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renamings and delete bn_bp stuff

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This commit is contained in:
Tiago Gomes
2012-04-05 23:00:48 +01:00
parent b28ee8fb3a
commit d1b25f0864
31 changed files with 230 additions and 1323 deletions
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84
packages/CLPBN/clpbn/bp/FactorGraph.cpp
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@@ -18,17 +18,17 @@ bool FactorGraph::orderFactorVariables = false;
FactorGraph::FactorGraph (const FactorGraph& fg)
{
const FgVarSet& vars = fg.getVarNodes();
const VarNodes& vars = fg.varNodes();
for (unsigned i = 0; i < vars.size(); i++) {
FgVarNode* varNode = new FgVarNode (vars[i]);
VarNode* varNode = new VarNode (vars[i]);
addVariable (varNode);
}
const FgFacSet& facs = fg.getFactorNodes();
const FactorNodes& facs = fg.factorNodes();
for (unsigned i = 0; i < facs.size(); i++) {
FgFacNode* facNode = new FgFacNode (facs[i]);
FactorNode* facNode = new FactorNode (facs[i]);
addFactor (facNode);
const FgVarSet& neighs = facs[i]->neighbors();
const VarNodes& neighs = facs[i]->neighbors();
for (unsigned j = 0; j < neighs.size(); j++) {
addEdge (facNode, varNodes_[neighs[j]->getIndex()]);
}
@@ -68,7 +68,7 @@ FactorGraph::readFromUaiFormat (const char* fileName)
while (is.peek() == '#' || is.peek() == '\n') getline (is, line);
for (unsigned i = 0; i < nVars; i++) {
addVariable (new FgVarNode (i, domainSizes[i]));
addVariable (new VarNode (i, domainSizes[i]));
}
unsigned nFactors;
@@ -77,21 +77,21 @@ FactorGraph::readFromUaiFormat (const char* fileName)
while (is.peek() == '#' || is.peek() == '\n') getline (is, line);
unsigned nFactorVars;
is >> nFactorVars;
VarNodes neighs;
Vars neighs;
for (unsigned j = 0; j < nFactorVars; j++) {
unsigned vid;
is >> vid;
FgVarNode* neigh = getFgVarNode (vid);
VarNode* neigh = getVarNode (vid);
if (!neigh) {
cerr << "error: invalid variable identifier (" << vid << ")" << endl;
abort();
}
neighs.push_back (neigh);
}
FgFacNode* fn = new FgFacNode (new Factor (neighs));
FactorNode* fn = new FactorNode (new Factor (neighs));
addFactor (fn);
for (unsigned j = 0; j < neighs.size(); j++) {
addEdge (fn, static_cast<FgVarNode*> (neighs[j]));
addEdge (fn, static_cast<VarNode*> (neighs[j]));
}
}
@@ -162,15 +162,15 @@ FactorGraph::readFromLibDaiFormat (const char* fileName)
vids.push_back (vid);
}
VarNodes neighs;
Vars neighs;
unsigned nParams = 1;
for (unsigned j = 0; j < nVars; j++) {
unsigned dsize;
while ((is.peek()) == '#') getline (is, line);
is >> dsize;
FgVarNode* var = getFgVarNode (vids[j]);
VarNode* var = getVarNode (vids[j]);
if (var == 0) {
var = new FgVarNode (vids[j], dsize);
var = new VarNode (vids[j], dsize);
addVariable (var);
} else {
if (var->range() != dsize) {
@@ -199,10 +199,10 @@ FactorGraph::readFromLibDaiFormat (const char* fileName)
if (Globals::logDomain) {
Util::toLog (params);
}
FgFacNode* fn = new FgFacNode (new Factor (neighs, params));
FactorNode* fn = new FactorNode (new Factor (neighs, params));
addFactor (fn);
for (unsigned j = 0; j < neighs.size(); j++) {
addEdge (fn, static_cast<FgVarNode*> (neighs[j]));
addEdge (fn, static_cast<VarNode*> (neighs[j]));
}
}
is.close();
@@ -224,7 +224,7 @@ FactorGraph::~FactorGraph (void)
void
FactorGraph::addVariable (FgVarNode* vn)
FactorGraph::addVariable (VarNode* vn)
{
varNodes_.push_back (vn);
vn->setIndex (varNodes_.size() - 1);
@@ -234,7 +234,7 @@ FactorGraph::addVariable (FgVarNode* vn)
void
FactorGraph::addFactor (FgFacNode* fn)
FactorGraph::addFactor (FactorNode* fn)
{
facNodes_.push_back (fn);
fn->setIndex (facNodes_.size() - 1);
@@ -245,7 +245,7 @@ FactorGraph::addFactor (FgFacNode* fn)
void
FactorGraph::addFactor (const Factor& factor)
{
FgFacNode* fn = new FgFacNode (factor);
FactorNode* fn = new FactorNode (factor);
addFactor (fn);
const VarIds& vids = factor.arguments();
for (unsigned i = 0; i < vids.size(); i++) {
@@ -257,7 +257,7 @@ FactorGraph::addFactor (const Factor& factor)
}
}
if (found == false) {
FgVarNode* vn = new FgVarNode (vids[i], factor.range (i));
VarNode* vn = new VarNode (vids[i], factor.range (i));
addVariable (vn);
addEdge (vn, fn);
}
@@ -267,7 +267,7 @@ FactorGraph::addFactor (const Factor& factor)
void
FactorGraph::addEdge (FgVarNode* vn, FgFacNode* fn)
FactorGraph::addEdge (VarNode* vn, FactorNode* fn)
{
vn->addNeighbor (fn);
fn->addNeighbor (vn);
@@ -276,7 +276,7 @@ FactorGraph::addEdge (FgVarNode* vn, FgFacNode* fn)
void
FactorGraph::addEdge (FgFacNode* fn, FgVarNode* vn)
FactorGraph::addEdge (FactorNode* fn, VarNode* vn)
{
fn->addNeighbor (vn);
vn->addNeighbor (fn);
@@ -284,28 +284,6 @@ FactorGraph::addEdge (FgFacNode* fn, FgVarNode* vn)
VarNode*
FactorGraph::getVariableNode (VarId vid) const
{
FgVarNode* vn = getFgVarNode (vid);
assert (vn);
return vn;
}
VarNodes
FactorGraph::getVariableNodes (void) const
{
VarNodes vars;
for (unsigned i = 0; i < varNodes_.size(); i++) {
vars.push_back (varNodes_[i]);
}
return vars;
}
bool
FactorGraph::isTree (void) const
{
@@ -348,7 +326,7 @@ FactorGraph::setIndexes (void)
void
FactorGraph::printGraphicalModel (void) const
FactorGraph::print (void) const
{
for (unsigned i = 0; i < varNodes_.size(); i++) {
cout << "var id = " << varNodes_[i]->varId() << endl;
@@ -390,7 +368,7 @@ FactorGraph::exportToGraphViz (const char* fileName) const
out << "\"" << ", shape=box]" << endl;
}
for (unsigned i = 0; i < facNodes_.size(); i++) {
const FgVarSet& myVars = facNodes_[i]->neighbors();
const VarNodes& myVars = facNodes_[i]->neighbors();
for (unsigned j = 0; j < myVars.size(); j++) {
out << '"' << facNodes_[i]->getLabel() << '"' ;
out << " -- " ;
@@ -422,7 +400,7 @@ FactorGraph::exportToUaiFormat (const char* fileName) const
out << facNodes_.size() << endl;
for (unsigned i = 0; i < facNodes_.size(); i++) {
const FgVarSet& factorVars = facNodes_[i]->neighbors();
const VarNodes& factorVars = facNodes_[i]->neighbors();
out << factorVars.size();
for (unsigned j = 0; j < factorVars.size(); j++) {
out << " " << factorVars[j]->getIndex();
@@ -458,7 +436,7 @@ FactorGraph::exportToLibDaiFormat (const char* fileName) const
}
out << facNodes_.size() << endl << endl;
for (unsigned i = 0; i < facNodes_.size(); i++) {
const FgVarSet& factorVars = facNodes_[i]->neighbors();
const VarNodes& factorVars = facNodes_[i]->neighbors();
out << factorVars.size() << endl;
for (int j = factorVars.size() - 1; j >= 0; j--) {
out << factorVars[j]->varId() << " " ;
@@ -503,13 +481,13 @@ FactorGraph::containsCycle (void) const
bool
FactorGraph::containsCycle (
const FgVarNode* v,
const FgFacNode* p,
const VarNode* v,
const FactorNode* p,
vector<bool>& visitedVars,
vector<bool>& visitedFactors) const
{
visitedVars[v->getIndex()] = true;
const FgFacSet& adjacencies = v->neighbors();
const FactorNodes& adjacencies = v->neighbors();
for (unsigned i = 0; i < adjacencies.size(); i++) {
int w = adjacencies[i]->getIndex();
if (!visitedFactors[w]) {
@@ -528,13 +506,13 @@ FactorGraph::containsCycle (
bool
FactorGraph::containsCycle (
const FgFacNode* v,
const FgVarNode* p,
const FactorNode* v,
const VarNode* p,
vector<bool>& visitedVars,
vector<bool>& visitedFactors) const
{
visitedFactors[v->getIndex()] = true;
const FgVarSet& adjacencies = v->neighbors();
const VarNodes& adjacencies = v->neighbors();
for (unsigned i = 0; i < adjacencies.size(); i++) {
int w = adjacencies[i]->getIndex();
if (!visitedVars[w]) {