public void testMdlToGraph() {
List models = TestInference.createTestModels();
for (Iterator mdlIt = models.iterator(); mdlIt.hasNext(); ) {
UndirectedModel mdl = (UndirectedModel) mdlIt.next();
UndirectedGraph g = Graphs.mdlToGraph(mdl);
Set vertices = g.vertexSet();
// check the number of vertices
assertEquals(mdl.numVariables(), vertices.size());
// check the number of edges
int numEdgePtls = 0;
for (Iterator factorIt = mdl.factors().iterator(); factorIt.hasNext(); ) {
Factor factor = (Factor) factorIt.next();
if (factor.varSet().size() == 2) numEdgePtls++;
}
assertEquals(numEdgePtls, g.edgeSet().size());
// check that the neighbors of each vertex contain at least some of what they're supposed to
Iterator it = vertices.iterator();
while (it.hasNext()) {
Variable var = (Variable) it.next();
assertTrue(vertices.contains(var));
Set neighborsInG = new HashSet(GraphHelper.neighborListOf(g, var));
neighborsInG.add(var);
Iterator factorIt = mdl.allFactorsContaining(var).iterator();
while (factorIt.hasNext()) {
Factor factor = (Factor) factorIt.next();
assertTrue(neighborsInG.containsAll(factor.varSet()));
}
}
}
}
/**
* Tests that models can be created that have multiple factors over the same edge, and that
* potentialOfEdge returns the product in that case.
*/
public void testMultipleEdgePotentials() {
Variable v1 = new Variable(2);
Variable v2 = new Variable(2);
Variable[] vars = new Variable[] {v1, v2};
FactorGraph mdl = new FactorGraph(vars);
Factor ptl1 = new TableFactor(vars, new double[] {0.5, 0.5, 0.5, 0.5});
mdl.addFactor(ptl1);
Factor ptl2 = new TableFactor(vars, new double[] {0.25, 0.25, 0.5, 0.5});
mdl.addFactor(ptl2);
try {
mdl.factorOf(v1, v2);
fail();
} catch (RuntimeException e) {
}
Collection factors = mdl.allFactorsContaining(new HashVarSet(vars));
assertEquals(2, factors.size());
assertTrue(factors.contains(ptl1));
assertTrue(factors.contains(ptl2));
double[] vals = {0.125, 0.125, 0.25, 0.25};
Factor total = TableFactor.multiplyAll(factors);
Factor expected = new TableFactor(vars, vals);
assertTrue(
"Arrays not equal\n Expected "
+ ArrayUtils.toString(vals)
+ "\n Actual "
+ ArrayUtils.toString(((TableFactor) total).toValueArray()),
expected.almostEquals(total, 1e-10));
}
private void verifyCachesConsistent(FactorGraph mdl) {
Factor pot, pot2, pot3;
for (Iterator it = mdl.factors().iterator(); it.hasNext(); ) {
pot = (Factor) it.next();
// System.out.println("Testing model "+i+" potential "+pot);
Object[] vars = pot.varSet().toArray();
switch (vars.length) {
case 1:
pot2 = mdl.factorOf((Variable) vars[0]);
assertTrue(pot == pot2);
break;
case 2:
Variable var1 = (Variable) vars[0];
Variable var2 = (Variable) vars[1];
pot2 = mdl.factorOf(var1, var2);
pot3 = mdl.factorOf(var2, var1);
assertTrue(pot == pot2);
assertTrue(pot2 == pot3);
break;
// Factors of size > 2 aren't now cached.
default:
break;
}
}
}
private double sumValues(List ptlList, Assignment assn) {
double sum = 0;
for (Iterator it = ptlList.iterator(); it.hasNext(); ) {
Factor ptl = (Factor) it.next();
sum += ptl.logValue(assn);
}
return sum;
}
public void testFactorOfSet() {
Variable[] vars = new Variable[3];
for (int i = 0; i < vars.length; i++) {
vars[i] = new Variable(2);
}
Factor factor = new TableFactor(vars, new double[] {0, 1, 2, 3, 4, 5, 6, 7});
FactorGraph fg = new FactorGraph(vars);
fg.addFactor(factor);
assertTrue(factor == fg.factorOf(factor.varSet()));
HashSet set = new HashSet(factor.varSet());
assertTrue(factor == fg.factorOf(set));
set.remove(vars[0]);
assertTrue(null == fg.factorOf(set));
}
// backtracking search for a feasible assignment
private Assignment initialAssignmentRec(FactorGraph mdl, Assignment assn, int fi) {
if (fi >= mdl.factors().size()) return assn;
Factor f = mdl.getFactor(fi);
Factor sliced = f.slice(assn);
if (sliced.varSet().isEmpty()) {
double val = f.value(assn);
if (val > 1e-50) {
return initialAssignmentRec(mdl, assn, fi + 1);
} else {
return null;
}
}
for (AssignmentIterator it = sliced.assignmentIterator(); it.hasNext(); ) {
double val = sliced.value(it);
if (val > 1e-50) {
Assignment new_assn = Assignment.union(assn, it.assignment());
Assignment assn_ret = initialAssignmentRec(mdl, new_assn, fi + 1);
if (assn_ret != null) return assn_ret;
}
it.advance();
}
return null;
}
private void initJtCpts(FactorGraph mdl, JunctionTree jt) {
for (Iterator it = jt.getVerticesIterator(); it.hasNext(); ) {
VarSet c = (VarSet) it.next();
// DiscreteFactor ptl = createBlankFactor (c);
// jt.setCPF(c, ptl);
jt.setCPF(c, new ConstantFactor(1.0));
}
for (Iterator it = mdl.factors().iterator(); it.hasNext(); ) {
Factor ptl = (Factor) it.next();
VarSet parent = jt.findParentCluster(ptl.varSet());
assert parent != null : "Unable to find parent cluster for ptl " + ptl + "in jt " + jt;
Factor cpf = jt.getCPF(parent);
Factor newCpf = cpf.multiply(ptl);
jt.setCPF(parent, newCpf);
/* debug
if (jt.isNaN()) {
throw new RuntimeException ("Got a NaN");
}
*/
}
}