SFLSSegmentor3D.h

Go to the documentation of this file.

#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