X-Git-Url: http://git.tuebingen.mpg.de/?p=libdai.git;a=blobdiff_plain;f=include%2Fdai%2Fjtree.h;h=aaff0e21adacb144366e8f2fb302b195a3018917;hp=e6bf12ffa45570267056045c299d37ac0537d1bf;hb=87c6827445f8fd67801efb6e818771e16229313b;hpb=7e77161d381c0062fb7159276d09633a0cce6a63

diff --git a/include/dai/jtree.h b/include/dai/jtree.h
index e6bf12f..aaff0e2 100644
--- a/include/dai/jtree.h
+++ b/include/dai/jtree.h
@@ -1,6 +1,7 @@
-/*  Copyright (C) 2006-2008  Joris Mooij  [j dot mooij at science dot ru dot nl]
-    Radboud University Nijmegen, The Netherlands
-    
+/*  Copyright (C) 2006-2008  Joris Mooij  [joris dot mooij at tuebingen dot mpg dot de]
+    Radboud University Nijmegen, The Netherlands /
+    Max Planck Institute for Biological Cybernetics, Germany
+
     This file is part of libDAI.
 
     libDAI is free software; you can redistribute it and/or modify
@@ -19,6 +20,11 @@
 */
 
 
+/// \file
+/// \brief Defines class JTree
+/// \todo Improve documentation
+
+
 #ifndef __defined_libdai_jtree_h
 #define __defined_libdai_jtree_h
 
@@ -32,64 +38,104 @@
 #include <dai/clustergraph.h>
 #include <dai/weightedgraph.h>
 #include <dai/enum.h>
+#include <dai/properties.h>
 
 
 namespace dai {
 
 
+/// Exact inference algorithm using junction tree
 class JTree : public DAIAlgRG {
-    protected:
-        DEdgeVec             _RTree;     // rooted tree
-        std::vector<Factor>  _Qa;
-        std::vector<Factor>  _Qb;
+    private:
         std::vector<std::vector<Factor> >  _mes;
         double               _logZ;
 
+    public:
+        /// Rooted tree
+        DEdgeVec             RTree;
+        
+        /// Outer region beliefs
+        std::vector<Factor>  Qa;
+        
+        /// Inner region beliefs
+        std::vector<Factor>  Qb;
+
+        /// Parameters of this inference algorithm
+        struct Properties {
+            /// Enumeration of possible JTree updates
+            DAI_ENUM(UpdateType,HUGIN,SHSH)
+
+            /// Verbosity
+            size_t verbose;
+
+            /// Type of updates
+            UpdateType updates;
+        } props;
+
+        /// Name of this inference algorithm
+        static const char *Name;
 
     public:
-        ENUM2(UpdateType,HUGIN,SHSH)
-        UpdateType Updates() const { return GetPropertyAs<UpdateType>("updates"); }
-
-        JTree() : DAIAlgRG(), _RTree(), _Qa(), _Qb(), _mes(), _logZ() {};
-        JTree( const JTree& x ) : DAIAlgRG(x), _RTree(x._RTree), _Qa(x._Qa), _Qb(x._Qb), _mes(x._mes), _logZ(x._logZ) {};
-        JTree* clone() const { return new JTree(*this); }
-        JTree & operator=( const JTree& x ) {
-            if( this != &x ) {
-                DAIAlgRG::operator=(x);
-                _RTree  = x._RTree;
-                _Qa     = x._Qa;
-                _Qb     = x._Qb;
-                _mes    = x._mes;
-                _logZ   = x._logZ;
-            }
-            return *this;
-        }
-        JTree( const FactorGraph &fg, const Properties &opts, bool automatic=true );
+        /// Default constructor
+        JTree() : DAIAlgRG(), _mes(), _logZ(), RTree(), Qa(), Qb(), props() {}
+
+        /// Construct from FactorGraph fg and PropertySet opts
+        JTree( const FactorGraph &fg, const PropertySet &opts, bool automatic=true );
+
+
+        /// @name General InfAlg interface
+        //@{
+        virtual JTree* clone() const { return new JTree(*this); }
+        virtual JTree* create() const { return new JTree(); }
+        virtual std::string identify() const;
+        virtual Factor belief( const Var &n ) const;
+        virtual Factor belief( const VarSet &ns ) const;
+        virtual std::vector<Factor> beliefs() const;
+        virtual Real logZ() const;
+        virtual void init() {}
+        virtual void init( const VarSet &/*ns*/ ) {}
+        virtual double run();
+        virtual double maxDiff() const { return 0.0; }
+        virtual size_t Iterations() const { return 1UL; }
+        //@}
+
+
+        /// @name Additional interface specific for JTree
+        //@{ 
         void GenerateJT( const std::vector<VarSet> &Cliques );
 
+        /// Returns reference the message from outer region alpha to its _beta'th neighboring inner region
         Factor & message( size_t alpha, size_t _beta ) { return _mes[alpha][_beta]; }   
+        /// Returns const reference to the message from outer region alpha to its _beta'th neighboring inner region
         const Factor & message( size_t alpha, size_t _beta ) const { return _mes[alpha][_beta]; }   
 
-        static const char *Name;
-        std::string identify() const;
-        void init() { assert( checkProperties() ); }
+        /// Runs junction-tree with HUGIN updates
         void runHUGIN();
-        void runShaferShenoy();
-        double run();
-        Factor belief( const Var &n ) const;
-        Factor belief( const VarSet &ns ) const;
-        std::vector<Factor> beliefs() const;
-        Complex logZ() const;
 
-        void init( const VarSet &/*ns*/ ) {}
-        void undoProbs( const VarSet &ns ) { RegionGraph::undoProbs( ns ); init( ns ); }
+        /// Runs junction-tree with Shafer-Shenoy updates
+        void runShaferShenoy();
 
+        /// Finds an efficient tree for calculating the marginal of some variables
         size_t findEfficientTree( const VarSet& ns, DEdgeVec &Tree, size_t PreviousRoot=(size_t)-1 ) const;
+
+        /// Calculates the marginal of a set of variables
         Factor calcMarginal( const VarSet& ns );
-        bool checkProperties();
+        //@}
+
+    private:
+        void setProperties( const PropertySet &opts );
+        PropertySet getProperties() const;
+        std::string printProperties() const;
 };
 
 
+/// Calculates upper bound to the treewidth of a FactorGraph
+/** \relates JTree
+ *  \return a pair (number of variables in largest clique, number of states in largest clique)
+ */
+std::pair<size_t,size_t> treewidth( const FactorGraph & fg );
+
+
 } // end of namespace dai