Add support to markov networks

packages/CLPBN/clpbn/bp/FactorGraph.cpp

@@ -9,6 +9,7 @@
 #include "FactorGraph.h"
 #include "Factor.h"
 #include "BayesNet.h"
+#include "BayesBall.h"
 #include "Util.h"
 
 
@@ -205,13 +206,13 @@ FactorGraph::readFromLibDaiFormat (const char* fileName)
         var = new FgVarNode (vids[j], dsize);
         addVariable (var);
       } else {
-        if (var->nrStates() != dsize) {
+        if (var->range() != dsize) {
           cerr << "error: variable `" << vids[j] << "' appears in two or " ;
           cerr << "more factors with different domain sizes" << endl;
         }
       }
       neighs.push_back (var);
-      nParams *= var->nrStates();
+      nParams *= var->range();
     }
     Params params (nParams, 0);
     unsigned nNonzeros;
@@ -274,6 +275,30 @@ FactorGraph::addFactor (FgFacNode* fn)
 
 
 
+void
+FactorGraph::addFactor (const Factor& factor)
+{
+  FgFacNode* fn = new FgFacNode (factor);
+  addFactor (fn);
+  const VarIds& vids = factor.arguments();
+  for (unsigned i = 0; i < vids.size(); i++) {
+    bool found = false;
+    for (unsigned j = 0; j < varNodes_.size(); j++) {
+      if (varNodes_[j]->varId() == vids[i]) {
+        addEdge (varNodes_[j], fn);
+        found = true;
+      }
+    }
+    if (found == false) {
+      FgVarNode* vn = new FgVarNode (vids[i], factor.range (i));
+      addVariable (vn);
+      addEdge (vn, fn);
+    }
+  }
+}
+
+
+
 void
 FactorGraph::addEdge (FgVarNode* vn, FgFacNode* fn)
 {
@@ -322,6 +347,26 @@ FactorGraph::isTree (void) const
 
 
 
+DAGraph&
+FactorGraph::getStructure (void)
+{
+  assert (fromBayesNet_);
+  if (structure_.empty()) {
+    for (unsigned i = 0; i < varNodes_.size(); i++) {
+      structure_.addNode (new DAGraphNode (varNodes_[i]));
+    }
+    for (unsigned i = 0; i < facNodes_.size(); i++) {
+      const VarIds& vids = facNodes_[i]->factor()->arguments();
+      for (unsigned j = 1; j < vids.size(); j++) {
+        structure_.addEdge (vids[j], vids[0]);
+      }
+    }
+  }
+  return structure_;
+}
+
+
+
 void
 FactorGraph::setIndexes (void)
 {
@@ -339,11 +384,11 @@ void
 FactorGraph::printGraphicalModel (void) const
 {
   for (unsigned i = 0; i < varNodes_.size(); i++) {
-    cout << "VarId       = " << varNodes_[i]->varId() << endl;
-    cout << "Label       = " << varNodes_[i]->label() << endl;
-    cout << "Nr States   = " << varNodes_[i]->nrStates() << endl;
-    cout << "Evidence    = " << varNodes_[i]->getEvidence() << endl;
-    cout << "Factors     = " ;
+    cout << "var id   = " << varNodes_[i]->varId() << endl;
+    cout << "label    = " << varNodes_[i]->label() << endl;
+    cout << "range    = " << varNodes_[i]->range() << endl;
+    cout << "evidence = " << varNodes_[i]->getEvidence() << endl;
+    cout << "factors  = " ;
     for (unsigned j = 0; j < varNodes_[i]->neighbors().size(); j++) {
       cout << varNodes_[i]->neighbors()[j]->getLabel() << " " ;
     }
@@ -351,7 +396,6 @@ FactorGraph::printGraphicalModel (void) const
   }
   for (unsigned i = 0; i < facNodes_.size(); i++) {
     facNodes_[i]->factor()->print();
-    cout << endl;
   }
 }
 
@@ -366,22 +410,18 @@ FactorGraph::exportToGraphViz (const char* fileName) const
     cerr << "FactorGraph::exportToDotFile()" << endl;
     abort();
   }
-
   out << "graph \"" << fileName << "\" {" << endl;
-
   for (unsigned i = 0; i < varNodes_.size(); i++) {
     if (varNodes_[i]->hasEvidence()) {
       out << '"' << varNodes_[i]->label() << '"' ;
       out << " [style=filled, fillcolor=yellow]" << endl;
     }
   }
-
   for (unsigned i = 0; i < facNodes_.size(); i++) {
     out << '"' << facNodes_[i]->getLabel() << '"' ;
     out << " [label=\"" << facNodes_[i]->getLabel(); 
     out << "\"" << ", shape=box]" << endl;
   }
-
   for (unsigned i = 0; i < facNodes_.size(); i++) {
     const FgVarSet& myVars = facNodes_[i]->neighbors();
     for (unsigned j = 0; j < myVars.size(); j++) {
@@ -390,7 +430,6 @@ FactorGraph::exportToGraphViz (const char* fileName) const
       out << '"' << myVars[j]->label() << '"' << endl;
     }
   }
-
   out << "}" << endl;
   out.close();
 }
@@ -410,7 +449,7 @@ FactorGraph::exportToUaiFormat (const char* fileName) const
   out << "MARKOV" << endl;
   out << varNodes_.size() << endl;
   for (unsigned i = 0; i < varNodes_.size(); i++) {
-    out << varNodes_[i]->nrStates() << " " ;
+    out << varNodes_[i]->range() << " " ;
   }
   out << endl;
 
@@ -459,7 +498,7 @@ FactorGraph::exportToLibDaiFormat (const char* fileName) const
     }
     out << endl;
     for (unsigned j = 0; j < factorVars.size(); j++) {
-      out << factorVars[j]->nrStates() << " " ;
+      out << factorVars[j]->range() << " " ;
     }
     out << endl;
     Params params = facNodes_[i]->factor()->params();
@@ -496,10 +535,11 @@ FactorGraph::containsCycle (void) const
 
 
 bool
-FactorGraph::containsCycle (const FgVarNode* v,
-                            const FgFacNode* p,
-                            vector<bool>& visitedVars,
-                            vector<bool>& visitedFactors) const
+FactorGraph::containsCycle (
+    const FgVarNode* v,
+    const FgFacNode* p,
+    vector<bool>& visitedVars,
+    vector<bool>& visitedFactors) const
 {
   visitedVars[v->getIndex()] = true;
   const FgFacSet& adjacencies = v->neighbors();
@@ -520,10 +560,11 @@ FactorGraph::containsCycle (const FgVarNode* v,
 
 
 bool
-FactorGraph::containsCycle (const FgFacNode* v,
-                            const FgVarNode* p,
-                            vector<bool>& visitedVars,
-                            vector<bool>& visitedFactors) const
+FactorGraph::containsCycle (
+    const FgFacNode* v,
+    const FgVarNode* p,
+    vector<bool>& visitedVars,
+    vector<bool>& visitedFactors) const
 {
   visitedFactors[v->getIndex()] = true;
   const FgVarSet& adjacencies = v->neighbors();