use of cbit.vcell.math.Function 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());
}
}
use of cbit.vcell.math.Function in project vcell by virtualcell.
the class NFsimXMLWriter method getListOfFunctions.
private static Element getListOfFunctions(MathDescription mathDesc, SimulationSymbolTable simulationSymbolTable) throws SolverException {
Element listOfParametersElement = new Element("ListOfFunctions");
for (Variable var : simulationSymbolTable.getVariables()) {
Double value = null;
if (var instanceof Constant || var instanceof Function) {
Expression valExpression = var.getExpression();
Expression substitutedValExpr = null;
try {
substitutedValExpr = simulationSymbolTable.substituteFunctions(valExpression);
} catch (Exception e) {
e.printStackTrace(System.out);
throw new SolverException("Constant or Function " + var.getName() + " substitution failed : exp = \"" + var.getExpression().infix() + "\": " + e.getMessage());
}
try {
value = substitutedValExpr.evaluateConstant();
} catch (ExpressionException e) {
System.out.println("constant or function " + var.getName() + " = " + substitutedValExpr.infix() + " does not have a constant value");
}
Element functionElement = new Element("Function");
functionElement.setAttribute("id", var.getName());
if (value != null) {
// parameter, see getListOfParameters() above
continue;
} else {
Element listOfReferencesElement = new Element("ListOfReferences");
String[] references = valExpression.getSymbols();
for (int i = 0; i < references.length; i++) {
String reference = references[i];
Element referenceElement = new Element("Reference");
referenceElement.setAttribute("name", reference);
Variable referenceVariable = simulationSymbolTable.getVariable(reference);
Double referenceValue = null;
Expression referenceExpression = referenceVariable.getExpression();
Expression substitutedReferenceExpression = null;
if (referenceExpression != null) {
try {
substitutedReferenceExpression = simulationSymbolTable.substituteFunctions(referenceExpression);
} catch (Exception e) {
e.printStackTrace(System.out);
throw new SolverException("Constant or Function " + var.getName() + " substitution failed : exp = \"" + var.getExpression().infix() + "\": " + e.getMessage());
}
try {
referenceValue = substitutedReferenceExpression.evaluateConstant();
} catch (ExpressionException e) {
System.out.println("constant or function " + var.getName() + " = " + substitutedValExpr.infix() + " does not have a constant value");
}
}
if (referenceVariable instanceof ParticleObservable) {
referenceElement.setAttribute("type", "Observable");
} else if (referenceVariable instanceof Function) {
if (referenceValue != null) {
referenceElement.setAttribute("type", "ConstantExpression");
} else {
referenceElement.setAttribute("type", "Function");
}
} else {
// constant
referenceElement.setAttribute("type", "ConstantExpression");
}
listOfReferencesElement.addContent(referenceElement);
}
functionElement.addContent(listOfReferencesElement);
Element expressionElement = new Element("Expression");
String functionExpression = valExpression.infix();
expressionElement.setText(functionExpression);
functionElement.addContent(expressionElement);
}
listOfParametersElement.addContent(functionElement);
}
}
return listOfParametersElement;
}
use of cbit.vcell.math.Function in project vcell by virtualcell.
the class NFsimXMLWriter method getListOfParameters.
private static Element getListOfParameters(MathDescription mathDesc, SimulationSymbolTable simulationSymbolTable) throws SolverException {
Element listOfParametersElement = new Element("ListOfParameters");
for (Variable var : simulationSymbolTable.getVariables()) {
Double value = null;
if (var instanceof Constant || var instanceof Function) {
Expression valExpression = var.getExpression();
Expression substitutedValExpr = null;
try {
substitutedValExpr = simulationSymbolTable.substituteFunctions(valExpression);
} catch (Exception e) {
e.printStackTrace(System.out);
throw new SolverException("Constant or Function " + var.getName() + " substitution failed : exp = \"" + var.getExpression().infix() + "\": " + e.getMessage());
}
try {
value = substitutedValExpr.evaluateConstant();
} catch (ExpressionException e) {
System.out.println("constant or function " + var.getName() + " = " + substitutedValExpr.infix() + " does not have a constant value");
}
Element parameterElement = new Element("Parameter");
parameterElement.setAttribute("id", var.getName());
if (value != null) {
parameterElement.setAttribute("type", "Constant");
parameterElement.setAttribute("value", value.toString());
} else {
// function, see getListOfFunctions() below
continue;
}
listOfParametersElement.addContent(parameterElement);
}
}
return listOfParametersElement;
}
use of cbit.vcell.math.Function in project vcell by virtualcell.
the class XmlReader method readParameters.
private void readParameters(List<Element> parameterElements, ParameterContext parameterContext, HashMap<String, ParameterRoleEnum> roleHash, ParameterRoleEnum userDefinedRole, HashSet<String> xmlRolesTagsToIgnore, Model model) throws XmlParseException {
String contextName = parameterContext.getNameScope().getName();
try {
//
// prepopulate varHash with reserved symbols
//
VariableHash varHash = new VariableHash();
addResevedSymbols(varHash, model);
//
for (Element xmlParam : parameterElements) {
String parsedParamName = unMangle(xmlParam.getAttributeValue(XMLTags.NameAttrTag));
String parsedRoleString = xmlParam.getAttributeValue(XMLTags.ParamRoleAttrTag);
String parsedExpressionString = xmlParam.getText();
//
if (xmlRolesTagsToIgnore.contains(parsedRoleString)) {
varHash.removeVariable(parsedParamName);
continue;
}
Expression paramExp = null;
if (parsedExpressionString.trim().length() > 0) {
paramExp = unMangleExpression(parsedExpressionString);
}
if (varHash.getVariable(parsedParamName) == null) {
Domain domain = null;
varHash.addVariable(new Function(parsedParamName, paramExp, domain));
} else {
if (model.getReservedSymbolByName(parsedParamName) != null) {
varHash.removeVariable(parsedParamName);
Domain domain = null;
varHash.addVariable(new Function(parsedParamName, paramExp, domain));
}
}
//
// get the parameter for this xml role string
//
ParameterRoleEnum paramRole = roleHash.get(parsedRoleString);
if (paramRole == null) {
throw new XmlParseException("parameter '" + parsedParamName + "' has unexpected role '" + parsedRoleString + "' in '" + contextName + "'");
}
//
if (paramRole != userDefinedRole) {
LocalParameter paramWithSameRole = parameterContext.getLocalParameterFromRole(paramRole);
if (paramWithSameRole == null) {
throw new XmlParseException("can't find parameter with role '" + parsedRoleString + "' in '" + contextName + "'");
}
//
if (!paramWithSameRole.getName().equals(parsedParamName)) {
//
// first rename other parameters with same name
//
LocalParameter paramWithSameNameButDifferentRole = parameterContext.getLocalParameterFromName(parsedParamName);
if (paramWithSameNameButDifferentRole != null) {
//
// find available name
//
int n = 0;
String newName = parsedParamName + "_" + n++;
while (parameterContext.getEntry(newName) != null) {
newName = parsedParamName + "_" + n++;
}
parameterContext.renameLocalParameter(parsedParamName, newName);
}
//
// then rename parameter with correct role
//
parameterContext.renameLocalParameter(paramWithSameRole.getName(), parsedParamName);
}
}
}
//
// create unresolved parameters for all unresolved symbols
//
String unresolvedSymbol = varHash.getFirstUnresolvedSymbol();
while (unresolvedSymbol != null) {
try {
Domain domain = null;
// will turn into an UnresolvedParameter.
varHash.addVariable(new Function(unresolvedSymbol, new Expression(0.0), domain));
} catch (MathException e) {
e.printStackTrace(System.out);
throw new XmlParseException(e.getMessage());
}
parameterContext.addUnresolvedParameter(unresolvedSymbol);
unresolvedSymbol = varHash.getFirstUnresolvedSymbol();
}
//
// in topological order, add parameters to model (getting units also).
// note that all pre-defined parameters already have the correct names
// here we set expressions on pre-defined parameters and add user-defined parameters
//
Variable[] sortedVariables = varHash.getTopologicallyReorderedVariables();
ModelUnitSystem modelUnitSystem = model.getUnitSystem();
for (int i = sortedVariables.length - 1; i >= 0; i--) {
if (sortedVariables[i] instanceof Function) {
Function paramFunction = (Function) sortedVariables[i];
Element xmlParam = null;
for (int j = 0; j < parameterElements.size(); j++) {
Element tempParam = (Element) parameterElements.get(j);
if (paramFunction.getName().equals(unMangle(tempParam.getAttributeValue(XMLTags.NameAttrTag)))) {
xmlParam = tempParam;
break;
}
}
if (xmlParam == null) {
// must have been an unresolved parameter
continue;
}
String symbol = xmlParam.getAttributeValue(XMLTags.VCUnitDefinitionAttrTag);
VCUnitDefinition unit = null;
if (symbol != null) {
unit = modelUnitSystem.getInstance(symbol);
}
LocalParameter tempParam = parameterContext.getLocalParameterFromName(paramFunction.getName());
if (tempParam == null) {
tempParam = parameterContext.addLocalParameter(paramFunction.getName(), new Expression(0.0), userDefinedRole, unit, userDefinedRole.getDescription());
parameterContext.setParameterValue(tempParam, paramFunction.getExpression(), true);
} else {
if (tempParam.getExpression() != null) {
// if the expression is null, it should remain null.
parameterContext.setParameterValue(tempParam, paramFunction.getExpression(), true);
}
tempParam.setUnitDefinition(unit);
}
}
}
} catch (PropertyVetoException | ExpressionException | MathException e) {
e.printStackTrace(System.out);
throw new XmlParseException("Exception while setting parameters for '" + contextName + "': " + e.getMessage(), e);
}
}
use of cbit.vcell.math.Function in project vcell by virtualcell.
the class XmlReader method getElectricalStimulus.
/**
* This method process Electrical Stimulus, also called Clamps.
* Creation date: (6/6/2002 4:46:18 PM)
* @return cbit.vcell.mapping.ElectricalStimulus
* @param param org.jdom.Element
*/
private ElectricalStimulus getElectricalStimulus(Element param, SimulationContext currentSimulationContext) throws XmlParseException {
ElectricalStimulus clampStimulus = null;
// get name
// String name = unMangle( param.getAttributeValue(XMLTags.NameAttrTag) );
// get Electrode
Electrode electrode = getElectrode(param.getChild(XMLTags.ElectrodeTag, vcNamespace), currentSimulationContext);
if (param.getAttributeValue(XMLTags.TypeAttrTag).equalsIgnoreCase(XMLTags.VoltageClampTag)) {
// is a voltage clamp
clampStimulus = new VoltageClampStimulus(electrode, "voltClampElectrode", new Expression(0.0), currentSimulationContext);
} else if (param.getAttributeValue(XMLTags.TypeAttrTag).equalsIgnoreCase(XMLTags.CurrentDensityClampTag) || param.getAttributeValue(XMLTags.TypeAttrTag).equalsIgnoreCase(XMLTags.CurrentDensityClampTag_oldName)) {
// is a current density clamp
clampStimulus = new CurrentDensityClampStimulus(electrode, "currDensityClampElectrode", new Expression(0.0), currentSimulationContext);
} else if (param.getAttributeValue(XMLTags.TypeAttrTag).equalsIgnoreCase(XMLTags.TotalCurrentClampTag)) {
// is a "total" current clamp
clampStimulus = new TotalCurrentClampStimulus(electrode, "totalCurrClampElectrode", new Expression(0.0), currentSimulationContext);
}
try {
// transaction begin flag ... yeah, this is a hack
clampStimulus.reading(true);
// Read all of the parameters
List<Element> list = param.getChildren(XMLTags.ParameterTag, vcNamespace);
// add constants that may be used in the electrical stimulus.
VariableHash varHash = new VariableHash();
Model model = currentSimulationContext.getModel();
addResevedSymbols(varHash, model);
//
for (Element xmlParam : list) {
String paramName = unMangle(xmlParam.getAttributeValue(XMLTags.NameAttrTag));
String role = xmlParam.getAttributeValue(XMLTags.ParamRoleAttrTag);
String paramExpStr = xmlParam.getText();
Expression paramExp = unMangleExpression(paramExpStr);
try {
if (varHash.getVariable(paramName) == null) {
Domain domain = null;
varHash.addVariable(new Function(paramName, paramExp, domain));
} else {
if (model.getReservedSymbolByName(paramName) != null) {
varHash.removeVariable(paramName);
Domain domain = null;
varHash.addVariable(new Function(paramName, paramExp, domain));
}
}
} catch (MathException e) {
e.printStackTrace(System.out);
throw new XmlParseException("error reordering parameters according to dependencies:", e);
}
LocalParameter tempParam = null;
if (!role.equals(XMLTags.ParamRoleUserDefinedTag)) {
if (role.equals(XMLTags.ParamRoleTotalCurrentTag)) {
if (clampStimulus instanceof TotalCurrentClampStimulus) {
tempParam = ((TotalCurrentClampStimulus) clampStimulus).getCurrentParameter();
} else {
varHash.removeVariable(paramName);
continue;
}
} else if (role.equals(XMLTags.ParamRoleTotalCurrentDensityTag) || role.equals(XMLTags.ParamRoleTotalCurrentDensityOldNameTag)) {
if (clampStimulus instanceof CurrentDensityClampStimulus) {
tempParam = ((CurrentDensityClampStimulus) clampStimulus).getCurrentDensityParameter();
} else {
varHash.removeVariable(paramName);
continue;
}
} else if (role.equals(XMLTags.ParamRolePotentialDifferenceTag)) {
if (clampStimulus instanceof VoltageClampStimulus) {
tempParam = ((VoltageClampStimulus) clampStimulus).getVoltageParameter();
} else {
varHash.removeVariable(paramName);
continue;
}
}
} else {
continue;
}
if (tempParam == null) {
throw new XmlParseException("parameter with role '" + role + "' not found in electricalstimulus");
}
//
if (!tempParam.getName().equals(paramName)) {
LocalParameter multNameParam = clampStimulus.getLocalParameter(paramName);
int n = 0;
while (multNameParam != null) {
String tempName = paramName + "_" + n++;
clampStimulus.renameParameter(paramName, tempName);
multNameParam = clampStimulus.getLocalParameter(tempName);
}
clampStimulus.renameParameter(tempParam.getName(), paramName);
}
}
//
// create unresolved parameters for all unresolved symbols
//
String unresolvedSymbol = varHash.getFirstUnresolvedSymbol();
while (unresolvedSymbol != null) {
try {
Domain domain = null;
// will turn into an UnresolvedParameter.
varHash.addVariable(new Function(unresolvedSymbol, new Expression(0.0), domain));
} catch (MathException e) {
e.printStackTrace(System.out);
throw new XmlParseException(e.getMessage());
}
clampStimulus.addUnresolvedParameter(unresolvedSymbol);
unresolvedSymbol = varHash.getFirstUnresolvedSymbol();
}
Variable[] sortedVariables = varHash.getTopologicallyReorderedVariables();
ModelUnitSystem modelUnitSystem = model.getUnitSystem();
for (int i = sortedVariables.length - 1; i >= 0; i--) {
if (sortedVariables[i] instanceof Function) {
Function paramFunction = (Function) sortedVariables[i];
Element xmlParam = null;
for (int j = 0; j < list.size(); j++) {
Element tempParam = (Element) list.get(j);
if (paramFunction.getName().equals(unMangle(tempParam.getAttributeValue(XMLTags.NameAttrTag)))) {
xmlParam = tempParam;
break;
}
}
if (xmlParam == null) {
// must have been an unresolved parameter
continue;
}
String symbol = xmlParam.getAttributeValue(XMLTags.VCUnitDefinitionAttrTag);
VCUnitDefinition unit = null;
if (symbol != null) {
unit = modelUnitSystem.getInstance(symbol);
}
LocalParameter tempParam = clampStimulus.getLocalParameter(paramFunction.getName());
if (tempParam == null) {
clampStimulus.addUserDefinedParameter(paramFunction.getName(), paramFunction.getExpression(), unit);
} else {
if (tempParam.getExpression() != null) {
// if the expression is null, it should remain null.
clampStimulus.setParameterValue(tempParam, paramFunction.getExpression());
}
tempParam.setUnitDefinition(unit);
}
}
}
} catch (java.beans.PropertyVetoException e) {
e.printStackTrace(System.out);
throw new XmlParseException("Exception while setting parameters for simContext : " + currentSimulationContext.getName(), e);
} catch (ExpressionException e) {
e.printStackTrace(System.out);
throw new XmlParseException("Exception while settings parameters for simContext : " + currentSimulationContext.getName(), e);
} finally {
clampStimulus.reading(false);
}
return clampStimulus;
}
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