vDynamicModel.hh

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/*
This file is part of CASToR.

    CASToR is free software: you can redistribute it and/or modify it under the
    terms of the GNU General Public License as published by the Free Software
    Foundation, either version 3 of the License, or (at your option) any later
    version.

    CASToR is distributed in the hope that it will be useful, but WITHOUT ANY
    WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
    FOR A PARTICULAR PURPOSE.  See the GNU General Public License for more
    details.

    You should have received a copy of the GNU General Public License along with
    CASToR (in file GNU_GPL.TXT). If not, see <http://www.gnu.org/licenses/>.

Copyright 2017-2020 all CASToR contributors listed below:

    --> Didier BENOIT, Claude COMTAT, Marina FILIPOVIC, Thibaut MERLIN, Mael MILLARDET, Simon STUTE, Valentin VIELZEUF, Zacharias CHALAMPALAKIS

This is CASToR version 3.1.
*/

#ifndef VDYNAMICMODEL_HH
#define VDYNAMICMODEL_HH 1

#include "gVariables.hh"
#include "oImageDimensionsAndQuantification.hh"
#include "oOptimizerManager.hh"
// #include "oArterialInputCurve.hh"

class oImageSpace;

class vDynamicModel
{
  // -----------------------------------------------------------------------------------------
  // Constructor & Destructor
  public:
    vDynamicModel();
    virtual ~vDynamicModel();


  // -----------------------------------------------------------------------------------------
  // Public member functions related to the initialization of the model
  public:
    inline void SetImageDimensionsAndQuantification(oImageDimensionsAndQuantification* ap_ImageDimensionsAndQuantification)
                           {mp_ID = ap_ImageDimensionsAndQuantification;}
    inline void SetVerbose(int a_verbose) 
               {m_verbose = a_verbose;}
    virtual int CheckParameters();
    virtual int CheckSpecificParameters() = 0;
    int ReadAndCheckConfigurationFile(string a_fileOptions);
    virtual int ReadAndCheckConfigurationFileSpecific() = 0;
    virtual int ReadAndCheckOptionsList(string a_listOptions) = 0;
    int Initialize();
    virtual int InitializeSpecific() = 0;
    virtual void ShowHelpModelSpecific() = 0;
     void ShowHelp() ;


  // -----------------------------------------------------------------------------------------
  // Public member functions called by the main iterative algorithm class
  public:
    virtual int EstimateModel(oImageSpace* ap_Image, int a_ite, int a_sset);
    virtual int EstimateModelParameters(oImageSpace* ap_Image, int a_ite, int a_sset) = 0;
    virtual int EstimateImage(oImageSpace* ap_Image, int a_ite, int a_sset);
    virtual int EstimateImageWithModel(oImageSpace* ap_Image, int a_ite, int a_sset) = 0;
    int SaveParametricImages(int a_iteration, int a_subset = -1);
    virtual int ApplyOutputFOVMaskingOnParametricImages();

    inline bool GetAICflag()  {return m_AICfileProvided; }
    inline bool GetModelBasisFunctionsRequiredFlag()  {return m_ModelSpecificBasisFunctionsRequired; }
    inline int GetNbTimeBasisFunctions() {return m_nbTimeBF; }
    inline FLTNB** GetTimeBasisFunctions() {return m2p_nestedModelTimeBasisFunctions; }

    virtual void ComputeOutputParImage();
    inline void SetUseModelInReconstruction(bool a_useModelInReconstruction)
           {m_useModelInReconstruction=a_useModelInReconstruction;}

    int NNLS( FLTNB **A,
              int m,
              int n,
              FLTNB *B,
              FLTNB *X,
              FLTNB *rnorm,
              FLTNB *wp,
              FLTNB *zzp,
              int *indexp );


  private:
  
    int NNLS_LSS_H12( int mode,
                      int lpivot,
                      int l1,
                      int m,
                      FLTNB *u,
                      int u_dim1,
                      FLTNB *up,
                      FLTNB *cm,
                      int ice,
                      int icv,
                      int ncv );

    void NNLS_LSS_G1(FLTNB a, FLTNB b, FLTNB *cterm, FLTNB *sterm, FLTNB *sig);


  // -----------------------------------------------------------------------------------------
  // Data members
  protected:
    oImageDimensionsAndQuantification* mp_ID; 
    int m_verbose;                            
    int m_nbTimeBF;                           
    int m_nbWeightFactors;                    
    int m_nbModelParam;                       
    int m_nbRGModelParam;                     
    int m_nbCGModelParam;                     
    string m_AICfile;                         
  oArterialInputCurve* mp_ArterialInputCurve; 
    FLTNB** m2p_parametricImages;      
    FLTNB* mp_blackListedvoxelsImage;  
    FLTNB** m2p_nestedModelTimeBasisFunctions;  
    FLTNB** m2p_outputParImages;       
    FLTNB** m2p_RGParametricImages; 
    FLTNB** m2p_CGParametricImages; 
    string      m_fileOptions;            
    string      m_listOptions;            
    bool        m_checked;                
    bool        m_initialized;            
    bool        m_useModelInReconstruction; 
    bool        m_saveParImageFlag;       
    bool        m_saveBlacklistedImageMaskFlag;   
    bool        m_AICfileProvided;        
    bool        m_ModelSpecificBasisFunctionsRequired;  
    bool        m_noImageUpdateFlag;      
    bool        m_noParametersUpdateFlag; 
    int         m_startIteUpdateFlag;     
    FLTNB*      mp_maskModel;             
    INTNB       m_nbVoxelsMask;           
    // NNLS function
    FLTNB*    mp_w;             
    FLTNB***  m3p_nnlsA;        
    FLTNB**   m2p_nnlsB;        
    FLTNB**   m2p_nnlsMat;      
    FLTNB**   m2p_nnlsX;        
    FLTNB**   m2p_nnlsWp;       
    int**     m2p_nnlsIdx;      
    uint16_t  m_nnlsN=0;      
};

// ----------------------------------------------------------------------
// Part of code that manages the auto declaration of children classes
// ----------------------------------------------------------------------

// Macro for the function that creates the object
#define FUNCTION_DYNAMICMODEL(CLASS) \
  static vDynamicModel *make_dynamic_model() { return new CLASS(); };

// Macro for the class that links the appropriate function to the map of objects
#define CLASS_DYNAMICMODEL(NAME,CLASS)                                                               \
  class NAME##DynamicModelCreator                                                                    \
  {                                                                                                  \
    public:                                                                                          \
      NAME##DynamicModelCreator()                                                                    \
        { sAddonManager::GetInstance()->mp_listOfDynamicModels[#NAME] = CLASS::make_dynamic_model; } \
  };                                                                                                 \
  static NAME##DynamicModelCreator DynamicModelCreator##NAME;

#endif