void CScanTask::fixBuild81()
{
CScanProblem * pProblem = dynamic_cast< CScanProblem * >(mpProblem);
if (pProblem == NULL) return;
pProblem->fixBuild81();
return;
}
bool ScanWidget::taskFinishedEvent()
{
if (!mpTask) return false;
CScanProblem* pProblem = dynamic_cast<CScanProblem*>(mpTask->getProblem());
if (!pProblem) return false;
if (pProblem->getSubtask() != CTaskEnum::Task::parameterFitting)
return false;
protectedNotify(ListViews::ObjectType::MODELPARAMETERSET, ListViews::ADD);
return true;
}
bool CScanTask::initSubtask(const OutputFlag & /* of */,
COutputHandler * pOutputHandler,
std::ostream * pOstream)
{
if (!mpProblem) fatalError();
CScanProblem * pProblem = dynamic_cast<CScanProblem *>(mpProblem);
if (!pProblem) fatalError();
//get the parameters from the problem
CCopasiTask::Type type = *(CCopasiTask::Type*) pProblem->getValue("Subtask").pUINT;
CCopasiDataModel* pDataModel = getObjectDataModel();
assert(pDataModel != NULL);
switch (type)
{
case CCopasiTask::steadyState:
mpSubtask = dynamic_cast<CCopasiTask*>
((*pDataModel->getTaskList())["Steady-State"]);
break;
case CCopasiTask::timeCourse:
mpSubtask = dynamic_cast<CCopasiTask*>
((*pDataModel->getTaskList())["Time-Course"]);
break;
case CCopasiTask::mca:
mpSubtask = dynamic_cast<CCopasiTask*>
((*pDataModel->getTaskList())["Metabolic Control Analysis"]);
break;
case CCopasiTask::lyap:
mpSubtask = dynamic_cast<CCopasiTask*>
((*pDataModel->getTaskList())["Lyapunov Exponents"]);
break;
case CCopasiTask::optimization:
mpSubtask = dynamic_cast<CCopasiTask*>
((*pDataModel->getTaskList())["Optimization"]);
break;
case CCopasiTask::parameterFitting:
mpSubtask = dynamic_cast<CCopasiTask*>
((*pDataModel->getTaskList())["Parameter Estimation"]);
break;
case CCopasiTask::sens:
mpSubtask = dynamic_cast<CCopasiTask*>
((*pDataModel->getTaskList())["Sensitivities"]);
break;
case CCopasiTask::lna:
mpSubtask = dynamic_cast<CCopasiTask*>
((*pDataModel->getTaskList())["Linear Noise Approximation"]);
break;
case CCopasiTask::tssAnalysis :
mpSubtask = dynamic_cast<CCopasiTask*>
((*pDataModel->getTaskList())[CCopasiTask::TypeName[tssAnalysis]]);
break;
case CCopasiTask::crosssection:
mpSubtask = dynamic_cast<CCopasiTask*>
((*pDataModel->getTaskList())["Cross Section"]);
break;
default:
mpSubtask = NULL;
}
mOutputInSubtask = * pProblem->getValue("Output in subtask").pBOOL;
mUseInitialValues = !pProblem->getContinueFromCurrentState();
if (!mpSubtask) return false;
mpSubtask->getProblem()->setModel(pDataModel->getModel()); //TODO
mpSubtask->setCallBack(NULL);
if (mOutputInSubtask)
return mpSubtask->initialize(OUTPUT, pOutputHandler, pOstream);
else
return mpSubtask->initialize(NO_OUTPUT, pOutputHandler, pOstream);
return true;
}
bool ScanWidget::saveTaskProtected()
{
if (mIsLoading)
return true; // currently loading the widget list cannot be trusted
saveCommon();
CScanTask* scanTask =
dynamic_cast< CScanTask * >(mpObject);
if (!scanTask) return false;
CScanProblem *scanProblem = dynamic_cast<CScanProblem *>(scanTask->getProblem());
if (!scanProblem) return false;
const std::vector< QWidget * > & widgetList = scrollview->getWidgetList();
size_t newSize = widgetList.size() - 1; // The last widget is reserved for the subtask.
size_t oldSize = scanProblem->getNumberOfScanItems();
size_t i, imax = std::min(newSize, oldSize);
mChanged = false;
for (i = 0; i < imax; ++i)
{
QWidget * pWidget = widgetList[i];
if (pWidget->objectName() == "CScanWidgetScan")
{
mChanged |= static_cast< CScanWidgetScan * >(pWidget)->save(scanProblem->getScanItem(i));
}
else if (pWidget->objectName() == "CScanWidgetRandom")
{
mChanged |= static_cast< CScanWidgetRandom * >(pWidget)->save(scanProblem->getScanItem(i));
}
else if (pWidget->objectName() == "CScanWidgetRepeat")
{
mChanged |= static_cast< CScanWidgetRepeat * >(pWidget)->save(scanProblem->getScanItem(i));
}
}
for (; i < newSize; ++i)
{
mChanged = true;
QWidget * pWidget = widgetList[i];
CCopasiParameterGroup * pItem = scanProblem->addScanItem(CScanProblem::SCAN_LINEAR);
if (pWidget->objectName() == "CScanWidgetScan")
{
static_cast< CScanWidgetScan * >(pWidget)->save(pItem);
}
else if (pWidget->objectName() == "CScanWidgetRandom")
{
static_cast< CScanWidgetRandom * >(pWidget)->save(pItem);
}
else if (pWidget->objectName() == "CScanWidgetRepeat")
{
static_cast< CScanWidgetRepeat * >(pWidget)->save(pItem);
}
}
for (; i < oldSize; ++i)
{
mChanged = true;
scanProblem->removeScanItem(newSize);
}
// the subtask
const CScanWidgetTask * tmpT = dynamic_cast<CScanWidgetTask*>(widgetList[newSize]);
if (tmpT != NULL)
{
mChanged |= tmpT->save(scanProblem);
}
// :TODO Bug 322: This should only be called when actual changes have been saved.
// However we do not check whether the scan item are mChanged we delete all
// and create them new.
if (mChanged)
{
if (mpDataModel != NULL)
{
mpDataModel->changed();
}
mChanged = false;
}
return true;
}
bool ScanWidget::loadTaskProtected()
{
if (mIsLoading)
return true; // currently loading
mIsLoading = true;
loadCommon();
CScanTask* scanTask =
dynamic_cast< CScanTask * >(mpObject);
if (!scanTask) return false;
CScanProblem *scanProblem = dynamic_cast<CScanProblem *>(scanTask->getProblem());
if (!scanProblem) return false;
scrollview->clearWidgetList();
//std::vector<QWidget*> & widgetList = scrollview->getWidgetList();
//+++
CScanWidgetScan* tmp1;
CScanWidgetRepeat* tmp2;
CScanWidgetRandom* tmp3;
//CScanWidgetBreak* tmp4;
// the scan items
assert(CRootContainer::getDatamodelList()->size() > 0);
size_t i, imax = scanProblem->getNumberOfScanItems();
for (i = 0; i < imax; ++i)
{
CScanProblem::Type type = scanProblem->getScanItem(i)->getValue< CScanProblem::Type >("Type");
switch (type)
{
//+++
case CScanProblem::SCAN_LINEAR:
tmp1 = new CScanWidgetScan(scrollview);
tmp1->load(scanProblem->getScanItem(i));
scrollview->addWidget(tmp1);
break;
case CScanProblem::SCAN_REPEAT:
tmp2 = new CScanWidgetRepeat(scrollview);
tmp2->load(scanProblem->getScanItem(i));
scrollview->addWidget(tmp2);
break;
case CScanProblem::SCAN_RANDOM:
tmp3 = new CScanWidgetRandom(scrollview);
tmp3->load(scanProblem->getScanItem(i));
scrollview->addWidget(tmp3);
break;
default:
break;
}
}
// the widget for the subtask
CScanWidgetTask* tmpT = new CScanWidgetTask(scrollview);
tmpT->load(scanProblem);
scrollview->addWidget(tmpT, false); //false: no control buttons (up/down/del)
mChanged = false;
mIsLoading = false;
return true;
}
/**
* Creates the simulations for SEDML.
*/
std::string CSEDMLExporter::createScanTask(CCopasiDataModel& dataModel, const std::string & modelId)
{
// need L1V2 to export repeated tasks
if (mpSEDMLDocument->getVersion() != 2) return "";
CScanTask* pTask = dynamic_cast<CScanTask*>((*dataModel.getTaskList())["Scan"]);
if (pTask == NULL) return "";
CScanProblem* pProblem = dynamic_cast<CScanProblem*>(pTask->getProblem());
size_t numItems = pProblem->getNumberOfScanItems();
if (numItems == 0)
return "";
if (pProblem->getSubtask() != CCopasiTask::steadyState &&
pProblem->getSubtask() != CCopasiTask::timeCourse)
{
CCopasiMessage(CCopasiMessage::WARNING, "This version of COPASI only allows the export of time course or steady state scans.");
return "";
}
std::string subTaskId;
if (pProblem->getSubtask() == CCopasiTask::steadyState)
{
subTaskId = createSteadyStateTask(dataModel, modelId);
}
else
{
subTaskId = mpTimecourseTask->getId();
}
SedRepeatedTask* task = mpSEDMLDocument->createRepeatedTask();
std::string taskId = SEDMLUtils::getNextId("task", mpSEDMLDocument->getNumTasks());
task->setId(taskId);
task->setResetModel(!pProblem->getContinueFromCurrentState());
// craete ranges / changes
for (size_t i = 0; i < numItems; ++i)
{
CCopasiParameterGroup* current = pProblem->getScanItem(i);
CScanProblem::Type type = (CScanProblem::Type)(*current->getParameter("Type")->getValue().pUINT);
// ignore random items
if (type == CScanProblem::SCAN_RANDOM)
{
CCopasiMessage(CCopasiMessage::WARNING, "This version of COPASI cannot export random scan items, they will be ignored.");
continue;
}
int numSteps = (*current->getParameter("Number of steps")->getValue().pUINT);
// handle repeats
if (type == CScanProblem::SCAN_REPEAT)
{
SedUniformRange *range = task->createUniformRange();
range->setId(SEDMLUtils::getNextId("range", task->getNumRanges()));
range->setStart(0);
range->setEnd(numSteps);
range->setNumberOfPoints(numSteps);
range->setType("linear");
if (task->isSetRangeId())
task->setRangeId(range->getId());
continue;
}
// handle scans
if (type == CScanProblem::SCAN_LINEAR)
{
double min = (*current->getParameter("Minimum")->getValue().pDOUBLE);
double max = (*current->getParameter("Maximum")->getValue().pDOUBLE);
bool log = (*current->getParameter("log")->getValue().pBOOL);
SedUniformRange *range = task->createUniformRange();
range->setId(SEDMLUtils::getNextId("range", task->getNumRanges()));
range->setStart(min);
range->setEnd(max);
range->setNumberOfPoints(numSteps);
range->setType(log ? "log" : "linear");
const CRegisteredObjectName& cn = (*current->getParameter("Object")->getValue().pCN);
std::string xpath = SEDMLUtils::getXPathForObject(*static_cast<const CCopasiObject*>(dataModel.getObject(cn)));
if (xpath.empty())
{
CCopasiMessage(CCopasiMessage::WARNING, "This version of COPASI cannot export the selected scan object, it will be ignored.");
continue;
}
SedSetValue *change = task->createTaskChange();
change->setModelReference(modelId);
if (xpath == SEDML_TIME_URN)
{
change->setSymbol(xpath);
}
else
{
change->setTarget(xpath);
}
change->setRange(range->getId());
change->setMath(SBML_parseFormula(range->getId().c_str()));
continue;
}
}
if (!task->isSetRangeId() && task->getNumRanges() > 0)
task->setRangeId(task->getRange(0)->getId());
// create subtask
SedSubTask* subTask = task->createSubTask();
subTask->setOrder(1);
subTask->setTask(subTaskId);
return taskId;
}
int main(int argc, char *argv[])
{
// Parse the commandline options
// first argument is the SBML filename
// second argument is the endtime
// third argument is the step number
// fourth argument is the filename where the results are to be written
// fifth argument is the tmp directory (this is not needed)
// the rest of the arguments are species names for the result
try
{
// Create the root container.
CCopasiRootContainer::init(0, NULL, false);
}
catch (copasi::autoexcept &e)
{}
catch (copasi::option_error &e)
{}
if (argc < 5)
{
std::cout << "Usage: stochastic-testsuite METHOD SBMLFILENAME ENDTIME STEPNUMBER REPEATS OUTFILENAME SPECIESID1 SPECIESID2 ..." << std::endl;
exit(1);
}
const char* pMethodType = argv[1];
const char* pSBMLFilename = argv[2];
const char* pEndTime = argv[3];
const char* pStepNumber = argv[4];
const char* pRepeats = argv[5];
const char* pOutputFilename = argv[6];
unsigned int NUMARGS = 7;
/*
std::cout << "Input : " << pSBMLFilename << std::endl;
std::cout << "Endtime : " << pEndTime << std::endl;
std::cout << "Stepnumber: " << pStepNumber << std::endl;
std::cout << "Repeats : " << pRepeats << std::endl;
std::cout << "Output file: " << pOutputFilename << std::endl;
*/
char** pSBMLSpeciesIds = new char * [argc - NUMARGS];
unsigned int i, iMax = argc;
CTrajectoryTask* pTrajectoryTask = NULL;
CScanTask* pScanTask = NULL;
std::string CWD = COptions::getPWD();
double endTime = strToDouble(pEndTime, &pEndTime);
double stepNumber = strToDouble(pStepNumber, &pStepNumber);
char** pTmpP = (char**)(&pRepeats);
long int repeats = strtol(pRepeats, pTmpP , 10);
CCopasiMethod::SubType MethodType;
if (!strcmp(pMethodType, "stochastic"))
{
MethodType = CCopasiMethod::stochastic;
}
else if (!strcmp(pMethodType, "directMethod"))
{
MethodType = CCopasiMethod::directMethod;
}
else if (!strcmp(pMethodType, "tauLeap"))
{
MethodType = CCopasiMethod::tauLeap;
}
else if (!strcmp(pMethodType, "adaptiveSA"))
{
MethodType = CCopasiMethod::adaptiveSA;
}
else if (!strcmp(pMethodType, "LSODA"))
{
MethodType = CCopasiMethod::deterministic;
}
else
{
std::cerr << "Invalid method type. Valid options are:" << std::endl;
std::cerr << " stochastic" << std::endl;
std::cerr << " directMethod" << std::endl;
std::cerr << " tauLeap" << std::endl;
}
if (endTime == 0.0)
{
std::cerr << "Invalid endtime " << pEndTime << std::endl;
exit(1);
}
if (stepNumber == 0.0)
{
std::cerr << "Invalid step number " << pStepNumber << std::endl;
exit(1);
}
for (i = NUMARGS; i < iMax; ++i)
{
pSBMLSpeciesIds[i - NUMARGS] = argv[i];
//std::cout << "Copying pointer to " << argv[i] << "." << std::endl;
}
try
{
// Create the global data model.
CCopasiDataModel* pDataModel = CCopasiRootContainer::addDatamodel();
// Import the SBML File
pDataModel->importSBML(pSBMLFilename);
//pDataModel->getModel()->forceCompile();
// create a report with the correct filename and all the species against
// time.
CReportDefinitionVector* pReports = pDataModel->getReportDefinitionList();
CReportDefinition* pReport = pReports->createReportDefinition("Report", "Output for stochastic testsuite run");
pReport->setTaskType(CCopasiTask::timeCourse);
pReport->setIsTable(false);
CCopasiReportSeparator Separator(std::string(","));
pReport->setSeparator(Separator);
std::vector<CRegisteredObjectName> * pHeader = pReport->getHeaderAddr();
std::vector<CRegisteredObjectName> * pBody = pReport->getBodyAddr();
// Add time column
pHeader->push_back(CCopasiStaticString("time").getCN());
pBody->push_back(CCopasiObjectName(pDataModel->getModel()->getCN() + ",Reference=Time"));
iMax = iMax - NUMARGS;
const CCopasiVector<CMetab>& metabolites = pDataModel->getModel()->getMetabolites();
for (i = 0; i < iMax; ++i)
{
pHeader->push_back(Separator.getCN());
pBody->push_back(Separator.getCN());
unsigned int j, jMax = metabolites.size();
std::string SBMLId = unQuote(pSBMLSpeciesIds[i]);
for (j = 0; j < jMax; ++j)
{
if (metabolites[j]->getSBMLId() == SBMLId)
{
break;
}
}
if (j == jMax)
{
std::cerr << "Could not find a metabolite for the SBML id \"" << pSBMLSpeciesIds[i] << "\"" << std::endl;
exit(1);
}
pHeader->push_back(CCopasiStaticString(SBMLId).getCN());
pBody->push_back(metabolites[j]->getObject(CCopasiObjectName("Reference=ParticleNumber"))->getCN());
}
// create a trajectory task
pTrajectoryTask = new CTrajectoryTask();
pTrajectoryTask->setMethodType(MethodType);
pTrajectoryTask->getProblem()->setModel(pDataModel->getModel());
pTrajectoryTask->setScheduled(false);
//pTrajectoryTask->getReport().setReportDefinition(pReport);
//pTrajectoryTask->getReport().setTarget(CWD + "/" + pOutputFilename);
//pTrajectoryTask->getReport().setAppend(false);
CTrajectoryProblem* pProblem = dynamic_cast<CTrajectoryProblem*>(pTrajectoryTask->getProblem());
pProblem->setStepNumber((const unsigned C_INT32)stepNumber);
pProblem->setDuration((const C_FLOAT64)endTime);
pProblem->setTimeSeriesRequested(true);
pProblem->setTimeSeriesRequested(false);
//pProblem->setInitialState(pDataModel->getModel()->getInitialState());
CCopasiVectorN< CCopasiTask > & TaskList = * pDataModel->getTaskList();
TaskList.remove("Time-Course");
TaskList.add(pTrajectoryTask, true);
// create a scan task
pScanTask = new CScanTask(pDataModel);
CScanProblem* pScanProblem = dynamic_cast<CScanProblem*>(pScanTask->getProblem());
pScanProblem->setModel(pDataModel->getModel());
pScanTask->setScheduled(true);
pScanTask->getReport().setReportDefinition(pReport);
pScanTask->getReport().setTarget(CWD + "/" + pOutputFilename);
pScanTask->getReport().setAppend(false);
pScanProblem->setSubtask(CCopasiTask::timeCourse);
pScanProblem->createScanItem(CScanProblem::SCAN_REPEAT, repeats);
pScanProblem->setOutputInSubtask(true);
pScanProblem->setContinueFromCurrentState(false);
TaskList.remove("Scan");
TaskList.add(pScanTask, true);
// save the file for control purposes
std::string saveFilename = pSBMLFilename;
saveFilename = saveFilename.substr(0, saveFilename.length() - 4) + ".cps";
pDataModel->saveModel(saveFilename, NULL, true);
// Run the trajectory task
pScanTask->initialize(CCopasiTask::OUTPUT_SE, pDataModel, NULL);
pScanTask->process(true);
pScanTask->restore();
// create another report that will write to the directory where the input file came from
// this can be used for debugging
// create a trajectory task
// pScanTask->getReport().setTarget(pOutputFilename);
// pScanTask->initialize(CCopasiTask::OUTPUT_SE, pDataModel, NULL);
// pScanTask->process(true);
// pScanTask->restore();
}
catch (CCopasiException Exception)
{
std::cerr << Exception.getMessage().getText() << std::endl;
}
CCopasiRootContainer::destroy();
return 0;
}
bool CScanTask::initSubtask(const OutputFlag & /* of */,
COutputHandler * pOutputHandler,
std::ostream * pOstream)
{
if (!mpProblem) fatalError();
CScanProblem * pProblem = dynamic_cast<CScanProblem *>(mpProblem);
if (!pProblem) fatalError();
//get the parameters from the problem
CTaskEnum::Task type = (CTaskEnum::Task) pProblem->getValue< unsigned C_INT32 >("Subtask");
CDataModel* pDataModel = getObjectDataModel();
assert(pDataModel != NULL);
switch (type)
{
case CTaskEnum::Task::steadyState:
mpSubtask = dynamic_cast<CCopasiTask*>
(&pDataModel->getTaskList()->operator[]("Steady-State"));
break;
case CTaskEnum::Task::timeCourse:
mpSubtask = dynamic_cast<CCopasiTask*>
(&pDataModel->getTaskList()->operator[]("Time-Course"));
break;
case CTaskEnum::Task::mca:
mpSubtask = dynamic_cast<CCopasiTask*>
(&pDataModel->getTaskList()->operator[]("Metabolic Control Analysis"));
break;
case CTaskEnum::Task::lyap:
mpSubtask = dynamic_cast<CCopasiTask*>
(&pDataModel->getTaskList()->operator[]("Lyapunov Exponents"));
break;
case CTaskEnum::Task::optimization:
mpSubtask = dynamic_cast<CCopasiTask*>
(&pDataModel->getTaskList()->operator[]("Optimization"));
break;
case CTaskEnum::Task::parameterFitting:
mpSubtask = dynamic_cast<CCopasiTask*>
(&pDataModel->getTaskList()->operator[]("Parameter Estimation"));
break;
case CTaskEnum::Task::sens:
mpSubtask = dynamic_cast<CCopasiTask*>
(&pDataModel->getTaskList()->operator[]("Sensitivities"));
break;
case CTaskEnum::Task::lna:
mpSubtask = dynamic_cast<CCopasiTask*>
(&pDataModel->getTaskList()->operator[]("Linear Noise Approximation"));
break;
case CTaskEnum::Task::tssAnalysis :
mpSubtask = dynamic_cast<CCopasiTask*>
(&pDataModel->getTaskList()->operator[](CTaskEnum::TaskName[CTaskEnum::Task::tssAnalysis]));
break;
case CTaskEnum::Task::crosssection:
mpSubtask = dynamic_cast<CCopasiTask*>
(&pDataModel->getTaskList()->operator[]("Cross Section"));
break;
default:
mpSubtask = NULL;
}
mOutputInSubtask = pProblem->getValue< bool >("Output in subtask");
mUseInitialValues = !pProblem->getContinueFromCurrentState();
if (!mpSubtask) return false;
mpSubtask->setMathContainer(mpContainer); //TODO
mpSubtask->setCallBack(NULL);
if (mOutputInSubtask)
return mpSubtask->initialize(OUTPUT, pOutputHandler, pOstream);
else
return mpSubtask->initialize(NO_OUTPUT, pOutputHandler, pOstream);
return true;
}
