/*  fwdmodel_asl_dynangio.cc -kinetic curve modelling for ASL Dynamic Angio data

    Michael Chappell, IBME & FMRIB Image Analysis Group

    Copyright (C) 2010 University of Oxford  */

/*  Part of FSL - FMRIB's Software Library
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    fsl@fmrib.ox.ac.uk
    
    Developed at FMRIB (Oxford Centre for Functional Magnetic Resonance
    Imaging of the Brain), Department of Clinical Neurology, Oxford
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#include "fwdmodel_asl_dynangio.h"

#include <iostream>
#include <newmatio.h>
#include <stdexcept>
#include "newimage/newimageall.h"
#include "miscmaths/miscprob.h"
using namespace NEWIMAGE;
#include "easylog.h"

string DynAngioFwdModel::ModelVersion() const
{
  return "$Id: fwdmodel_asl_dynangio.cc,v 1.2 2011/03/10 13:56:06 chappell Exp $";
}

void DynAngioFwdModel::HardcodedInitialDists(MVNDist& prior, 
    MVNDist& posterior) const
{
    Tracer_Plus tr("DynAngioFwdModel::HardcodedInitialDists");
    assert(prior.means.Nrows() == NumParams());

     SymmetricMatrix precisions = IdentityMatrix(NumParams()) * 1e-12;

     // Set priors
     // abv
     prior.means(1) = 0;
     precisions(1,1) = 1e-12;

     // transit delay
     prior.means(2) = 0.1;
     precisions(2,2) = 10;
     
     // bolus duration
     prior.means(3) = seqtau;
     if (taufix) precisions(3,3) = 1e99;
     else        precisions(3,3) = 10;
     
     // T1b
     prior.means(4) = t1b;
     precisions(4,4) = 100;
     
     //dispersion parameters
     //default to 0 and known
     prior.means(disp_index()) = 0;
     prior.means(disp_index()+1) = 0;
     precisions(disp_index(),disp_index()) = 1e12;
     precisions(disp_index()+1,disp_index()+1) = 1e12;

     if (disptype=="gamma") {
     prior.means(disp_index()) = 1.1; //-1;//0.05;
     prior.means(disp_index()+1) = 0.1; //1.1; //0.7; //2;
     precisions(disp_index(),disp_index()) = 1; //10; //400;
     precisions(disp_index()+1,disp_index()+1) = 100; //1;
     }

     if (disptype=="gvf") {
       prior.means(disp_index()) = 1.1;//0.05;
       prior.means(disp_index()+1) = 0.7;
       precisions(disp_index(),disp_index()) = 1; //400;
       precisions(disp_index()+1,disp_index()+1) = 10;

     }

     if (disptype=="gauss") {
       prior.means(disp_index()) = -1.6;
       precisions(disp_index(),disp_index()) = 1;
     }
     if (disptype=="sgauss") {
       prior.means(disp_index()) = -1.4;
       precisions(disp_index(),disp_index()) = 1;
     }
     if (disptype=="gallichan") {
       prior.means(disp_index()) = 0.2;
       precisions(disp_index(),disp_index()) = 0.1;
     }

     prior.means(7) = 0;
     precisions(7,7) = 0.1;

    // Set precsions on priors
    prior.SetPrecisions(precisions);
    
    // Set initial posterior
    posterior = prior;

    // For parameters with uniformative prior chosoe more sensible inital posterior
    posterior.means(1) = 1;
    precisions(1,1) = 1;

    // for dispersion parameters - initialise to a realtively non dispersed case
    if (disptype=="gamma" || disptype=="gvf") {
    prior.means(disp_index()) = 5;
    prior.means(disp_index()) = 1;
    }
    
    posterior.SetPrecisions(precisions);
    
}    
    
    

void DynAngioFwdModel::Evaluate(const ColumnVector& params, ColumnVector& result) const
{
  Tracer_Plus tr("DynAngioFwdModel::Evaluate");

    // ensure that values are reasonable
    // negative check
  ColumnVector paramcpy = params;
   for (int i=1;i<=NumParams();i++) {
      if (params(i)<0) { paramcpy(i) = 0; }
      }
  
     // sensible limits on transit times
  if (params(2)>timax-0.2) { paramcpy(2) = timax-0.2; }

  // parameters that are inferred - extract and give sensible names
  float abv;
  float delt;
  float tau;
  float T_1b;

  bool outresult=true;

  abv = params(1);
  delt = params(2);
  tau = params(3);
  T_1b = params(4);

  float floor;
  floor = params(7);

  if (abv < 0 || delt<0 || tau < 0 || T_1b < 0 ) {
    //delt=0;
    outresult=true;
  }

  if (outresult) {
  // Look-locker readout
  T_1b = 1/( 1/T_1b - log(cos(FA))/dti); //assume that all the blood has seen the small FAs


  // deal with different dispersion models
   ColumnVector kcblood(tis.Nrows());

    // generate the kinetic curves
    if (disptype=="none") {
      kcblood=kcblood_nodisp(tis,delt,tau,T_1b,false);
    //cout << kcblood << endl;
    }
    else if (disptype=="gamma") {
      float p;
      float s;
      s = exp( params(disp_index()) );
      //float k=exp(params(disp_index()+1));;
      //p = (k-1)/s; //possibly define that parameter as (k-1) ?
      p = params(disp_index()+1);
      if (p<0) p=0;

      kcblood=kcblood_gammadisp(tis,delt,tau,T_1b,s,p,false);
    //cout << kcblood << endl;
    }
    else if (disptype=="gvf") {
      float p;
      float s;
      //float sp = exp(params(disp_index()));
      s = exp( params(disp_index()) );
      //if (sp>10) sp=10;
      p = params(disp_index()+1); //sp/s;
      

      kcblood=kcblood_gvf(tis,delt,T_1b,s,p,false);
    //cout << kcblood << endl;
    }
    else if (disptype=="gauss") {
      float sig;
      sig = exp( params(disp_index()) );
      // we will only have diserpsion SD (leading edge)
      // assume trailing edge is related to leading edge as Hrabe did
      float sig2;      
      if (delt > 0) {
	sig2  = sig*sqrt( (delt+tau)/delt );
      }
      else sig2 = sig;

      //cout << sig << endl;
      kcblood = kcblood_gaussdisp(tis,delt,tau,T_1b,sig,sig2,false);
      //cout << kcblood.t() << endl;
    }
    else if (disptype=="sgauss") {
      float k;
      k = exp( params(disp_index()) );
      
      kcblood = kcblood_spatialgaussdisp(tis,delt,tau,T_1b,k,false);
    }
    else if (disptype=="gallichan") {
      float xV;
      xV = params(disp_index());

      kcblood = kcblood_gallichan(tis,delt,tau,T_1b,xV,false);
    }
    else {
      throw Exception("Unrecognised dispersion model ");
    }

    // Nan catching

    bool cont=true;
    int it=1;
    while (cont) {
      if (isnan(kcblood(it)) || isinf(kcblood(it)) ) { 
      
      LOG << "Warning NaN or Inf in kcblood" << endl;
      LOG << "params: " << params.t() << endl;
      LOG << "kcblood: " << kcblood.t() << endl;
      cont =false;
      kcblood=1e12;
 }
    it++;
    if (it>kcblood.Nrows()) cont=false;
  }

    // assemble the result
    result = floor + abv*kcblood;
  }
  else {
    result.ReSize(tis.Nrows());
    result = 0;
  }

  return;
}


DynAngioFwdModel::DynAngioFwdModel(ArgsType& args)
{
    string scanParams = args.ReadWithDefault("scan-params","cmdline");
    
    if (scanParams == "cmdline")
    {
      // specify command line parameters here
      //dispersion model
      disptype=args.ReadWithDefault("disp","gamma");

      //repeats = convertTo<int>(args.Read("repeats")); // number of repeats in data
      t1b = convertTo<double>(args.ReadWithDefault("t1b","1.66"));

      seqtau = convertTo<double>(args.ReadWithDefault("tau","1000")); //bolus length as set by sequence (default of 1000 is effectively infinite

      // special options
      taufix = args.ReadBool("taufix");
     
      // Deal with tis
      tis.ReSize(1); //will add extra values onto end as needed
      tis(1) = atof(args.Read("ti1").c_str());
      
      while (true) //get the rest of the tis
	{
	  int N = tis.Nrows()+1;
	  string tiString = args.ReadWithDefault("ti"+stringify(N), "stop!");
	  if (tiString == "stop!") break; //we have run out of tis
	 
	  // append the new ti onto the end of the list
	  ColumnVector tmp(1);
	  tmp = convertTo<double>(tiString);
	  tis &= tmp; //vertical concatenation

	}
      timax = tis.Maximum(); //dtermine the final TI
      //determine the TI interval (assume it is even throughout)
      dti = tis(2)-tis(1);

      float fadeg = convertTo<double>(args.ReadWithDefault("fa","30"));
      FA = fadeg * M_PI/180;
	
      // add information about the parameters to the log
      LOG << "Inference using Dynamic Angio model" << endl;
      LOG << "TIs: ";
      for (int i=1; i <= tis.Nrows(); i++)
	LOG << tis(i) << " ";
      LOG << endl;
	  
    }

    else
        throw invalid_argument("Only --scan-params=cmdline is accepted at the moment");    
    
 
}

void DynAngioFwdModel::ModelUsage()
{ 
  cout << "To be added"
       << endl
    ;
}

void DynAngioFwdModel::DumpParameters(const ColumnVector& vec,
                                    const string& indent) const
{
    
}

void DynAngioFwdModel::NameParams(vector<string>& names) const
{
  names.clear();
  
  names.push_back("aBV");
  names.push_back("delt");
  names.push_back("tau");
  names.push_back("T_1b");

  names.push_back("disp1");
  names.push_back("disp2");

}



void DynAngioFwdModel::SetupARD( const MVNDist& theta, MVNDist& thetaPrior, double& Fard)
{
  
}

void DynAngioFwdModel::UpdateARD(
				const MVNDist& theta,
				MVNDist& thetaPrior, double& Fard) const
{
  
  }