extract a slice from a 3D image

diff --git a/itk/clitkExtractSliceFilter.h b/itk/clitkExtractSliceFilter.h
new file mode 100644 (file)
index 0000000..93d3cd0
--- /dev/null
+++ b/itk/clitkExtractSliceFilter.h
@@ -0,0 +1,118 @@
+/*=========================================================================
+  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://oncora1.lyon.fnclcc.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 CLITKEXTRACTSLICEFILTER_H
+#define CLITKEXTRACTSLICEFILTER_H
+
+// clitk
+#include "clitkFilterBase.h"
+
+// itk
+#include "itkPasteImageFilter.h"
+
+// itk ENST
+#include "RelativePositionPropImageFilter.h"
+
+namespace clitk {
+  
+  //--------------------------------------------------------------------
+  /*
+    Let A be an initial label image.
+    Let B be a label image with an object. 
+    Let o be an orientation relatively to the B object (for example RightTo, AntTo, InferiorTo ...)
+
+    This filter removes (=set background) from A all points that are
+    not in the wanted o orientation. It uses downsampled version for
+    faster processing, and (try to) take into account discretization
+    problem. Uses [Bloch 1999].
+  */
+  //--------------------------------------------------------------------
+  
+  template <class ImageType>
+  class ITK_EXPORT ExtractSliceFilter:
+    public clitk::FilterBase, 
+    public itk::ImageToImageFilter<ImageType, 
+                                   std::vector<typename itk::Image<typename ImageType::PixelType, 
+                                                                   ImageType::ImageDimension-1>::Pointer> > 
+  {
+
+  public:
+    /** Standard class typedefs. */
+    typedef itk::ImageToImageFilter<ImageType, ImageType> Superclass;
+    typedef ExtractSliceFilter                              Self;
+    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(ExtractSliceFilter, ImageToImageFilter);
+    FILTERBASE_INIT;
+
+    /** Some convenient typedefs. */
+    typedef typename ImageType::ConstPointer ImageConstPointer;
+    typedef typename ImageType::Pointer      ImagePointer;
+    typedef typename ImageType::RegionType   RegionType; 
+    typedef typename ImageType::PixelType    PixelType;
+    typedef typename ImageType::SpacingType  SpacingType;
+    typedef typename ImageType::SizeType     SizeType;
+    
+    /** ImageDimension constants */
+    itkStaticConstMacro(ImageDimension, unsigned int, ImageType::ImageDimension);
+
+    /** Slice image type **/
+    typedef itk::Image<PixelType, ImageDimension-1> SliceType;
+    typedef typename SliceType::Pointer             SliceTypePointer;
+
+    /** Input : initial image and object */
+    void SetInput(const ImageType * image);
+    
+    // Options
+    itkGetConstMacro(Direction, int);
+    itkSetMacro(Direction, int);
+
+  protected:
+    ExtractSliceFilter();
+    virtual ~ExtractSliceFilter() {}
+    
+    int m_Direction;
+
+    virtual void GenerateOutputInformation();
+    virtual void GenerateInputRequestedRegion();
+    virtual void GenerateData();
+
+    ImagePointer input;
+    ImagePointer object;
+    std::vector<SliceTypePointer> output;
+
+  private:
+    ExtractSliceFilter(const Self&); //purposely not implemented
+    void operator=(const Self&); //purposely not implemented
+    
+  }; // end class
+  //--------------------------------------------------------------------
+
+} // end namespace clitk
+//--------------------------------------------------------------------
+
+#ifndef ITK_MANUAL_INSTANTIATION
+#include "clitkExtractSliceFilter.txx"
+#endif
+
+#endif

diff --git a/itk/clitkExtractSliceFilter.txx b/itk/clitkExtractSliceFilter.txx
new file mode 100644 (file)
index 0000000..40f7982
--- /dev/null
+++ b/itk/clitkExtractSliceFilter.txx
@@ -0,0 +1,106 @@
+/*=========================================================================
+  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://oncora1.lyon.fnclcc.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
+  ======================================================================-====*/
+
+// clitk
+#include "clitkCommon.h"
+
+
+//--------------------------------------------------------------------
+template <class ImageType>
+clitk::ExtractSliceFilter<ImageType>::
+ExtractSliceFilter():
+  clitk::FilterBase(),
+  itk::ImageToImageFilter<ImageType, ImageType>()
+{
+  this->SetNumberOfRequiredInputs(1);
+  SetDirection(2);
+}
+//--------------------------------------------------------------------
+
+
+//--------------------------------------------------------------------
+template <class ImageType>
+void 
+clitk::ExtractSliceFilter<ImageType>::
+SetInput(const ImageType * image) {
+  // Process object is not const-correct so the const casting is required.
+  this->SetNthInput(0, const_cast<ImageType *>(image));
+}
+//--------------------------------------------------------------------
+  
+
+//--------------------------------------------------------------------
+template <class ImageType>
+void 
+clitk::ExtractSliceFilter<ImageType>::
+GenerateOutputInformation() { 
+  DD("GenerateOutputInformation");
+  ImagePointer input = dynamic_cast<ImageType*>(itk::ProcessObject::GetInput(0));
+  //   ImagePointer outputImage = this->GetOutput(0);
+  //   outputImage->SetRegions(input->GetLargestPossibleRegion());
+  
+  output = this->GetOutput(0);
+  
+  // create vector
+  typename SliceType::RegionType SliceRegionType;
+  typename SliceType::SizeType SliceSizeType;
+  typename SliceType::IndexType SliceIndexType;
+  // SliceRegionType region;
+
+  // create region
+  // loop ExtractImageFilter with region updated, push_back
+
+
+}
+//--------------------------------------------------------------------
+
+
+//--------------------------------------------------------------------
+template <class ImageType>
+void 
+clitk::ExtractSliceFilter<ImageType>::
+GenerateInputRequestedRegion() {
+  DD("GenerateInputRequestedRegion");
+  // Call default
+  itk::ImageToImageFilter<ImageType, ImageType>::GenerateInputRequestedRegion();
+  // Get input pointers and set requested region to common region
+  ImagePointer input = dynamic_cast<ImageType*>(itk::ProcessObject::GetInput(0));
+  input->SetRequestedRegion(input->GetLargestPossibleRegion());
+}
+//--------------------------------------------------------------------
+
+//--------------------------------------------------------------------
+template <class ImageType>
+void 
+clitk::ExtractSliceFilter<ImageType>::
+GenerateData() {
+  DD("GenerateData");
+
+  // Get input pointer
+  input = dynamic_cast<ImageType*>(itk::ProcessObject::GetInput(0));
+
+
+
+  //--------------------------------------------------------------------
+  //--------------------------------------------------------------------  
+  // Final Step -> set output
+  //this->SetNthOutput(0, working_image);
+  return;
+}
+//--------------------------------------------------------------------
+