itkHessianToShikataMeasureImageFilter.h

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 *  Copyright Insight Software Consortium
 *
 *  Licensed under the Apache License, Version 2.0 (the "License");
 *  you may not use this file except in compliance with the License.
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#ifndef __itkHessianToShikataMeasureImageFilter_h
#define __itkHessianToShikataMeasureImageFilter_h

#include "itkSymmetricSecondRankTensor.h"
#include "itkImageToImageFilter.h"

namespace itk
{
/** \class HessianToShikataMeasureImageFilter
 * \brief A filter to enhance M-dimensional objects in N-dimensional images
 *
 * The objectness measure is a generalization of Frangi's vesselness measure,
 * which is based on the analysis of the the Hessian eigen system. The filter
 * can enhance blob-like structures (M=0), vessel-like structures (M=1), 2D
 * plate-like structures (M=2), hyper-plate-like structures (M=3) in N-dimensional
 * images, with M<N.
 * The filter takes an image of a Hessian pixels ( SymmetricSecondRankTensor pixels
 * pixels ) and produces an enhanced image. The Hessian input image can be produced
 * using itk::HessianRecursiveGaussianImageFilter.
 *
 *
 * \par References
 * Frangi, AF, Niessen, WJ, Vincken, KL, & Viergever, MA (1998). Multiscale Vessel
 * Enhancement Filtering. In Wells, WM, Colchester, A, & Delp, S, Editors, MICCAI '98
 * Medical Image Computing and Computer-Assisted Intervention, Lecture Notes in Computer
 * Science, pages 130-137, Springer Verlag, 1998.
 *
 * Additional information can be from in the Insight Journal:
 * http://hdl.handle.net/1926/576
 *
 * \author Luca Antiga Ph.D.  Medical Imaging Unit,
 *                            Bioengineering Deparment, Mario Negri Institute, Italy.
 *
 * \sa MultiScaleHessianBasedMeasureImageFilter
 * \sa Hessian3DToVesselnessMeasureImageFilter
 * \sa HessianSmoothedRecursiveGaussianImageFilter
 * \sa SymmetricEigenAnalysisImageFilter
 * \sa SymmetricSecondRankTensor
 *
 * \ingroup IntensityImageFilters TensorObjects
 *
 * \ingroup ITK-Review
 */
template< typename TInputImage, typename TScalarImage, typename TOutputImage >
class ITK_EXPORT HessianToShikataMeasureImageFilter:public
  ImageToImageFilter< TInputImage, TOutputImage >
{
public:
  /** Standard class typedefs. */
  typedef HessianToShikataMeasureImageFilter Self;

  typedef ImageToImageFilter< TInputImage, TOutputImage > Superclass;

  typedef SmartPointer< Self >       Pointer;
  typedef SmartPointer< const Self > ConstPointer;

  typedef typename Superclass::InputImageType  InputImageType;
  typedef typename Superclass::OutputImageType OutputImageType;
  typedef typename InputImageType::PixelType   InputPixelType;
  typedef typename OutputImageType::PixelType  OutputPixelType;
  typedef typename OutputImageType::RegionType OutputImageRegionType;
  typedef TScalarImage ScalarImageType;
  typedef TInputImage HessianImageType;


  /** Image dimension */
  itkStaticConstMacro(ImageDimension, unsigned int, ::itk::GetImageDimension< InputImageType >::ImageDimension);

  typedef double                                                                    EigenValueType;
  typedef itk::FixedArray< EigenValueType, itkGetStaticConstMacro(ImageDimension) > EigenValueArrayType;

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

  /** Runtime information support. */
  itkTypeMacro(HessianToShikataMeasureImageFilter, ImageToImageFilter);




  void SetInputHessianImage(const HessianImageType* hessian);


  void SetInputScalarImage(const ScalarImageType* scalarImage);



  itkSetMacro(SigmaF, double);
  itkGetConstMacro(SigmaF, double);

//
//  /** Set/Get Alpha, the weight corresponding to R_A
//   * (the ratio of the smallest eigenvalue that has to be large to the larger ones).
//   * Smaller values lead to increased sensitivity to the object dimensionality. */
//  itkSetMacro(Alpha, double);
//  itkGetConstMacro(Alpha, double);
//
//  /** Set/Get Beta, the weight corresponding to R_B
//   * (the ratio of the largest eigenvalue that has to be small to the larger ones).
//   * Smaller values lead to increased sensitivity to the object dimensionality. */
//  itkSetMacro(Beta, double);
//  itkGetConstMacro(Beta, double);
//
//  /** Set/Get Gamma, the weight corresponding to S
//   * (the Frobenius norm of the Hessian matrix, or second-order structureness) */
//  itkSetMacro(Gamma, double);
//  itkGetConstMacro(Gamma, double);

  /** Toggle scaling the objectness measure with the magnitude of the largest
    absolute eigenvalue */
  itkSetMacro(ScaleObjectnessMeasure, bool);
  itkGetConstMacro(ScaleObjectnessMeasure, bool);
  itkBooleanMacro(ScaleObjectnessMeasure);

//  /** Set/Get the dimensionality of the object (0: points (blobs),
//   * 1: lines (vessels), 2: planes (plate-like structures), 3: hyper-planes.
//   * ObjectDimension must be smaller than ImageDimension. */
//  itkSetMacro(ObjectDimension, unsigned int);
//  itkGetConstMacro(ObjectDimension, unsigned int);

  /** Enhance bright structures on a dark background if true, the opposite if
    false. */
  itkSetMacro(BrightObject, bool);
  itkGetConstMacro(BrightObject, bool);
  itkBooleanMacro(BrightObject);

#ifdef ITK_USE_CONCEPT_CHECKING
  /** Begin concept checking */
  itkConceptMacro( DoubleConvertibleToOutputCheck, ( Concept::Convertible< double, OutputPixelType > ) );
  /** End concept checking */
#endif
protected:
  HessianToShikataMeasureImageFilter();
  ~HessianToShikataMeasureImageFilter() {}
  void PrintSelf(std::ostream & os, Indent indent) const;

  void BeforeThreadedGenerateData(void);

  void ThreadedGenerateData(const OutputImageRegionType & outputRegionForThread, ThreadIdType threadId);

private:
  HessianToShikataMeasureImageFilter(const Self &); //purposely not
                                                       // implemented
  void operator=(const Self &);                        //purposely not
                                                       // implemented

  // functor used to sort the eigenvalues are to be sorted
  // |e1|<=|e2|<=...<=|eN|
//  struct AbsLessEqualCompare {
//    bool operator()(EigenValueType a, EigenValueType b)
//    {
//      return vnl_math_abs(a) <= vnl_math_abs(b);
//    }
//  };

  struct LessEqualCompare {
    bool operator()(EigenValueType a, EigenValueType b)
    {
      return a <= b;
    }
  };



  // From Shikata's paper
  double      m_SigmaF;



//  double       m_Alpha;
//  double       m_Beta;
//  double       m_Gamma;
  unsigned int m_ObjectDimension;
  bool         m_BrightObject;
  bool         m_ScaleObjectnessMeasure;
};
} // end namespace itk

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

#endif