Fixed previous partial commit which left everything broken

diff --git a/ChangeLog b/ChangeLog
index e003b28..28fe4ae 100644 (file)
--- a/ChangeLog
+++ b/ChangeLog
@@ -81,14 +81,17 @@ libDAI-0.2.2 (2008-??-??)
       removed MakeFactorCavity(size_t)
       removed ExactMarginal(const VarSet &)
       removed ExactlogZ()
-      moved isConnected() to BipartiteGraph
       removed updatedFactor(size_t)
       removed _normtype and NormType()
-      WriteToDotFile(const char *filename) -> display( std::ostream& os )
+      removed hasShortLoops(...) and removeShortLoops(...)
+      WriteToDotFile(const char *filename) -> printDot( std::ostream& os )
       undoProb(size_t) -> restoreFactor(size_t)
       saveProb(size_t) -> backupFactor(size_t)
       undoProbs(const VarSet &) -> restoreFactors(const VarSet &)
       saveProbs(const VarSet &) -> backupFactors(const VarSet &)
+      ReadFromFile(const char*) returns void (throws on error)
+      WriteToFile(const char*) returns void (throws on error)
+      removed hasNegatives()
   - RegionGraph::
       nr_ORs() -> nrORs()
       nr_IRs() -> nrIRs()

diff --git a/example.cpp b/example.cpp
index 9e72056..6056ce4 100644 (file)
--- a/example.cpp
+++ b/example.cpp
@@ -35,47 +35,43 @@ int main( int argc, char *argv[] ) {
         return 1;
     } else {
         FactorGraph fg;
+        fg.ReadFromFile(argv[1]);
 
-        if( fg.ReadFromFile(argv[1]) ) {
-            cout << "Error reading " << argv[1] << endl;
-            return 2;
-        } else {
-            size_t  maxiter = 10000;
-            double  tol = 1e-9;
-            size_t  verb = 1;
-
-            PropertySet opts;
-            opts.Set("maxiter",maxiter);
-            opts.Set("tol",tol);
-            opts.Set("verbose",verb);
-
-            JTree jt( fg, opts("updates",string("HUGIN")) );
-            jt.init();
-            jt.run();
-
-            BP bp(fg, opts("updates",string("SEQFIX"))("logdomain",false));
-            bp.init();
-            bp.run();
-
-            cout << "Exact single node marginals:" << endl;
-            for( size_t i = 0; i < fg.nrVars(); i++ )
-                cout << jt.belief(fg.var(i)) << endl;
-
-            cout << "Approximate (loopy belief propagation) single node marginals:" << endl;
-            for( size_t i = 0; i < fg.nrVars(); i++ )
-                cout << bp.belief(fg.var(i)) << endl;
-
-            cout << "Exact factor marginals:" << endl;
-            for( size_t I = 0; I < fg.nrFactors(); I++ )
-                cout << jt.belief(fg.factor(I).vars()) << endl;
-
-            cout << "Approximate (loopy belief propagation) factor marginals:" << endl;
-            for( size_t I = 0; I < fg.nrFactors(); I++ )
-                cout << bp.belief(fg.factor(I).vars()) << "=" << bp.beliefF(I) << endl;
-
-            cout << "Exact log partition sum: " << jt.logZ() << endl;
-            cout << "Approximate (loopy belief propagation) log partition sum: " << bp.logZ() << endl;
-        }
+        size_t  maxiter = 10000;
+        double  tol = 1e-9;
+        size_t  verb = 1;
+
+        PropertySet opts;
+        opts.Set("maxiter",maxiter);
+        opts.Set("tol",tol);
+        opts.Set("verbose",verb);
+
+        JTree jt( fg, opts("updates",string("HUGIN")) );
+        jt.init();
+        jt.run();
+
+        BP bp(fg, opts("updates",string("SEQFIX"))("logdomain",false));
+        bp.init();
+        bp.run();
+
+        cout << "Exact single node marginals:" << endl;
+        for( size_t i = 0; i < fg.nrVars(); i++ )
+            cout << jt.belief(fg.var(i)) << endl;
+
+        cout << "Approximate (loopy belief propagation) single node marginals:" << endl;
+        for( size_t i = 0; i < fg.nrVars(); i++ )
+            cout << bp.belief(fg.var(i)) << endl;
+
+        cout << "Exact factor marginals:" << endl;
+        for( size_t I = 0; I < fg.nrFactors(); I++ )
+            cout << jt.belief(fg.factor(I).vars()) << endl;
+
+        cout << "Approximate (loopy belief propagation) factor marginals:" << endl;
+        for( size_t I = 0; I < fg.nrFactors(); I++ )
+            cout << bp.belief(fg.factor(I).vars()) << "=" << bp.beliefF(I) << endl;
+
+        cout << "Exact log partition sum: " << jt.logZ() << endl;
+        cout << "Approximate (loopy belief propagation) log partition sum: " << bp.logZ() << endl;
     }
 
     return 0;

diff --git a/include/dai/bipgraph.h b/include/dai/bipgraph.h
index b385476..d9b83e6 100644 (file)
--- a/include/dai/bipgraph.h
+++ b/include/dai/bipgraph.h
@@ -291,7 +291,7 @@ class BipartiteGraph {
         bool isTree() const;
 
         /// Stream to output stream os in graphviz .dot syntax
-        void display( std::ostream& os ) const;
+        void printDot( std::ostream& os ) const;
 
         /// Checks internal consistency
         void check() const;

diff --git a/include/dai/bp.h b/include/dai/bp.h
index 61981f2..48c2957 100644 (file)
--- a/include/dai/bp.h
+++ b/include/dai/bp.h
@@ -104,7 +104,7 @@ class BP : public DAIAlgFG {
         Real logZ() const;
 
         void init( const VarSet &ns );
-        void undoProbs( const VarSet &ns ) { FactorGraph::undoProbs(ns); init(ns); }
+        void restoreFactors( const VarSet &ns ) { FactorGraph::restoreFactors(ns); init(ns); }
 
         /// Set Props according to the PropertySet opts, where the values can be stored as std::strings or as the type of the corresponding Props member
         void setProperties( const PropertySet &opts );

diff --git a/include/dai/daialg.h b/include/dai/daialg.h
index 61ee8dc..5d3226e 100644 (file)
--- a/include/dai/daialg.h
+++ b/include/dai/daialg.h
@@ -67,14 +67,14 @@ class InfAlg {
         virtual double run() = 0;
 
         /// Save factor I
-        virtual void saveProb( size_t I ) = 0;
+        virtual void backupFactor( size_t I ) = 0;
         /// Save Factors involving ns
-        virtual void saveProbs( const VarSet &ns ) = 0;
+        virtual void backupFactors( const VarSet &ns ) = 0;
 
         /// Restore factor I
-        virtual void undoProb( size_t I ) = 0;
+        virtual void restoreFactor( size_t I ) = 0;
         /// Restore Factors involving ns
-        virtual void undoProbs( const VarSet &ns ) = 0;
+        virtual void restoreFactors( const VarSet &ns ) = 0;
 
         /// Clamp variable n to value i (i.e. multiply with a Kronecker delta \f$\delta_{x_n, i}\f$)
         virtual void clamp( const Var & n, size_t i ) = 0;
@@ -105,15 +105,15 @@ class DAIAlg : public InfAlg, public T {
         /// Copy constructor
         DAIAlg( const DAIAlg & x ) : InfAlg(x), T(x) {}
 
-        /// Save factor I (using T::saveProb)
-        void saveProb( size_t I ) { T::saveProb( I ); }
-        /// Save Factors involving ns (using T::saveProbs)
-        void saveProbs( const VarSet &ns ) { T::saveProbs( ns ); }
+        /// Save factor I (using T::backupFactor)
+        void backupFactor( size_t I ) { T::backupFactor( I ); }
+        /// Save Factors involving ns (using T::backupFactors)
+        void backupFactors( const VarSet &ns ) { T::backupFactors( ns ); }
 
-        /// Restore factor I (using T::undoProb)
-        void undoProb( size_t I ) { T::undoProb( I ); }
-        /// Restore Factors involving ns (using T::undoProbs)
-        void undoProbs( const VarSet &ns ) { T::undoProbs( ns ); }
+        /// Restore factor I (using T::restoreFactor)
+        void restoreFactor( size_t I ) { T::restoreFactor( I ); }
+        /// Restore Factors involving ns (using T::restoreFactors)
+        void restoreFactors( const VarSet &ns ) { T::restoreFactors( ns ); }
 
         /// Clamp variable n to value i (i.e. multiply with a Kronecker delta \f$\delta_{x_n, i}\f$) (using T::clamp)
         void clamp( const Var & n, size_t i ) { T::clamp( n, i ); }

diff --git a/include/dai/exactinf.h b/include/dai/exactinf.h
index 3c398dd..204c28f 100644 (file)
--- a/include/dai/exactinf.h
+++ b/include/dai/exactinf.h
@@ -117,7 +117,7 @@ class ExactInf : public DAIAlgFG {
         static const char *Name;
 
         void create();
-        void undoProbs( const VarSet &ns ) { FactorGraph::undoProbs(ns); init(ns); }
+        void restoreFactors( const VarSet &ns ) { FactorGraph::restoreFactors(ns); init(ns); }
         void setProperties( const PropertySet &opts );
         PropertySet getProperties() const;
         std::string printProperties() const;

diff --git a/include/dai/factorgraph.h b/include/dai/factorgraph.h
index 0659ded..2a99be6 100644 (file)
--- a/include/dai/factorgraph.h
+++ b/include/dai/factorgraph.h
@@ -42,13 +42,13 @@ class FactorGraph {
         typedef BipartiteGraph::Edge      Edge;
 
     private:
-        std::map<size_t,Factor>  _backupFactors;
+        std::map<size_t,Factor>  _backup;
 
     public:
         /// Default constructor
-        FactorGraph() : G(), vars(), factors(), _backupFactors() {}
+        FactorGraph() : G(), vars(), factors(), _backup() {}
         /// Copy constructor
-        FactorGraph(const FactorGraph & x) : G(x.G), vars(x.vars), factors(x.factors), _backupFactors(x._backupFactors) {}
+        FactorGraph(const FactorGraph & x) : G(x.G), vars(x.vars), factors(x.factors), _backup(x._backup) {}
         /// Construct FactorGraph from vector of Factors
         FactorGraph(const std::vector<Factor> &P);
         // Construct a FactorGraph from given factor and variable iterators
@@ -61,7 +61,7 @@ class FactorGraph {
                 G          = x.G;
                 vars       = x.vars;
                 factors    = x.factors;
-                _backupFactors = x._backupFactors;
+                _backup = x._backup;
             }
             return *this;
         }
@@ -185,7 +185,7 @@ class FactorGraph {
 
         void ReadFromFile(const char *filename);
         void WriteToFile(const char *filename) const;
-        void display( std::ostream& os ) const;
+        void printDot( std::ostream& os ) const;
         
         std::vector<VarSet> Cliques() const;
 
@@ -199,7 +199,6 @@ class FactorGraph {
         bool isPairwise() const;
         bool isBinary() const;
 
-    private:
         void restoreFactor( size_t I );
         void backupFactor( size_t I );
         void restoreFactors( const VarSet &ns );
@@ -211,7 +210,7 @@ class FactorGraph {
 
 // assumes that the set of variables in [var_begin,var_end) is the union of the variables in the factors in [fact_begin, fact_end)
 template<typename FactorInputIterator, typename VarInputIterator>
-FactorGraph::FactorGraph(FactorInputIterator fact_begin, FactorInputIterator fact_end, VarInputIterator var_begin, VarInputIterator var_end, size_t nr_fact_hint, size_t nr_var_hint ) : G(), _backupFactors() {
+FactorGraph::FactorGraph(FactorInputIterator fact_begin, FactorInputIterator fact_end, VarInputIterator var_begin, VarInputIterator var_end, size_t nr_fact_hint, size_t nr_var_hint ) : G(), _backup() {
     // add factors
     size_t nrEdges = 0;
     factors.reserve( nr_fact_hint );

diff --git a/include/dai/hak.h b/include/dai/hak.h
index b782fd9..0c5fd5e 100644 (file)
--- a/include/dai/hak.h
+++ b/include/dai/hak.h
@@ -101,7 +101,7 @@ class HAK : public DAIAlgRG {
         Real logZ () const;
 
         void init( const VarSet &ns );
-        void undoProbs( const VarSet &ns ) { RegionGraph::undoProbs( ns ); init( ns ); }
+        void restoreFactors( const VarSet &ns ) { RegionGraph::restoreFactors( ns ); init( ns ); }
         void setProperties( const PropertySet &opts );
         PropertySet getProperties() const;
         std::string printProperties() const;

diff --git a/include/dai/jtree.h b/include/dai/jtree.h
index 5517865..17d8cf2 100644 (file)
--- a/include/dai/jtree.h
+++ b/include/dai/jtree.h
@@ -87,7 +87,7 @@ class JTree : public DAIAlgRG {
         Real logZ() const;
 
         void init( const VarSet &/*ns*/ ) {}
-        void undoProbs( const VarSet &ns ) { RegionGraph::undoProbs( ns ); init( ns ); }
+        void restoreFactors( const VarSet &ns ) { RegionGraph::restoreFactors( ns ); init( ns ); }
 
         size_t findEfficientTree( const VarSet& ns, DEdgeVec &Tree, size_t PreviousRoot=(size_t)-1 ) const;
         Factor calcMarginal( const VarSet& ns );

diff --git a/include/dai/lc.h b/include/dai/lc.h
index 422f6f1..0648ce1 100644 (file)
--- a/include/dai/lc.h
+++ b/include/dai/lc.h
@@ -110,10 +110,10 @@ class LC : public DAIAlgFG {
         void clamp( const Var &/*n*/, size_t /*i*/ ) { 
             DAI_THROW(NOT_IMPLEMENTED);
         }
-        void undoProbs( const VarSet &/*ns*/ ) { 
+        void restoreFactors( const VarSet &/*ns*/ ) { 
             DAI_THROW(NOT_IMPLEMENTED);
         }
-        void saveProbs( const VarSet &/*ns*/ ) { 
+        void backupFactors( const VarSet &/*ns*/ ) { 
             DAI_THROW(NOT_IMPLEMENTED);
         }
         virtual void makeCavity(const Var & /*n*/) { 

diff --git a/include/dai/mf.h b/include/dai/mf.h
index c5ae9b6..2b6113d 100644 (file)
--- a/include/dai/mf.h
+++ b/include/dai/mf.h
@@ -78,7 +78,7 @@ class MF : public DAIAlgFG {
         Real logZ() const;
 
         void init( const VarSet &ns );
-        void undoProbs( const VarSet &ns ) { FactorGraph::undoProbs(ns); init(ns); }
+        void restoreFactors( const VarSet &ns ) { FactorGraph::restoreFactors(ns); init(ns); }
         void setProperties( const PropertySet &opts );
         PropertySet getProperties() const;
         std::string printProperties() const;

diff --git a/include/dai/regiongraph.h b/include/dai/regiongraph.h
index 6268d76..24cf3d2 100644 (file)
--- a/include/dai/regiongraph.h
+++ b/include/dai/regiongraph.h
@@ -183,11 +183,11 @@ class RegionGraph : public FactorGraph {
         /// We have to overload FactorGraph::makeCavity because the corresponding outer regions have to be recomputed
         void makeCavity( size_t i ) { FactorGraph::makeCavity( i ); RecomputeORs( var(i) ); }
 
-        /// We have to overload FactorGraph::undoProbs because the corresponding outer regions have to be recomputed
-        void undoProbs( const VarSet &ns ) { FactorGraph::restoreFactors( ns ); RecomputeORs( ns ); }
+        /// We have to overload FactorGraph::restoreFactors because the corresponding outer regions have to be recomputed
+        void restoreFactors( const VarSet &ns ) { FactorGraph::restoreFactors( ns ); RecomputeORs( ns ); }
 
-        /// We have to overload FactorGraph::undoProb because the corresponding outer regions have to be recomputed
-        void undoProb( size_t I ) { FactorGraph::restoreFactor( I ); RecomputeOR( I ); }
+        /// We have to overload FactorGraph::restoreFactor because the corresponding outer regions have to be recomputed
+        void restoreFactor( size_t I ) { FactorGraph::restoreFactor( I ); RecomputeOR( I ); }
 
         /// Send RegionGraph to output stream
         friend std::ostream & operator << ( std::ostream & os, const RegionGraph & rg );

diff --git a/include/dai/treeep.h b/include/dai/treeep.h
index 4080644..684fae3 100644 (file)
--- a/include/dai/treeep.h
+++ b/include/dai/treeep.h
@@ -128,7 +128,7 @@ class TreeEP : public JTree {
         bool offtree( size_t I ) const { return (fac2OR[I] == -1U); }
 
         void init( const VarSet &/*ns*/ ) { init(); }
-        void undoProbs( const VarSet &ns ) { RegionGraph::undoProbs( ns ); init( ns ); }
+        void restoreFactors( const VarSet &ns ) { RegionGraph::restoreFactors( ns ); init( ns ); }
 
         void setProperties( const PropertySet &opts );
         PropertySet getProperties() const;

diff --git a/src/bipgraph.cpp b/src/bipgraph.cpp
index 6632ee5..d27b8c0 100644 (file)
--- a/src/bipgraph.cpp
+++ b/src/bipgraph.cpp
@@ -227,7 +227,7 @@ bool BipartiteGraph::isTree() const {
 }
 
 
-void BipartiteGraph::display( std::ostream& os ) const {
+void BipartiteGraph::printDot( std::ostream& os ) const {
     using namespace std;
     os << "graph G {" << endl;
     os << "node[shape=circle,width=0.4,fixedsize=true];" << endl;

diff --git a/src/daialg.cpp b/src/daialg.cpp
index e199670..b8adfb9 100644 (file)
--- a/src/daialg.cpp
+++ b/src/daialg.cpp
@@ -41,7 +41,7 @@ Factor calcMarginal( const InfAlg & obj, const VarSet & ns, bool reInit ) {
     Real logZ0 = 0.0;
     for( State s(ns); s.valid(); s++ ) {
         // save unclamped factors connected to ns
-        clamped->saveProbs( ns );
+        clamped->backupFactors( ns );
 
         // set clamping Factors to delta functions
         for( VarSet::const_iterator n = ns.begin(); n != ns.end(); n++ )
@@ -64,7 +64,7 @@ Factor calcMarginal( const InfAlg & obj, const VarSet & ns, bool reInit ) {
         Pns[s] = Z;
         
         // restore clamped factors
-        clamped->undoProbs( ns );
+        clamped->restoreFactors( ns );
     }
 
     delete clamped;
@@ -99,7 +99,7 @@ vector<Factor> calcPairBeliefs( const InfAlg & obj, const VarSet& ns, bool reIni
         // clamp Var j to its possible values
         for( size_t j_val = 0; j_val < vns[j].states(); j_val++ ) {
             // save unclamped factors connected to ns
-            clamped->saveProbs( ns );
+            clamped->backupFactors( ns );
             
             clamped->clamp( vns[j], j_val );
             if( reInit )
@@ -127,7 +127,7 @@ vector<Factor> calcPairBeliefs( const InfAlg & obj, const VarSet& ns, bool reIni
                 }
 
             // restore clamped factors
-            clamped->undoProbs( ns );
+            clamped->restoreFactors( ns );
         }
     }
     
@@ -178,7 +178,7 @@ vector<Factor> calcPairBeliefsNew( const InfAlg & obj, const VarSet& ns, bool re
             for( size_t j_val = 0; j_val < nj->states(); j_val++ ) 
                 for( size_t k_val = 0; k_val < nk->states(); k_val++ ) {
                     // save unclamped factors connected to ns
-                    clamped->saveProbs( ns );
+                    clamped->backupFactors( ns );
             
                     clamped->clamp( *nj, j_val );
                     clamped->clamp( *nk, k_val );
@@ -199,7 +199,7 @@ vector<Factor> calcPairBeliefsNew( const InfAlg & obj, const VarSet& ns, bool re
                     pairbelief[j_val + (k_val * nj->states())] = Z_xj;
 
                     // restore clamped factors
-                    clamped->undoProbs( ns );
+                    clamped->restoreFactors( ns );
                 }
         
             result.push_back( pairbelief );

diff --git a/src/factorgraph.cpp b/src/factorgraph.cpp
index 1a25f8d..922e9e6 100644 (file)
--- a/src/factorgraph.cpp
+++ b/src/factorgraph.cpp
@@ -38,7 +38,7 @@ namespace dai {
 using namespace std;
 
 
-FactorGraph::FactorGraph( const std::vector<Factor> &P ) : G(), _undoProbs() {
+FactorGraph::FactorGraph( const std::vector<Factor> &P ) : G(), _backup() {
     // add factors, obtain variables
     set<Var> _vars;
     factors.reserve( P.size() );
@@ -281,7 +281,7 @@ void FactorGraph::WriteToFile( const char *filename ) const {
 }
 
 
-void FactorGraph::display( ostream &os ) const {
+void FactorGraph::printDot( std::ostream &os ) const {
     os << "graph G {" << endl;
     os << "node[shape=circle,width=0.4,fixedsize=true];" << endl;
     for( size_t i = 0; i < nrVars(); i++ )
@@ -334,18 +334,18 @@ void FactorGraph::clamp( const Var & n, size_t i, bool backup ) {
 
 
 void FactorGraph::backupFactor( size_t I ) {
-    map<size_t,Factor>::iterator it = _backupFactors.find( I );
-    if( it != _backupFactors.end() )
+    map<size_t,Factor>::iterator it = _backup.find( I );
+    if( it != _backup.end() )
         DAI_THROW( MULTIPLE_UNDO );
-    _backupFactors[I] = factor(I);
+    _backup[I] = factor(I);
 }
 
 
 void FactorGraph::restoreFactor( size_t I ) {
-    map<size_t,Factor>::iterator it = _backupFactors.find( I );
-    if( it != _backupFactors.end() ) {
+    map<size_t,Factor>::iterator it = _backup.find( I );
+    if( it != _backup.end() ) {
         setFactor(I, it->second);
-        _backupFactors.erase(it);
+        _backup.erase(it);
     }
 }
 
@@ -359,10 +359,10 @@ void FactorGraph::backupFactors( const VarSet &ns ) {
 
 void FactorGraph::restoreFactors( const VarSet &ns ) {
     map<size_t,Factor> facs;
-    for( map<size_t,Factor>::iterator uI = _backupFactors.begin(); uI != _backupFactors.end(); ) {
+    for( map<size_t,Factor>::iterator uI = _backup.begin(); uI != _backup.end(); ) {
         if( factor(uI->first).vars().intersects( ns ) ) {
             facs.insert( *uI );
-            _backupFactors.erase(uI++);
+            _backup.erase(uI++);
         } else
             uI++;
     }
@@ -371,8 +371,8 @@ void FactorGraph::restoreFactors( const VarSet &ns ) {
 
 
 void FactorGraph::restoreFactors() {
-    setFactors( _backupFactors );
-    _backupFactors.clear();
+    setFactors( _backup );
+    _backup.clear();
 }
 
 void FactorGraph::backupFactors( const std::set<size_t> & facs ) {
@@ -451,7 +451,7 @@ FactorGraph FactorGraph::maximalFactors() const {
     for( size_t I = 0; I < nrFactors(); I++ )
         facs[newindex[maxfac[I]]] *= factor(I);
 
-    return FactorGraph( facs.begin(), facs.end(), vars().begin(), vars().end(), facs.size(), nrVars() );
+    return FactorGraph( facs.begin(), facs.end(), vars.begin(), vars.end(), facs.size(), nrVars() );
 }
 
 

diff --git a/src/treeep.cpp b/src/treeep.cpp
index 8be99fe..54d168d 100644 (file)
--- a/src/treeep.cpp
+++ b/src/treeep.cpp
@@ -200,7 +200,7 @@ double TreeEPSubTree::logZ( const std::vector<Factor> &Qa, const std::vector<Fac
 TreeEP::TreeEP( const FactorGraph &fg, const PropertySet &opts ) : JTree(fg, opts("updates",string("HUGIN")), false), props(), maxdiff(0.0) {
     setProperties( opts );
 
-    assert( fg.G.isConnected() );
+    assert( fg.isConnected() );
 
     if( opts.hasKey("tree") ) {
         ConstructRG( opts.GetAs<DEdgeVec>("tree") );

diff --git a/tests/test.cpp b/tests/test.cpp
index 76ea915..507201e 100644 (file)
--- a/tests/test.cpp
+++ b/tests/test.cpp
@@ -231,88 +231,85 @@ int main( int argc, char *argv[] ) {
         }
 
         FactorGraph fg;
-        if( fg.ReadFromFile(filename.c_str()) ) {
-            cout << "Error reading " << filename << endl;
-            return 2;
-        } else {
-            vector<Factor> q0;
-            double logZ0 = 0.0;
-
-            cout << "# " << filename << endl;
+        fg.ReadFromFile(filename.c_str());
+
+        vector<Factor> q0;
+        double logZ0 = 0.0;
+
+        cout << "# " << filename << endl;
+        cout.width( 40 );
+        cout << left << "# METHOD" << "  ";
+        if( report_time ) {
+            cout.width( 10 );
+            cout << right << "SECONDS" << "   ";
+        }
+        cout.width( 10 );
+        cout << "MAX ERROR" << "  ";
+        cout.width( 10 );
+        cout << "AVG ERROR" << "  ";
+        cout.width( 10 );
+        cout << "LOGZ ERROR" << "  ";
+        cout.width( 10 );
+        cout << "MAXDIFF" << endl;
+
+        for( size_t m = 0; m < methods.size(); m++ ) {
+            pair<string, PropertySet> meth = parseMethod( methods[m], Aliases );
+
+            if( vm.count("tol") )
+                meth.second.Set("tol",tol);
+            if( vm.count("maxiter") )
+                meth.second.Set("maxiter",maxiter);
+            if( vm.count("verbose") )
+                meth.second.Set("verbose",verbose);
+            TestAI piet(fg, meth.first, meth.second );
+            piet.doAI();
+            if( m == 0 ) {
+                q0 = piet.q;
+                logZ0 = piet.logZ;
+            }
+            piet.calcErrs(q0);
+
             cout.width( 40 );
-            cout << left << "# METHOD" << "  ";
+//                cout << left << piet.identify() << "  ";
+            cout << left << methods[m] << "  ";
             if( report_time ) {
                 cout.width( 10 );
-                cout << right << "SECONDS" << "   ";
+                cout << right << piet.time << "    ";
             }
-            cout.width( 10 );
-            cout << "MAX ERROR" << "  ";
-            cout.width( 10 );
-            cout << "AVG ERROR" << "  ";
-            cout.width( 10 );
-            cout << "LOGZ ERROR" << "  ";
-            cout.width( 10 );
-            cout << "MAXDIFF" << endl;
-
-            for( size_t m = 0; m < methods.size(); m++ ) {
-                pair<string, PropertySet> meth = parseMethod( methods[m], Aliases );
-
-                if( vm.count("tol") )
-                    meth.second.Set("tol",tol);
-                if( vm.count("maxiter") )
-                    meth.second.Set("maxiter",maxiter);
-                if( vm.count("verbose") )
-                    meth.second.Set("verbose",verbose);
-                TestAI piet(fg, meth.first, meth.second );
-                piet.doAI();
-                if( m == 0 ) {
-                    q0 = piet.q;
-                    logZ0 = piet.logZ;
-                }
-                piet.calcErrs(q0);
 
-                cout.width( 40 );
-//                cout << left << piet.identify() << "  ";
-                cout << left << methods[m] << "  ";
-                if( report_time ) {
-                    cout.width( 10 );
-                    cout << right << piet.time << "    ";
+            if( m > 0 ) {
+                cout.setf( ios_base::scientific );
+                cout.precision( 3 );
+                cout.width( 10 ); 
+                double me = clipdouble( piet.maxErr(), 1e-9 );
+                cout << me << "  ";
+                cout.width( 10 );
+                double ae = clipdouble( piet.avgErr(), 1e-9 );
+                cout << ae << "  ";
+                cout.width( 10 );
+                if( piet.has_logZ ) {
+                    double le = clipdouble( piet.logZ / logZ0 - 1.0, 1e-9 );
+                    cout << le << "  ";
+                } else {
+                    cout << "N/A         ";
                 }
-
-                if( m > 0 ) {
-                    cout.setf( ios_base::scientific );
-                    cout.precision( 3 );
-                    cout.width( 10 ); 
-                    double me = clipdouble( piet.maxErr(), 1e-9 );
-                    cout << me << "  ";
-                    cout.width( 10 );
-                    double ae = clipdouble( piet.avgErr(), 1e-9 );
-                    cout << ae << "  ";
-                    cout.width( 10 );
-                    if( piet.has_logZ ) {
-                        double le = clipdouble( piet.logZ / logZ0 - 1.0, 1e-9 );
-                        cout << le << "  ";
-                    } else {
-                        cout << "N/A         ";
-                    }
-                    cout.width( 10 );
-                    if( piet.has_maxdiff ) {
-                        double md = clipdouble( piet.maxdiff, 1e-9 );
-                        if( isnan( me ) )
-                            md = me;
-                        if( isnan( ae ) )
-                            md = ae;
-                        cout << md << endl;
-                    } else {
-                        cout << "N/A       ";
-                    }
-                } else
-                    cout << endl;
-
-                if( marginals ) {
-                    for( size_t i = 0; i < piet.q.size(); i++ )
-                        cout << "# " << piet.q[i] << endl;
+                cout.width( 10 );
+                if( piet.has_maxdiff ) {
+                    double md = clipdouble( piet.maxdiff, 1e-9 );
+                    if( isnan( me ) )
+                        md = me;
+                    if( isnan( ae ) )
+                        md = ae;
+                    cout << md << endl;
+                } else {
+                    cout << "N/A       ";
                 }
+            } else
+                cout << endl;
+
+            if( marginals ) {
+                for( size_t i = 0; i < piet.q.size(); i++ )
+                    cout << "# " << piet.q[i] << endl;
             }
         }
     } catch(const char *e) {

diff --git a/utils/createfg.cpp b/utils/createfg.cpp
index 4feb946..8796f55 100644 (file)
--- a/utils/createfg.cpp
+++ b/utils/createfg.cpp
@@ -652,7 +652,7 @@ int main( int argc, char *argv[] ) {
                 throw "Please specify all required arguments";
             do {
                 MakeHOIFG( N, K, k, beta, fg );
-            } while( !fg.G.isConnected() );
+            } while( !fg.isConnected() );
 
             cout << "# N = " << N << endl;
             cout << "# K = " << K << endl;

diff --git a/utils/fg2dot.cpp b/utils/fg2dot.cpp
index d50c776..c0c7cc2 100644 (file)
--- a/utils/fg2dot.cpp
+++ b/utils/fg2dot.cpp
@@ -20,6 +20,7 @@
 
 
 #include <iostream>
+#include <fstream>
 #include <cstdlib>
 #include <string>
 #include <dai/factorgraph.h>
@@ -40,29 +41,22 @@ int main( int argc, char *argv[] ) {
         FactorGraph fg;
         char *infile = argv[1];
 
-        if( fg.ReadFromFile( infile ) ) {
-            cerr << "Error reading file " << infile << endl;
-            return 2;
-        } else {
-            if( string( argv[2] ) != "-" ) 
-                fg.WriteToDotFile( argv[2] );
-            else {
-                cout << "graph G {" << endl;
-                cout << "graph[size=\"9,9\"];" << endl;
-                cout << "node[shape=circle,width=0.4,fixedsize=true];" << endl;
-                for( size_t i = 0; i < fg.nrVars(); i++ )
-                    cout << "\tx" << fg.var(i).label() << ";" << endl;
-                cout << "node[shape=box,style=filled,color=lightgrey,width=0.3,height=0.3,fixedsize=true];" << endl;
-                for( size_t I = 0; I < fg.nrFactors(); I++ )
-                    cout << "\tp" << I << ";" << endl;
-                for( size_t i = 0; i < fg.nrVars(); i++ )
-                    foreach( const FactorGraph::Neighbor &I, fg.nbV(i) )
-                        cout << "\tx" << fg.var(i).label() << " -- p" << I << ";" << endl;
-                cout << "}" << endl;
-            }
+        fg.ReadFromFile( infile );
 
-            return 0;
+        ostream *os = &cout;
+        ofstream outfile;
+        if( string( argv[2] ) != "-" ) {
+            outfile.open( argv[2] );
+            if( !outfile.is_open() ) {
+                cerr << "Cannot open " << argv[2] << " for writing" << endl;
+                return 1;
+            }
+            os = &outfile;
         }
+
+        fg.printDot( *os );
+
+        return 0;
     }
 }
 

diff --git a/utils/fginfo.cpp b/utils/fginfo.cpp
index 5498b3c..78bb85e 100644 (file)
--- a/utils/fginfo.cpp
+++ b/utils/fginfo.cpp
@@ -38,33 +38,31 @@ int main( int argc, char *argv[] ) {
         FactorGraph fg;
         char *infile = argv[1];
 
-        if( fg.ReadFromFile( infile ) ) {
-            cerr << "Error reading file " << infile << endl;
-            return 2;
-        } else {
-            cout << "Number of variables: " << fg.nrVars() << endl;
-            cout << "Number of factors:   " << fg.nrFactors() << endl;
-            cout << "Connected:           " << fg.G.isConnected() << endl;
+        fg.ReadFromFile( infile );
+        cout << "Number of variables:   " << fg.nrVars() << endl;
+        cout << "Number of factors:     " << fg.nrFactors() << endl;
+        cout << "Connected:             " << fg.isConnected() << endl;
+        cout << "Binary variables?      " << fg.isBinary() << endl;
+        cout << "Pairwise interactions? " << fg.isPairwise() << endl;
 //          cout << "Treewidth:           " << endl;
 
-            double cavsum_lcbp = 0.0;
-            double cavsum_lcbp2 = 0.0;
-            size_t max_Delta_size = 0;
-            for( size_t i = 0; i < fg.nrVars(); i++ ) {
-                VarSet di = fg.delta(i);
-                size_t Ds = fg.Delta(i).states();
-                if( Ds > max_Delta_size )
-                    max_Delta_size = Ds;
-                cavsum_lcbp += di.states();
-                for( VarSet::const_iterator j = di.begin(); j != di.end(); j++ )
-                    cavsum_lcbp2 += j->states();
-            }
-            cout << "Maximum pancake has " << max_Delta_size << " states" << endl;
-            cout << "LCBP with full cavities needs " << cavsum_lcbp << " BP runs" << endl;
-            cout << "LCBP with only pairinteractions needs " << cavsum_lcbp2 << " BP runs" << endl;
-
-            return 0;
+        double cavsum_lcbp = 0.0;
+        double cavsum_lcbp2 = 0.0;
+        size_t max_Delta_size = 0;
+        for( size_t i = 0; i < fg.nrVars(); i++ ) {
+            VarSet di = fg.delta(i);
+            size_t Ds = fg.Delta(i).states();
+            if( Ds > max_Delta_size )
+                max_Delta_size = Ds;
+            cavsum_lcbp += di.states();
+            for( VarSet::const_iterator j = di.begin(); j != di.end(); j++ )
+                cavsum_lcbp2 += j->states();
         }
+        cout << "Maximum pancake has " << max_Delta_size << " states" << endl;
+        cout << "LCBP with full cavities needs " << cavsum_lcbp << " BP runs" << endl;
+        cout << "LCBP with only pairinteractions needs " << cavsum_lcbp2 << " BP runs" << endl;
+
+        return 0;
     }
 }