remove duplicated file

diff --git a/registration/clitkExtractImageFilter.h b/registration/clitkExtractImageFilter.h
deleted file mode 100644 (file)
index 1e797bc..0000000
--- a/registration/clitkExtractImageFilter.h
+++ /dev/null
@@ -1,113 +0,0 @@
-/*=========================================================================
-  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://www.centreleonberard.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 __clitkExtractImageFilter_h
-#define __clitkExtractImageFilter_h
-#include "itkImageToImageFilter.h"
-#include "itkSmartPointer.h"
-#include "itkExtractImageFilterRegionCopier.h"
-
-namespace clitk
-{
-
-template <class TInputImage, class TOutputImage>
-class ITK_EXPORT ExtractImageFilter:
-    public itk::ImageToImageFilter<TInputImage,TOutputImage>
-{
-public:
-  /** Standard class typedefs. */
-  typedef ExtractImageFilter         Self;
-  typedef itk::ImageToImageFilter<TInputImage,TOutputImage>  Superclass;
-  typedef itk::SmartPointer<Self>  Pointer;
-  typedef itk::SmartPointer<const Self>  ConstPointer;
-
-  /** Method for creation through the object factory. */
-  itkNewMacro(Self);  
-
-  /** Run-time type information (and related methods). */
-  itkTypeMacro(ExtractImageFilter, ImageToImageFilter);
-
-  /** Image type information. */
-  typedef TInputImage  InputImageType;
-  typedef TOutputImage OutputImageType;
-
-  /** Typedef to describe the output and input image region types. */
-  typedef typename TOutputImage::RegionType OutputImageRegionType;
-  typedef typename TInputImage::RegionType InputImageRegionType;
-
-  /** Typedef to describe the type of pixel. */
-  typedef typename TOutputImage::PixelType OutputImagePixelType;
-  typedef typename TInputImage::PixelType InputImagePixelType;
-
-  /** Typedef to describe the output and input image index and size types. */
-  typedef typename TOutputImage::IndexType OutputImageIndexType;
-  typedef typename TInputImage::IndexType InputImageIndexType;
-  typedef typename TOutputImage::SizeType OutputImageSizeType;
-  typedef typename TInputImage::SizeType InputImageSizeType;
-
-  /** ImageDimension enumeration */
-  itkStaticConstMacro(InputImageDimension, unsigned int,
-                      TInputImage::ImageDimension);
-  itkStaticConstMacro(OutputImageDimension, unsigned int,
-                      TOutputImage::ImageDimension);
-
-  typedef itk::ImageToImageFilterDetail::ExtractImageFilterRegionCopier<
-    itkGetStaticConstMacro(InputImageDimension), 
-    itkGetStaticConstMacro(OutputImageDimension)> ExtractImageFilterRegionCopierType;
-
-  void SetExtractionRegion(InputImageRegionType extractRegion);
-  itkGetMacro(ExtractionRegion, InputImageRegionType);
-
-#ifdef ITK_USE_CONCEPT_CHECKING
-  /** Begin concept checking */
-  itkConceptMacro(InputCovertibleToOutputCheck,
-                 (itk::Concept::Convertible<InputImagePixelType, OutputImagePixelType>));
-  /** End concept checking */
-#endif
-
-protected:
-  ExtractImageFilter();
-  ~ExtractImageFilter() {};
-  void PrintSelf(std::ostream& os, itk::Indent indent) const;
-
-
-  virtual void GenerateOutputInformation();
-
-
-  virtual void CallCopyOutputRegionToInputRegion(InputImageRegionType &destRegion,
-                                                 const OutputImageRegionType &srcRegion);
-
-
-  void ThreadedGenerateData(const OutputImageRegionType& outputRegionForThread,
-                            int threadId );
-  InputImageRegionType m_ExtractionRegion;
-  OutputImageRegionType m_OutputImageRegion;
-
-private:
-  ExtractImageFilter(const Self&); //purposely not implemented
-  void operator=(const Self&); //purposely not implemented
-  
-};
-
-  
-} // end namespace itk
-  
-#ifndef ITK_MANUAL_INSTANTIATION
-#include "clitkExtractImageFilter.txx"
-#endif
-  
-#endif

diff --git a/registration/clitkExtractImageFilter.txx b/registration/clitkExtractImageFilter.txx
deleted file mode 100644 (file)
index d321f9e..0000000
--- a/registration/clitkExtractImageFilter.txx
+++ /dev/null
@@ -1,274 +0,0 @@
-/*=========================================================================
-  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://www.centreleonberard.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 _clitkExtractImageFilter_txx
-#define _clitkExtractImageFilter_txx
-#include "clitkExtractImageFilter.h"
-#include "itkImageRegionIterator.h"
-#include "itkImageRegionConstIterator.h"
-#include "itkObjectFactory.h"
-#include "itkExtractImageFilterRegionCopier.h"
-#include "itkProgressReporter.h"
-
-
-namespace clitk
-{
-
-/**
- *
- */
-template <class TInputImage, class TOutputImage>
-ExtractImageFilter<TInputImage,TOutputImage>
-::ExtractImageFilter() 
-{
-}
-
-
-/**
- *
- */
-template <class TInputImage, class TOutputImage>
-void 
-ExtractImageFilter<TInputImage,TOutputImage>
-::PrintSelf(std::ostream& os, itk::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;
-
-  /**
-   * check to see if the number of non-zero entries in the extraction region
-   * matches the number of dimensions in the output image.  
-   **/
-  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();
-}
-
-
-
-/** 
- * ExtractImageFilter can produce an image which is a different resolution
- * than its input image.  As such, ExtractImageFilter needs to provide an
- * implementation for GenerateOutputInformation() in order to inform
- * the pipeline execution model.  The original documentation of this
- * method is below.
- *
- * \sa ProcessObject::GenerateOutputInformaton() 
- */
-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 itk::ImageBase<InputImageDimension> *phyData;
-
-  phyData
-    = dynamic_cast<const itk::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
-      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[i][dim];
-              ++nonZeroCount2;
-              }
-            }
-          nonZeroCount++;
-          }
-        }
-      }
-
-    // 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(itk::ImageBase<InputImageDimension>*).name() );
-    }
-}
-
-/** 
-   * ExtractImageFilter can be implemented as a multithreaded filter.
-   * Therefore, this implementation provides a ThreadedGenerateData()
-   * routine which is called for each processing thread. The output
-   * image data is allocated automatically by the superclass prior to
-   * calling ThreadedGenerateData().  ThreadedGenerateData can only
-   * write to the portion of the output image specified by the
-   * parameter "outputRegionForThread"
-   *
-   * \sa ImageToImageFilter::ThreadedGenerateData(),
-   *     ImageToImageFilter::GenerateData() 
-   */
-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
- itk::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 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() )
-    {
-    // copy the input pixel to the output
-    outIt.Set( static_cast<OutputImagePixelType>(inIt.Get()));
-    ++outIt; 
-    ++inIt; 
-    progress.CompletedPixel();
-    }
-}
-
-} // end namespace clitk
-
-#endif