Examples with AnalysisTask cbit.vcell.modelopt.AnalysisTask used on opensource projects

Example 6 with AnalysisTask

use of cbit.vcell.modelopt.AnalysisTask in project vcell by virtualcell.

the class XmlReader method getSimulationContext.

/**
 * This method returns a SimulationContext from a XML representation.
 * Creation date: (4/2/2001 3:19:01 PM)
 * @return cbit.vcell.mapping.SimulationContext
 * @param param org.jdom.Element
 */
private SimulationContext getSimulationContext(Element param, BioModel biomodel) throws XmlParseException {
    // get the attributes
    // name
    String name = unMangle(param.getAttributeValue(XMLTags.NameAttrTag));
    boolean bStoch = false;
    boolean bRuleBased = false;
    boolean bUseConcentration = true;
    boolean bRandomizeInitCondition = false;
    boolean bInsufficientIterations = false;
    boolean bInsufficientMaxMolecules = false;
    // default is true for now
    boolean bMassConservationModelReduction = true;
    NetworkConstraints nc = null;
    Element ncElement = param.getChild(XMLTags.RbmNetworkConstraintsTag, vcNamespace);
    if (ncElement != null) {
        // one network constraint element
        nc = getAppNetworkConstraints(ncElement, biomodel.getModel());
    } else {
        if (legacyNetworkConstraints != null) {
            nc = legacyNetworkConstraints;
        }
    }
    if ((param.getAttributeValue(XMLTags.StochAttrTag) != null) && (param.getAttributeValue(XMLTags.StochAttrTag).equals("true"))) {
        bStoch = true;
    }
    if (bStoch) {
        // stochastic and using concentration vs amount
        if ((param.getAttributeValue(XMLTags.ConcentrationAttrTag) != null) && (param.getAttributeValue(XMLTags.ConcentrationAttrTag).equals("false"))) {
            bUseConcentration = false;
        }
        // stochastic and randomizing initial conditions or not (for non-spatial)
        if ((param.getAttributeValue(XMLTags.RandomizeInitConditionTag) != null) && (param.getAttributeValue(XMLTags.RandomizeInitConditionTag).equals("true"))) {
            bRandomizeInitCondition = true;
        }
    }
    if ((param.getAttributeValue(XMLTags.MassConservationModelReductionTag) != null) && (param.getAttributeValue(XMLTags.MassConservationModelReductionTag).equals("false"))) {
        bMassConservationModelReduction = false;
    }
    if ((param.getAttributeValue(XMLTags.InsufficientIterationsTag) != null) && (param.getAttributeValue(XMLTags.InsufficientIterationsTag).equals("true"))) {
        bInsufficientIterations = true;
    }
    if ((param.getAttributeValue(XMLTags.InsufficientMaxMoleculesTag) != null) && (param.getAttributeValue(XMLTags.InsufficientMaxMoleculesTag).equals("true"))) {
        bInsufficientMaxMolecules = true;
    }
    if ((param.getAttributeValue(XMLTags.RuleBasedAttrTag) != null) && (param.getAttributeValue(XMLTags.RuleBasedAttrTag).equals("true"))) {
        bRuleBased = true;
        if ((param.getAttributeValue(XMLTags.ConcentrationAttrTag) != null) && (param.getAttributeValue(XMLTags.ConcentrationAttrTag).equals("false"))) {
            bUseConcentration = false;
        }
        if ((param.getAttributeValue(XMLTags.RandomizeInitConditionTag) != null) && (param.getAttributeValue(XMLTags.RandomizeInitConditionTag).equals("true"))) {
            // we propagate the flag but we don't use it for now
            bRandomizeInitCondition = true;
        }
    }
    // Retrieve Geometry
    Geometry newgeometry = null;
    try {
        newgeometry = getGeometry(param.getChild(XMLTags.GeometryTag, vcNamespace));
    } catch (Throwable e) {
        e.printStackTrace();
        String stackTrace = null;
        try {
            java.io.ByteArrayOutputStream bos = new java.io.ByteArrayOutputStream();
            java.io.PrintStream ps = new java.io.PrintStream(bos);
            e.printStackTrace(ps);
            ps.flush();
            bos.flush();
            stackTrace = new String(bos.toByteArray());
            ps.close();
            bos.close();
        } catch (Exception e2) {
        // do Nothing
        }
        throw new XmlParseException("A Problem occurred while retrieving the geometry for the simulationContext " + name, e);
    }
    // Retrieve MathDescription(if there is no MathDescription skip it)
    MathDescription newmathdesc = null;
    Element xmlMathDescription = param.getChild(XMLTags.MathDescriptionTag, vcNamespace);
    if (xmlMathDescription != null) {
        newmathdesc = getMathDescription(xmlMathDescription, newgeometry);
        if (biomodel.getVersion() != null && biomodel.getVersion().getVersionKey() != null) {
            Long lpcBMKey = Long.valueOf(biomodel.getVersion().getVersionKey().toString());
            // MathDescription.originalHasLowPrecisionConstants.remove(lpcBMKey);
            try {
                Enumeration<Constant> myenum = newmathdesc.getConstants();
                while (myenum.hasMoreElements()) {
                    Constant nextElement = myenum.nextElement();
                    String name2 = nextElement.getName();
                    ReservedSymbol reservedSymbolByName = biomodel.getModel().getReservedSymbolByName(name2);
                    if (reservedSymbolByName != null && nextElement.getExpression() != null && reservedSymbolByName.getExpression() != null) {
                        // System.out.println(name2);
                        boolean equals = nextElement.getExpression().infix().equals(reservedSymbolByName.getExpression().infix());
                        // System.out.println("--"+" "+nextElement.getExpression().infix() +" "+reservedSymbolByName.getExpression().infix()+" "+equals);
                        if (!equals) {
                            TreeSet<String> treeSet = MathDescription.originalHasLowPrecisionConstants.get(lpcBMKey);
                            if (treeSet == null) {
                                treeSet = new TreeSet<>();
                                MathDescription.originalHasLowPrecisionConstants.put(lpcBMKey, treeSet);
                            }
                            treeSet.add(newmathdesc.getVersion().getVersionKey().toString());
                            break;
                        }
                    }
                }
            } catch (Exception e) {
                // TODO Auto-generated catch block
                e.printStackTrace();
            }
        }
    }
    // Retrieve Version (Metada)
    Version version = getVersion(param.getChild(XMLTags.VersionTag, vcNamespace));
    // ------ Create SimContext ------
    SimulationContext newsimcontext = null;
    try {
        newsimcontext = new SimulationContext(biomodel.getModel(), newgeometry, newmathdesc, version, bStoch, bRuleBased);
    } catch (java.beans.PropertyVetoException e) {
        e.printStackTrace(System.out);
        throw new XmlParseException("A propertyveto exception was generated when creating the new SimulationContext " + name, e);
    }
    // set attributes
    try {
        newsimcontext.setName(name);
        // Add annotation
        String annotation = param.getChildText(XMLTags.AnnotationTag, vcNamespace);
        if (annotation != null) /* && annotation.length()>0*/
        {
            newsimcontext.setDescription(unMangle(annotation));
        }
        // set if using concentration
        newsimcontext.setUsingConcentration(bUseConcentration);
        // set mass conservation model reduction flag
        newsimcontext.setUsingMassConservationModelReduction(bMassConservationModelReduction);
        // set if randomizing init condition or not (for stochastic applications
        if (bStoch) {
            newsimcontext.setRandomizeInitConditions(bRandomizeInitCondition);
        }
        if (bInsufficientIterations) {
            newsimcontext.setInsufficientIterations(bInsufficientIterations);
        }
        if (bInsufficientMaxMolecules) {
            newsimcontext.setInsufficientMaxMolecules(bInsufficientMaxMolecules);
        }
        if (nc != null) {
            newsimcontext.setNetworkConstraints(nc);
        }
    } catch (java.beans.PropertyVetoException e) {
        e.printStackTrace(System.out);
        throw new XmlParseException("Exception", e);
    }
    String tempchar = param.getAttributeValue(XMLTags.CharacteristicSizeTag);
    if (tempchar != null) {
        try {
            newsimcontext.setCharacteristicSize(Double.valueOf(tempchar));
        } catch (java.beans.PropertyVetoException e) {
            e.printStackTrace(System.out);
            throw new XmlParseException("A PropertyVetoException was fired when setting the CharacteristicSize " + tempchar, e);
        }
    }
    // Retrieve DataContext
    Element dataContextElement = param.getChild(XMLTags.DataContextTag, vcNamespace);
    if (dataContextElement != null) {
        DataContext dataContext = newsimcontext.getDataContext();
        ArrayList<DataSymbol> dataSymbols = getDataSymbols(dataContextElement, dataContext, newsimcontext.getModel().getUnitSystem());
        for (int i = 0; i < dataSymbols.size(); i++) {
            dataContext.addDataSymbol(dataSymbols.get(i));
        }
    }
    // Retrieve spatialObjects and add to simContext
    Element spatialObjectsElement = param.getChild(XMLTags.SpatialObjectsTag, vcNamespace);
    if (spatialObjectsElement != null) {
        SpatialObject[] spatialObjects = getSpatialObjects(newsimcontext, spatialObjectsElement);
        try {
            newsimcontext.setSpatialObjects(spatialObjects);
        } catch (PropertyVetoException e) {
            e.printStackTrace(System.out);
            throw new RuntimeException("Error adding spatialObjects to simulationContext", e);
        }
    }
    // Retrieve application parameters and add to simContext
    Element appParamsElement = param.getChild(XMLTags.ApplicationParametersTag, vcNamespace);
    if (appParamsElement != null) {
        SimulationContextParameter[] appParameters = getSimulationContextParams(appParamsElement, newsimcontext);
        try {
            newsimcontext.setSimulationContextParameters(appParameters);
        } catch (PropertyVetoException e) {
            e.printStackTrace(System.out);
            throw new RuntimeException("Error adding application parameters to simulationContext", e);
        }
    }
    // 
    // -Process the GeometryContext-
    // 
    Element tempelement = param.getChild(XMLTags.GeometryContextTag, vcNamespace);
    LinkedList<StructureMapping> maplist = new LinkedList<StructureMapping>();
    // Retrieve FeatureMappings
    Iterator<Element> iterator = tempelement.getChildren(XMLTags.FeatureMappingTag, vcNamespace).iterator();
    while (iterator.hasNext()) {
        maplist.add(getFeatureMapping((Element) (iterator.next()), newsimcontext));
    }
    // Retrieve MembraneMappings
    iterator = tempelement.getChildren(XMLTags.MembraneMappingTag, vcNamespace).iterator();
    while (iterator.hasNext()) {
        maplist.add(getMembraneMapping((Element) (iterator.next()), newsimcontext));
    }
    // Add these mappings to the internal geometryContext of this simcontext
    StructureMapping[] structarray = new StructureMapping[maplist.size()];
    maplist.toArray(structarray);
    try {
        newsimcontext.getGeometryContext().setStructureMappings(structarray);
        newsimcontext.getGeometryContext().refreshStructureMappings();
        newsimcontext.refreshSpatialObjects();
    } catch (MappingException e) {
        e.printStackTrace();
        throw new XmlParseException("A MappingException was fired when trying to set the StructureMappings array to the Geometrycontext of the SimContext " + name, e);
    } catch (java.beans.PropertyVetoException e) {
        e.printStackTrace(System.out);
        throw new XmlParseException("A PopertyVetoException was fired when trying to set the StructureMappings array to the Geometrycontext of the SimContext " + name, e);
    }
    // 
    // -Process the ReactionContext-
    // 
    tempelement = param.getChild(XMLTags.ReactionContextTag, vcNamespace);
    // Retrieve ReactionSpecs
    List<Element> children = tempelement.getChildren(XMLTags.ReactionSpecTag, vcNamespace);
    if (children.size() != 0) {
        if (children.size() != biomodel.getModel().getReactionSteps().length) {
            throw new XmlParseException("The number of reactions is not consistent.\n" + "Model reactions=" + biomodel.getModel().getReactionSteps().length + ", Reaction specs=" + children.size());
        }
        // *NOTE: Importing a model from other languages does not generates reaction specs.
        // A more robust code will read the reactions in the source file and replace the ones created by the default by the VirtualCell framework.
        ReactionSpec[] reactionSpecs = new ReactionSpec[children.size()];
        int rSpecCounter = 0;
        for (Element rsElement : children) {
            reactionSpecs[rSpecCounter] = getReactionSpec(rsElement, newsimcontext);
            rSpecCounter++;
        }
        try {
            newsimcontext.getReactionContext().setReactionSpecs(reactionSpecs);
        } catch (java.beans.PropertyVetoException e) {
            e.printStackTrace(System.out);
            throw new XmlParseException("A PropertyVetoException occurred while setting the ReactionSpecs to the SimContext " + name, e);
        }
    }
    // Retrieve ReactionRuleSpecs
    Element reactionRuleSpecsElement = tempelement.getChild(XMLTags.ReactionRuleSpecsTag, vcNamespace);
    if (reactionRuleSpecsElement != null) {
        ReactionRuleSpec[] reactionRuleSpecs = getReactionRuleSpecs(newsimcontext, reactionRuleSpecsElement);
        try {
            newsimcontext.getReactionContext().setReactionRuleSpecs(reactionRuleSpecs);
        } catch (PropertyVetoException e) {
            e.printStackTrace(System.out);
            throw new XmlParseException("A PropertyVetoException occurred while setting the ReactionRuleSpecs to the SimContext " + name, e);
        }
    }
    children = tempelement.getChildren(XMLTags.SpeciesContextSpecTag, vcNamespace);
    getSpeciesContextSpecs(children, newsimcontext.getReactionContext(), biomodel.getModel());
    // Retrieve output functions
    Element outputFunctionsElement = param.getChild(XMLTags.OutputFunctionsTag, vcNamespace);
    if (outputFunctionsElement != null) {
        ArrayList<AnnotatedFunction> outputFunctions = getOutputFunctions(outputFunctionsElement);
        try {
            // construct OutputFnContext from mathDesc in newSimContext and add output functions that were read in from XML.
            OutputFunctionContext outputFnContext = newsimcontext.getOutputFunctionContext();
            for (AnnotatedFunction outputFunction : outputFunctions) {
                outputFnContext.addOutputFunction(outputFunction);
            }
        } catch (PropertyVetoException e) {
            e.printStackTrace(System.out);
            throw new XmlParseException(e);
        }
    }
    // Retrieve Electrical context
    org.jdom.Element electElem = param.getChild(XMLTags.ElectricalContextTag, vcNamespace);
    // this information is optional!
    if (electElem != null) {
        if (electElem.getChild(XMLTags.ClampTag, vcNamespace) != null) {
            // read clamp
            ElectricalStimulus[] electArray = new ElectricalStimulus[1];
            electArray[0] = getElectricalStimulus(electElem.getChild(XMLTags.ClampTag, vcNamespace), newsimcontext);
            try {
                newsimcontext.setElectricalStimuli(electArray);
            } catch (java.beans.PropertyVetoException e) {
                e.printStackTrace(System.out);
                throw new XmlParseException(e);
            }
        }
        // read ground electrode
        if (electElem.getChild(XMLTags.ElectrodeTag, vcNamespace) != null) {
            Electrode groundElectrode = getElectrode(electElem.getChild(XMLTags.ElectrodeTag, vcNamespace), newsimcontext);
            try {
                newsimcontext.setGroundElectrode(groundElectrode);
            } catch (java.beans.PropertyVetoException e) {
                e.printStackTrace(System.out);
                throw new XmlParseException(e);
            }
        }
    }
    // Retrieve (bio)events and add to simContext
    tempelement = param.getChild(XMLTags.BioEventsTag, vcNamespace);
    if (tempelement != null) {
        BioEvent[] bioEvents = getBioEvents(newsimcontext, tempelement);
        try {
            newsimcontext.setBioEvents(bioEvents);
        } catch (PropertyVetoException e) {
            e.printStackTrace(System.out);
            throw new RuntimeException("Error adding events to simulationContext", e);
        }
    }
    // Retrieve spatialProcesses and add to simContext
    tempelement = param.getChild(XMLTags.SpatialProcessesTag, vcNamespace);
    if (tempelement != null) {
        SpatialProcess[] spatialProcesses = getSpatialProcesses(newsimcontext, tempelement);
        try {
            newsimcontext.setSpatialProcesses(spatialProcesses);
        } catch (PropertyVetoException e) {
            e.printStackTrace(System.out);
            throw new RuntimeException("Error adding spatialProcesses to simulationContext", e);
        }
    }
    // Retrieve rate rules and add to simContext
    tempelement = param.getChild(XMLTags.RateRulesTag, vcNamespace);
    if (tempelement != null) {
        RateRule[] rateRules = getRateRules(newsimcontext, tempelement);
        try {
            newsimcontext.setRateRules(rateRules);
        } catch (PropertyVetoException e) {
            e.printStackTrace(System.out);
            throw new RuntimeException("Error adding rate rules to simulationContext", e);
        }
    }
    tempelement = param.getChild(XMLTags.AssignmentRulesTag, vcNamespace);
    if (tempelement != null) {
        AssignmentRule[] assignmentRules = getAssignmentRules(newsimcontext, tempelement);
        try {
            newsimcontext.setAssignmentRules(assignmentRules);
        } catch (PropertyVetoException e) {
            e.printStackTrace(System.out);
            throw new RuntimeException("Error adding assignment rules to simulationContext", e);
        }
    }
    org.jdom.Element analysisTaskListElement = param.getChild(XMLTags.AnalysisTaskListTag, vcNamespace);
    if (analysisTaskListElement != null) {
        children = analysisTaskListElement.getChildren(XMLTags.ParameterEstimationTaskTag, vcNamespace);
        if (children.size() != 0) {
            Vector<ParameterEstimationTask> analysisTaskList = new Vector<ParameterEstimationTask>();
            for (Element parameterEstimationTaskElement : children) {
                try {
                    ParameterEstimationTask parameterEstimationTask = ParameterEstimationTaskXMLPersistence.getParameterEstimationTask(parameterEstimationTaskElement, newsimcontext);
                    analysisTaskList.add(parameterEstimationTask);
                } catch (Exception e) {
                    e.printStackTrace(System.out);
                    throw new XmlParseException("An Exception occurred when parsing AnalysisTasks of SimContext " + name, e);
                }
            }
            try {
                AnalysisTask[] analysisTasks = (AnalysisTask[]) BeanUtils.getArray(analysisTaskList, AnalysisTask.class);
                newsimcontext.setAnalysisTasks(analysisTasks);
            } catch (java.beans.PropertyVetoException e) {
                e.printStackTrace(System.out);
                throw new XmlParseException("A PropertyVetoException occurred when setting the AnalysisTasks of the SimContext " + name, e);
            }
        }
    }
    // Microscope Measurement
    org.jdom.Element element = param.getChild(XMLTags.MicroscopeMeasurement, vcNamespace);
    if (element != null) {
        getMicroscopeMeasurement(element, newsimcontext);
    }
    for (GeometryClass gc : newsimcontext.getGeometry().getGeometryClasses()) {
        try {
            StructureSizeSolver.updateUnitStructureSizes(newsimcontext, gc);
        } catch (Exception e) {
            e.printStackTrace();
        }
    }
    newsimcontext.getGeometryContext().enforceHierarchicalBoundaryConditions(newsimcontext.getModel().getStructureTopology());
    return newsimcontext;
}

Example 7 with AnalysisTask

use of cbit.vcell.modelopt.AnalysisTask in project vcell by virtualcell.

the class Xmlproducer method getXML.

/**
 * This method returns a XML representation of a SimulationContext object.
 * Creation date: (2/22/2001 2:15:14 PM)
 * @return Element
 * @param param cbit.vcell.mapping.SimulationContext
 */
public Element getXML(SimulationContext param, BioModel bioModel) throws XmlParseException {
    SimulationContext.Application applicationType = param.getApplicationType();
    Element simulationcontext = new Element(XMLTags.SimulationSpecTag);
    // add attributes
    String name = mangle(param.getName());
    simulationcontext.setAttribute(XMLTags.NameAttrTag, name);
    // set isStoch, isUsingConcentration attributes
    if (applicationType == Application.NETWORK_STOCHASTIC) {
        simulationcontext.setAttribute(XMLTags.StochAttrTag, "true");
        setBooleanAttribute(simulationcontext, XMLTags.ConcentrationAttrTag, param.isUsingConcentration());
        // write out 'randomizeInitConditin' flag only if non-spatial stochastic simContext
        if (param.getGeometry().getDimension() == 0) {
            setBooleanAttribute(simulationcontext, XMLTags.RandomizeInitConditionTag, param.isRandomizeInitCondition());
        }
    } else {
        simulationcontext.setAttribute(XMLTags.StochAttrTag, "false");
        simulationcontext.setAttribute(XMLTags.ConcentrationAttrTag, "true");
    }
    final boolean ruleBased = param.getApplicationType() == SimulationContext.Application.RULE_BASED_STOCHASTIC;
    setBooleanAttribute(simulationcontext, XMLTags.RuleBasedAttrTag, ruleBased);
    if (ruleBased) {
        setBooleanAttribute(simulationcontext, XMLTags.ConcentrationAttrTag, param.isUsingConcentration());
        if (param.getGeometry().getDimension() == 0) {
            // we don't use it yet but we do propagate it
            setBooleanAttribute(simulationcontext, XMLTags.RandomizeInitConditionTag, param.isRandomizeInitCondition());
        }
    }
    setBooleanAttribute(simulationcontext, XMLTags.MassConservationModelReductionTag, param.isUsingMassConservationModelReduction());
    setBooleanAttribute(simulationcontext, XMLTags.InsufficientIterationsTag, param.isInsufficientIterations());
    setBooleanAttribute(simulationcontext, XMLTags.InsufficientMaxMoleculesTag, param.isInsufficientMaxMolecules());
    NetworkConstraints constraints = param.getNetworkConstraints();
    if (constraints != null) {
        simulationcontext.addContent(getXML(constraints, param));
    }
    // add annotation
    if (param.getDescription() != null) /*&& param.getDescription().length()>0*/
    {
        Element annotationElem = new Element(XMLTags.AnnotationTag);
        annotationElem.setText(mangle(param.getDescription()));
        simulationcontext.addContent(annotationElem);
    }
    if (param.getCharacteristicSize() != null) {
        simulationcontext.setAttribute(XMLTags.CharacteristicSizeTag, param.getCharacteristicSize().toString());
    }
    // write Geometry (or GeometryRef???)
    try {
        simulationcontext.addContent(getXML(param.getGeometryContext().getGeometry()));
    } catch (XmlParseException e) {
        e.printStackTrace();
        throw new XmlParseException("A problem occurred when trying to process the geometry for the simulationContext " + name, e);
    }
    // write GeometryContext (geometric mapping)
    simulationcontext.addContent(getXML(param.getGeometryContext()));
    // write ReactionContext (parameter/variable mapping)
    simulationcontext.addContent(getXML(param.getReactionContext()));
    // check if there is anything to write first for the electrical context
    if (param.getElectricalStimuli().length == 1 || param.getGroundElectrode() != null) {
        // create ElectricalContext
        Element electricalElement = new Element(XMLTags.ElectricalContextTag);
        // Write the electrical stimuli
        if (param.getElectricalStimuli().length == 1) {
            // write clamp
            electricalElement.addContent(getXML(param.getElectricalStimuli(0)));
        // Element clampElem = new Element(XMLTags.ClampTag);
        // clampElem.addContent(getXML(param.getElectricalStimuli(0)));
        // if (param.getElectricalStimuli()[0] instanceof VoltageClampStimulus) {
        // //this is a VOLTAGE clamp
        // clampElem.setAttribute(XMLTags.TypeAttrTag, XMLTags.VoltageClampTag);
        // clampElem.setAttribute( XMLTags.NameAttrTag, this.mangle((param.getElectricalStimuli()[0]).getName()) );
        // String tempExp = this.mangleExpression( ((VoltageClampStimulus)param.getElectricalStimuli()[0]).getVoltageParameter().getExpression() );
        // clampElem.setAttribute(XMLTags.ExpressionAttrTag, tempExp);
        // //add probe-electrode
        // clampElem.addContent(getXML(param.getElectricalStimuli()[0].getElectrode()));
        // } else {
        // //this is a CURRENT clamp
        // clampElem.setAttribute(XMLTags.TypeAttrTag, XMLTags.CurrentClampTag);
        // clampElem.setAttribute( XMLTags.NameAttrTag, this.mangle((param.getElectricalStimuli()[0]).getName()) );
        // String tempExp = this.mangleExpression( ((CurrentClampStimulus)param.getElectricalStimuli()[0]).getCurrentParameter().getExpression() );
        // clampElem.setAttribute(XMLTags.ExpressionAttrTag, tempExp);
        // //add probe-electrode
        // clampElem.addContent(getXML(param.getElectricalStimuli()[0].getElectrode()));
        // }
        // electricalElement.addContent(clampElem);
        // 
        } else if (param.getElectricalStimuli().length > 1) {
            // **ONLY ONE ELECTRODE IS SUPPORTED RIGHT NOW!
            throw new IllegalArgumentException("More than one electrode is not supported!");
        }
        // Process the Ground electrode
        if (param.getGroundElectrode() != null) {
            // write the ground electrode
            electricalElement.addContent(getXML(param.getGroundElectrode()));
        }
        simulationcontext.addContent(electricalElement);
    }
    // Add Mathdescription (if present)
    if (param.getMathDescription() != null) {
        simulationcontext.addContent(getXML(param.getMathDescription()));
    }
    if (param.getOutputFunctionContext() != null) {
        ArrayList<AnnotatedFunction> outputFunctions = param.getOutputFunctionContext().getOutputFunctionsList();
        if (outputFunctions != null && outputFunctions.size() > 0) {
            // get output functions
            simulationcontext.addContent(getXML(outputFunctions));
        }
    }
    // Add Simulations to the simulationSpec
    if (bioModel != null) {
        cbit.vcell.solver.Simulation[] simulations = bioModel.getSimulations(param);
        for (int i = 0; simulations != null && i < simulations.length; i++) {
            simulationcontext.addContent(getXML(simulations[i]));
        }
    }
    // Add AnalysisTasks
    if (param.getAnalysisTasks() != null && param.getAnalysisTasks().length > 0) {
        // if the task is empty (no parameters set up, no reference data), we shall not save it
        if (param.getAnalysisTasks().length == 1) {
            AnalysisTask task = param.getAnalysisTasks()[0];
            if (task instanceof ParameterEstimationTask) {
                if (!((ParameterEstimationTask) task).isEmpty()) {
                    simulationcontext.addContent(getXML(param.getAnalysisTasks()));
                }
            }
        } else // have more than one analysis task
        {
            simulationcontext.addContent(getXML(param.getAnalysisTasks()));
        }
    }
    // Add (Bio)events
    BioEvent[] bioEvents = param.getBioEvents();
    if (bioEvents != null && bioEvents.length > 0) {
        simulationcontext.addContent(getXML(bioEvents));
    }
    SimulationContextParameter[] appParams = param.getSimulationContextParameters();
    if (appParams != null && appParams.length > 0) {
        simulationcontext.addContent(getXML(appParams));
    }
    SpatialObject[] spatialObjects = param.getSpatialObjects();
    if (spatialObjects != null && spatialObjects.length > 0) {
        simulationcontext.addContent(getXML(spatialObjects));
    }
    SpatialProcess[] spatialProcesses = param.getSpatialProcesses();
    if (spatialProcesses != null && spatialProcesses.length > 0) {
        simulationcontext.addContent(getXML(spatialProcesses));
    }
    // Add rate rules
    RateRule[] rateRules = param.getRateRules();
    if (param.getRateRules() != null && rateRules.length > 0) {
        simulationcontext.addContent(getXML(rateRules));
    }
    AssignmentRule[] assignmentRules = param.getAssignmentRules();
    if (param.getAssignmentRules() != null && assignmentRules.length > 0) {
        simulationcontext.addContent(getXML(assignmentRules));
    }
    // Add Datacontext
    if (param.getDataContext() != null && param.getDataContext().getDataSymbols().length > 0) {
        simulationcontext.addContent(getXML(param.getDataContext(), param.getModel().getUnitSystem()));
    }
    // Add Metadata (if any)
    if (param.getVersion() != null) {
        simulationcontext.addContent(getXML(param.getVersion(), param));
    }
    // Add microscope measurements
    simulationcontext.addContent(getXML(param.getMicroscopeMeasurement()));
    return simulationcontext;
}

Example 8 with AnalysisTask

use of cbit.vcell.modelopt.AnalysisTask in project vcell by virtualcell.

the class ParameterEstimationPanel method newParameterEstimationTaskButton_ActionPerformed.

private void newParameterEstimationTaskButton_ActionPerformed() {
    try {
        String parameterEstimationName = "task0";
        if (simulationContext == null) {
            return;
        }
        AnalysisTask[] analysisTasks = simulationContext.getAnalysisTasks();
        boolean found = true;
        while (found) {
            found = false;
            parameterEstimationName = TokenMangler.getNextEnumeratedToken(parameterEstimationName);
            for (int i = 0; analysisTasks != null && i < analysisTasks.length; i++) {
                if (analysisTasks[i].getName().equals(parameterEstimationName)) {
                    found = true;
                    continue;
                }
            }
        }
        String newParameterEstimationName = null;
        try {
            newParameterEstimationName = DialogUtils.showInputDialog0(this, "name for new parameter estimation set", parameterEstimationName);
        } catch (UtilCancelException ex) {
        // user canceled; it's ok
        }
        if (newParameterEstimationName != null) {
            if (newParameterEstimationName.length() == 0) {
                PopupGenerator.showErrorDialog(this, "Error:\n name for new parameter estimation can't be empty");
            } else {
                final String finalname = newParameterEstimationName;
                AsynchClientTask task1 = new AsynchClientTask("init task", AsynchClientTask.TASKTYPE_NONSWING_BLOCKING) {

                    @Override
                    public void run(Hashtable<String, Object> hashTable) throws Exception {
                        ParameterEstimationTask newParameterEstimationTask = new ParameterEstimationTask(simulationContext);
                        newParameterEstimationTask.setName(finalname);
                        hashTable.put("newParameterEstimationTask", newParameterEstimationTask);
                    }
                };
                AsynchClientTask task2 = new AsynchClientTask("add task", AsynchClientTask.TASKTYPE_SWING_BLOCKING) {

                    @Override
                    public void run(Hashtable<String, Object> hashTable) throws Exception {
                        ParameterEstimationTask newParameterEstimationTask = (ParameterEstimationTask) hashTable.get("newParameterEstimationTask");
                        simulationContext.addAnalysisTask(newParameterEstimationTask);
                        getAnalysisTaskComboBox().setSelectedItem(newParameterEstimationTask);
                        refreshAnalysisTaskEnables();
                    }
                };
                ClientTaskDispatcher.dispatch(this, new Hashtable<String, Object>(), new AsynchClientTask[] { task1, task2 });
            }
        }
    } catch (Exception e) {
        e.printStackTrace(System.out);
        DialogUtils.showErrorDialog(this, e.getMessage(), e);
    }
}

Example 9 with AnalysisTask

use of cbit.vcell.modelopt.AnalysisTask in project vcell by virtualcell.

the class AnalysisTaskComboBoxModel method propertyChange.

/**
 * This method gets called when a bound property is changed.
 * @param evt A PropertyChangeEvent object describing the event source
 *   	and the property that has changed.
 */
public void propertyChange(java.beans.PropertyChangeEvent evt) {
    if (evt.getSource() == getSimulationContext() && evt.getPropertyName().equals("analysisTasks")) {
        AnalysisTask oldSelected = (AnalysisTask) getSelectedItem();
        AnalysisTask[] oldAnalysisTasks = (AnalysisTask[]) evt.getOldValue();
        if (oldAnalysisTasks != null && oldAnalysisTasks.length > 0) {
            for (int i = 0; i < oldAnalysisTasks.length; i++) {
                oldAnalysisTasks[i].removePropertyChangeListener(this);
            }
            fireIntervalRemoved(this, 0, oldAnalysisTasks.length - 1);
        }
        AnalysisTask[] newAnalysisTasks = (AnalysisTask[]) evt.getNewValue();
        if (newAnalysisTasks != null && newAnalysisTasks.length > 0) {
            for (int i = 0; i < newAnalysisTasks.length; i++) {
                newAnalysisTasks[i].addPropertyChangeListener(this);
            }
            fireIntervalAdded(this, 0, newAnalysisTasks.length - 1);
        }
        if (newAnalysisTasks == null || newAnalysisTasks.length == 0) {
            setSelectedItem(null);
        } else {
            AnalysisTask newSelected = null;
            if (oldSelected != null) {
                for (int i = 0; i < newAnalysisTasks.length; i++) {
                    if (oldSelected.getName().equals(newAnalysisTasks[i].getName())) {
                        newSelected = newAnalysisTasks[i];
                        break;
                    }
                }
            }
            if (newSelected == null) {
                newSelected = newAnalysisTasks[0];
            }
            setSelectedItem(newSelected);
        }
    }
    if (evt.getSource() instanceof AnalysisTask) {
        if (evt.getPropertyName().equals("name")) {
            fireContentsChanged(this, 0, getSize() - 1);
        }
    }
}