Merge branch 'master' of git@git.tuebingen.mpg.de:libdai

Conflicts:

	include/dai/lc.h
	include/dai/mr.h
	src/alldai.cpp
	src/lc.cpp
	tests/test.cpp

diff --cc include/dai/bp.h
Simple merge

diff --cc include/dai/daialg.h
index fdb0ee7,bfb2b84..61ee8dc
--- 1/include/dai/daialg.h
--- 2/include/dai/daialg.h
+++ b/include/dai/daialg.h
@@@ -82,38 -156,15 +82,14 @@@ class InfAlg 
          /// Set all factors interacting with var(i) to 1
          virtual void makeCavity( size_t i ) = 0;
  
-         /// Get index of variable n
-         virtual size_t findVar( const Var & n ) const = 0;
- 
-         /// Get index of first factor involving ns
-         virtual size_t findFactor( const VarSet &ns ) const = 0;
- 
-         /// Get number of variables
-         virtual size_t nrVars() const = 0;
- 
-         /// Get number of factors
-         virtual size_t nrFactors() const = 0;
- 
-         /// Get const reference to variable i
-         virtual const Var & var(size_t i) const = 0;
- 
-         /// Get reference to variable i
-         virtual Var & var(size_t i) = 0;
- 
-         /// Get const reference to factor I
-         virtual const Factor & factor( size_t I ) const = 0;
- 
-         /// Get reference to factor I
-         virtual Factor & factor( size_t I ) = 0;
+         /// Get reference to underlying FactorGraph
+         virtual FactorGraph &fg() = 0;
  
-         /// Factor I has been updated
-         virtual void updatedFactor( size_t I ) = 0;
+         /// Get const reference to underlying FactorGraph
+         virtual const FactorGraph &fg() const = 0;
  
 -        /// Checks whether all necessary properties have been set
 -        /// and casts string-valued properties to other values if necessary
 -        virtual bool checkProperties() = 0;
 +        /// Return maximum difference between beliefs in the last pass
 +        virtual double maxDiff() const = 0;
  };
  
  

diff --cc include/dai/hak.h
Simple merge

diff --cc include/dai/jtree.h
Simple merge

diff --cc include/dai/lc.h
index 57037d9,4af42dc..f1fab99
--- 1/include/dai/lc.h
--- 2/include/dai/lc.h
+++ b/include/dai/lc.h
@@@ -27,7 -27,7 +27,8 @@@
  #include <dai/daialg.h>
  #include <dai/enum.h>
  #include <dai/factorgraph.h>
 +#include <dai/properties.h>
+ #include <dai/exceptions.h>
  
  
  namespace dai {
@@@ -92,22 -82,33 +93,35 @@@ class LC : public DAIAlgFG 
  
          std::string identify() const;
          Factor belief (const Var &n) const { return( _beliefs[findVar(n)] ); }
-         Factor belief (const VarSet &/*ns*/) const { assert( 0 == 1 ); }
+         Factor belief (const VarSet &/*ns*/) const { 
+             DAI_THROW(NOT_IMPLEMENTED);
+             return Factor(); 
+         }
          std::vector<Factor> beliefs() const { return _beliefs; }
-         Complex logZ() const { return NAN; }
+         Real logZ() const { 
+             DAI_THROW(NOT_IMPLEMENTED);
+             return 0.0; 
+         }
          void CalcBelief (size_t i);
 -        const Factor & belief (size_t i) const { return _beliefs[i]; };
 -        const Factor & pancake (size_t i) const { return _pancakes[i]; };
 -        const Factor & cavitydist (size_t i) const { return _cavitydists[i]; };
 +        const Factor &belief (size_t i) const { return _beliefs[i]; };
 +        const Factor &pancake (size_t i) const { return _pancakes[i]; };
 +        const Factor &cavitydist (size_t i) const { return _cavitydists[i]; };
  
-         void clamp( const Var &/*n*/, size_t /*i*/ ) { assert( 0 == 1 ); }
-         void undoProbs( const VarSet &/*ns*/ ) { assert( 0 == 1 ); }
-         void saveProbs( const VarSet &/*ns*/ ) { assert( 0 == 1 ); }
-         virtual void makeCavity(const Var & /*n*/) { assert( 0 == 1 ); }
- 
+         void clamp( const Var &/*n*/, size_t /*i*/ ) { 
+             DAI_THROW(NOT_IMPLEMENTED);
+         }
+         void undoProbs( const VarSet &/*ns*/ ) { 
+             DAI_THROW(NOT_IMPLEMENTED);
+         }
+         void saveProbs( const VarSet &/*ns*/ ) { 
+             DAI_THROW(NOT_IMPLEMENTED);
+         }
+         virtual void makeCavity(const Var & /*n*/) { 
+             DAI_THROW(NOT_IMPLEMENTED);
+         }
 -        bool checkProperties();
 +        void setProperties( const PropertySet &opts );
 +        PropertySet getProperties() const;
 +        double maxDiff() const { return maxdiff; }
  };
  
  

diff --cc include/dai/mf.h
Simple merge

diff --cc include/dai/mr.h
index f3cee73,2dfb2b9..41610e7
--- 1/include/dai/mr.h
--- 2/include/dai/mr.h
+++ b/include/dai/mr.h
@@@ -28,7 -28,7 +28,8 @@@
  #include <dai/factorgraph.h>
  #include <dai/daialg.h>
  #include <dai/enum.h>
 +#include <dai/properties.h>
+ #include <dai/exceptions.h>
  
  
  namespace dai {
@@@ -77,10 -72,16 +78,16 @@@ class MR : public DAIAlgFG 
          void solveM();
          double run();
          Factor belief( const Var &n ) const;
-         Factor belief( const VarSet &/*ns*/ ) const { assert( 0 == 1 ); }
+         Factor belief( const VarSet &/*ns*/ ) const { 
+             DAI_THROW(NOT_IMPLEMENTED);
+             return Factor(); 
+         }
          std::vector<Factor> beliefs() const;
-         Complex logZ() const { return NAN; }
+         Real logZ() const { 
+             DAI_THROW(NOT_IMPLEMENTED);
+             return 0.0; 
+         }
 -        void init() { assert( checkProperties() ); }
 +        void init() {}
          static const char *Name;
          std::string identify() const;
          double _tJ(size_t i, sub_nb A);
@@@ -95,11 -96,10 +102,11 @@@
          void sum_subs(size_t j, sub_nb A, double *sum_even, double *sum_odd);
  
          double sign(double a) { return (a >= 0) ? 1.0 : -1.0; }
-         MR* clone() const { assert( 0 == 1 ); }
+         MR* clone() const { return new MR(*this); }
  
 -        bool checkProperties();
 -
 +        void setProperties( const PropertySet &opts );
 +        PropertySet getProperties() const;
 +        double maxDiff() const { return maxdiff; }
  }; 
  
  

diff --cc include/dai/treeep.h
Simple merge

diff --cc src/alldai.cpp
index cca6ec2,40e0343..05359ba
--- 1/src/alldai.cpp
--- 2/src/alldai.cpp
+++ b/src/alldai.cpp
@@@ -21,7 -21,7 +21,8 @@@
  
  #include <string>
  #include <dai/alldai.h>
 +#include <dai/properties.h>
+ #include <dai/exceptions.h>
  
  
  namespace dai {
@@@ -56,10 -56,11 +57,10 @@@ InfAlg *newInfAlg( const string &name, 
          return new JTree (fg, opts);
  #endif
  #ifdef WITH_MR
 -    else if( name == MR::Name )
 +    if( name == MR::Name )
          return new MR (fg, opts);
  #endif
-     throw "Unknown inference algorithm";
 -    else
 -        DAI_THROW(UNKNOWN_DAI_ALGORITHM);
++    DAI_THROW(UNKNOWN_DAI_ALGORITHM);
  }
  
  

diff --cc src/bp.cpp
index 94680d6,bb8a21f..0352565
--- 1/src/bp.cpp
--- 2/src/bp.cpp
+++ b/src/bp.cpp
@@@ -172,10 -170,10 +172,10 @@@ void BP::calcNewMessage( size_t i, size
      const ind_t ind = index(i,_I);
      for( size_t r = 0; r < prod.size(); ++r )
          marg[ind[r]] += prod[r];
-     marg.normalize( _normtype );
+     marg.normalize( Prob::NORMPROB );
      
      // Store result
 -    if( logDomain )
 +    if( props.logdomain )
          newMessage(i,_I) = marg.log();
      else
          newMessage(i,_I) = marg;

diff --cc src/daialg.cpp
Simple merge

diff --cc src/hak.cpp
Simple merge

diff --cc src/jtree.cpp
Simple merge

diff --cc src/lc.cpp
index 2e795d4,a2c1797..d8da46c
--- 1/src/lc.cpp
--- 2/src/lc.cpp
+++ b/src/lc.cpp
@@@ -124,16 -118,16 +124,16 @@@ double LC::CalcCavityDist (size_t i, co
          InfAlg *cav = newInfAlg( name, *this, opts );
          cav->makeCavity( i );
  
 -        if( Cavity() == CavityType::FULL )
 -            Bi = calcMarginal( *cav, cav->fg().delta(i), reInit() );
 -        else if( Cavity() == CavityType::PAIR )
 -            Bi = calcMarginal2ndO( *cav, cav->fg().delta(i), reInit() );
 -        else if( Cavity() == CavityType::PAIR2 ) {
 -            vector<Factor> pairbeliefs = calcPairBeliefsNew( *cav, cav->fg().delta(i), reInit() );
 +        if( props.cavity == Properties::CavityType::FULL )
-             Bi = calcMarginal( *cav, cav->delta(i), props.reinit );
++            Bi = calcMarginal( *cav, cav->fg().delta(i), props.reinit );
 +        else if( props.cavity == Properties::CavityType::PAIR )
-             Bi = calcMarginal2ndO( *cav, cav->delta(i), props.reinit );
++            Bi = calcMarginal2ndO( *cav, cav->fg().delta(i), props.reinit );
 +        else if( props.cavity == Properties::CavityType::PAIR2 ) {
-             vector<Factor> pairbeliefs = calcPairBeliefsNew( *cav, cav->delta(i), props.reinit );
++            vector<Factor> pairbeliefs = calcPairBeliefsNew( *cav, cav->fg().delta(i), props.reinit );
              for( size_t ij = 0; ij < pairbeliefs.size(); ij++ )
                  Bi *= pairbeliefs[ij];
 -        } else if( Cavity() == CavityType::PAIRINT ) {
 -            Bi = calcMarginal( *cav, cav->fg().delta(i), reInit() );
 +        } else if( props.cavity == Properties::CavityType::PAIRINT ) {
-             Bi = calcMarginal( *cav, cav->delta(i), props.reinit );
++            Bi = calcMarginal( *cav, cav->fg().delta(i), props.reinit );
              
              // Set interactions of order > 2 to zero
              size_t N = delta(i).size();
@@@ -144,8 -138,8 +144,8 @@@
              x2x::w2logp (N, p);
  //            x2x::logpnorm (N, p);
              x2x::logp2p (N, p);
 -        } else if( Cavity() == CavityType::PAIRCUM ) {
 -            Bi = calcMarginal( *cav, cav->fg().delta(i), reInit() );
 +        } else if( props.cavity == Properties::CavityType::PAIRCUM ) {
-             Bi = calcMarginal( *cav, cav->delta(i), props.reinit );
++            Bi = calcMarginal( *cav, cav->fg().delta(i), props.reinit );
              
              // Set cumulants of order > 2 to zero
              size_t N = delta(i).size();
@@@ -156,10 -150,10 +156,10 @@@
              x2x::c2m (N, p, N);
              x2x::m2p (N, p);
          }
 -        maxdiff = cav->MaxDiff();
 +        maxdiff = cav->maxDiff();
          delete cav;
      }
-     Bi.normalize( _normtype );
+     Bi.normalize( Prob::NORMPROB );
      _cavitydists[i] = Bi;
  
      return maxdiff;

diff --cc src/mf.cpp
Simple merge

diff --cc src/mr.cpp
Simple merge

diff --cc src/properties.cpp
index 2b131b3,b259914..d62d6d5
--- 1/src/properties.cpp
--- 2/src/properties.cpp
+++ b/src/properties.cpp
@@@ -38,38 -39,38 +39,38 @@@ std::ostream& operator<< (std::ostream 
          os << boost::any_cast<double>(p.second);
      else if( p.second.type() == typeid(bool) )
          os << boost::any_cast<bool>(p.second);
 -    else if( p.second.type() == typeid(Properties) )
 -        os << boost::any_cast<Properties>(p.second);
 +    else if( p.second.type() == typeid(PropertySet) )
 +        os << boost::any_cast<PropertySet>(p.second);
  #ifdef WITH_BP
 -    else if( p.second.type() == typeid(BP::UpdateType) )
 -        os << boost::any_cast<BP::UpdateType>(p.second);
 +    else if( p.second.type() == typeid(BP::Properties::UpdateType) )
 +        os << boost::any_cast<BP::Properties::UpdateType>(p.second);
  #endif
  #ifdef WITH_HAK
 -    else if( p.second.type() == typeid(HAK::ClustersType) )
 -        os << boost::any_cast<HAK::ClustersType>(p.second);
 +    else if( p.second.type() == typeid(HAK::Properties::ClustersType) )
 +        os << boost::any_cast<HAK::Properties::ClustersType>(p.second);
  #endif
  #ifdef WITH_JTREE
 -    else if( p.second.type() == typeid(JTree::UpdateType) )
 -        os << boost::any_cast<JTree::UpdateType>(p.second);
 +    else if( p.second.type() == typeid(JTree::Properties::UpdateType) )
 +        os << boost::any_cast<JTree::Properties::UpdateType>(p.second);
  #endif
  #ifdef WITH_MR
 -    else if( p.second.type() == typeid(MR::UpdateType) )
 -        os << boost::any_cast<MR::UpdateType>(p.second);
 -    else if( p.second.type() == typeid(MR::InitType) )
 -        os << boost::any_cast<MR::InitType>(p.second);
 +    else if( p.second.type() == typeid(MR::Properties::UpdateType) )
 +        os << boost::any_cast<MR::Properties::UpdateType>(p.second);
 +    else if( p.second.type() == typeid(MR::Properties::InitType) )
 +        os << boost::any_cast<MR::Properties::InitType>(p.second);
  #endif
  #ifdef WITH_TREEEP
 -    else if( p.second.type() == typeid(TreeEP::TypeType) )
 -        os << boost::any_cast<TreeEP::TypeType>(p.second);
 +    else if( p.second.type() == typeid(TreeEP::Properties::TypeType) )
 +        os << boost::any_cast<TreeEP::Properties::TypeType>(p.second);
  #endif
  #ifdef WITH_LC
 -    else if( p.second.type() == typeid(LC::CavityType) )
 -        os << boost::any_cast<LC::CavityType>(p.second);
 -    else if( p.second.type() == typeid(LC::UpdateType) )
 -        os << boost::any_cast<LC::UpdateType>(p.second);
 +    else if( p.second.type() == typeid(LC::Properties::CavityType) )
 +        os << boost::any_cast<LC::Properties::CavityType>(p.second);
 +    else if( p.second.type() == typeid(LC::Properties::UpdateType) )
 +        os << boost::any_cast<LC::Properties::UpdateType>(p.second);
  #endif
      else
-         throw "Unknown property type";
+         DAI_THROW(UNKNOWN_PROPERTY_TYPE);
      return( os );
  }
  

diff --cc src/treeep.cpp
Simple merge

diff --cc tests/test.cpp
index 02ca982,fe42f43..d33880f
--- 1/tests/test.cpp
--- 2/tests/test.cpp
+++ b/tests/test.cpp
@@@ -46,8 -47,9 +47,9 @@@ class TestAI 
          double          logZ;
          double          maxdiff;
          double          time;
+         bool            has_logZ;
  
-         TestAI( const FactorGraph &fg, const string &_name, const PropertySet &opts ) : obj(NULL), name(_name), err(), q(), logZ(0.0), maxdiff(0.0), time(0) {
 -        TestAI( const FactorGraph &fg, const string &_name, const Properties &opts ) : obj(NULL), name(_name), err(), q(), logZ(0.0), maxdiff(0.0), time(0), has_logZ(true) {
++        TestAI( const FactorGraph &fg, const string &_name, const PropertySet &opts ) : obj(NULL), name(_name), err(), q(), logZ(0.0), maxdiff(0.0), time(0), has_logZ(true) {
              double tic = toc();
              obj = newInfAlg( name, fg, opts );
              time += toc() - tic;
@@@ -104,8 -106,13 +106,13 @@@
                  obj->init();
                  obj->run();
                  time += toc() - tic;
-                 logZ = real(obj->logZ());
+                 try {
+                     logZ = obj->logZ();
+                     has_logZ = true;
+                 } catch( Exception &e ) {
+                     has_logZ = false;
+                 }
 -                maxdiff = obj->MaxDiff();
 +                maxdiff = obj->maxDiff();
                  q = allBeliefs();
              };
          }