void ParameterScanWorker::run()
{
workerStarted();
//The user may have aborted the minization... check here..
if(mHost.isBeingTerminated())
{
//user did set the terminate flag to true.. discard any data and get out of the
//plugin execute code..
RRPLOG(lInfo)<<"The ParameterScanWorker was terminated.. aborting";
workerFinished();
return;
}
//Create arrayed data
ArrayedParameter para(mHost.mParameter.getValueReference());
StringList selList(mHost.mSelectionList.getValue());
RoadRunner rr;
rr.load(mHost.mSBML.getValue());
//Make sure time is the first column in the selectin list
if(selList.size() && compareNoCase(selList[0], "time") != true)
{
selList.InsertAt(0,"time");
}
rr.setSelections(selList);
TelluriumData& data = mHost.mOutputData.getValueReference();
data.clear();
for(int i = 0; i < para.getNumberOfIncrements() + 1; i++)
{
rr::SimulateOptions options;
options.flags |= rr::SimulateOptions::RESET_MODEL;
options.start = mHost.mStartTime.getValue();
options.duration = mHost.mEndTime.getValue() - mHost.mStartTime.getValue();
options.steps = mHost.mNumberOfPointsPerSimulation.getValue() - 1;
//Set parameter
rr.setValue(para.getName(), para.getCurrentValue());
const RoadRunnerData *rrData = rr.simulate(&options);
TelluriumData *temp = new TelluriumData(*rrData);
data.append(*temp);
delete temp;
para.increment();
}
//The Arrayed parameter need to be added to the data.
data.setArrayedParameter(para);
workerFinished();
}
/**
* perform a stochastic ensemble calculation.
*
* :param: r an existing roadrunner obj, loaded with a mode.
* :param: n how many ensembles to run.
* :param: seed the seed value, use None to continue with previous
* random number stream.
* :param: start start time
* :param: stop stop time
* :param: ntps how many points display in the result.
*/
DoubleMatrix ensemble(RoadRunner &r, int n, unsigned long seed, double start, double stop, int npts) {
// set the seed value of the integrator
Integrator *itg = r.getIntegrator(Integrator::GILLESPIE);
itg->setItem("seed", seed);
// setup the simulation
// create a sim opt obj, loads itself with
// default values in ctor.
SimulateOptions o;
o.start = start;
o.duration = stop;
o.steps = npts;
// we should reset the model each time we simulate,
// set the RESET_MODEL bit.
o.flags |= SimulateOptions::RESET_MODEL;
o.integrator = Integrator::GILLESPIE;
// make a result var
DoubleMatrix result(npts+1, n+1);
for (int i = 0; i < n; ++i) {
const DoubleMatrix &sim = *r.simulate(&o);
// copy result data colum
for (int row = 0; row < npts+1; ++row) {
result(row, i+1) = sim(row, 1);
}
}
// copy result time column
const DoubleMatrix &sim = *r.getSimulationData();
// copy result data colum
for (int row = 0; row < npts+1; ++row) {
result(row, 0) = sim(row, 0);
}
return result;
}
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(int argc, char** argv)
{
std::string in_dir;
std::string out_dir;
std::string test_name;
unsigned int level = 0;
unsigned int version = 0;
double start_time = 0.0;
double duration = 0.0;
std::list<std::string> variables;
std::set<std::string> amounts;
std::set<std::string> concentrations;
double absolute_error = 0.0;
double relative_error = 0.0;
if (argc < 6)
{
std::cerr << "Usage: rr-sbml-benchmrk INPUT_DIRECTORY TESTNAME OUTPUTDIRECTORY SBMLLEVEL SBMLVERSION [steps override] [durration] [compiler] [-stiff]" << std::endl;
exit(1);
}
in_dir = argv[1];
test_name = argv[2];
out_dir = argv[3];
level = strtol(argv[4], NULL, 10);
version = strtol(argv[5], NULL, 10);
if (level < 1 || level > 3)
{
std::cerr << "SBML Level " << level << " Version " << version << " not supported." << std::endl;
exit(1);
}
if (level == 1 && (version < 1 || version > 2))
{
std::cerr << "SBML Level " << level << " Version " << version << " not supported." << std::endl;
exit(1);
}
std::ostringstream os;
os << in_dir << "/" << test_name << "/" << test_name << "-settings.txt";
// open the settings file and parse it
std::cout << "parsing file: " << os.str() << std::endl;
std::ifstream f;
std::string settingsFile = in_dir + "/" + test_name + "/" + test_name + "-settings.txt";
std::string sbmlFile;
{
stringstream os;
os << in_dir << "/" << test_name << "/" << test_name << "-sbml-l" << level << "v" << version << ".xml";
sbmlFile = os.str();
}
std::string output_filename;
if (!out_dir.empty() || out_dir.compare("/dev/null") != 0)
{
stringstream os;
os.str("");
os << out_dir << "/" << test_name << ".csv";
output_filename = os.str();
}
RoadRunner roadRunner;
LoadSBMLOptions opt;
// don't generate cache for models
opt.modelGeneratorOpt = opt.modelGeneratorOpt | LoadSBMLOptions::RECOMPILE;
// no mutable initial conditions
opt.modelGeneratorOpt = opt.modelGeneratorOpt & ~LoadSBMLOptions::MUTABLE_INITIAL_CONDITIONS;
// read only model
opt.modelGeneratorOpt = opt.modelGeneratorOpt | LoadSBMLOptions::READ_ONLY;
opt.modelGeneratorOpt = opt.modelGeneratorOpt | LoadSBMLOptions::OPTIMIZE_CFG_SIMPLIFICATION;
opt.modelGeneratorOpt = opt.modelGeneratorOpt | LoadSBMLOptions::OPTIMIZE_GVN;
std::cout << "loading file: " << sbmlFile << std::endl;
roadRunner.load(sbmlFile, &opt);
SimulateOptions settings;
settings.loadSBMLSettings(settingsFile);
// override steps
if (argc > 6)
{
int steps = strtol(argv[6], NULL, 0);
if (steps > 0) {
settings.steps = steps;
}
}
if (argc > 7)
{
double dur = atof(argv[7]);
if (dur > 0) {
settings.duration = dur;
}
}
for (int i = 0; i < argc; ++i) {
if (string(argv[i]).find("stiff") != string::npos) {
roadRunner.getIntegrator()->setValue("stiff", true);
}
}
std::cout << "running for " << settings.steps << ", duration " << settings.duration << std::endl;
std::cout << "absolute: " << roadRunner.getIntegrator()->getValue("absolute_tolerance").convert<bool>() << std::endl;
std::cout << "relative: " << roadRunner.getIntegrator()->getValue("relative_tolerance").convert<bool>() << std::endl;
std::cout << "stiff: " << (roadRunner.getIntegrator()->getValue("stiff").convert<bool>() ? "True" : "False") << std::endl;
roadRunner.setSimulateOptions(settings);
const DoubleMatrix& result = *roadRunner.simulate(0);
if (!output_filename.empty())
{
ofstream output;
output.open(output_filename.c_str());
int rows = result.numRows();
int cols = result.numCols();
for (int i = 0; i < rows; ++i)
{
for (int j = 0; j < cols; ++j)
{
output << result(i, j);
if (j + 1 < cols)
{
output << ", ";
}
else
{
output << "\n";
}
}
}
}
return 0;
}