SRC=src
LIB=lib
-# Extensions (library, object, executable, MEX file extensions)
+# Extensions (library, object, executable, matlab compiled MEX file)
LE=.a
OE=.o
EE=
CCO=-o
# Flags for the C++ compiler
-CCFLAGS=-Wno-deprecated -Wall -W -Wextra -fpic -I./include -Llib -O3 #-pg
+CCFLAGS=-O3 -Wno-deprecated -Wall -W -Wextra -fpic -Iinclude -Llib
ifdef DEBUG
CCFLAGS:=$(CCFLAGS) -g -DDAI_DEBUG
endif
ifdef WITH_MATLAB
# Replace the following by the directory where Matlab has been installed
-MATLABDIR=/opt/matlab/bin
-# Replace the following with the extension of compiled MEX files on this platform, e.g. .mexglx for x86
-MEX=$(MATLABDIR)/mex
-MEXFLAGS=-I.
+MATLABDIR=/agbs/share/sw/matlab
+MEX=$(MATLABDIR)/bin/mex
+MEXFLAGS=-Iinclude CXX\#$(CC) CXXFLAGS\#'-O3 -Wno-deprecated -Wall -W -Wextra -fpic'
ifdef DEBUG
MEXFLAGS:=$(MEXFLAGS) -g -DDAI_DEBUG
endif
.PHONY : clean
clean :
- -rm *$(OE)
- -rm matlab/*$(ME) matlab/*$(OE)
+ -rm *$(OE)
+ -rm matlab/*$(ME)
-rm example$(EE) tests/testdai$(EE) utils/fg2dot$(EE) utils/createfg$(EE) utils/fginfo$(EE)
-rm -R doc
-rm -R lib
# MATLAB INTERFACE
###################
-matlab/dai.$(ME) : matlab/dai.cpp $(HEADERS) matlab/matlab$(OE) $(LIB)/libdai$(LE)
- $(MEX) $(MEXFLAGS) -o matlab/dai matlab/dai.cpp matlab/matlab$(OE) $(LIB)/libdai$(LE)
+matlab/dai$(ME) : $(SRC)/matlab/dai.cpp $(HEADERS) matlab$(OE) $(LIB)/libdai$(LE)
+ $(MEX) $(MEXFLAGS) -o matlab/dai $(SRC)/matlab/dai.cpp matlab$(OE) $(LIB)/libdai$(LE)
-matlab/dai_readfg.$(ME) : matlab/dai_readfg.cpp $(HEADERS) factorgraph$(OE) matlab/matlab$(OE) exceptions$(OE)
- $(MEX) $(MEXFLAGS) -o matlab/dai_readfg matlab/dai_readfg.cpp factorgraph$(OE) matlab/matlab$(OE) exceptions$(OE)
+matlab/dai_readfg$(ME) : $(SRC)/matlab/dai_readfg.cpp $(HEADERS) factorgraph$(OE) matlab$(OE) exceptions$(OE)
+ $(MEX) $(MEXFLAGS) -o matlab/dai_readfg $(SRC)/matlab/dai_readfg.cpp factorgraph$(OE) matlab$(OE) exceptions$(OE)
-matlab/dai_writefg.$(ME) : matlab/dai_writefg.cpp $(HEADERS) factorgraph$(OE) matlab/matlab$(OE) exceptions$(OE)
- $(MEX) $(MEXFLAGS) -o matlab/dai_writefg matlab/dai_writefg.cpp factorgraph$(OE) matlab/matlab$(OE) exceptions$(OE)
+matlab/dai_writefg$(ME) : $(SRC)/matlab/dai_writefg.cpp $(HEADERS) factorgraph$(OE) matlab$(OE) exceptions$(OE)
+ $(MEX) $(MEXFLAGS) -o matlab/dai_writefg $(SRC)/matlab/dai_writefg.cpp factorgraph$(OE) matlab$(OE) exceptions$(OE)
-matlab/dai_potstrength.$(ME) : matlab/dai_potstrength.cpp $(HEADERS) matlab/matlab$(OE) exceptions$(OE)
- $(MEX) $(MEXFLAGS) -o matlab/dai_potstrength matlab/dai_potstrength.cpp matlab/matlab$(OE) exceptions$(OE)
+matlab/dai_potstrength$(ME) : $(SRC)/matlab/dai_potstrength.cpp $(HEADERS) matlab$(OE) exceptions$(OE)
+ $(MEX) $(MEXFLAGS) -o matlab/dai_potstrength $(SRC)/matlab/dai_potstrength.cpp matlab$(OE) exceptions$(OE)
-matlab/matlab$(OE) : matlab/matlab.cpp matlab/matlab.h $(HEADERS)
- $(MEX) $(MEXFLAGS) -outdir matlab -c matlab/matlab.cpp
+matlab$(OE) : $(SRC)/matlab/matlab.cpp $(INC)/matlab/matlab.h $(HEADERS)
+ $(MEX) $(MEXFLAGS) -c $(SRC)/matlab/matlab.cpp
# UTILS
SRC=src\r
LIB=lib\r
\r
-# Extensions (library, object, executable, MEX file extensions)\r
+# Extensions (library, object, executable, matlab compiled MEX file)\r
LE=.lib\r
OE=.obj\r
EE=.exe\r
CCO=/Fe\r
\r
# Flags for the C++ compiler\r
-CCFLAGS=/I./include /IC:\boost_1_36_0 /EHsc /Ox\r
+CCFLAGS=/Iinclude /IC:\boost_1_36_0 /EHsc /Ox\r
!IFDEF DEBUG\r
CCFLAGS=$(CCFLAGS) /Zi /DDAI_DEBUG\r
!ENDIF\r
\r
!IFDEF WITH_MATLAB\r
# Replace the following by the directory where Matlab has been installed\r
-MATLABDIR=/opt/matlab/bin\r
-# Replace the following with the extension of compiled MEX files on this platform, e.g. .mexglx for x86\r
-MEX=$(MATLABDIR)/mex\r
-MEXFLAGS=-I.\r
+MATLABDIR=c:\matlab\r
+MEX=$(MATLABDIR)\bin\mex\r
+MEXFLAGS=-Iinclude CXX\#$(CC) CXXFLAGS\#"/EHsc /Ox"\r
!IFDEF DEBUG\r
MEXFLAGS=$(MEXFLAGS) -g /DDAI_DEBUG\r
!ENDIF\r
doxygen doxygen.conf\r
\r
clean :\r
- del *$(OE) *.ilk *.pdb *$(EE) matlab\*$(ME) matlab\*$(OE) tests\testdai$(EE) tests\*.pdb tests\*.ilk utils\*$(EE) utils\*.pdb utils\*.ilk $(LIB)\libdai$(LE)\r
+ del *$(OE) *.ilk *.pdb *$(EE) matlab\*$(ME) tests\testdai$(EE) tests\*.pdb tests\*.ilk utils\*$(EE) utils\*.pdb utils\*.ilk $(LIB)\libdai$(LE)\r
\r
!INCLUDE Makefile.shared\r
--- /dev/null
+/* 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
+ it under the terms of the GNU General Public License as published by
+ the Free Software Foundation; either version 2 of the License, or
+ (at your option) any later version.
+
+ libDAI is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ GNU General Public License for more details.
+
+ You should have received a copy of the GNU General Public License
+ along with libDAI; if not, write to the Free Software
+ Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
+*/
+
+
+#ifndef __defined_libdai_matlab_h
+#define __defined_libdai_matlab_h
+
+
+#include "mex.h"
+#include <dai/factor.h>
+
+
+namespace dai {
+
+
+#ifdef SMALLMEM
+ typedef int mwSize;
+ typedef int mwIndex;
+#endif
+
+
+/// Convert vector<Factor> structure to a cell vector of CPTAB-like structs
+mxArray *Factors2mx(const std::vector<Factor> &Ps);
+
+/// Convert cell vector of CPTAB-like structs to vector<Factor>
+std::vector<Factor> mx2Factors(const mxArray *psi, long verbose);
+
+/// Convert CPTAB-like struct to Factor
+Factor mx2Factor(const mxArray *psi);
+
+
+} // end of namespace dai
+
+
+#endif
+++ /dev/null
-/* 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
- it under the terms of the GNU General Public License as published by
- the Free Software Foundation; either version 2 of the License, or
- (at your option) any later version.
-
- libDAI is distributed in the hope that it will be useful,
- but WITHOUT ANY WARRANTY; without even the implied warranty of
- MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- GNU General Public License for more details.
-
- You should have received a copy of the GNU General Public License
- along with libDAI; if not, write to the Free Software
- Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
-*/
-
-
-/*=================================================================*
- * *
- * This is a MEX-file for MATLAB. *
- * *
- * [logZ,q,md] = dai(psi,method,opts); *
- * *
- *=================================================================*/
-
-
-#include <iostream>
-#include <dai/matlab/matlab.h>
-#include "mex.h"
-#include <dai/alldai.h>
-
-
-using namespace std;
-using namespace dai;
-
-
-/* Input Arguments */
-
-#define PSI_IN prhs[0]
-#define METHOD_IN prhs[1]
-#define OPTS_IN prhs[2]
-#define NR_IN 3
-
-
-/* Output Arguments */
-
-#define LOGZ_OUT plhs[0]
-#define Q_OUT plhs[1]
-#define MD_OUT plhs[2]
-#define NR_OUT 3
-
-
-void mexFunction( int nlhs, mxArray *plhs[], int nrhs, const mxArray*prhs[] )
-{
- size_t buflen;
-
- /* Check for proper number of arguments */
- if( (nrhs != NR_IN) || (nlhs != NR_OUT) ) {
- mexErrMsgTxt("Usage: [logZ,q,md] = dai(psi,method,opts)\n\n"
- "\n"
- "INPUT: psi = linear cell array containing the factors \n"
- " psi{i} should be a structure with a Member field\n"
- " and a P field, like a CPTAB).\n"
- " method = name of the method (see README)\n"
- " opts = string of options (see README)\n"
- "\n"
- "OUTPUT: logZ = approximation of the logarithm of the partition sum.\n"
- " q = linear cell array containing all final beliefs.\n"
- " md = maxdiff (final linf-dist between new and old single node beliefs).\n");
- }
-
- char *method;
- char *opts;
-
-
- // Get psi and construct factorgraph
- vector<Factor> factors = mx2Factors(PSI_IN, 0);
- FactorGraph fg(factors);
- long nr_v = fg.nrVars();
-
- // Get method
- buflen = mxGetN( METHOD_IN ) + 1;
- method = (char *)mxCalloc( buflen, sizeof(char) );
- mxGetString( METHOD_IN, method, buflen );
-
- // Get options string
- buflen = mxGetN( OPTS_IN ) + 1;
- opts = (char *)mxCalloc( buflen, sizeof(char) );
- mxGetString( OPTS_IN, opts, buflen );
- // Convert to options object props
- stringstream ss;
- ss << opts;
- Properties props;
- ss >> props;
-
- // Construct InfAlg object, init and run
- InfAlg *obj = newInfAlg( method, fg, props );
- obj->init();
- obj->run();
-
-
- // Save logZ
- double logZ = obj->logZ();
-
- // Save maxdiff
- double maxdiff = obj->MaxDiff();
-
-
- // Hand over results to MATLAB
- LOGZ_OUT = mxCreateDoubleMatrix(1,1,mxREAL);
- *(mxGetPr(LOGZ_OUT)) = logZ;
-
- Q_OUT = Factors2mx(obj->beliefs());
-
- MD_OUT = mxCreateDoubleMatrix(1,1,mxREAL);
- *(mxGetPr(MD_OUT)) = maxdiff;
-
-
- return;
-}
+++ /dev/null
-/* 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
- it under the terms of the GNU General Public License as published by
- the Free Software Foundation; either version 2 of the License, or
- (at your option) any later version.
-
- libDAI is distributed in the hope that it will be useful,
- but WITHOUT ANY WARRANTY; without even the implied warranty of
- MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- GNU General Public License for more details.
-
- You should have received a copy of the GNU General Public License
- along with libDAI; if not, write to the Free Software
- Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
-*/
-
-
-/*=================================================================*
- * *
- * This is a MEX-file for MATLAB. *
- * *
- * N = dai_potstrength(psi,i,j); *
- * *
- *=================================================================*/
-
-
-#include <iostream>
-#include "mex.h"
-#include <dai/matlab/matlab.h>
-#include <dai/factor.h>
-
-
-using namespace std;
-using namespace dai;
-
-
-/* Input Arguments */
-
-#define PSI_IN prhs[0]
-#define I_IN prhs[1]
-#define J_IN prhs[2]
-#define NR_IN 3
-
-
-/* Output Arguments */
-
-#define N_OUT plhs[0]
-#define NR_OUT 1
-
-
-void mexFunction( int nlhs, mxArray *plhs[], int nrhs, const mxArray*prhs[] )
-{
- long ilabel, jlabel;
-
- // Check for proper number of arguments
- if ((nrhs != NR_IN) || (nlhs != NR_OUT)) {
- mexErrMsgTxt("Usage: N = dai_potstrength(psi,i,j);\n\n"
- "\n"
- "INPUT: psi = structure with a Member field and a P field, like a CPTAB.\n"
- " i = label of a variable in psi.\n"
- " j = label of another variable in psi.\n"
- "\n"
- "OUTPUT: N = strength of psi in direction i->j.\n");
- }
-
- // Get input parameters
- Factor psi = mx2Factor(PSI_IN);
- ilabel = (long)*mxGetPr(I_IN);
- jlabel = (long)*mxGetPr(J_IN);
-
- // Find variable in psi with label ilabel
- Var i;
- for( VarSet::const_iterator n = psi.vars().begin(); n != psi.vars().end(); n++ )
- if( n->label() == ilabel ) {
- i = *n;
- break;
- }
- assert( i.label() == ilabel );
-
- // Find variable in psi with label jlabel
- Var j;
- for( VarSet::const_iterator n = psi.vars().begin(); n != psi.vars().end(); n++ )
- if( n->label() == jlabel ) {
- j = *n;
- break;
- }
- assert( j.label() == jlabel );
-
- // Calculate N(psi,i,j);
- double N = psi.strength( i, j );
-
- // Hand over result to MATLAB
- N_OUT = mxCreateDoubleMatrix(1,1,mxREAL);
- *(mxGetPr(N_OUT)) = N;
-
- return;
-}
+++ /dev/null
-/* 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
- it under the terms of the GNU General Public License as published by
- the Free Software Foundation; either version 2 of the License, or
- (at your option) any later version.
-
- libDAI is distributed in the hope that it will be useful,
- but WITHOUT ANY WARRANTY; without even the implied warranty of
- MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- GNU General Public License for more details.
-
- You should have received a copy of the GNU General Public License
- along with libDAI; if not, write to the Free Software
- Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
-*/
-
-
-/*=================================================================*
- * *
- * This is a MEX-file for MATLAB. *
- * *
- * [psi] = dai_readfg(filename); *
- * *
- *=================================================================*/
-
-
-#include <iostream>
-#include "mex.h"
-#include <dai/matlab/matlab.h>
-#include <dai/factorgraph.h>
-
-
-using namespace std;
-using namespace dai;
-
-
-/* Input Arguments */
-
-#define FILENAME_IN prhs[0]
-#define NR_IN 1
-
-
-/* Output Arguments */
-
-#define PSI_OUT plhs[0]
-#define NR_OUT 1
-
-
-void mexFunction( int nlhs, mxArray *plhs[], int nrhs, const mxArray*prhs[] )
-{
- char *filename;
-
-
- // Check for proper number of arguments
- if ((nrhs != NR_IN) || (nlhs != NR_OUT)) {
- mexErrMsgTxt("Usage: [psi] = dai_readfg(filename);\n\n"
- "\n"
- "INPUT: filename = filename of a .fg file\n"
- "\n"
- "OUTPUT: psi = linear cell array containing the factors\n"
- " (psi{i} is a structure with a Member field\n"
- " and a P field, like a CPTAB).\n");
- }
-
- // Get input parameters
- size_t buflen;
- buflen = mxGetN( FILENAME_IN ) + 1;
- filename = (char *)mxCalloc( buflen, sizeof(char) );
- mxGetString( FILENAME_IN, filename, buflen );
-
-
- // Read factorgraph
- FactorGraph fg;
- try {
- fg.ReadFromFile( filename );
- } catch( std::exception &e ) {
- mexErrMsgTxt( e.what() );
- }
-
-
- // Save factors
- vector<Factor> psi;
- for( size_t I = 0; I < fg.nrFactors(); I++ )
- psi.push_back(fg.factor(I));
-
-
- // Hand over results to MATLAB
- PSI_OUT = Factors2mx(psi);
-
-
- return;
-}
+++ /dev/null
-/* 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
- it under the terms of the GNU General Public License as published by
- the Free Software Foundation; either version 2 of the License, or
- (at your option) any later version.
-
- libDAI is distributed in the hope that it will be useful,
- but WITHOUT ANY WARRANTY; without even the implied warranty of
- MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- GNU General Public License for more details.
-
- You should have received a copy of the GNU General Public License
- along with libDAI; if not, write to the Free Software
- Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
-*/
-
-
-/*=================================================================*
- * *
- * This is a MEX-file for MATLAB. *
- * *
- * dai_writefg(psi, filename); *
- * *
- *=================================================================*/
-
-
-#include <iostream>
-#include "mex.h"
-#include <dai/matlab/matlab.h>
-#include <dai/factorgraph.h>
-
-
-using namespace std;
-using namespace dai;
-
-
-/* Input Arguments */
-
-#define PSI_IN prhs[0]
-#define FILENAME_IN prhs[1]
-#define NR_IN 2
-
-
-/* Output Arguments */
-
-#define NR_OUT 0
-
-
-void mexFunction( int nlhs, mxArray *plhs[], int nrhs, const mxArray*prhs[] )
-{
- char *filename;
-
-
- // Check for proper number of arguments
- if ((nrhs != NR_IN) || (nlhs != NR_OUT)) {
- mexErrMsgTxt("Usage: dai_writefg(psi,filename);\n\n"
- "\n"
- "INPUT: psi = linear cell array containing the factors\n"
- " (psi{i} should be a structure with a Member field\n"
- " and a P field, like a CPTAB).\n"
- " filename = filename of a .fg file\n");
- }
-
- // Get input parameters
- vector<Factor> factors = mx2Factors(PSI_IN,0);
-
- size_t buflen;
- buflen = mxGetN( FILENAME_IN ) + 1;
- filename = (char *)mxCalloc( buflen, sizeof(char) );
- mxGetString( FILENAME_IN, filename, buflen );
-
- // Construct factorgraph
- FactorGraph fg(factors);
- long nr_v = fg.nrVars();
- long nr_f = fg.nrFactors();
-
- try {
- fg.WriteToFile( filename );
- } catch( std::exception &e ) {
- mexErrMsgTxt( e.what() );
- }
-
- return;
-}
+++ /dev/null
-/* 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
- it under the terms of the GNU General Public License as published by
- the Free Software Foundation; either version 2 of the License, or
- (at your option) any later version.
-
- libDAI is distributed in the hope that it will be useful,
- but WITHOUT ANY WARRANTY; without even the implied warranty of
- MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- GNU General Public License for more details.
-
- You should have received a copy of the GNU General Public License
- along with libDAI; if not, write to the Free Software
- Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
-*/
-
-
-#include <iostream>
-#include <dai/matlab/matlab.h>
-
-
-namespace dai {
-
-
-using namespace std;
-
-
-/* Convert vector<Factor> structure to a cell vector of CPTAB-like structs */
-mxArray *Factors2mx(const vector<Factor> &Ps) {
- size_t nr = Ps.size();
-
- mxArray *psi = mxCreateCellMatrix(nr,1);
-
- const char *fieldnames[2];
- fieldnames[0] = "Member";
- fieldnames[1] = "P";
-
- size_t I_ind = 0;
- for( vector<Factor>::const_iterator I = Ps.begin(); I != Ps.end(); I++, I_ind++ ) {
- mxArray *Bi = mxCreateStructMatrix(1,1,2,fieldnames);
-
- mxArray *BiMember = mxCreateDoubleMatrix(1,I->vars().size(),mxREAL);
- double *BiMember_data = mxGetPr(BiMember);
- size_t i = 0;
- vector<mwSize> dims;
- for( VarSet::const_iterator j = I->vars().begin(); j != I->vars().end(); j++,i++ ) {
- BiMember_data[i] = j->label();
- dims.push_back( j->states() );
- }
-
- mxArray *BiP = mxCreateNumericArray(I->vars().size(), &(*(dims.begin())), mxDOUBLE_CLASS, mxREAL);
- double *BiP_data = mxGetPr(BiP);
- for( size_t j = 0; j < I->states(); j++ )
- BiP_data[j] = (*I)[j];
-
- mxSetField(Bi,0,"Member",BiMember);
- mxSetField(Bi,0,"P",BiP);
-
- mxSetCell(psi, I_ind, Bi);
- }
- return( psi );
-}
-
-
-/* Convert cell vector of CPTAB-like structs to vector<Factor> */
-vector<Factor> mx2Factors(const mxArray *psi, long verbose) {
- set<Var> vars;
- vector<Factor> factors;
-
- int n1 = mxGetM(psi);
- int n2 = mxGetN(psi);
- if( n2 != 1 && n1 != 1 )
- mexErrMsgTxt("psi should be a Nx1 or 1xN cell matrix.");
- size_t nr_f = n1;
- if( n1 == 1 )
- nr_f = n2;
-
- // interpret psi, linear cell array of cptabs
- for( size_t cellind = 0; cellind < nr_f; cellind++ ) {
- if( verbose >= 3 )
- cout << "reading factor " << cellind << ": " << endl;
- mxArray *cell = mxGetCell(psi, cellind);
- mxArray *mx_member = mxGetField(cell, 0, "Member");
- size_t nr_mem = mxGetN(mx_member);
- double *members = mxGetPr(mx_member);
- const mwSize *dims = mxGetDimensions(mxGetField(cell,0,"P"));
- double *factordata = mxGetPr(mxGetField(cell, 0, "P"));
-
- // add variables
- VarSet factorvars;
- vector<long> labels(nr_mem,0);
- if( verbose >= 3 )
- cout << " vars: ";
- for( size_t mi = 0; mi < nr_mem; mi++ ) {
- labels[mi] = (long)members[mi];
- if( verbose >= 3 )
- cout << labels[mi] << "(" << dims[mi] << ") ";
- vars.insert( Var(labels[mi], dims[mi]) );
- factorvars |= Var(labels[mi], dims[mi]);
- }
- factors.push_back(Factor(factorvars));
-
- // calculate permutation matrix
- vector<size_t> perm(nr_mem,0);
- VarSet::iterator j = factorvars.begin();
- for( size_t mi = 0; mi < nr_mem; mi++,j++ ) {
- long gezocht = j->label();
- vector<long>::iterator piet = find(labels.begin(),labels.end(),gezocht);
- perm[mi] = piet - labels.begin();
- }
-
- if( verbose >= 3 ) {
- cout << endl << " perm: ";
- for( vector<size_t>::iterator r=perm.begin(); r!=perm.end(); r++ )
- cout << *r << " ";
- cout << endl;
- }
-
- // read Factor
- vector<size_t> di(nr_mem,0);
- size_t prod = 1;
- for( size_t k = 0; k < nr_mem; k++ ) {
- di[k] = dims[k];
- prod *= dims[k];
- }
- Permute permindex( di, perm );
- for( size_t li = 0; li < prod; li++ )
- factors.back()[permindex.convert_linear_index(li)] = factordata[li];
- }
-
- if( verbose >= 3 ) {
- for(vector<Factor>::const_iterator I=factors.begin(); I!=factors.end(); I++ )
- cout << *I << endl;
- }
-
- return( factors );
-}
-
-
-/* Convert CPTAB-like struct to Factor */
-Factor mx2Factor(const mxArray *psi) {
- mxArray *mx_member = mxGetField(psi, 0, "Member");
- size_t nr_mem = mxGetN(mx_member);
- double *members = mxGetPr(mx_member);
- const mwSize *dims = mxGetDimensions(mxGetField(psi,0,"P"));
- double *factordata = mxGetPr(mxGetField(psi, 0, "P"));
-
- // add variables
- VarSet vars;
- vector<long> labels(nr_mem,0);
- for( size_t mi = 0; mi < nr_mem; mi++ ) {
- labels[mi] = (long)members[mi];
- vars |= Var(labels[mi], dims[mi]);
- }
- Factor factor(vars);
-
- // calculate permutation matrix
- vector<size_t> perm(nr_mem,0);
- VarSet::iterator j = vars.begin();
- for( size_t mi = 0; mi < nr_mem; mi++,j++ ) {
- long gezocht = j->label();
- vector<long>::iterator piet = find(labels.begin(),labels.end(),gezocht);
- perm[mi] = piet - labels.begin();
- }
-
- // read Factor
- vector<size_t> di(nr_mem,0);
- size_t prod = 1;
- for( size_t k = 0; k < nr_mem; k++ ) {
- di[k] = dims[k];
- prod *= dims[k];
- }
- Permute permindex( di, perm );
- for( size_t li = 0; li < prod; li++ )
- factor[permindex.convert_linear_index(li)] = factordata[li];
-
- return( factor );
-}
-
-
-}
+++ /dev/null
-/* 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
- it under the terms of the GNU General Public License as published by
- the Free Software Foundation; either version 2 of the License, or
- (at your option) any later version.
-
- libDAI is distributed in the hope that it will be useful,
- but WITHOUT ANY WARRANTY; without even the implied warranty of
- MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- GNU General Public License for more details.
-
- You should have received a copy of the GNU General Public License
- along with libDAI; if not, write to the Free Software
- Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
-*/
-
-
-#ifndef __defined_libdai_matlab_h
-#define __defined_libdai_matlab_h
-
-
-#include "mex.h"
-#include <dai/factor.h>
-
-
-namespace dai {
-
-
-#ifdef SMALLMEM
- typedef int mwSize;
- typedef int mwIndex;
-#endif
-
-
-/// Convert vector<Factor> structure to a cell vector of CPTAB-like structs
-mxArray *Factors2mx(const std::vector<Factor> &Ps);
-
-/// Convert cell vector of CPTAB-like structs to vector<Factor>
-std::vector<Factor> mx2Factors(const mxArray *psi, long verbose);
-
-/// Convert CPTAB-like struct to Factor
-Factor mx2Factor(const mxArray *psi);
-
-
-} // end of namespace dai
-
-
-#endif
const char *BP::Name = "BP";
+#define DAI_BP_FAST 1
+
+
void BP::setProperties( const PropertySet &opts ) {
assert( opts.hasKey("tol") );
assert( opts.hasKey("maxiter") );
newEP.message = Prob( var(i).states() );
newEP.newMessage = Prob( var(i).states() );
- newEP.index.reserve( factor(I).states() );
- for( IndexFor k( var(i), factor(I).vars() ); k >= 0; ++k )
- newEP.index.push_back( k );
+ if( DAI_BP_FAST ) {
+ newEP.index.reserve( factor(I).states() );
+ for( IndexFor k( var(i), factor(I).vars() ); k >= 0; ++k )
+ newEP.index.push_back( k );
+ }
newEP.residual = 0.0;
_edges[i].push_back( newEP );
// calculate updated message I->i
size_t I = nbV(i,_I);
- if( 0 == 1 ) {
+ if( !DAI_BP_FAST ) {
/* UNOPTIMIZED (SIMPLE TO READ, BUT SLOW) VERSION */
Factor prod( factor( I ) );
foreach( const Neighbor &j, nbF(I) )
Factor BP::beliefF (size_t I) const {
- if( 0 == 1 ) {
+ if( !DAI_BP_FAST ) {
/* UNOPTIMIZED (SIMPLE TO READ, BUT SLOW) VERSION */
Factor prod( factor(I) );
--- /dev/null
+/* 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
+ it under the terms of the GNU General Public License as published by
+ the Free Software Foundation; either version 2 of the License, or
+ (at your option) any later version.
+
+ libDAI is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ GNU General Public License for more details.
+
+ You should have received a copy of the GNU General Public License
+ along with libDAI; if not, write to the Free Software
+ Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
+*/
+
+
+/*=================================================================*
+ * *
+ * This is a MEX-file for MATLAB. *
+ * *
+ * [logZ,q,md] = dai(psi,method,opts); *
+ * *
+ *=================================================================*/
+
+
+#include <iostream>
+#include <dai/matlab/matlab.h>
+#include "mex.h"
+#include <dai/alldai.h>
+
+
+using namespace std;
+using namespace dai;
+
+
+/* Input Arguments */
+
+#define PSI_IN prhs[0]
+#define METHOD_IN prhs[1]
+#define OPTS_IN prhs[2]
+#define NR_IN 3
+
+
+/* Output Arguments */
+
+#define LOGZ_OUT plhs[0]
+#define Q_OUT plhs[1]
+#define MD_OUT plhs[2]
+#define NR_OUT 3
+
+
+void mexFunction( int nlhs, mxArray *plhs[], int nrhs, const mxArray*prhs[] )
+{
+ size_t buflen;
+
+ /* Check for proper number of arguments */
+ if( (nrhs != NR_IN) || (nlhs != NR_OUT) ) {
+ mexErrMsgTxt("Usage: [logZ,q,md] = dai(psi,method,opts)\n\n"
+ "\n"
+ "INPUT: psi = linear cell array containing the factors \n"
+ " psi{i} should be a structure with a Member field\n"
+ " and a P field, like a CPTAB).\n"
+ " method = name of the method (see README)\n"
+ " opts = string of options (see README)\n"
+ "\n"
+ "OUTPUT: logZ = approximation of the logarithm of the partition sum.\n"
+ " q = linear cell array containing all final beliefs.\n"
+ " md = maxdiff (final linf-dist between new and old single node beliefs).\n");
+ }
+
+ char *method;
+ char *opts;
+
+
+ // Get psi and construct factorgraph
+ vector<Factor> factors = mx2Factors(PSI_IN, 0);
+ FactorGraph fg(factors);
+
+ // Get method
+ buflen = mxGetN( METHOD_IN ) + 1;
+ method = (char *)mxCalloc( buflen, sizeof(char) );
+ mxGetString( METHOD_IN, method, buflen );
+
+ // Get options string
+ buflen = mxGetN( OPTS_IN ) + 1;
+ opts = (char *)mxCalloc( buflen, sizeof(char) );
+ mxGetString( OPTS_IN, opts, buflen );
+ // Convert to options object props
+ stringstream ss;
+ ss << opts;
+ PropertySet props;
+ ss >> props;
+
+ // Construct InfAlg object, init and run
+ InfAlg *obj = newInfAlg( method, fg, props );
+ obj->init();
+ obj->run();
+
+
+ // Save logZ
+ double logZ = obj->logZ();
+
+ // Save maxdiff
+ double maxdiff = obj->maxDiff();
+
+
+ // Hand over results to MATLAB
+ LOGZ_OUT = mxCreateDoubleMatrix(1,1,mxREAL);
+ *(mxGetPr(LOGZ_OUT)) = logZ;
+
+ Q_OUT = Factors2mx(obj->beliefs());
+
+ MD_OUT = mxCreateDoubleMatrix(1,1,mxREAL);
+ *(mxGetPr(MD_OUT)) = maxdiff;
+
+
+ return;
+}
--- /dev/null
+/* 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
+ it under the terms of the GNU General Public License as published by
+ the Free Software Foundation; either version 2 of the License, or
+ (at your option) any later version.
+
+ libDAI is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ GNU General Public License for more details.
+
+ You should have received a copy of the GNU General Public License
+ along with libDAI; if not, write to the Free Software
+ Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
+*/
+
+
+/*=================================================================*
+ * *
+ * This is a MEX-file for MATLAB. *
+ * *
+ * N = dai_potstrength(psi,i,j); *
+ * *
+ *=================================================================*/
+
+
+#include <iostream>
+#include "mex.h"
+#include <dai/matlab/matlab.h>
+#include <dai/factor.h>
+
+
+using namespace std;
+using namespace dai;
+
+
+/* Input Arguments */
+
+#define PSI_IN prhs[0]
+#define I_IN prhs[1]
+#define J_IN prhs[2]
+#define NR_IN 3
+
+
+/* Output Arguments */
+
+#define N_OUT plhs[0]
+#define NR_OUT 1
+
+
+void mexFunction( int nlhs, mxArray *plhs[], int nrhs, const mxArray*prhs[] )
+{
+ long ilabel, jlabel;
+
+ // Check for proper number of arguments
+ if ((nrhs != NR_IN) || (nlhs != NR_OUT)) {
+ mexErrMsgTxt("Usage: N = dai_potstrength(psi,i,j);\n\n"
+ "\n"
+ "INPUT: psi = structure with a Member field and a P field, like a CPTAB.\n"
+ " i = label of a variable in psi.\n"
+ " j = label of another variable in psi.\n"
+ "\n"
+ "OUTPUT: N = strength of psi in direction i->j.\n");
+ }
+
+ // Get input parameters
+ Factor psi = mx2Factor(PSI_IN);
+ ilabel = (long)*mxGetPr(I_IN);
+ jlabel = (long)*mxGetPr(J_IN);
+
+ // Find variable in psi with label ilabel
+ Var i;
+ for( VarSet::const_iterator n = psi.vars().begin(); n != psi.vars().end(); n++ )
+ if( n->label() == ilabel ) {
+ i = *n;
+ break;
+ }
+ assert( i.label() == ilabel );
+
+ // Find variable in psi with label jlabel
+ Var j;
+ for( VarSet::const_iterator n = psi.vars().begin(); n != psi.vars().end(); n++ )
+ if( n->label() == jlabel ) {
+ j = *n;
+ break;
+ }
+ assert( j.label() == jlabel );
+
+ // Calculate N(psi,i,j);
+ double N = psi.strength( i, j );
+
+ // Hand over result to MATLAB
+ N_OUT = mxCreateDoubleMatrix(1,1,mxREAL);
+ *(mxGetPr(N_OUT)) = N;
+
+ return;
+}
--- /dev/null
+/* 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
+ it under the terms of the GNU General Public License as published by
+ the Free Software Foundation; either version 2 of the License, or
+ (at your option) any later version.
+
+ libDAI is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ GNU General Public License for more details.
+
+ You should have received a copy of the GNU General Public License
+ along with libDAI; if not, write to the Free Software
+ Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
+*/
+
+
+/*=================================================================*
+ * *
+ * This is a MEX-file for MATLAB. *
+ * *
+ * [psi] = dai_readfg(filename); *
+ * *
+ *=================================================================*/
+
+
+#include <iostream>
+#include "mex.h"
+#include <dai/matlab/matlab.h>
+#include <dai/factorgraph.h>
+
+
+using namespace std;
+using namespace dai;
+
+
+/* Input Arguments */
+
+#define FILENAME_IN prhs[0]
+#define NR_IN 1
+
+
+/* Output Arguments */
+
+#define PSI_OUT plhs[0]
+#define NR_OUT 1
+
+
+void mexFunction( int nlhs, mxArray *plhs[], int nrhs, const mxArray*prhs[] )
+{
+ char *filename;
+
+
+ // Check for proper number of arguments
+ if ((nrhs != NR_IN) || (nlhs != NR_OUT)) {
+ mexErrMsgTxt("Usage: [psi] = dai_readfg(filename);\n\n"
+ "\n"
+ "INPUT: filename = filename of a .fg file\n"
+ "\n"
+ "OUTPUT: psi = linear cell array containing the factors\n"
+ " (psi{i} is a structure with a Member field\n"
+ " and a P field, like a CPTAB).\n");
+ }
+
+ // Get input parameters
+ size_t buflen;
+ buflen = mxGetN( FILENAME_IN ) + 1;
+ filename = (char *)mxCalloc( buflen, sizeof(char) );
+ mxGetString( FILENAME_IN, filename, buflen );
+
+
+ // Read factorgraph
+ FactorGraph fg;
+ try {
+ fg.ReadFromFile( filename );
+ } catch( std::exception &e ) {
+ mexErrMsgTxt( e.what() );
+ }
+
+
+ // Save factors
+ vector<Factor> psi;
+ for( size_t I = 0; I < fg.nrFactors(); I++ )
+ psi.push_back(fg.factor(I));
+
+
+ // Hand over results to MATLAB
+ PSI_OUT = Factors2mx(psi);
+
+
+ return;
+}
--- /dev/null
+/* 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
+ it under the terms of the GNU General Public License as published by
+ the Free Software Foundation; either version 2 of the License, or
+ (at your option) any later version.
+
+ libDAI is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ GNU General Public License for more details.
+
+ You should have received a copy of the GNU General Public License
+ along with libDAI; if not, write to the Free Software
+ Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
+*/
+
+
+/*=================================================================*
+ * *
+ * This is a MEX-file for MATLAB. *
+ * *
+ * dai_writefg(psi, filename); *
+ * *
+ *=================================================================*/
+
+
+#include <iostream>
+#include "mex.h"
+#include <dai/matlab/matlab.h>
+#include <dai/factorgraph.h>
+
+
+using namespace std;
+using namespace dai;
+
+
+/* Input Arguments */
+
+#define PSI_IN prhs[0]
+#define FILENAME_IN prhs[1]
+#define NR_IN 2
+
+
+/* Output Arguments */
+
+#define NR_OUT 0
+
+
+void mexFunction( int nlhs, mxArray * /*plhs*/[], int nrhs, const mxArray*prhs[] )
+{
+ char *filename;
+
+
+ // Check for proper number of arguments
+ if ((nrhs != NR_IN) || (nlhs != NR_OUT)) {
+ mexErrMsgTxt("Usage: dai_writefg(psi,filename);\n\n"
+ "\n"
+ "INPUT: psi = linear cell array containing the factors\n"
+ " (psi{i} should be a structure with a Member field\n"
+ " and a P field, like a CPTAB).\n"
+ " filename = filename of a .fg file\n");
+ }
+
+ // Get input parameters
+ vector<Factor> factors = mx2Factors(PSI_IN,0);
+
+ size_t buflen;
+ buflen = mxGetN( FILENAME_IN ) + 1;
+ filename = (char *)mxCalloc( buflen, sizeof(char) );
+ mxGetString( FILENAME_IN, filename, buflen );
+
+ // Construct factorgraph
+ FactorGraph fg(factors);
+
+ try {
+ fg.WriteToFile( filename );
+ } catch( std::exception &e ) {
+ mexErrMsgTxt( e.what() );
+ }
+
+ return;
+}
--- /dev/null
+/* 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
+ it under the terms of the GNU General Public License as published by
+ the Free Software Foundation; either version 2 of the License, or
+ (at your option) any later version.
+
+ libDAI is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ GNU General Public License for more details.
+
+ You should have received a copy of the GNU General Public License
+ along with libDAI; if not, write to the Free Software
+ Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
+*/
+
+
+#include <iostream>
+#include <dai/matlab/matlab.h>
+
+
+namespace dai {
+
+
+using namespace std;
+
+
+/* Convert vector<Factor> structure to a cell vector of CPTAB-like structs */
+mxArray *Factors2mx(const vector<Factor> &Ps) {
+ size_t nr = Ps.size();
+
+ mxArray *psi = mxCreateCellMatrix(nr,1);
+
+ const char *fieldnames[2];
+ fieldnames[0] = "Member";
+ fieldnames[1] = "P";
+
+ size_t I_ind = 0;
+ for( vector<Factor>::const_iterator I = Ps.begin(); I != Ps.end(); I++, I_ind++ ) {
+ mxArray *Bi = mxCreateStructMatrix(1,1,2,fieldnames);
+
+ mxArray *BiMember = mxCreateDoubleMatrix(1,I->vars().size(),mxREAL);
+ double *BiMember_data = mxGetPr(BiMember);
+ size_t i = 0;
+ vector<mwSize> dims;
+ for( VarSet::const_iterator j = I->vars().begin(); j != I->vars().end(); j++,i++ ) {
+ BiMember_data[i] = j->label();
+ dims.push_back( j->states() );
+ }
+
+ mxArray *BiP = mxCreateNumericArray(I->vars().size(), &(*(dims.begin())), mxDOUBLE_CLASS, mxREAL);
+ double *BiP_data = mxGetPr(BiP);
+ for( size_t j = 0; j < I->states(); j++ )
+ BiP_data[j] = (*I)[j];
+
+ mxSetField(Bi,0,"Member",BiMember);
+ mxSetField(Bi,0,"P",BiP);
+
+ mxSetCell(psi, I_ind, Bi);
+ }
+ return( psi );
+}
+
+
+/* Convert cell vector of CPTAB-like structs to vector<Factor> */
+vector<Factor> mx2Factors(const mxArray *psi, long verbose) {
+ set<Var> vars;
+ vector<Factor> factors;
+
+ int n1 = mxGetM(psi);
+ int n2 = mxGetN(psi);
+ if( n2 != 1 && n1 != 1 )
+ mexErrMsgTxt("psi should be a Nx1 or 1xN cell matrix.");
+ size_t nr_f = n1;
+ if( n1 == 1 )
+ nr_f = n2;
+
+ // interpret psi, linear cell array of cptabs
+ for( size_t cellind = 0; cellind < nr_f; cellind++ ) {
+ if( verbose >= 3 )
+ cout << "reading factor " << cellind << ": " << endl;
+ mxArray *cell = mxGetCell(psi, cellind);
+ mxArray *mx_member = mxGetField(cell, 0, "Member");
+ size_t nr_mem = mxGetN(mx_member);
+ double *members = mxGetPr(mx_member);
+ const mwSize *dims = mxGetDimensions(mxGetField(cell,0,"P"));
+ double *factordata = mxGetPr(mxGetField(cell, 0, "P"));
+
+ // add variables
+ VarSet factorvars;
+ vector<long> labels(nr_mem,0);
+ if( verbose >= 3 )
+ cout << " vars: ";
+ for( size_t mi = 0; mi < nr_mem; mi++ ) {
+ labels[mi] = (long)members[mi];
+ if( verbose >= 3 )
+ cout << labels[mi] << "(" << dims[mi] << ") ";
+ vars.insert( Var(labels[mi], dims[mi]) );
+ factorvars |= Var(labels[mi], dims[mi]);
+ }
+ factors.push_back(Factor(factorvars));
+
+ // calculate permutation matrix
+ vector<size_t> perm(nr_mem,0);
+ VarSet::iterator j = factorvars.begin();
+ for( size_t mi = 0; mi < nr_mem; mi++,j++ ) {
+ long gezocht = j->label();
+ vector<long>::iterator piet = find(labels.begin(),labels.end(),gezocht);
+ perm[mi] = piet - labels.begin();
+ }
+
+ if( verbose >= 3 ) {
+ cout << endl << " perm: ";
+ for( vector<size_t>::iterator r=perm.begin(); r!=perm.end(); r++ )
+ cout << *r << " ";
+ cout << endl;
+ }
+
+ // read Factor
+ vector<size_t> di(nr_mem,0);
+ size_t prod = 1;
+ for( size_t k = 0; k < nr_mem; k++ ) {
+ di[k] = dims[k];
+ prod *= dims[k];
+ }
+ Permute permindex( di, perm );
+ for( size_t li = 0; li < prod; li++ )
+ factors.back()[permindex.convert_linear_index(li)] = factordata[li];
+ }
+
+ if( verbose >= 3 ) {
+ for(vector<Factor>::const_iterator I=factors.begin(); I!=factors.end(); I++ )
+ cout << *I << endl;
+ }
+
+ return( factors );
+}
+
+
+/* Convert CPTAB-like struct to Factor */
+Factor mx2Factor(const mxArray *psi) {
+ mxArray *mx_member = mxGetField(psi, 0, "Member");
+ size_t nr_mem = mxGetN(mx_member);
+ double *members = mxGetPr(mx_member);
+ const mwSize *dims = mxGetDimensions(mxGetField(psi,0,"P"));
+ double *factordata = mxGetPr(mxGetField(psi, 0, "P"));
+
+ // add variables
+ VarSet vars;
+ vector<long> labels(nr_mem,0);
+ for( size_t mi = 0; mi < nr_mem; mi++ ) {
+ labels[mi] = (long)members[mi];
+ vars |= Var(labels[mi], dims[mi]);
+ }
+ Factor factor(vars);
+
+ // calculate permutation matrix
+ vector<size_t> perm(nr_mem,0);
+ VarSet::iterator j = vars.begin();
+ for( size_t mi = 0; mi < nr_mem; mi++,j++ ) {
+ long gezocht = j->label();
+ vector<long>::iterator piet = find(labels.begin(),labels.end(),gezocht);
+ perm[mi] = piet - labels.begin();
+ }
+
+ // read Factor
+ vector<size_t> di(nr_mem,0);
+ size_t prod = 1;
+ for( size_t k = 0; k < nr_mem; k++ ) {
+ di[k] = dims[k];
+ prod *= dims[k];
+ }
+ Permute permindex( di, perm );
+ for( size_t li = 0; li < prod; li++ )
+ factor[permindex.convert_linear_index(li)] = factordata[li];
+
+ return( factor );
+}
+
+
+}
cout << "Girth: infinity" << endl;
}
+ map<size_t,size_t> facsizes;
+ for( size_t I = 0; I < fg.nrFactors(); I++ ) {
+ size_t Isize = fg.factor(I).vars().size();
+ if( facsizes.count( Isize ) )
+ facsizes[Isize]++;
+ else
+ facsizes[Isize] = 1;
+ }
+ cout << "Factor sizes: ";
+ for( map<size_t,size_t>::const_iterator it = facsizes.begin(); it != facsizes.end(); it++ )
+ cout << it->first << "(" << it->second << ") ";
+ cout << endl;
+
return 0;
}
}
projects / libdai.git / commitdiff