File: itkSurfaceImageCurvature.h

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

  Program:   Advanced Normalization Tools
  Module:    $RCSfile: itkSurfaceImageCurvature.h,v $
  Language:  C++
  Date:      $Date: 2008/11/15 23:46:06 $
  Version:   $Revision: 1.12 $

  Copyright (c) ConsortiumOfANTS. All rights reserved.
  See accompanying COPYING.txt or 
 http://sourceforge.net/projects/advants/files/ANTS/ANTSCopyright.txt 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 _SurfaceImageCurvature_h
#define _SurfaceImageCurvature_h


#include "itkNeighborhoodIterator.h"

#include "itkSurfaceCurvatureBase.h"
#include "itkGradientRecursiveGaussianImageFilter.h"
#include "itkGradientImageFilter.h"

namespace itk
{

/** \class SurfaceImageCurvature
 * 
 * This class takes a surface as input and creates a local
 * geometric frame for each surface point.  
 *
 *
 */
template < typename TSurface >
           class SurfaceImageCurvature : 
           public SurfaceCurvatureBase < TSurface ,
             3 >
{
public:

  /** Standard class typedefs. */
  typedef SurfaceImageCurvature Self;
  typedef SurfaceCurvatureBase<TSurface> Superclass;
  typedef SmartPointer<Self> Pointer;
  typedef SmartPointer<const Self>  ConstPointer;

  /** Run-time type information (and related methods). */
  itkTypeMacro(SurfaceImageCurvature,SurfaceCurvatureBase);

  /** Method for creation through the object factory. */
  itkNewMacro(Self);

  /** Image related types. */
  typedef typename TSurface::PixelType     PixelType;
  enum { ImageDimension = TSurface::ImageDimension };
  typedef Image<PixelType,itkGetStaticConstMacro(ImageDimension)>            
    ImageType; 
  typedef typename ImageType::IndexType     IndexType;
  typedef typename ImageType::SizeType      SizeType;
  typedef ImageRegionIteratorWithIndex<ImageType> ImageIteratorType;
  /** Image dimension. */
  itkStaticConstMacro(SurfaceDimension, unsigned int, TSurface::ImageDimension);

  typedef typename Superclass::RealType     RealType;
  typedef typename Superclass::PointType    VectorType;
  typedef typename Superclass::PointType    FixedVectorType;
  typedef typename Superclass::PointType    PointType;
  typedef typename Superclass::MatrixType   MatrixType;

  typedef  Image<RealType,itkGetStaticConstMacro(ImageDimension)>            
    OutputImageType; 
  typedef ImageRegionIteratorWithIndex<OutputImageType> OutputImageIteratorType; 
  
  typedef typename OutputImageType::Pointer      OutputImagePointer;

  typedef Image<MatrixType,itkGetStaticConstMacro(ImageDimension)>            
    FrameImageType;

  
  /** Gradient filtering */
  typedef CovariantVector<RealType,
          itkGetStaticConstMacro(ImageDimension)> GradientPixelType;
  typedef Image<GradientPixelType,
               itkGetStaticConstMacro(ImageDimension)> GradientImageType;
  typedef SmartPointer<GradientImageType>     GradientImagePointer;
  typedef GradientRecursiveGaussianImageFilter< OutputImageType,GradientImageType > 
          GradientImageFilterType;  
  typedef GradientImageFilter< OutputImageType > 
          GradientImageFilterType2;  
  typedef typename GradientImageFilterType::Pointer GradientImageFilterPointer;
 
  typedef NeighborhoodIterator<ImageType>  NeighborhoodIteratorType;

  /** Find all points within some distance of the origin. 
    * The argument gives the number of times to apply the 
    * mean shift algorithm to find the best neighborhood.
    */
  void FindNeighborhood(unsigned int numMeanShifts=0);

  void  FindEuclideanNeighborhood(PointType p);

  void  FindGeodesicNeighborhood();


  /** This applies one of the algorithms for finding the local curvature
      and frame.  The default is joshi. */
  void ComputeFrameOverDomain(unsigned int which=0);

  ImageType* GetInput();
  void SetInput(typename ImageType::Pointer input);
  OutputImageType* GetOutput();

  /** Apply the level set curvature equation over the whole image */
  void LevelSetMeanCurvature();


  /** Use the gradient of the image to estimate the normals everywhere.
   *  Also compute area, if boolean is set.
  */
  void EstimateNormalsFromGradient();


  /** Use the Weingarten map to estimate the curvature.*/
  void WeingartenMap();

  /** Computes a neighborhood surface area function everywhere*/
  void ComputeSurfaceArea();

  /** Use the gradient estimated normal to get the local frame.
      Requires call to SetNormal to find tangents. */
  void EstimateFrameFromGradient(IndexType);


  /** Implemented version of virtual function from parent class.
      Here, we just sum the computed function, held in CurvatureImage,
      over a neighborhood */
  RealType IntegrateFunctionOverNeighborhood(bool norm=false);

  /** Get the neighborhood integral for every surface point.*/
  RealType IntegrateFunctionOverSurface(bool norm=false);

  /** Postprocess the curvature function by, e.g., gaussian
      smoothing of the curvature (and perhaps frame) 
      in the local neighbhorhood. */
  void PostProcessGeometry();

  itkSetMacro(NeighborhoodRadius,RealType);
  itkGetMacro(NeighborhoodRadius,RealType);

  itkSetMacro(UseLabel,bool);
  itkGetMacro(UseLabel,bool);


  itkSetMacro(kSign,float);
  itkSetMacro(Sigma,float);

  itkSetMacro(Threshold,float);
  
  itkGetMacro(FunctionImage,OutputImagePointer);
  itkSetMacro(FunctionImage,OutputImagePointer);

  void ProcessLabelImage();

  float CurvatureAtIndex(IndexType index)
  {      
	  PointType p;
      for (unsigned int k=0; k<ImageDimension; k++) 
      {
        p[k]=(RealType) index[k];
      }
      this->SetOrigin(p);
      this->EstimateFrameFromGradient(index);
      this->FindNeighborhood();
	  this->WeingartenMap();
      float fval=this->m_GaussianKappa;
	  float kpix;
      fval=this->m_MeanKappa;
      if (fabs(fval) > 1) fval/=fval;
      kpix=kpix+m_kSign*fval; 

    return kpix;
  }

  inline bool IsValidSurface(PixelType pix, IndexType ind)
    {
      //   std::cout << "m_UseLabel "<< m_UseLabel << " pix " << pix << " Thresh " << m_Threshold << " ind " << ind << std::endl;
      if (this->m_UseLabel)
      {
        if ( pix == this->m_SurfaceLabel ) return true; else return false;
      }
      else
      {
        if (pix > this->m_Threshold ) return true;
          else return false;
      }
    }

protected:

  SurfaceImageCurvature();
  ~SurfaceImageCurvature(){};

  void CopyImageToFunctionImage( OutputImagePointer,OutputImagePointer);

  
  /** This function changes the values of the label image for use with 
      the fast marching image filter. */
  

private:

  PixelType                     m_SurfaceLabel;
  OutputImagePointer            m_FunctionImage;
  RealType                      m_NeighborhoodRadius;
  SizeType                      m_ImageSize;
  GradientImagePointer          m_GradientImage;
  NeighborhoodIteratorType      m_ti;
  NeighborhoodIteratorType      m_ti2;
  bool                          m_UseLabel;
  float                         m_kSign;
  float                         m_Sigma;
  float                         m_Threshold;
};



} // namespace itk

#ifndef ITK_MANUAL_INSTANTIATION
#include "itkSurfaceImageCurvature.txx"
#endif

#endif