include/optimizer/iPenaltyMarkovRandomField.hh

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#ifndef IPENALTYMARKOVRANDOMFIELD_HH
#define IPENALTYMARKOVRANDOMFIELD_HH 1

#include "vPenalty.hh"
#include "sAddonManager.hh"
#include "sOutputManager.hh"

#define MRF_POTENTIAL_QUADRATIC 0
#define MRF_POTENTIAL_RELATIVE_DIFFERENCE 1
#define MRF_POTENTIAL_GEMAN_MCCLURE 2
#define MRF_POTENTIAL_GREEN 3
#define MRF_POTENTIAL_HEBERT_LEAHY 4
#define MRF_POTENTIAL_HUBER 5

#define MRF_PROXIMITY_NONE 0
#define MRF_PROXIMITY_VOXEL 1
#define MRF_PROXIMITY_EUCLIDIAN 2
#define MRF_PROXIMITY_GAUSSIAN 3

#define MRF_SIMILARITY_NONE 0
#define MRF_SIMILARITY_BOWSHER 1

#define MRF_NEIGHBORHOOD_SPHERE 0
#define MRF_NEIGHBORHOOD_BOX 1
#define MRF_NEIGHBORHOOD_6_NEAREST 2

#define MRF_NOT_DEFINED -1

#define MRF_NEIGHBOR_X 0
#define MRF_NEIGHBOR_Y 1
#define MRF_NEIGHBOR_Z 2

class iPenaltyMarkovRandomField : public vPenalty
{
  // -------------------------------------------------------------------
  // Constructor & Destructor
  public:

    iPenaltyMarkovRandomField();
    ~iPenaltyMarkovRandomField();

  // -------------------------------------------------------------------
  // Public member functions
  public:
    // Function for automatic insertion (put the class name as the parameter and do not add semi-column at the end of the line)
    FUNCTION_PENALTY(iPenaltyMarkovRandomField)
    int ReadConfigurationFile(const string& a_configurationFile);
    int ReadOptionsList(const string& a_optionsList);
    int LocalPreProcessingStep(int a_tbf, int a_rbf, int a_cbf, INTNB a_voxel, int a_th);
    FLTNB ComputePenaltyValue(FLTNB* ap_image, INTNB a_voxel, int a_th);
    FLTNB ComputeFirstDerivative(FLTNB* ap_image, INTNB a_voxel, int a_th);
    FLTNB ComputeSecondDerivative(FLTNB* ap_image, INTNB a_voxel, int a_th);
    int BuildSpecificNeighborhood(INTNB a_voxel, int a_th);
    
  // -------------------------------------------------------------------
  // Public Get & Set functions
  public:
    inline int GetPotentialType() {return m_potentialType;}
    inline FLTNB* GetProximityKernel() {return mp_proximityKernel;}
    inline FLTNB* GetSimilarityFactors(int a_th) {return m2p_similarityFactors[a_th];}
    inline INTNB GetNeighborhoodMaxNbVoxels() {return m_neighborhoodMaxNbVoxels;}
    inline INTNB** GetNeighborhoodIndices() {return m2p_neighborhoodIndices;}

  // -------------------------------------------------------------------
  // Private member functions
  private:
    void ShowHelpSpecific();
    int CheckSpecificParameters();
    int InitializeSpecific();
    int BuildNeighborhoodKernel();
    int BuildProximityFactors();
    int ComputeSimilarityFactors(int a_tbf, int a_rbf, int a_cbf, INTNB a_voxel, int a_th);

  // -------------------------------------------------------------------
  // Data members
  private:
    // Potential functions
    int m_potentialType;                      
    FLTNB m_potentialRelativeDifferenceGamma; 
    FLTNB m_potentialGemanMcClureDelta;       
    FLTNB m_potentialGreenLogCoshDelta;       
    FLTNB m_potentialHebertLeahyMu;           
    FLTNB m_potentialHuberDelta;              
    // Proximity factors
    int m_proximityType;                      
    FLTNB m_proximityGaussianFWHM;            
    FLTNB* mp_proximityKernel;                
    // Similarity factors
    int m_similarityType;                     
    FLTNB m_similarityBowsherThreshold;       
    FLTNB** m2p_similarityFactors;            
    INTNB m_similarityBowsherNbVoxels;        
    // Neighborhood
    int       m_neighborhoodShape;             
    FLTNB     m_neighborhoodSphereRadius;      
    int       m_neighborhoodBoxOrder;          
    int       m_neighborhoodBoxExcludeCorners; 
    INTNB     m_neighborhoodMaxNbVoxels;       
    INTNB** m2p_neighborhoodKernel;            
    INTNB*   mp_neighborhoodNbVoxels;          
    INTNB** m2p_neighborhoodIndices;           
    INTNB** m2p_helper_bowsher;                
};

// Class for automatic insertion (set here the visible optimizer's name as the first parameter,
// put the class name as the second parameter and do NOT add semi-colon at the end of the line)
CLASS_PENALTY(MRF,iPenaltyMarkovRandomField)

#endif