Example 1 with MathMapping
use of cbit.vcell.mapping.MathMapping in project vcell by virtualcell.
the class ParameterMappingPanel method jMenuItemPaste_ActionPerformed.
/**
* Comment
*/
private void jMenuItemPaste_ActionPerformed(java.awt.event.ActionEvent actionEvent) {
java.util.Vector<String> pasteDescriptionsV = new java.util.Vector<String>();
java.util.Vector<Expression> newExpressionsV = new java.util.Vector<Expression>();
java.util.Vector<ParameterMappingSpec> changedParametersV = new java.util.Vector<ParameterMappingSpec>();
try {
if (actionEvent.getSource() == getJMenuItemPaste() || actionEvent.getSource() == getJMenuItemPasteAll()) {
Object pasteThis = VCellTransferable.getFromClipboard(VCellTransferable.OBJECT_FLAVOR);
SimulationContext sc = getParameterEstimationTask().getModelOptimizationSpec().getSimulationContext();
MathSymbolMapping msm = null;
Exception mathMappingException = null;
try {
MathMapping mm = sc.createNewMathMapping();
msm = mm.getMathSymbolMapping();
} catch (Exception e) {
mathMappingException = e;
e.printStackTrace(System.out);
}
// if(msm == null){
// try{
// getParameterEstimationTask().refreshMappings();
// msm = getParameterEstimationTask().getMathSymbolMapping();
// }catch(Exception e){
// e.printStackTrace();
// }
// }
int[] rows = null;
if (actionEvent.getSource() == getJMenuItemPasteAll()) {
rows = new int[getScrollPaneTable().getRowCount()];
for (int i = 0; i < rows.length; i += 1) {
rows[i] = i;
}
} else {
rows = getScrollPaneTable().getSelectedRows();
}
//
// Check paste
//
StringBuffer errors = null;
for (int i = 0; i < rows.length; i += 1) {
ParameterMappingSpec pms = parameterMappingTableModel.getValueAt(rows[i]);
try {
if (pasteThis instanceof VCellTransferable.ResolvedValuesSelection) {
VCellTransferable.ResolvedValuesSelection rvs = (VCellTransferable.ResolvedValuesSelection) pasteThis;
for (int j = 0; j < rvs.getPrimarySymbolTableEntries().length; j += 1) {
ParameterMappingSpec pasteDestination = null;
Parameter clipboardBiologicalParameter = null;
if (rvs.getPrimarySymbolTableEntries()[j] instanceof Parameter) {
clipboardBiologicalParameter = (Parameter) rvs.getPrimarySymbolTableEntries()[j];
} else if (rvs.getAlternateSymbolTableEntries() != null && rvs.getAlternateSymbolTableEntries()[j] instanceof Parameter) {
clipboardBiologicalParameter = (Parameter) rvs.getAlternateSymbolTableEntries()[j];
}
if (clipboardBiologicalParameter == null) {
Variable pastedMathVariable = null;
if (rvs.getPrimarySymbolTableEntries()[j] instanceof Variable) {
pastedMathVariable = (Variable) rvs.getPrimarySymbolTableEntries()[j];
} else if (rvs.getAlternateSymbolTableEntries() != null && rvs.getAlternateSymbolTableEntries()[j] instanceof Variable) {
pastedMathVariable = (Variable) rvs.getAlternateSymbolTableEntries()[j];
}
if (pastedMathVariable != null) {
if (msm == null) {
throw mathMappingException;
}
Variable localMathVariable = msm.findVariableByName(pastedMathVariable.getName());
if (localMathVariable != null) {
SymbolTableEntry[] localBiologicalSymbolArr = msm.getBiologicalSymbol(localMathVariable);
for (int k = 0; k < localBiologicalSymbolArr.length; k += 1) {
if (localBiologicalSymbolArr[k] == pms.getModelParameter()) {
pasteDestination = pms;
break;
}
}
}
}
} else {
if (pms.getModelParameter().getName().equals(clipboardBiologicalParameter.getName()) && pms.getModelParameter().getClass().equals(clipboardBiologicalParameter.getClass()) && pms.getModelParameter().getNameScope().getName().equals(clipboardBiologicalParameter.getNameScope().getName())) {
pasteDestination = pms;
}
}
if (pasteDestination != null) {
changedParametersV.add(pasteDestination);
newExpressionsV.add(rvs.getExpressionValues()[j]);
pasteDescriptionsV.add(VCellCopyPasteHelper.formatPasteList(pms.getModelParameter().getNameScope().getName(), pms.getModelParameter().getName(), pasteDestination.getCurrent() + "", rvs.getExpressionValues()[j].infix()));
}
}
}
} catch (Throwable e) {
if (errors == null) {
errors = new StringBuffer();
}
errors.append(pms.getModelParameter().getName() + " (" + e.getClass().getName() + ") " + e.getMessage() + "\n");
}
}
if (errors != null) {
throw new Exception(errors.toString());
}
}
} catch (Throwable e) {
PopupGenerator.showErrorDialog(this, "Paste failed during pre-check (no changes made).\n" + e.getMessage(), e);
return;
}
// Do paste
try {
if (pasteDescriptionsV.size() > 0) {
String[] pasteDescriptionArr = new String[pasteDescriptionsV.size()];
pasteDescriptionsV.copyInto(pasteDescriptionArr);
ParameterMappingSpec[] changedParametersArr = new ParameterMappingSpec[changedParametersV.size()];
changedParametersV.copyInto(changedParametersArr);
Expression[] newExpressionsArr = new Expression[newExpressionsV.size()];
newExpressionsV.copyInto(newExpressionsArr);
VCellCopyPasteHelper.chooseApplyPaste(this, pasteDescriptionArr, changedParametersArr, newExpressionsArr);
} else {
PopupGenerator.showInfoDialog(this, "No paste items match the destination (no changes made).");
}
} catch (Throwable e) {
PopupGenerator.showErrorDialog(this, "Paste Error\n" + e.getMessage(), e);
}
}
Also used :
Variable(cbit.vcell.math.Variable)
VCellTransferable(cbit.vcell.desktop.VCellTransferable)
SymbolTableEntry(cbit.vcell.parser.SymbolTableEntry)
ParameterMappingSpec(cbit.vcell.modelopt.ParameterMappingSpec)
SimulationContext(cbit.vcell.mapping.SimulationContext)
MathSymbolMapping(cbit.vcell.mapping.MathSymbolMapping)
Expression(cbit.vcell.parser.Expression)
MathMapping(cbit.vcell.mapping.MathMapping)
ModelParameter(cbit.vcell.model.Model.ModelParameter)
Parameter(cbit.vcell.model.Parameter)
UnresolvedParameter(cbit.vcell.model.Kinetics.UnresolvedParameter)
Example 2 with MathMapping
use of cbit.vcell.mapping.MathMapping 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());
}
}
Also used :
Task(org.jlibsedml.Task)
SubTask(org.jlibsedml.SubTask)
RepeatedTask(org.jlibsedml.RepeatedTask)
HashMap(java.util.HashMap)
ArrayList(java.util.ArrayList)
SpeciesContext(cbit.vcell.model.SpeciesContext)
ConstantArraySpec(cbit.vcell.solver.ConstantArraySpec)
ExpressionException(cbit.vcell.parser.ExpressionException)
ChangeAttribute(org.jlibsedml.ChangeAttribute)
ComputeChange(org.jlibsedml.ComputeChange)
SolverTaskDescription(cbit.vcell.solver.SolverTaskDescription)
SubTask(org.jlibsedml.SubTask)
AnnotatedFunction(cbit.vcell.solver.AnnotatedFunction)
Curve(org.jlibsedml.Curve)
SBMLExporter(org.vcell.sbml.vcell.SBMLExporter)
XmlParseException(cbit.vcell.xml.XmlParseException)
VectorRange(org.jlibsedml.VectorRange)
UniformRange(org.jlibsedml.UniformRange)
Range(org.jlibsedml.Range)
Algorithm(org.jlibsedml.Algorithm)
MathOverrides(cbit.vcell.solver.MathOverrides)
ModelParameter(cbit.vcell.model.Model.ModelParameter)
DataGenerator(org.jlibsedml.DataGenerator)
MathMapping(cbit.vcell.mapping.MathMapping)
UniformTimeCourse(org.jlibsedml.UniformTimeCourse)
Plot2D(org.jlibsedml.Plot2D)
SbmlException(org.vcell.sbml.SbmlException)
VectorRange(org.jlibsedml.VectorRange)
SolverDescription(cbit.vcell.solver.SolverDescription)
ReservedSymbol(cbit.vcell.model.Model.ReservedSymbol)
StructureMapping(cbit.vcell.mapping.StructureMapping)
TimeBounds(cbit.vcell.solver.TimeBounds)
AnnotatedFunction(cbit.vcell.solver.AnnotatedFunction)
Function(cbit.vcell.math.Function)
SymbolTableEntry(cbit.vcell.parser.SymbolTableEntry)
ASTCi(org.jmathml.ASTCi)
RepeatedTask(org.jlibsedml.RepeatedTask)
ASTNode(org.jmathml.ASTNode)
Structure(cbit.vcell.model.Structure)
SimulationJob(cbit.vcell.solver.SimulationJob)
Pair(org.vcell.util.Pair)
ModelUnitSystem(cbit.vcell.model.ModelUnitSystem)
SimulationContext(cbit.vcell.mapping.SimulationContext)
MathSymbolMapping(cbit.vcell.mapping.MathSymbolMapping)
SbmlException(org.vcell.sbml.SbmlException)
TransformerException(javax.xml.transform.TransformerException)
XmlParseException(cbit.vcell.xml.XmlParseException)
IOException(java.io.IOException)
ExpressionException(cbit.vcell.parser.ExpressionException)
ParserConfigurationException(javax.xml.parsers.ParserConfigurationException)
SBMLSupport(org.jlibsedml.modelsupport.SBMLSupport)
Simulation(cbit.vcell.solver.Simulation)
Expression(cbit.vcell.parser.Expression)
BioModel(cbit.vcell.biomodel.BioModel)
UniformRange(org.jlibsedml.UniformRange)
BioModel(cbit.vcell.biomodel.BioModel)
Model(org.jlibsedml.Model)
StructureMappingParameter(cbit.vcell.mapping.StructureMapping.StructureMappingParameter)
KineticsParameter(cbit.vcell.model.Kinetics.KineticsParameter)
ModelParameter(cbit.vcell.model.Model.ModelParameter)
SpeciesContextSpecParameter(cbit.vcell.mapping.SpeciesContextSpec.SpeciesContextSpecParameter)
ProxyParameter(cbit.vcell.model.ProxyParameter)
Parameter(org.jlibsedml.Parameter)
XPathTarget(org.jlibsedml.XPathTarget)
SetValue(org.jlibsedml.SetValue)
Example 3 with MathMapping
use of cbit.vcell.mapping.MathMapping in project vcell by virtualcell.
the class ClientRequestManager method createRuleBasedBioModelFromApplication.
public void createRuleBasedBioModelFromApplication(final BioModelWindowManager requester, final String name, final SimulationContext simContext) {
if (simContext == null) {
PopupGenerator.showErrorDialog(requester, "Selected Application is null, cannot generate corresponding bio model");
return;
}
AsynchClientTask task1 = new AsynchClientTask("Creating BioModel from BioModel Application", AsynchClientTask.TASKTYPE_NONSWING_BLOCKING) {
@Override
public void run(Hashtable<String, Object> hashTable) throws Exception {
MathMappingCallback dummyCallback = new MathMappingCallback() {
public void setProgressFraction(float percentDone) {
}
public void setMessage(String message) {
}
public boolean isInterrupted() {
return false;
}
};
MathMapping transformedMathMapping = simContext.createNewMathMapping(dummyCallback, NetworkGenerationRequirements.ComputeFullStandardTimeout);
// simContext.setMathDescription(transformedMathMapping.getMathDescription());
BioModel newBioModel = new BioModel(null);
SimulationContext transformedSimContext = transformedMathMapping.getTransformation().transformedSimContext;
Model model = transformedSimContext.getModel();
// for(ReactionStep rs : model.getReactionSteps()) {
// model.removeReactionStep(rs);
// }
newBioModel.setModel(model);
hashTable.put("newBioModel", newBioModel);
}
};
AsynchClientTask task2 = new AsynchClientTask("Creating BioModel from BioModel Application", AsynchClientTask.TASKTYPE_SWING_BLOCKING) {
@Override
public void run(Hashtable<String, Object> hashTable) throws Exception {
BioModel newBioModel = (BioModel) hashTable.get("newBioModel");
DocumentWindowManager windowManager = createDocumentWindowManager(newBioModel);
getMdiManager().createNewDocumentWindow(windowManager);
}
};
ClientTaskDispatcher.dispatch(requester.getComponent(), new Hashtable<String, Object>(), new AsynchClientTask[] { task1, task2 }, false);
}
Also used :
AsynchClientTask(cbit.vcell.client.task.AsynchClientTask)
MathMappingCallback(cbit.vcell.mapping.SimulationContext.MathMappingCallback)
Hashtable(java.util.Hashtable)
BioModel(cbit.vcell.biomodel.BioModel)
MathMapping(cbit.vcell.mapping.MathMapping)
ASTModel(org.vcell.model.bngl.ASTModel)
MathModel(cbit.vcell.mathmodel.MathModel)
Model(cbit.vcell.model.Model)
ListSelectionModel(javax.swing.ListSelectionModel)
BioModel(cbit.vcell.biomodel.BioModel)
CSGObject(cbit.vcell.geometry.CSGObject)
SimulationContext(cbit.vcell.mapping.SimulationContext)
Example 4 with MathMapping
use of cbit.vcell.mapping.MathMapping 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;
}
Also used :
MembraneMapping(cbit.vcell.mapping.MembraneMapping)
ImageException(cbit.image.ImageException)
KeyValue(org.vcell.util.document.KeyValue)
Extent(org.vcell.util.Extent)
SurfaceClass(cbit.vcell.geometry.SurfaceClass)
MathDescription(cbit.vcell.math.MathDescription)
VCImage(cbit.image.VCImage)
SpeciesContext(cbit.vcell.model.SpeciesContext)
SpeciesContextSpec(cbit.vcell.mapping.SpeciesContextSpec)
Feature(cbit.vcell.model.Feature)
TimeBounds(cbit.vcell.solver.TimeBounds)
Function(cbit.vcell.math.Function)
GroupAccessNone(org.vcell.util.document.GroupAccessNone)
TimeStep(cbit.vcell.solver.TimeStep)
SimulationVersion(org.vcell.util.document.SimulationVersion)
FeatureMapping(cbit.vcell.mapping.FeatureMapping)
SubVolume(cbit.vcell.geometry.SubVolume)
ImageSubVolume(cbit.vcell.geometry.ImageSubVolume)
Membrane(cbit.vcell.model.Membrane)
Species(cbit.vcell.model.Species)
ImageSubVolume(cbit.vcell.geometry.ImageSubVolume)
UniformOutputTimeSpec(cbit.vcell.solver.UniformOutputTimeSpec)
FieldFunctionArguments(cbit.vcell.field.FieldFunctionArguments)
VCImageUncompressed(cbit.image.VCImageUncompressed)
SimulationContext(cbit.vcell.mapping.SimulationContext)
ROI(cbit.vcell.VirtualMicroscopy.ROI)
ImageException(cbit.image.ImageException)
UserCancelException(org.vcell.util.UserCancelException)
BigDecimal(java.math.BigDecimal)
Date(java.util.Date)
Geometry(cbit.vcell.geometry.Geometry)
Simulation(cbit.vcell.solver.Simulation)
Expression(cbit.vcell.parser.Expression)
BioModel(cbit.vcell.biomodel.BioModel)
Model(cbit.vcell.model.Model)
BioModel(cbit.vcell.biomodel.BioModel)
MathMapping(cbit.vcell.mapping.MathMapping)
Example 5 with MathMapping
use of cbit.vcell.mapping.MathMapping in project vcell by virtualcell.
the class TestingFrameworkWindowManager method addTestCases.
/**
* Insert the method's description here.
* Creation date: (4/10/2003 11:27:32 AM)
* @param testCase cbit.vcell.numericstestingframework.TestCase
*/
public String addTestCases(final TestSuiteInfoNew tsInfo, final TestCaseNew[] testCaseArray, int regrRefFlag, ClientTaskStatusSupport pp) {
if (tsInfo == null) {
throw new IllegalArgumentException("TestSuiteInfo cannot be null");
}
if (testCaseArray == null || testCaseArray.length == 0) {
throw new IllegalArgumentException("TestCases cannot be null / empty");
}
// make modifiable list
List<TestCaseNew> testCases = new ArrayList<>(Arrays.asList(testCaseArray));
StringBuffer errors = new StringBuffer();
// When a testCase (mathmodel/biomodel) is added to a testSuite, a new version of the mathModel/biomodel should be created.
// Also, the simulations in the original mathmodel/biomodel should be rid of their parent simulation reference.
pp.setMessage("Getting testSuite");
pp.setProgress(1);
TestSuiteNew testSuite = null;
try {
testSuite = getRequestManager().getDocumentManager().getTestSuite(tsInfo.getTSKey());
} catch (Throwable e) {
throw new RuntimeException("couldn't get test suite " + tsInfo.getTSID() + "\n" + e.getClass().getName() + " mesg=" + e.getMessage() + "\n");
}
if (testSuite != null && testSuite.getTSInfoNew().isLocked()) {
throw new RuntimeException("Cannot addTestCases to locked table");
}
if (testSuite != null) {
// Saving BioModels
TestCaseNew[] existingTestCases = testSuite.getTestCases();
java.util.HashMap<KeyValue, BioModel> bioModelHashMap = new java.util.HashMap<KeyValue, BioModel>();
// if(existingTestCases != null){
// Find BioModels, Using the same BM reference for sibling Applications
int pcounter = 0;
// use iterator to allow removal of test case from collection if exception
Iterator<TestCaseNew> iter = testCases.iterator();
while (iter.hasNext()) {
TestCaseNew testCase = iter.next();
pp.setProgress(Math.max(1, ((int) ((pcounter++ / (double) (testCases.size() * 3)) * 100))));
pp.setMessage("Checking " + testCase.getVersion().getName());
try {
if (testCase instanceof TestCaseNewBioModel) {
TestCaseNewBioModel bioTestCase = (TestCaseNewBioModel) testCase;
//
if (bioModelHashMap.get(bioTestCase.getBioModelInfo().getVersion().getVersionKey()) == null) {
pp.setMessage("Getting BM " + testCase.getVersion().getName());
BioModel bioModel = getRequestManager().getDocumentManager().getBioModel(bioTestCase.getBioModelInfo().getVersion().getVersionKey());
if (!bioModel.getVersion().getOwner().equals(getRequestManager().getDocumentManager().getUser())) {
throw new Exception("BioModel does not belong to VCELLTESTACCOUNT, cannot proceed with test!");
}
//
// if biomodel already exists in same testsuite, then use this BioModel edition
//
BioModel newBioModel = null;
if (existingTestCases != null) {
for (int j = 0; newBioModel == null && j < existingTestCases.length; j++) {
if (existingTestCases[j] instanceof TestCaseNewBioModel) {
TestCaseNewBioModel existingTestCaseBioModel = (TestCaseNewBioModel) existingTestCases[j];
//
if (existingTestCaseBioModel.getBioModelInfo().getVersion().getBranchID().equals(bioTestCase.getBioModelInfo().getVersion().getBranchID())) {
//
if (existingTestCaseBioModel.getBioModelInfo().getVersion().getVersionKey().equals(bioTestCase.getBioModelInfo().getVersion().getVersionKey())) {
//
// same, store this "unchanged" in bioModelHashMap
//
newBioModel = bioModel;
} else {
//
throw new Exception("can't add new test case using (" + bioTestCase.getBioModelInfo().getVersion().getName() + " " + bioTestCase.getBioModelInfo().getVersion().getDate() + ")\n" + "a test case already exists with different edition of same BioModel dated " + existingTestCaseBioModel.getBioModelInfo().getVersion().getDate());
}
}
}
}
}
if (newBioModel == null) {
pp.setMessage("Saving BM " + testCase.getVersion().getName());
//
// some older models have membrane voltage variable names which are not unique
// (e.g. membranes 'pm' and 'nm' both have membrane voltage variables named 'Voltage_Membrane0')
//
// if this is the case, we will try to repair the conflict (for math testing purposes only) by renaming the voltage variables to their default values.
//
// Ordinarily, the conflict will be identified as an "Error" issue and the user will be prompted to repair before saving or math generation.
//
bioModel.refreshDependencies();
boolean bFoundIdentifierConflictUponLoading = hasDuplicateIdentifiers(bioModel);
if (bFoundIdentifierConflictUponLoading) {
//
// look for two MembraneVoltage instances with same variable name, rename all
//
HashSet<String> membraneVoltageVarNames = new HashSet<String>();
ArrayList<MembraneVoltage> membraneVoltageVars = new ArrayList<MembraneVoltage>();
for (Structure struct : bioModel.getModel().getStructures()) {
if (struct instanceof Membrane) {
MembraneVoltage membraneVoltage = ((Membrane) struct).getMembraneVoltage();
if (membraneVoltage != null) {
membraneVoltageVars.add(membraneVoltage);
membraneVoltageVarNames.add(membraneVoltage.getName());
}
}
}
if (membraneVoltageVars.size() != membraneVoltageVarNames.size()) {
// rename them all to the default names
for (MembraneVoltage memVoltage : membraneVoltageVars) {
memVoltage.setName(Membrane.getDefaultMembraneVoltageName(memVoltage.getMembrane().getName()));
}
}
}
SimulationContext[] simContexts = bioModel.getSimulationContexts();
for (int j = 0; j < simContexts.length; j++) {
simContexts[j].clearVersion();
GeometrySurfaceDescription gsd = simContexts[j].getGeometry().getGeometrySurfaceDescription();
if (gsd != null) {
GeometricRegion[] grArr = gsd.getGeometricRegions();
if (grArr == null) {
gsd.updateAll();
}
}
MathMapping mathMapping = simContexts[j].createNewMathMapping();
// for older models that do not have absolute compartment sizes set, but have relative sizes (SVR/VF); or if there is only one compartment with size not set,
// compute absolute compartment sizes using relative sizes and assuming a default value of '1' for one of the compartments.
// Otherwise, the math generation will fail, since for the relaxed topology (VCell 5.3 and later) absolute compartment sizes are required.
GeometryContext gc = simContexts[j].getGeometryContext();
if (simContexts[j].getGeometry().getDimension() == 0 && ((gc.isAllSizeSpecifiedNull() && !gc.isAllVolFracAndSurfVolSpecifiedNull()) || (gc.getModel().getStructures().length == 1 && gc.isAllSizeSpecifiedNull()))) {
// choose the first structure in model and set its size to '1'.
Structure struct = simContexts[j].getModel().getStructure(0);
double structSize = 1.0;
StructureSizeSolver.updateAbsoluteStructureSizes(simContexts[j], struct, structSize, struct.getStructureSize().getUnitDefinition());
}
simContexts[j].setMathDescription(mathMapping.getMathDescription());
}
Simulation[] sims = bioModel.getSimulations();
String[] simNames = new String[sims.length];
for (int j = 0; j < sims.length; j++) {
// prevents parent simulation (from the original mathmodel) reference connection
// Otherwise it will refer to data from previous (parent) simulation.
sims[j].clearVersion();
simNames[j] = sims[j].getName();
// if(sims[j].getSolverTaskDescription().getSolverDescription().equals(SolverDescription.FiniteVolume)){
// sims[j].getSolverTaskDescription().setSolverDescription(SolverDescription.FiniteVolumeStandalone);
// }
}
newBioModel = getRequestManager().getDocumentManager().save(bioModel, simNames);
}
bioModelHashMap.put(bioTestCase.getBioModelInfo().getVersion().getVersionKey(), newBioModel);
}
}
} catch (Throwable e) {
String identifier = testCase.getVersion() != null ? "Name=" + testCase.getVersion().getName() : "TCKey=" + testCase.getTCKey();
if (lg.isInfoEnabled()) {
lg.info(identifier, e);
}
errors.append("Error collecting BioModel for TestCase " + identifier + '\n' + e.getClass().getName() + " " + e.getMessage() + '\n');
// remove to avoid further processing attempts
iter.remove();
}
}
// }
// then process each BioModelTestCase individually
// if(bioModelHashMap != null){
pcounter = 0;
for (TestCaseNew testCase : testCases) {
pp.setProgress(Math.max(1, ((int) ((pcounter++ / (double) (testCases.size() * 3)) * 100))));
pp.setMessage("Checking " + testCase.getVersion().getName());
try {
AddTestCasesOP testCaseOP = null;
if (testCase instanceof TestCaseNewBioModel) {
pp.setMessage("Processing BM " + testCase.getVersion().getName());
TestCaseNewBioModel bioTestCase = (TestCaseNewBioModel) testCase;
BioModel newBioModel = (BioModel) bioModelHashMap.get(bioTestCase.getBioModelInfo().getVersion().getVersionKey());
if (newBioModel == null) {
throw new Exception("BioModel not found");
}
SimulationContext simContext = null;
for (int j = 0; j < newBioModel.getSimulationContexts().length; j++) {
if (newBioModel.getSimulationContext(j).getName().equals(bioTestCase.getSimContextName())) {
simContext = newBioModel.getSimulationContext(j);
}
}
Simulation[] newSimulations = simContext.getSimulations();
AddTestCriteriaOPBioModel[] testCriteriaOPs = new AddTestCriteriaOPBioModel[newSimulations.length];
for (int j = 0; j < newSimulations.length; j++) {
TestCriteriaNewBioModel tcritOrigForSimName = null;
for (int k = 0; bioTestCase.getTestCriterias() != null && k < bioTestCase.getTestCriterias().length; k += 1) {
if (bioTestCase.getTestCriterias()[k].getSimInfo().getName().equals(newSimulations[j].getName())) {
tcritOrigForSimName = (TestCriteriaNewBioModel) bioTestCase.getTestCriterias()[k];
break;
}
}
KeyValue regressionBioModelKey = null;
KeyValue regressionBioModelSimKey = null;
if (bioTestCase.getType().equals(TestCaseNew.REGRESSION)) {
if (regrRefFlag == TestingFrameworkWindowManager.COPY_REGRREF) {
regressionBioModelKey = (tcritOrigForSimName != null && tcritOrigForSimName.getRegressionBioModelInfo() != null ? tcritOrigForSimName.getRegressionBioModelInfo().getVersion().getVersionKey() : null);
regressionBioModelSimKey = (tcritOrigForSimName != null && tcritOrigForSimName.getRegressionSimInfo() != null ? tcritOrigForSimName.getRegressionSimInfo().getVersion().getVersionKey() : null);
} else if (regrRefFlag == TestingFrameworkWindowManager.ASSIGNORIGINAL_REGRREF) {
regressionBioModelKey = (tcritOrigForSimName != null ? bioTestCase.getBioModelInfo().getVersion().getVersionKey() : null);
regressionBioModelSimKey = (tcritOrigForSimName != null ? tcritOrigForSimName.getSimInfo().getVersion().getVersionKey() : null);
} else if (regrRefFlag == TestingFrameworkWindowManager.ASSIGNNEW_REGRREF) {
regressionBioModelKey = newBioModel.getVersion().getVersionKey();
regressionBioModelSimKey = newSimulations[j].getVersion().getVersionKey();
} else {
throw new IllegalArgumentException(this.getClass().getName() + ".addTestCases(...) BIOMODEL Unknown Regression Operation Flag");
}
}
testCriteriaOPs[j] = new AddTestCriteriaOPBioModel(testCase.getTCKey(), newSimulations[j].getVersion().getVersionKey(), regressionBioModelKey, regressionBioModelSimKey, (tcritOrigForSimName != null ? tcritOrigForSimName.getMaxAbsError() : new Double(1e-16)), (tcritOrigForSimName != null ? tcritOrigForSimName.getMaxRelError() : new Double(1e-9)), null);
}
testCaseOP = new AddTestCasesOPBioModel(new BigDecimal(tsInfo.getTSKey().toString()), newBioModel.getVersion().getVersionKey(), simContext.getKey(), bioTestCase.getType(), bioTestCase.getAnnotation(), testCriteriaOPs);
getRequestManager().getDocumentManager().doTestSuiteOP(testCaseOP);
}
} catch (Throwable e) {
errors.append("Error processing Biomodel for TestCase " + (testCase.getVersion() != null ? "Name=" + testCase.getVersion().getName() : "TCKey=" + testCase.getTCKey()) + "\n" + e.getClass().getName() + " " + e.getMessage() + "\n");
}
}
// }
// Process MathModels
pcounter = 0;
for (TestCaseNew testCase : testCases) {
pp.setProgress(Math.max(1, ((int) ((pcounter++ / (double) (testCases.size() * 3)) * 100))));
pp.setMessage("Checking " + testCase.getVersion().getName());
try {
AddTestCasesOP testCaseOP = null;
if (testCase instanceof TestCaseNewMathModel) {
TestCaseNewMathModel mathTestCase = (TestCaseNewMathModel) testCase;
pp.setMessage("Getting MathModel " + testCase.getVersion().getName());
MathModel mathModel = getRequestManager().getDocumentManager().getMathModel(mathTestCase.getMathModelInfo().getVersion().getVersionKey());
if (!mathModel.getVersion().getOwner().equals(getRequestManager().getDocumentManager().getUser())) {
throw new Exception("MathModel does not belong to VCELLTESTACCOUNT, cannot proceed with test!");
}
Simulation[] sims = mathModel.getSimulations();
String[] simNames = new String[sims.length];
for (int j = 0; j < sims.length; j++) {
// prevents parent simulation (from the original mathmodel) reference connection
// Otherwise it will refer to data from previous (parent) simulation.
sims[j].clearVersion();
simNames[j] = sims[j].getName();
// if(sims[j].getSolverTaskDescription().getSolverDescription().equals(SolverDescription.FiniteVolume)){
// sims[j].getSolverTaskDescription().setSolverDescription(SolverDescription.FiniteVolumeStandalone);
// }
}
pp.setMessage("Saving MathModel " + testCase.getVersion().getName());
MathModel newMathModel = getRequestManager().getDocumentManager().save(mathModel, simNames);
Simulation[] newSimulations = newMathModel.getSimulations();
AddTestCriteriaOPMathModel[] testCriteriaOPs = new AddTestCriteriaOPMathModel[newSimulations.length];
for (int j = 0; j < newSimulations.length; j++) {
TestCriteriaNewMathModel tcritOrigForSimName = null;
for (int k = 0; mathTestCase.getTestCriterias() != null && k < mathTestCase.getTestCriterias().length; k += 1) {
if (mathTestCase.getTestCriterias()[k].getSimInfo().getName().equals(newSimulations[j].getName())) {
tcritOrigForSimName = (TestCriteriaNewMathModel) mathTestCase.getTestCriterias()[k];
break;
}
}
KeyValue regressionMathModelKey = null;
KeyValue regressionMathModelSimKey = null;
if (mathTestCase.getType().equals(TestCaseNew.REGRESSION)) {
if (regrRefFlag == TestingFrameworkWindowManager.COPY_REGRREF) {
regressionMathModelKey = (tcritOrigForSimName != null && tcritOrigForSimName.getRegressionMathModelInfo() != null ? tcritOrigForSimName.getRegressionMathModelInfo().getVersion().getVersionKey() : null);
regressionMathModelSimKey = (tcritOrigForSimName != null && tcritOrigForSimName.getRegressionSimInfo() != null ? tcritOrigForSimName.getRegressionSimInfo().getVersion().getVersionKey() : null);
} else if (regrRefFlag == TestingFrameworkWindowManager.ASSIGNORIGINAL_REGRREF) {
regressionMathModelKey = (tcritOrigForSimName != null ? mathTestCase.getMathModelInfo().getVersion().getVersionKey() : null);
regressionMathModelSimKey = (tcritOrigForSimName != null ? tcritOrigForSimName.getSimInfo().getVersion().getVersionKey() : null);
} else if (regrRefFlag == TestingFrameworkWindowManager.ASSIGNNEW_REGRREF) {
regressionMathModelKey = newMathModel.getVersion().getVersionKey();
regressionMathModelSimKey = newSimulations[j].getVersion().getVersionKey();
} else {
throw new IllegalArgumentException(this.getClass().getName() + ".addTestCases(...) MATHMODEL Unknown Regression Operation Flag");
}
}
testCriteriaOPs[j] = new AddTestCriteriaOPMathModel(testCase.getTCKey(), newSimulations[j].getVersion().getVersionKey(), regressionMathModelKey, regressionMathModelSimKey, (tcritOrigForSimName != null ? tcritOrigForSimName.getMaxAbsError() : new Double(1e-16)), (tcritOrigForSimName != null ? tcritOrigForSimName.getMaxRelError() : new Double(1e-9)), null);
}
testCaseOP = new AddTestCasesOPMathModel(new BigDecimal(tsInfo.getTSKey().toString()), newMathModel.getVersion().getVersionKey(), mathTestCase.getType(), mathTestCase.getAnnotation(), testCriteriaOPs);
getRequestManager().getDocumentManager().doTestSuiteOP(testCaseOP);
}
} catch (Throwable e) {
errors.append("Error processing MathModel for TestCase " + (testCase.getVersion() != null ? "Name=" + testCase.getVersion().getName() : "TCKey=" + testCase.getTCKey()) + "\n" + e.getClass().getName() + " " + e.getMessage() + "\n");
}
}
}
if (errors.length() > 0) {
return errors.toString();
}
return null;
}
Also used :
AddTestCriteriaOPBioModel(cbit.vcell.numericstest.AddTestCriteriaOPBioModel)
AddTestCasesOPBioModel(cbit.vcell.numericstest.AddTestCasesOPBioModel)
ArrayList(java.util.ArrayList)
TestCriteriaNewMathModel(cbit.vcell.numericstest.TestCriteriaNewMathModel)
GeometryContext(cbit.vcell.mapping.GeometryContext)
HashSet(java.util.HashSet)
TestSuiteNew(cbit.vcell.numericstest.TestSuiteNew)
TestCaseNew(cbit.vcell.numericstest.TestCaseNew)
GeometricRegion(cbit.vcell.geometry.surface.GeometricRegion)
AddTestCriteriaOPMathModel(cbit.vcell.numericstest.AddTestCriteriaOPMathModel)
MathMapping(cbit.vcell.mapping.MathMapping)
MathModel(cbit.vcell.mathmodel.MathModel)
AddTestCasesOPMathModel(cbit.vcell.numericstest.AddTestCasesOPMathModel)
TestCaseNewMathModel(cbit.vcell.numericstest.TestCaseNewMathModel)
TestCriteriaNewMathModel(cbit.vcell.numericstest.TestCriteriaNewMathModel)
EditTestCriteriaOPMathModel(cbit.vcell.numericstest.EditTestCriteriaOPMathModel)
AddTestCriteriaOPMathModel(cbit.vcell.numericstest.AddTestCriteriaOPMathModel)
KeyValue(org.vcell.util.document.KeyValue)
GeometrySurfaceDescription(cbit.vcell.geometry.surface.GeometrySurfaceDescription)
TestCriteriaNewBioModel(cbit.vcell.numericstest.TestCriteriaNewBioModel)
AddTestCasesOP(cbit.vcell.numericstest.AddTestCasesOP)
TestCaseNewBioModel(cbit.vcell.numericstest.TestCaseNewBioModel)
AddTestCasesOPMathModel(cbit.vcell.numericstest.AddTestCasesOPMathModel)
Membrane(cbit.vcell.model.Membrane)
Structure(cbit.vcell.model.Structure)
SimulationContext(cbit.vcell.mapping.SimulationContext)
ObjectNotFoundException(org.vcell.util.ObjectNotFoundException)
DataAccessException(org.vcell.util.DataAccessException)
UserCancelException(org.vcell.util.UserCancelException)
BigDecimal(java.math.BigDecimal)
Simulation(cbit.vcell.solver.Simulation)
MembraneVoltage(cbit.vcell.model.Membrane.MembraneVoltage)
TestCaseNewBioModel(cbit.vcell.numericstest.TestCaseNewBioModel)
TestCriteriaNewBioModel(cbit.vcell.numericstest.TestCriteriaNewBioModel)
AddTestCasesOPBioModel(cbit.vcell.numericstest.AddTestCasesOPBioModel)
BioModel(cbit.vcell.biomodel.BioModel)
EditTestCriteriaOPBioModel(cbit.vcell.numericstest.EditTestCriteriaOPBioModel)
AddTestCriteriaOPBioModel(cbit.vcell.numericstest.AddTestCriteriaOPBioModel)
TestCaseNewMathModel(cbit.vcell.numericstest.TestCaseNewMathModel)
Aggregations
MathMapping (cbit.vcell.mapping.MathMapping)21
SimulationContext (cbit.vcell.mapping.SimulationContext)16
MathDescription (cbit.vcell.math.MathDescription)13
BioModel (cbit.vcell.biomodel.BioModel)12
Expression (cbit.vcell.parser.Expression)10
Simulation (cbit.vcell.solver.Simulation)10
Model (cbit.vcell.model.Model)8
KeyValue (org.vcell.util.document.KeyValue)8
TimeBounds (cbit.vcell.solver.TimeBounds)7
UniformOutputTimeSpec (cbit.vcell.solver.UniformOutputTimeSpec)7
Geometry (cbit.vcell.geometry.Geometry)6
MathSymbolMapping (cbit.vcell.mapping.MathSymbolMapping)6
SpeciesContextSpec (cbit.vcell.mapping.SpeciesContextSpec)6
SpeciesContext (cbit.vcell.model.SpeciesContext)6
ExpressionException (cbit.vcell.parser.ExpressionException)6
SimulationVersion (org.vcell.util.document.SimulationVersion)6
Variable (cbit.vcell.math.Variable)5
SymbolTableEntry (cbit.vcell.parser.SymbolTableEntry)5
IOException (java.io.IOException)5
ArrayList (java.util.ArrayList)5
