void lmWorker::calculateChiSquare()
{
//Calculate ChiSquare(s)
TelluriumData& modelData = *(TelluriumData*) mTheHost.mModelData.getValuePointer();
TelluriumData& obsData = *(TelluriumData*) mTheHost.mExperimentalData.getValuePointer();
Plugin* chi = mTheHost.mPM->getPlugin("tel_chisquare");
if(!chi)
{
throw(Exception("Failed to get chisquare plugin in lmfit plugin"));
}
Property<TelluriumData>* para = dynamic_cast<Property<TelluriumData>*>(chi->getProperty("ExperimentalData"));
para->setValue(obsData);
para = dynamic_cast<Property<TelluriumData>*>(chi->getProperty("ModelData"));
para->setValue(modelData);
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"));
Property<double>* rChiSquare = dynamic_cast< Property<double>* >(chi->getProperty("ReducedChiSquare"));
mTheHost.mChiSquare.setValue(chiSquare->getValue());
mTheHost.mReducedChiSquare.setValue(rChiSquare->getValue());
Log(lInfo)<<"Chi Square = "<<chiSquare->getValue();
Log(lInfo)<<"Reduced Chi Square = "<<rChiSquare->getValue();
}
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();
}
bool TestModel::execute(bool inThread)
{
Log(lDebug)<<"Executing the TestModel plugin by Totte Karlsson";
RoadRunner rr;
rr.load(mModel);
rr::SimulateOptions opt;
opt.start = 0;
opt.duration = 10;
opt.steps = 14;
TelluriumData data(rr.simulate(&opt));
mTestData.setValue(data);
//Add noise
const PluginManager* PM = this->getPluginManager();
Plugin* noise = PM->getPlugin("AddNoise");
if(!noise)
{
stringstream msg;
msg<<"The TestModel plugin dependes on the AddNoise plugin, which is not yet loaded.";
throw(Exception(msg.str()));
}
mTestDataWithNoise.setValue(mTestData.getValue());
noise->setPropertyValue("Sigma", mSigma.getValueHandle());
noise->setPropertyValue("InputData", mTestDataWithNoise.getValueHandle());
noise->execute();
mTestDataWithNoise.setValue(noise->getPropertyValueHandle("InputData"));
//Add weights
addWeights();
return true;
}
int main()
{
try
{
//Create a RoadRunner object
RoadRunner rr("r:\\installs\\cg\\xe3\\debug\\rr_support");
//Get the plugin manager
PluginManager& plugins = rr.getPluginManager();
if(!plugins.load())
{
clog<<"Failed loading plugins..\n";
}
if(plugins.getNumberOfPlugins() > 0)
{
cout<<"The following plugins are loaded:\n";
for(int i = 0; i < plugins.getNumberOfPlugins(); i++)
{
Plugin* aPlugin = plugins[i];
cout<<"Plugin "<<i<<": "<<aPlugin->getName()<<"\n";
cout<<aPlugin->getInfo();
aPlugin->execute();
}
}
plugins.unload();
Pause(true);
rr.~RoadRunner();
}
catch(const rr::Exception& ex)
{
clog<<"There was a problem: "<<ex.what();
}
return 0;
}
