include/dai/factorgraph.h

   1 /*  Copyright (C) 2006-2008  Joris Mooij  [j dot mooij at science dot ru dot nl]
   2     Radboud University Nijmegen, The Netherlands
   3
   4     This file is part of libDAI.
   5
   6     libDAI is free software; you can redistribute it and/or modify
   7     it under the terms of the GNU General Public License as published by
   8     the Free Software Foundation; either version 2 of the License, or
   9     (at your option) any later version.
  10
  11     libDAI is distributed in the hope that it will be useful,
  12     but WITHOUT ANY WARRANTY; without even the implied warranty of
  13     MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  14     GNU General Public License for more details.
  15
  16     You should have received a copy of the GNU General Public License
  17     along with libDAI; if not, write to the Free Software
  18     Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA  02110-1301  USA
  19 */
  20
  21
  22 #ifndef __defined_libdai_factorgraph_h
  23 #define __defined_libdai_factorgraph_h
  24
  25
  26 #include <iostream>
  27 #include <map>
  28 #include <dai/bipgraph.h>
  29 #include <dai/factor.h>
  30
  31
  32 namespace dai {
  33
  34
  35 class FactorGraph {
  36     public:
  37         BipartiteGraph         G;
  38         std::vector<Var>       vars;
  39         typedef BipartiteGraph::Neighbor  Neighbor;
  40         typedef BipartiteGraph::Neighbors Neighbors;
  41         typedef BipartiteGraph::Edge      Edge;
  42
  43     private:
  44         std::vector<Factor>      _factors;
  45         std::map<size_t,Factor>  _backup;
  46
  47     public:
  48         /// Default constructor
  49         FactorGraph() : G(), vars(), _factors(), _backup() {}
  50         /// Copy constructor
  51         FactorGraph(const FactorGraph & x) : G(x.G), vars(x.vars), _factors(x._factors), _backup(x._backup) {}
  52         /// Construct FactorGraph from vector of Factors
  53         FactorGraph(const std::vector<Factor> &P);
  54         // Construct a FactorGraph from given factor and variable iterators
  55         template<typename FactorInputIterator, typename VarInputIterator>
  56         FactorGraph(FactorInputIterator fact_begin, FactorInputIterator fact_end, VarInputIterator var_begin, VarInputIterator var_end, size_t nr_fact_hint = 0, size_t nr_var_hint = 0 );
  57
  58         /// Assignment operator
  59         FactorGraph & operator=(const FactorGraph & x) {
  60             if( this != &x ) {
  61                 G          = x.G;
  62                 vars       = x.vars;
  63                 _factors   = x._factors;
  64                 _backup    = x._backup;
  65             }
  66             return *this;
  67         }
  68         virtual ~FactorGraph() {}
  69
  70         /// Create (virtual default constructor)
  71         virtual FactorGraph* create() const {
  72             return new FactorGraph(*this);
  73         }
  74
  75         /// Clone (virtual copy constructor)
  76         virtual FactorGraph* clone() const {
  77             return new FactorGraph();
  78         }
  79
  80         // aliases
  81         Var & var(size_t i) { return vars[i]; }
  82         /// Get const reference to i'th variable
  83         const Var & var(size_t i) const { return vars[i]; }
  84         /// Get const reference to I'th factor
  85         Factor & factor(size_t I) { return _factors[I]; }
  86         /// Get const reference to I'th factor
  87         const Factor & factor(size_t I) const { return _factors[I]; }
  88         /// Get const reference to all factors
  89         const std::vector<Factor> & factors() const { return _factors; }
  90
  91         /// Get number of variables
  92         size_t nrVars() const { return vars.size(); }
  93         /// Get number of factors
  94         size_t nrFactors() const { return _factors.size(); }
  95         size_t nrEdges() const { return G.nrEdges(); }
  96
  97         /// Provides read access to neighbors of variable
  98         const Neighbors & nbV( size_t i ) const { return G.nb1(i); }
  99         /// Provides full access to neighbors of variable
 100         Neighbors & nbV( size_t i ) { return G.nb1(i); }
 101         /// Provides read access to neighbors of factor
 102         const Neighbors & nbF( size_t I ) const { return G.nb2(I); }
 103         /// Provides full access to neighbors of factor
 104         Neighbors & nbF( size_t I ) { return G.nb2(I); }
 105         /// Provides read access to neighbor of variable
 106         const Neighbor & nbV( size_t i, size_t _I ) const { return G.nb1(i)[_I]; }
 107         /// Provides full access to neighbor of variable
 108         Neighbor & nbV( size_t i, size_t _I ) { return G.nb1(i)[_I]; }
 109         /// Provides read access to neighbor of factor
 110         const Neighbor & nbF( size_t I, size_t _i ) const { return G.nb2(I)[_i]; }
 111         /// Provides full access to neighbor of factor
 112         Neighbor & nbF( size_t I, size_t _i ) { return G.nb2(I)[_i]; }
 113
 114         /// Get index of variable n
 115         size_t findVar( const Var & n ) const {
 116             size_t i = find( vars.begin(), vars.end(), n ) - vars.begin();
 117             assert( i != nrVars() );
 118             return i;
 119         }
 120
 121         /// Get set of indexes for set of variables
 122         std::set<size_t> findVars( VarSet &ns ) const {
 123             std::set<size_t> indexes;
 124             for( VarSet::const_iterator n = ns.begin(); n != ns.end(); n++ )
 125                 indexes.insert( findVar( *n ) );
 126             return indexes;
 127         }
 128
 129         /// Get index of first factor involving ns
 130         size_t findFactor(const VarSet &ns) const {
 131             size_t I;
 132             for( I = 0; I < nrFactors(); I++ )
 133                 if( factor(I).vars() == ns )
 134                     break;
 135             assert( I != nrFactors() );
 136             return I;
 137         }
 138
 139         /// Return all variables that occur in a factor involving the i'th variable, itself included
 140         VarSet Delta( unsigned i ) const;
 141
 142         /// Return all variables that occur in a factor involving some variable in ns, ns itself included
 143         VarSet Delta( const VarSet &ns ) const;
 144
 145         /// Return all variables that occur in a factor involving the i'th variable, n itself excluded
 146         VarSet delta( unsigned i ) const;
 147
 148         /// Return all variables that occur in a factor involving some variable in ns, ns itself excluded
 149         VarSet delta( const VarSet & ns ) const {
 150             return Delta( ns ) / ns;
 151         }
 152
 153         /// Set the content of the I'th factor and make a backup of its old content if backup == true
 154         virtual void setFactor( size_t I, const Factor &newFactor, bool backup = false ) {
 155             assert( newFactor.vars() == factor(I).vars() );
 156             if( backup )
 157                 backupFactor( I );
 158             _factors[I] = newFactor;
 159         }
 160
 161         /// Set the contents of all factors as specified by facs and make a backup of the old contents if backup == true
 162         virtual void setFactors( const std::map<size_t, Factor> & facs, bool backup = false ) {
 163             for( std::map<size_t, Factor>::const_iterator fac = facs.begin(); fac != facs.end(); fac++ ) {
 164                 if( backup )
 165                     backupFactor( fac->first );
 166                 setFactor( fac->first, fac->second );
 167             }
 168         }
 169
 170         /// Clamp variable n to value i (i.e. multiply with a Kronecker delta \f$\delta_{x_n, i}\f$);
 171         /// If backup == true, make a backup of all factors that are changed
 172         virtual void clamp( const Var & n, size_t i, bool backup = false );
 173
 174         /// Set all factors interacting with the i'th variable 1
 175         virtual void makeCavity( unsigned i, bool backup = false );
 176
 177         /// Backup the factors specified by indices in facs
 178         virtual void backupFactors( const std::set<size_t> & facs );
 179
 180         /// Restore all factors to the backup copies
 181         virtual void restoreFactors();
 182
 183         bool isConnected() const { return G.isConnected(); }
 184         bool isTree() const { return G.isTree(); }
 185
 186         friend std::ostream& operator << (std::ostream& os, const FactorGraph& fg);
 187         friend std::istream& operator >> (std::istream& is, FactorGraph& fg);
 188
 189         void ReadFromFile(const char *filename);
 190         void WriteToFile(const char *filename) const;
 191         void printDot( std::ostream& os ) const;
 192
 193         std::vector<VarSet> Cliques() const;
 194
 195         // Clamp variable v_i to value state (i.e. multiply with a Kronecker delta \f$\delta_{x_{v_i},x}\f$);
 196         // This version changes the factor graph structure and thus returns a newly constructed FactorGraph
 197         // and keeps the current one constant, contrary to clamp()
 198         FactorGraph clamped( const Var & v_i, size_t x ) const;
 199
 200         FactorGraph maximalFactors() const;
 201
 202         bool isPairwise() const;
 203         bool isBinary() const;
 204
 205         void restoreFactor( size_t I );
 206         void backupFactor( size_t I );
 207         void restoreFactors( const VarSet &ns );
 208         void backupFactors( const VarSet &ns );
 209         /// Part of constructors (creates edges, neighbors and adjacency matrix)
 210         void createGraph( size_t nrEdges );
 211 };
 212
 213
 214 // 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)
 215 template<typename FactorInputIterator, typename VarInputIterator>
 216 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() {
 217     // add factors
 218     size_t nrEdges = 0;
 219     _factors.reserve( nr_fact_hint );
 220     for( FactorInputIterator p2 = fact_begin; p2 != fact_end; ++p2 ) {
 221         _factors.push_back( *p2 );
 222         nrEdges += p2->vars().size();
 223     }
 224
 225     // add variables
 226     vars.reserve( nr_var_hint );
 227     for( VarInputIterator p1 = var_begin; p1 != var_end; ++p1 )
 228         vars.push_back( *p1 );
 229
 230     // create graph structure
 231     createGraph( nrEdges );
 232 }
 233
 234
 235 } // end of namespace dai
 236
 237
 238 #endif