Examples with SimulationContext cbit.vcell.mapping.SimulationContext used on opensource projects

Example 66 with SimulationContext

use of cbit.vcell.mapping.SimulationContext 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 });
}

Example 67 with SimulationContext

use of cbit.vcell.mapping.SimulationContext in project vcell by virtualcell.

the class SimulationListPanel method quickRun.

/*
	private void particleView() {
		int row = getScrollPaneTable().getSelectedRow();
		if (row < 0) {
			return;
		}
		Simulation selectedSim = getSimulationListTableModel1().getValueAt(row);
		getSimulationWorkspace().getClientSimManager().runSmoldynParticleView(selectedSim);
	}
	*/
private void quickRun(ViewerType viewerType) {
    int row = getScrollPaneTable().getSelectedRow();
    if (row < 0) {
        return;
    }
    activateConsole();
    Simulation selectedSim = getSimulationListTableModel1().getValueAt(row);
    SolverDescription solverDescription = selectedSim.getSolverTaskDescription().getSolverDescription();
    if (solverDescription.equals(SolverDescription.FiniteVolume)) {
        if (getSimulationWorkspace().getSimulationOwner() instanceof SimulationContext) {
            String option = DialogUtils.showOKCancelWarningDialog(SimulationListPanel.this, "Deprecated Solver", VCellErrorMessages.getSemiFVSolverCompiledSolverDeprecated(selectedSim));
            if (option.equals(SimpleUserMessage.OPTION_CANCEL)) {
                return;
            }
            try {
                selectedSim.getSolverTaskDescription().setSolverDescription(SolverDescription.FiniteVolumeStandalone);
                selectedSim.setIsDirty(true);
            } catch (PropertyVetoException e) {
                e.printStackTrace();
            }
        }
    }
    getSimulationWorkspace().getClientSimManager().runQuickSimulation(selectedSim, viewerType);
}

Example 68 with SimulationContext

use of cbit.vcell.mapping.SimulationContext in project vcell by virtualcell.

the class SimulationListPanel method runSimulations.

/**
 * Comment
 */
private void runSimulations() {
    final ArrayList<Simulation> simList = new ArrayList<Simulation>();
    int[] selections = getScrollPaneTable().getSelectedRows();
    for (int i = 0; i < selections.length; i++) {
        Simulation sim = (Simulation) (ivjSimulationListTableModel1.getValueAt(selections[i]));
        if (sim.getSolverTaskDescription().getSolverDescription().equals(SolverDescription.FiniteVolume)) {
            if (getSimulationWorkspace().getSimulationOwner() instanceof SimulationContext) {
                String option = DialogUtils.showOKCancelWarningDialog(SimulationListPanel.this, "Deprecated Solver", VCellErrorMessages.getSemiFVSolverCompiledSolverDeprecated(sim));
                if (option.equals(SimpleUserMessage.OPTION_CANCEL)) {
                    return;
                }
                try {
                    sim.getSolverTaskDescription().setSolverDescription(SolverDescription.FiniteVolumeStandalone);
                    sim.setIsDirty(true);
                } catch (PropertyVetoException e) {
                    e.printStackTrace();
                }
            }
        }
        simList.add(sim);
    }
    if (simList.size() > 0) {
        activateConsole();
        Simulation[] toRun = simList.toArray(new Simulation[0]);
        getSimulationWorkspace().runSimulations(toRun, this);
    }
}

Example 69 with SimulationContext

use of cbit.vcell.mapping.SimulationContext in project vcell by virtualcell.

the class VFrapXmlHelper method ReplaceVFrapNamesWithSymbolNames.

// 
// replace vFrap default names in field function arguments with data symbol names -----
// 
public static void ReplaceVFrapNamesWithSymbolNames(BioModel bioModel) throws ExpressionException {
    SimulationContext simContext = bioModel.getSimulationContexts()[0];
    SpeciesContextSpec[] scsArray = simContext.getReactionContext().getSpeciesContextSpecs();
    for (SpeciesContextSpec scs : scsArray) {
        // vFrap('a','c',0.0,'volume')
        Expression exp = scs.getInitialConditionParameter().getExpression();
        FieldFunctionArguments[] fieldFunctionArgs = FieldUtilities.getFieldFunctionArguments(exp);
        if (fieldFunctionArgs != null && fieldFunctionArgs.length > 0) {
            for (FieldFunctionArguments args : fieldFunctionArgs) {
                for (DataSymbol ds : simContext.getDataContext().getDataSymbols()) {
                    if (ds instanceof FieldDataSymbol) {
                        FieldDataSymbol fieldDataSymbol = (FieldDataSymbol) ds;
                        // String extDataIdentName = fieldDataSymbol.getExternalDataIdentifier().getName();	// name of field data
                        // String argsFieldName = args.getFieldName();				// roiData
                        // fieldDataSymbol.getFieldDataVarTime() == args.getTime().evaluateConstant()
                        // name of data symbol  ex: postbleach_first_ccccF
                        String dataSymbolName = fieldDataSymbol.getName();
                        // name in expression as it comes from vFrap   ex: postbleach_first
                        String argsVariableName = args.getVariableName();
                        if (dataSymbolName.startsWith(argsVariableName)) {
                            // vcField('roiData','postbleach_first',0.0,'Volume')
                            String oldExpression = args.infix();
                            exp.substituteInPlace(new Expression(oldExpression), new Expression(dataSymbolName));
                            exp.bindExpression(simContext);
                        }
                    }
                }
            }
        }
    }
}

Example 70 with SimulationContext

use of cbit.vcell.mapping.SimulationContext in project vcell by virtualcell.

the class BioModelWindowManager method updateApplicationHash.

/**
 * Insert the method's description here.
 * Creation date: (6/1/2004 2:33:41 AM)
 */
private void updateApplicationHash(boolean reset) {
    SimulationContext[] scs = getBioModel().getSimulationContexts();
    Enumeration<SimulationContext> en = getApplicationsHash().keys();
    while (en.hasMoreElements()) {
        SimulationContext sc = (SimulationContext) en.nextElement();
        ApplicationComponents appComponents = getApplicationsHash().get(sc);
        if (!getBioModel().contains(sc)) {
            if (reset) {
                // find one with the same name, if available
                SimulationContext found = null;
                if (scs != null) {
                    for (int i = 0; i < scs.length; i++) {
                        if (scs[i].getName().equals(sc.getName())) {
                            found = scs[i];
                            break;
                        }
                    }
                }
                if (found != null) {
                    // update hash
                    getApplicationsHash().remove(sc);
                    getApplicationsHash().put(found, appComponents);
                    appComponents.resetSimulationContext(found);
                    // check simulation data windows
                    updateSimulationDataViewers(appComponents, found);
                    // rewire listener
                    sc.removePropertyChangeListener(this);
                    found.removePropertyChangeListener(this);
                    found.addPropertyChangeListener(this);
                } else {
                    // we didn't find one, so remove from hash and close all of its windows
                    remove(appComponents, sc);
                }
            } else {
                // shouldn't have it
                remove(appComponents, sc);
            }
        }
    }
}