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yap-6.3/packages/CLPBN/horus/FactorGraph.cpp

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#include <cassert>
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#include <algorithm>
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#include <iostream>
#include "FactorGraph.h"
#include "BayesBall.h"
#include "Util.h"
namespace Horus {
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bool FactorGraph::exportLd_ = false;
bool FactorGraph::exportUai_ = false;
bool FactorGraph::exportGv_ = false;
bool FactorGraph::printFg_ = false;
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FactorGraph::FactorGraph (const FactorGraph& fg)
{
clone (fg);
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}
FactorGraph::~FactorGraph()
{
for (size_t i = 0; i < varNodes_.size(); i++) {
delete varNodes_[i];
}
for (size_t i = 0; i < facNodes_.size(); i++) {
delete facNodes_[i];
}
}
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void
FactorGraph::addFactor (const Factor& factor)
{
FacNode* fn = new FacNode (factor);
addFacNode (fn);
const VarIds& vids = fn->factor().arguments();
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for (size_t i = 0; i < vids.size(); i++) {
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VarMap::const_iterator it = varMap_.find (vids[i]);
if (it != varMap_.end()) {
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addEdge (it->second, fn);
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} else {
VarNode* vn = new VarNode (vids[i], fn->factor().range (i));
addVarNode (vn);
addEdge (vn, fn);
}
}
}
void
FactorGraph::addVarNode (VarNode* vn)
{
varNodes_.push_back (vn);
vn->setIndex (varNodes_.size() - 1);
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varMap_.insert (std::make_pair (vn->varId(), vn));
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}
void
FactorGraph::addFacNode (FacNode* fn)
{
facNodes_.push_back (fn);
fn->setIndex (facNodes_.size() - 1);
}
void
FactorGraph::addEdge (VarNode* vn, FacNode* fn)
{
vn->addNeighbor (fn);
fn->addNeighbor (vn);
}
bool
FactorGraph::isTree() const
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{
return !containsCycle();
}
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BayesBallGraph&
FactorGraph::getStructure()
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{
assert (bayesFactors_);
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if (structure_.empty()) {
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for (size_t i = 0; i < varNodes_.size(); i++) {
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structure_.addNode (new BBNode (varNodes_[i]));
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}
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for (size_t i = 0; i < facNodes_.size(); i++) {
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const VarIds& vids = facNodes_[i]->factor().arguments();
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for (size_t j = 1; j < vids.size(); j++) {
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structure_.addEdge (vids[j], vids[0]);
}
}
}
return structure_;
}
void
FactorGraph::print() const
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{
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using std::cout;
using std::endl;
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for (size_t i = 0; i < varNodes_.size(); i++) {
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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 = " ;
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for (size_t j = 0; j < varNodes_[i]->neighbors().size(); j++) {
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cout << varNodes_[i]->neighbors()[j]->getLabel() << " " ;
}
cout << endl << endl;
}
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for (size_t i = 0; i < facNodes_.size(); i++) {
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facNodes_[i]->factor().print();
}
}
void
FactorGraph::exportToLibDai (const char* fileName) const
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{
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std::ofstream out (fileName);
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if (!out.is_open()) {
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std::cerr << "Error: couldn't open file '" << fileName << "'." ;
std::cerr << std::endl;
return;
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}
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out << facNodes_.size() << std::endl << std::endl;
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for (size_t i = 0; i < facNodes_.size(); i++) {
Factor f (facNodes_[i]->factor());
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out << f.nrArguments() << std::endl;
out << Util::elementsToString (f.arguments()) << std::endl;
out << Util::elementsToString (f.ranges()) << std::endl;
VarIds args = f.arguments();
std::reverse (args.begin(), args.end());
f.reorderArguments (args);
if (Globals::logDomain) {
Util::exp (f.params());
}
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out << f.size() << std::endl;
for (size_t j = 0; j < f.size(); j++) {
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out << j << " " << f[j] << std::endl;
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}
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out << std::endl;
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}
out.close();
}
void
FactorGraph::exportToUai (const char* fileName) const
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{
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std::ofstream out (fileName);
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if (!out.is_open()) {
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std::cerr << "Error: couldn't open file '" << fileName << "'." ;
std::cerr << std::endl;
return;
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}
out << (bayesFactors_ ? "BAYES" : "MARKOV") ;
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out << std::endl << std::endl;
out << varNodes_.size() << std::endl;
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VarNodes sortedVns = varNodes_;
std::sort (sortedVns.begin(), sortedVns.end(), sortByVarId());
for (size_t i = 0; i < sortedVns.size(); i++) {
out << ((i != 0) ? " " : "") << sortedVns[i]->range();
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}
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out << std::endl << facNodes_.size() << std::endl;
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for (size_t i = 0; i < facNodes_.size(); i++) {
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VarIds args = facNodes_[i]->factor().arguments();
if (bayesFactors_) {
std::swap (args.front(), args.back());
}
out << args.size() << " " << Util::elementsToString (args);
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out << std::endl;
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}
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out << std::endl;
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for (size_t i = 0; i < facNodes_.size(); i++) {
Factor f = facNodes_[i]->factor();
if (bayesFactors_) {
VarIds args = f.arguments();
std::swap (args.front(), args.back());
f.reorderArguments (args);
}
Params params = f.params();
if (Globals::logDomain) {
Util::exp (params);
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}
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out << params.size() << std::endl << " " ;
out << Util::elementsToString (params);
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out << std::endl << std::endl;
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}
out.close();
}
void
FactorGraph::exportToGraphViz (const char* fileName) const
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{
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std::ofstream out (fileName);
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if (!out.is_open()) {
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std::cerr << "Error: couldn't open file '" << fileName << "'." ;
std::cerr << std::endl;
return;
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}
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out << "graph \"" << fileName << "\" {" << std::endl;
for (size_t i = 0; i < varNodes_.size(); i++) {
if (varNodes_[i]->hasEvidence()) {
out << '"' << varNodes_[i]->label() << '"' ;
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out << " [style=filled, fillcolor=yellow]" << std::endl;
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}
}
for (size_t i = 0; i < facNodes_.size(); i++) {
out << '"' << facNodes_[i]->getLabel() << '"' ;
out << " [label=\"" << facNodes_[i]->getLabel();
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out << "\"" << ", shape=box]" << std::endl;
}
for (size_t i = 0; i < facNodes_.size(); i++) {
const VarNodes& myVars = facNodes_[i]->neighbors();
for (size_t j = 0; j < myVars.size(); j++) {
out << '"' << facNodes_[i]->getLabel() << '"' ;
out << " -- " ;
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out << '"' << myVars[j]->label() << '"' << std::endl;
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}
}
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out << "}" << std::endl;
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out.close();
}
FactorGraph&
FactorGraph::operator= (const FactorGraph& fg)
{
if (this != &fg) {
for (size_t i = 0; i < varNodes_.size(); i++) {
delete varNodes_[i];
}
varNodes_.clear();
for (size_t i = 0; i < facNodes_.size(); i++) {
delete facNodes_[i];
}
facNodes_.clear();
varMap_.clear();
clone (fg);
}
return *this;
}
FactorGraph
FactorGraph::readFromUaiFormat (const char* fileName)
{
std::ifstream is (fileName);
if (!is.is_open()) {
std::cerr << "Error: couldn't open file '" << fileName << "'." ;
std::cerr << std::endl;
exit (EXIT_FAILURE);
}
FactorGraph fg;
ignoreLines (is);
std::string line;
getline (is, line);
if (line == "BAYES") {
fg.bayesFactors_ = true;
} else if (line == "MARKOV") {
fg.bayesFactors_ = false;
} else {
std::cerr << "Error: the type of network is missing." << std::endl;
exit (EXIT_FAILURE);
}
// read the number of vars
ignoreLines (is);
unsigned nrVars;
is >> nrVars;
// read the range of each var
ignoreLines (is);
Ranges ranges (nrVars);
for (unsigned i = 0; i < nrVars; i++) {
is >> ranges[i];
}
unsigned nrFactors;
unsigned nrArgs;
unsigned vid;
is >> nrFactors;
std::vector<VarIds> allVarIds;
std::vector<Ranges> allRanges;
for (unsigned i = 0; i < nrFactors; i++) {
ignoreLines (is);
is >> nrArgs;
allVarIds.push_back ({ });
allRanges.push_back ({ });
for (unsigned j = 0; j < nrArgs; j++) {
is >> vid;
if (vid >= ranges.size()) {
std::cerr << "Error: invalid variable identifier `" << vid << "'" ;
std::cerr << ". Identifiers must be between 0 and " ;
std::cerr << ranges.size() - 1 << "." << std::endl;
exit (EXIT_FAILURE);
}
allVarIds.back().push_back (vid);
allRanges.back().push_back (ranges[vid]);
}
}
// read the parameters
unsigned nrParams;
for (unsigned i = 0; i < nrFactors; i++) {
ignoreLines (is);
is >> nrParams;
if (nrParams != Util::sizeExpected (allRanges[i])) {
std::cerr << "Error: invalid number of parameters for factor nº " ;
std::cerr << i << ", " << Util::sizeExpected (allRanges[i]);
std::cerr << " expected, " << nrParams << " given." << std::endl;
exit (EXIT_FAILURE);
}
Params params (nrParams);
for (unsigned j = 0; j < nrParams; j++) {
is >> params[j];
}
if (Globals::logDomain) {
Util::log (params);
}
Factor f (allVarIds[i], allRanges[i], params);
if (fg.bayesFactors_ && allVarIds[i].size() > 1) {
// In this format the child is the last variable,
// move it to be the first
std::swap (allVarIds[i].front(), allVarIds[i].back());
f.reorderArguments (allVarIds[i]);
}
fg.addFactor (f);
}
is.close();
return fg;
}
FactorGraph
FactorGraph::readFromLibDaiFormat (const char* fileName)
{
std::ifstream is (fileName);
if (!is.is_open()) {
std::cerr << "Error: couldn't open file '" << fileName << "'." ;
std::cerr << std::endl;
exit (EXIT_FAILURE);
}
FactorGraph fg;
ignoreLines (is);
unsigned nrFactors;
unsigned nrArgs;
VarId vid;
is >> nrFactors;
for (unsigned i = 0; i < nrFactors; i++) {
ignoreLines (is);
// read the factor arguments
is >> nrArgs;
VarIds vids;
for (unsigned j = 0; j < nrArgs; j++) {
ignoreLines (is);
is >> vid;
vids.push_back (vid);
}
// read ranges
Ranges ranges (nrArgs);
for (unsigned j = 0; j < nrArgs; j++) {
ignoreLines (is);
is >> ranges[j];
VarNode* var = fg.getVarNode (vids[j]);
if (var && ranges[j] != var->range()) {
std::cerr << "Error: variable `" << vids[j] << "' appears" ;
std::cerr << " in two or more factors with a different range." ;
std::cerr << std::endl;
exit (EXIT_FAILURE);
}
}
// read parameters
ignoreLines (is);
unsigned nNonzeros;
is >> nNonzeros;
Params params (Util::sizeExpected (ranges), 0);
for (unsigned j = 0; j < nNonzeros; j++) {
ignoreLines (is);
unsigned index;
is >> index;
ignoreLines (is);
double val;
is >> val;
params[index] = val;
}
if (Globals::logDomain) {
Util::log (params);
}
std::reverse (vids.begin(), vids.end());
std::reverse (ranges.begin(), ranges.end());
Factor f (vids, ranges, params);
std::reverse (vids.begin(), vids.end());
f.reorderArguments (vids);
fg.addFactor (f);
}
is.close();
return fg;
}
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void
FactorGraph::clone (const FactorGraph& fg)
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{
const VarNodes& varNodes = fg.varNodes();
for (size_t i = 0; i < varNodes.size(); i++) {
addVarNode (new VarNode (varNodes[i]));
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}
const FacNodes& facNodes = fg.facNodes();
for (size_t i = 0; i < facNodes.size(); i++) {
FacNode* facNode = new FacNode (facNodes[i]->factor());
addFacNode (facNode);
const VarNodes& neighs = facNodes[i]->neighbors();
for (size_t j = 0; j < neighs.size(); j++) {
addEdge (varNodes_[neighs[j]->getIndex()], facNode);
}
}
bayesFactors_ = fg.bayesianFactors();
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}
bool
FactorGraph::containsCycle() const
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{
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std::vector<bool> visitedVars (varNodes_.size(), false);
std::vector<bool> visitedFactors (facNodes_.size(), false);
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for (size_t i = 0; i < varNodes_.size(); i++) {
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int v = varNodes_[i]->getIndex();
if (!visitedVars[v]) {
if (containsCycle (varNodes_[i], 0, visitedVars, visitedFactors)) {
return true;
}
}
}
return false;
}
bool
FactorGraph::containsCycle (
const VarNode* v,
const FacNode* p,
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std::vector<bool>& visitedVars,
std::vector<bool>& visitedFactors) const
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{
visitedVars[v->getIndex()] = true;
const FacNodes& adjacencies = v->neighbors();
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for (size_t i = 0; i < adjacencies.size(); i++) {
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int w = adjacencies[i]->getIndex();
if (!visitedFactors[w]) {
if (containsCycle (adjacencies[i], v, visitedVars, visitedFactors)) {
return true;
}
}
else if (visitedFactors[w] && adjacencies[i] != p) {
return true;
}
}
return false; // no cycle detected in this component
}
bool
FactorGraph::containsCycle (
const FacNode* v,
const VarNode* p,
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std::vector<bool>& visitedVars,
std::vector<bool>& visitedFactors) const
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{
visitedFactors[v->getIndex()] = true;
const VarNodes& adjacencies = v->neighbors();
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for (size_t i = 0; i < adjacencies.size(); i++) {
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int w = adjacencies[i]->getIndex();
if (!visitedVars[w]) {
if (containsCycle (adjacencies[i], v, visitedVars, visitedFactors)) {
return true;
}
}
else if (visitedVars[w] && adjacencies[i] != p) {
return true;
}
}
return false; // no cycle detected in this component
}
void
FactorGraph::ignoreLines (std::ifstream& is)
{
std::string ignoreStr;
while (is.peek() == '#' || is.peek() == '\n') {
getline (is, ignoreStr);
}
}
} // namespace Horus
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