diogo/yap-6.3
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new release from Tiago

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This commit is contained in:
Vítor Santos Costa
2011-12-12 15:29:51 +00:00
parent 03391e3feb
commit 33bf0bc0f5
33 changed files with 5943 additions and 1167 deletions
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154
packages/CLPBN/clpbn/bp/HorusCli.cpp
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@@ -5,15 +5,18 @@
#include "BayesNet.h"
#include "FactorGraph.h"
#include "SPSolver.h"
#include "BPSolver.h"
#include "CountingBP.h"
#include "VarElimSolver.h"
#include "BnBpSolver.h"
#include "FgBpSolver.h"
#include "CbpSolver.h"
#include "StatesIndexer.h"
using namespace std;
void BayesianNetwork (int, const char* []);
void markovNetwork (int, const char* []);
void runSolver (Solver*, const VarSet&);
void processArguments (BayesNet&, int, const char* []);
void processArguments (FactorGraph&, int, const char* []);
void runSolver (Solver*, const VarNodes&);
const string USAGE = "usage: \
./hcli FILE [VARIABLE | OBSERVED_VARIABLE=EVIDENCE]..." ;
@@ -21,33 +24,7 @@ const string USAGE = "usage: \
int
main (int argc, const char* argv[])
{
/*
FactorGraph fg;
FgVarNode* varNode1 = new FgVarNode (0, 2);
FgVarNode* varNode2 = new FgVarNode (1, 2);
FgVarNode* varNode3 = new FgVarNode (2, 2);
fg.addVariable (varNode1);
fg.addVariable (varNode2);
fg.addVariable (varNode3);
Distribution* dist = new Distribution (ParamSet() = {1.2, 1.4, 2.0, 0.4});
fg.addFactor (new Factor (FgVarSet() = {varNode1, varNode2}, dist));
fg.addFactor (new Factor (FgVarSet() = {varNode3, varNode2}, dist));
//fg.printGraphicalModel();
//SPSolver sp (fg);
//sp.runSolver();
//sp.printAllPosterioris();
//ParamSet p = sp.getJointDistributionOf (VidSet() = {0, 1, 2});
//cout << Util::parametersToString (p) << endl;
CountingBP cbp (fg);
//cbp.runSolver();
//cbp.printAllPosterioris();
ParamSet p2 = cbp.getJointDistributionOf (VidSet() = {0, 1, 2});
cout << Util::parametersToString (p2) << endl;
fg.freeDistributions();
Statistics::printCompressingStats ("compressing.stats");
return 0;
*/
{
if (!argv[1]) {
cerr << "error: no graphical model specified" << endl;
cerr << USAGE << endl;
@@ -56,12 +33,20 @@ main (int argc, const char* argv[])
const string& fileName = argv[1];
const string& extension = fileName.substr (fileName.find_last_of ('.') + 1);
if (extension == "xml") {
BayesianNetwork (argc, argv);
BayesNet bn;
bn.readFromBifFormat (argv[1]);
processArguments (bn, argc, argv);
} else if (extension == "uai") {
markovNetwork (argc, argv);
FactorGraph fg;
fg.readFromUaiFormat (argv[1]);
processArguments (fg, argc, argv);
} else if (extension == "fg") {
FactorGraph fg;
fg.readFromLibDaiFormat (argv[1]);
processArguments (fg, argc, argv);
} else {
cerr << "error: the graphical model must be defined either " ;
cerr << "in a xml file or uai file" << endl;
cerr << "in a xml, uai or libDAI file" << endl;
exit (0);
}
return 0;
@@ -70,12 +55,9 @@ main (int argc, const char* argv[])
void
BayesianNetwork (int argc, const char* argv[])
processArguments (BayesNet& bn, int argc, const char* argv[])
{
BayesNet bn (argv[1]);
//bn.printGraphicalModel();
VarSet queryVars;
VarNodes queryVars;
for (int i = 2; i < argc; i++) {
const string& arg = argv[i];
if (arg.find ('=') == std::string::npos) {
@@ -86,6 +68,7 @@ BayesianNetwork (int argc, const char* argv[])
cerr << "error: there isn't a variable labeled of " ;
cerr << "`" << arg << "'" ;
cerr << endl;
bn.freeDistributions();
exit (0);
}
} else {
@@ -95,11 +78,13 @@ BayesianNetwork (int argc, const char* argv[])
if (label.empty()) {
cerr << "error: missing left argument" << endl;
cerr << USAGE << endl;
bn.freeDistributions();
exit (0);
}
if (state.empty()) {
cerr << "error: missing right argument" << endl;
cerr << USAGE << endl;
bn.freeDistributions();
exit (0);
}
BayesNode* node = bn.getBayesNode (label);
@@ -109,42 +94,54 @@ BayesianNetwork (int argc, const char* argv[])
} else {
cerr << "error: `" << state << "' " ;
cerr << "is not a valid state for " ;
cerr << "`" << node->getLabel() << "'" ;
cerr << "`" << node->label() << "'" ;
cerr << endl;
bn.freeDistributions();
exit (0);
}
} else {
cerr << "error: there isn't a variable labeled of " ;
cerr << "`" << label << "'" ;
cerr << endl;
bn.freeDistributions();
exit (0);
}
}
}
Solver* solver;
if (SolverOptions::convertBn2Fg) {
FactorGraph* fg = new FactorGraph (bn);
fg->printGraphicalModel();
solver = new SPSolver (*fg);
runSolver (solver, queryVars);
delete fg;
} else {
solver = new BPSolver (bn);
runSolver (solver, queryVars);
Solver* solver = 0;
FactorGraph* fg = 0;
switch (InfAlgorithms::infAlgorithm) {
case InfAlgorithms::VE:
fg = new FactorGraph (bn);
solver = new VarElimSolver (*fg);
break;
case InfAlgorithms::BN_BP:
solver = new BnBpSolver (bn);
break;
case InfAlgorithms::FG_BP:
fg = new FactorGraph (bn);
fg->printGraphicalModel();
solver = new FgBpSolver (*fg);
break;
case InfAlgorithms::CBP:
fg = new FactorGraph (bn);
solver = new CbpSolver (*fg);
break;
default:
assert (false);
}
runSolver (solver, queryVars);
delete fg;
bn.freeDistributions();
}
void
markovNetwork (int argc, const char* argv[])
processArguments (FactorGraph& fg, int argc, const char* argv[])
{
FactorGraph fg (argv[1]);
//fg.printGraphicalModel();
VarSet queryVars;
VarNodes queryVars;
for (int i = 2; i < argc; i++) {
const string& arg = argv[i];
if (arg.find ('=') == std::string::npos) {
@@ -152,19 +149,21 @@ markovNetwork (int argc, const char* argv[])
cerr << "error: `" << arg << "' " ;
cerr << "is not a valid variable id" ;
cerr << endl;
fg.freeDistributions();
exit (0);
}
Vid vid;
VarId vid;
stringstream ss;
ss << arg;
ss >> vid;
Variable* queryVar = fg.getFgVarNode (vid);
VarNode* queryVar = fg.getFgVarNode (vid);
if (queryVar) {
queryVars.push_back (queryVar);
} else {
cerr << "error: there isn't a variable with " ;
cerr << "`" << vid << "' as id" ;
cerr << endl;
fg.freeDistributions();
exit (0);
}
} else {
@@ -172,53 +171,73 @@ markovNetwork (int argc, const char* argv[])
if (arg.substr (0, pos).empty()) {
cerr << "error: missing left argument" << endl;
cerr << USAGE << endl;
fg.freeDistributions();
exit (0);
}
if (arg.substr (pos + 1).empty()) {
cerr << "error: missing right argument" << endl;
cerr << USAGE << endl;
fg.freeDistributions();
exit (0);
}
if (!Util::isInteger (arg.substr (0, pos))) {
cerr << "error: `" << arg.substr (0, pos) << "' " ;
cerr << "is not a variable id" ;
cerr << endl;
fg.freeDistributions();
exit (0);
}
Vid vid;
VarId vid;
stringstream ss;
ss << arg.substr (0, pos);
ss >> vid;
Variable* var = fg.getFgVarNode (vid);
VarNode* var = fg.getFgVarNode (vid);
if (var) {
if (!Util::isInteger (arg.substr (pos + 1))) {
cerr << "error: `" << arg.substr (pos + 1) << "' " ;
cerr << "is not a state index" ;
cerr << endl;
fg.freeDistributions();
exit (0);
}
int stateIndex;
stringstream ss;
ss << arg.substr (pos + 1);
ss >> stateIndex;
if (var->isValidStateIndex (stateIndex)) {
if (var->isValidState (stateIndex)) {
var->setEvidence (stateIndex);
} else {
cerr << "error: `" << stateIndex << "' " ;
cerr << "is not a valid state index for variable " ;
cerr << "`" << var->getVarId() << "'" ;
cerr << "`" << var->varId() << "'" ;
cerr << endl;
fg.freeDistributions();
exit (0);
}
} else {
cerr << "error: there isn't a variable with " ;
cerr << "`" << vid << "' as id" ;
cerr << endl;
fg.freeDistributions();
exit (0);
}
}
}
Solver* solver = new SPSolver (fg);
Solver* solver = 0;
switch (InfAlgorithms::infAlgorithm) {
case InfAlgorithms::VE:
solver = new VarElimSolver (fg);
break;
case InfAlgorithms::BN_BP:
case InfAlgorithms::FG_BP:
solver = new FgBpSolver (fg);
break;
case InfAlgorithms::CBP:
solver = new CbpSolver (fg);
break;
default:
assert (false);
}
runSolver (solver, queryVars);
fg.freeDistributions();
}
@@ -226,11 +245,11 @@ markovNetwork (int argc, const char* argv[])
void
runSolver (Solver* solver, const VarSet& queryVars)
runSolver (Solver* solver, const VarNodes& queryVars)
{
VidSet vids;
VarIdSet vids;
for (unsigned i = 0; i < queryVars.size(); i++) {
vids.push_back (queryVars[i]->getVarId());
vids.push_back (queryVars[i]->varId());
}
if (queryVars.size() == 0) {
solver->runSolver();
@@ -239,6 +258,7 @@ runSolver (Solver* solver, const VarSet& queryVars)
solver->runSolver();
solver->printPosterioriOf (vids[0]);
} else {
solver->runSolver();
solver->printJointDistributionOf (vids);
}
delete solver;