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

Example 96 with SimulationContext

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

the class ParameterEstimationRunTaskPanel method saveSolutionAsNewSimulation.

private void saveSolutionAsNewSimulation() {
    try {
        OptimizationSpec optSpec = parameterEstimationTask.getModelOptimizationMapping().getOptimizationSpec();
        if (optSpec == null) {
            throw new RuntimeException("optimization not yet performed");
        }
        // 
        // add new simulation to the Application (other bookkeeping required?)
        // 
        String newSimName = DialogUtils.showInputDialog0(this, "Enter name for new simulation", "Fitted");
        newSimName = (newSimName == null ? null : newSimName.trim());
        if (newSimName == null || newSimName.length() == 0) {
            throw new Exception("New Simulation name cannot be 0 characters");
        }
        SimulationContext simContext = parameterEstimationTask.getModelOptimizationSpec().getSimulationContext();
        MathMappingCallback dummyCallback = new MathMappingCallback() {

            @Override
            public void setProgressFraction(float fractionDone) {
            }

            @Override
            public void setMessage(String message) {
            }

            @Override
            public boolean isInterrupted() {
                return false;
            }
        };
        Simulation newSim = simContext.addNewSimulation(newSimName, dummyCallback, NetworkGenerationRequirements.ComputeFullStandardTimeout);
        parameterEstimationTask.getModelOptimizationMapping().applySolutionToMathOverrides(newSim, parameterEstimationTask.getOptimizationResultSet());
        DialogUtils.showInfoDialog(this, "created simulation \"" + newSim.getName() + "\"");
    } catch (UtilCancelException e) {
    // ignore, user cancelled operation
    } catch (Exception e) {
        e.printStackTrace(System.out);
        DialogUtils.showErrorDialog(this, e.getMessage(), e);
    }
}

Example 97 with SimulationContext

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

the class ParameterMappingPanel method jMenuItemCopy_ActionPerformed.

/**
 * Comment
 */
private void jMenuItemCopy_ActionPerformed(java.awt.event.ActionEvent actionEvent) {
    if (actionEvent.getSource() == getJMenuItemCopy() || actionEvent.getSource() == getJMenuItemCopyAll()) {
        try {
            // 
            // Copy Optimization Parameters (Initial Guess or Solution)
            // 
            int[] rows = null;
            if (actionEvent.getSource() == getJMenuItemCopyAll()) {
                rows = new int[getScrollPaneTable().getRowCount()];
                for (int i = 0; i < rows.length; i += 1) {
                    rows[i] = i;
                }
            } else {
                rows = getScrollPaneTable().getSelectedRows();
            }
            SimulationContext sc = getParameterEstimationTask().getModelOptimizationSpec().getSimulationContext();
            MathSymbolMapping msm = null;
            try {
                MathMapping mm = sc.createNewMathMapping();
                msm = mm.getMathSymbolMapping();
            } catch (Exception e) {
                e.printStackTrace(System.out);
                DialogUtils.showWarningDialog(this, "current math not valid, some paste operations will be limited\n\nreason: " + e.getMessage());
            }
            boolean bInitialGuess = (getScrollPaneTable().getSelectedColumn() == ParameterMappingTableModel.COLUMN_CURRENTVALUE);
            ParameterMappingSpec[] parameterMappingSpecs = new ParameterMappingSpec[rows.length];
            java.util.Vector<SymbolTableEntry> primarySymbolTableEntriesV = new java.util.Vector<SymbolTableEntry>();
            java.util.Vector<SymbolTableEntry> alternateSymbolTableEntriesV = new java.util.Vector<SymbolTableEntry>();
            java.util.Vector<Expression> resolvedValuesV = new java.util.Vector<Expression>();
            // 
            // Create formatted string for text/spreadsheet pasting.
            // 
            StringBuffer sb = new StringBuffer();
            sb.append("\"Parameters for (Optimization Task)" + getParameterEstimationTask().getName() + " -> " + "(BioModel)" + getParameterEstimationTask().getModelOptimizationSpec().getSimulationContext().getBioModel().getName() + " -> " + "(App)" + getParameterEstimationTask().getModelOptimizationSpec().getSimulationContext().getName() + "\"\n");
            sb.append("\"Parameter Name\"\t\"" + (bInitialGuess ? "Initial Guess" : "Solution") + "\"\n");
            for (int i = 0; i < rows.length; i += 1) {
                ParameterMappingSpec pms = parameterMappingTableModel.getValueAt(rows[i]);
                parameterMappingSpecs[i] = pms;
                primarySymbolTableEntriesV.add(pms.getModelParameter());
                if (msm != null) {
                    alternateSymbolTableEntriesV.add(msm.getVariable(pms.getModelParameter()));
                } else {
                    alternateSymbolTableEntriesV.add(null);
                }
                Double resolvedValue = null;
                if (!bInitialGuess) {
                    resolvedValue = getParameterEstimationTask().getCurrentSolution(pms);
                }
                if (resolvedValue == null) {
                    resolvedValue = new Double(pms.getCurrent());
                }
                resolvedValuesV.add(new Expression(resolvedValue.doubleValue()));
                sb.append("\"" + parameterMappingSpecs[i].getModelParameter().getName() + "\"\t" + resolvedValue + "\n");
            }
            // 
            // Send to clipboard
            // 
            VCellTransferable.ResolvedValuesSelection rvs = new VCellTransferable.ResolvedValuesSelection((SymbolTableEntry[]) BeanUtils.getArray(primarySymbolTableEntriesV, SymbolTableEntry.class), (SymbolTableEntry[]) BeanUtils.getArray(alternateSymbolTableEntriesV, SymbolTableEntry.class), (Expression[]) BeanUtils.getArray(resolvedValuesV, Expression.class), sb.toString());
            VCellTransferable.sendToClipboard(rvs);
        } catch (Throwable e) {
            PopupGenerator.showErrorDialog(this, "ParameterMappingPanel copy failed.  " + e.getMessage(), e);
        }
    }
}

Example 98 with SimulationContext

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

the class BioModel method addNewSimulationContext.

/**
 * Insert the method's description here.
 * Creation date: (1/19/01 3:31:00 PM)
 * @param simulationContext cbit.vcell.mapping.SimulationContext
 * @exception java.beans.PropertyVetoException The exception description.
 */
public SimulationContext addNewSimulationContext(String newSimulationContextName, SimulationContext.Application app) throws java.beans.PropertyVetoException {
    SimulationContext simContext = new SimulationContext(getModel(), new Geometry("non-spatial", 0), null, null, app);
    simContext.setName(newSimulationContextName);
    addSimulationContext(simContext);
    return simContext;
}

Example 99 with SimulationContext

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

the class ModelUnitConverter method createBioModelWithNewUnitSystem.

public static BioModel createBioModelWithNewUnitSystem(BioModel oldBioModel, ModelUnitSystem newUnitSystem) throws ExpressionException, XmlParseException {
    // new BioModel has new unit system applied to all built-in units ... but expressions still need to be corrected (see below).
    BioModel newBioModel = XmlHelper.cloneBioModelWithNewUnitSystem(oldBioModel, newUnitSystem);
    Model newModel = newBioModel.getModel();
    Model oldModel = oldBioModel.getModel();
    for (Parameter p : newBioModel.getModel().getModelParameters()) {
        convertVarsWithUnitFactors(oldBioModel.getModel(), newBioModel.getModel(), p);
    }
    for (ReactionStep reactionStep : newBioModel.getModel().getReactionSteps()) {
        SymbolTable oldSymbolTable = oldBioModel.getModel().getReactionStep(reactionStep.getName());
        SymbolTable newSymbolTable = reactionStep;
        for (Parameter p : reactionStep.getKinetics().getUnresolvedParameters()) {
            convertVarsWithUnitFactors(oldSymbolTable, newSymbolTable, p);
        }
        for (Parameter p : reactionStep.getKinetics().getKineticsParameters()) {
            convertVarsWithUnitFactors(oldSymbolTable, newSymbolTable, p);
        }
    }
    for (ReactionRule reactionRule : newBioModel.getModel().getRbmModelContainer().getReactionRuleList()) {
        SymbolTable oldSymbolTable = oldBioModel.getModel().getRbmModelContainer().getReactionRule(reactionRule.getName()).getKineticLaw().getScopedSymbolTable();
        SymbolTable newSymbolTable = reactionRule.getKineticLaw().getScopedSymbolTable();
        for (Parameter p : reactionRule.getKineticLaw().getUnresolvedParameters()) {
            convertVarsWithUnitFactors(oldSymbolTable, newSymbolTable, p);
        }
        for (Parameter p : reactionRule.getKineticLaw().getLocalParameters()) {
            convertVarsWithUnitFactors(oldSymbolTable, newSymbolTable, p);
        }
    }
    for (SimulationContext simContext : newBioModel.getSimulationContexts()) {
        SimulationContext oldSimContext = oldBioModel.getSimulationContext(simContext.getName());
        // ArrayList<Parameter> parameterList = new ArrayList<Parameter>();
        for (StructureMapping mapping : simContext.getGeometryContext().getStructureMappings()) {
            Structure oldStructure = oldModel.getStructure(mapping.getStructure().getName());
            StructureMapping oldMapping = oldSimContext.getGeometryContext().getStructureMapping(oldStructure);
            for (Parameter p : mapping.computeApplicableParameterList()) {
                convertVarsWithUnitFactors(oldMapping, mapping, p);
            }
        }
        for (SpeciesContextSpec spec : simContext.getReactionContext().getSpeciesContextSpecs()) {
            SpeciesContext oldSpeciesContext = oldModel.getSpeciesContext(spec.getSpeciesContext().getName());
            SpeciesContextSpec oldSpec = oldSimContext.getReactionContext().getSpeciesContextSpec(oldSpeciesContext);
            for (Parameter p : spec.computeApplicableParameterList()) {
                convertVarsWithUnitFactors(oldSpec, spec, p);
            }
        }
        for (int i = 0; i < simContext.getElectricalStimuli().length; i++) {
            ElectricalStimulus newElectricalStimulus = simContext.getElectricalStimuli()[i];
            ElectricalStimulus oldElectricalStimulus = oldSimContext.getElectricalStimuli()[i];
            for (Parameter p : newElectricalStimulus.getParameters()) {
                convertVarsWithUnitFactors(oldElectricalStimulus.getNameScope().getScopedSymbolTable(), newElectricalStimulus.getNameScope().getScopedSymbolTable(), p);
            }
        }
        // convert events : trigger and delay parameters and event assignments
        for (int i = 0; simContext.getBioEvents() != null && oldSimContext.getBioEvents() != null && i < simContext.getBioEvents().length; i++) {
            BioEvent newBioEvent = simContext.getBioEvents()[i];
            BioEvent oldBioEvent = oldSimContext.getBioEvent(newBioEvent.getName());
            for (Parameter p : newBioEvent.getEventParameters()) {
                convertVarsWithUnitFactors(oldBioEvent.getNameScope().getScopedSymbolTable(), newBioEvent.getNameScope().getScopedSymbolTable(), p);
            }
            // for each event assignment expression
            for (int e = 0; e < newBioEvent.getEventAssignments().size(); e++) {
                ScopedSymbolTable newSymbolTable = newBioEvent.getNameScope().getScopedSymbolTable();
                ScopedSymbolTable oldSymbolTable = oldBioEvent.getNameScope().getScopedSymbolTable();
                EventAssignment newEventAssignment = newBioEvent.getEventAssignments().get(e);
                EventAssignment oldEventAssignment = oldBioEvent.getEventAssignments().get(e);
                VCUnitDefinition oldTargetUnit = oldEventAssignment.getTarget().getUnitDefinition();
                VCUnitDefinition newTargetUnit = newEventAssignment.getTarget().getUnitDefinition();
                Expression eventAssgnExpr = newEventAssignment.getAssignmentExpression();
                convertExprWithUnitFactors(oldSymbolTable, newSymbolTable, oldTargetUnit, newTargetUnit, eventAssgnExpr);
            }
        }
        /**
         * @TODO: If rate rule variable unit is TBD, we still need to handle the rate expression unit.
         */
        // convert rate rules
        RateRule[] rateRules = simContext.getRateRules();
        if (rateRules != null && rateRules.length > 0) {
            for (RateRule rateRule : rateRules) {
                RateRule oldRateRule = oldSimContext.getRateRule(rateRule.getName());
                ScopedSymbolTable oldSymbolTable = oldRateRule.getSimulationContext();
                ScopedSymbolTable newSymbolTable = rateRule.getSimulationContext();
                VCUnitDefinition oldTargetUnit = oldRateRule.getRateRuleVar().getUnitDefinition();
                VCUnitDefinition newTargetUnit = rateRule.getRateRuleVar().getUnitDefinition();
                Expression rateRuleExpr = rateRule.getRateRuleExpression();
                convertExprWithUnitFactors(oldSymbolTable, newSymbolTable, oldTargetUnit, newTargetUnit, rateRuleExpr);
            }
        }
    }
    // end  for - simulationContext
    return newBioModel;
}

Example 100 with SimulationContext

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

the class ClientDocumentManager method saveAsNew.

/**
 * Insert the method's description here.
 * Creation date: (1/19/01 11:27:52 AM)
 */
public BioModel saveAsNew(BioModel bioModel, java.lang.String newName, String[] independentSims) throws DataAccessException {
    try {
        String bioModelXML = null;
        try {
            bioModel.getVCMetaData().cleanupMetadata();
            bioModelXML = XmlHelper.bioModelToXML(bioModel);
        } catch (XmlParseException e) {
            e.printStackTrace(System.out);
            throw new DataAccessException(e.getMessage());
        }
        String savedBioModelXML = sessionManager.getUserMetaDbServer().saveBioModelAs(new BigString(bioModelXML), newName, independentSims).toString();
        BioModel savedBioModel = getBioModelFromDatabaseXML(new XMLHolder<BioModel>(savedBioModelXML));
        KeyValue savedKey = savedBioModel.getVersion().getVersionKey();
        if (xmlHash.get(savedKey) == null) {
            xmlHash.put(savedKey, savedBioModelXML);
        }
        BioModelInfo savedBioModelInfo = new BioModelInfo(savedBioModel.getVersion(), savedBioModel.getModel().getKey(), savedBioModel.createBioModelChildSummary(), VCellSoftwareVersion.fromSystemProperty());
        bioModelInfoHash.put(savedKey, savedBioModelInfo);
        SimulationContext[] scArr = savedBioModel.getSimulationContexts();
        for (int i = 0; i < scArr.length; i++) {
            updateGeometryRelatedHashes(scArr[i].getGeometry());
        }
        fireDatabaseInsert(new DatabaseEvent(this, DatabaseEvent.INSERT, null, savedBioModelInfo));
        return savedBioModel;
    } catch (RemoteProxyException e) {
        e.printStackTrace(System.out);
        throw new DataAccessException(VCellErrorMessages.FAIL_SAVE_MESSAGE + "\n\n" + e.getMessage());
    }
}