Fixed NAN related bugs for Visual C++.

diff --git a/Makefile.win b/Makefile.win
index 7a12f2e..77252af 100755 (executable)
--- a/Makefile.win
+++ b/Makefile.win
@@ -135,7 +135,7 @@ doc : $(INC)/*.h $(SRC)/*.cpp doxygen.conf
        doxygen doxygen.conf\r
 \r
 clean :\r
        doxygen doxygen.conf\r
 \r
 clean :\r

-       del *.obj example.exe matlab\*.$(MEXEXT) matlab\*.obj tests/test.exe utils\fg2dot.exe utils\createfg.exe utils\remove_short_loops.exe utils\fginfo.exe $(LIB)\libdai.lib\r
+       del *.obj example.exe matlab\*.$(MEXEXT) matlab\*.obj tests\test.exe utils\fg2dot.exe utils\createfg.exe utils\remove_short_loops.exe utils\fginfo.exe $(LIB)\libdai.lib\r

 \r
 \r
 bipgraph.obj : $(SRC)/bipgraph.cpp $(HEADERS)\r
 \r
 \r
 bipgraph.obj : $(SRC)/bipgraph.cpp $(HEADERS)\r

diff --git a/STATUS b/STATUS
new file mode 100644 (file)
index 0000000..f34afcc
--- /dev/null
+++ b/STATUS
@@ -0,0 +1,55 @@
+- Idea: a FactorGraph and a RegionGraph are often equipped with
+extra properties for nodes and edges. The code to initialize those
+is often quite similar; maybe this can be abstracted to classes
+like ExtFactorGraph and ExtRegionGraph (Ext stands for Extended), e.g.
+template <typename NodeProperties, typename EdgeProperties>
+class ExtFactorGraph : public FactorGraph {
+       public:
+               std::vector<NodeProperties>               nodeProps;
+               std::vector<std::vector<EdgeProperties> > edgeProps;
+       // blabla
+}
+A disadvantage of this approach may be worse cachability.
+- http://www.boost.org/development/requirements.html#Design_and_Programming
+- Would it be a good idea to cache second-order neighborhoods (delta's) in BipGraph?
+- Would it be a good idea to add the variable label -> index hashmap in FactorGraph,
+  to replace the linear searches that are performed every time for findVar()?
+  No, a better idea is to avoid calls to findVar() as much as possible.
+- Can the FactorGraph constructors be optimized further?
+- Move FactorGraph::_normType somewhere else (maybe to InfAlg or DAIAlg<T>)
+- Remove updatedFactor
+- Add Exceptions framework; this can e.g. be used as follows: if *.logZ() is
+called, it can return an exception if this method is not implemented, and the
+caller can catch this exception and handle it correctly. Then, you don't need
+a hasLogZ function/constant that tells whether this functionality is available.
+- Add an option to tests/test that it doesn't report the time needed; this is
+useful for the regression testing.
+
+DONE IN PREVIOUS COMMITS:
+- Added a few methods to BipartiteGraph
+- Improved ClusterGraph implementation (taken from SVN head)
+- Improved MaxSpanningTree algorithm (using boost::graph library, taken from SVN head)
+- Updated doxygen.conf
+- Made compatible with Visual C++
+- Merged improved index.h from svn
+- Rename stateSpace -> states
+- Optimized Diffs
+- Renamed Regenerate() -> create() 
+
+TODO FOR RELEASE:
+- Test Visual C++ compatibility
+- Figure out which libraries are required and document in README
+  boost headers, boost::program_options library
+
+FILES IN SVN HEAD THAT ARE NO LONGER RELEVANT FOR GIT MASTER
+diffs.h
+index.h
+util.h
+util.cpp
+bipgraph.h
+weightedgraph.h
+clustergraph.h
+clustergraph.cpp
+varset.h
+var.h
+utils/createfg.cpp

diff --git a/include/dai/lc.h b/include/dai/lc.h
index 7ded83e..2de05f5 100644 (file)
--- a/include/dai/lc.h
+++ b/include/dai/lc.h
@@ -83,7 +83,7 @@ class LC : public DAIAlgFG {
         Factor belief (const Var &n) const { return( _beliefs[findVar(n)] ); }
         Factor belief (const VarSet &/*ns*/) const { assert( 0 == 1 ); return Factor(); }
         std::vector<Factor> beliefs() const { return _beliefs; }
         Factor belief (const Var &n) const { return( _beliefs[findVar(n)] ); }
         Factor belief (const VarSet &/*ns*/) const { assert( 0 == 1 ); return Factor(); }
         std::vector<Factor> beliefs() const { return _beliefs; }

-        Complex logZ() const { return NAN; }
+        Complex logZ() const { /*assert( 0 == 1 );*/ return 0.0; }

         void CalcBelief (size_t i);
         const Factor & belief (size_t i) const { return _beliefs[i]; };
         const Factor & pancake (size_t i) const { return _pancakes[i]; };
         void CalcBelief (size_t i);
         const Factor & belief (size_t i) const { return _beliefs[i]; };
         const Factor & pancake (size_t i) const { return _pancakes[i]; };

diff --git a/include/dai/mr.h b/include/dai/mr.h
index eb0726d..d786527 100644 (file)
--- a/include/dai/mr.h
+++ b/include/dai/mr.h
@@ -73,7 +73,7 @@ class MR : public DAIAlgFG {
         Factor belief( const Var &n ) const;
         Factor belief( const VarSet &/*ns*/ ) const { assert( 0 == 1 ); return Factor(); }
         std::vector<Factor> beliefs() const;
         Factor belief( const Var &n ) const;
         Factor belief( const VarSet &/*ns*/ ) const { assert( 0 == 1 ); return Factor(); }
         std::vector<Factor> beliefs() const;

-        Complex logZ() const { return NAN; }
+        Complex logZ() const { /*assert( 0 == 1 );*/ return 0.0; }

         void init() { assert( checkProperties() ); }
         static const char *Name;
         std::string identify() const;
         void init() { assert( checkProperties() ); }
         static const char *Name;
         std::string identify() const;

diff --git a/include/dai/util.h b/include/dai/util.h
index 4c093e0..900f275 100644 (file)
--- a/include/dai/util.h
+++ b/include/dai/util.h
@@ -32,7 +32,6 @@
 
 
 #ifdef WINDOWS
 
 
 #ifdef WINDOWS

-    #include <xmath.h> // for NAN

     #include <map>
 #else
     #include <tr1/unordered_map>
     #include <map>
 #else
     #include <tr1/unordered_map>

diff --git a/src/lc.cpp b/src/lc.cpp
index 57c84d5..e3349ce 100644 (file)
--- a/src/lc.cpp
+++ b/src/lc.cpp
@@ -282,7 +282,7 @@ double LC::run() {
         }
     if( hasNaNs ) {
         cout << "LC::run:  initial _pancakes has NaNs!" << endl;
         }
     if( hasNaNs ) {
         cout << "LC::run:  initial _pancakes has NaNs!" << endl;

-        return NAN;
+        return -1.0;

     }
 
     size_t nredges = nrEdges();
     }
 
     size_t nredges = nrEdges();


@@ -306,7 +306,7 @@ double LC::run() {
             size_t _I = update_seq[t].second;
             _pancakes[i] = NewPancake( i, _I, hasNaNs);
             if( hasNaNs )
             size_t _I = update_seq[t].second;
             _pancakes[i] = NewPancake( i, _I, hasNaNs);
             if( hasNaNs )

-                return NAN;
+                return -1.0;

             CalcBelief( i );
         }
 
             CalcBelief( i );
         }
 

diff --git a/src/mr.cpp b/src/mr.cpp
index 5a3a7c8..2c84702 100644 (file)
--- a/src/mr.cpp
+++ b/src/mr.cpp
@@ -562,7 +562,7 @@ double MR::run() {
 
         return 0.0;
     } else
 
         return 0.0;
     } else

-        return NAN;
+        return -1.0;

 }
 
 
 }
 
 

diff --git a/src/regiongraph.cpp b/src/regiongraph.cpp
index 79fb5f9..8078279 100644 (file)
--- a/src/regiongraph.cpp
+++ b/src/regiongraph.cpp
@@ -114,7 +114,7 @@ RegionGraph::RegionGraph( const FactorGraph &fg, const std::vector<VarSet> &cl )
     // Create inner regions - store them in the bipartite graph
     IRs.reserve( betas.size() );
     for( set<VarSet>::const_iterator beta = betas.begin(); beta != betas.end(); beta++ )
     // Create inner regions - store them in the bipartite graph
     IRs.reserve( betas.size() );
     for( set<VarSet>::const_iterator beta = betas.begin(); beta != betas.end(); beta++ )

-        IRs.push_back( Region(*beta,NAN) );
+        IRs.push_back( Region(*beta,0.0) );

     
     // Create edges
     vector<pair<size_t,size_t> > edges;
     
     // Create edges
     vector<pair<size_t,size_t> > edges;


@@ -142,8 +142,9 @@ void RegionGraph::Calc_Counting_Numbers() {
     // Calculates counting numbers of inner regions based upon counting numbers of outer regions
     
     vector<vector<size_t> > ancestors(nrIRs());
     // Calculates counting numbers of inner regions based upon counting numbers of outer regions
     
     vector<vector<size_t> > ancestors(nrIRs());

+    vector<bool> assigned(nrIRs(), false);

     for( size_t beta = 0; beta < nrIRs(); beta++ ) {
     for( size_t beta = 0; beta < nrIRs(); beta++ ) {

-        IR(beta).c() = NAN;
+        IR(beta).c() = 0.0;

         for( size_t beta2 = 0; beta2 < nrIRs(); beta2++ )
             if( (beta2 != beta) && IR(beta2) >> IR(beta) )
                 ancestors[beta].push_back(beta2);
         for( size_t beta2 = 0; beta2 < nrIRs(); beta2++ )
             if( (beta2 != beta) && IR(beta2) >> IR(beta) )
                 ancestors[beta].push_back(beta2);


@@ -153,18 +154,19 @@ void RegionGraph::Calc_Counting_Numbers() {
     do {
         new_counting = false;
         for( size_t beta = 0; beta < nrIRs(); beta++ ) {
     do {
         new_counting = false;
         for( size_t beta = 0; beta < nrIRs(); beta++ ) {

-            if( isnan( IR(beta).c() ) ) {
-                bool has_nan_ancestor = false;
-                for( vector<size_t>::const_iterator beta2 = ancestors[beta].begin(); (beta2 != ancestors[beta].end()) && !has_nan_ancestor; beta2++ )
-                    if( isnan( IR(*beta2).c() ) )
-                        has_nan_ancestor = true;
-                if( !has_nan_ancestor ) {
+            if( !assigned[beta] ) {
+                bool has_unassigned_ancestor = false;
+                for( vector<size_t>::const_iterator beta2 = ancestors[beta].begin(); (beta2 != ancestors[beta].end()) && !has_unassigned_ancestor; beta2++ )
+                    if( !assigned[*beta2] )
+                        has_unassigned_ancestor = true;
+                if( !has_unassigned_ancestor ) {

                     double c = 1.0;
                     foreach( const Neighbor &alpha, nbIR(beta) )
                         c -= OR(alpha).c();
                     for( vector<size_t>::const_iterator beta2 = ancestors[beta].begin(); beta2 != ancestors[beta].end(); beta2++ )
                         c -= IR(*beta2).c();
                     IR(beta).c() = c;
                     double c = 1.0;
                     foreach( const Neighbor &alpha, nbIR(beta) )
                         c -= OR(alpha).c();
                     for( vector<size_t>::const_iterator beta2 = ancestors[beta].begin(); beta2 != ancestors[beta].end(); beta2++ )
                         c -= IR(*beta2).c();
                     IR(beta).c() = c;

+                    assigned[beta] = true;

                     new_counting = true;
                 }
             }
                     new_counting = true;
                 }
             }

diff --git a/tests/testall.bat b/tests/testall.bat
new file mode 100755 (executable)
index 0000000..0241a04
--- /dev/null
+++ b/tests/testall.bat
@@ -0,0 +1 @@
+test --aliases aliases.conf --filename %1 --methods JTREE_HUGIN JTREE_SHSH BP_SEQFIX BP_SEQRND BP_SEQMAX BP_PARALL BP_SEQFIX_LOG BP_SEQRND_LOG BP_SEQMAX_LOG BP_PARALL_LOG MF_SEQRND TREEEP TREEEPWC GBP_MIN GBP_DELTA GBP_LOOP3 GBP_LOOP4 HAK_MIN HAK_DELTA HAK_LOOP3 HAK_LOOP4 MR_RESPPROP_FULL MR_CLAMPING_FULL MR_EXACT_FULL MR_RESPPROP_LINEAR MR_CLAMPING_LINEAR MR_EXACT_LINEAR LCBP_FULLCAV_SEQFIX LCBP_FULLCAVin_SEQFIX LCBP_FULLCAV_SEQRND LCBP_FULLCAVin_SEQRND LCBP_FULLCAV_NONE LCBP_FULLCAVin_NONE LCBP_PAIRCAV_SEQFIX LCBP_PAIRCAVin_SEQFIX LCBP_PAIRCAV_SEQRND LCBP_PAIRCAVin_SEQRND LCBP_PAIRCAV_NONE LCBP_PAIRCAVin_NONE LCBP_UNICAV_SEQFIX LCBP_UNICAV_SEQRND