt or http://www.mitk.org for details.

===================================================================*/
#ifndef _itkRegularizedIVIMLocalVariationImageFilter_txx
#define _itkRegularizedIVIMLocalVariationImageFilter_txx

#include "itkConstShapedNeighborhoodIterator.h"
#include "itkNeighborhoodInnerProduct.h"
#include "itkImageRegionIterator.h"
#include "itkNeighborhoodAlgorithm.h"
#include "itkZeroFluxNeumannBoundaryCondition.h"
#include "itkOffset.h"
#include "itkProgressReporter.h"
#include "itkVectorImage.h"

#include <vector>
#include <algorithm>

namespace itk
{

  template <class TInputImage, class TOutputImage>
  RegularizedIVIMLocalVariationImageFilter<TInputImage, TOutputImage>
    ::RegularizedIVIMLocalVariationImageFilter()
  {}

  template <class TInputImage, class TOutputImage>
  void
    RegularizedIVIMLocalVariationImageFilter<TInputImage, TOutputImage>
    ::GenerateInputRequestedRegion() throw (InvalidRequestedRegionError)
  {
    // call the superclass' implementation of this method
    Superclass::GenerateInputRequestedRegion();

    // get pointers to the input and output
    typename Superclass::InputImagePointer inputPtr =
      const_cast< TInputImage * >( this->GetInput() );
    typename Superclass::OutputImagePointer outputPtr = this->GetOutput();

    if ( !inputPtr || !outputPtr )
    {
      return;
    }

    // get a copy of the input requested region (should equal the output
    // requested region)
    typename TInputImage::RegionType inputRequestedRegion;
    inputRequestedRegion = inputPtr->GetRequestedRegion();

    // pad the input requested region by 1
    inputRequestedRegion.PadByRadius( 1 );

    // crop the input requested region at the input's largest possible region
    if ( inputRequestedRegion.Crop(inputPtr->GetLargestPossibleRegion()) )
    {
      inputPtr->SetRequestedRegion( inputRequestedRegion );
      return;
    }
    else
    {
      // Couldn't crop the region (requested region is outside the largest
      // possible region).  Throw an exception.

      // store what we tried to request (prior to trying to crop)
      inputPtr->SetRequestedRegion( inputRequestedRegion );

      // build an exception
      InvalidRequestedRegionError e(__FILE__, __LINE__);
      e.SetLocation(ITK_LOCATION);
      e.SetDescription("Requested region outside possible region.");
      e.SetDataObject(inputPtr);
      throw e;
    }
  }

  template< class TInputImage, class TOutputImage>
  void
    RegularizedIVIMLocalVariationImageFilter< TInputImage, TOutputImage>
    ::ThreadedGenerateData(const OutputImageRegionType& outputRegionForThread,
    ThreadIdType threadId)
  {

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

    itk::Size<InputImageDimension> size;
    for( int i=0; i<InputImageDimension; i++)
      size[i] = 1;

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

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

    ZeroFluxNeumannBoundaryCondition<InputImageType> nbc;
    std::vector<InputPixelType> pixels;

    // Process each of the boundary faces.  These are N-d regions which border
    // the edge of the buffer.
    for ( typename NeighborhoodAlgorithm::
      ImageBoundaryFacesCalculator<InputImageType>::FaceListType::iterator
      fit=faceList.begin(); fit != faceList.end(); ++fit)
    {

      // iterators over output and input
      ImageRegionIterator<OutputImageType>
        output_image_it(output, *fit);
      ImageRegionConstIterator<InputImageType>
        input_image_it(input.GetPointer(), *fit);

      // neighborhood iterator for input image
      ConstShapedNeighborhoodIterator<InputImageType>
        input_image_neighbors_it(size, input, *fit);
      typename ConstShapedNeighborhoodIterator<InputImageType>::
        OffsetType offset;
      input_image_neighbors_it.OverrideBoundaryCondition(&nbc);
      input_image_neighbors_it.ClearActiveList();
      for(int i=0; i<InputImageDimension; i++)
      {
        offset.Fill(0);
        offset[i] = -1;
        input_image_neighbors_it.ActivateOffset(offset);
        offset[i] = 1;
        input_image_neighbors_it.ActivateOffset(offset);
      }
      input_image_neighbors_it.GoToBegin();
      //const unsigned int neighborhoodSize = InputImageDimension*2;

      while ( ! input_image_neighbors_it.IsAtEnd() )
      {
        // collect all the pixels in the neighborhood, note that we use
        // GetPixel on the NeighborhoodIterator to honor the boundary conditions
        typename OutputImageType::PixelType locVariation = 0;
        typename ConstShapedNeighborhoodIterator<InputImageType>::
          ConstIterator input_neighbors_it;
        for (input_neighbors_it = input_image_neighbors_it.Begin();
          ! input_neighbors_it.IsAtEnd();
          input_neighbors_it++)
        {
            typename TInputImage::PixelType diffVec =
              input_neighbors_it.Get()-input_image_it.Get();
            locVariation += IVIMSquaredEuclideanMetric
              <typename TInputImage::PixelType>::Calc(diffVec);
        }
        locVariation = sqrt(locVariation + 0.0001);
        output_image_it.Set(locVariation);

        // update iterators
        ++input_image_neighbors_it;
        ++output_image_it;
        ++input_image_it;

        // report progress
        progress.CompletedPixel();
      }
    }
  }

  /**
  * Standard "PrintSelf" method
  */
  template <class TInputImage, class TOutput>
  void
    RegularizedIVIMLocalVariationImageFilter<TInputImage, TOutput>
    ::PrintSelf(
    std::ostream& os,
    Indent indent) const
  {
    Superclass::PrintSelf( os, indent );
  }

} // end namespace itk

#endif //_itkRegularizedIVIMLocalVariationImageFilter_txx