SFLSSegmentor3D.h

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#ifndef SFLSSegmentor3D_h_
#define SFLSSegmentor3D_h_

#include "SFLS.h"

#include <list>
#include <vector>

// douher
// #include "cArray3D.h"

// itk
#include "itkImage.h"

template <typename TPixel>
class CSFLSSegmentor3D : public CSFLS
{
public:
  typedef CSFLSSegmentor3D<TPixel> Self;

  typedef CSFLS SuperClassType;

  typedef SuperClassType::NodeType   NodeType;
  typedef SuperClassType::CSFLSLayer CSFLSLayer;
  // typedef boost::shared_ptr< Self > Pointer;

  typedef itk::Image<TPixel, 3>        TImage;
  typedef itk::Image<float, 3>         TFloatImage;
  typedef itk::Image<double, 3>        TDoubleImage;
  typedef itk::Image<char, 3>          TCharImage;
  typedef itk::Image<unsigned char, 3> TUCharImage;
  typedef itk::Image<short, 3>         TShortImage;

  typedef TImage      ImageType;
  typedef TFloatImage LSImageType;
  typedef TCharImage  LabelImageType;
  typedef TUCharImage MaskImageType;
  typedef TShortImage ShortImageType;

  typedef typename TImage::IndexType  TIndex;
  typedef typename TImage::SizeType   TSize;
  typedef typename TImage::RegionType TRegion;

  CSFLSSegmentor3D();
  virtual ~CSFLSSegmentor3D() = default;

  /* New */
  // static Pointer New() { return Pointer(new Self); }

  /* ============================================================
   * functions         */
  void basicInit();

  void setNumIter(unsigned long n);

  void setImage(typename ImageType::Pointer img);
  void setMask(typename MaskImageType::Pointer mask);

  virtual void computeForce() = 0;

  void normalizeForce();

  //     double maxPhi(long ix, long iy, long iz, double level);
  //     double minPhi(long ix, long iy, long iz, double level);
  bool getPhiOfTheNbhdWhoIsClosestToZeroLevelInLayerCloserToZeroLevel(long ix, long iy, long iz, double& thePhi);

  void oneStepLevelSetEvolution();

  // void getSFLSFromPhi();

  void initializeSFLS()
  {
    initializeSFLSFromMask();
  }
  void initializeSFLSFromMask(); // m_insideVoxelCount is first computed here

  void initializeLabel();

  void initializePhi();

  virtual void doSegmenation() = 0;

  // geometry
  double computeKappa(long ix, long iy, long iz);

  void setMaxVolume(double v); // v is in mL

  void setMaxRunningTime(double t); // t in min

  // about evolution history
  void keepZeroLayerHistory(bool b)
  {
    m_keepZeroLayerHistory = b;
  }
  CSFLSLayer getZeroLayerAtIteration(unsigned long i);

  void writeZeroLayerAtIterationToFile(unsigned long i, const char* name);

  void writeZeroLayerToFile(const char* namePrefix);

  void setCurvatureWeight(double a);

  LSImageType::Pointer getLevelSetFunction();

  /* ============================================================
   * data     */
  // CSFLS::Pointer mp_sfls;

  typename ImageType::Pointer mp_img;
  typename LabelImageType::Pointer mp_label;
  typename MaskImageType::Pointer mp_mask; // 0, non-0 mask for object
  typename LSImageType::Pointer mp_phi;

  //  std::list< double > m_force;
  std::vector<double> m_force;

  double m_timeStep;

  unsigned long m_numIter;
protected:
  double m_curvatureWeight;

  bool m_done;

  long m_nx;
  long m_ny;
  long m_nz;

  double m_dx; // in mm
  double m_dy; // in mm
  double m_dz; // in mm

  long   m_insideVoxelCount;
  double m_insideVolume;

  double m_maxVolume;      // max physical volume, in mm^3
  double m_maxRunningTime; // in sec

  /*----------------------------------------------------------------------
    These two record the pts which change status

    Because they are created and visited sequentially, and when not
    needed, are clear-ed as a whole. No random insertion or removal is
    needed. So use vector is faster than list.  */
  CSFLSLayer m_lIn2out;
  CSFLSLayer m_lOut2in;

  void updateInsideVoxelCount();

  inline bool doubleEqual(double a, double b, double eps = 1e-10)
  {
    return a - b < eps && b - a < eps;
  }

  bool                    m_keepZeroLayerHistory;
  std::vector<CSFLSLayer> m_zeroLayerHistory;

};

#include "SFLSSegmentor3D.txx"

#endif