457 lines
11 KiB
C++
457 lines
11 KiB
C++
#include <set>
|
|
#include <vector>
|
|
#include <algorithm>
|
|
|
|
#include <iostream>
|
|
#include <fstream>
|
|
#include <sstream>
|
|
|
|
#include "FactorGraph.h"
|
|
#include "Factor.h"
|
|
#include "BayesNet.h"
|
|
#include "BayesBall.h"
|
|
#include "Util.h"
|
|
|
|
|
|
FactorGraph::FactorGraph (const FactorGraph& fg)
|
|
{
|
|
const VarNodes& varNodes = fg.varNodes();
|
|
for (size_t i = 0; i < varNodes.size(); i++) {
|
|
addVarNode (new VarNode (varNodes[i]));
|
|
}
|
|
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();
|
|
}
|
|
|
|
|
|
|
|
void
|
|
FactorGraph::readFromUaiFormat (const char* fileName)
|
|
{
|
|
std::ifstream is (fileName);
|
|
if (!is.is_open()) {
|
|
cerr << "error: cannot read from file " << fileName << endl;
|
|
abort();
|
|
}
|
|
ignoreLines (is);
|
|
string line;
|
|
getline (is, line);
|
|
if (line != "MARKOV") {
|
|
cerr << "error: the network must be a MARKOV network " << endl;
|
|
abort();
|
|
}
|
|
// 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;
|
|
vector<VarIds> factorVarIds;
|
|
vector<Ranges> factorRanges;
|
|
for (unsigned i = 0; i < nrFactors; i++) {
|
|
ignoreLines (is);
|
|
is >> nrArgs;
|
|
factorVarIds.push_back ({ });
|
|
factorRanges.push_back ({ });
|
|
for (unsigned j = 0; j < nrArgs; j++) {
|
|
is >> vid;
|
|
if (vid >= ranges.size()) {
|
|
cerr << "error: invalid variable identifier `" << vid << "'" << endl;
|
|
cerr << "identifiers must be between 0 and " << ranges.size() - 1 ;
|
|
cerr << endl;
|
|
abort();
|
|
}
|
|
factorVarIds.back().push_back (vid);
|
|
factorRanges.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 (factorRanges[i])) {
|
|
cerr << "error: invalid number of parameters for factor nº " << i ;
|
|
cerr << ", expected: " << Util::sizeExpected (factorRanges[i]);
|
|
cerr << ", given: " << nrParams << endl;
|
|
abort();
|
|
}
|
|
Params params (nrParams);
|
|
for (unsigned j = 0; j < nrParams; j++) {
|
|
is >> params[j];
|
|
}
|
|
if (Globals::logDomain) {
|
|
Util::log (params);
|
|
}
|
|
addFactor (Factor (factorVarIds[i], factorRanges[i], params));
|
|
}
|
|
is.close();
|
|
}
|
|
|
|
|
|
|
|
void
|
|
FactorGraph::readFromLibDaiFormat (const char* fileName)
|
|
{
|
|
std::ifstream is (fileName);
|
|
if (!is.is_open()) {
|
|
cerr << "error: cannot read from file " << fileName << endl;
|
|
abort();
|
|
}
|
|
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 = getVarNode (vids[j]);
|
|
if (var != 0 && ranges[j] != var->range()) {
|
|
cerr << "error: variable `" << vids[j] << "' appears in two or " ;
|
|
cerr << "more factors with a different range" << endl;
|
|
}
|
|
}
|
|
// 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());
|
|
Factor f (vids, ranges, params);
|
|
std::reverse (vids.begin(), vids.end());
|
|
f.reorderArguments (vids);
|
|
addFactor (f);
|
|
}
|
|
is.close();
|
|
}
|
|
|
|
|
|
|
|
FactorGraph::~FactorGraph (void)
|
|
{
|
|
for (size_t i = 0; i < varNodes_.size(); i++) {
|
|
delete varNodes_[i];
|
|
}
|
|
for (size_t i = 0; i < facNodes_.size(); i++) {
|
|
delete facNodes_[i];
|
|
}
|
|
}
|
|
|
|
|
|
|
|
void
|
|
FactorGraph::addFactor (const Factor& factor)
|
|
{
|
|
FacNode* fn = new FacNode (factor);
|
|
addFacNode (fn);
|
|
const VarIds& vids = fn->factor().arguments();
|
|
for (size_t i = 0; i < vids.size(); i++) {
|
|
VarMap::const_iterator it = varMap_.find (vids[i]);
|
|
if (it != varMap_.end()) {
|
|
addEdge (it->second, fn);
|
|
} 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);
|
|
varMap_.insert (make_pair (vn->varId(), vn));
|
|
}
|
|
|
|
|
|
|
|
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 (void) const
|
|
{
|
|
return !containsCycle();
|
|
}
|
|
|
|
|
|
|
|
DAGraph&
|
|
FactorGraph::getStructure (void)
|
|
{
|
|
assert (bayesFactors_);
|
|
if (structure_.empty()) {
|
|
for (size_t i = 0; i < varNodes_.size(); i++) {
|
|
structure_.addNode (new DAGraphNode (varNodes_[i]));
|
|
}
|
|
for (size_t i = 0; i < facNodes_.size(); i++) {
|
|
const VarIds& vids = facNodes_[i]->factor().arguments();
|
|
for (size_t j = 1; j < vids.size(); j++) {
|
|
structure_.addEdge (vids[j], vids[0]);
|
|
}
|
|
}
|
|
}
|
|
return structure_;
|
|
}
|
|
|
|
|
|
|
|
void
|
|
FactorGraph::print (void) const
|
|
{
|
|
for (size_t i = 0; i < varNodes_.size(); i++) {
|
|
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 (size_t j = 0; j < varNodes_[i]->neighbors().size(); j++) {
|
|
cout << varNodes_[i]->neighbors()[j]->getLabel() << " " ;
|
|
}
|
|
cout << endl << endl;
|
|
}
|
|
for (size_t i = 0; i < facNodes_.size(); i++) {
|
|
facNodes_[i]->factor().print();
|
|
}
|
|
}
|
|
|
|
|
|
|
|
void
|
|
FactorGraph::exportToGraphViz (const char* fileName) const
|
|
{
|
|
ofstream out (fileName);
|
|
if (!out.is_open()) {
|
|
cerr << "error: cannot open file to write at " ;
|
|
cerr << "FactorGraph::exportToDotFile()" << endl;
|
|
abort();
|
|
}
|
|
out << "graph \"" << fileName << "\" {" << endl;
|
|
for (size_t i = 0; i < varNodes_.size(); i++) {
|
|
if (varNodes_[i]->hasEvidence()) {
|
|
out << '"' << varNodes_[i]->label() << '"' ;
|
|
out << " [style=filled, fillcolor=yellow]" << endl;
|
|
}
|
|
}
|
|
for (size_t i = 0; i < facNodes_.size(); i++) {
|
|
out << '"' << facNodes_[i]->getLabel() << '"' ;
|
|
out << " [label=\"" << facNodes_[i]->getLabel();
|
|
out << "\"" << ", shape=box]" << 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 << " -- " ;
|
|
out << '"' << myVars[j]->label() << '"' << endl;
|
|
}
|
|
}
|
|
out << "}" << endl;
|
|
out.close();
|
|
}
|
|
|
|
|
|
|
|
void
|
|
FactorGraph::exportToUaiFormat (const char* fileName) const
|
|
{
|
|
ofstream out (fileName);
|
|
if (!out.is_open()) {
|
|
cerr << "error: cannot open file " << fileName << endl;
|
|
abort();
|
|
}
|
|
out << "MARKOV" << endl;
|
|
out << varNodes_.size() << endl;
|
|
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();
|
|
}
|
|
out << endl << facNodes_.size() << endl;
|
|
for (size_t i = 0; i < facNodes_.size(); i++) {
|
|
VarIds args = facNodes_[i]->factor().arguments();
|
|
out << args.size() << " " << Util::elementsToString (args) << endl;
|
|
}
|
|
out << endl;
|
|
for (size_t i = 0; i < facNodes_.size(); i++) {
|
|
Params params = facNodes_[i]->factor().params();
|
|
if (Globals::logDomain) {
|
|
Util::exp (params);
|
|
}
|
|
out << params.size() << endl << " " ;
|
|
out << Util::elementsToString (params) << endl << endl;
|
|
}
|
|
out.close();
|
|
}
|
|
|
|
|
|
|
|
void
|
|
FactorGraph::exportToLibDaiFormat (const char* fileName) const
|
|
{
|
|
ofstream out (fileName);
|
|
if (!out.is_open()) {
|
|
cerr << "error: cannot open file " << fileName << endl;
|
|
abort();
|
|
}
|
|
out << facNodes_.size() << endl << endl;
|
|
for (size_t i = 0; i < facNodes_.size(); i++) {
|
|
Factor f (facNodes_[i]->factor());
|
|
out << f.nrArguments() << endl;
|
|
out << Util::elementsToString (f.arguments()) << endl;
|
|
out << Util::elementsToString (f.ranges()) << endl;
|
|
VarIds args = f.arguments();
|
|
std::reverse (args.begin(), args.end());
|
|
f.reorderArguments (args);
|
|
if (Globals::logDomain) {
|
|
Util::exp (f.params());
|
|
}
|
|
out << f.size() << endl;
|
|
for (size_t j = 0; j < f.size(); j++) {
|
|
out << j << " " << f[j] << endl;
|
|
}
|
|
out << endl;
|
|
}
|
|
out.close();
|
|
}
|
|
|
|
|
|
|
|
void
|
|
FactorGraph::ignoreLines (std::ifstream& is) const
|
|
{
|
|
string ignoreStr;
|
|
while (is.peek() == '#' || is.peek() == '\n') {
|
|
getline (is, ignoreStr);
|
|
}
|
|
}
|
|
|
|
|
|
|
|
bool
|
|
FactorGraph::containsCycle (void) const
|
|
{
|
|
vector<bool> visitedVars (varNodes_.size(), false);
|
|
vector<bool> visitedFactors (facNodes_.size(), false);
|
|
for (size_t i = 0; i < varNodes_.size(); i++) {
|
|
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,
|
|
vector<bool>& visitedVars,
|
|
vector<bool>& visitedFactors) const
|
|
{
|
|
visitedVars[v->getIndex()] = true;
|
|
const FacNodes& adjacencies = v->neighbors();
|
|
for (size_t i = 0; i < adjacencies.size(); i++) {
|
|
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,
|
|
vector<bool>& visitedVars,
|
|
vector<bool>& visitedFactors) const
|
|
{
|
|
visitedFactors[v->getIndex()] = true;
|
|
const VarNodes& adjacencies = v->neighbors();
|
|
for (size_t i = 0; i < adjacencies.size(); i++) {
|
|
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
|
|
}
|
|
|