double nmWorker::getChi(const Properties& parameters)
{
Log(lDebug)<<"Getting chisquare using parameters: "<<parameters;
//Reset RoadRunner
mHost.mRRI->reset();
for(int i = 0; i < parameters.count(); i++)
{
Property<double> *para = (Property<double>*) (parameters[i]);
mHost.mRRI->setValue(para->getName(), para->getValue());
}
TelluriumData* expData = (TelluriumData*) mHost.mExperimentalData.getValueHandle();
rr::SimulateOptions options;
options.start = expData->getTimeStart();
options.duration = expData->getTimeEnd() - expData->getTimeStart();
options.steps = expData->rSize() - 1;
options.flags = options.flags | rr::SimulateOptions::RESET_MODEL;
rr::RoadRunnerData *modelData = NULL;
if(mHost.mRRI->simulate(&options))
{
modelData = mHost.mRRI->getSimulationResult();
}
TelluriumData& obsData = *(TelluriumData*) mHost.mExperimentalData.getValuePointer();
Plugin* chi = mHost.mPM->getPlugin("tel_chisquare");
Property<TelluriumData>* para = dynamic_cast<Property<TelluriumData>*>(chi->getProperty("ExperimentalData"));
para->setValue(obsData);
para = dynamic_cast<Property<TelluriumData>*>(chi->getProperty("ModelData"));
para->setValue(TelluriumData(*(modelData)));
Property<int>* intPara = dynamic_cast< Property<int>* >(chi->getProperty("NrOfModelParameters"));
intPara->setValue(getNumberOfParameters());
//Calculate Chi square
chi->execute();
Property<double>* chiSquare = dynamic_cast< Property<double>* >(chi->getProperty("ChiSquare"));
return chiSquare->getValue();
}
double lmWorker::getChi(const Properties& parameters)
{
RRPLOG(lDebug)<<"Getting chisquare using parameters: "<<parameters;
//Reset RoadRunner
mRRI->reset();
for(int i = 0; i < parameters.count(); i++)
{
Property<double> *para = (Property<double>*) (parameters[i]);
mRRI->setValue(para->getName(), para->getValue());
}
rr::SimulateOptions options;
options.start = mLMData.timeStart;
options.duration = mLMData.timeEnd - mLMData.timeStart;
options.steps = mLMData.nrOfTimePoints - 1;
mRRI->reset();
const DoubleMatrix* modelData = NULL;
if(mRRI->simulate(&options))
{
modelData = mRRI->getSimulationData();
}
TelluriumData& obsData = *(TelluriumData*) mTheHost.mExperimentalData.getValuePointer();
Plugin* chi = mTheHost.mPM->getPlugin("tel_chisquare");
Property<TelluriumData>* para = dynamic_cast<Property<TelluriumData>*>(chi->getProperty("ExperimentalData"));
para->setValue(obsData);
para = dynamic_cast<Property<TelluriumData>*>(chi->getProperty("ModelData"));
TelluriumData td;
td.setData(*modelData);
para->setValue(td);
Property<int>* intPara = dynamic_cast< Property<int>* >(chi->getProperty("NrOfModelParameters"));
intPara->setValue(mLMData.nrOfParameters);
//Calculate Chi square
chi->execute();
Property<double>* chiSquare = dynamic_cast< Property<double>* >(chi->getProperty("ChiSquare"));
return chiSquare->getValue();
}
void nmWorker::createModelData(TelluriumData* _data)
{
TelluriumData& data = *(_data);
TelluriumData* expData = (TelluriumData*) mHost.mExperimentalData.getValueHandle();
Properties& outParas = * (Properties*) mHost.mOutputParameterList.getValueHandle();
int nrOfParameters = outParas.count();
//We now have the parameters
StringList selList("time");
selList.append(mHost.mModelDataSelectionList.getValue());
data.reSize(expData->rSize(), selList.count());
mHost.mRRI->reset();
mHost.mRRI->setSelections(selList);
for(int i = 0; i < nrOfParameters; i++)
{
mHost.mRRI->setValue(outParas[i]->getName(), * (double*) outParas[i]->getValueHandle());
}
rr::SimulateOptions options;
options.start = expData->getTimeStart();
options.duration = expData->getTimeEnd() - expData->getTimeStart();
options.steps = expData->rSize() - 1;
options.flags = options.flags | rr::SimulateOptions::RESET_MODEL;
if(mHost.mRRI->simulate(&options))
{
data = * (mHost.mRRI->getSimulationResult());
}
}
bool TelluriumData::append(const TelluriumData& dataToAppend)
{
//When appending data, the number of rows have to match with current data
if(mTheData.RSize() > 0)
{
if(dataToAppend.rSize() != rSize())
{
return false;
}
}
else
{
//Starting with an empty data object. Simple assignment
(*this) = dataToAppend;
return true;
}
int originalColSize = cSize();
//Copy our data to temp data object
TelluriumData temp;
temp = (*this);
int newCSize = originalColSize + dataToAppend.cSize();
//Check if first column is 'time'.. if so, ignore
bool isFirstColTime = dataToAppend.isFirstColumnTime();
if(isFirstColTime)
{
newCSize -= 1;
}
mTheData.resize(dataToAppend.rSize(), newCSize);
//First, copy back 'original' data
for(int row = 0; row < temp.rSize(); row++)
{
for( int col = 0; col < temp.cSize(); col++)
{
mTheData(row, col) = temp(row, col);
}
}
//Append the data
for(int col = isFirstColTime ? 1 : 0, colNr = 0; col < dataToAppend.cSize(); col++, colNr++)
{
for(int row = 0; row < mTheData.RSize(); row++)
{
int destCol = originalColSize + colNr;
mTheData(row, destCol) = dataToAppend(row, col);
}
}
//Add column names
for(int col = isFirstColTime ? 1 : 0; col < dataToAppend.cSize(); col++)
{
mColumnNames.add(dataToAppend.getColumnName(col));
}
return true;
}
