Use a static method to create a FactorGraph
This commit is contained in:
Tiago Gomes
parent
2ef1651c6a
commit
bc04d28092
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@ -18,20 +18,7 @@ bool FactorGraph::printFg_ = false;
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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 (size_t 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 (size_t 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 (size_t 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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bayesFactors_ = fg.bayesianFactors();
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clone (fg);
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}
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@ -48,157 +35,6 @@ FactorGraph::~FactorGraph()
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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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std::cerr << "Error: couldn't open file '" << fileName << "'." ;
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std::cerr << std::endl;
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exit (EXIT_FAILURE);
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}
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ignoreLines (is);
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std::string line;
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getline (is, line);
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if (line == "BAYES") {
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bayesFactors_ = true;
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} else if (line == "MARKOV") {
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bayesFactors_ = false;
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} else {
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std::cerr << "Error: the type of network is missing." << std::endl;
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exit (EXIT_FAILURE);
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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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std::vector<VarIds> allVarIds;
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std::vector<Ranges> allRanges;
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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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allVarIds.push_back ({ });
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allRanges.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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std::cerr << "Error: invalid variable identifier `" << vid << "'" ;
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std::cerr << ". Identifiers must be between 0 and " ;
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std::cerr << ranges.size() - 1 << "." << std::endl;
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exit (EXIT_FAILURE);
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}
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allVarIds.back().push_back (vid);
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allRanges.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::sizeExpected (allRanges[i])) {
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std::cerr << "Error: invalid number of parameters for factor nº " ;
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std::cerr << i << ", " << Util::sizeExpected (allRanges[i]);
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std::cerr << " expected, " << nrParams << " given." << std::endl;
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exit (EXIT_FAILURE);
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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::log (params);
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}
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Factor f (allVarIds[i], allRanges[i], params);
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if (bayesFactors_ && allVarIds[i].size() > 1) {
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// In this format the child is the last variable,
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// move it to be the first
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std::swap (allVarIds[i].front(), allVarIds[i].back());
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f.reorderArguments (allVarIds[i]);
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}
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addFactor (f);
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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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std::cerr << "Error: couldn't open file '" << fileName << "'." ;
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std::cerr << std::endl;
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exit (EXIT_FAILURE);
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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 && ranges[j] != var->range()) {
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std::cerr << "Error: variable `" << vids[j] << "' appears" ;
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std::cerr << " in two or more factors with a different range." ;
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std::cerr << std::endl;
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exit (EXIT_FAILURE);
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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::sizeExpected (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::log (params);
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}
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std::reverse (vids.begin(), vids.end());
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std::reverse (ranges.begin(), ranges.end());
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Factor f (vids, ranges, params);
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std::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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void
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FactorGraph::addFactor (const Factor& factor)
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{
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@ -412,13 +248,198 @@ FactorGraph::exportToGraphViz (const char* fileName) const
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void
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FactorGraph::ignoreLines (std::ifstream& is) const
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FactorGraph&
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FactorGraph::operator= (const FactorGraph& fg)
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{
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std::string ignoreStr;
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while (is.peek() == '#' || is.peek() == '\n') {
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getline (is, ignoreStr);
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if (this != &fg) {
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for (size_t i = 0; i < varNodes_.size(); i++) {
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delete varNodes_[i];
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}
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varNodes_.clear();
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for (size_t i = 0; i < facNodes_.size(); i++) {
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delete facNodes_[i];
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}
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facNodes_.clear();
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varMap_.clear();
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clone (fg);
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}
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return *this;
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}
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FactorGraph
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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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std::cerr << "Error: couldn't open file '" << fileName << "'." ;
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std::cerr << std::endl;
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exit (EXIT_FAILURE);
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}
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FactorGraph fg;
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ignoreLines (is);
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std::string line;
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getline (is, line);
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if (line == "BAYES") {
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fg.bayesFactors_ = true;
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} else if (line == "MARKOV") {
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fg.bayesFactors_ = false;
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} else {
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std::cerr << "Error: the type of network is missing." << std::endl;
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exit (EXIT_FAILURE);
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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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std::vector<VarIds> allVarIds;
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std::vector<Ranges> allRanges;
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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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allVarIds.push_back ({ });
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allRanges.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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std::cerr << "Error: invalid variable identifier `" << vid << "'" ;
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std::cerr << ". Identifiers must be between 0 and " ;
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std::cerr << ranges.size() - 1 << "." << std::endl;
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exit (EXIT_FAILURE);
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}
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allVarIds.back().push_back (vid);
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allRanges.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::sizeExpected (allRanges[i])) {
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std::cerr << "Error: invalid number of parameters for factor nº " ;
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std::cerr << i << ", " << Util::sizeExpected (allRanges[i]);
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std::cerr << " expected, " << nrParams << " given." << std::endl;
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exit (EXIT_FAILURE);
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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::log (params);
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}
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Factor f (allVarIds[i], allRanges[i], params);
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if (fg.bayesFactors_ && allVarIds[i].size() > 1) {
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// In this format the child is the last variable,
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// move it to be the first
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std::swap (allVarIds[i].front(), allVarIds[i].back());
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f.reorderArguments (allVarIds[i]);
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}
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fg.addFactor (f);
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}
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is.close();
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return fg;
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}
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FactorGraph
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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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std::cerr << "Error: couldn't open file '" << fileName << "'." ;
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std::cerr << std::endl;
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exit (EXIT_FAILURE);
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}
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FactorGraph fg;
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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 = fg.getVarNode (vids[j]);
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if (var && ranges[j] != var->range()) {
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std::cerr << "Error: variable `" << vids[j] << "' appears" ;
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std::cerr << " in two or more factors with a different range." ;
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std::cerr << std::endl;
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exit (EXIT_FAILURE);
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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::sizeExpected (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::log (params);
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}
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std::reverse (vids.begin(), vids.end());
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std::reverse (ranges.begin(), ranges.end());
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Factor f (vids, ranges, params);
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std::reverse (vids.begin(), vids.end());
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f.reorderArguments (vids);
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fg.addFactor (f);
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}
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is.close();
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return fg;
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}
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void
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FactorGraph::clone (const FactorGraph& fg)
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{
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const VarNodes& varNodes = fg.varNodes();
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for (size_t 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 (size_t 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 (size_t 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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bayesFactors_ = fg.bayesianFactors();
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}
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@ -489,5 +510,16 @@ FactorGraph::containsCycle (
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return false; // no cycle detected in this component
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}
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void
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FactorGraph::ignoreLines (std::ifstream& is)
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{
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std::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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} // namespace Horus
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@ -86,10 +86,6 @@ class FactorGraph {
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VarNode* getVarNode (VarId vid) const;
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void readFromUaiFormat (const char*);
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void readFromLibDaiFormat (const char*);
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void addFactor (const Factor& factor);
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void addVarNode (VarNode*);
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@ -110,6 +106,12 @@ class FactorGraph {
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void exportToGraphViz (const char*) const;
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FactorGraph& operator= (const FactorGraph&);
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static FactorGraph readFromUaiFormat (const char*);
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static FactorGraph readFromLibDaiFormat (const char*);
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static bool exportToLibDai() { return exportLd_; }
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static bool exportToUai() { return exportUai_; }
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@ -137,7 +139,7 @@ class FactorGraph {
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private:
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typedef std::unordered_map<unsigned, VarNode*> VarMap;
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void ignoreLines (std::ifstream&) const;
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void clone (const FactorGraph& fg);
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bool containsCycle() const;
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@ -147,6 +149,8 @@ class FactorGraph {
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bool containsCycle (const FacNode*, const VarNode*,
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std::vector<bool>&, std::vector<bool>&) const;
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static void ignoreLines (std::ifstream&);
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VarNodes varNodes_;
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FacNodes facNodes_;
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VarMap varMap_;
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@ -157,8 +161,6 @@ class FactorGraph {
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static bool exportUai_;
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static bool exportGv_;
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static bool printFg_;
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DISALLOW_ASSIGN (FactorGraph);
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};
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@ -100,9 +100,9 @@ readFactorGraph (Horus::FactorGraph& fg, const char* s)
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std::string fileName (s);
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std::string extension = fileName.substr (fileName.find_last_of ('.') + 1);
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if (extension == "uai") {
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fg.readFromUaiFormat (fileName.c_str());
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fg = Horus::FactorGraph::readFromUaiFormat (fileName.c_str());
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} else if (extension == "fg") {
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fg.readFromLibDaiFormat (fileName.c_str());
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fg = Horus::FactorGraph::readFromLibDaiFormat (fileName.c_str());
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} else {
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std::cerr << "Error: the probabilistic graphical model must be " ;
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std::cerr << "defined either in a UAI or libDAI file." << std::endl;
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