itkExtractImageFilter.txx

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

  Program:   Insight Segmentation & Registration Toolkit
  Module:    $RCSfile: itkExtractImageFilter.txx,v $
  Language:  C++
  Date:      $Date: 2008-11-09 16:51:04 $
  Version:   $Revision: 1.28 $

  Copyright (c) Insight Software Consortium. All rights reserved.
  See ITKCopyright.txt or http://www.itk.org/HTML/Copyright.htm for details.

     This software is distributed WITHOUT ANY WARRANTY; without even 
     the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
     PURPOSE.  See the above copyright notices for more information.

=========================================================================*/
#ifndef __itkExtractImageFilter_txx
#define __itkExtractImageFilter_txx

#include "itkExtractImageFilter.h"
#include "itkImageRegionIterator.h"
#include "itkImageRegionConstIterator.h"
#include "itkObjectFactory.h"
#include "itkExtractImageFilterRegionCopier.h"
#include "itkProgressReporter.h"


namespace itk
{

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


template <class TInputImage, class TOutputImage>
void 
ExtractImageFilter<TInputImage,TOutputImage>
::PrintSelf(std::ostream& os, Indent indent) const
{
  Superclass::PrintSelf(os,indent);

  os << indent << "ExtractionRegion: " << m_ExtractionRegion << std::endl;
  os << indent << "OutputImageRegion: " << m_OutputImageRegion << std::endl;
}


template<class TInputImage, class TOutputImage>
void 
ExtractImageFilter<TInputImage,TOutputImage>
::CallCopyOutputRegionToInputRegion(InputImageRegionType &destRegion,
                                    const OutputImageRegionType &srcRegion)
{
  ExtractImageFilterRegionCopierType extractImageRegionCopier;
  extractImageRegionCopier(destRegion, srcRegion, m_ExtractionRegion);
}


template <class TInputImage, class TOutputImage>
void 
ExtractImageFilter<TInputImage,TOutputImage>
::SetExtractionRegion(InputImageRegionType extractRegion)
{
  m_ExtractionRegion = extractRegion;

  unsigned int nonzeroSizeCount = 0;
  InputImageSizeType inputSize = extractRegion.GetSize();
  OutputImageSizeType outputSize;
  OutputImageIndexType outputIndex;

  for (unsigned int i = 0; i < InputImageDimension; ++i)
    {
    if (inputSize[i])
      { 
      outputSize[nonzeroSizeCount] = inputSize[i];
      outputIndex[nonzeroSizeCount] = extractRegion.GetIndex()[i];
      nonzeroSizeCount++;
      }
    }
    
  if (nonzeroSizeCount != OutputImageDimension)
    {
    itkExceptionMacro("Extraction Region not consistent with output image");
    }

  m_OutputImageRegion.SetSize(outputSize);
  m_OutputImageRegion.SetIndex(outputIndex);
  this->Modified();
}

template <class TInputImage, class TOutputImage>
void 
ExtractImageFilter<TInputImage,TOutputImage>
::GenerateOutputInformation()
{
  // do not call the superclass' implementation of this method since
  // this filter allows the input and the output to be of different dimensions
 
  // get pointers to the input and output
  typename Superclass::OutputImagePointer      outputPtr = this->GetOutput();
  typename Superclass::InputImageConstPointer  inputPtr  = this->GetInput();

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

  // Set the output image size to the same value as the extraction region.
  outputPtr->SetLargestPossibleRegion( m_OutputImageRegion );

  // Set the output spacing and origin
  const ImageBase<InputImageDimension> *phyData;

  phyData
    = dynamic_cast<const ImageBase<InputImageDimension>*>(this->GetInput());

  if (phyData)
    {
    // Copy what we can from the image from spacing and origin of the input
    // This logic needs to be augmented with logic that select which
    // dimensions to copy

    unsigned int i;
    const typename InputImageType::SpacingType& 
      inputSpacing = inputPtr->GetSpacing();
    const typename InputImageType::DirectionType&
      inputDirection = inputPtr->GetDirection();
    const typename InputImageType::PointType&
      inputOrigin = inputPtr->GetOrigin();

    typename OutputImageType::SpacingType outputSpacing;
    typename OutputImageType::DirectionType outputDirection;
    typename OutputImageType::PointType outputOrigin;

    if ( static_cast<unsigned int>(OutputImageDimension) > 
         static_cast<unsigned int>(InputImageDimension )    )
      {
      // copy the input to the output and fill the rest of the
      // output with zeros.
      for (i=0; i < InputImageDimension; ++i)
        {
        outputSpacing[i] = inputSpacing[i];
        outputOrigin[i] = inputOrigin[i];
        for (unsigned int dim = 0; dim < InputImageDimension; ++dim)
          {
          outputDirection[i][dim] = inputDirection[i][dim];
          }
        }
      for (; i < OutputImageDimension; ++i)
        {
        outputSpacing[i] = 1.0;
        outputOrigin[i] = 0.0;
        for (unsigned int dim = 0; dim < InputImageDimension; ++dim)
          {
          outputDirection[i][dim] = 0.0;
          }
        outputDirection[i][i] = 1.0;
        }
      }
    else
      {
      // copy the non-collapsed part of the input spacing and origing to the output
      outputDirection.SetIdentity();
      int nonZeroCount = 0;
      for (i=0; i < InputImageDimension; ++i)
        {
        if (m_ExtractionRegion.GetSize()[i])
          {
          outputSpacing[nonZeroCount] = inputSpacing[i];
          outputOrigin[nonZeroCount] = inputOrigin[i];
          int nonZeroCount2 = 0;
          for (unsigned int dim = 0; dim < InputImageDimension; ++dim)
            {
            if (m_ExtractionRegion.GetSize()[dim])
              {
              outputDirection[nonZeroCount][nonZeroCount2] =
                inputDirection[nonZeroCount][dim];
              ++nonZeroCount2;
              }
            }
          nonZeroCount++;
          }
        }
      }
    // This is a temporary fix to get over the problems with using OrientedImages to
    // a non-degenerate extracted image to be created.  It still needs to be determined
    // how to compute the correct outputDirection from all possible input directions.
    if (vnl_determinant(outputDirection.GetVnlMatrix()) == 0.0)
      {
      outputDirection.SetIdentity();
      }

    // set the spacing and origin
    outputPtr->SetSpacing( outputSpacing );
    outputPtr->SetDirection( outputDirection );
    outputPtr->SetOrigin( outputOrigin );
    outputPtr->SetNumberOfComponentsPerPixel(
    inputPtr->GetNumberOfComponentsPerPixel() );
    }
  else
    {
    // pointer could not be cast back down
    itkExceptionMacro(<< "itk::ExtractImageFilter::GenerateOutputInformation "
                      << "cannot cast input to "
                      << typeid(ImageBase<InputImageDimension>*).name() );
    }
}

template <class TInputImage, class TOutputImage>
void 
ExtractImageFilter<TInputImage,TOutputImage>
::ThreadedGenerateData(const OutputImageRegionType& outputRegionForThread,
                       int threadId)
{
  itkDebugMacro(<<"Actually executing");

  // Get the input and output pointers
  typename Superclass::InputImageConstPointer  inputPtr = this->GetInput();
  typename Superclass::OutputImagePointer outputPtr = this->GetOutput();

  // support progress methods/callbacks
  ProgressReporter progress(this, threadId, outputRegionForThread.GetNumberOfPixels());
  
  // Define the portion of the input to walk for this thread
  InputImageRegionType inputRegionForThread;
  this->CallCopyOutputRegionToInputRegion(inputRegionForThread, outputRegionForThread);
  
  // Define the iterators.
  typedef ImageRegionIterator<TOutputImage>     OutputIterator;
  typedef ImageRegionConstIterator<TInputImage> InputIterator;

  OutputIterator outIt(outputPtr, outputRegionForThread);
  InputIterator inIt(inputPtr, inputRegionForThread);

  // walk the output region, and sample the input image
  while( !outIt.IsAtEnd() )
    {
    // copy the input pixel to the output
    outIt.Set( static_cast<OutputImagePixelType>(inIt.Get()));
    ++outIt; 
    ++inIt; 
    progress.CompletedPixel();
    }
}

} // end namespace itk

#endif