Removed remove_short_loops functionality.

diff --git a/ChangeLog b/ChangeLog
index 3db77fc..00460a0 100644 (file)
--- a/ChangeLog
+++ b/ChangeLog
@@ -4,6 +4,7 @@ libDAI-0.2.2 (2008-??-??)
 * Now compiles also under Visual C++.
 * Added Exceptions framework.
 * Replaced ENUM2,ENUM3,ENUM4,ENUM5,ENUM6 by single DAI_ENUM macro.
+* Removed utils/remove_short_loops and matlab/remove_short_loops.
 * Added more features to utils/createfg for creating factor graphs.
 * Pervasive change of BipartiteGraph implementation (based on an idea by
   Giuseppe Passino). BipartiteGraph no longer stores the node properties 
@@ -50,6 +51,14 @@ libDAI-0.2.2 (2008-??-??)
   std::set<Var>, which yields a significant speed improvement.
 * Improved MaxSpanningTreePrims algorithm (uses boost::graph)
 * Small optimization in Diffs
+* Replaced Complex with real numbers (negative potentials is just not
+  used enough to warrant the additional "complexity" :))
+* Moved Properties and MaxDiff frameworks from InfAlg to each individual
+  inference algorithm, because the Properties framework was not as 
+  convenient as I hoped, and not every inference algorithm needs a maxdiff
+  variable. Also, replaced some FactorGraph functionality in InfAlg by a
+  function that returns the FactorGraph. The result is cleaner (less 
+  entangled) code.
 * Improved ClusterGraph implementation, yielding significant speedups
   for the JunctionTree algorithm on large factorgraphs.
 * Improved documetation
@@ -71,6 +80,8 @@ libDAI-0.2.2 (2008-??-??)
       removed ExactMarginal(const VarSet &)
       removed ExactlogZ()
       moved isConnected() to BipartiteGraph
+      removed updatedFactor(size_t)
+      removed _normtype and NormType()
   - RegionGraph::
       nr_ORs() -> nrORs()
       nr_IRs() -> nrIRs()
@@ -85,6 +96,7 @@ libDAI-0.2.2 (2008-??-??)
   - Factor::max() -> Factor::maxVal()
   - toc() in util.h now returns seconds as a double
   - VarSet::operator&&
+  - Properties -> PropertySet
 
 
 libDAI-0.2.1 (2008-05-26)

diff --git a/Makefile b/Makefile
index 5740a10..bde5a6f 100644 (file)
--- a/Makefile
+++ b/Makefile
@@ -109,14 +109,14 @@ endif
 all : $(TARGETS)
        echo -e "\a"
 
-matlabs : matlab/dai.$(MEXEXT) matlab/dai_readfg.$(MEXEXT) matlab/dai_writefg.$(MEXEXT) matlab/dai_removeshortloops.$(MEXEXT) matlab/dai_potstrength.$(MEXEXT)
+matlabs : matlab/dai.$(MEXEXT) matlab/dai_readfg.$(MEXEXT) matlab/dai_writefg.$(MEXEXT) matlab/dai_potstrength.$(MEXEXT)
 
 $(LIB)/libdai.a : bipgraph.o daialg.o alldai.o clustergraph.o factorgraph.o properties.o regiongraph.o util.o weightedgraph.o x2x.o exceptions.o $(OBJECTS)
        ar rcs $(LIB)/libdai.a bipgraph.o daialg.o alldai.o clustergraph.o factorgraph.o properties.o regiongraph.o util.o weightedgraph.o x2x.o exceptions.o $(OBJECTS)
 
 tests : tests/test
 
-utils : utils/createfg utils/fg2dot utils/remove_short_loops utils/fginfo
+utils : utils/createfg utils/fg2dot utils/fginfo
 
 testregression : tests/test
        echo Testing...this can take a while...
@@ -126,7 +126,7 @@ doc : $(INC)/*.h $(SRC)/*.cpp doxygen.conf
        doxygen doxygen.conf
 
 clean :
-       rm *.o example matlab/*.$(MEXEXT) matlab/*.o tests/test utils/fg2dot utils/createfg utils/remove_short_loops utils/fginfo $(LIB)/libdai.a; echo
+       rm *.o example matlab/*.$(MEXEXT) matlab/*.o tests/test utils/fg2dot utils/createfg utils/fginfo $(LIB)/libdai.a; echo
        rm -R doc; echo
 
 bipgraph.o : $(SRC)/bipgraph.cpp $(HEADERS)
@@ -208,9 +208,6 @@ matlab/dai_readfg.$(MEXEXT) : matlab/dai_readfg.cpp $(HEADERS) factorgraph.o mat
 matlab/dai_writefg.$(MEXEXT) : matlab/dai_writefg.cpp $(HEADERS) factorgraph.o matlab/matlab.o
        $(MEX) $(MEXFLAGS) -o matlab/dai_writefg matlab/dai_writefg.cpp factorgraph.o matlab/matlab.o
 
-matlab/dai_removeshortloops.$(MEXEXT) : matlab/dai_removeshortloops.cpp $(HEADERS) factorgraph.o matlab/matlab.o
-       $(MEX) $(MEXFLAGS) -o matlab/dai_removeshortloops matlab/dai_removeshortloops.cpp factorgraph.o matlab/matlab.o
-
 matlab/dai_potstrength.$(MEXEXT) : matlab/dai_potstrength.cpp $(HEADERS) matlab/matlab.o
        $(MEX) $(MEXFLAGS) -o matlab/dai_potstrength matlab/dai_potstrength.cpp matlab/matlab.o
 
@@ -227,8 +224,5 @@ utils/createfg : utils/createfg.cpp $(HEADERS) factorgraph.o weightedgraph.o uti
 utils/fg2dot : utils/fg2dot.cpp $(HEADERS) factorgraph.o exceptions.o
        $(CC) $(CCFLAGS) -o utils/fg2dot utils/fg2dot.cpp factorgraph.o exceptions.o
 
-utils/remove_short_loops : utils/remove_short_loops.cpp $(HEADERS) factorgraph.o exceptions.o
-       $(CC) $(CCFLAGS) -o utils/remove_short_loops utils/remove_short_loops.cpp factorgraph.o exceptions.o
-
 utils/fginfo : utils/fginfo.cpp $(HEADERS) factorgraph.o bipgraph.o exceptions.o
        $(CC) $(CCFLAGS) -o utils/fginfo utils/fginfo.cpp factorgraph.o bipgraph.o exceptions.o

diff --git a/STATUS b/STATUS
index 3c2a492..be9e25f 100644 (file)
--- a/STATUS
+++ b/STATUS
@@ -40,6 +40,7 @@ var.h
 utils/createfg.cpp
 exceptions.h
 exceptions.cpp
+enum.h
 
 DOCUMENTATION READY:
 - bipgraph.h, bipgraph.cpp

diff --git a/matlab/dai_removeshortloops.cpp b/matlab/dai_removeshortloops.cpp
deleted file mode 100644 (file)
index 4c0ac1e..0000000
--- a/matlab/dai_removeshortloops.cpp
+++ /dev/null
@@ -1,78 +0,0 @@
-/*  Copyright (C) 2006-2008  Joris Mooij  [j dot mooij at science dot ru dot nl]
-    Radboud University Nijmegen, The Netherlands
-    
-    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_out] = dai_removeshortloops(psi_in);                     *
- *                                                                 * 
- *=================================================================*/
-
-
-#include <iostream>
-#include "mex.h"
-#include "matlab.h"
-#include "factorgraph.h"
-
-
-using namespace std;
-
-
-/* Input Arguments */
-
-#define PSI_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[] ) { 
-    // Check for proper number of arguments
-    if ((nrhs != NR_IN) || (nlhs != NR_OUT)) { 
-        mexErrMsgTxt("Usage: [psi_out] = dai_removeshortloops(psi_in);\n\n"
-        "\n"
-        "INPUT:  psi_in     = 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"
-        "\n"
-        "OUTPUT: psi_out    = linear cell array containing the factors of psi_in,\n"
-        "                     where factors have been merged to prevent short loops\n"
-        "                     of length 4 in the factor graph (i.e. loops of type\n"
-        "                     var1-factor1-var2-factor2-var1),\n");
-    } 
-    
-    // Get the factors from PSI_IN
-    vector<Factor> psi = mx2Factors(PSI_IN, 0);
-
-    // Remove the short loops
-    RemoveShortLoops(psi);
-
-    // Hand over results to MATLAB
-    PSI_OUT = Factors2mx(psi);
-
-    
-    return;
-}

diff --git a/matlab/dai_removeshortloops.m b/matlab/dai_removeshortloops.m
deleted file mode 100644 (file)
index 264ed7e..0000000
--- a/matlab/dai_removeshortloops.m
+++ /dev/null
@@ -1,10 +0,0 @@
-% [psi_out] = dai_removeshortloops (psi_in)
-%       
-%    INPUT:  psi_in     = linear cell array containing the factors
-%                         (psi{i} is a structure with a Member field
-%                         and a P field, like a CPTAB).
-%      
-%    OUTPUT: psi_out    = linear cell array containing the factors of psi_in,
-%                         where factors have been merged to prevent short loops
-%                         of length 4 in the factor graph (i.e. loops of type
-%                         var1-factor1-var2-factor2-var1).

diff --git a/utils/remove_short_loops.cpp b/utils/remove_short_loops.cpp
deleted file mode 100644 (file)
index 09427df..0000000
--- a/utils/remove_short_loops.cpp
+++ /dev/null
@@ -1,65 +0,0 @@
-/*  Copyright (C) 2006-2008  Joris Mooij  [j dot mooij at science dot ru dot nl]
-    Radboud University Nijmegen, The Netherlands
-    
-    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 <cstdlib>
-#include <dai/factorgraph.h>
-
-
-using namespace dai;
-using namespace std;
-
-
-int main( int argc, char *argv[] ) {
-    if( argc != 3 ) {
-        cout << "Usage: " << argv[0] << " <in.fg> <out.fg>" << endl << endl;
-        cout << "Merges short loops (of length 4 in the factor graph) in <in.fg>" << endl;
-        cout << "and writes result to <out.fg>." << endl;
-        cout << "Returns 2 in case of error reading <in.fg>, 1 if there are no" << endl;
-        cout << "short loops present and 0 if short loops have been merged." << endl;
-        return 1;
-    } else {
-        // Read factorgraph
-        FactorGraph fg;
-        char *infile = argv[1];
-
-        if( fg.ReadFromFile( infile ) ) {
-            cerr << "Error reading file " << infile << endl;
-            return 2;
-        } else {
-            vector<Factor> fg_facs;
-
-            fg_facs.reserve( fg.nrFactors() );
-            for( size_t I = 0; I < fg.nrFactors(); I++ )
-                fg_facs.push_back( fg.factor(I) );
-
-            if( hasShortLoops( fg_facs) ) {
-                RemoveShortLoops( fg_facs );
-                FactorGraph newfg( fg_facs );
-                newfg.WriteToFile( argv[2] );
-                return 0;
-            } else {
-                fg.WriteToFile( argv[2] );
-                return 1;
-            }
-        }
-    }
-}