*** empty log message ***

fibre.h

@@ -222,11 +222,15 @@ namespace FIBRE{
 	return true;
       else{
 	//m_f_prior=-(log(m_lam) + (m_lam-1)*log(1-m_f));
-	if(m_lam_jump)
-	  m_f_prior=log(1-m_f)+2*log(fabs(log(1-m_f))); //marginalised with uniform prior on lambda
-	else
+	if(opts.no_ard.value()){
 	  m_f_prior=0;
-	
+	}
+	else{
+	  if(m_lam_jump)
+	    m_f_prior=log(1-m_f)+2*log(fabs(log(1-m_f))); //marginalised with uniform prior on lambda
+	  else
+	    m_f_prior=0;
+	}
 	m_f_prior=opts.fudge.value()*m_f_prior;
 	return false;
       }
@@ -459,7 +463,9 @@ namespace FIBRE{
     inline float get_d() const{ return m_d;}
     inline void set_d(const float d){ m_d=d; }
     
-
+    inline float get_energy() const { return m_likelihood_en+m_prior_en;}
+    inline float get_likelihood_energy() const { return m_likelihood_en;}
+    
     inline float get_S0() const{ return m_S0;}
     inline void set_S0(const float S0){ m_S0=S0; }
     

xfibres.cc

@@ -127,6 +127,7 @@ class Samples{
   xfibresOptions& opts;
   Matrix m_dsamples;
   Matrix m_S0samples;
+  Matrix m_lik_energy;
   vector<Matrix> m_thsamples;
   vector<Matrix> m_phsamples;
   vector<Matrix> m_fsamples;
@@ -149,6 +150,7 @@ public:
     m_dsamples=0;
     m_S0samples.ReSize(nsamples,nvoxels);
     m_S0samples=0;
+    m_lik_energy.ReSize(nsamples,nvoxels);
    
     for(int f=0;f<opts.nfibres.value();f++){
       m_thsamples.push_back(m_S0samples);
@@ -164,6 +166,7 @@ public:
   void record(Multifibre& mfib, int vox, int samp){
     m_dsamples(samp,vox)=mfib.get_d();
     m_S0samples(samp,vox)=mfib.get_S0();
+    m_lik_energy(samp,vox)=mfib.get_likelihood_energy();
     for(int f=0;f<opts.nfibres.value();f++){
       m_thsamples[f](samp,vox)=mfib.fibres()[f].get_th();
       m_phsamples[f](samp,vox)=mfib.fibres()[f].get_ph();
@@ -181,12 +184,14 @@ public:
     vector<Matrix> phsamples_out=m_phsamples;
     vector<Matrix> fsamples_out=m_fsamples;
     vector<Matrix> lamsamples_out=m_lamsamples;
-
+    
     Log& logger = LogSingleton::getInstance();
     tmp.setmatrix(m_dsamples,mask);
     save_volume4D(tmp,logger.appendDir("dsamples"));
     tmp.setmatrix(m_S0samples,mask);
     save_volume4D(tmp,logger.appendDir("S0samples"));
+    tmp.setmatrix(m_lik_energy,mask);
+    save_volume4D(tmp,logger.appendDir("lik_energy"));
     
     //Sort the output based on mean_fsamples
     // 

xfibresoptions.h

@@ -42,6 +42,7 @@ class xfibresOptions {
   Option<int> sampleevery;
   Option<int> updateproposalevery;
   Option<int> seed;
+  Option<bool> no_ard;
   void parse_command_line(int argc, char** argv,  Log& logger);
   
  private:
@@ -105,6 +106,8 @@ class xfibresOptions {
 	false,requires_argument),
   seed(string("--seed"),8665904,string("seed for pseudo random number generator"),
        false,requires_argument),
+  no_ard(string("--noard"),false,string("Turn ARD off on all fibres"),
+       false,no_argument),
    options("xfibres", "xfibres -k <filename>\n xfibres --verbose\n")
    {
      
@@ -125,6 +128,7 @@ class xfibresOptions {
        options.add(sampleevery);
        options.add(updateproposalevery);
        options.add(seed);
+       options.add(no_ard);
        
      }
      catch(X_OptionError& e) {