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Merge branch 'master' of /cygdrive/z/vitor/Yap/yap-6.3

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U-WIN-U2045GN0RNQ\Vítor Santos Costa
2011-07-25 17:09:43 +01:00
parent 840e287cda beffc7b69d
commit 4fe1833ece
81 changed files with 4239 additions and 2447 deletions
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342
packages/CLPBN/clpbn/bp/BayesNet.cpp
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@@ -1,30 +1,24 @@
#include <cstdlib>
#include <cassert>
#include <iostream>
#include <fstream>
#include <sstream>
#include <iomanip>
#include <cassert>
#include <cstdlib>
#include <map>
#include "xmlParser/xmlParser.h"
#include "BayesNet.h"
BayesNet::BayesNet (void)
{
}
BayesNet::BayesNet (const char* fileName)
{
map<string, Domain> domains;
XMLNode xMainNode = XMLNode::openFileHelper (fileName, "BIF");
// only the first network is parsed, others are ignored
XMLNode xNode = xMainNode.getChildNode ("NETWORK");
int nVars = xNode.nChildNode ("VARIABLE");
for (int i = 0; i < nVars; i++) {
unsigned nVars = xNode.nChildNode ("VARIABLE");
for (unsigned i = 0; i < nVars; i++) {
XMLNode var = xNode.getChildNode ("VARIABLE", i);
string type = var.getAttribute ("TYPE");
if (type != "nature") {
@@ -32,9 +26,9 @@ BayesNet::BayesNet (const char* fileName)
abort();
}
Domain domain;
string label = var.getChildNode("NAME").getText();
int domainSize = var.nChildNode ("OUTCOME");
for (int j = 0; j < domainSize; j++) {
string varLabel = var.getChildNode("NAME").getText();
unsigned dsize = var.nChildNode ("OUTCOME");
for (unsigned j = 0; j < dsize; j++) {
if (var.getChildNode("OUTCOME", j).getText() == 0) {
stringstream ss;
ss << j + 1;
@@ -43,37 +37,37 @@ BayesNet::BayesNet (const char* fileName)
domain.push_back (var.getChildNode("OUTCOME", j).getText());
}
}
domains.insert (make_pair (label, domain));
domains.insert (make_pair (varLabel, domain));
}
int nDefs = xNode.nChildNode ("DEFINITION");
unsigned nDefs = xNode.nChildNode ("DEFINITION");
if (nVars != nDefs) {
cerr << "error: different number of variables and definitions";
cerr << endl;
cerr << "error: different number of variables and definitions" << endl;
abort();
}
queue<int> indexes;
for (int i = 0; i < nDefs; i++) {
queue<unsigned> indexes;
for (unsigned i = 0; i < nDefs; i++) {
indexes.push (i);
}
while (!indexes.empty()) {
int index = indexes.front();
unsigned index = indexes.front();
indexes.pop();
XMLNode def = xNode.getChildNode ("DEFINITION", index);
string label = def.getChildNode("FOR").getText();
string varLabel = def.getChildNode("FOR").getText();
map<string, Domain>::const_iterator iter;
iter = domains.find (label);
iter = domains.find (varLabel);
if (iter == domains.end()) {
cerr << "error: unknow variable `" << label << "'" << endl;
cerr << "error: unknow variable `" << varLabel << "'" << endl;
abort();
}
bool processItLatter = false;
NodeSet parents;
int nParams = iter->second.size();
BnNodeSet parents;
unsigned nParams = iter->second.size();
for (int j = 0; j < def.nChildNode ("GIVEN"); j++) {
string parentLabel = def.getChildNode("GIVEN", j).getText();
BayesNode* parentNode = getNode (parentLabel);
BayesNode* parentNode = getBayesNode (parentLabel);
if (parentNode) {
nParams *= parentNode->getDomainSize();
parents.push_back (parentNode);
@@ -95,7 +89,7 @@ BayesNet::BayesNet (const char* fileName)
}
if (!processItLatter) {
int count = 0;
unsigned count = 0;
ParamSet params (nParams);
stringstream s (def.getChildNode("TABLE").getText());
while (!s.eof() && count < nParams) {
@@ -104,11 +98,11 @@ BayesNet::BayesNet (const char* fileName)
}
if (count != nParams) {
cerr << "error: invalid number of parameters " ;
cerr << "for variable `" << label << "'" << endl;
cerr << "for variable `" << varLabel << "'" << endl;
abort();
}
params = reorderParameters (params, iter->second.size());
addNode (label, iter->second, parents, params);
addNode (varLabel, iter->second, parents, params);
}
}
setIndexes();
@@ -118,7 +112,6 @@ BayesNet::BayesNet (const char* fileName)
BayesNet::~BayesNet (void)
{
Statistics::writeStats();
for (unsigned i = 0; i < nodes_.size(); i++) {
delete nodes_[i];
}
@@ -127,25 +120,25 @@ BayesNet::~BayesNet (void)
BayesNode*
BayesNet::addNode (unsigned varId)
BayesNet::addNode (Vid vid)
{
indexMap_.insert (make_pair (varId, nodes_.size()));
nodes_.push_back (new BayesNode (varId));
indexMap_.insert (make_pair (vid, nodes_.size()));
nodes_.push_back (new BayesNode (vid));
return nodes_.back();
}
BayesNode*
BayesNet::addNode (unsigned varId,
BayesNet::addNode (Vid vid,
unsigned dsize,
int evidence,
NodeSet& parents,
BnNodeSet& parents,
Distribution* dist)
{
indexMap_.insert (make_pair (varId, nodes_.size()));
indexMap_.insert (make_pair (vid, nodes_.size()));
nodes_.push_back (new BayesNode (
varId, dsize, evidence, parents, dist));
vid, dsize, evidence, parents, dist));
return nodes_.back();
}
@@ -154,7 +147,7 @@ BayesNet::addNode (unsigned varId,
BayesNode*
BayesNet::addNode (string label,
Domain domain,
NodeSet& parents,
BnNodeSet& parents,
ParamSet& params)
{
indexMap_.insert (make_pair (nodes_.size(), nodes_.size()));
@@ -169,9 +162,9 @@ BayesNet::addNode (string label,
BayesNode*
BayesNet::getNode (unsigned varId) const
BayesNet::getBayesNode (Vid vid) const
{
IndexMap::const_iterator it = indexMap_.find(varId);
IndexMap::const_iterator it = indexMap_.find (vid);
if (it == indexMap_.end()) {
return 0;
} else {
@@ -182,7 +175,7 @@ BayesNet::getNode (unsigned varId) const
BayesNode*
BayesNet::getNode (string label) const
BayesNet::getBayesNode (string label) const
{
BayesNode* node = 0;
for (unsigned i = 0; i < nodes_.size(); i++) {
@@ -196,6 +189,15 @@ BayesNet::getNode (string label) const
Variable*
BayesNet::getVariable (Vid vid) const
{
return getBayesNode (vid);
}
void
BayesNet::addDistribution (Distribution* dist)
{
@@ -219,15 +221,15 @@ BayesNet::getDistribution (unsigned distId) const
const NodeSet&
BayesNet::getNodes (void) const
const BnNodeSet&
BayesNet::getBayesNodes (void) const
{
return nodes_;
}
int
unsigned
BayesNet::getNumberOfNodes (void) const
{
return nodes_.size();
@@ -235,10 +237,10 @@ BayesNet::getNumberOfNodes (void) const
NodeSet
BnNodeSet
BayesNet::getRootNodes (void) const
{
NodeSet roots;
BnNodeSet roots;
for (unsigned i = 0; i < nodes_.size(); i++) {
if (nodes_[i]->isRoot()) {
roots.push_back (nodes_[i]);
@@ -249,10 +251,10 @@ BayesNet::getRootNodes (void) const
NodeSet
BnNodeSet
BayesNet::getLeafNodes (void) const
{
NodeSet leafs;
BnNodeSet leafs;
for (unsigned i = 0; i < nodes_.size(); i++) {
if (nodes_[i]->isLeaf()) {
leafs.push_back (nodes_[i]);
@@ -276,30 +278,32 @@ BayesNet::getVariables (void) const
BayesNet*
BayesNet::pruneNetwork (BayesNode* queryNode) const
BayesNet::getMinimalRequesiteNetwork (Vid vid) const
{
NodeSet queryNodes;
queryNodes.push_back (queryNode);
return pruneNetwork (queryNodes);
return getMinimalRequesiteNetwork (VidSet() = {vid});
}
BayesNet*
BayesNet::pruneNetwork (const NodeSet& interestedVars) const
BayesNet::getMinimalRequesiteNetwork (const VidSet& queryVids) const
{
/*
cout << "interested vars: " ;
for (unsigned i = 0; i < interestedVars.size(); i++) {
cout << interestedVars[i]->getLabel() << " " ;
BnNodeSet queryVars;
for (unsigned i = 0; i < queryVids.size(); i++) {
assert (getBayesNode (queryVids[i]));
queryVars.push_back (getBayesNode (queryVids[i]));
}
cout << endl;
*/
// cout << "query vars: " ;
// for (unsigned i = 0; i < queryVars.size(); i++) {
// cout << queryVars[i]->getLabel() << " " ;
// }
// cout << endl;
vector<StateInfo*> states (nodes_.size(), 0);
Scheduling scheduling;
for (NodeSet::const_iterator it = interestedVars.begin();
it != interestedVars.end(); it++) {
for (BnNodeSet::const_iterator it = queryVars.begin();
it != queryVars.end(); it++) {
scheduling.push (ScheduleInfo (*it, false, true));
}
@@ -378,18 +382,18 @@ BayesNet::constructGraph (BayesNet* bn,
states[i]->markedOnTop;
}
if (isRequired) {
NodeSet parents;
BnNodeSet parents;
if (states[i]->markedOnTop) {
const NodeSet& ps = nodes_[i]->getParents();
const BnNodeSet& ps = nodes_[i]->getParents();
for (unsigned j = 0; j < ps.size(); j++) {
BayesNode* parent = bn->getNode (ps[j]->getVarId());
BayesNode* parent = bn->getBayesNode (ps[j]->getVarId());
if (!parent) {
parent = bn->addNode (ps[j]->getVarId());
}
parents.push_back (parent);
}
}
BayesNode* node = bn->getNode (nodes_[i]->getVarId());
BayesNode* node = bn->getBayesNode (nodes_[i]->getVarId());
if (node) {
node->setData (nodes_[i]->getDomainSize(),
nodes_[i]->getEvidence(), parents,
@@ -411,65 +415,6 @@ BayesNet::constructGraph (BayesNet* bn,
bn->setIndexes();
}
/*
void
BayesNet::constructGraph (BayesNet* bn,
const vector<StateInfo*>& states) const
{
for (unsigned i = 0; i < nodes_.size(); i++) {
if (states[i]) {
if (nodes_[i]->hasEvidence() && states[i]->visited) {
NodeSet parents;
if (states[i]->markedOnTop) {
const NodeSet& ps = nodes_[i]->getParents();
for (unsigned j = 0; j < ps.size(); j++) {
BayesNode* parent = bn->getNode (ps[j]->getVarId());
if (parent == 0) {
parent = bn->addNode (ps[j]->getVarId());
}
parents.push_back (parent);
}
}
BayesNode* n = bn->getNode (nodes_[i]->getVarId());
if (n) {
n->setData (nodes_[i]->getDomainSize(),
nodes_[i]->getEvidence(), parents,
nodes_[i]->getDistribution());
} else {
bn->addNode (nodes_[i]->getVarId(),
nodes_[i]->getDomainSize(),
nodes_[i]->getEvidence(), parents,
nodes_[i]->getDistribution());
}
} else if (states[i]->markedOnTop) {
NodeSet parents;
const NodeSet& ps = nodes_[i]->getParents();
for (unsigned j = 0; j < ps.size(); j++) {
BayesNode* parent = bn->getNode (ps[j]->getVarId());
if (parent == 0) {
parent = bn->addNode (ps[j]->getVarId());
}
parents.push_back (parent);
}
BayesNode* n = bn->getNode (nodes_[i]->getVarId());
if (n) {
n->setData (nodes_[i]->getDomainSize(),
nodes_[i]->getEvidence(), parents,
nodes_[i]->getDistribution());
} else {
bn->addNode (nodes_[i]->getVarId(),
nodes_[i]->getDomainSize(),
nodes_[i]->getEvidence(), parents,
nodes_[i]->getDistribution());
}
}
}
}
}*/
bool
@@ -480,70 +425,6 @@ BayesNet::isSingleConnected (void) const
vector<DomainConf>
BayesNet::getDomainConfigurationsOf (const NodeSet& nodes)
{
int nConfs = 1;
for (unsigned i = 0; i < nodes.size(); i++) {
nConfs *= nodes[i]->getDomainSize();
}
vector<DomainConf> confs (nConfs);
for (int i = 0; i < nConfs; i++) {
confs[i].resize (nodes.size());
}
int nReps = 1;
for (int i = nodes.size() - 1; i >= 0; i--) {
int index = 0;
while (index < nConfs) {
for (int j = 0; j < nodes[i]->getDomainSize(); j++) {
for (int r = 0; r < nReps; r++) {
confs[index][i] = j;
index++;
}
}
}
nReps *= nodes[i]->getDomainSize();
}
return confs;
}
vector<string>
BayesNet::getInstantiations (const NodeSet& parents_)
{
int nParents = parents_.size();
int rowSize = 1;
for (unsigned i = 0; i < parents_.size(); i++) {
rowSize *= parents_[i]->getDomainSize();
}
int nReps = 1;
vector<string> headers (rowSize);
for (int i = nParents - 1; i >= 0; i--) {
Domain domain = parents_[i]->getDomain();
int index = 0;
while (index < rowSize) {
for (int j = 0; j < parents_[i]->getDomainSize(); j++) {
for (int r = 0; r < nReps; r++) {
if (headers[index] != "") {
headers[index] = domain[j] + "," + headers[index];
} else {
headers[index] = domain[j];
}
index++;
}
}
}
nReps *= parents_[i]->getDomainSize();
}
return headers;
}
void
BayesNet::setIndexes (void)
{
@@ -565,7 +446,7 @@ BayesNet::freeDistributions (void)
void
BayesNet::printNetwork (void) const
BayesNet::printGraphicalModel (void) const
{
for (unsigned i = 0; i < nodes_.size(); i++) {
cout << *nodes_[i];
@@ -575,32 +456,11 @@ BayesNet::printNetwork (void) const
void
BayesNet::printNetworkToFile (const char* fileName) const
BayesNet::exportToDotFormat (const char* fileName,
bool showNeighborless,
CVidSet& highlightVids) const
{
string s = "../../" ;
s += fileName;
ofstream out (s.c_str());
if (!out.is_open()) {
cerr << "error: cannot open file to write at " ;
cerr << "BayesNet::printToFile()" << endl;
abort();
}
for (unsigned i = 0; i < nodes_.size(); i++) {
out << *nodes_[i];
}
out.close();
}
void
BayesNet::exportToDotFile (const char* fileName,
bool showNeighborless,
const NodeSet& highlightNodes) const
{
string s = "../../" ;
s+= fileName;
ofstream out (s.c_str());
ofstream out (fileName);
if (!out.is_open()) {
cerr << "error: cannot open file to write at " ;
cerr << "BayesNet::exportToDotFile()" << endl;
@@ -608,13 +468,6 @@ BayesNet::exportToDotFile (const char* fileName,
}
out << "digraph \"" << fileName << "\" {" << endl;
for (unsigned i = 0; i < nodes_.size(); i++) {
const NodeSet& childs = nodes_[i]->getChilds();
for (unsigned j = 0; j < childs.size(); j++) {
out << '"' << nodes_[i]->getLabel() << '"' << " -> " ;
out << '"' << childs[j]->getLabel() << '"' << endl;
}
}
for (unsigned i = 0; i < nodes_.size(); i++) {
if (showNeighborless || nodes_[i]->hasNeighbors()) {
@@ -627,9 +480,24 @@ BayesNet::exportToDotFile (const char* fileName,
}
}
for (unsigned i = 0; i < highlightNodes.size(); i++) {
out << '"' << highlightNodes[i]->getLabel() << '"' ;
out << " [shape=box]" << endl;
for (unsigned i = 0; i < highlightVids.size(); i++) {
BayesNode* node = getBayesNode (highlightVids[i]);
if (node) {
out << '"' << node->getLabel() << '"' ;
// out << " [shape=polygon, sides=6]" << endl;
out << " [shape=box3d]" << endl;
} else {
cout << "error: invalid variable id: " << highlightVids[i] << endl;
abort();
}
}
for (unsigned i = 0; i < nodes_.size(); i++) {
const BnNodeSet& childs = nodes_[i]->getChilds();
for (unsigned j = 0; j < childs.size(); j++) {
out << '"' << nodes_[i]->getLabel() << '"' << " -> " ;
out << '"' << childs[j]->getLabel() << '"' << endl;
}
}
out << "}" << endl;
@@ -639,11 +507,9 @@ BayesNet::exportToDotFile (const char* fileName,
void
BayesNet::exportToBifFile (const char* fileName) const
BayesNet::exportToBifFormat (const char* fileName) const
{
string s = "../../" ;
s += fileName;
ofstream out (s.c_str());
ofstream out (fileName);
if(!out.is_open()) {
cerr << "error: cannot open file to write at " ;
cerr << "BayesNet::exportToBifFile()" << endl;
@@ -666,7 +532,7 @@ BayesNet::exportToBifFile (const char* fileName) const
for (unsigned i = 0; i < nodes_.size(); i++) {
out << "<DEFINITION>" << endl;
out << "\t<FOR>" << nodes_[i]->getLabel() << "</FOR>" << endl;
const NodeSet& parents = nodes_[i]->getParents();
const BnNodeSet& parents = nodes_[i]->getParents();
for (unsigned j = 0; j < parents.size(); j++) {
out << "\t<GIVEN>" << parents[j]->getLabel();
out << "</GIVEN>" << endl;
@@ -682,7 +548,7 @@ BayesNet::exportToBifFile (const char* fileName) const
}
out << "</NETWORK>" << endl;
out << "</BIF>" << endl << endl;
out.close();
out.close();
}
@@ -731,8 +597,8 @@ vector<int>
BayesNet::getAdjacentNodes (int v) const
{
vector<int> adjacencies;
const NodeSet& parents = nodes_[v]->getParents();
const NodeSet& childs = nodes_[v]->getChilds();
const BnNodeSet& parents = nodes_[v]->getParents();
const BnNodeSet& childs = nodes_[v]->getChilds();
for (unsigned i = 0; i < parents.size(); i++) {
adjacencies.push_back (parents[i]->getIndex());
}
@@ -745,8 +611,8 @@ BayesNet::getAdjacentNodes (int v) const
ParamSet
BayesNet::reorderParameters (const ParamSet& params,
int domainSize) const
BayesNet::reorderParameters (CParamSet params,
unsigned domainSize) const
{
// the interchange format for bayesian networks keeps the probabilities
// in the following order:
@@ -773,15 +639,15 @@ BayesNet::reorderParameters (const ParamSet& params,
ParamSet
BayesNet::revertParameterReorder (const ParamSet& params,
int domainSize) const
BayesNet::revertParameterReorder (CParamSet params,
unsigned domainSize) const
{
unsigned count = 0;
unsigned rowSize = params.size() / domainSize;
ParamSet reordered;
while (reordered.size() < params.size()) {
unsigned idx = count;
for (int i = 0; i < domainSize; i++) {
for (unsigned i = 0; i < domainSize; i++) {
reordered.push_back (params[idx]);
idx += rowSize;
}