iRCPGSAlgorithm.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 2017-2019 all CASToR contributors listed below:

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

This is CASToR version 3.0.
*/


#ifndef IRCPGSALGORITHM_HH
#define IRCPGSALGORITHM_HH 1


#include "vAlgorithm.hh"
#include <functional>


class iRCPGSAlgorithm : public vAlgorithm
{
  // Constructor & Destructor
  public:
    iRCPGSAlgorithm();
    ~iRCPGSAlgorithm();
    
    int InitSpecificOptions(string a_specificOptions);
    void ShowHelpSpecific();

  // Protected overriden virtual member functions
  protected:
    int StepBeforeIterationLoop();
    int StepAfterIterationLoop();
    int StepBeforeSubsetLoop(int a_iteration);
    int StepAfterSubsetLoop(int a_iteration);
    int StepPreProcessInsideSubsetLoop(int a_iteration, int a_subset);
    int StepInnerLoopInsideSubsetLoop(int a_iteration, int a_subset, int a_bed);
    int StepPostProcessInsideSubsetLoop(int a_iteration, int a_subset);
    int StepImageOutput(int a_iteration, int a_subset = -1);
    int ReadConfigurationFile(const string& a_configurationFile);
    
  // Private member functions
  private:
    int SampleConditionalCompleteData(int a_iteration, int a_subset, int a_bed);
    int SampleConditionalClustering(int a_iteration);
    int SampleConditionalClusterIntensity();
    int UpdateVisitedVoxels();
    int InitializeHelperVar();
    int ProcessMultiModalInfo();
    int GenerateCurrentImage();
    int ComputeFellowVoxelsList(vector<INTNB>& a_fellow_voxels, int a_current_voxel);
    int ComputeSumsPerClusters(int a_iteration);
    int SaveIntermediaryData(int a_iteration);
    
    
  // Private data members
  private:
    // algorithm parameters
    int m_ddCRP; 
    int m_backprojection; 
    int m_neighbourhood; 
    HPFLTNB m_gammaShape; 
    HPFLTNB m_gammaRate; 
    HPFLTNB m_ddcrpAlpha; 
    INTNB m_multiModalLag; 
    HPFLTNB m_ddcrpAlphaIncrement; 
    HPFLTNB* mp_multiModalNoiseSigma; 
    HPFLTNB* mp_multiModalParam; 
    INTNB* mp_voxelClusterMapping;
    HPFLTNB* mp_clusterValues;
    HPFLTNB** mp_clusterN;
    HPFLTNB* mp_clusterSensitivity;
    HPFLTNB** mpp_clusterMultiModal;
    INTNB* mp_clusterCount;
    INTNB* mp_nextLink;
    vector<INTNB>* mpv_parentLinks;
    vector<INTNB> mv_newClusters;
    INTNB* mp_listVoxelIndices;
    INTNB** mp_listEventsIndices;
    INTNB**** m4p_EventsBackprojectionTrace;
    bool* mp_listRelevantVoxelIndices;
    HPFLTNB* temp_count_multimodal; 
    HPFLTNB m_ddcrpLogAlpha; 
    HPFLTNB m_currentMeanClusterVolume; 
    HPFLTNB m_meanClusterVolumeMin; 
    HPFLTNB m_meanClusterVolumeMax; 
    FLTNB* mp_permanentBackwardImage; 
};

#endif