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 { return new FactorGraph(*this); }
  72
  73         /// Clone (virtual copy constructor)
  74         virtual FactorGraph* clone() const { return new FactorGraph(); }
  75
  76         // aliases
  77         Var & var(size_t i) { return vars[i]; }
  78         /// Get const reference to i'th variable
  79         const Var & var(size_t i) const { return vars[i]; }
  80         /// Get const reference to I'th factor
  81         Factor & factor(size_t I) { return _factors[I]; }
  82         /// Get const reference to I'th factor
  83         const Factor & factor(size_t I) const { return _factors[I]; }
  84         /// Get const reference to all factors
  85         const std::vector<Factor> & factors() const { return _factors; }
  86
  87         /// Get number of variables
  88         size_t nrVars() const { return vars.size(); }
  89         /// Get number of factors
  90         size_t nrFactors() const { return _factors.size(); }
  91         size_t nrEdges() const { return G.nrEdges(); }
  92
  93         /// Provides read access to neighbors of variable
  94         const Neighbors & nbV( size_t i ) const { return G.nb1(i); }
  95         /// Provides full access to neighbors of variable
  96         Neighbors & nbV( size_t i ) { return G.nb1(i); }
  97         /// Provides read access to neighbors of factor
  98         const Neighbors & nbF( size_t I ) const { return G.nb2(I); }
  99         /// Provides full access to neighbors of factor
 100         Neighbors & nbF( size_t I ) { return G.nb2(I); }
 101         /// Provides read access to neighbor of variable
 102         const Neighbor & nbV( size_t i, size_t _I ) const { return G.nb1(i)[_I]; }
 103         /// Provides full access to neighbor of variable
 104         Neighbor & nbV( size_t i, size_t _I ) { return G.nb1(i)[_I]; }
 105         /// Provides read access to neighbor of factor
 106         const Neighbor & nbF( size_t I, size_t _i ) const { return G.nb2(I)[_i]; }
 107         /// Provides full access to neighbor of factor
 108         Neighbor & nbF( size_t I, size_t _i ) { return G.nb2(I)[_i]; }
 109
 110         /// Get index of variable n
 111         size_t findVar( const Var & n ) const {
 112             size_t i = find( vars.begin(), vars.end(), n ) - vars.begin();
 113             assert( i != nrVars() );
 114             return i;
 115         }
 116
 117         /// Get set of indexes for set of variables
 118         std::set<size_t> findVars( VarSet &ns ) const {
 119             std::set<size_t> indexes;
 120             for( VarSet::const_iterator n = ns.begin(); n != ns.end(); n++ )
 121                 indexes.insert( findVar( *n ) );
 122             return indexes;
 123         }
 124
 125         /// Get index of first factor involving ns
 126         size_t findFactor(const VarSet &ns) const {
 127             size_t I;
 128             for( I = 0; I < nrFactors(); I++ )
 129                 if( factor(I).vars() == ns )
 130                     break;
 131             assert( I != nrFactors() );
 132             return I;
 133         }
 134
 135         /// Return all variables that occur in a factor involving the i'th variable, itself included
 136         VarSet Delta( unsigned i ) const;
 137
 138         /// Return all variables that occur in a factor involving some variable in ns, ns itself included
 139         VarSet Delta( const VarSet &ns ) const;
 140
 141         /// Return all variables that occur in a factor involving the i'th variable, n itself excluded
 142         VarSet delta( unsigned i ) const;
 143
 144         /// Return all variables that occur in a factor involving some variable in ns, ns itself excluded
 145         VarSet delta( const VarSet & ns ) const {
 146             return Delta( ns ) / ns;
 147         }
 148
 149         /// Set the content of the I'th factor and make a backup of its old content if backup == true
 150         virtual void setFactor( size_t I, const Factor &newFactor, bool backup = false ) {
 151             assert( newFactor.vars() == factor(I).vars() );
 152             if( backup )
 153                 backupFactor( I );
 154             _factors[I] = newFactor;
 155         }
 156
 157         /// Set the contents of all factors as specified by facs and make a backup of the old contents if backup == true
 158         virtual void setFactors( const std::map<size_t, Factor> & facs, bool backup = false ) {
 159             for( std::map<size_t, Factor>::const_iterator fac = facs.begin(); fac != facs.end(); fac++ ) {
 160                 if( backup )
 161                     backupFactor( fac->first );
 162                 setFactor( fac->first, fac->second );
 163             }
 164         }
 165
 166         /// Clamp variable n to value i (i.e. multiply with a Kronecker delta \f$\delta_{x_n, i}\f$);
 167         /// If backup == true, make a backup of all factors that are changed
 168         virtual void clamp( const Var & n, size_t i, bool backup = false );
 169
 170         /// Set all factors interacting with the i'th variable 1
 171         virtual void makeCavity( unsigned i, bool backup = false );
 172
 173         /// Backup the factors specified by indices in facs
 174         virtual void backupFactors( const std::set<size_t> & facs );
 175
 176         /// Restore all factors to the backup copies
 177         virtual void restoreFactors();
 178
 179         bool isConnected() const { return G.isConnected(); }
 180         bool isTree() const { return G.isTree(); }
 181
 182         friend std::ostream& operator << (std::ostream& os, const FactorGraph& fg);
 183         friend std::istream& operator >> (std::istream& is, FactorGraph& fg);
 184
 185         void ReadFromFile(const char *filename);
 186         void WriteToFile(const char *filename) const;
 187         void printDot( std::ostream& os ) const;
 188
 189         std::vector<VarSet> Cliques() const;
 190
 191         // Clamp variable v_i to value state (i.e. multiply with a Kronecker delta \f$\delta_{x_{v_i},x}\f$);
 192         // This version changes the factor graph structure and thus returns a newly constructed FactorGraph
 193         // and keeps the current one constant, contrary to clamp()
 194         FactorGraph clamped( const Var & v_i, size_t x ) const;
 195
 196         FactorGraph maximalFactors() const;
 197
 198         bool isPairwise() const;
 199         bool isBinary() const;
 200
 201         void restoreFactor( size_t I );
 202         void backupFactor( size_t I );
 203         void restoreFactors( const VarSet &ns );
 204         void backupFactors( const VarSet &ns );
 205         /// Part of constructors (creates edges, neighbors and adjacency matrix)
 206         void constructGraph( size_t nrEdges );
 207 };
 208
 209
 210 // 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)
 211 template<typename FactorInputIterator, typename VarInputIterator>
 212 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() {
 213     // add factors
 214     size_t nrEdges = 0;
 215     _factors.reserve( nr_fact_hint );
 216     for( FactorInputIterator p2 = fact_begin; p2 != fact_end; ++p2 ) {
 217         _factors.push_back( *p2 );
 218         nrEdges += p2->vars().size();
 219     }
 220
 221     // add variables
 222     vars.reserve( nr_var_hint );
 223     for( VarInputIterator p1 = var_begin; p1 != var_end; ++p1 )
 224         vars.push_back( *p1 );
 225
 226     // create graph structure
 227     constructGraph( nrEdges );
 228 }
 229
 230
 231 } // end of namespace dai
 232
 233
 234 #endif