ok, second try
This commit is contained in:
Tiago Gomes
465
packages/CLPBN/horus/FactorGraph.cpp
Normal file
465
packages/CLPBN/horus/FactorGraph.cpp
Normal file
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#include <set>
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#include <vector>
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#include <algorithm>
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#include <iostream>
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#include <fstream>
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#include <sstream>
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#include "FactorGraph.h"
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#include "Factor.h"
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#include "BayesNet.h"
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#include "BayesBall.h"
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#include "Util.h"
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FactorGraph::FactorGraph (const FactorGraph& fg)
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{
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const VarNodes& varNodes = fg.varNodes();
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for (unsigned i = 0; i < varNodes.size(); i++) {
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addVarNode (new VarNode (varNodes[i]));
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}
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const FacNodes& facNodes = fg.facNodes();
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for (unsigned i = 0; i < facNodes.size(); i++) {
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FacNode* facNode = new FacNode (facNodes[i]->factor());
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addFacNode (facNode);
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const VarNodes& neighs = facNodes[i]->neighbors();
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for (unsigned j = 0; j < neighs.size(); j++) {
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addEdge (varNodes_[neighs[j]->getIndex()], facNode);
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}
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}
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fromBayesNet_ = fg.isFromBayesNetwork();
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}
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void
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FactorGraph::readFromUaiFormat (const char* fileName)
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{
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std::ifstream is (fileName);
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if (!is.is_open()) {
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cerr << "error: cannot read from file " << fileName << endl;
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abort();
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}
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ignoreLines (is);
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string line;
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getline (is, line);
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if (line != "MARKOV") {
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cerr << "error: the network must be a MARKOV network " << endl;
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abort();
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}
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// read the number of vars
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ignoreLines (is);
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unsigned nrVars;
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is >> nrVars;
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// read the range of each var
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ignoreLines (is);
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Ranges ranges (nrVars);
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for (unsigned i = 0; i < nrVars; i++) {
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is >> ranges[i];
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}
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unsigned nrFactors;
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unsigned nrArgs;
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unsigned vid;
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is >> nrFactors;
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vector<VarIds> factorVarIds;
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vector<Ranges> factorRanges;
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for (unsigned i = 0; i < nrFactors; i++) {
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ignoreLines (is);
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is >> nrArgs;
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factorVarIds.push_back ({ });
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factorRanges.push_back ({ });
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for (unsigned j = 0; j < nrArgs; j++) {
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is >> vid;
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if (vid >= ranges.size()) {
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cerr << "error: invalid variable identifier `" << vid << "'" << endl;
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cerr << "identifiers must be between 0 and " << ranges.size() - 1 ;
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cerr << endl;
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abort();
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}
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factorVarIds.back().push_back (vid);
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factorRanges.back().push_back (ranges[vid]);
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}
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}
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// read the parameters
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unsigned nrParams;
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for (unsigned i = 0; i < nrFactors; i++) {
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ignoreLines (is);
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is >> nrParams;
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if (nrParams != Util::expectedSize (factorRanges[i])) {
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cerr << "error: invalid number of parameters for factor nº " << i ;
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cerr << ", expected: " << Util::expectedSize (factorRanges[i]);
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cerr << ", given: " << nrParams << endl;
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abort();
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}
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Params params (nrParams);
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for (unsigned j = 0; j < nrParams; j++) {
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is >> params[j];
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}
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if (Globals::logDomain) {
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Util::toLog (params);
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}
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addFactor (Factor (factorVarIds[i], factorRanges[i], params));
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}
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is.close();
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}
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void
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FactorGraph::readFromLibDaiFormat (const char* fileName)
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{
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std::ifstream is (fileName);
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if (!is.is_open()) {
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cerr << "error: cannot read from file " << fileName << endl;
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abort();
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}
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ignoreLines (is);
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unsigned nrFactors;
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unsigned nrArgs;
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VarId vid;
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is >> nrFactors;
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for (unsigned i = 0; i < nrFactors; i++) {
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ignoreLines (is);
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// read the factor arguments
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is >> nrArgs;
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VarIds vids;
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for (unsigned j = 0; j < nrArgs; j++) {
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ignoreLines (is);
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is >> vid;
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vids.push_back (vid);
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}
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// read ranges
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Ranges ranges (nrArgs);
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for (unsigned j = 0; j < nrArgs; j++) {
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ignoreLines (is);
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is >> ranges[j];
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VarNode* var = getVarNode (vids[j]);
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if (var != 0 && ranges[j] != var->range()) {
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cerr << "error: variable `" << vids[j] << "' appears in two or " ;
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cerr << "more factors with a different range" << endl;
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}
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}
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// read parameters
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ignoreLines (is);
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unsigned nNonzeros;
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is >> nNonzeros;
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Params params (Util::expectedSize (ranges), 0);
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for (unsigned j = 0; j < nNonzeros; j++) {
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ignoreLines (is);
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unsigned index;
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is >> index;
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ignoreLines (is);
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double val;
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is >> val;
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params[index] = val;
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}
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if (Globals::logDomain) {
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Util::toLog (params);
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}
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reverse (vids.begin(), vids.end());
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Factor f (vids, ranges, params);
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reverse (vids.begin(), vids.end());
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f.reorderArguments (vids);
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addFactor (f);
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}
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is.close();
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}
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FactorGraph::~FactorGraph (void)
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{
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for (unsigned i = 0; i < varNodes_.size(); i++) {
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delete varNodes_[i];
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}
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for (unsigned i = 0; i < facNodes_.size(); i++) {
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delete facNodes_[i];
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}
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}
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void
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FactorGraph::addFactor (const Factor& factor)
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{
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FacNode* fn = new FacNode (factor);
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addFacNode (fn);
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const VarIds& vids = fn->factor().arguments();
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for (unsigned i = 0; i < vids.size(); i++) {
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VarMap::const_iterator it = varMap_.find (vids[i]);
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if (it != varMap_.end()) {
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addEdge (it->second, fn);
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} else {
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VarNode* vn = new VarNode (vids[i], fn->factor().range (i));
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addVarNode (vn);
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addEdge (vn, fn);
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}
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}
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}
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void
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FactorGraph::addVarNode (VarNode* vn)
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{
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varNodes_.push_back (vn);
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vn->setIndex (varNodes_.size() - 1);
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varMap_.insert (make_pair (vn->varId(), vn));
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}
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void
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FactorGraph::addFacNode (FacNode* fn)
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{
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facNodes_.push_back (fn);
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fn->setIndex (facNodes_.size() - 1);
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}
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void
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FactorGraph::addEdge (VarNode* vn, FacNode* fn)
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{
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vn->addNeighbor (fn);
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fn->addNeighbor (vn);
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}
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bool
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FactorGraph::isTree (void) const
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{
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return !containsCycle();
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}
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DAGraph&
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FactorGraph::getStructure (void)
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{
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assert (fromBayesNet_);
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if (structure_.empty()) {
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for (unsigned i = 0; i < varNodes_.size(); i++) {
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structure_.addNode (new DAGraphNode (varNodes_[i]));
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}
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for (unsigned i = 0; i < facNodes_.size(); i++) {
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const VarIds& vids = facNodes_[i]->factor().arguments();
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for (unsigned j = 1; j < vids.size(); j++) {
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structure_.addEdge (vids[j], vids[0]);
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}
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}
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}
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return structure_;
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}
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void
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FactorGraph::print (void) const
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{
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for (unsigned i = 0; i < varNodes_.size(); i++) {
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cout << "var id = " << varNodes_[i]->varId() << endl;
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cout << "label = " << varNodes_[i]->label() << endl;
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cout << "range = " << varNodes_[i]->range() << endl;
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cout << "evidence = " << varNodes_[i]->getEvidence() << endl;
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cout << "factors = " ;
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for (unsigned j = 0; j < varNodes_[i]->neighbors().size(); j++) {
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cout << varNodes_[i]->neighbors()[j]->getLabel() << " " ;
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}
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cout << endl << endl;
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}
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for (unsigned i = 0; i < facNodes_.size(); i++) {
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facNodes_[i]->factor().print();
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}
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}
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void
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FactorGraph::exportToGraphViz (const char* fileName) const
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{
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ofstream out (fileName);
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if (!out.is_open()) {
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cerr << "error: cannot open file to write at " ;
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cerr << "FactorGraph::exportToDotFile()" << endl;
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abort();
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}
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out << "graph \"" << fileName << "\" {" << endl;
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for (unsigned i = 0; i < varNodes_.size(); i++) {
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if (varNodes_[i]->hasEvidence()) {
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out << '"' << varNodes_[i]->label() << '"' ;
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out << " [style=filled, fillcolor=yellow]" << endl;
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}
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}
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for (unsigned i = 0; i < facNodes_.size(); i++) {
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out << '"' << facNodes_[i]->getLabel() << '"' ;
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out << " [label=\"" << facNodes_[i]->getLabel();
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out << "\"" << ", shape=box]" << endl;
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}
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for (unsigned i = 0; i < facNodes_.size(); i++) {
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const VarNodes& myVars = facNodes_[i]->neighbors();
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for (unsigned j = 0; j < myVars.size(); j++) {
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out << '"' << facNodes_[i]->getLabel() << '"' ;
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out << " -- " ;
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out << '"' << myVars[j]->label() << '"' << endl;
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}
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}
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out << "}" << endl;
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out.close();
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}
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void
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FactorGraph::exportToUaiFormat (const char* fileName) const
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{
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ofstream out (fileName);
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if (!out.is_open()) {
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cerr << "error: cannot open file " << fileName << endl;
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abort();
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}
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out << "MARKOV" << endl;
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out << varNodes_.size() << endl;
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for (unsigned i = 0; i < varNodes_.size(); i++) {
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out << varNodes_[i]->range() << " " ;
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}
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out << endl;
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out << facNodes_.size() << endl;
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for (unsigned i = 0; i < facNodes_.size(); i++) {
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const VarNodes& factorVars = facNodes_[i]->neighbors();
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out << factorVars.size();
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for (unsigned j = 0; j < factorVars.size(); j++) {
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out << " " << factorVars[j]->getIndex();
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}
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out << endl;
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}
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for (unsigned i = 0; i < facNodes_.size(); i++) {
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Params params = facNodes_[i]->factor().params();
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if (Globals::logDomain) {
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Util::fromLog (params);
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}
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out << endl << params.size() << endl << " " ;
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for (unsigned j = 0; j < params.size(); j++) {
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out << params[j] << " " ;
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}
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out << endl;
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}
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out.close();
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}
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void
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FactorGraph::exportToLibDaiFormat (const char* fileName) const
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{
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ofstream out (fileName);
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if (!out.is_open()) {
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cerr << "error: cannot open file " << fileName << endl;
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abort();
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}
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out << facNodes_.size() << endl << endl;
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for (unsigned i = 0; i < facNodes_.size(); i++) {
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const VarNodes& factorVars = facNodes_[i]->neighbors();
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out << factorVars.size() << endl;
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for (int j = factorVars.size() - 1; j >= 0; j--) {
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out << factorVars[j]->varId() << " " ;
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}
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out << endl;
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for (unsigned j = 0; j < factorVars.size(); j++) {
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out << factorVars[j]->range() << " " ;
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}
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out << endl;
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Params params = facNodes_[i]->factor().params();
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if (Globals::logDomain) {
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Util::fromLog (params);
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}
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out << params.size() << endl;
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for (unsigned j = 0; j < params.size(); j++) {
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out << j << " " << params[j] << endl;
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}
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out << endl;
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}
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out.close();
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}
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void
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FactorGraph::ignoreLines (std::ifstream& is) const
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{
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string ignoreStr;
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while (is.peek() == '#' || is.peek() == '\n') {
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getline (is, ignoreStr);
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}
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}
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bool
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FactorGraph::containsCycle (void) const
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{
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vector<bool> visitedVars (varNodes_.size(), false);
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vector<bool> visitedFactors (facNodes_.size(), false);
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for (unsigned i = 0; i < varNodes_.size(); i++) {
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int v = varNodes_[i]->getIndex();
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if (!visitedVars[v]) {
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if (containsCycle (varNodes_[i], 0, visitedVars, visitedFactors)) {
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return true;
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}
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}
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}
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return false;
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}
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bool
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FactorGraph::containsCycle (
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const VarNode* v,
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const FacNode* p,
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vector<bool>& visitedVars,
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vector<bool>& visitedFactors) const
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{
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visitedVars[v->getIndex()] = true;
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const FacNodes& adjacencies = v->neighbors();
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for (unsigned i = 0; i < adjacencies.size(); i++) {
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int w = adjacencies[i]->getIndex();
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if (!visitedFactors[w]) {
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if (containsCycle (adjacencies[i], v, visitedVars, visitedFactors)) {
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return true;
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}
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}
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else if (visitedFactors[w] && adjacencies[i] != p) {
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return true;
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}
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}
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return false; // no cycle detected in this component
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}
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bool
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FactorGraph::containsCycle (
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const FacNode* v,
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const VarNode* p,
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vector<bool>& visitedVars,
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vector<bool>& visitedFactors) const
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{
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visitedFactors[v->getIndex()] = true;
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const VarNodes& adjacencies = v->neighbors();
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for (unsigned i = 0; i < adjacencies.size(); i++) {
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int w = adjacencies[i]->getIndex();
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if (!visitedVars[w]) {
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if (containsCycle (adjacencies[i], v, visitedVars, visitedFactors)) {
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return true;
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}
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}
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else if (visitedVars[w] && adjacencies[i] != p) {
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return true;
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}
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}
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return false; // no cycle detected in this component
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}
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