void CBKInfEngine::
Get1_5Clusters(int nnodesPerSlice, intVector& interfNds, intVecVector& clusters,
intVecVector* clusters1_5Sl) const
{
int nInterfNds = interfNds.size();
clusters1_5Sl->assign( clusters.begin(), clusters.end() );
clusters1_5Sl->insert( clusters1_5Sl->end(), clusters.begin(), clusters.end() );
int nClusters = clusters.size();
int i,j;
for( i = 0; i < nClusters; i++ )
{
int nnodesPerClust = clusters[i].size();
for( j = 0; j < nnodesPerClust; j++ )
{
intVector::iterator loc = std::find( interfNds.begin(),
interfNds.end(), clusters[i][j] );
(*clusters1_5Sl)[i][j] = loc - interfNds.begin();
(*clusters1_5Sl)[i + nClusters][j] += nInterfNds;
}
}
}
void CSamplingInfEngine::
GetObsDimsWithVls(intVector &domain, int nonObsNode, const CEvidence* pEv,
intVector *dims, intVector *vls) const
{
int nnodes = domain.size();
dims->resize(nnodes - 1);
vls->resize(nnodes - 1);
int* it = &domain.front();
int* itDims = &dims->front();
int* itVls = &vls->front();
int i;
for( i = 0; i < nnodes; i++, it++ )
{
if( *it != nonObsNode )
{
*itDims = i;
*itVls = pEv->GetValueBySerialNumber(*it)->GetInt();//only if all nds are tabular!!
itDims++;
itVls++;
}
}
}
bool CBKInfEngine::
CheckClustersValidity( intVecVector& clusters, intVector& interfNds )
{
if( clusters.empty() )
{
return false;
}
intVector::iterator interfNdsLit = interfNds.begin();
intVector::iterator interfNdsRit = interfNds.end();
int i;
for( i = 0; i < clusters.size(); i++ )
{
if( clusters[i].empty() )
{
return false;
}
else
{
int j;
for( j = 0; j < clusters[i].size(); j++ )
{
if( std::find(interfNdsLit, interfNdsRit, clusters[i][j]) == interfNdsRit )
{
return false;
}
}
}
}
return true;
}
CMlStaticStructLearn::CMlStaticStructLearn(CStaticGraphicalModel *pGrModel,
ELearningTypes LearnType,
EOptimizeTypes AlgorithmType,
EScoreFunTypes ScoreType, int nMaxFanIn,
intVector& vAncestor, intVector& vDescent)
:CStaticLearningEngine(pGrModel, LearnType),
m_pResultBNet(NULL), m_pResultDAG(NULL)
{
int nnodes = pGrModel->GetNumberOfNodes();
m_nNodes = nnodes;
int i;
for (i = 0; i<nnodes; i++) m_vResultRenaming.push_back(i);
m_ScoreType = ScoreType;
m_Algorithm = AlgorithmType;
m_nMaxFanIn = nMaxFanIn;
m_ScoreMethod = MaxLh;
m_priorType = Dirichlet;
m_K2alfa = 0;
m_vAncestor.assign(vAncestor.begin(), vAncestor.end());
m_vDescent.assign(vDescent.begin(),vDescent.end());
PNL_CHECK_RANGES(nMaxFanIn, 1, nnodes);
intVector ranges(nMaxFanIn);
for(i=0; i<nMaxFanIn; i++) ranges[i] = nnodes+1;
float max = 0.0f;
m_pNodeScoreCache = (CSparseMatrix<float>**)malloc(nnodes * sizeof(CSparseMatrix<float>*));
for(i=0; i<nnodes; i++)
{
m_pNodeScoreCache[i] = CSparseMatrix<float>::Create(nMaxFanIn,
&ranges.front(), max, 0);
}
}
// enforce epicardium properties on boundary nodes (boundary between
// epicardium and endocardium mesh)
void AnisotropyGenerator::eliminateSpecificSurface(InputFileData* InputData,
AnisotropyCondition& condition,
intVector& surfElems,
int surfID,
std::ofstream& logFile) {
using namespace std;
vector<ConditionParticle>& ptcls = condition.getParticles();
vector<ConditionElement>& elems = condition.getElements();
bool notSame = false;
for(int j = 1;j < surfElems.size();j++) {
if(elems[surfElems[j - 1]].getSurfaceID()
!= elems[surfElems[j]].getSurfaceID()) {
notSame = true;
}
}
if(notSame == true) {
intVector dummyVec;
for(int k = 0;k < surfElems.size();k++) {
if(elems[surfElems[k]].getSurfaceID() == surfID) {
dummyVec.push_back(surfElems[k]);
}
}
surfElems = dummyVec;
}
}
/**********************************************************************************
* AUTHOR : Naveen Sundar G.
* DATE : 10-AUGUST-2007
* NAME : toIntVector
* DESCRIPTION : This method converts the feature instance to an intVector.
* ARGUMENTS : The integer vector passed by reference
* RETURNS : 0 on success.
* NOTES :
* CHANGE HISTROY
* Author Date Description of change
*************************************************************************************/
int L7ShapeFeature::toIntVector(intVector& intVec)
{
intVec.push_back(m_x);
intVec.push_back(m_y);
intVec.push_back(m_xFirstDerv);
intVec.push_back(m_yFirstDerv);
intVec.push_back(m_xSecondDerv);
intVec.push_back(m_ySecondDerv);
intVec.push_back(m_curvature);
intVec.push_back(m_penUp);
return SUCCESS;
}
void CMNet::CreateTabularPotential( const intVector& domain,
const floatVector& data )
{
AllocFactor( domain.size(), &domain.front() );
pFactorVector factors;
int numFactors = GetFactors( domain.size(), &domain.front(), &factors );
if( numFactors != 1 )
{
PNL_THROW( CInconsistentSize,
"domain must be the same as corresponding domain size got from graph" );
}
factors[0]->AllocMatrix( &data.front(), matTable );
}
//-------------------------------------------------------------------------------
void CSoftMaxCPD::BuildCurrentEvidenceMatrix(float ***full_evid, float ***evid,intVector family,int numEv)
{
int i, j;
*evid = new float* [family.size()];
for (i = 0; i < family.size(); i++)
{
(*evid)[i] = new float [numEv];
}
for (i = 0; i < numEv; i++)
{
for (j = 0; j < family.size(); j++)
{
(*evid)[j][i] = (*full_evid)[family[j]][i];
}
}
}
bool
DatabaseCorrelation::GetCorrelatedTimeStates(int state, intVector &states) const
{
bool retval = false;
if(state >= 0 && state < numStates)
{
states.clear();
int index = state;
for(size_t i = 0; i < databaseNames.size(); ++i)
{
states.push_back(indices[index]);
index += numStates;
}
retval = true;
}
return retval;
}
void
Dyna3DFile::GetMaterials(intVector &matnos, stringVector &matnames, doubleVector &matdens)
{
for(int i = 0; i < materialCards.size(); ++i)
{
matnos.push_back(materialCards[i].materialNumber);
matnames.push_back(materialCards[i].materialName);
matdens.push_back(materialCards[i].density);
}
}
void CGaussianCPD::AllocDistribution( const floatVector& mean,
const floatVector& cov, float normCoeff,
const floatVecVector& weights,
const intVector& parentCombination )
{
if( weights.size() )
{
pnlVector<const float*> pWeights;
int numWeights = weights.size();
pWeights.resize( numWeights );
for( int i = 0; i < numWeights; i++ )
{
pWeights[i] = &weights[i].front();
}
AllocDistribution( &mean.front(), &cov.front(), normCoeff,
&pWeights.front(), &parentCombination.front() );
}
else
{
AllocDistribution( &mean.front(), &cov.front(), normCoeff, NULL,
&parentCombination.front() );
}
}
// compute the distribution of correspondence statuses in this order:
// connected, paused, observed, expected, blacklisted, alternate, silent
void SM_ComputeDistribution( intVector &dist )
{
// reset the distribution
dist.clear();
for (int i=0; i<3; i++)
dist.push_back( 0 );
// populate the distribution
for ( corresVector::iterator iter = cq.begin(); iter != cq.end(); iter++ ) {
switch ( iter->status() ) {
case _CONNECTED:
dist[0]++;
break;
case _EXPECTED:
dist[1]++;
break;
case _BLACKLISTED:
dist[2]++;
break;
default:
assert( false );
}
}
}
avtSpeciesMetaData::avtSpeciesMetaData(const std::string &n,
const std::string &meshn, const std::string &matn,
int nummat, const intVector &ns, const std::vector<stringVector> &sn)
: AttributeSubject(avtSpeciesMetaData::TypeMapFormatString)
{
// Initialize all.
*this = avtSpeciesMetaData();
// Override members
name = n;
originalName = name;
meshName = meshn;
materialName = matn;
numMaterials = nummat;
ClearSpecies();
for (size_t i=0; i<ns.size(); i++)
AddSpecies(avtMatSpeciesMetaData(ns[i], sn[i]));
validVariable = true;
}
float CMlStaticStructLearn::ScoreFamily(intVector vFamily)
{
int nParents = vFamily.size() - 1;
PNL_CHECK_RANGES(nParents, 0, m_nMaxFanIn);
intVector indexes(m_nMaxFanIn,0);
int i;
for(i=0; i<nParents; i++)
{
indexes[i] = vFamily[i]+1;
}
int node = vFamily[nParents];
float score;
float defval = m_pNodeScoreCache[node]->GetDefaultValue();
score = m_pNodeScoreCache[node]->GetElementByIndexes(&indexes.front());
if(score == defval)
{
score = ComputeFamilyScore(vFamily);
m_pNodeScoreCache[node]->SetElementByIndexes(score, &indexes.front());
}
return score;
}
void CGibbsSamplingInfEngine::
MarginalNodes( const intVector& queryNdsIn, int notExpandJPD )
{
MarginalNodes( &queryNdsIn.front(), queryNdsIn.size(), notExpandJPD );
}
void CExInfEngine< INF_ENGINE, MODEL, FLAV, FALLBACK_ENGINE1, FALLBACK_ENGINE2 >::MarginalNodes( intVector const &queryNds, int notExpandJPD )
{
MarginalNodes(&queryNds.front(), queryNds.size(), notExpandJPD );
}
CFactor::CFactor( EDistributionType dt,
EFactorType pt,
const int *domain, int nNodes, CModelDomain* pMD,
const intVector& obsIndices )
: m_Domain( domain, domain + nNodes )
{
/*fill enum fields:*/
m_DistributionType = dt;
m_FactorType = pt;
m_pMD = pMD;
m_factNumInHeap = m_pMD->AttachFactor(this);
int i;
pConstNodeTypeVector nt;
intVector dom = intVector( domain, domain+nNodes );
pMD->GetVariableTypes( dom, &nt );
m_obsPositions.assign( obsIndices.begin(), obsIndices.end() );
int numObsNodesHere = obsIndices.size();
switch (dt)
{
case dtScalar:
{
if( pt == ftCPD )
{
PNL_THROW( CInvalidOperation, "scalar is only potential - to multiply" );
}
//if there are observed nodes - get corresponding node types
if( numObsNodesHere )
{
if ( numObsNodesHere != nNodes )
{
PNL_THROW( CInconsistentType,
"all nodes in scalar distribution must be observed" )
}
//need to find observed nodes in domain and check including their changed types
for( i = 0; i < numObsNodesHere; i++ )
{
nt[obsIndices[i]] = nt[obsIndices[i]]->IsDiscrete() ? pMD->GetObsTabVarType():
pMD->GetObsGauVarType();
}
}
m_CorrespDistribFun = CScalarDistribFun::Create(nNodes, &nt.front());
break;
}
case dtTree:
{
if( pt != ftCPD )
{
PNL_THROW( CInvalidOperation, "Tree is only CPD" );
}
m_CorrespDistribFun = CTreeDistribFun::Create(nNodes, &nt.front());
break;
}
case dtTabular:
{
if(( pt == ftPotential )&&( numObsNodesHere ))
{
//need to find observed nodes in domain and check including their changed types
for( i = 0; i < numObsNodesHere; i++ )
{
//change node type for this node
nt[obsIndices[i]] = nt[obsIndices[i]]->IsDiscrete() ? pMD->GetObsTabVarType():
pMD->GetObsGauVarType();
}
}
//check all node types corresponds Tabular distribution
for( i = 0; i < nNodes; i++ )
{
if((!(( nt[i]->IsDiscrete() )||
( !nt[i]->IsDiscrete()&&(nt[i]->GetNodeSize() == 0)))))
{
PNL_THROW( CInconsistentType,
"node types must corresponds Tabular type" );
}
}
m_CorrespDistribFun = CTabularDistribFun::Create( nNodes,
&nt.front(), NULL );
break;
}
case dtGaussian:
{
switch (pt)
{
case ftPotential:
{
//need to find observed nodes in domain and check including their changed types
for( i = 0; i < numObsNodesHere; i++ )
{
//change node type for this node
nt[obsIndices[i]] = nt[obsIndices[i]]->IsDiscrete() ?
pMD->GetObsTabVarType():pMD->GetObsGauVarType();
}
for( i = 0; i < nNodes; i++ )
{
if( nt[i]->IsDiscrete() && (nt[i]->GetNodeSize() != 1))
{
PNL_THROW( CInvalidOperation,
"Gaussian potential must be of Gaussian nodes only" )
}
}
m_CorrespDistribFun =
CGaussianDistribFun::CreateInMomentForm( 1, nNodes,
&nt.front(), NULL, NULL, NULL );
break;
}
case ftCPD:
{
//can check if there are both Continuous & Discrete nodes
int noDiscrete = 1;
for( int i = 0; i < nNodes; i++ )
{
if( nt[i]->IsDiscrete() )
{
noDiscrete = 0;
break;
}
}
if( noDiscrete )
{
m_CorrespDistribFun =
CGaussianDistribFun::CreateInMomentForm( 0, nNodes,
&nt.front(), NULL, NULL, NULL );
break;
}
else
{
m_CorrespDistribFun =
CCondGaussianDistribFun::Create( 0, nNodes, &nt.front() );
break;
}
}
default:
{
PNL_THROW( CBadConst,
"no competent type as EFactorType" );
break;
}
}
break;
}
case dtMixGaussian:
{
switch(pt)
{
case ftCPD:
{
//check if where is discrete node - mixture node
int noDiscrete = 1;
for( int i = 0; i < nNodes; i++ )
{
if( nt[i]->IsDiscrete() )
{
noDiscrete = 0;
break;
}
}
if( !noDiscrete )
{
m_CorrespDistribFun = CCondGaussianDistribFun::Create( 0,
nNodes, &nt.front() );
}
else
{
PNL_THROW( CInconsistentType,
"mixture Gaussian CPD must have mixture node - discrete" );
}
break;
}
default:
{
PNL_THROW( CNotImplemented, "mixture gaussian potential" );
}
}
break;
}
case dtSoftMax:
{
switch (pt)
{
case ftPotential:
{
PNL_THROW( CNotImplemented, "only CPD yet" );
break;
}
case ftCPD:
{
//can check if there are both Continuous & Discrete nodes
int noDiscrete = 1;
for( int i = 0; i < nNodes-1; i++ )
{
if( nt[i]->IsDiscrete() )
{
noDiscrete = 0;
break;
}
}
if( noDiscrete )
{
m_CorrespDistribFun =
CSoftMaxDistribFun::Create( nNodes,
&nt.front(), NULL, NULL );
break;
}
else
{
m_CorrespDistribFun =
CCondSoftMaxDistribFun::Create( nNodes, &nt.front() );
break;
}
/*
//can check if there are both Continuous & Discrete nodes
m_CorrespDistribFun =
CSoftMaxDistribFun::CreateUnitFunctionDistribution( nNodes, &nt.front() );
break;
*/
}
default:
{
PNL_THROW( CBadConst,
"no competent type as EFactorType" );
break;
}
}
break;
}
default:
{
PNL_THROW ( CBadConst,
"we have no such factor type at EDistributionType");
}
}
}
void CGaussianCPD::SetCoefficientVec( float coeff,
const intVector& parentCombination )
{
SetCoefficient( coeff, &parentCombination.front() );
}
void CGraphicalModel::AllocFactor( const intVector& domainIn)
{
AllocFactor( domainIn.size(), &domainIn.front() );
};
float CMlStaticStructLearn::ComputeFamilyScore(intVector vFamily)
{
int nFamily = vFamily.size();
CCPD* iCPD = this->CreateRandomCPD(nFamily, &vFamily.front(), m_pGrModel);
CTabularDistribFun *pDistribFun;
int ncases = m_Vector_pEvidences.size();
const CEvidence * pEv;
float score;
float pred = 0;
EDistributionType NodeType;
switch (m_ScoreMethod)
{
case MaxLh :
if ( !((iCPD->GetDistribFun()->GetDistributionType() == dtSoftMax)
|| (iCPD->GetDistribFun()->GetDistributionType() == dtCondSoftMax)))
{
iCPD->UpdateStatisticsML( &m_Vector_pEvidences.front(), ncases );
score = iCPD->ProcessingStatisticalData(ncases);
}
else
{
float **evid = NULL;
float **full_evid = NULL;
BuildFullEvidenceMatrix(&full_evid);
CSoftMaxCPD* SoftMaxFactor = static_cast<CSoftMaxCPD*>(iCPD);
SoftMaxFactor->BuildCurrentEvidenceMatrix(&full_evid, &evid,
vFamily,m_Vector_pEvidences.size());
SoftMaxFactor->InitLearnData();
SoftMaxFactor->SetMaximizingMethod(mmGradient);
SoftMaxFactor->MaximumLikelihood(evid, m_Vector_pEvidences.size(),
0.00001f, 0.01f);
SoftMaxFactor->CopyLearnDataToDistrib();
if (SoftMaxFactor->GetDistribFun()->GetDistributionType() == dtSoftMax)
{
score = ((CSoftMaxDistribFun*)SoftMaxFactor->GetDistribFun())->CalculateLikelihood(evid,ncases);
}
else
{
score = ((CCondSoftMaxDistribFun*)SoftMaxFactor->GetDistribFun())->CalculateLikelihood(evid,ncases);
};
for (int k = 0; k < SoftMaxFactor->GetDomainSize(); k++)
{
delete [] evid[k];
}
delete [] evid;
int i;
intVector obsNodes;
(m_Vector_pEvidences[0])->GetAllObsNodes(&obsNodes);
for (i=0; i<obsNodes.size(); i++)
{
delete [] full_evid[i];
}
delete [] full_evid;
};
break;
case PreAs :
int i;
NodeType = iCPD->GetDistributionType();
switch (NodeType)
{
case dtTabular :
for(i = 0; i < ncases; i++)
{
pConstEvidenceVector tempEv(0);
tempEv.push_back(m_Vector_pEvidences[i]);
iCPD->UpdateStatisticsML(&tempEv.front(), tempEv.size());
iCPD->ProcessingStatisticalData(tempEv.size());
pred += log(((CTabularCPD*)iCPD)->GetMatrixValue(m_Vector_pEvidences[i]));
}
break;
case dtGaussian :
for(i = 0; i < ncases; i += 1 )
{
pConstEvidenceVector tempEv(0);
tempEv.push_back(m_Vector_pEvidences[i]);
iCPD->UpdateStatisticsML(&tempEv.front(), tempEv.size());
float tmp = 0;
if (i != 0)
{
tmp =iCPD->ProcessingStatisticalData(1);
pred +=tmp;
}
}
break;
case dtSoftMax:
PNL_THROW(CNotImplemented,
"This type score method has not been implemented yet");
break;
default:
PNL_THROW(CNotImplemented,
"This type score method has not been implemented yet");
break;
};
score = pred;
break;
case MarLh :
{
//проверка того, что потенциал дискретный
if (iCPD->GetDistributionType() != dtTabular)
{
PNL_THROW(CNotImplemented,
"This type of score method has been implemented only for discrete nets");
}
int DomainSize;
const int * domain;
switch(m_priorType)
{
case Dirichlet:
iCPD->GetDomain(&DomainSize, &domain);
pDistribFun = static_cast<CTabularDistribFun *>(iCPD->GetDistribFun());
pDistribFun->InitPseudoCounts();
for (i=0; i<ncases; i++)
{
pEv = m_Vector_pEvidences[i];
const CEvidence *pEvidences[] = { pEv };
pDistribFun->BayesUpdateFactor(pEvidences, 1, domain);
}
score = pDistribFun->CalculateBayesianScore();
break;
case K2:
iCPD->GetDomain(&DomainSize, &domain);
pDistribFun = static_cast<CTabularDistribFun *>(iCPD->GetDistribFun());
pDistribFun->InitPseudoCounts(m_K2alfa);
for (i=0; i<ncases; i++)
{
pEv = m_Vector_pEvidences[i];
const CEvidence *pEvidences[] = { pEv };
pDistribFun->BayesUpdateFactor(pEvidences, 1, domain);
}
score = pDistribFun->CalculateBayesianScore();
break;
case BDeu:
iCPD->GetDomain(&DomainSize, &domain);
pDistribFun = static_cast<CTabularDistribFun *>(iCPD->GetDistribFun());
pDistribFun->InitPseudoCounts();
for (i=0; i<ncases; i++)
{
pEv = m_Vector_pEvidences[i];
const CEvidence *pEvidences[] = { pEv };
pDistribFun->BayesUpdateFactor(pEvidences, 1, domain);
}
score = pDistribFun->CalculateBayesianScore() / iCPD->GetNumberOfFreeParameters();
break;
default:
PNL_THROW(CNotImplemented,
"This type of prior has not been implemented yet");
break;
}
break;
}
default :
PNL_THROW(CNotImplemented,
"This type score method has not been implemented yet");
break;
}
int dim = iCPD->GetNumberOfFreeParameters();
switch (m_ScoreType)
{
case BIC :
score -= 0.5f * float(dim) * float(log(float(ncases)));
break;
case AIC :
score -= 0.5f * float(dim);
break;
case WithoutFine:
break;
case VAR :
PNL_THROW(CNotImplemented,
"This type score function has not been implemented yet");
break;
default:
PNL_THROW(CNotImplemented,
"This type score function has not been implemented yet");
break;
}
delete iCPD;
return score;
}
void
DatabaseCorrelation::AddDatabase(const std::string &database, int nStates,
const doubleVector ×, const intVector &cycles)
{
// If the database is already in the correlation, maybe we should
// remove it and then add it again in case the length changed like
// when we add time states to a file.
if(UsesDatabase(database))
return;
//
// Add the times and cycles for the new database to the correlation so
// we can access them later and perhaps use them to correlate.
//
for(int i = 0; i < nStates; ++i)
{
double t = ((i < times.size()) ? times[i] : 0.);
databaseTimes.push_back(t);
int c = ((i < cycles.size()) ? cycles[i] : 0);
databaseCycles.push_back(c);
}
if(method == IndexForIndexCorrelation)
{
if(numStates >= nStates)
{
//
// The number of states in the correlation is larger than
// the number of states in the database so we can append
// the database's states to the end of the indices and
// repeat the last frames.
//
for(int i = 0; i < numStates; ++i)
{
int state = (i < nStates) ? i : (nStates - 1);
indices.push_back(state);
}
}
else
{
//
// The number of states for the current database is larger
// than the number of states in the correlation. The correlation
// must be lengthened.
//
indices.clear();
for(size_t i = 0; i < databaseNames.size(); ++i)
{
for(int j = 0; j < nStates; ++j)
{
int state = (j < databaseNStates[i]) ? j :
(databaseNStates[i]-1);
indices.push_back(state);
}
}
// Add the new database to the correlation.
for(int i = 0; i < nStates; ++i)
indices.push_back(i);
numStates = nStates;
}
databaseNames.push_back(database);
databaseNStates.push_back(nStates);
}
else if(method == StretchedIndexCorrelation)
{
databaseNames.push_back(database);
databaseNStates.push_back(nStates);
indices.clear();
int maxStates = (numStates > nStates) ? numStates : nStates;
for(size_t i = 0; i < databaseNames.size(); ++i)
{
for(int j = 0; j < maxStates; ++j)
{
float t = float(j) / float(maxStates - 1);
int state = int(t * (databaseNStates[i] - 1) + 0.5);
indices.push_back(state);
}
}
numStates = maxStates;
}
else if(method == UserDefinedCorrelation)
{
if(numStates > nStates)
{
//
// The database being added has fewer states so we need to
// repeat the last states.
//
// We'll have to pass in the user-defined indices and append them to the indices vector
}
else
{
}
}
else if(method == TimeCorrelation)
{
databaseNames.push_back(database);
databaseNStates.push_back(nStates);
// Align time for all databases on the same time axis so we can count the
// number of times and make that be the new number of states.
std::map<double, intVector> timeAlignmentMap;
int index = 0;
for(size_t i = 0; i < databaseNames.size(); ++i)
for(int j = 0; j < databaseNStates[i]; ++j, ++index)
timeAlignmentMap[databaseTimes[index]].push_back(i);
//
// Set the condensed times vector
//
condensedTimes.clear();
for(std::map<double,intVector>::const_iterator p = timeAlignmentMap.begin();
p != timeAlignmentMap.end(); ++p)
{
condensedTimes.push_back(p->first);
}
// Now there is a map that has for each time in all of the databases
// a list of the databases that contain that time.
indices.clear();
for(size_t i = 0; i < databaseNames.size(); ++i)
{
int state = 0;
std::map<double, intVector>::const_iterator pos = timeAlignmentMap.begin();
for(; pos != timeAlignmentMap.end(); ++pos)
{
// Look to see if the current database is in the list of databases
// for the current time. If so, we need to increment the state after
// we use it.
intVector::const_iterator dbIndex =
std::find(pos->second.begin(), pos->second.end(), i);
indices.push_back(state);
if(dbIndex != pos->second.end() && state < databaseNStates[i] - 1)
++state;
}
}
numStates = timeAlignmentMap.size();
}
else if(method == CycleCorrelation)
{
databaseNames.push_back(database);
databaseNStates.push_back(nStates);
// Align cycle for all databases on the same time axis so we can count the
// number of cycles and make that be the new number of states.
std::map<int, intVector> cycleAlignmentMap;
int index = 0;
for(size_t i = 0; i < databaseNames.size(); ++i)
for(int j = 0; j < databaseNStates[i]; ++j, ++index)
cycleAlignmentMap[databaseCycles[index]].push_back(i);
//
// Set the condensed cycles vector
//
condensedCycles.clear();
for(std::map<int,intVector>::const_iterator p = cycleAlignmentMap.begin();
p != cycleAlignmentMap.end(); ++p)
{
condensedCycles.push_back(p->first);
}
// Now there is a map that has for each time in all of the databases
// a list of the databases that contain that time.
indices.clear();
for(size_t i = 0; i < databaseNames.size(); ++i)
{
int state = 0;
std::map<int, intVector>::const_iterator pos = cycleAlignmentMap.begin();
for(; pos != cycleAlignmentMap.end(); ++pos)
{
// Look to see if the current database is in the list of databases
// for the current time. If so, we need to increment the state after
// we use it.
intVector::const_iterator dbIndex =
std::find(pos->second.begin(), pos->second.end(), i);
indices.push_back(state);
if(dbIndex != pos->second.end() && state < databaseNStates[i] - 1)
++state;
}
}
numStates = cycleAlignmentMap.size();
}
}
void CNodeValues::ToggleNodeStateBySerialNumber( const intVector& numsOfNds )
{
int numNds = numsOfNds.size();
const int* pNumsOfNds = &numsOfNds.front();
ToggleNodeStateBySerialNumber( numNds, pNumsOfNds );
}
void CSoftMaxCPD::AllocDistribution(const floatVector& weights,
const floatVector& offsets, const intVector& parentCombination)
{
AllocDistribution(&weights.front(), &offsets.front(),
&parentCombination.front());
}
int CGraphicalModel::GetFactors( const intVector& subdomainIn,
pFactorVector *paramsOut ) const
{
return GetFactors( subdomainIn.size(), &subdomainIn.front(),
paramsOut );
};
//! Calculate the Weight function
dbVector Interpolation::weightCalc(dbVector& iPoint, intVector& neighbours,
dbMatrix& coords, dbVector& radiusVec, InputFileData* InputData,
ofstream& logFile) {
dbVector weightVec(neighbours.size(), 1);
int choice = InputData->getValue("MLSWeightFunc");
switch (choice) {
// *************************************************************************
// Cubic spline
case 0:
for (int i = 0; i < neighbours.size(); i++) {
weightVec[i] = cubicSplineWgtCalc(iPoint, coords[neighbours[i]],
radiusVec, logFile);
}
break;
// *************************************************************************
// Gaussian
case 1:
for (int i = 0; i < neighbours.size(); i++) {
weightVec[i] = gaussianWgtCalc(iPoint, coords[neighbours[i]],
radiusVec, logFile);
}
break;
// *************************************************************************
// Regularised
case 2: {
double weightSum = 0;
for (int i = 0; i < neighbours.size(); i++) {
weightVec[i] = regularizedWgtCalc(iPoint, coords[neighbours[i]],
radiusVec, logFile);
weightSum += weightVec[i];
}
for (int i = 0; i < neighbours.size(); i++) {
weightVec[i] = weightVec[i] / weightSum;
}
break;
}
// *************************************************************************
// Regularised modified
case 3: {
int ndim = iPoint.size();
double weight = 0;
for (int d = 0; d < ndim; d++) {
dbVector weightDimVec(weightVec.size(), 0);
double weightSum = 0;
for (int i = 0; i < neighbours.size(); i++) {
weightDimVec[i] = regularizedWgtCalc_mod(iPoint,
coords[neighbours[i]], radiusVec, d, logFile);
weightSum += weightDimVec[i];
}
for (int i = 0; i < neighbours.size(); i++) {
weightVec[i] *= weightDimVec[i] / weightSum;
}
}
break;
}
default:
logFile << "ERROR: In Interpolation::weightCalc, MLSWeightFunc = "
<< choice << "doesn't exist" << endl;
cout << "ERROR: In Interpolation::weightCalc, MLSWeightFunc = "
<< choice << "doesn't exist" << endl;
MPI_Abort(MPI_COMM_WORLD, 1);
}
return weightVec;
}
avtDataObject_p
IceTNetworkManager::Render(
bool checkThreshold, intVector networkIds,
bool getZBuffer, int annotMode, int windowID,
bool leftEye)
{
int t0 = visitTimer->StartTimer();
DataNetwork *origWorkingNet = workingNet;
avtDataObject_p retval;
EngineVisWinInfo &viswinInfo = viswinMap[windowID];
viswinInfo.markedForDeletion = false;
VisWindow *viswin = viswinInfo.viswin;
std::vector<avtPlot_p>& imageBasedPlots = viswinInfo.imageBasedPlots;
renderings = 0;
TRY
{
this->StartTimer();
RenderSetup(windowID, networkIds, getZBuffer,
annotMode, leftEye, checkThreshold);
bool plotDoingTransparencyOutsideTransparencyActor = false;
for(size_t i = 0 ; i < networkIds.size() ; i++)
{
workingNet = NULL;
UseNetwork(networkIds[i]);
if(this->workingNet->GetPlot()->ManagesOwnTransparency())
{
plotDoingTransparencyOutsideTransparencyActor = true;
}
}
workingNet = NULL;
// We can't easily figure out a compositing order, which IceT requires
// in order to properly composite transparent geometry. Thus if there
// is some transparency, fallback to our parent implementation.
avtTransparencyActor* trans = viswin->GetTransparencyActor();
bool transparenciesExist = trans->TransparenciesExist()
|| plotDoingTransparencyOutsideTransparencyActor;
if (transparenciesExist)
{
debug2 << "Encountered transparency: falling back to old "
"SR / compositing routines." << std::endl;
retval = NetworkManager::RenderInternal();
}
else
{
bool needZB = !imageBasedPlots.empty() ||
renderState.shadowMap ||
renderState.depthCues;
// Confusingly, we need to set the input to be *opposite* of what VisIt
// wants. This is due to (IMHO) poor naming in the IceT case; on the
// input side:
// ICET_DEPTH_BUFFER_BIT set: do Z-testing
// ICET_DEPTH_BUFFER_BIT not set: do Z-based compositing.
// On the output side:
// ICET_DEPTH_BUFFER_BIT set: readback of Z buffer is allowed
// ICET_DEPTH_BUFFER_BIT not set: readback of Z does not work.
// In VisIt's case, we calculated a `need Z buffer' predicate based
// around the idea that we need the Z buffer to do Z-compositing.
// However, IceT \emph{always} needs the Z buffer internally -- the
// flag only differentiates between `compositing' methodologies
// (painter-style or `over' operator) on input.
GLenum inputs = ICET_COLOR_BUFFER_BIT;
GLenum outputs = ICET_COLOR_BUFFER_BIT;
// Scratch all that, I guess. That might be the correct way to go
// about things in the long run, but IceT only gives us back half an
// image if we don't set the depth buffer bit. The compositing is a
// bit wrong, but there's not much else we can do..
// Consider removing the `hack' if a workaround is found.
if (/*hack*/true/*hack*/) // || !this->MemoMultipass(viswin))
{
inputs |= ICET_DEPTH_BUFFER_BIT;
}
if(needZB)
{
outputs |= ICET_DEPTH_BUFFER_BIT;
}
ICET(icetInputOutputBuffers(inputs, outputs));
// If there is a backdrop image, we need to tell IceT so that it can
// composite correctly.
if(viswin->GetBackgroundMode() != AnnotationAttributes::Solid)
{
ICET(icetEnable(ICET_CORRECT_COLORED_BACKGROUND));
}
else
{
ICET(icetDisable(ICET_CORRECT_COLORED_BACKGROUND));
}
if (renderState.renderOnViewer)
{
RenderCleanup();
avtDataObject_p dobj = NULL;
CATCH_RETURN2(1, dobj);
}
debug5 << "Rendering " << viswin->GetNumPrimitives()
<< " primitives." << endl;
int width, height, width_start, height_start;
// This basically gets the width and the height.
// The distinction is for 2D rendering, where we only want the
// width and the height of the viewport.
viswin->GetCaptureRegion(width_start, height_start, width, height,
renderState.viewportedMode);
this->TileLayout(width, height);
CallInitializeProgressCallback(this->RenderingStages());
// IceT mode is different from the standard network manager; we don't
// need to create any compositor or anything: it's all done under the
// hood.
// Whether or not to do multipass rendering (opaque first, translucent
// second) is all handled in the callback; from our perspective, we
// just say draw, read back the image, and post-process it.
// IceT sometimes omits large parts of Curve plots when using the
// REDUCE strategy. Use a different compositing strategy for Curve
// plots to avoid the problem.
if(viswin->GetWindowMode() == WINMODE_CURVE)
ICET(icetStrategy(ICET_STRATEGY_VTREE));
else
ICET(icetStrategy(ICET_STRATEGY_REDUCE));
ICET(icetDrawFunc(render));
ICET(icetDrawFrame());
// Now that we're done rendering, we need to post process the image.
debug3 << "IceTNM: Starting readback." << std::endl;
avtImage_p img = this->Readback(viswin, needZB);
// Now its essentially back to the same behavior as our parent:
// shadows
// depth cueing
// post processing
if (renderState.shadowMap)
this->RenderShadows(img);
if (renderState.depthCues)
this->RenderDepthCues(img);
// If the engine is doing more than just 3D annotations,
// post-process the composited image.
RenderPostProcess(img);
CopyTo(retval, img);
}
RenderCleanup();
}
CATCHALL
{
RenderCleanup();
RETHROW;
}
ENDTRY
workingNet = origWorkingNet;
visitTimer->StopTimer(t0, "Ice-T Render");
return retval;
}
float CGaussianCPD::GetCoefficientVec( const intVector& parentCombination )
{
return GetCoefficient( &parentCombination.front() );
}
void
avtFVCOMParticleFileFormat::GetCycles(intVector &cyc)
{
const char *mName = "avtFVCOMParticleFileObject::GetCycles: ";
debug4 << mName << endl;
int ncid;
ncid=fileObject->GetFileHandle();
size_t ntimesteps;
int time_id;
int status = nc_inq_dimid(ncid, "time", &time_id);
if (status != NC_NOERR) fileObject-> HandleError(status);
status = nc_inq_dimlen(ncid, time_id, &ntimesteps);
if (status != NC_NOERR) fileObject-> HandleError(status);
char varname[NC_MAX_NAME+1];
nc_type vartype;
int varndims;
int vardims[NC_MAX_VAR_DIMS];
int varnatts;
int cycle_id;
status = nc_inq_varid (ncid, "cycle", &cycle_id);
if (status != NC_NOERR)
{
fileObject-> HandleError(status);
debug4 << "Could not find variable: cycle" << endl;
return;
}
// Now get variable type!
status = nc_inq_var(ncid, cycle_id, varname, &vartype, &varndims,
vardims, &varnatts);
if (status != NC_NOERR) fileObject-> HandleError(status);
if (varndims != 1 )
{
debug4 << mName << "Cycles has the wrong dimensions" << endl;
}
else if (varndims == 1)
{
if(vartype == NC_INT)
{
debug4 << "IINT returned to cyc as NC_INT" << endl;
int *ci = new int[ntimesteps+1];
fileObject->ReadVariableInto("iint", INTEGERARRAY_TYPE, ci);
for(int n=0; n<ntimesteps; ++n)
{
cyc.push_back(ci[n]);
}
delete [] ci;
}
else if(vartype == NC_FLOAT )
{
debug4 << "iint is float: Returned to cyc as INT" << endl;
float *cf = new float[ntimesteps+1];
fileObject->ReadVariableInto("cycle", FLOATARRAY_TYPE, cf);
for(int n=0; n<ntimesteps; ++n)
{
cyc.push_back(int(cf[n]));
}
delete [] cf;
}
}
else
{
debug4 << "Could not return cycles: Wrong variable type" << endl;
}
}
//! Coordinate generator
//! Points are defined along the columns of coords and their dimensional
//! coordinates along the rows
void Interpolation::MLSUnitTest_meshMultiDim(double& length, double& nodal_dist,
int& ndim, dbMatrix& coords, int& numCoords, intVector SBM_dim,
dbVector SBM_coeff, ofstream& logFile) {
// Define the coordinate list in a specific dimension
dbVector coordList;
for (int i = 0; (i) * nodal_dist <= length; i++)
coordList.push_back(i * nodal_dist);
printVector(coordList, "coordList", logFile);
dbMatrix x;
x.push_back(coordList);
if (ndim > 1) {
for (int i = 1; i < ndim; i++) {
int dimLookup = i + 1;
int position = findIntVecPos(dimLookup, 0, SBM_dim.size(), SBM_dim);
logFile << "Position: " << position << endl;
dbMatrix xBlock = x;
int xBlockSize = xBlock[0].size();
x.clear();
x.resize(i + 1);
for (int j = 0; j < coordList.size(); j++) {
// Select a particular coordinate
double coordSelect = coordList[j];
// Find if dimension needs to be factored
dbMatrix x_add = xBlock;
if (position != -1) {
logFile << "Dim factored" << endl;
x_add.push_back(
dbVector(xBlockSize,
SBM_coeff[position] * coordSelect));
//dbMatrix x_add = [SBM_coeff*coordSelect*ones(1,xBlockSize);xBlock];
} else {
// Repeat the previous block for each selected coordinate
//x_add = [coordSelect*ones(1,xBlockSize);xBlock];
x_add.push_back(dbVector(xBlockSize, coordSelect));
}
printMatrix(x_add, "x_add", logFile);
//x = [x x_add];
for (int k = 0; k < x_add.size(); k++) {
for (int l = 0; l < x_add[k].size(); l++) {
x[k].push_back(x_add[k][l]);
}
}
printMatrix(x, "x", logFile);
}
}
}
// Transposing the coordinate matrix
coords.resize(x[0].size());
for (int i = 0; i < coords.size(); i++) {
coords[i].resize(ndim);
for (int j = 0; j < ndim; j++)
coords[i][j] = x[j][i];
}
numCoords = coords.size();
}