use of cbit.vcell.mapping.SimulationContext.MathMappingCallback in project vcell by virtualcell.
the class SimulationListPanel method newSimulation.
/**
* Comment
*/
private void newSimulation(final NetworkGenerationRequirements networkGenerationRequirements) {
AsynchClientTask task1 = new AsynchClientTask("new simulation", AsynchClientTask.TASKTYPE_NONSWING_BLOCKING) {
@Override
public void run(Hashtable<String, Object> hashTable) throws Exception {
MathMappingCallback mathMappingCallback = new MathMappingCallbackTaskAdapter(getClientTaskStatusSupport());
if (getSimulationWorkspace().getSimulationOwner() instanceof SimulationContext) {
SimulationContext simulationContext = (SimulationContext) getSimulationWorkspace().getSimulationOwner();
simulationContext.refreshMathDescription(mathMappingCallback, networkGenerationRequirements);
}
}
};
AsynchClientTask task2 = new AsynchClientTask("new simulation", AsynchClientTask.TASKTYPE_SWING_BLOCKING) {
@Override
public void run(Hashtable<String, Object> hashTable) throws Exception {
MathMappingCallback mathMappingCallback = new MathMappingCallbackTaskAdapter(getClientTaskStatusSupport());
int newSimIndex = getSimulationWorkspace().newSimulation(SimulationListPanel.this, mathMappingCallback, networkGenerationRequirements);
getScrollPaneTable().getSelectionModel().setSelectionInterval(newSimIndex, newSimIndex);
getScrollPaneTable().scrollRectToVisible(getScrollPaneTable().getCellRect(newSimIndex, 0, true));
}
};
ClientTaskDispatcher.dispatch(this, new Hashtable<String, Object>(), new AsynchClientTask[] { task1, task2 });
}
use of cbit.vcell.mapping.SimulationContext.MathMappingCallback in project vcell by virtualcell.
the class ParameterEstimationRunTaskPanel method solve.
private void solve() throws NumberFormatException {
CopasiOptimizationMethod com = optimizationMethodParameterTableModel.copasiOptimizationMethod;
OptimizationSolverSpec optSolverSpec = new OptimizationSolverSpec(com);
// get num runs for stochstic opt mehtods before starting solving...
if (com.getType().isStochasticMethod()) {
int numRuns = Integer.parseInt(((String) numberOfRunComboBox.getSelectedItem()));
optSolverSpec.setNumOfRuns(numRuns);
}
parameterEstimationTask.setOptimizationSolverSpec(optSolverSpec);
parameterEstimationTask.getModelOptimizationSpec().setComputeProfileDistributions(computeProfileDistributionsCheckBox.isSelected());
optSolverCallbacks.reset();
Double endValue = com.getEndValue();
optSolverCallbacks.setEvaluation(0, Double.POSITIVE_INFINITY, 0, endValue, 0);
// (endValue != null);
getRunStatusDialog().showProgressBar(com);
Collection<AsynchClientTask> taskList = ClientRequestManager.updateMath(this, parameterEstimationTask.getSimulationContext(), false, NetworkGenerationRequirements.ComputeFullStandardTimeout);
AsynchClientTask task1 = new AsynchClientTask("checking issues", AsynchClientTask.TASKTYPE_NONSWING_BLOCKING) {
@Override
public void run(Hashtable<String, Object> hashTable) throws Exception {
getClientTaskStatusSupport().setProgress(0);
StringBuffer issueText = new StringBuffer();
java.util.Vector<Issue> issueList = new java.util.Vector<Issue>();
IssueContext issueContext = new IssueContext();
parameterEstimationTask.gatherIssues(issueContext, issueList);
boolean bFailed = false;
for (int i = 0; i < issueList.size(); i++) {
Issue issue = (Issue) issueList.elementAt(i);
issueText.append(issue.getMessage() + "\n");
if (issue.getSeverity() == Issue.SEVERITY_ERROR) {
bFailed = true;
break;
}
}
if (bFailed) {
throw new OptimizationException(issueText.toString());
}
parameterEstimationTask.refreshMappings();
}
};
taskList.add(task1);
AsynchClientTask task2 = new AsynchClientTask("Starting param esitmation job...", AsynchClientTask.TASKTYPE_NONSWING_BLOCKING) {
@Override
public void run(Hashtable<String, Object> hashTable) throws Exception {
MathMappingCallback mathMappingCallback = new MathMappingCallbackTaskAdapter(getClientTaskStatusSupport());
// OptimizationResultSet optResultSet = CopasiOptimizationSolver.solveLocalPython(new ParameterEstimationTaskSimulatorIDA(),parameterEstimationTask,optSolverCallbacks,mathMappingCallback);
OptimizationResultSet optResultSet = CopasiOptimizationSolver.solveRemoteApi(new ParameterEstimationTaskSimulatorIDA(), parameterEstimationTask, optSolverCallbacks, mathMappingCallback, getClientTaskStatusSupport());
hashTable.put(ORS_KEY, optResultSet);
}
};
taskList.add(task2);
AsynchClientTask setResultTask = new AsynchClientTask("set results", AsynchClientTask.TASKTYPE_SWING_BLOCKING) {
@Override
public void run(Hashtable<String, Object> hashTable) throws Exception {
OptimizationResultSet optResultSet = (OptimizationResultSet) hashTable.get(ORS_KEY);
parameterEstimationTask.setOptimizationResultSet(optResultSet);
}
};
taskList.add(setResultTask);
ClientTaskDispatcher.dispatch(this, new Hashtable<String, Object>(), taskList.toArray(new AsynchClientTask[taskList.size()]), getRunStatusDialog(), true, true, true, null, false);
}
use of cbit.vcell.mapping.SimulationContext.MathMappingCallback in project vcell by virtualcell.
the class StochtestRunService method computeTrials.
private void computeTrials(SimulationContext simContext, StochtestRun stochtestRun, File baseDirectory, OutputTimeSpec outputTimeSpec, double endTime, int numTrials) throws PropertyVetoException, IOException {
//
// make simulation
//
MathMappingCallback callback = new MathMappingCallback() {
@Override
public void setProgressFraction(float fractionDone) {
}
@Override
public void setMessage(String message) {
}
@Override
public boolean isInterrupted() {
return false;
}
};
NetworkGenerationRequirements networkGenerationRequirements = NetworkGenerationRequirements.getComputeFull(bngTimeoutMS);
simContext.refreshMathDescription(callback, networkGenerationRequirements);
Simulation sim = simContext.addNewSimulation("stochtestrun_" + stochtestRun.key, callback, networkGenerationRequirements);
sim.setSimulationOwner(simContext);
//
// get variables to save
//
simContext.getModel().getSpeciesContexts();
ArrayList<String> varNameList = new ArrayList<String>();
for (SpeciesContextSpec scs : simContext.getReactionContext().getSpeciesContextSpecs()) {
varNameList.add(scs.getSpeciesContext().getName());
}
String[] varNames = varNameList.toArray(new String[0]);
//
// get time points to save
//
ArrayList<Double> sampleTimeList = new ArrayList<Double>();
if (outputTimeSpec instanceof UniformOutputTimeSpec) {
double dT = ((UniformOutputTimeSpec) outputTimeSpec).getOutputTimeStep();
int currTimeIndex = 0;
while (currTimeIndex * dT <= (endTime + 1e-8)) {
sampleTimeList.add(currTimeIndex * dT);
currTimeIndex++;
}
}
double[] sampleTimes = new double[sampleTimeList.size()];
for (int i = 0; i < sampleTimes.length; i++) {
sampleTimes[i] = sampleTimeList.get(i);
}
//
// run N trials and save data
//
TimeSeriesMultitrialData sampleData = new TimeSeriesMultitrialData(sim.getName(), varNames, sampleTimes, numTrials);
runsolver(sim, baseDirectory, numTrials, sampleData);
StochtestFileUtils.writeData(sampleData, StochtestFileUtils.getStochtestRunDataFile(baseDir, stochtestRun));
}
use of cbit.vcell.mapping.SimulationContext.MathMappingCallback in project vcell by virtualcell.
the class BioModelEditor method popupMenuActionPerformed.
@Override
protected void popupMenuActionPerformed(DocumentEditorPopupMenuAction action, String actionCommand) {
Model model = bioModel.getModel();
final SimulationContext selectedSimulationContext = getSelectedSimulationContext();
switch(action) {
case add_new:
try {
Object obj = documentEditorTree.getLastSelectedPathComponent();
if (obj == null || !(obj instanceof BioModelNode)) {
return;
}
BioModelNode selectedNode = (BioModelNode) obj;
Object userObject = selectedNode.getUserObject();
if (userObject instanceof DocumentEditorTreeFolderNode) {
DocumentEditorTreeFolderClass folderClass = ((DocumentEditorTreeFolderNode) userObject).getFolderClass();
Object newObject = null;
switch(folderClass) {
case REACTIONS_NODE:
// TODO: should add a Add New Rule menu item
newObject = model.createSimpleReaction(model.getStructure(0));
break;
case STRUCTURES_NODE:
newObject = model.createFeature();
break;
case SPECIES_NODE:
newObject = model.createSpeciesContext(model.getStructure(0));
break;
case MOLECULAR_TYPES_NODE:
MolecularType mt = model.getRbmModelContainer().createMolecularType();
model.getRbmModelContainer().addMolecularType(mt, true);
newObject = mt;
break;
case OBSERVABLES_NODE:
if (bioModel.getModel().getRbmModelContainer().getMolecularTypeList().isEmpty()) {
PopupGenerator.showInfoDialog(this, VCellErrorMessages.MustBeRuleBased);
return;
}
RbmObservable o = model.getRbmModelContainer().createObservable(RbmObservable.ObservableType.Molecules);
model.getRbmModelContainer().addObservable(o);
SpeciesPattern sp = new SpeciesPattern();
o.addSpeciesPattern(sp);
newObject = o;
break;
case SIMULATIONS_NODE:
if (selectedSimulationContext != null) {
AsynchClientTask task1 = new AsynchClientTask("new simulation", AsynchClientTask.TASKTYPE_NONSWING_BLOCKING) {
@Override
public void run(Hashtable<String, Object> hashTable) throws Exception {
MathMappingCallback callback = new MathMappingCallbackTaskAdapter(getClientTaskStatusSupport());
selectedSimulationContext.refreshMathDescription(callback, NetworkGenerationRequirements.AllowTruncatedStandardTimeout);
}
};
AsynchClientTask task2 = new AsynchClientTask("new simulation", AsynchClientTask.TASKTYPE_SWING_BLOCKING) {
@Override
public void run(Hashtable<String, Object> hashTable) throws Exception {
MathMappingCallback callback = new MathMappingCallbackTaskAdapter(getClientTaskStatusSupport());
Object newsim = selectedSimulationContext.addNewSimulation(SimulationOwner.DEFAULT_SIM_NAME_PREFIX, callback, NetworkGenerationRequirements.AllowTruncatedStandardTimeout);
selectionManager.setSelectedObjects(new Object[] { newsim });
}
};
ClientTaskDispatcher.dispatch(this, new Hashtable<String, Object>(), new AsynchClientTask[] { task1, task2 });
}
break;
default:
break;
}
if (newObject != null) {
selectionManager.setSelectedObjects(new Object[] { newObject });
}
}
} catch (Exception ex) {
DialogUtils.showErrorDialog(this, ex.getMessage());
}
break;
case add_new_app_deterministic:
newApplication(Application.NETWORK_DETERMINISTIC);
break;
case add_new_app_stochastic:
newApplication(Application.NETWORK_STOCHASTIC);
break;
case add_new_app_rulebased:
{
// if(model.getStructures().length > 1) {
// DialogUtils.showErrorDialog(this, VCellErrorMessages.NFSimAppNotAllowedForMultipleStructures);
// return;
// }
newApplication(Application.RULE_BASED_STOCHASTIC);
break;
}
case copyName:
String name = bioModel.getName();
StringSelection data = new StringSelection(name);
Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
c.setContents(data, data);
break;
case copy_app:
ApplicationActionCommand acc = ApplicationActionCommand.lookup(actionCommand);
switch(acc.actionType()) {
case COPY_AS_IS:
copyApplication();
break;
case COPY_CHANGE:
boolean bothSpatial = acc.isSourceSpatial() && acc.isDestSpatial();
// if(acc.getAppType().equals(SimulationContext.Application.RULE_BASED_STOCHASTIC) && model.getStructures().length > 1) {
// DialogUtils.showErrorDialog(this, VCellErrorMessages.NFSimAppNotAllowedForMultipleStructures);
// return;
// }
copyApplication(bothSpatial, acc.getAppType());
break;
case CREATE:
// not used in this menu
throw new UnsupportedOperationException();
}
break;
case app_new_biomodel:
if (actionCommand.equals(GuiConstants.MENU_TEXT_APP_NEWBIOMODEL)) {
createNewBiomodelFromApp();
}
break;
case delete:
try {
if (selectedSimulationContext != null) {
String confirm = PopupGenerator.showOKCancelWarningDialog(this, "Deleting application", "You are going to delete the Application '" + selectedSimulationContext.getName() + "'. Continue?");
if (confirm.equals(UserMessage.OPTION_CANCEL)) {
return;
}
deleteSimulationcontexts(new SimulationContext[] { selectedSimulationContext });
}
} catch (Exception ex) {
DialogUtils.showErrorDialog(this, ex.getMessage());
}
break;
case deleteChoose:
try {
SimulationContext[] allSimContexts = Arrays.copyOf(getBioModelWindowManager().getVCDocument().getSimulationContexts(), getBioModelWindowManager().getVCDocument().getSimulationContexts().length);
Arrays.sort(allSimContexts, new Comparator<SimulationContext>() {
@Override
public int compare(SimulationContext o1, SimulationContext o2) {
return o1.getName().compareToIgnoreCase(o2.getName());
}
});
String[][] rowDataOrig = new String[allSimContexts.length][2];
for (int i = 0; i < allSimContexts.length; i++) {
rowDataOrig[i][0] = allSimContexts[i].getName();
rowDataOrig[i][1] = allSimContexts[i].getSimulations().length + "";
}
final String DELETE = "Delete";
final String CANCEL = "Cancel";
TableListResult result = DialogUtils.showComponentOptionsTableList(this, "Select Applications (and associated Simulations) to delete.", new String[] { "Application", "# of Sims" }, rowDataOrig, ListSelectionModel.MULTIPLE_INTERVAL_SELECTION, null, new String[] { DELETE, CANCEL }, CANCEL, null);
if (result != null && result.selectedOption != null && result.selectedOption.equals(DELETE) && result.selectedTableRows != null && result.selectedTableRows.length > 0) {
ArrayList<SimulationContext> deleteTheseSimcontexts = new ArrayList<SimulationContext>();
for (int i = 0; i < result.selectedTableRows.length; i++) {
deleteTheseSimcontexts.add(allSimContexts[result.selectedTableRows[i]]);
}
deleteSimulationcontexts(deleteTheseSimcontexts.toArray(new SimulationContext[0]));
}
} catch (Exception ex) {
DialogUtils.showErrorDialog(this, ex.getMessage());
}
break;
default:
break;
}
}
use of cbit.vcell.mapping.SimulationContext.MathMappingCallback in project vcell by virtualcell.
the class BioModelEditorApplicationsPanel method compareButtonPressed.
private void compareButtonPressed() {
int[] rows = table.getSelectedRows();
if (rows == null || rows.length != 2) {
return;
}
try {
SimulationContext simContext1 = tableModel.getValueAt(rows[0]);
SimulationContext simContext2 = tableModel.getValueAt(rows[1]);
BioModel bioModel = simContext1.getBioModel();
MathMappingCallback callback = new MathMappingCallback() {
@Override
public void setProgressFraction(float fractionDone) {
Thread.dumpStack();
System.out.println("---> stdout mathMapping: progress = " + (fractionDone * 100.0) + "% done");
}
@Override
public void setMessage(String message) {
Thread.dumpStack();
System.out.println("---> stdout mathMapping: message = " + message);
}
@Override
public boolean isInterrupted() {
return false;
}
};
simContext1.refreshMathDescription(callback, NetworkGenerationRequirements.ComputeFullStandardTimeout);
simContext2.refreshMathDescription(callback, NetworkGenerationRequirements.ComputeFullStandardTimeout);
Xmlproducer xmlProducer = new Xmlproducer(false);
String simContext1XML = XmlUtil.xmlToString(xmlProducer.getXML(simContext1, bioModel));
String simContext2XML = XmlUtil.xmlToString(xmlProducer.getXML(simContext2, bioModel));
DiffConfiguration comparisonSetting = DiffConfiguration.COMPARE_DOCS_OTHER;
XmlTreeDiff diffTree = XmlHelper.compareMerge(simContext1XML, simContext2XML, comparisonSetting, true);
String baselineDesc = "application " + simContext1.getName();
String modifiedDesc = "application " + simContext2.getName();
TMLPanel comparePanel = new TMLPanel();
comparePanel.setXmlTreeDiff(diffTree);
comparePanel.setBaselineVersionDescription(baselineDesc);
comparePanel.setModifiedVersionDescription(modifiedDesc);
ChildWindowManager childWindowManager = ChildWindowManager.findChildWindowManager(this);
String title = "comparing application " + simContext1.getName() + " and " + simContext2.getName();
ChildWindow childWindow = childWindowManager.addChildWindow(comparePanel, diffTree, title, true);
childWindow.setSize(new Dimension(600, 600));
childWindow.show();
} catch (XmlParseException e) {
e.printStackTrace();
DialogUtils.showErrorDialog(this, "failed to compare applications: \n\n" + e.getMessage());
}
}
Aggregations