Experimental code for Tiago Gomes bp solver.

2011-02-23 15:31:56 +00:00
parent 4a5ba35937
commit 29e46cbab9
39 changed files with 39941 additions and 245 deletions
--- a/packages/CLPBN/clpbn/bp/BifInterface.cpp
+++ b/packages/CLPBN/clpbn/bp/BifInterface.cpp
@@ -0,0 +1,117 @@
+#include <iostream>
+#include <sstream>
+#include <map>
+
+#include "xmlParser/xmlParser.h"
+
+#include "BifInterface.h"
+#include "BayesianNetwork.h"
+#include "BayesianNode.h" 
+
+
+void
+BifInterface::createNetworkFromXML (BayesianNetwork* bn, const char* fileName)
+{
+  map<string, vector<string> > domains;
+  XMLNode xMainNode = XMLNode::openFileHelper (fileName, "BIF");
+  // only the first network is parsed, others are ignored
+  XMLNode xNode = xMainNode.getChildNode ("NETWORK");
+  int nVars = xNode.nChildNode ("VARIABLE");
+  for (int i = 0; i < nVars; i++) {
+    XMLNode var = xNode.getChildNode ("VARIABLE", i);
+    string type = var.getAttribute ("TYPE");
+    if (type != "nature") {
+      cerr << "error: only \"nature\" variables are supported" << endl;
+      abort();
+    }
+    vector<string> domain;
+    string varName = var.getChildNode("NAME").getText();
+    int domainSize = var.nChildNode ("OUTCOME");
+    for (int j = 0; j < domainSize; j++) {
+      domain.push_back (var.getChildNode("OUTCOME", j).getText());
+    }
+    domains.insert (make_pair (varName, domain));
+  }
+
+  int nDefs = xNode.nChildNode ("DEFINITION");
+  if (nVars != nDefs) {
+    cerr << "error: different number of variables and definitions";
+    cerr << endl;
+  }
+
+  for (int i = 0; i < nDefs; i++) {
+    XMLNode def = xNode.getChildNode ("DEFINITION", i);
+    string nodeName = def.getChildNode("FOR").getText();
+    map<string, vector<string> >::const_iterator iter = domains.find (nodeName);
+    if (iter == domains.end()) {
+      cerr << "error: unknow variable `" << nodeName << "'" << endl;
+      abort();
+    }
+    vector<BayesianNode*> parents;
+    int nParams = iter->second.size();
+    for (int j = 0; j < def.nChildNode ("GIVEN"); j++) {
+      string parentName = def.getChildNode("GIVEN", j).getText();
+      BayesianNode* parentNode = bn->getNode (parentName);
+      if (parentNode) {
+        nParams *= parentNode->getDomainSize();
+        parents.push_back (parentNode);
+      }
+      else {
+        cerr << "error: unknow variable `" << parentName << "'" << endl;
+        abort();
+      }
+    }
+
+    int c = 0;
+    double* params = new double [nParams];
+    stringstream s (def.getChildNode("TABLE").getText());
+    while (!s.eof() && c < nParams) {
+      s >> params[c];
+      c++;
+    }
+    if (c != nParams) {
+      cerr << "error: invalid number of parameters " ;
+      cerr << "for variable `" << nodeName << "'" << endl;
+      abort();
+    }
+   
+    params = reorderParameters (params, nParams, iter->second.size());
+    bn->addNode (nodeName, parents, params, nParams, iter->second);
+  }
+}
+
+
+double*
+BifInterface::reorderParameters (double* params, 
+                                 int nParams,
+                                 int domainSize)
+{
+  // the interchange format for bayesian networks saves the probabilities 
+  // in the following order:
+  // p(a1|b1,c1) p(a2|b1,c1) p(a1|b1,c2) p(a2|b1,c2) p(a1|b2,c1) p(a2|b2,c1)
+  // p(a1|b2,c2) p(a2|b2,c2).
+  //
+  // however, in clpbn we keep the probabilities in this order:
+  // p(a1|b1,c1) p(a1|b1,c2) p(a1|b2,c1) p(a1|b2,c2) p(a2|b1,c1) p(a2|b1,c2)
+  // p(a2|b2,c1) p(a2|b2,c2).
+
+  int count         = 0;
+  int index1        = 0;
+  int index2        = 0;
+  int rowSize       = nParams / domainSize;
+  double* reordered = new double [nParams];
+
+  while (index1 < nParams) {
+    index2 = count;
+    for (int i = 0; i < domainSize; i++) {
+      reordered[index2] = params[index1];
+      index1 += 1;
+      index2 += rowSize;
+    }
+    count++;
+  }
+
+  delete [] params;
+  return reordered;
+}
+