int main()
{
itk::RGBPixel<unsigned char> rgbPixel;
std::cout << Helpers::length(rgbPixel) << std::endl;
std::cout << Helpers::index(rgbPixel, 2) << std::endl;
itk::VariableLengthVector<float> varVec(4);
std::cout << Helpers::length(varVec) << std::endl;
std::cout << Helpers::index(varVec, 1) << std::endl;
itk::CovariantVector<float, 5> covVec;
std::cout << Helpers::length(covVec) << std::endl;
std::cout << Helpers::index(covVec, 1) << std::endl;
return 0;
}
void dfgEm(DfgInfo & dfgInfo, string const & varDataFile, string const & facDataFile, string const & subVarDataFile, number_t minDeltaLogLik, unsigned maxIter,
string const & logStateMapsFile, string const & logFactorPotentialsFile, string const & logVariablesFile, string const & logFactorGraphFile, string const & logFile)
{
DFG & dfg = dfgInfo.dfg; // convenient
AbstractBaseFactorSet & factorSet = dfgInfo.facSet;
unsigned iter = 0;
number_t logLik = 0;
number_t prevLogLik = 0;
number_t deltaLogLik = 0;
// setup input data structures
VarData varData(varDataFile, dfgInfo.varNames);
FacData * facDataPtr = NULL;
VarData * subVarDataPtr = NULL;
if (facDataFile.size() != 0) {
facDataPtr = new FacData(facDataFile, dfgInfo.facNames);
}
if (subVarDataFile.size() != 0) {
subVarDataPtr = new VarData(subVarDataFile, dfgInfo.subNames);
}
else if( dfgInfo.subNames.size() > 0 ){
errorAbort("DfgDataWrap.cpp::164::main There are subscribed factors but no subscribed variable file were provided");
}
// init variables
// input data variables
string idVar;
vector<symbol_t> varVec( varData.count() ); // for input data
// dfg variables
stateMaskVec_t stateMaskVec( dfgInfo.varNames.size() );
vector<matrix_t> facExpCounts; // Expectation counts
initAccFactorMarginals(facExpCounts, dfg);
vector<xmatrix_t> tmpFacMar; // workspace
dfg.initFactorMarginals(tmpFacMar);
xnumber_t normConst;
// open log file
ofstream f;
if ( logFile.size() ) {
f.open(logFile.c_str(), ios::out);
if (!f)
errorAbort("Cannot open file: " + logFile + "\n");
f << "minDeltaLogLik: " << minDeltaLogLik << endl;
f << "maxIter: " << maxIter << endl;
f << endl;
f << "iter" << "\t" << "logLik" << "\t" << "deltaLogLik" << endl;
}
while ( ( (deltaLogLik > minDeltaLogLik) or iter == 0) and iter < maxIter) {
logLik = 0;
reset(facExpCounts);
// reset varData and facData
varData.reset(varDataFile, dfgInfo.varNames);
if (facDataFile.size() != 0) {
facDataPtr->reset(facDataFile, dfgInfo.facNames);
}
if (subVarDataFile.size() != 0) {
subVarDataPtr->reset(subVarDataFile, dfgInfo.subNames);
}
unsigned lineCount = 0;
while ( varData.next(idVar, varVec) ) {
lineCount++;
resetFactorPotential(facDataPtr, idVar, lineCount, dfgInfo.dfg);
updateFactorPotentials(subVarDataPtr, idVar, lineCount, dfgInfo);
dfgInfo.stateMaskMapSet.symbols2StateMasks( stateMaskVec, varVec, varData.map() );
// //debug begin
// string facName("CpG_P_1.likelihood");
// unsigned facIdx = find(dfgInfo.facNames.begin(), dfgInfo.facNames.end(), facName) - dfgInfo.facNames.begin();
// cout << "factor name: " << facName << "; facIdx: " << facIdx << "; potential " << dfg.getFactor(facIdx).potential << endl;
// //debug end
calcFacAccMarAndNormConst(facExpCounts, tmpFacMar, normConst, stateMaskVec, dfg);
logLik += - log(normConst);
}
factorSet.submitCounts(facExpCounts);
factorSet.optimizeParameters();
dfg.resetFactorPotentials( factorSet.mkFactorVec() );
factorSet.clearCounts();
deltaLogLik = abs(prevLogLik - logLik); // set at abs(-logLik) in iter 0
if ( logFile.size() )
f << iter << "\t" << logLik << "\t" << deltaLogLik << endl;
if ( logStateMapsFile.size() )
writeDfgInfo(dfgInfo, logStateMapsFile, logFactorPotentialsFile, logVariablesFile, logFactorGraphFile);
//
// // debug
// cout << "from dfgEm:" << endl;
// cout << "iter: " << iter << endl;
// cout << "logLik: " << logLik << endl;
// cout << "prevLogLik: " << prevLogLik << endl;
// cout << "deltaLogLik: " << deltaLogLik << endl;
// cout << "minDeltaLogLik: " << minDeltaLogLik << endl;
// cout << "maxIter: " << maxIter << endl;
// cout << "( ( (deltaLogLik > minDeltaLogLik) or iter == 0) and iter < maxIter): " << ( ( (deltaLogLik > minDeltaLogLik) or iter == 0) and iter < maxIter) << endl;
//
// //debug begin
// cout << endl << "iteration #: " << iter << endl << endl;
// //debug end
prevLogLik = logLik;
iter++;
}
// clean up
if (facDataPtr != NULL)
delete facDataPtr;
}