diogo/yap-6.3
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Factor nodes now contain a factor object instead of a pointer. Refactor the way .fg and .uai formats are readed.
This commit is contained in:
Tiago Gomes
2012-04-09 15:40:51 +01:00
parent f1d52c0389
commit 6986e8c0d7
16 changed files with 233 additions and 310 deletions
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256
packages/CLPBN/clpbn/bp/FactorGraph.cpp
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@@ -18,21 +18,20 @@ bool FactorGraph::orderFactorVariables = false;
FactorGraph::FactorGraph (const FactorGraph& fg)
{
const VarNodes& vars = fg.varNodes();
for (unsigned i = 0; i < vars.size(); i++) {
VarNode* varNode = new VarNode (vars[i]);
addVariable (varNode);
const VarNodes& varNodes = fg.varNodes();
for (unsigned i = 0; i < varNodes.size(); i++) {
addVarNode (new VarNode (varNodes[i]));
}
const FactorNodes& facs = fg.factorNodes();
for (unsigned i = 0; i < facs.size(); i++) {
FactorNode* facNode = new FactorNode (facs[i]);
addFactor (facNode);
const VarNodes& neighs = facs[i]->neighbors();
const FactorNodes& facNodes = fg.factorNodes();
for (unsigned i = 0; i < facNodes.size(); i++) {
FactorNode* facNode = new FactorNode (facNodes[i]->factor());
addFactorNode (facNode);
const VarNodes& neighs = facNodes[i]->neighbors();
for (unsigned j = 0; j < neighs.size(); j++) {
addEdge (facNode, varNodes_[neighs[j]->getIndex()]);
}
}
setIndexes();
}
@@ -40,82 +39,70 @@ FactorGraph::FactorGraph (const FactorGraph& fg)
void
FactorGraph::readFromUaiFormat (const char* fileName)
{
ifstream is (fileName);
ifstream is (fileName);
if (!is.is_open()) {
cerr << "error: cannot read from file " + std::string (fileName) << endl;
abort();
}
ignoreLines (is);
string line;
while (is.peek() == '#' || is.peek() == '\n') getline (is, line);
getline (is, line);
if (line != "MARKOV") {
cerr << "error: the network must be a MARKOV network " << endl;
abort();
}
while (is.peek() == '#' || is.peek() == '\n') getline (is, line);
unsigned nVars;
is >> nVars;
while (is.peek() == '#' || is.peek() == '\n') getline (is, line);
vector<int> domainSizes (nVars);
for (unsigned i = 0; i < nVars; i++) {
unsigned ds;
is >> ds;
domainSizes[i] = ds;
// 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];
}
while (is.peek() == '#' || is.peek() == '\n') getline (is, line);
for (unsigned i = 0; i < nVars; i++) {
addVariable (new VarNode (i, domainSizes[i]));
}
unsigned nFactors;
is >> nFactors;
for (unsigned i = 0; i < nFactors; i++) {
while (is.peek() == '#' || is.peek() == '\n') getline (is, line);
unsigned nFactorVars;
is >> nFactorVars;
Vars neighs;
for (unsigned j = 0; j < nFactorVars; j++) {
unsigned vid;
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;
VarNode* neigh = getVarNode (vid);
if (!neigh) {
cerr << "error: invalid variable identifier (" << vid << ")" << endl;
if (vid >= ranges.size()) {
cerr << "error: invalid variable identifier `" << vid << "'" << endl;
cerr << "identifiers must be between 0 and " << ranges.size() - 1 ;
cerr << endl;
abort();
}
neighs.push_back (neigh);
}
FactorNode* fn = new FactorNode (new Factor (neighs));
addFactor (fn);
for (unsigned j = 0; j < neighs.size(); j++) {
addEdge (fn, static_cast<VarNode*> (neighs[j]));
factorVarIds.back().push_back (vid);
factorRanges.back().push_back (ranges[vid]);
}
}
for (unsigned i = 0; i < nFactors; i++) {
while (is.peek() == '#' || is.peek() == '\n') getline (is, line);
unsigned nParams;
is >> nParams;
if (facNodes_[i]->params().size() != nParams) {
cerr << "error: invalid number of parameters for factor " ;
cerr << facNodes_[i]->getLabel() ;
cerr << ", expected: " << facNodes_[i]->params().size();
cerr << ", given: " << nParams << endl;
// read the parameters
unsigned nrParams;
for (unsigned i = 0; i < nrFactors; i++) {
ignoreLines (is);
is >> nrParams;
if (nrParams != Util::expectedSize (factorRanges[i])) {
cerr << "error: invalid number of parameters for factor nº " << i ;
cerr << ", expected: " << Util::expectedSize (factorRanges[i]);
cerr << ", given: " << nrParams << endl;
abort();
}
Params params (nParams);
for (unsigned j = 0; j < nParams; j++) {
double param;
is >> param;
params[j] = param;
Params params (nrParams);
for (unsigned j = 0; j < nrParams; j++) {
is >> params[j];
}
if (Globals::logDomain) {
Util::toLog (params);
}
facNodes_[i]->factor()->setParams (params);
addFactor (Factor (factorVarIds[i], factorRanges[i], params));
}
is.close();
setIndexes();
@@ -131,79 +118,51 @@ FactorGraph::readFromLibDaiFormat (const char* fileName)
cerr << "error: cannot read from file " + std::string (fileName) << endl;
abort();
}
string line;
unsigned nFactors;
while ((is.peek()) == '#') getline (is, line);
is >> nFactors;
if (is.fail()) {
cerr << "error: cannot read the number of factors" << endl;
abort();
}
getline (is, line);
if (is.fail() || line.size() > 0) {
cerr << "error: cannot read the number of factors" << endl;
abort();
}
for (unsigned i = 0; i < nFactors; i++) {
unsigned nVars;
while ((is.peek()) == '#') getline (is, line);
is >> nVars;
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 < nVars; j++) {
VarId vid;
while ((is.peek()) == '#') getline (is, line);
for (unsigned j = 0; j < nrArgs; j++) {
ignoreLines (is);
is >> vid;
vids.push_back (vid);
}
Vars neighs;
unsigned nParams = 1;
for (unsigned j = 0; j < nVars; j++) {
unsigned dsize;
while ((is.peek()) == '#') getline (is, line);
is >> dsize;
// 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) {
var = new VarNode (vids[j], dsize);
addVariable (var);
} else {
if (var->range() != dsize) {
cerr << "error: variable `" << vids[j] << "' appears in two or " ;
cerr << "more factors with different domain sizes" << endl;
}
if (var != 0 && ranges[j] != var->range()) {
cerr << "error: variable `" << vids[j] << "' appears in two or " ;
cerr << "more factors with a different range" << endl;
}
neighs.push_back (var);
nParams *= var->range();
}
Params params (nParams, 0);
// read parameters
ignoreLines (is);
unsigned nNonzeros;
while ((is.peek()) == '#') getline (is, line);
is >> nNonzeros;
Params params (Util::expectedSize (ranges), 0);
for (unsigned j = 0; j < nNonzeros; j++) {
ignoreLines (is);
unsigned index;
double val;
while ((is.peek()) == '#') getline (is, line);
is >> index;
while ((is.peek()) == '#') getline (is, line);
ignoreLines (is);
double val;
is >> val;
params[index] = val;
}
reverse (neighs.begin(), neighs.end());
reverse (vids.begin(), vids.end());
if (Globals::logDomain) {
Util::toLog (params);
}
FactorNode* fn = new FactorNode (new Factor (neighs, params));
addFactor (fn);
for (unsigned j = 0; j < neighs.size(); j++) {
addEdge (fn, static_cast<VarNode*> (neighs[j]));
}
addFactor (Factor (vids, ranges, params));
}
is.close();
setIndexes();
@@ -223,30 +182,11 @@ FactorGraph::~FactorGraph (void)
void
FactorGraph::addVariable (VarNode* vn)
{
varNodes_.push_back (vn);
vn->setIndex (varNodes_.size() - 1);
varMap_.insert (make_pair (vn->varId(), varNodes_.size() - 1));
}
void
FactorGraph::addFactor (FactorNode* fn)
{
facNodes_.push_back (fn);
fn->setIndex (facNodes_.size() - 1);
}
void
FactorGraph::addFactor (const Factor& factor)
{
FactorNode* fn = new FactorNode (factor);
addFactor (fn);
addFactorNode (fn);
const VarIds& vids = factor.arguments();
for (unsigned i = 0; i < vids.size(); i++) {
bool found = false;
@@ -258,7 +198,7 @@ FactorGraph::addFactor (const Factor& factor)
}
if (found == false) {
VarNode* vn = new VarNode (vids[i], factor.range (i));
addVariable (vn);
addVarNode (vn);
addEdge (vn, fn);
}
}
@@ -266,6 +206,25 @@ FactorGraph::addFactor (const Factor& factor)
void
FactorGraph::addVarNode (VarNode* vn)
{
varNodes_.push_back (vn);
vn->setIndex (varNodes_.size() - 1);
varMap_.insert (make_pair (vn->varId(), varNodes_.size() - 1));
}
void
FactorGraph::addFactorNode (FactorNode* fn)
{
facNodes_.push_back (fn);
fn->setIndex (facNodes_.size() - 1);
}
void
FactorGraph::addEdge (VarNode* vn, FactorNode* fn)
{
@@ -301,7 +260,7 @@ FactorGraph::getStructure (void)
structure_.addNode (new DAGraphNode (varNodes_[i]));
}
for (unsigned i = 0; i < facNodes_.size(); i++) {
const VarIds& vids = facNodes_[i]->factor()->arguments();
const VarIds& vids = facNodes_[i]->factor().arguments();
for (unsigned j = 1; j < vids.size(); j++) {
structure_.addEdge (vids[j], vids[0]);
}
@@ -340,7 +299,7 @@ FactorGraph::print (void) const
cout << endl << endl;
}
for (unsigned i = 0; i < facNodes_.size(); i++) {
facNodes_[i]->factor()->print();
facNodes_[i]->factor().print();
}
}
@@ -446,7 +405,7 @@ FactorGraph::exportToLibDaiFormat (const char* fileName) const
out << factorVars[j]->range() << " " ;
}
out << endl;
Params params = facNodes_[i]->factor()->params();
Params params = facNodes_[i]->factor().params();
if (Globals::logDomain) {
Util::fromLog (params);
}
@@ -461,6 +420,17 @@ FactorGraph::exportToLibDaiFormat (const char* fileName) const
void
FactorGraph::ignoreLines (std::ifstream& is) const
{
string ignoreStr;
while (is.peek() == '#' || is.peek() == '\n') {
getline (is, ignoreStr);
}
}
bool
FactorGraph::containsCycle (void) const
{