-/* 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
#include <iostream>
+#include <iomanip>
#include <iterator>
#include <map>
#include <set>
FactorGraph::FactorGraph( const std::vector<Factor> &P ) : G(), _backup() {
// add factors, obtain variables
- set<Var> _vars;
- factors.reserve( P.size() );
+ set<Var> varset;
+ _factors.reserve( P.size() );
size_t nrEdges = 0;
for( vector<Factor>::const_iterator p2 = P.begin(); p2 != P.end(); p2++ ) {
- factors.push_back( *p2 );
- copy( p2->vars().begin(), p2->vars().end(), inserter( _vars, _vars.begin() ) );
+ _factors.push_back( *p2 );
+ copy( p2->vars().begin(), p2->vars().end(), inserter( varset, varset.begin() ) );
nrEdges += p2->vars().size();
}
- // add _vars
- vars.reserve( _vars.size() );
- for( set<Var>::const_iterator p1 = _vars.begin(); p1 != _vars.end(); p1++ )
- vars.push_back( *p1 );
+ // add vars
+ _vars.reserve( varset.size() );
+ for( set<Var>::const_iterator p1 = varset.begin(); p1 != varset.end(); p1++ )
+ _vars.push_back( *p1 );
// create graph structure
- createGraph( nrEdges );
+ constructGraph( nrEdges );
}
-/// Part of constructors (creates edges, neighbours and adjacency matrix)
-void FactorGraph::createGraph( size_t nrEdges ) {
+void FactorGraph::constructGraph( size_t nrEdges ) {
// create a mapping for indices
hash_map<size_t, size_t> hashmap;
- for( size_t i = 0; i < vars.size(); i++ )
+ for( size_t i = 0; i < vars().size(); i++ )
hashmap[var(i).label()] = i;
// create edge list
}
// create bipartite graph
- G.create( nrVars(), nrFactors(), edges.begin(), edges.end() );
+ G.construct( nrVars(), nrFactors(), edges.begin(), edges.end() );
}
+/// Writes a FactorGraph to an output stream
ostream& operator << (ostream& os, const FactorGraph& fg) {
os << fg.nrFactors() << endl;
nr_nonzeros++;
os << nr_nonzeros << endl;
for( size_t k = 0; k < fg.factor(I).states(); k++ )
- if( fg.factor(I)[k] != 0.0 ) {
- char buf[20];
- sprintf(buf,"%18.14g", fg.factor(I)[k]);
- os << k << " " << buf << endl;
- }
+ if( fg.factor(I)[k] != 0.0 )
+ os << k << " " << setw(os.precision()+4) << fg.factor(I)[k] << endl;
}
return(os);
}
+/// Reads a FactorGraph from an input stream
istream& operator >> (istream& is, FactorGraph& fg) {
long verbose = 0;
- try {
- vector<Factor> factors;
- size_t nr_Factors;
- string line;
-
+ vector<Factor> facs;
+ size_t nr_Factors;
+ string line;
+
+ while( (is.peek()) == '#' )
+ getline(is,line);
+ is >> nr_Factors;
+ if( is.fail() )
+ DAI_THROW(INVALID_FACTORGRAPH_FILE);
+ if( verbose >= 2 )
+ cerr << "Reading " << nr_Factors << " factors..." << endl;
+
+ getline (is,line);
+ if( is.fail() )
+ DAI_THROW(INVALID_FACTORGRAPH_FILE);
+
+ map<long,size_t> vardims;
+ for( size_t I = 0; I < nr_Factors; I++ ) {
+ if( verbose >= 3 )
+ cerr << "Reading factor " << I << "..." << endl;
+ size_t nr_members;
while( (is.peek()) == '#' )
getline(is,line);
- is >> nr_Factors;
- if( is.fail() )
- DAI_THROW(INVALID_FACTORGRAPH_FILE);
- if( verbose >= 2 )
- cout << "Reading " << nr_Factors << " factors..." << endl;
-
- getline (is,line);
- if( is.fail() )
- DAI_THROW(INVALID_FACTORGRAPH_FILE);
-
- map<long,size_t> vardims;
- for( size_t I = 0; I < nr_Factors; I++ ) {
- if( verbose >= 3 )
- cout << "Reading factor " << I << "..." << endl;
- size_t nr_members;
+ is >> nr_members;
+ if( verbose >= 3 )
+ cerr << " nr_members: " << nr_members << endl;
+
+ vector<long> labels;
+ for( size_t mi = 0; mi < nr_members; mi++ ) {
+ long mi_label;
while( (is.peek()) == '#' )
getline(is,line);
- is >> nr_members;
- if( verbose >= 3 )
- cout << " nr_members: " << nr_members << endl;
-
- vector<long> labels;
- for( size_t mi = 0; mi < nr_members; mi++ ) {
- long mi_label;
- while( (is.peek()) == '#' )
- getline(is,line);
- is >> mi_label;
- labels.push_back(mi_label);
- }
- if( verbose >= 3 )
- cout << " labels: " << labels << endl;
-
- vector<size_t> dims;
- for( size_t mi = 0; mi < nr_members; mi++ ) {
- size_t mi_dim;
- while( (is.peek()) == '#' )
- getline(is,line);
- is >> mi_dim;
- dims.push_back(mi_dim);
- }
- if( verbose >= 3 )
- cout << " dimensions: " << dims << endl;
-
- // add the Factor
- VarSet I_vars;
- for( size_t mi = 0; mi < nr_members; mi++ ) {
- map<long,size_t>::iterator vdi = vardims.find( labels[mi] );
- if( vdi != vardims.end() ) {
- // check whether dimensions are consistent
- if( vdi->second != dims[mi] )
- DAI_THROW(INVALID_FACTORGRAPH_FILE);
- } else
- vardims[labels[mi]] = dims[mi];
- I_vars |= Var(labels[mi], dims[mi]);
- }
- factors.push_back( Factor( I_vars, 0.0 ) );
-
- // calculate permutation sigma (internally, members are sorted)
- vector<size_t> sigma(nr_members,0);
- VarSet::iterator j = I_vars.begin();
- for( size_t mi = 0; mi < nr_members; mi++,j++ ) {
- long search_for = j->label();
- vector<long>::iterator j_loc = find(labels.begin(),labels.end(),search_for);
- sigma[mi] = j_loc - labels.begin();
- }
- if( verbose >= 3 )
- cout << " sigma: " << sigma << endl;
-
- // calculate multindices
- Permute permindex( dims, sigma );
-
- // read values
- size_t nr_nonzeros;
+ is >> mi_label;
+ labels.push_back(mi_label);
+ }
+ if( verbose >= 3 )
+ cerr << " labels: " << labels << endl;
+
+ vector<size_t> dims;
+ for( size_t mi = 0; mi < nr_members; mi++ ) {
+ size_t mi_dim;
while( (is.peek()) == '#' )
getline(is,line);
- is >> nr_nonzeros;
- if( verbose >= 3 )
- cout << " nonzeroes: " << nr_nonzeros << endl;
- for( size_t k = 0; k < nr_nonzeros; k++ ) {
- size_t li;
- double val;
- while( (is.peek()) == '#' )
- getline(is,line);
- is >> li;
- while( (is.peek()) == '#' )
- getline(is,line);
- is >> val;
-
- // store value, but permute indices first according
- // to internal representation
- factors.back()[permindex.convert_linear_index( li )] = val;
- }
+ is >> mi_dim;
+ dims.push_back(mi_dim);
+ }
+ if( verbose >= 3 )
+ cerr << " dimensions: " << dims << endl;
+
+ // add the Factor
+ VarSet I_vars;
+ for( size_t mi = 0; mi < nr_members; mi++ ) {
+ map<long,size_t>::iterator vdi = vardims.find( labels[mi] );
+ if( vdi != vardims.end() ) {
+ // check whether dimensions are consistent
+ if( vdi->second != dims[mi] )
+ DAI_THROW(INVALID_FACTORGRAPH_FILE);
+ } else
+ vardims[labels[mi]] = dims[mi];
+ I_vars |= Var(labels[mi], dims[mi]);
+ }
+ facs.push_back( Factor( I_vars, 0.0 ) );
+
+ // calculate permutation sigma (internally, members are sorted)
+ vector<size_t> sigma(nr_members,0);
+ VarSet::iterator j = I_vars.begin();
+ for( size_t mi = 0; mi < nr_members; mi++,j++ ) {
+ long search_for = j->label();
+ vector<long>::iterator j_loc = find(labels.begin(),labels.end(),search_for);
+ sigma[mi] = j_loc - labels.begin();
}
-
if( verbose >= 3 )
- cout << "factors:" << factors << endl;
+ cerr << " sigma: " << sigma << endl;
+
+ // calculate multindices
+ Permute permindex( dims, sigma );
+
+ // read values
+ size_t nr_nonzeros;
+ while( (is.peek()) == '#' )
+ getline(is,line);
+ is >> nr_nonzeros;
+ if( verbose >= 3 )
+ cerr << " nonzeroes: " << nr_nonzeros << endl;
+ for( size_t k = 0; k < nr_nonzeros; k++ ) {
+ size_t li;
+ double val;
+ while( (is.peek()) == '#' )
+ getline(is,line);
+ is >> li;
+ while( (is.peek()) == '#' )
+ getline(is,line);
+ is >> val;
- fg = FactorGraph(factors);
- } catch (char *e) {
- cout << e << endl;
+ // store value, but permute indices first according
+ // to internal representation
+ facs.back()[permindex.convert_linear_index( li )] = val;
+ }
}
+ if( verbose >= 3 )
+ cerr << "factors:" << facs << endl;
+
+ fg = FactorGraph(facs);
+
return is;
}
}
-void FactorGraph::WriteToFile( const char *filename ) const {
+void FactorGraph::WriteToFile( const char *filename, size_t precision ) const {
ofstream outfile;
outfile.open( filename );
if( outfile.is_open() ) {
+ outfile.precision( precision );
outfile << *this;
outfile.close();
} else
}
+void FactorGraph::clampVar( size_t i, const vector<size_t> &is, bool backup ) {
+ Var n = var(i);
+ Factor mask_n( n, 0.0 );
+
+ foreach( size_t i, is ) {
+ assert( i <= n.states() );
+ mask_n[i] = 1.0;
+ }
+
+ map<size_t, Factor> newFacs;
+ for( size_t I = 0; I < nrFactors(); I++ )
+ if( factor(I).vars().contains( n ) ) {
+ newFacs[I] = factor(I) * mask_n;
+ }
+ setFactors( newFacs, backup );
+}
+
+
+void FactorGraph::clampFactor( size_t I, const vector<size_t> &is, bool backup ) {
+ size_t st = factor(I).states();
+ Factor newF( factor(I).vars(), 0.0 );
+
+ foreach( size_t i, is ) {
+ assert( i <= st );
+ newF[i] = factor(I)[i];
+ }
+
+ setFactor( I, newF, backup );
+}
+
+
void FactorGraph::backupFactor( size_t I ) {
map<size_t,Factor>::iterator it = _backup.find( I );
if( it != _backup.end() )
_backup.clear();
}
+
void FactorGraph::backupFactors( const std::set<size_t> & facs ) {
for( std::set<size_t>::const_iterator fac = facs.begin(); fac != facs.end(); fac++ )
backupFactor( *fac );
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() );
}
projects / libdai.git / blobdiff