Examples with TimeBounds cbit.vcell.solver.TimeBounds used on opensource projects

Example 1 with TimeBounds

use of cbit.vcell.solver.TimeBounds in project vcell by virtualcell.

the class SEDMLExporter method translateBioModelToSedML.

private void translateBioModelToSedML(String savePath) {
    sbmlFilePathStrAbsoluteList.clear();
    // models
    try {
        SimulationContext[] simContexts = vcBioModel.getSimulationContexts();
        cbit.vcell.model.Model vcModel = vcBioModel.getModel();
        // "urn:sedml:language:sbml";
        String sbmlLanguageURN = SUPPORTED_LANGUAGE.SBML_GENERIC.getURN();
        String bioModelName = TokenMangler.mangleToSName(vcBioModel.getName());
        // String usrHomeDirPath = ResourceUtil.getUserHomeDir().getAbsolutePath();
        // to get Xpath string for variables.
        SBMLSupport sbmlSupport = new SBMLSupport();
        // for model count, task subcount
        int simContextCnt = 0;
        // for dtaGenerator count.
        int varCount = 0;
        boolean bSpeciesAddedAsDataGens = false;
        String sedmlNotesStr = "";
        for (SimulationContext simContext : simContexts) {
            String simContextName = simContext.getName();
            // export all applications that are not spatial stochastic
            if (!(simContext.getGeometry().getDimension() > 0 && simContext.isStoch())) {
                // to compute and set the sizes of the remaining structures.
                if (!simContext.getGeometryContext().isAllSizeSpecifiedPositive()) {
                    Structure structure = simContext.getModel().getStructure(0);
                    double structureSize = 1.0;
                    StructureMapping structMapping = simContext.getGeometryContext().getStructureMapping(structure);
                    StructureSizeSolver.updateAbsoluteStructureSizes(simContext, structure, structureSize, structMapping.getSizeParameter().getUnitDefinition());
                }
                // Export the application itself to SBML, with default overrides
                String sbmlString = null;
                int level = 2;
                int version = 4;
                boolean isSpatial = simContext.getGeometry().getDimension() > 0 ? true : false;
                SimulationJob simJob = null;
                // if (simContext.getGeometry().getDimension() > 0) {
                // sbmlString = XmlHelper.exportSBML(vcBioModel, 2, 4, 0, true, simContext, null);
                // } else {
                // sbmlString = XmlHelper.exportSBML(vcBioModel, 2, 4, 0, false, simContext, null);
                // }
                // 
                // TODO: we need to salvage from the SBMLExporter info about the fate of local parameters
                // some of them may stay as locals, some others may become globals
                // Any of these, if used in a repeated task or change or whatever, needs to be used in a consistent way,
                // that is, if a param becomes a global in SBML, we need to refer at it in SEDML as the same global
                // 
                // We'll use:
                // Map<Pair <String reaction, String param>, String global>		- if local converted to global
                // Set<Pair <String reaction, String param>>	(if needed?)	- if local stays local
                // 
                // local to global translation map
                Map<Pair<String, String>, String> l2gMap = null;
                if (vcBioModel instanceof BioModel) {
                    try {
                        // check if model to be exported to SBML has units compatible with SBML default units (default units in SBML can be assumed only until SBML Level2)
                        ModelUnitSystem forcedModelUnitSystem = simContext.getModel().getUnitSystem();
                        if (level < 3 && !ModelUnitSystem.isCompatibleWithDefaultSBMLLevel2Units(forcedModelUnitSystem)) {
                            forcedModelUnitSystem = ModelUnitSystem.createDefaultSBMLLevel2Units();
                        }
                        // create new Biomodel with new (SBML compatible)  unit system
                        BioModel modifiedBiomodel = ModelUnitConverter.createBioModelWithNewUnitSystem(simContext.getBioModel(), forcedModelUnitSystem);
                        // extract the simContext from new Biomodel. Apply overrides to *this* modified simContext
                        SimulationContext simContextFromModifiedBioModel = modifiedBiomodel.getSimulationContext(simContext.getName());
                        SBMLExporter sbmlExporter = new SBMLExporter(modifiedBiomodel, level, version, isSpatial);
                        sbmlExporter.setSelectedSimContext(simContextFromModifiedBioModel);
                        // no sim job
                        sbmlExporter.setSelectedSimulationJob(null);
                        sbmlString = sbmlExporter.getSBMLFile();
                        l2gMap = sbmlExporter.getLocalToGlobalTranslationMap();
                    } catch (ExpressionException | SbmlException e) {
                        e.printStackTrace(System.out);
                        throw new XmlParseException(e);
                    }
                } else {
                    throw new RuntimeException("unsupported Document Type " + vcBioModel.getClass().getName() + " for SBML export");
                }
                String sbmlFilePathStrAbsolute = savePath + FileUtils.WINDOWS_SEPARATOR + bioModelName + "_" + simContextName + ".xml";
                String sbmlFilePathStrRelative = bioModelName + "_" + simContextName + ".xml";
                XmlUtil.writeXMLStringToFile(sbmlString, sbmlFilePathStrAbsolute, true);
                sbmlFilePathStrAbsoluteList.add(sbmlFilePathStrRelative);
                String simContextId = TokenMangler.mangleToSName(simContextName);
                sedmlModel.addModel(new Model(simContextId, simContextName, sbmlLanguageURN, sbmlFilePathStrRelative));
                // required for mathOverrides, if any
                MathMapping mathMapping = simContext.createNewMathMapping();
                MathSymbolMapping mathSymbolMapping = mathMapping.getMathSymbolMapping();
                // create sedml simulation objects and tasks (mapping each sim with current simContext)
                int simCount = 0;
                String taskRef = null;
                int overrideCount = 0;
                for (Simulation vcSimulation : simContext.getSimulations()) {
                    List<DataGenerator> dataGeneratorsOfSim = new ArrayList<DataGenerator>();
                    // if simContext is non-spatial stochastic, check if sim is histogram
                    SolverTaskDescription simTaskDesc = vcSimulation.getSolverTaskDescription();
                    if (simContext.getGeometry().getDimension() == 0 && simContext.isStoch()) {
                        long numOfTrials = simTaskDesc.getStochOpt().getNumOfTrials();
                        if (numOfTrials > 1) {
                            String msg = "\n\t" + simContextName + " ( " + vcSimulation.getName() + " ) : export of non-spatial stochastic simulation with histogram option to SEDML not supported at this time.";
                            sedmlNotesStr += msg;
                            continue;
                        }
                    }
                    // create Algorithm and sedmlSimulation (UniformtimeCourse)
                    SolverDescription vcSolverDesc = simTaskDesc.getSolverDescription();
                    // String kiSAOIdStr = getKiSAOIdFromSimulation(vcSolverDesc);	// old way of doing it, going directly to the web site
                    String kiSAOIdStr = vcSolverDesc.getKisao();
                    Algorithm sedmlAlgorithm = new Algorithm(kiSAOIdStr);
                    TimeBounds vcSimTimeBounds = simTaskDesc.getTimeBounds();
                    double startingTime = vcSimTimeBounds.getStartingTime();
                    String simName = vcSimulation.getName();
                    UniformTimeCourse utcSim = new UniformTimeCourse(TokenMangler.mangleToSName(simName), simName, startingTime, startingTime, vcSimTimeBounds.getEndingTime(), (int) simTaskDesc.getExpectedNumTimePoints(), sedmlAlgorithm);
                    // if solver is not CVODE, add a note to utcSim to indicate actual solver name
                    if (!vcSolverDesc.equals(SolverDescription.CVODE)) {
                        String simNotesStr = "Actual Solver Name : '" + vcSolverDesc.getDisplayLabel() + "'.";
                        utcSim.addNote(createNotesElement(simNotesStr));
                    }
                    sedmlModel.addSimulation(utcSim);
                    // add SEDML tasks (map simulation to model:simContext)
                    // repeated tasks
                    MathOverrides mathOverrides = vcSimulation.getMathOverrides();
                    if (mathOverrides != null && mathOverrides.hasOverrides()) {
                        String[] overridenConstantNames = mathOverrides.getOverridenConstantNames();
                        String[] scannedConstantsNames = mathOverrides.getScannedConstantNames();
                        HashMap<String, String> scannedParamHash = new HashMap<String, String>();
                        HashMap<String, String> unscannedParamHash = new HashMap<String, String>();
                        for (String name : scannedConstantsNames) {
                            scannedParamHash.put(name, name);
                        }
                        for (String name : overridenConstantNames) {
                            if (!scannedParamHash.containsKey(name)) {
                                unscannedParamHash.put(name, name);
                            }
                        }
                        if (!unscannedParamHash.isEmpty() && scannedParamHash.isEmpty()) {
                            // only parameters with simple overrides (numeric/expression) no scans
                            // create new model with change for each parameter that has override; add simple task
                            String overriddenSimContextId = simContextId + "_" + overrideCount;
                            String overriddenSimContextName = simContextName + " modified";
                            Model sedModel = new Model(overriddenSimContextId, overriddenSimContextName, sbmlLanguageURN, simContextId);
                            overrideCount++;
                            for (String unscannedParamName : unscannedParamHash.values()) {
                                SymbolTableEntry ste = getSymbolTableEntryForModelEntity(mathSymbolMapping, unscannedParamName);
                                Expression unscannedParamExpr = mathOverrides.getActualExpression(unscannedParamName, 0);
                                if (unscannedParamExpr.isNumeric()) {
                                    // if expression is numeric, add ChangeAttribute to model created above
                                    XPathTarget targetXpath = getTargetAttributeXPath(ste, l2gMap);
                                    ChangeAttribute changeAttribute = new ChangeAttribute(targetXpath, unscannedParamExpr.infix());
                                    sedModel.addChange(changeAttribute);
                                } else {
                                    // non-numeric expression : add 'computeChange' to modified model
                                    ASTNode math = Libsedml.parseFormulaString(unscannedParamExpr.infix());
                                    XPathTarget targetXpath = getTargetXPath(ste, l2gMap);
                                    ComputeChange computeChange = new ComputeChange(targetXpath, math);
                                    String[] exprSymbols = unscannedParamExpr.getSymbols();
                                    for (String symbol : exprSymbols) {
                                        String symbolName = TokenMangler.mangleToSName(symbol);
                                        SymbolTableEntry ste1 = vcModel.getEntry(symbol);
                                        if (ste != null) {
                                            if (ste1 instanceof SpeciesContext || ste1 instanceof Structure || ste1 instanceof ModelParameter) {
                                                XPathTarget ste1_XPath = getTargetXPath(ste1, l2gMap);
                                                org.jlibsedml.Variable sedmlVar = new org.jlibsedml.Variable(symbolName, symbolName, taskRef, ste1_XPath.getTargetAsString());
                                                computeChange.addVariable(sedmlVar);
                                            } else {
                                                double doubleValue = 0.0;
                                                if (ste1 instanceof ReservedSymbol) {
                                                    doubleValue = getReservedSymbolValue(ste1);
                                                }
                                                Parameter sedmlParameter = new Parameter(symbolName, symbolName, doubleValue);
                                                computeChange.addParameter(sedmlParameter);
                                            }
                                        } else {
                                            throw new RuntimeException("Symbol '" + symbol + "' used in expression for '" + unscannedParamName + "' not found in model.");
                                        }
                                    }
                                    sedModel.addChange(computeChange);
                                }
                            }
                            sedmlModel.addModel(sedModel);
                            String taskId = "tsk_" + simContextCnt + "_" + simCount;
                            Task sedmlTask = new Task(taskId, taskId, sedModel.getId(), utcSim.getId());
                            sedmlModel.addTask(sedmlTask);
                            // to be used later to add dataGenerators : one set of DGs per model (simContext).
                            taskRef = taskId;
                        } else if (!scannedParamHash.isEmpty() && unscannedParamHash.isEmpty()) {
                            // only parameters with scans : only add 1 Task and 1 RepeatedTask
                            String taskId = "tsk_" + simContextCnt + "_" + simCount;
                            Task sedmlTask = new Task(taskId, taskId, simContextId, utcSim.getId());
                            sedmlModel.addTask(sedmlTask);
                            String repeatedTaskId = "repTsk_" + simContextCnt + "_" + simCount;
                            // TODO: temporary solution - we use as range here the first range
                            String scn = scannedConstantsNames[0];
                            String rId = "range_" + simContextCnt + "_" + simCount + "_" + scn;
                            RepeatedTask rt = new RepeatedTask(repeatedTaskId, repeatedTaskId, true, rId);
                            // to be used later to add dataGenerators - in our case it has to be the repeated task
                            taskRef = repeatedTaskId;
                            SubTask subTask = new SubTask("0", taskId);
                            rt.addSubtask(subTask);
                            for (String scannedConstName : scannedConstantsNames) {
                                ConstantArraySpec constantArraySpec = mathOverrides.getConstantArraySpec(scannedConstName);
                                String rangeId = "range_" + simContextCnt + "_" + simCount + "_" + scannedConstName;
                                // list of Ranges, if sim is parameter scan.
                                if (constantArraySpec != null) {
                                    Range r = null;
                                    System.out.println("     " + constantArraySpec.toString());
                                    if (constantArraySpec.getType() == ConstantArraySpec.TYPE_INTERVAL) {
                                        // ------ Uniform Range
                                        r = new UniformRange(rangeId, constantArraySpec.getMinValue(), constantArraySpec.getMaxValue(), constantArraySpec.getNumValues());
                                        rt.addRange(r);
                                    } else {
                                        // ----- Vector Range
                                        cbit.vcell.math.Constant[] cs = constantArraySpec.getConstants();
                                        ArrayList<Double> values = new ArrayList<Double>();
                                        for (int i = 0; i < cs.length; i++) {
                                            String value = cs[i].getExpression().infix();
                                            values.add(Double.parseDouble(value));
                                        }
                                        r = new VectorRange(rangeId, values);
                                        rt.addRange(r);
                                    }
                                    // list of Changes
                                    SymbolTableEntry ste = getSymbolTableEntryForModelEntity(mathSymbolMapping, scannedConstName);
                                    XPathTarget target = getTargetXPath(ste, l2gMap);
                                    // ASTNode math1 = new ASTCi(r.getId());		// was scannedConstName
                                    ASTNode math1 = Libsedml.parseFormulaString(r.getId());
                                    SetValue setValue = new SetValue(target, r.getId(), simContextId);
                                    setValue.setMath(math1);
                                    rt.addChange(setValue);
                                } else {
                                    throw new RuntimeException("No scan ranges found for scanned parameter : '" + scannedConstName + "'.");
                                }
                            }
                            sedmlModel.addTask(rt);
                        } else {
                            // both scanned and simple parameters : create new model with change for each simple override; add RepeatedTask
                            // create new model with change for each unscanned parameter that has override
                            String overriddenSimContextId = simContextId + "_" + overrideCount;
                            String overriddenSimContextName = simContextName + " modified";
                            Model sedModel = new Model(overriddenSimContextId, overriddenSimContextName, sbmlLanguageURN, simContextId);
                            overrideCount++;
                            String taskId = "tsk_" + simContextCnt + "_" + simCount;
                            Task sedmlTask = new Task(taskId, taskId, overriddenSimContextId, utcSim.getId());
                            sedmlModel.addTask(sedmlTask);
                            // scanned parameters
                            String repeatedTaskId = "repTsk_" + simContextCnt + "_" + simCount;
                            // TODO: temporary solution - we use as range here the first range
                            String scn = scannedConstantsNames[0];
                            String rId = "range_" + simContextCnt + "_" + simCount + "_" + scn;
                            RepeatedTask rt = new RepeatedTask(repeatedTaskId, repeatedTaskId, true, rId);
                            // to be used later to add dataGenerators - in our case it has to be the repeated task
                            taskRef = repeatedTaskId;
                            SubTask subTask = new SubTask("0", taskId);
                            rt.addSubtask(subTask);
                            for (String scannedConstName : scannedConstantsNames) {
                                ConstantArraySpec constantArraySpec = mathOverrides.getConstantArraySpec(scannedConstName);
                                String rangeId = "range_" + simContextCnt + "_" + simCount + "_" + scannedConstName;
                                // list of Ranges, if sim is parameter scan.
                                if (constantArraySpec != null) {
                                    Range r = null;
                                    System.out.println("     " + constantArraySpec.toString());
                                    if (constantArraySpec.getType() == ConstantArraySpec.TYPE_INTERVAL) {
                                        // ------ Uniform Range
                                        r = new UniformRange(rangeId, constantArraySpec.getMinValue(), constantArraySpec.getMaxValue(), constantArraySpec.getNumValues());
                                        rt.addRange(r);
                                    } else {
                                        // ----- Vector Range
                                        cbit.vcell.math.Constant[] cs = constantArraySpec.getConstants();
                                        ArrayList<Double> values = new ArrayList<Double>();
                                        for (int i = 0; i < cs.length; i++) {
                                            String value = cs[i].getExpression().infix() + ", ";
                                            values.add(Double.parseDouble(value));
                                        }
                                        r = new VectorRange(rangeId, values);
                                        rt.addRange(r);
                                    }
                                    // use scannedParamHash to store rangeId for that param, since it might be needed if unscanned param has a scanned param in expr.
                                    if (scannedParamHash.get(scannedConstName).equals(scannedConstName)) {
                                        // the hash was originally populated as <scannedParamName, scannedParamName>. Replace 'value' with rangeId for scannedParam
                                        scannedParamHash.put(scannedConstName, r.getId());
                                    }
                                    // create setValue for scannedConstName
                                    SymbolTableEntry ste2 = getSymbolTableEntryForModelEntity(mathSymbolMapping, scannedConstName);
                                    XPathTarget target1 = getTargetXPath(ste2, l2gMap);
                                    ASTNode math1 = new ASTCi(scannedConstName);
                                    SetValue setValue1 = new SetValue(target1, r.getId(), sedModel.getId());
                                    setValue1.setMath(math1);
                                    rt.addChange(setValue1);
                                } else {
                                    throw new RuntimeException("No scan ranges found for scanned parameter : '" + scannedConstName + "'.");
                                }
                            }
                            // for unscanned parameter overrides
                            for (String unscannedParamName : unscannedParamHash.values()) {
                                SymbolTableEntry ste = getSymbolTableEntryForModelEntity(mathSymbolMapping, unscannedParamName);
                                Expression unscannedParamExpr = mathOverrides.getActualExpression(unscannedParamName, 0);
                                if (unscannedParamExpr.isNumeric()) {
                                    // if expression is numeric, add ChangeAttribute to model created above
                                    XPathTarget targetXpath = getTargetAttributeXPath(ste, l2gMap);
                                    ChangeAttribute changeAttribute = new ChangeAttribute(targetXpath, unscannedParamExpr.infix());
                                    sedModel.addChange(changeAttribute);
                                } else {
                                    // check for any scanned parameter in unscanned parameter expression
                                    ASTNode math = Libsedml.parseFormulaString(unscannedParamExpr.infix());
                                    String[] exprSymbols = unscannedParamExpr.getSymbols();
                                    boolean bHasScannedParameter = false;
                                    String scannedParamNameInUnscannedParamExp = null;
                                    for (String symbol : exprSymbols) {
                                        if (scannedParamHash.get(symbol) != null) {
                                            bHasScannedParameter = true;
                                            scannedParamNameInUnscannedParamExp = new String(symbol);
                                            // @TODO check for multiple scannedParameters in expression.
                                            break;
                                        }
                                    }
                                    // (scanned parameter in expr) ? (add setValue for unscanned param in repeatedTask) : (add computeChange to modifiedModel)
                                    if (bHasScannedParameter && scannedParamNameInUnscannedParamExp != null) {
                                        // create setValue for unscannedParamName (which contains a scanned param in its expression)
                                        SymbolTableEntry entry = getSymbolTableEntryForModelEntity(mathSymbolMapping, unscannedParamName);
                                        XPathTarget target = getTargetXPath(entry, l2gMap);
                                        String rangeId = scannedParamHash.get(scannedParamNameInUnscannedParamExp);
                                        // @TODO: we have no range??
                                        SetValue setValue = new SetValue(target, rangeId, sedModel.getId());
                                        setValue.setMath(math);
                                        rt.addChange(setValue);
                                    } else {
                                        // non-numeric expression : add 'computeChange' to modified model
                                        XPathTarget targetXpath = getTargetXPath(ste, l2gMap);
                                        ComputeChange computeChange = new ComputeChange(targetXpath, math);
                                        for (String symbol : exprSymbols) {
                                            String symbolName = TokenMangler.mangleToSName(symbol);
                                            SymbolTableEntry ste1 = vcModel.getEntry(symbol);
                                            // ste1 could be a math parameter, hence the above could return null
                                            if (ste1 == null) {
                                                ste1 = simContext.getMathDescription().getEntry(symbol);
                                            }
                                            if (ste1 != null) {
                                                if (ste1 instanceof SpeciesContext || ste1 instanceof Structure || ste1 instanceof ModelParameter) {
                                                    XPathTarget ste1_XPath = getTargetXPath(ste1, l2gMap);
                                                    org.jlibsedml.Variable sedmlVar = new org.jlibsedml.Variable(symbolName, symbolName, taskRef, ste1_XPath.getTargetAsString());
                                                    computeChange.addVariable(sedmlVar);
                                                } else {
                                                    double doubleValue = 0.0;
                                                    if (ste1 instanceof ReservedSymbol) {
                                                        doubleValue = getReservedSymbolValue(ste1);
                                                    } else if (ste instanceof Function) {
                                                        try {
                                                            doubleValue = ste.getExpression().evaluateConstant();
                                                        } catch (Exception e) {
                                                            e.printStackTrace(System.out);
                                                            throw new RuntimeException("Unable to evaluate function '" + ste.getName() + "' used in '" + unscannedParamName + "' expression : ", e);
                                                        }
                                                    } else {
                                                        doubleValue = ste.getConstantValue();
                                                    }
                                                    // TODO: shouldn't be s1_init_uM which is a math symbol, should be s0 (so use the ste-something from above)
                                                    // TODO: revert to Variable, not Parameter
                                                    Parameter sedmlParameter = new Parameter(symbolName, symbolName, doubleValue);
                                                    computeChange.addParameter(sedmlParameter);
                                                }
                                            } else {
                                                throw new RuntimeException("Symbol '" + symbol + "' used in expression for '" + unscannedParamName + "' not found in model.");
                                            }
                                        }
                                        sedModel.addChange(computeChange);
                                    }
                                }
                            }
                            sedmlModel.addModel(sedModel);
                            sedmlModel.addTask(rt);
                        }
                    } else {
                        // no math overrides, add basic task.
                        String taskId = "tsk_" + simContextCnt + "_" + simCount;
                        Task sedmlTask = new Task(taskId, taskId, simContextId, utcSim.getId());
                        sedmlModel.addTask(sedmlTask);
                        // to be used later to add dataGenerators : one set of DGs per model (simContext).
                        taskRef = taskId;
                    }
                    // add one dataGenerator for 'time' for entire SEDML model.
                    // (using the id of the first task in model for 'taskRef' field of var since
                    String timeDataGenPrefix = DATAGENERATOR_TIME_NAME + "_" + taskRef;
                    DataGenerator timeDataGen = sedmlModel.getDataGeneratorWithId(timeDataGenPrefix);
                    if (timeDataGen == null) {
                        // org.jlibsedml.Variable timeVar = new org.jlibsedml.Variable(DATAGENERATOR_TIME_SYMBOL, DATAGENERATOR_TIME_SYMBOL, sedmlModel.getTasks().get(0).getId(), VariableSymbol.TIME);
                        org.jlibsedml.Variable timeVar = new org.jlibsedml.Variable(DATAGENERATOR_TIME_SYMBOL, DATAGENERATOR_TIME_SYMBOL, taskRef, VariableSymbol.TIME);
                        ASTNode math = Libsedml.parseFormulaString(DATAGENERATOR_TIME_SYMBOL);
                        timeDataGen = new DataGenerator(timeDataGenPrefix, timeDataGenPrefix, math);
                        timeDataGen.addVariable(timeVar);
                        sedmlModel.addDataGenerator(timeDataGen);
                        dataGeneratorsOfSim.add(timeDataGen);
                    }
                    // add dataGenerators for species
                    // get species list from SBML model.
                    String dataGenIdPrefix = "dataGen_" + taskRef;
                    String[] varNamesList = SimSpec.fromSBML(sbmlString).getVarsList();
                    for (String varName : varNamesList) {
                        org.jlibsedml.Variable sedmlVar = new org.jlibsedml.Variable(varName, varName, taskRef, sbmlSupport.getXPathForSpecies(varName));
                        ASTNode varMath = Libsedml.parseFormulaString(varName);
                        // "dataGen_" + varCount; - old code
                        String dataGenId = dataGenIdPrefix + "_" + TokenMangler.mangleToSName(varName);
                        DataGenerator dataGen = new DataGenerator(dataGenId, dataGenId, varMath);
                        dataGen.addVariable(sedmlVar);
                        sedmlModel.addDataGenerator(dataGen);
                        dataGeneratorsOfSim.add(dataGen);
                        varCount++;
                    }
                    // add DataGenerators for output functions here
                    ArrayList<AnnotatedFunction> outputFunctions = simContext.getOutputFunctionContext().getOutputFunctionsList();
                    for (AnnotatedFunction annotatedFunction : outputFunctions) {
                        Expression functionExpr = annotatedFunction.getExpression();
                        ASTNode funcMath = Libsedml.parseFormulaString(functionExpr.infix());
                        // "dataGen_" + varCount; - old code
                        String dataGenId = dataGenIdPrefix + "_" + TokenMangler.mangleToSName(annotatedFunction.getName());
                        DataGenerator dataGen = new DataGenerator(dataGenId, dataGenId, funcMath);
                        String[] functionSymbols = functionExpr.getSymbols();
                        for (String symbol : functionSymbols) {
                            String symbolName = TokenMangler.mangleToSName(symbol);
                            // try to get symbol from model, if null, try simContext.mathDesc
                            SymbolTableEntry ste = vcModel.getEntry(symbol);
                            if (ste == null) {
                                ste = simContext.getMathDescription().getEntry(symbol);
                            }
                            if (ste instanceof SpeciesContext || ste instanceof Structure || ste instanceof ModelParameter) {
                                XPathTarget targetXPath = getTargetXPath(ste, l2gMap);
                                org.jlibsedml.Variable sedmlVar = new org.jlibsedml.Variable(symbolName, symbolName, taskRef, targetXPath.getTargetAsString());
                                dataGen.addVariable(sedmlVar);
                            } else {
                                double value = 0.0;
                                if (ste instanceof Function) {
                                    try {
                                        value = ste.getExpression().evaluateConstant();
                                    } catch (Exception e) {
                                        e.printStackTrace(System.out);
                                        throw new RuntimeException("Unable to evaluate function '" + ste.getName() + "' for output function '" + annotatedFunction.getName() + "'.", e);
                                    }
                                } else {
                                    value = ste.getConstantValue();
                                }
                                Parameter sedmlParameter = new Parameter(symbolName, symbolName, value);
                                dataGen.addParameter(sedmlParameter);
                            }
                        }
                        sedmlModel.addDataGenerator(dataGen);
                        dataGeneratorsOfSim.add(dataGen);
                        varCount++;
                    }
                    simCount++;
                    // ignoring output for spatial deterministic (spatial stochastic is not exported to SEDML) and non-spatial stochastic applications with histogram
                    if (!(simContext.getGeometry().getDimension() > 0)) {
                        // ignore Output (Plot2d)  for non-spatial stochastic simulation with histogram.
                        boolean bSimHasHistogram = false;
                        if (simContext.isStoch()) {
                            long numOfTrials = simTaskDesc.getStochOpt().getNumOfTrials();
                            if (numOfTrials > 1) {
                                // not histogram {
                                bSimHasHistogram = true;
                            }
                        }
                        if (!bSimHasHistogram) {
                            String plot2dId = "plot2d_" + TokenMangler.mangleToSName(vcSimulation.getName());
                            Plot2D sedmlPlot2d = new Plot2D(plot2dId, simContext.getName() + "plots");
                            sedmlPlot2d.addNote(createNotesElement("Plot of all variables and output functions from application '" + simContext.getName() + "' ; simulation '" + vcSimulation.getName() + "' in VCell model"));
                            List<DataGenerator> dataGenerators = sedmlModel.getDataGenerators();
                            String xDataRef = sedmlModel.getDataGeneratorWithId(DATAGENERATOR_TIME_NAME + "_" + taskRef).getId();
                            // add a curve for each dataGenerator in SEDML model
                            int curveCnt = 0;
                            for (DataGenerator dataGenerator : dataGeneratorsOfSim) {
                                // no curve for time, since time is xDateReference
                                if (dataGenerator.getId().equals(xDataRef)) {
                                    continue;
                                }
                                String curveId = "curve_" + curveCnt++;
                                Curve curve = new Curve(curveId, curveId, false, false, xDataRef, dataGenerator.getId());
                                sedmlPlot2d.addCurve(curve);
                            }
                            sedmlModel.addOutput(sedmlPlot2d);
                        }
                    }
                }
            // end - for 'sims'
            } else {
                // end if (!(simContext.getGeometry().getDimension() > 0 && simContext.isStoch()))
                String msg = "\n\t" + simContextName + " : export of spatial stochastic (Smoldyn solver) applications to SEDML not supported at this time.";
                sedmlNotesStr += msg;
            }
            // end : if-else simContext is not spatial stochastic
            simContextCnt++;
        }
        // if sedmlNotesStr is not null, there were some applications that could not be exported to SEDML (eg., spatial stochastic). Create a notes element and add it to sedml Model.
        if (sedmlNotesStr.length() > 0) {
            sedmlNotesStr = "\n\tThe following applications in the VCell model were not exported to VCell : " + sedmlNotesStr;
            sedmlModel.addNote(createNotesElement(sedmlNotesStr));
        }
        // error check : if there are no non-spatial deterministic applications (=> no models in SEDML document), complain.
        if (sedmlModel.getModels().isEmpty()) {
            throw new RuntimeException("No applications in biomodel to export to Sedml.");
        }
    } catch (Exception e) {
        e.printStackTrace(System.out);
        throw new RuntimeException("Error adding model to SEDML document : " + e.getMessage());
    }
}

Example 2 with TimeBounds

use of cbit.vcell.solver.TimeBounds in project vcell by virtualcell.

the class SmoldynFileWriter method writeSimulationTimes.

private void writeSimulationTimes() {
    // write simulation times
    TimeBounds timeBounds = simulation.getSolverTaskDescription().getTimeBounds();
    TimeStep timeStep = simulation.getSolverTaskDescription().getTimeStep();
    printWriter.println("# simulation times");
    printWriter.println(SmoldynVCellMapper.SmoldynKeyword.time_start + " " + timeBounds.getStartingTime());
    printWriter.println(SmoldynVCellMapper.SmoldynKeyword.time_stop + " " + timeBounds.getEndingTime());
    printWriter.println(SmoldynVCellMapper.SmoldynKeyword.time_step + " " + timeStep.getDefaultTimeStep());
    printWriter.println();
}

Example 3 with TimeBounds

use of cbit.vcell.solver.TimeBounds in project vcell by virtualcell.

the class RbmNetworkGenerator method runNFSim.

public static void runNFSim(PrintWriter writer, RbmModelContainer rbmModelContainer, SimulationContext sc, NetworkGenerationRequirements networkGenerationRequirements) {
    // ex: simulate_nf({t_end=>100,n_steps=>50});
    writer.print("simulate_nf({");
    if (sc.getBioModel() == null || sc.getSimulations() == null || sc.getSimulations().length == 0) {
        writer.print("t_end=>100,n_steps=>50");
        writer.println("})");
        return;
    }
    // we just pick whatever the first simulation has, it'll get too complicated to offer the user a list of simulations and ask him to choose
    SolverTaskDescription solverTaskDescription = sc.getSimulations(0).getSolverTaskDescription();
    TimeBounds tb = solverTaskDescription.getTimeBounds();
    double dtime = tb.getEndingTime() - tb.getStartingTime();
    if (solverTaskDescription.getOutputTimeSpec() instanceof UniformOutputTimeSpec) {
        UniformOutputTimeSpec uots = (UniformOutputTimeSpec) solverTaskDescription.getOutputTimeSpec();
        double interval = uots.getOutputTimeStep();
        int steps = (int) Math.round(dtime / interval);
        writer.print("t_end=>" + dtime + ",n_steps=>" + steps);
    } else if (solverTaskDescription.getOutputTimeSpec() instanceof DefaultOutputTimeSpec) {
        // currently unsupported, but some old simulations have it
        writer.print("t_end=>" + dtime + ",n_steps=>50");
    } else {
        writer.print("t_end=>100,n_steps=>50");
    }
    writer.println("})");
}

Example 4 with TimeBounds

use of cbit.vcell.solver.TimeBounds in project vcell by virtualcell.

the class ParameterEstimationTaskSimulatorIDA method getRowColumnRestultSetByBestEstimations.

public RowColumnResultSet getRowColumnRestultSetByBestEstimations(ParameterEstimationTask parameterEstimationTask, String[] paramNames, double[] paramValues) throws Exception {
    // create a temp simulation based on math description
    KeyValue key = new KeyValue("" + Math.abs(new Random().nextLong()));
    SimulationVersion dummyVersion = new SimulationVersion(key, "name", new User("temp", new KeyValue("1")), null, null, null, null, null, null, null);
    Simulation simulation = new Simulation(dummyVersion, parameterEstimationTask.getSimulationContext().getMathDescription());
    ReferenceData refData = parameterEstimationTask.getModelOptimizationSpec().getReferenceData();
    double[] times = refData.getDataByColumn(0);
    double endTime = times[times.length - 1];
    ExplicitOutputTimeSpec exTimeSpec = new ExplicitOutputTimeSpec(times);
    // set simulation ending time and output interval
    simulation.getSolverTaskDescription().setTimeBounds(new TimeBounds(0, endTime));
    simulation.getSolverTaskDescription().setOutputTimeSpec(exTimeSpec);
    // set parameters as math overrides
    MathOverrides mathOverrides = simulation.getMathOverrides();
    for (int i = 0; i < paramNames.length; i++) {
        mathOverrides.putConstant(new Constant(paramNames[i], new Expression(paramValues[i])));
    }
    SimulationTask simTask = new SimulationTask(new SimulationJob(simulation, 0, null), 0);
    IDASolverStandalone idaSolver = new IDASolverStandalone(simTask, ResourceUtil.getLocalSimDir("temp"), false);
    // startSolver();
    idaSolver.runSolver();
    Thread.sleep(1000);
    long startTimeMS = System.currentTimeMillis();
    while (idaSolver.getSolverStatus().isRunning() && System.currentTimeMillis() < (startTimeMS + 10000L)) {
        Thread.sleep(500);
    }
    ODESolverResultSet resultset = idaSolver.getODESolverResultSet();
    return resultset;
}

Example 5 with TimeBounds

use of cbit.vcell.solver.TimeBounds in project vcell by virtualcell.

the class FRAPStudy method createNewRefBioModel.

public static BioModel createNewRefBioModel(FRAPStudy sourceFrapStudy, String baseDiffusionRate, TimeStep tStep, KeyValue simKey, User owner, FieldDataIdentifierSpec psfFDIS, int startingIndexForRecovery) throws Exception {
    if (owner == null) {
        throw new Exception("Owner is not defined");
    }
    ROI cellROI_2D = sourceFrapStudy.getFrapData().getRoi(FRAPData.VFRAP_ROI_ENUM.ROI_CELL.name());
    Extent extent = sourceFrapStudy.getFrapData().getImageDataset().getExtent();
    TimeBounds timeBounds = FRAPOptData.getEstimatedRefTimeBound(sourceFrapStudy);
    double timeStepVal = FRAPOptData.REFERENCE_DIFF_DELTAT;
    int numX = cellROI_2D.getRoiImages()[0].getNumX();
    int numY = cellROI_2D.getRoiImages()[0].getNumY();
    int numZ = cellROI_2D.getRoiImages().length;
    short[] shortPixels = cellROI_2D.getRoiImages()[0].getPixels();
    byte[] bytePixels = new byte[numX * numY * numZ];
    final byte EXTRACELLULAR_PIXVAL = 0;
    final byte CYTOSOL_PIXVAL = 1;
    for (int i = 0; i < bytePixels.length; i++) {
        if (shortPixels[i] != 0) {
            bytePixels[i] = CYTOSOL_PIXVAL;
        }
    }
    VCImage maskImage;
    try {
        maskImage = new VCImageUncompressed(null, bytePixels, extent, numX, numY, numZ);
    } catch (ImageException e) {
        e.printStackTrace();
        throw new RuntimeException("failed to create mask image for geometry");
    }
    Geometry geometry = new Geometry("geometry", maskImage);
    if (geometry.getGeometrySpec().getNumSubVolumes() != 2) {
        throw new Exception("Cell ROI has no ExtraCellular.");
    }
    int subVolume0PixVal = ((ImageSubVolume) geometry.getGeometrySpec().getSubVolume(0)).getPixelValue();
    geometry.getGeometrySpec().getSubVolume(0).setName((subVolume0PixVal == EXTRACELLULAR_PIXVAL ? EXTRACELLULAR_NAME : CYTOSOL_NAME));
    int subVolume1PixVal = ((ImageSubVolume) geometry.getGeometrySpec().getSubVolume(1)).getPixelValue();
    geometry.getGeometrySpec().getSubVolume(1).setName((subVolume1PixVal == CYTOSOL_PIXVAL ? CYTOSOL_NAME : EXTRACELLULAR_NAME));
    geometry.getGeometrySurfaceDescription().updateAll();
    BioModel bioModel = new BioModel(null);
    bioModel.setName("unnamed");
    Model model = new Model("model");
    bioModel.setModel(model);
    Feature extracellular = model.addFeature(EXTRACELLULAR_NAME);
    Feature cytosol = model.addFeature(CYTOSOL_NAME);
    Membrane plasmaMembrane = model.addMembrane(PLASMAMEMBRANE_NAME);
    String roiDataName = FRAPStudy.ROI_EXTDATA_NAME;
    final int ONE_DIFFUSION_SPECIES_COUNT = 1;
    final int MOBILE_SPECIES_INDEX = 0;
    Expression[] diffusionConstants = new Expression[ONE_DIFFUSION_SPECIES_COUNT];
    Species[] species = new Species[ONE_DIFFUSION_SPECIES_COUNT];
    SpeciesContext[] speciesContexts = new SpeciesContext[ONE_DIFFUSION_SPECIES_COUNT];
    Expression[] initialConditions = new Expression[ONE_DIFFUSION_SPECIES_COUNT];
    // Mobile Species
    diffusionConstants[MOBILE_SPECIES_INDEX] = new Expression(baseDiffusionRate);
    species[MOBILE_SPECIES_INDEX] = new Species(SPECIES_NAME_PREFIX_MOBILE, "Mobile bleachable species");
    speciesContexts[MOBILE_SPECIES_INDEX] = new SpeciesContext(null, species[MOBILE_SPECIES_INDEX].getCommonName(), species[MOBILE_SPECIES_INDEX], cytosol);
    FieldFunctionArguments postBleach_first = new FieldFunctionArguments(roiDataName, "postbleach_first", new Expression(0), VariableType.VOLUME);
    FieldFunctionArguments prebleach_avg = new FieldFunctionArguments(roiDataName, "prebleach_avg", new Expression(0), VariableType.VOLUME);
    Expression expPostBleach_first = new Expression(postBleach_first.infix());
    Expression expPreBleach_avg = new Expression(prebleach_avg.infix());
    initialConditions[MOBILE_SPECIES_INDEX] = Expression.div(expPostBleach_first, expPreBleach_avg);
    SimulationContext simContext = new SimulationContext(bioModel.getModel(), geometry);
    bioModel.addSimulationContext(simContext);
    FeatureMapping cytosolFeatureMapping = (FeatureMapping) simContext.getGeometryContext().getStructureMapping(cytosol);
    FeatureMapping extracellularFeatureMapping = (FeatureMapping) simContext.getGeometryContext().getStructureMapping(extracellular);
    MembraneMapping plasmaMembraneMapping = (MembraneMapping) simContext.getGeometryContext().getStructureMapping(plasmaMembrane);
    SubVolume cytSubVolume = geometry.getGeometrySpec().getSubVolume(CYTOSOL_NAME);
    SubVolume exSubVolume = geometry.getGeometrySpec().getSubVolume(EXTRACELLULAR_NAME);
    SurfaceClass pmSurfaceClass = geometry.getGeometrySurfaceDescription().getSurfaceClass(exSubVolume, cytSubVolume);
    cytosolFeatureMapping.setGeometryClass(cytSubVolume);
    extracellularFeatureMapping.setGeometryClass(exSubVolume);
    plasmaMembraneMapping.setGeometryClass(pmSurfaceClass);
    cytosolFeatureMapping.getUnitSizeParameter().setExpression(new Expression(1.0));
    extracellularFeatureMapping.getUnitSizeParameter().setExpression(new Expression(1.0));
    plasmaMembraneMapping.getUnitSizeParameter().setExpression(new Expression(1.0));
    for (int i = 0; i < initialConditions.length; i++) {
        model.addSpecies(species[i]);
        model.addSpeciesContext(speciesContexts[i]);
    }
    for (int i = 0; i < speciesContexts.length; i++) {
        SpeciesContextSpec scs = simContext.getReactionContext().getSpeciesContextSpec(speciesContexts[i]);
        scs.getInitialConditionParameter().setExpression(initialConditions[i]);
        scs.getDiffusionParameter().setExpression(diffusionConstants[i]);
    }
    MathMapping mathMapping = simContext.createNewMathMapping();
    MathDescription mathDesc = mathMapping.getMathDescription();
    // Add PSF function
    mathDesc.addVariable(new Function(Simulation.PSF_FUNCTION_NAME, new Expression(psfFDIS.getFieldFuncArgs().infix()), null));
    simContext.setMathDescription(mathDesc);
    SimulationVersion simVersion = new SimulationVersion(simKey, "sim1", owner, new GroupAccessNone(), new KeyValue("0"), new BigDecimal(0), new Date(), VersionFlag.Current, "", null);
    Simulation newSimulation = new Simulation(simVersion, simContext.getMathDescription());
    newSimulation.getSolverTaskDescription().setSolverDescription(SolverDescription.FiniteVolumeStandalone);
    simContext.addSimulation(newSimulation);
    newSimulation.getSolverTaskDescription().setTimeBounds(timeBounds);
    newSimulation.getSolverTaskDescription().setOutputTimeSpec(new UniformOutputTimeSpec(timeStepVal));
    newSimulation.getMeshSpecification().setSamplingSize(cellROI_2D.getISize());
    newSimulation.getSolverTaskDescription().setTimeStep(new TimeStep(timeStepVal, timeStepVal, timeStepVal));
    return bioModel;
}