/*  lsmcmcmanager.h

    Mark Woolrich - FMRIB Image Analysis Group

    Copyright (C) 2002 University of Oxford  */

/*  Part of FSL - FMRIB's Software Library
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    Developed at FMRIB (Oxford Centre for Functional Magnetic Resonance
    Imaging of the Brain), Department of Clinical Neurology, Oxford
    University, Oxford, UK
    
    
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#if !defined(lsmcmcmanager_h)
#define lsmcmcmanager_h

#include <iostream>
#include <fstream>
#include <string>
#include <vector>
#include "newimage/newimageall.h"
#include "model.h"
#include "bintoptions.h"

using namespace NEWMAT;
using namespace MISCMATHS;
using namespace NEWIMAGE;

namespace Bint {

  class LSMCMCParameter;
  class LSMCMCPrecParameter;

  class LSMCMCVoxelManager
  {
  public:

    LSMCMCVoxelManager(ForwardModel& pmodel,int pburnin, int pnjumps, int psampleevery, int pupdateproposalevery, float pacceptancerate, int pdebuglevel, bool panalmargprec, int pnsamples) : model(pmodel), burnin(pburnin), njumps(pnjumps), sampleevery(psampleevery), updateproposalevery(pupdateproposalevery), acceptancerate(pacceptancerate), nsamples(pnsamples), nparams(0), sumsquares(0), likelihood(0), debuglevel(pdebuglevel), analmargprec(panalmargprec) {}
  
    virtual ~LSMCMCVoxelManager();

    void run();
    void jump();
    void sample();

    void setupparams(float prec);
    void setdata(const ColumnVector& pdata);

    void calcsumsquares();
    float calclikelihood();

    void restoresumsquares(){ sumsquares = sumsquares_old; }

    void restorelikelihood(){ likelihood = likelihood_old; }

    int getnsamples() const {return nsamples;}
    const vector<float>& getsamples(int p);
    const vector<float>& getprecsamples();
    const string& getparamname(int p);
    int getnparams() const {return nparams;}

    int getdebuglevel() const {return debuglevel;}
    float getlikelihood() const {return likelihood;}
    int getntpts() const {return ntpts;}
    const vector<LSMCMCParameter*>& getmcmcparams() const {return mcmcparams;}

  protected:

    ForwardModel& model;

    vector<LSMCMCParameter*> mcmcparams;

    Parameter* precparam;
    LSMCMCPrecParameter* precmcmcparam;
    GammaPrior* precparamprior;

    int burnin;
    int njumps;
    int sampleevery;
    int updateproposalevery; 
    float acceptancerate;

    int nsamples;
    int ntpts;
    int nparams;
    float sumsquares;
    float likelihood;

    int debuglevel;
    bool analmargprec;

    float sumsquares_old;
    float likelihood_old;
    bool updateprec;
    ColumnVector data;    

  private:

    LSMCMCVoxelManager();
    const LSMCMCVoxelManager& operator=(LSMCMCVoxelManager& par);     
    LSMCMCVoxelManager(LSMCMCVoxelManager& des);
  };

class McmcParameter
  {
  public:
    
    McmcParameter(Parameter& pparam, int pnsamples, int pupdateproposalevery, float pacceptancerate, int pdebuglevel) :       
      param(pparam),
      val(pparam.getinitvalue()),
      naccepted(0),
      nrejected(0),
      proposal_std(pparam.getinitstd()),
      jumpcount(0),
      debuglevel(pdebuglevel),
      updateproposalevery(pupdateproposalevery),
      acceptancerate(pacceptancerate)
    {
      samples.reserve(pnsamples);
    }
    
    // get new energy taking into account that this parameter's value has changed
    virtual float new_energy() = 0;

    // get energy assuming current value has not changed
    virtual float old_energy() = 0;

    // jump has been rejected: restore energies
    virtual void restore_energy() = 0;

    void update_proposal_std() {
      proposal_std *= acceptancerate/((1+nrejected)/float(1+naccepted+nrejected));
      //cout <<param.getname()<<endl;
      //cout<<"Nacc "<<naccepted<<endl;
      //cout<<"Nrej "<<nrejected<<endl;
      naccepted = 0;
      nrejected = 0;
    }

    virtual void setup() = 0;

//      virtual void reset(float pvalue, float pproposal_std)
//      {
//        naccepted = 0;
//        nrejected = 0;
//        proposal_std = pproposal_std;
//        val = pvalue;
//        jumpcount = 0;
//      }

    void jump();
    void sample(){samples.push_back(val);}    

    virtual ~McmcParameter(){}

    const float value() const {return val;}

    float& value() {return val;}

    const vector<float>& getsamples() const {return samples;}

    bool getallowtovary() const {return param.getallowtovary();}
    bool getsave() const {return param.getsave();}
  protected:

    Parameter& param;
    float val;
    int naccepted;
    int nrejected;
    float proposal_std;
    int jumpcount;
    vector<float> samples;
    int debuglevel;
    int updateproposalevery;
    float acceptancerate;

  private:

    McmcParameter();
    const McmcParameter& operator=(McmcParameter& par);     
    McmcParameter(McmcParameter& des);
  };


  class LSMCMCParameter : public McmcParameter
  {
  public:
    LSMCMCParameter(Parameter& pparam,int pnsamples, int pupdateproposalevery, float pacceptancerate,LSMCMCVoxelManager& plsmcmc) : 
      McmcParameter(pparam,pnsamples,pupdateproposalevery,pacceptancerate,plsmcmc.getdebuglevel()), lsmcmc(plsmcmc), prior_energy(0.0), prior_old_energy(0.0)
    {}

    ~LSMCMCParameter(){}
    
    void setup()
    {
      calc_prior();
    }

    float new_energy() 
    {      
      float energy = calc_prior();
      if(energy != float(MAX_EN)) 
	{
	  lsmcmc.calcsumsquares();
	  energy += lsmcmc.calclikelihood();
	}
	
      return energy;
    }

    float old_energy() 
    {
      float energy = prior_energy;
      
      if(energy != float(MAX_EN)) 
	{
	  energy += lsmcmc.getlikelihood();
	}

      return energy;
    }

    void restore_energy()
    {
      restoreprior();
      lsmcmc.restoresumsquares();
      lsmcmc.restorelikelihood();
    }

    float calc_prior() { 

      prior_old_energy = prior_energy; 
      prior_energy = param.getprior().calc_energy(val); 

      if(debuglevel==2)
	{
	  cout << "prior_old_energy=" << prior_old_energy << endl;
	  cout << "prior_energy=" << prior_energy << endl;
	}

      return prior_energy; 
    }  

    void restoreprior() { prior_energy = prior_old_energy; }

  protected:
    LSMCMCVoxelManager& lsmcmc;
    float prior_energy;
    float prior_old_energy;

  private:

    LSMCMCParameter();
    const LSMCMCParameter& operator=(LSMCMCParameter& par);     
    LSMCMCParameter(LSMCMCParameter& des);

  };

  class LSMCMCPrecParameter : public McmcParameter
  {
  public:
    LSMCMCPrecParameter(Parameter& pparam,int pnsamples, int pupdateproposalevery, float pacceptancerate,LSMCMCVoxelManager& plsmcmc) : 
      McmcParameter(pparam,pnsamples,pupdateproposalevery,pacceptancerate,plsmcmc.getdebuglevel()), lsmcmc(plsmcmc), extra_energy(0.0), extra_old_energy(0.0), N(plsmcmc.getntpts()), priormean(pparam.getinitvalue()), impropercount(0)
    {}

    ~LSMCMCPrecParameter(){}
    
    void setup()
    {      
      calc_extra();
    }

//     void reset(float pvalue, float pproposal_std)
//     { 
//       McmcParameter::reset(pvalue,pproposal_std);
//       extra_energy = 0.0;
//       impropercount = 0;
//       calc_extra();
//     }

    float new_energy() 
    {      
      return calc_extra() + lsmcmc.calclikelihood();
    }

    float old_energy() 
    {
      return extra_energy + lsmcmc.getlikelihood();
    }

    void restore_energy()
    {
      restoreextra();      
      lsmcmc.restorelikelihood();
    }

    float calc_extra();

    void restoreextra() { extra_energy = extra_old_energy; }

  protected:

    LSMCMCVoxelManager& lsmcmc;

    float extra_energy;
    float extra_old_energy;

    int N;

    float priormean;

    int impropercount;

 private:

    LSMCMCPrecParameter();
    const LSMCMCPrecParameter& operator=(LSMCMCPrecParameter& par);     
    LSMCMCPrecParameter(LSMCMCPrecParameter& des);

  };

  inline LSMCMCVoxelManager::~LSMCMCVoxelManager() { 
    mcmcparams.clear();
    if(!analmargprec) {
      delete precparam; delete precmcmcparam; delete precparamprior;
    }
  }
  
  inline const vector<float>& LSMCMCVoxelManager::getsamples(int p) {return mcmcparams[p]->getsamples();}
  inline const vector<float>& LSMCMCVoxelManager::getprecsamples() {return precmcmcparam->getsamples();}
  inline const string& LSMCMCVoxelManager::getparamname(int p) {return model.getparam(p).getname();}
  
  inline float LSMCMCVoxelManager::calclikelihood() 
  { 
    // calculates -log(likelihood):

    likelihood_old = likelihood;

    if(!analmargprec)
      {               
	likelihood = precmcmcparam->value()*sumsquares/2.0;
      }
    else
      {
	likelihood = ntpts/2.0*std::log(sumsquares);
      }

    if(debuglevel==2)
      {
	cout << "likelihood_old="<< likelihood_old << endl; 
	cout << "likelihood="<< likelihood << endl; 
      }
    
    return likelihood;   
  }

  class LSMCMCManager
  {
  public:
    // constructor
    LSMCMCManager(int pnjumps, int pnburnin, int psampleevery, int pupdateproposalevery, int pacceptancerate, int pdebuglevel, float pprecin, bool panalmargprec, ForwardModel& pmodel, const Matrix& pdata, const volume4D<float>& pmask) : 
      data(pdata),
      mask(pmask),      
      debuglevel(pdebuglevel),
      precin(pprecin),
      analmargprec(panalmargprec),
      nsamples((pnjumps-pnburnin)/psampleevery),
      voxelmanager(pmodel,pnburnin,pnjumps,psampleevery,pupdateproposalevery,pacceptancerate,pdebuglevel,analmargprec,nsamples),
      model(pmodel)
    {
    }

    LSMCMCManager(BintOptions& opts, ForwardModel& pmodel,const Matrix& pdata, const volume4D<float>& pmask) : 
      data(pdata),
      mask(pmask),      
      debuglevel(opts.debuglevel.value()),
      precin(opts.prec.value()),
      analmargprec(opts.analmargprec.value()),
      nsamples((opts.njumps.value()-opts.burnin.value())/opts.sampleevery.value()),
      voxelmanager(pmodel,opts.burnin.value(),opts.njumps.value(),opts.sampleevery.value(),opts.updateproposalevery.value(),opts.acceptancerate.value(),opts.debuglevel.value(),opts.analmargprec.value(),nsamples),
      model(pmodel)      
    {       
    }

    // load data from file in from file and set up starting values
    void setup();

    void run();

    // saves results in logging directory
    void save();     

    int getntpts() const {return ntpts;}
    int getnvoxels() const {return nvoxels;}
    
    const Matrix& getsamples(int paramnum) const {return samples[paramnum];}
    Matrix& getsamples(int paramnum) {return samples[paramnum];}
   
    // Destructor
    virtual ~LSMCMCManager() {}
 
  protected:     

    Matrix data;
    volume4D<float> mask;

    int ntpts;    
    int nvoxels;
    int nparams;

    vector<Matrix> samples;

    Matrix precsamples;

    vector<string> paramnames;

    int debuglevel;
    float precin;
    bool analmargprec;

    int nsamples;

    LSMCMCVoxelManager voxelmanager;
    
    ForwardModel& model;

  private:

    LSMCMCManager();
    const LSMCMCManager& operator=(LSMCMCManager& par);     
    LSMCMCManager(LSMCMCManager& des);

  };
}

#endif







