freSpatialRegionOfInterestImageFilter.txx

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

  Program:   F.R.E.E. - flexible registration evaluation engine
  Version:   v.1.0.0
  Date:      $Date: 2006/09/01 12:00:00 $
  Module:    $RCSfile: freSpatialRegionOfInterestImageFilter.txx,v $
  Language:  C++



  Copyright (c) 2007 Ralf o Floca (Department of Medical Informatics,
  Institute for Medical Biometry and Informatics, University of Heidelberg,
  Germany). All rights reserved.
  See FREECopyright.txt or http://www.mi.med.uni-hd.de/free/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 _freSpatialRegionOfInterestImageFilter_txx
#define _freSpatialRegionOfInterestImageFilter_txx

#include "freSpatialRegionOfInterestImageFilter.h"
#include "itkImageRegionIterator.h"
#include "itkImageRegionConstIterator.h"
#include "itkObjectFactory.h"
#include "itkProgressReporter.h"
#include "itkImage.h"

namespace FREE
{

template <class TInputImage, class TOutputImage>
SpatialRegionOfInterestImageFilter<TInputImage,TOutputImage>
::SpatialRegionOfInterestImageFilter() 
{
  m_CropByInput = true;
  m_OutsideValue = 0;
}

template <class TInputImage, class TOutputImage>
void
SpatialRegionOfInterestImageFilter<TInputImage,TOutputImage>
::SetSpatialRegionOfInterest(SpatialObjectType* pROI)
{
  itkDebugMacro("setting SpatialObject to " << pROI );
  if (this->m_SpatialObject != pROI)
    {
      this->m_SpatialObject = pROI;
      this->Modified();
    }
}

template <class TInputImage, class TOutputImage>
typename SpatialRegionOfInterestImageFilter<TInputImage,TOutputImage>::SpatialObjectType*
SpatialRegionOfInterestImageFilter<TInputImage,TOutputImage>
::GetSpatialRegionOfInterest()
{
  itkDebugMacro("returning SpatialObject address " << this->m_SpatialObject );
  return this->m_SpatialObject.GetPointer();
};

template <class TInputImage, class TOutputImage>
typename SpatialRegionOfInterestImageFilter<TInputImage,TOutputImage>::RegionType 
SpatialRegionOfInterestImageFilter<TInputImage,TOutputImage>
::GenerateLargestSpatialRegion(const TInputImage* pInput)
{
  if (this->m_SpatialObject.IsNull())
  {
    return pInput->GetLargestPossibleRegion();
  }
  else
  { //compute via bounding box of spatial object
    m_SpatialObject->ComputeBoundingBox();
    typename SpatialObjectType::BoundingBoxType::Pointer boundingBox = m_SpatialObject->GetBoundingBox();
    
    typename SpatialObjectType::BoundingBoxType::PointType minPoint = boundingBox->GetMinimum();
    typename SpatialObjectType::BoundingBoxType::PointType maxPoint = boundingBox->GetMaximum();

    IndexType minIndex;
    IndexType maxIndex;
    pInput->TransformPhysicalPointToIndex(minPoint,minIndex);
    pInput->TransformPhysicalPointToIndex(maxPoint,maxIndex);

    IndexType regionIndex;
    SizeType regionSize;
    for (unsigned int iIndex = 0; iIndex<ImageDimension; iIndex++)
    {
      regionIndex[iIndex] = minIndex[iIndex];
      regionSize[iIndex] = maxIndex[iIndex] - minIndex[iIndex];
    }

    RegionType region(regionIndex,regionSize);
    
    if (m_CropByInput) region.Crop(pInput->GetLargestPossibleRegion());
    
    return region;
  }
}

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

  os << indent << "OutsideValue:     " << m_OutsideValue << std::endl;
  os << indent << "SpatialObject:    " << m_SpatialObject << std::endl;
}



template <class TInputImage, class TOutputImage>
void 
SpatialRegionOfInterestImageFilter<TInputImage,TOutputImage>
::GenerateInputRequestedRegion()
{
  // call the superclass' implementation of this method
  Superclass::GenerateInputRequestedRegion();
  
  // get pointer to the input 
  typename Superclass::InputImagePointer  inputPtr = 
    const_cast< TInputImage * >( this->GetInput() );

  if( inputPtr )
    {
    // request the region of interest
    RegionType spatialROI = this->GenerateLargestSpatialRegion(inputPtr);
    inputPtr->SetRequestedRegion( spatialROI );
    }
}


template <class TInputImage, class TOutputImage>
void 
SpatialRegionOfInterestImageFilter<TInputImage,TOutputImage>
::EnlargeOutputRequestedRegion(itk::DataObject *output)
{
  // call the superclass' implementation of this method
  Superclass::EnlargeOutputRequestedRegion(output);
  
  // generate everything in the region of interest
  output->SetRequestedRegionToLargestPossibleRegion();
}




template <class TInputImage, class TOutputImage>
void 
SpatialRegionOfInterestImageFilter<TInputImage,TOutputImage>
::GenerateOutputInformation()
{
  // do not call the superclass' implementation of this method since
  // this filter allows the input 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;
    }

  RegionType spatialROI = this->GenerateLargestSpatialRegion(inputPtr);

  // Set the output image size to the same value as the region of interest.
  RegionType region;
  IndexType  start;
  start.Fill(0);

  region.SetSize( spatialROI.GetSize() );
  region.SetIndex( start );
 
  // Copy Information without modification.
  outputPtr->CopyInformation( inputPtr );

  // Adjust output region
  outputPtr->SetLargestPossibleRegion(region);

  // Correct origin of the extracted region.
  IndexType roiStart( spatialROI.GetIndex() );
  typename Superclass::OutputImageType::PointType  outputOrigin;
  typedef itk::Image< ITK_TYPENAME TInputImage::PixelType,
    Superclass::InputImageDimension > ImageType;
  typename ImageType::ConstPointer imagePtr =
    dynamic_cast< const ImageType * >( inputPtr.GetPointer() );
  if ( imagePtr )
    {
    // Input image supports TransformIndexToContinuousPoint
    inputPtr->TransformIndexToPhysicalPoint( roiStart, outputOrigin);
    }
  else
    {
    // Generic type of image
    const typename Superclass::InputImageType::PointType&
      inputOrigin = inputPtr->GetOrigin();

    const typename Superclass::InputImageType::SpacingType&
      spacing = inputPtr->GetSpacing() ;
 
    for( unsigned int i=0; i<ImageDimension; i++)
      {
      outputOrigin[i] = inputOrigin[i] + roiStart[i] * spacing[i];
      }
    }
  
  outputPtr->SetOrigin( outputOrigin );

}



template <class TInputImage, class TOutputImage>
void 
SpatialRegionOfInterestImageFilter<TInputImage,TOutputImage>
::ThreadedGenerateData(const RegionType& 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
  itk::ProgressReporter progress(this, threadId, outputRegionForThread.GetNumberOfPixels());
  
  RegionType spatialROI = this->GenerateLargestSpatialRegion(inputPtr);

  // Define the portion of the input to walk for this thread
  InputImageRegionType inputRegionForThread;
  inputRegionForThread.SetSize( outputRegionForThread.GetSize() );

  IndexType start;
  IndexType roiStart(    spatialROI.GetIndex()    );
  IndexType threadStart( outputRegionForThread.GetIndex() );
  for(unsigned int i=0; i<ImageDimension; i++)
    {
    start[i] = roiStart[i] + threadStart[i];
    }

  inputRegionForThread.SetIndex( start );
  
  // Define the iterators.
  typedef itk::ImageRegionIterator<TOutputImage> OutputIterator;
  typedef itk::ImageRegionConstIterator<TInputImage> InputIterator;

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

  // walk the output region, and sample the input image
  while( !outIt.IsAtEnd() )
    {
      //here is the adition to itk::RegionOfInterestImageFilter
      IndexType index = inIt.GetIndex();
      PointType point;
      inputPtr->TransformIndexToPhysicalPoint(index,point);
      if (m_SpatialObject->IsInside(point))
      {
        // copy the input pixel to the output
        outIt.Set( inIt.Get());
      }
      else
      { //use outside value
        outIt.Set( m_OutsideValue);
      }

      ++outIt; 
      ++inIt; 
      progress.CompletedPixel();
    }
}

} // end namespace itk

#endif

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