git HEAD
--------
+* Added io.h/io.cpp which currently provides functionality for reading
+ files in the UAI Approximate Inference Challenge fileformats
+ (supporting both the 2006/2008 evidence file format and the 2010
+ evidence file format)
+* Deprecated void tokenizeString( const string&, vector<string>&, const string& )
+ and replaced it with an improved version
+ vector<string> tokenizeString( const string&, bool, const string& )
* [Matt Dunham] Fixed a bug in Factors2mx in src/matlab/matlab.cpp:
segfault if factors depending on 0 variables were passed to MatLab
* Added source code for one of the winning solvers of the
endif
# Define conditional build targets
-NAMES:=graph dag bipgraph varset daialg alldai clustergraph factor factorgraph properties regiongraph util weightedgraph exceptions exactinf evidence emalg
+NAMES:=graph dag bipgraph varset daialg alldai clustergraph factor factorgraph properties regiongraph util weightedgraph exceptions exactinf evidence emalg io
ifdef WITH_BP
WITHFLAGS:=$(WITHFLAGS) -DDAI_WITH_BP
NAMES:=$(NAMES) bp
#include <ostream>
#include <cstdlib>
#include <dai/alldai.h>
-#include <dai/util.h>
-#include <dai/index.h>
-#include <dai/jtree.h>
+#include <dai/io.h>
using namespace std;
};
-/// Reads "evidence" (a mapping from observed variable labels to the observed values) from a UAI evidence file
-vector<map<size_t, size_t> > ReadUAIEvidenceFile( char* filename, size_t verbose ) {
- vector<map<size_t, size_t> > evid;
-
- // open file
- ifstream is;
- is.open( filename );
- if( is.is_open() ) {
- // read number of evidence cases
- size_t nr_evid;
- is >> nr_evid;
- if( is.fail() )
- DAI_THROWE(INVALID_EVIDENCE_FILE,"Cannot read number of evidence cases");
- if( verbose >= 2 )
- cout << "Reading " << nr_evid << " evidence cases..." << endl;
-
- evid.resize( nr_evid );
- for( size_t i = 0; i < nr_evid; i++ ) {
- // read number of variables
- size_t nr_obs;
- is >> nr_obs;
- if( is.fail() )
- DAI_THROWE(INVALID_EVIDENCE_FILE,"Evidence case " + toString(i) + ": Cannot read number of observations");
- if( verbose >= 2 )
- cout << "Evidence case " << i << ": reading " << nr_obs << " observations..." << endl;
-
- // for each observation, read the variable label and the observed value
- for( size_t j = 0; j < nr_obs; j++ ) {
- size_t label, val;
- is >> label;
- if( is.fail() )
- DAI_THROWE(INVALID_EVIDENCE_FILE,"Evidence case " + toString(i) + ": Cannot read label for " + toString(j) + "'th observed variable");
- is >> val;
- if( is.fail() )
- DAI_THROWE(INVALID_EVIDENCE_FILE,"Evidence case " + toString(i) + ": Cannot read value of " + toString(j) + "'th observed variable");
- if( verbose >= 3 )
- cout << " variable: " << label << ", value: " << val << endl;
- evid[i][label] = val;
- }
- }
-
- // close file
- is.close();
- } else
- DAI_THROWE(CANNOT_READ_FILE,"Cannot read from file " + std::string(filename));
-
- if( evid.size() == 0 )
- evid.resize( 1 );
-
- return evid;
-}
-
-
-/// Reads factor graph (as a pair of a variable vector and factor vector) from a UAI factor graph file
-void ReadUAIFGFile( const char *filename, size_t verbose, vector<Var>& vars, vector<Factor>& factors, vector<Permute>& permutations ) {
- vars.clear();
- factors.clear();
- permutations.clear();
-
- // open file
- ifstream is;
- is.open( filename );
- if( is.is_open() ) {
- size_t nrFacs, nrVars;
- string line;
-
- // read header line
- getline(is,line);
- if( is.fail() || (line != "BAYES" && line != "MARKOV" && line != "BAYES\r" && line != "MARKOV\r") )
- DAI_THROWE(INVALID_FACTORGRAPH_FILE,"UAI factor graph file should start with \"BAYES\" or \"MARKOV\"");
- if( verbose >= 2 )
- cout << "Reading " << line << " network..." << endl;
-
- // read number of variables
- is >> nrVars;
- if( is.fail() )
- DAI_THROWE(INVALID_FACTORGRAPH_FILE,"Cannot read number of variables");
- if( verbose >= 2 )
- cout << "Reading " << nrVars << " variables..." << endl;
-
- // for each variable, read its number of states
- vars.reserve( nrVars );
- for( size_t i = 0; i < nrVars; i++ ) {
- size_t dim;
- is >> dim;
- if( is.fail() )
- DAI_THROWE(INVALID_FACTORGRAPH_FILE,"Cannot read number of states of " + toString(i) + "'th variable");
- vars.push_back( Var( i, dim ) );
- }
-
- // read number of factors
- is >> nrFacs;
- if( is.fail() )
- DAI_THROWE(INVALID_FACTORGRAPH_FILE,"Cannot read number of factors");
- if( verbose >= 2 )
- cout << "Reading " << nrFacs << " factors..." << endl;
-
- // for each factor, read the variables on which it depends
- vector<vector<Var> > factorVars;
- factors.reserve( nrFacs );
- factorVars.reserve( nrFacs );
- for( size_t I = 0; I < nrFacs; I++ ) {
- if( verbose >= 3 )
- cout << "Reading factor " << I << "..." << endl;
-
- // read number of variables for factor I
- size_t I_nrVars;
- is >> I_nrVars;
- if( is.fail() )
- DAI_THROWE(INVALID_FACTORGRAPH_FILE,"Cannot read number of variables for " + toString(I) + "'th factor");
- if( verbose >= 3 )
- cout << " which depends on " << I_nrVars << " variables" << endl;
-
- // read the variable labels
- vector<long> I_labels;
- vector<size_t> I_dims;
- I_labels.reserve( I_nrVars );
- I_dims.reserve( I_nrVars );
- factorVars[I].reserve( I_nrVars );
- for( size_t _i = 0; _i < I_nrVars; _i++ ) {
- long label;
- is >> label;
- if( is.fail() )
- DAI_THROWE(INVALID_FACTORGRAPH_FILE,"Cannot read variable labels for " + toString(I) + "'th factor");
- I_labels.push_back( label );
- I_dims.push_back( vars[label].states() );
- factorVars[I].push_back( vars[label] );
- }
- if( verbose >= 3 )
- cout << " labels: " << I_labels << ", dimensions " << I_dims << endl;
-
- // add the factor and the labels
- factors.push_back( Factor( VarSet( factorVars[I].begin(), factorVars[I].end(), factorVars[I].size() ), (Real)0 ) );
- }
-
- // for each factor, read its values
- permutations.reserve( nrFacs );
- for( size_t I = 0; I < nrFacs; I++ ) {
- if( verbose >= 3 )
- cout << "Reading factor " << I << "..." << endl;
-
- // calculate permutation object, reversing the indexing in factorVars[I] first
- Permute permindex( factorVars[I], true );
- permutations.push_back( permindex );
-
- // read factor values
- size_t nrNonZeros;
- is >> nrNonZeros;
- if( is.fail() )
- DAI_THROWE(INVALID_FACTORGRAPH_FILE,"Cannot read number of nonzero factor values for " + toString(I) + "'th factor");
- if( verbose >= 3 )
- cout << " number of nonzero values: " << nrNonZeros << endl;
- DAI_ASSERT( nrNonZeros == factors[I].nrStates() );
- for( size_t li = 0; li < nrNonZeros; li++ ) {
- Real val;
- is >> val;
- if( is.fail() )
- DAI_THROWE(INVALID_FACTORGRAPH_FILE,"Cannot read factor values of " + toString(I) + "'th factor");
- // assign value after calculating its linear index corresponding to the permutation
- if( verbose >= 4 )
- cout << " " << li << "'th value " << val << " corresponds with index " << permindex.convertLinearIndex(li) << endl;
- factors[I].set( permindex.convertLinearIndex( li ), val );
- }
- }
- if( verbose >= 3 )
- cout << "variables:" << vars << endl;
- if( verbose >= 3 )
- cout << "factors:" << factors << endl;
-
- // close file
- is.close();
- } else
- DAI_THROWE(CANNOT_READ_FILE,"Cannot read from file " + std::string(filename));
-}
-
-
int main( int argc, char *argv[] ) {
if ( argc != 5 ) {
cout << "This program is part of libDAI - http://www.libdai.org/" << endl << endl;
} else {
double starttic = toc();
- size_t verbose = 1;
- size_t ia_verbose = 0;
- bool surgery = true;
+ size_t verbose = 1; // verbosity
+ size_t ia_verbose = 0; // verbosity of inference algorithms
+ bool surgery = true; // change factor graph structure based on evidence
if( verbose )
cout << "Solver: " << argv[0] << endl;
vector<Permute> permutations;
if( verbose )
cout << "Reading factor graph..." << endl;
- ReadUAIFGFile( argv[1], verbose, vars, facs0, permutations );
+ ReadUaiAieFactorGraphFile( argv[1], verbose, vars, facs0, permutations );
if( verbose )
cout << "Successfully read factor graph" << endl;
// read evidence
if( verbose )
cout << "Reading evidence..." << endl;
- vector<map<size_t,size_t> > evid = ReadUAIEvidenceFile( argv[2], verbose );
+ vector<map<size_t,size_t> > evid = ReadUaiAieEvidenceFile( argv[2], verbose );
if( verbose )
cout << "Successfully read " << evid.size() << " evidence cases" << endl;
// construct inference algorithm on clamped factor graph
if( verbose )
cout << " Constructing inference algorithm..." << endl;
- InfAlg *ia;
+ InfAlg *ia = NULL;
double tic = toc();
bool failed = false;
try {
--- /dev/null
+/* This file is part of libDAI - http://www.libdai.org/
+ *
+ * libDAI is licensed under the terms of the GNU General Public License version
+ * 2, or (at your option) any later version. libDAI is distributed without any
+ * warranty. See the file COPYING for more details.
+ *
+ * Copyright (C) 2010 Joris Mooij [joris dot mooij at libdai dot org]
+ */
+
+
+/// \file
+/// \brief Provides functionality for input/output of data structures in various file formats
+
+
+#ifndef __defined_libdai_io_h
+#define __defined_libdai_io_h
+
+
+#include <dai/factor.h>
+#include <vector>
+#include <map>
+
+
+namespace dai {
+
+
+/// Reads factor graph (as a pair of a variable vector and factor vector) from a file in the UAI approximate inference challenge format
+/** \param[in] filename The filename (usually ends with ".uai")
+ * \param[in] verbose The amount of output sent to cout
+ * \param[out] vars Array of variables read from the file
+ * \param[out] factors Array of factors read from the file
+ * \param[out] permutations Array of permutations, which permute between libDAI canonical ordering and ordering specified by the file
+ * \see http://www.cs.huji.ac.il/project/UAI10 and http://graphmod.ics.uci.edu/uai08
+ */
+void ReadUaiAieFactorGraphFile( const char *filename, size_t verbose, std::vector<Var>& vars, std::vector<Factor>& factors, std::vector<Permute>& permutations );
+
+
+/// Reads evidence (a mapping from observed variable labels to the observed values) from a file in the UAI approximate inference challenge format
+/** \param[in] filename The filename (usually ends with ".uai.evid")
+ * \param[in] verbose The amount of output sent to cout
+ * \see http://www.cs.huji.ac.il/project/UAI10 and http://graphmod.ics.uci.edu/uai08
+ */
+std::vector<std::map<size_t, size_t> > ReadUaiAieEvidenceFile( const char* filename, size_t verbose );
+
+
+} // end of namespace dai
+
+
+#endif
--- /dev/null
+/* This file is part of libDAI - http://www.libdai.org/
+ *
+ * libDAI is licensed under the terms of the GNU General Public License version
+ * 2, or (at your option) any later version. libDAI is distributed without any
+ * warranty. See the file COPYING for more details.
+ *
+ * Copyright (C) 2008-2010 Joris Mooij [joris dot mooij at libdai dot org]
+ */
+
+
+#include <dai/io.h>
+#include <dai/alldai.h>
+#include <iostream>
+#include <fstream>
+
+
+namespace dai {
+
+
+using namespace std;
+
+
+void ReadUaiAieFactorGraphFile( const char *filename, size_t verbose, std::vector<Var>& vars, std::vector<Factor>& factors, std::vector<Permute>& permutations ) {
+ vars.clear();
+ factors.clear();
+ permutations.clear();
+
+ // open file
+ ifstream is;
+ is.open( filename );
+ if( is.is_open() ) {
+ size_t nrFacs, nrVars;
+ string line;
+
+ // read header line
+ getline(is,line);
+ if( is.fail() || line.size() == 0 )
+ DAI_THROWE(INVALID_FACTORGRAPH_FILE,"UAI factor graph file should start with nonempty header line");
+ if( line[line.size() - 1] == '\r' )
+ line.resize( line.size() - 1 ); // for DOS text files
+ if( line != "BAYES" && line != "MARKOV" )
+ DAI_THROWE(INVALID_FACTORGRAPH_FILE,"UAI factor graph file should start with \"BAYES\" or \"MARKOV\"");
+ if( verbose >= 2 )
+ cout << "Reading " << line << " network..." << endl;
+
+ // read number of variables
+ is >> nrVars;
+ if( is.fail() )
+ DAI_THROWE(INVALID_FACTORGRAPH_FILE,"Cannot read number of variables");
+ if( verbose >= 2 )
+ cout << "Reading " << nrVars << " variables..." << endl;
+
+ // for each variable, read its number of states
+ vars.reserve( nrVars );
+ for( size_t i = 0; i < nrVars; i++ ) {
+ size_t dim;
+ is >> dim;
+ if( is.fail() )
+ DAI_THROWE(INVALID_FACTORGRAPH_FILE,"Cannot read number of states of " + toString(i) + "'th variable");
+ vars.push_back( Var( i, dim ) );
+ }
+
+ // read number of factors
+ is >> nrFacs;
+ if( is.fail() )
+ DAI_THROWE(INVALID_FACTORGRAPH_FILE,"Cannot read number of factors");
+ if( verbose >= 2 )
+ cout << "Reading " << nrFacs << " factors..." << endl;
+
+ // for each factor, read the variables on which it depends
+ vector<vector<Var> > factorVars;
+ factors.reserve( nrFacs );
+ factorVars.reserve( nrFacs );
+ for( size_t I = 0; I < nrFacs; I++ ) {
+ if( verbose >= 3 )
+ cout << "Reading factor " << I << "..." << endl;
+
+ // read number of variables for factor I
+ size_t I_nrVars;
+ is >> I_nrVars;
+ if( is.fail() )
+ DAI_THROWE(INVALID_FACTORGRAPH_FILE,"Cannot read number of variables for " + toString(I) + "'th factor");
+ if( verbose >= 3 )
+ cout << " which depends on " << I_nrVars << " variables" << endl;
+
+ // read the variable labels
+ vector<long> I_labels;
+ vector<size_t> I_dims;
+ I_labels.reserve( I_nrVars );
+ I_dims.reserve( I_nrVars );
+ factorVars[I].reserve( I_nrVars );
+ for( size_t _i = 0; _i < I_nrVars; _i++ ) {
+ long label;
+ is >> label;
+ if( is.fail() )
+ DAI_THROWE(INVALID_FACTORGRAPH_FILE,"Cannot read variable labels for " + toString(I) + "'th factor");
+ I_labels.push_back( label );
+ I_dims.push_back( vars[label].states() );
+ factorVars[I].push_back( vars[label] );
+ }
+ if( verbose >= 3 )
+ cout << " labels: " << I_labels << ", dimensions " << I_dims << endl;
+
+ // add the factor and the labels
+ factors.push_back( Factor( VarSet( factorVars[I].begin(), factorVars[I].end(), factorVars[I].size() ), (Real)0 ) );
+ }
+
+ // for each factor, read its values
+ permutations.reserve( nrFacs );
+ for( size_t I = 0; I < nrFacs; I++ ) {
+ if( verbose >= 3 )
+ cout << "Reading factor " << I << "..." << endl;
+
+ // calculate permutation object, reversing the indexing in factorVars[I] first
+ Permute permindex( factorVars[I], true );
+ permutations.push_back( permindex );
+
+ // read factor values
+ size_t nrNonZeros;
+ is >> nrNonZeros;
+ if( is.fail() )
+ DAI_THROWE(INVALID_FACTORGRAPH_FILE,"Cannot read number of nonzero factor values for " + toString(I) + "'th factor");
+ if( verbose >= 3 )
+ cout << " number of nonzero values: " << nrNonZeros << endl;
+ DAI_ASSERT( nrNonZeros == factors[I].nrStates() );
+ for( size_t li = 0; li < nrNonZeros; li++ ) {
+ Real val;
+ is >> val;
+ if( is.fail() )
+ DAI_THROWE(INVALID_FACTORGRAPH_FILE,"Cannot read factor values of " + toString(I) + "'th factor");
+ // assign value after calculating its linear index corresponding to the permutation
+ if( verbose >= 4 )
+ cout << " " << li << "'th value " << val << " corresponds with index " << permindex.convertLinearIndex(li) << endl;
+ factors[I].set( permindex.convertLinearIndex( li ), val );
+ }
+ }
+ if( verbose >= 3 )
+ cout << "variables:" << vars << endl;
+ if( verbose >= 3 )
+ cout << "factors:" << factors << endl;
+
+ // close file
+ is.close();
+ } else
+ DAI_THROWE(CANNOT_READ_FILE,"Cannot read from file " + std::string(filename));
+}
+
+
+std::vector<std::map<size_t, size_t> > ReadUaiAieEvidenceFile( const char* filename, size_t verbose ) {
+ vector<map<size_t, size_t> > evid;
+
+ // open file
+ ifstream is;
+ string line;
+ is.open( filename );
+ if( is.is_open() ) {
+ // read number of lines
+ getline( is, line );
+ if( is.fail() || line.size() == 0 )
+ DAI_THROWE(INVALID_EVIDENCE_FILE,"Cannot read header line of evidence file");
+ if( line[line.size() - 1] == '\r' )
+ line.resize( line.size() - 1 ); // for DOS text files
+ size_t nrLines = fromString<size_t>( line );
+ if( verbose >= 2 )
+ cout << "Reading " << nrLines << " evidence file lines..." << endl;
+
+ if( nrLines ) {
+ // detect version (pre-2010 or 2010)
+ streampos pos = is.tellg();
+ getline( is, line );
+ if( is.fail() || line.size() == 0 )
+ DAI_THROWE(INVALID_EVIDENCE_FILE,"Cannot read second line of evidence file");
+ if( line[line.size() - 1] == '\r' )
+ line.resize( line.size() - 1 ); // for DOS text files
+ vector<string> cols;
+ cols = tokenizeString( line, false, " \t" );
+ bool oldVersion = true;
+ if( cols.size() % 2 )
+ oldVersion = false;
+ if( verbose >= 2 ) {
+ if( oldVersion )
+ cout << "Detected old (2006, 2008) evidence file format" << endl;
+ else
+ cout << "Detected new (2010) evidence file format" << endl;
+ }
+ size_t nrEvid;
+ if( oldVersion ) {
+ nrEvid = 1;
+ is.seekg( 0 );
+ } else {
+ nrEvid = nrLines;
+ is.seekg( pos );
+ }
+
+ // read all evidence cases
+ if( verbose >= 2 )
+ cout << "Reading " << nrEvid << " evidence cases..." << endl;
+ evid.resize( nrEvid );
+ for( size_t i = 0; i < nrEvid; i++ ) {
+ // read number of variables
+ size_t nrObs;
+ is >> nrObs;
+ if( is.fail() )
+ DAI_THROWE(INVALID_EVIDENCE_FILE,"Evidence case " + toString(i) + ": Cannot read number of observations");
+ if( verbose >= 2 )
+ cout << "Evidence case " << i << ": reading " << nrObs << " observations..." << endl;
+
+ // for each observation, read the variable label and the observed value
+ for( size_t j = 0; j < nrObs; j++ ) {
+ size_t label, val;
+ is >> label;
+ if( is.fail() )
+ DAI_THROWE(INVALID_EVIDENCE_FILE,"Evidence case " + toString(i) + ": Cannot read label for " + toString(j) + "'th observed variable");
+ is >> val;
+ if( is.fail() )
+ DAI_THROWE(INVALID_EVIDENCE_FILE,"Evidence case " + toString(i) + ": Cannot read value of " + toString(j) + "'th observed variable");
+ if( verbose >= 3 )
+ cout << " variable: " << label << ", value: " << val << endl;
+ evid[i][label] = val;
+ }
+ }
+ }
+
+ // close file
+ is.close();
+ } else
+ DAI_THROWE(CANNOT_READ_FILE,"Cannot read from file " + std::string(filename));
+
+ if( evid.size() == 0 )
+ evid.resize( 1 );
+
+ return evid;
+}
+
+
+} // end of namespace dai
#include <iostream>
#include <fstream>
+#include <cstdlib>
#include <dai/alldai.h>
-#include <dai/util.h>
-#include <dai/index.h>
-#include <dai/jtree.h>
+#include <dai/io.h>
using namespace std;
using namespace dai;
-/// Reads "evidence" (a mapping from observed variable labels to the observed values) from a UAI evidence file
-map<size_t, size_t> ReadUAIEvidenceFile( char* filename ) {
- map<size_t, size_t> evid;
-
- // open file
- ifstream is;
- is.open( filename );
- if( is.is_open() ) {
- // read number of observed variables
- size_t nr_evid;
- is >> nr_evid;
- if( is.fail() )
- DAI_THROWE(INVALID_EVIDENCE_FILE,"Cannot read number of observed variables");
-
- // for each observation, read the variable label and the observed value
- for( size_t i = 0; i < nr_evid; i++ ) {
- size_t label, val;
- is >> label;
- if( is.fail() )
- DAI_THROWE(INVALID_EVIDENCE_FILE,"Cannot read label for " + toString(i) + "'th observed variable");
- is >> val;
- if( is.fail() )
- DAI_THROWE(INVALID_EVIDENCE_FILE,"Cannot read value of " + toString(i) + "'th observed variable");
- evid[label] = val;
- }
-
- // close file
- is.close();
- } else
- DAI_THROWE(CANNOT_READ_FILE,"Cannot read from file " + std::string(filename));
-
- return evid;
-}
-
-
-/// Reads factor graph (as a pair of a variable vector and factor vector) from a UAI factor graph file
-void ReadUAIFGFile( const char *filename, size_t verbose, vector<Var>& vars, vector<Factor>& factors, vector<Permute>& permutations ) {
- vars.clear();
- factors.clear();
- permutations.clear();
-
- // open file
- ifstream is;
- is.open( filename );
- if( is.is_open() ) {
- size_t nrFacs, nrVars;
- string line;
-
- // read header line
- getline(is,line);
- if( is.fail() || (line != "BAYES" && line != "MARKOV" && line != "BAYES\r" && line != "MARKOV\r") )
- DAI_THROWE(INVALID_FACTORGRAPH_FILE,"UAI factor graph file should start with \"BAYES\" or \"MARKOV\"");
- if( verbose >= 2 )
- cout << "Reading " << line << " network..." << endl;
-
- // read number of variables
- is >> nrVars;
- if( is.fail() )
- DAI_THROWE(INVALID_FACTORGRAPH_FILE,"Cannot read number of variables");
- if( verbose >= 2 )
- cout << "Reading " << nrVars << " variables..." << endl;
-
- // for each variable, read its number of states
- vars.reserve( nrVars );
- for( size_t i = 0; i < nrVars; i++ ) {
- size_t dim;
- is >> dim;
- if( is.fail() )
- DAI_THROWE(INVALID_FACTORGRAPH_FILE,"Cannot read number of states of " + toString(i) + "'th variable");
- vars.push_back( Var( i, dim ) );
- }
-
- // read number of factors
- is >> nrFacs;
- if( is.fail() )
- DAI_THROWE(INVALID_FACTORGRAPH_FILE,"Cannot read number of factors");
- if( verbose >= 2 )
- cout << "Reading " << nrFacs << " factors..." << endl;
-
- // for each factor, read the variables on which it depends
- vector<vector<Var> > factorVars;
- factors.reserve( nrFacs );
- factorVars.reserve( nrFacs );
- for( size_t I = 0; I < nrFacs; I++ ) {
- if( verbose >= 3 )
- cout << "Reading factor " << I << "..." << endl;
-
- // read number of variables for factor I
- size_t I_nrVars;
- is >> I_nrVars;
- if( is.fail() )
- DAI_THROWE(INVALID_FACTORGRAPH_FILE,"Cannot read number of variables for " + toString(I) + "'th factor");
- if( verbose >= 3 )
- cout << " which depends on " << I_nrVars << " variables" << endl;
-
- // read the variable labels
- vector<long> I_labels;
- vector<size_t> I_dims;
- I_labels.reserve( I_nrVars );
- I_dims.reserve( I_nrVars );
- factorVars[I].reserve( I_nrVars );
- for( size_t _i = 0; _i < I_nrVars; _i++ ) {
- long label;
- is >> label;
- if( is.fail() )
- DAI_THROWE(INVALID_FACTORGRAPH_FILE,"Cannot read variable labels for " + toString(I) + "'th factor");
- I_labels.push_back( label );
- I_dims.push_back( vars[label].states() );
- factorVars[I].push_back( vars[label] );
- }
- if( verbose >= 3 )
- cout << " labels: " << I_labels << ", dimensions " << I_dims << endl;
-
- // add the factor and the labels
- factors.push_back( Factor( VarSet( factorVars[I].begin(), factorVars[I].end(), factorVars[I].size() ), (Real)0 ) );
- }
-
- // for each factor, read its values
- permutations.reserve( nrFacs );
- for( size_t I = 0; I < nrFacs; I++ ) {
- if( verbose >= 3 )
- cout << "Reading factor " << I << "..." << endl;
-
- // calculate permutation object, reversing the indexing in factorVars[I] first
- Permute permindex( factorVars[I], true );
- permutations.push_back( permindex );
-
- // read factor values
- size_t nrNonZeros;
- is >> nrNonZeros;
- if( is.fail() )
- DAI_THROWE(INVALID_FACTORGRAPH_FILE,"Cannot read number of nonzero factor values for " + toString(I) + "'th factor");
- if( verbose >= 3 )
- cout << " number of nonzero values: " << nrNonZeros << endl;
- DAI_ASSERT( nrNonZeros == factors[I].nrStates() );
- for( size_t li = 0; li < nrNonZeros; li++ ) {
- Real val;
- is >> val;
- if( is.fail() )
- DAI_THROWE(INVALID_FACTORGRAPH_FILE,"Cannot read factor values of " + toString(I) + "'th factor");
- // assign value after calculating its linear index corresponding to the permutation
- if( verbose >= 4 )
- cout << " " << li << "'th value " << val << " corresponds with index " << permindex.convertLinearIndex(li) << endl;
- factors[I].set( permindex.convertLinearIndex( li ), val );
- }
- }
- if( verbose >= 3 )
- cout << "variables:" << vars << endl;
- if( verbose >= 3 )
- cout << "factors:" << factors << endl;
-
- // close file
- is.close();
- } else
- DAI_THROWE(CANNOT_READ_FILE,"Cannot read from file " + std::string(filename));
-}
-
-
int main( int argc, char *argv[] ) {
- if ( argc != 7 ) {
+ if ( argc != 4 ) {
cout << "This program is part of libDAI - http://www.libdai.org/" << endl << endl;
- cout << "Usage: ./uai2fg <filename.uai> <filename.uai.evid> <filename.fg> <type> <run_jtree> <verbose>" << endl << endl;
- cout << "Converts input files in the UAI 2008 approximate inference evaluation format" << endl;
- cout << "(see http://graphmod.ics.uci.edu/uai08/) to the libDAI factor graph format." << endl;
- cout << "Reads factor graph <filename.uai> and evidence <filename.uai.evid>" << endl;
- cout << "and writes the resulting clamped factor graph to <filename.fg>." << endl;
- cout << "If type==0, uses surgery (recommended), otherwise, uses just adds delta factors." << endl;
- cout << "If run_jtree!=0, runs a junction tree and reports the results in the UAI 2008 results file format." << endl;
+ cout << "Usage: ./uai2fg <basename> <surgery> <verbose>" << endl << endl;
+ cout << "Converts input files in the UAI 2006/2008/2010 approximate inference evaluation format" << endl;
+ cout << "(see http://graphmod.ics.uci.edu/uai08/ and http://www.cs.huji.ac.il/project/UAI10/)" << endl;
+ cout << "to the libDAI factor graph format." << endl << endl;
+ cout << "Reads factor graph <basename.uai> and evidence <basename.uai.evid>" << endl;
+ cout << "and writes the resulting clamped factor graphs to <basename.X.fg>," << endl;
+ cout << "where X=0,1,2,... enumerates the different evidence cases." << endl << endl;
+ cout << "If surgery!=0, uses surgery on the factor graph (recommended)," << endl;
+ cout << "otherwise, just adds delta factors to the factor graph." << endl;
return 1;
} else {
- long verbose = fromString<long>( argv[6] );
- long type = fromString<long>( argv[4] );
- bool run_jtree = fromString<bool>( argv[5] );
+ string basename( argv[1] );
+ bool surgery = fromString<size_t>( argv[2] );
+ size_t verbose = fromString<size_t>( argv[3] );
+ string uainame = basename + ".uai";
+ string evidname = uainame + ".evid";
+
+ // output command line options
+ if( verbose ) {
+ cout << "Factorgraph filename: " << uainame << endl;
+ cout << "Evidence filename: " << evidname << endl;
+ cout << "Output basename: " << basename << endl;
+ cout << "Surgery: " << surgery << endl;
+ }
// read factor graph
vector<Var> vars;
- vector<Factor> facs;
+ vector<Factor> facs0;
vector<Permute> permutations;
- ReadUAIFGFile( argv[1], verbose, vars, facs, permutations );
+ if( verbose )
+ cout << "Reading factor graph..." << endl;
+ ReadUaiAieFactorGraphFile( uainame.c_str(), verbose, vars, facs0, permutations );
+ if( verbose )
+ cout << "Successfully read factor graph" << endl;
// read evidence
- map<size_t,size_t> evid = ReadUAIEvidenceFile( argv[2] );
-
- // construct unclamped factor graph
- FactorGraph fg0( facs.begin(), facs.end(), vars.begin(), vars.end(), facs.size(), vars.size() );
-
- // change factor graph to reflect observed evidence
- if( type == 0 ) {
- // replace factors with clamped variables with slices
- for( size_t I = 0; I < facs.size(); I++ ) {
- for( map<size_t,size_t>::const_iterator e = evid.begin(); e != evid.end(); e++ ) {
- if( facs[I].vars() >> vars[e->first] ) {
- if( verbose >= 2 )
- cout << "Clamping " << e->first << " to value " << e->second << " in factor " << I << " = " << facs[I].vars() << endl;
- facs[I] = facs[I].slice( vars[e->first], e->second );
- if( verbose >= 2 )
- cout << "...remaining vars: " << facs[I].vars() << endl;
+ if( verbose )
+ cout << "Reading evidence..." << endl;
+ vector<map<size_t,size_t> > evid = ReadUaiAieEvidenceFile( evidname.c_str(), verbose );
+ if( verbose )
+ cout << "Successfully read " << evid.size() << " evidence cases" << endl;
+
+ // build output file names
+ vector<string> fgnames;
+ fgnames.reserve( evid.size() );
+ for( size_t ev = 0; ev < evid.size(); ev++ )
+ fgnames.push_back( basename + '.' + toString(ev) + ".fg" );
+
+ // construct clamped factor graphs which reflect observed evidence cases
+ if( verbose )
+ cout << "Constructing clamped factor graphs..." << endl;
+ vector<FactorGraph> fgs;
+ fgs.reserve( evid.size() );
+ for( size_t ev = 0; ev < evid.size(); ev++ ) {
+ if( verbose )
+ cout << " Evidence case " << ev << "..." << endl;
+ // copy vector of factors
+ vector<Factor> facs( facs0 );
+
+ // change factor graph to reflect observed evidence
+ if( verbose )
+ cout << " Applying evidence..." << endl;
+ if( surgery ) {
+ // replace factors with clamped variables with slices
+ for( size_t I = 0; I < facs.size(); I++ ) {
+ for( map<size_t,size_t>::const_iterator e = evid[ev].begin(); e != evid[ev].end(); e++ ) {
+ if( facs[I].vars() >> vars[e->first] ) {
+ if( verbose >= 2 )
+ cout << " Clamping " << e->first << " to value " << e->second << " in factor " << I << " = " << facs[I].vars() << endl;
+ facs[I] = facs[I].slice( vars[e->first], e->second );
+ if( verbose >= 2 )
+ cout << " ...remaining vars: " << facs[I].vars() << endl;
+ }
}
}
+ // remove empty factors
+ Real logZcorr = 0.0;
+ for( vector<Factor>::iterator I = facs.begin(); I != facs.end(); )
+ if( I->vars().size() == 0 ) {
+ logZcorr += std::log( (Real)(*I)[0] );
+ I = facs.erase( I );
+ } else
+ I++;
+ // multiply with logZcorr constant
+ if( facs.size() == 0 )
+ facs.push_back( Factor( VarSet(), std::exp(logZcorr) ) );
+ else
+ facs.front() *= std::exp(logZcorr);
}
- // remove empty factors
- double logZcorr = 0.0;
- for( vector<Factor>::iterator I = facs.begin(); I != facs.end(); )
- if( I->vars().size() == 0 ) {
- logZcorr += std::log( (Real)(*I)[0] );
- I = facs.erase( I );
- } else
- I++;
- // multiply with logZcorr constant
- if( facs.size() == 0 )
- facs.push_back( Factor( VarSet(), std::exp(logZcorr) ) );
- else
- facs.front() *= std::exp(logZcorr);
+ // add delta factors corresponding to observed variable values
+ for( map<size_t,size_t>::const_iterator e = evid[ev].begin(); e != evid[ev].end(); e++ )
+ facs.push_back( createFactorDelta( vars[e->first], e->second ) );
+
+ // construct clamped factor graph
+ if( verbose )
+ cout << " Constructing factor graph..." << endl;
+ fgs.push_back( FactorGraph( facs.begin(), facs.end(), vars.begin(), vars.end(), facs.size(), vars.size() ) );
+
+ // write it to a file
+ if( verbose )
+ cout << " Saving factor graph as " << fgnames[ev] << "..." << endl;
+ fgs[ev].WriteToFile( fgnames[ev].c_str() );
}
- // add delta factors corresponding to observed variable values
- for( map<size_t,size_t>::const_iterator e = evid.begin(); e != evid.end(); e++ )
- facs.push_back( createFactorDelta( vars[e->first], e->second ) );
-
- // construct clamped factor graph
- FactorGraph fg( facs.begin(), facs.end(), vars.begin(), vars.end(), facs.size(), vars.size() );
-
- // write it to a file
- fg.WriteToFile( argv[3] );
-
- // if requested, perform various inference tasks
- if( run_jtree ) {
- // construct junction tree on unclamped factor graph
- JTree jt0( fg0, PropertySet()("updates",string("HUGIN")) );
- jt0.init();
- jt0.run();
-
- // construct junction tree on clamped factor graph
- JTree jt( fg, PropertySet()("updates",string("HUGIN")) );
- jt.init();
- jt.run();
- // output probability of evidence
- cout.precision( 8 );
- if( evid.size() )
- cout << "z " << (jt.logZ() - jt0.logZ()) / dai::log((Real)10.0) << endl;
- else
- cout << "z " << jt.logZ() / dai::log((Real)10.0) << endl;
-
- // output variable marginals
- cout << "m " << jt.nrVars() << " ";
- for( size_t i = 0; i < jt.nrVars(); i++ ) {
- cout << jt.var(i).states() << " ";
- for( size_t s = 0; s < jt.var(i).states(); s++ )
- cout << jt.beliefV(i)[s] << " ";
- }
- cout << endl;
-
- // calculate MAP state
- jt.props.inference = JTree::Properties::InfType::MAXPROD;
- jt.init();
- jt.run();
- vector<size_t> MAP = jt.findMaximum();
- map<Var, size_t> state;
- for( size_t i = 0; i < MAP.size(); i++ )
- state[jt.var(i)] = MAP[i];
- double log_MAP_prob = 0.0;
- for( size_t I = 0; I < jt.nrFactors(); I++ )
- log_MAP_prob += dai::log( jt.factor(I)[calcLinearState( jt.factor(I).vars(), state )] );
-
- // output MAP state
- cout << "s ";
- if( evid.size() )
- cout << (log_MAP_prob - jt0.logZ()) / dai::log((Real)10.0) << " ";
- else
- cout << log_MAP_prob / dai::log((Real)10.0) << " ";
- cout << jt.nrVars() << " ";
- for( size_t i = 0; i < jt.nrVars(); i++ )
- cout << MAP[i] << " ";
- cout << endl;
- }
+ if( verbose )
+ cout << "Done!" << endl;
}
return 0;
projects / libdai.git / commitdiff