Example 6 with SpatialProcess
use of cbit.vcell.mapping.spatial.processes.SpatialProcess in project vcell by virtualcell.
the class BioModelParametersTableModel method propertyChange.
@Override
public void propertyChange(java.beans.PropertyChangeEvent evt) {
super.propertyChange(evt);
if (evt.getSource() instanceof EditableSymbolTableEntry) {
int changeRow = getRowIndex((EditableSymbolTableEntry) evt.getSource());
if (changeRow >= 0) {
fireTableRowsUpdated(changeRow, changeRow);
}
} else {
String propertyName = evt.getPropertyName();
if (evt.getSource() == bioModel.getModel()) {
if (propertyName.equals(Model.PROPERTY_NAME_MODEL_PARAMETERS)) {
ModelParameter[] oldValue = (ModelParameter[]) evt.getOldValue();
if (oldValue != null) {
for (EditableSymbolTableEntry parameter : oldValue) {
parameter.removePropertyChangeListener(this);
}
}
ModelParameter[] newValue = (ModelParameter[]) evt.getNewValue();
if (newValue != null) {
for (EditableSymbolTableEntry parameter : newValue) {
parameter.addPropertyChangeListener(this);
}
}
refreshData();
} else if (propertyName.equals(Model.PROPERTY_NAME_SPECIES_CONTEXTS)) {
SpeciesContext[] oldValue = (SpeciesContext[]) evt.getOldValue();
if (oldValue != null) {
for (SpeciesContext sc : oldValue) {
sc.removePropertyChangeListener(this);
}
}
SpeciesContext[] newValue = (SpeciesContext[]) evt.getNewValue();
if (newValue != null) {
for (SpeciesContext sc : newValue) {
sc.addPropertyChangeListener(this);
}
}
refreshData();
} else if (propertyName.equals(Model.PROPERTY_NAME_REACTION_STEPS)) {
ReactionStep[] oldValue = (ReactionStep[]) evt.getOldValue();
if (oldValue != null) {
for (ReactionStep reactionStep : oldValue) {
reactionStep.removePropertyChangeListener(this);
reactionStep.getKinetics().removePropertyChangeListener(this);
for (KineticsParameter kineticsEditableSymbolTableEntry : reactionStep.getKinetics().getKineticsParameters()) {
kineticsEditableSymbolTableEntry.removePropertyChangeListener(this);
}
for (ProxyParameter proxyEditableSymbolTableEntry : reactionStep.getKinetics().getProxyParameters()) {
proxyEditableSymbolTableEntry.removePropertyChangeListener(this);
}
for (UnresolvedParameter unresolvedEditableSymbolTableEntry : reactionStep.getKinetics().getUnresolvedParameters()) {
unresolvedEditableSymbolTableEntry.removePropertyChangeListener(this);
}
}
}
ReactionStep[] newValue = (ReactionStep[]) evt.getNewValue();
if (newValue != null) {
for (ReactionStep reactionStep : newValue) {
reactionStep.addPropertyChangeListener(this);
reactionStep.getKinetics().addPropertyChangeListener(this);
for (KineticsParameter kineticsEditableSymbolTableEntry : reactionStep.getKinetics().getKineticsParameters()) {
kineticsEditableSymbolTableEntry.addPropertyChangeListener(this);
}
for (ProxyParameter proxyEditableSymbolTableEntry : reactionStep.getKinetics().getProxyParameters()) {
proxyEditableSymbolTableEntry.addPropertyChangeListener(this);
}
for (UnresolvedParameter unresolvedEditableSymbolTableEntry : reactionStep.getKinetics().getUnresolvedParameters()) {
unresolvedEditableSymbolTableEntry.addPropertyChangeListener(this);
}
}
}
refreshData();
} else if (evt.getPropertyName().equals(RbmModelContainer.PROPERTY_NAME_REACTION_RULE_LIST)) {
List<ReactionRule> oldValue = (List<ReactionRule>) evt.getOldValue();
if (oldValue != null) {
for (ReactionRule rs : oldValue) {
rs.removePropertyChangeListener(this);
}
}
List<ReactionRule> newValue = (List<ReactionRule>) evt.getNewValue();
if (newValue != null) {
for (ReactionRule rs : newValue) {
rs.addPropertyChangeListener(this);
}
}
refreshData();
}
} else if (evt.getSource() == bioModel) {
if (propertyName.equals(BioModel.PROPERTY_NAME_SIMULATION_CONTEXTS)) {
SimulationContext[] oldValue = (SimulationContext[]) evt.getOldValue();
for (SimulationContext simulationContext : oldValue) {
simulationContext.removePropertyChangeListener(this);
simulationContext.getGeometryContext().removePropertyChangeListener(this);
for (StructureMapping mapping : simulationContext.getGeometryContext().getStructureMappings()) {
mapping.removePropertyChangeListener(this);
for (EditableSymbolTableEntry parameter : mapping.getParameters()) {
parameter.removePropertyChangeListener(this);
}
}
simulationContext.getReactionContext().removePropertyChangeListener(this);
for (SpeciesContextSpec spec : simulationContext.getReactionContext().getSpeciesContextSpecs()) {
spec.removePropertyChangeListener(this);
for (EditableSymbolTableEntry parameter : spec.getParameters()) {
parameter.removePropertyChangeListener(this);
}
}
for (ElectricalStimulus elect : simulationContext.getElectricalStimuli()) {
elect.removePropertyChangeListener(this);
for (EditableSymbolTableEntry parameter : elect.getParameters()) {
parameter.removePropertyChangeListener(this);
}
}
for (SpatialObject spatialObject : simulationContext.getSpatialObjects()) {
spatialObject.removePropertyChangeListener(this);
}
for (SpatialProcess spatialProcess : simulationContext.getSpatialProcesses()) {
spatialProcess.removePropertyChangeListener(this);
for (LocalParameter p : spatialProcess.getParameters()) {
p.removePropertyChangeListener(this);
}
}
for (SimulationContextParameter p : simulationContext.getSimulationContextParameters()) {
p.removePropertyChangeListener(this);
}
}
SimulationContext[] newValue = (SimulationContext[]) evt.getNewValue();
for (SimulationContext simulationContext : newValue) {
simulationContext.addPropertyChangeListener(this);
simulationContext.getGeometryContext().addPropertyChangeListener(this);
for (StructureMapping mapping : simulationContext.getGeometryContext().getStructureMappings()) {
mapping.addPropertyChangeListener(this);
for (EditableSymbolTableEntry parameter : mapping.getParameters()) {
parameter.addPropertyChangeListener(this);
}
}
simulationContext.getReactionContext().addPropertyChangeListener(this);
for (SpeciesContextSpec spec : simulationContext.getReactionContext().getSpeciesContextSpecs()) {
spec.addPropertyChangeListener(this);
for (EditableSymbolTableEntry parameter : spec.getParameters()) {
parameter.addPropertyChangeListener(this);
}
}
for (ElectricalStimulus elect : simulationContext.getElectricalStimuli()) {
elect.addPropertyChangeListener(this);
for (EditableSymbolTableEntry parameter : elect.getParameters()) {
parameter.addPropertyChangeListener(this);
}
}
for (SpatialObject spatialObject : simulationContext.getSpatialObjects()) {
spatialObject.addPropertyChangeListener(this);
}
for (SpatialProcess spatialProcess : simulationContext.getSpatialProcesses()) {
spatialProcess.addPropertyChangeListener(this);
for (LocalParameter p : spatialProcess.getParameters()) {
p.addPropertyChangeListener(this);
}
}
for (SimulationContextParameter p : simulationContext.getSimulationContextParameters()) {
p.addPropertyChangeListener(this);
}
}
refreshData();
}
} else if (evt.getSource() instanceof GeometryContext && evt.getPropertyName().equals(GeometryContext.PROPERTY_STRUCTURE_MAPPINGS)) {
StructureMapping[] oldValue = (StructureMapping[]) evt.getOldValue();
if (oldValue != null) {
for (StructureMapping mapping : oldValue) {
mapping.removePropertyChangeListener(this);
for (EditableSymbolTableEntry parameter : mapping.getParameters()) {
parameter.removePropertyChangeListener(this);
}
}
}
StructureMapping[] newValue = (StructureMapping[]) evt.getNewValue();
if (newValue != null) {
for (StructureMapping mapping : newValue) {
mapping.addPropertyChangeListener(this);
for (EditableSymbolTableEntry parameter : mapping.getParameters()) {
parameter.addPropertyChangeListener(this);
}
}
}
refreshData();
} else if (evt.getSource() instanceof ReactionStep && (evt.getPropertyName().equals(ReactionStep.PROPERTY_NAME_KINETICS))) {
Kinetics oldValue = (Kinetics) evt.getOldValue();
if (oldValue != null) {
oldValue.removePropertyChangeListener(this);
for (KineticsParameter kineticsEditableSymbolTableEntry : oldValue.getKineticsParameters()) {
kineticsEditableSymbolTableEntry.removePropertyChangeListener(this);
}
for (ProxyParameter proxyEditableSymbolTableEntry : oldValue.getProxyParameters()) {
proxyEditableSymbolTableEntry.removePropertyChangeListener(this);
}
for (UnresolvedParameter unresolvedEditableSymbolTableEntry : oldValue.getUnresolvedParameters()) {
unresolvedEditableSymbolTableEntry.removePropertyChangeListener(this);
}
}
Kinetics newValue = (Kinetics) evt.getNewValue();
if (newValue != null) {
newValue.addPropertyChangeListener(this);
for (KineticsParameter kineticsEditableSymbolTableEntry : newValue.getKineticsParameters()) {
kineticsEditableSymbolTableEntry.addPropertyChangeListener(this);
}
for (ProxyParameter proxyEditableSymbolTableEntry : newValue.getProxyParameters()) {
proxyEditableSymbolTableEntry.addPropertyChangeListener(this);
}
for (UnresolvedParameter unresolvedEditableSymbolTableEntry : newValue.getUnresolvedParameters()) {
unresolvedEditableSymbolTableEntry.addPropertyChangeListener(this);
}
}
refreshData();
} else if (evt.getSource() instanceof SimulationContext && evt.getPropertyName().equals(SimulationContext.PROPERTY_NAME_SPATIALPROCESSES)) {
SpatialProcess[] oldValue = (SpatialProcess[]) evt.getOldValue();
if (oldValue != null) {
for (SpatialProcess process : oldValue) {
process.removePropertyChangeListener(this);
for (EditableSymbolTableEntry parameter : process.getParameters()) {
parameter.removePropertyChangeListener(this);
}
}
}
SpatialProcess[] newValue = (SpatialProcess[]) evt.getNewValue();
if (newValue != null) {
for (SpatialProcess process : newValue) {
process.addPropertyChangeListener(this);
for (EditableSymbolTableEntry parameter : process.getParameters()) {
parameter.addPropertyChangeListener(this);
}
}
}
refreshData();
} else if (evt.getSource() instanceof SimulationContext && evt.getPropertyName().equals(SimulationContext.PROPERTY_NAME_SPATIALOBJECTS)) {
SpatialObject[] oldValue = (SpatialObject[]) evt.getOldValue();
if (oldValue != null) {
for (SpatialObject spatialObject : oldValue) {
spatialObject.removePropertyChangeListener(this);
}
}
SpatialObject[] newValue = (SpatialObject[]) evt.getNewValue();
if (newValue != null) {
for (SpatialObject spatialObject : newValue) {
spatialObject.addPropertyChangeListener(this);
}
}
refreshData();
} else if (evt.getSource() instanceof SpatialObject && evt.getPropertyName().equals(SpatialObject.PROPERTY_NAME_QUANTITYCATEGORIESENABLED)) {
refreshData();
} else if (evt.getSource() instanceof SimulationContext && evt.getPropertyName().equals(SimulationContext.PROPERTY_NAME_SIMULATIONCONTEXTPARAMETERS)) {
SimulationContextParameter[] oldValue = (SimulationContextParameter[]) evt.getOldValue();
if (oldValue != null) {
for (SimulationContextParameter param : oldValue) {
param.removePropertyChangeListener(this);
}
}
SimulationContextParameter[] newValue = (SimulationContextParameter[]) evt.getNewValue();
if (newValue != null) {
for (SimulationContextParameter param : newValue) {
param.addPropertyChangeListener(this);
}
}
refreshData();
} else if (evt.getSource() instanceof Kinetics && (evt.getPropertyName().equals(Kinetics.PROPERTY_NAME_KINETICS_PARAMETERS))) {
EditableSymbolTableEntry[] oldValue = (EditableSymbolTableEntry[]) evt.getOldValue();
if (oldValue != null) {
for (int i = 0; i < oldValue.length; i++) {
oldValue[i].removePropertyChangeListener(this);
}
}
EditableSymbolTableEntry[] newValue = (EditableSymbolTableEntry[]) evt.getNewValue();
if (newValue != null) {
for (int i = 0; i < newValue.length; i++) {
newValue[i].addPropertyChangeListener(this);
}
}
refreshData();
// } else if(evt.getSource() instanceof ReactionRuleEmbedded) {
// ReactionRuleEmbedded reactionRule = (ReactionRuleEmbedded) evt.getSource();
// int changeRow = getRowIndex(reactionRule);
// if (changeRow >= 0) {
// fireTableRowsUpdated(changeRow, changeRow);
// }
}
}
}
Also used :
UnresolvedParameter(cbit.vcell.model.Kinetics.UnresolvedParameter)
SpeciesContext(cbit.vcell.model.SpeciesContext)
SpeciesContextSpec(cbit.vcell.mapping.SpeciesContextSpec)
StructureMapping(cbit.vcell.mapping.StructureMapping)
SpatialObject(cbit.vcell.mapping.spatial.SpatialObject)
KineticsParameter(cbit.vcell.model.Kinetics.KineticsParameter)
SpatialProcess(cbit.vcell.mapping.spatial.processes.SpatialProcess)
ArrayList(java.util.ArrayList)
List(java.util.List)
GeometryContext(cbit.vcell.mapping.GeometryContext)
ReactionRule(cbit.vcell.model.ReactionRule)
SimulationContext(cbit.vcell.mapping.SimulationContext)
SimulationContextParameter(cbit.vcell.mapping.SimulationContext.SimulationContextParameter)
LocalParameter(cbit.vcell.mapping.ParameterContext.LocalParameter)
ModelParameter(cbit.vcell.model.Model.ModelParameter)
ElectricalStimulus(cbit.vcell.mapping.ElectricalStimulus)
ProxyParameter(cbit.vcell.model.ProxyParameter)
ReactionStep(cbit.vcell.model.ReactionStep)
Kinetics(cbit.vcell.model.Kinetics)
EditableSymbolTableEntry(cbit.vcell.model.EditableSymbolTableEntry)
Example 7 with SpatialProcess
use of cbit.vcell.mapping.spatial.processes.SpatialProcess in project vcell by virtualcell.
the class SimulationContext method gatherIssues.
public void gatherIssues(IssueContext issueContext, List<Issue> issueVector, boolean bIgnoreMathDescription) {
// issueContext = issueContext.newChildContext(ContextType.SimContext, this);
if (applicationType.equals(Application.RULE_BASED_STOCHASTIC)) {
for (ReactionRuleSpec rrs : getReactionContext().getReactionRuleSpecs()) {
if (rrs.isExcluded()) {
continue;
}
ReactionRule rr = rrs.getReactionRule();
if (rr.getReactantPatterns().size() > 2) {
String message = "NFSim doesn't support more than 2 reactants within a reaction rule.";
issueVector.add(new Issue(rr, issueContext, IssueCategory.Identifiers, message, Issue.Severity.WARNING));
}
if (rr.isReversible() && rr.getProductPatterns().size() > 2) {
String message = "NFSim doesn't support more than 2 products within a reversible reaction rule.";
issueVector.add(new Issue(rr, issueContext, IssueCategory.Identifiers, message, Issue.Severity.WARNING));
}
}
for (ReactionSpec rrs : getReactionContext().getReactionSpecs()) {
if (rrs.isExcluded()) {
continue;
}
ReactionStep rs = rrs.getReactionStep();
if (rs.getNumReactants() > 2) {
String message = "NFSim doesn't support more than 2 reactants within a reaction step.";
issueVector.add(new Issue(rs, issueContext, IssueCategory.Identifiers, message, Issue.Severity.WARNING));
}
if (rs.isReversible() && rs.getNumProducts() > 2) {
String message = "NFSim doesn't support more than 2 products within a reversible reaction step.";
issueVector.add(new Issue(rs, issueContext, IssueCategory.Identifiers, message, Issue.Severity.WARNING));
}
}
// we give warning when we have plain reactions with participants with patterns;
// making rules from these may result in inconsistent interpretation for the constant rates
boolean isParticipantWithPattern = false;
for (ReactionSpec rrs : getReactionContext().getReactionSpecs()) {
if (rrs.isExcluded()) {
continue;
}
ReactionStep rs = rrs.getReactionStep();
for (Reactant r : rs.getReactants()) {
if (r.getSpeciesContext().hasSpeciesPattern()) {
isParticipantWithPattern = true;
break;
}
}
if (isParticipantWithPattern) {
break;
}
for (Product p : rs.getProducts()) {
if (p.getSpeciesContext().hasSpeciesPattern()) {
isParticipantWithPattern = true;
break;
}
}
if (isParticipantWithPattern) {
break;
}
}
if (isParticipantWithPattern) {
String message = SimulationContext.rateWarning2;
String tooltip = SimulationContext.rateWarning;
issueVector.add(new Issue(this, issueContext, IssueCategory.Identifiers, message, tooltip, Issue.Severity.WARNING));
}
for (Structure struct : getModel().getStructures()) {
String name = struct.getName();
if (!name.equals(TokenMangler.fixTokenStrict(name))) {
String msg = "'" + name + "' not legal identifier for rule-based stochastic applications, try '" + TokenMangler.fixTokenStrict(name) + "'.";
issueVector.add(new Issue(struct, issueContext, IssueCategory.Identifiers, msg, Issue.Severity.ERROR));
}
}
}
if (fieldBioEvents != null) {
for (BioEvent bioEvent : fieldBioEvents) {
bioEvent.gatherIssues(issueContext, issueVector);
}
}
if (spatialObjects != null) {
for (SpatialObject spatialObject : spatialObjects) {
spatialObject.gatherIssues(issueContext, issueVector);
}
}
if (spatialProcesses != null) {
for (SpatialProcess spatialProcess : spatialProcesses) {
spatialProcess.gatherIssues(issueContext, issueVector);
}
}
if (applicationType.equals(Application.NETWORK_DETERMINISTIC) && getModel().getRbmModelContainer().getMolecularTypeList().size() > 0) {
// we're going to use network transformer to flatten (or we already did)
if (isInsufficientIterations()) {
issueVector.add(new Issue(this, issueContext, IssueCategory.RbmNetworkConstraintsBad, IssueInsufficientIterations, Issue.Severity.WARNING));
}
if (isInsufficientMaxMolecules()) {
issueVector.add(new Issue(this, issueContext, IssueCategory.RbmNetworkConstraintsBad, IssueInsufficientMolecules, Issue.Severity.WARNING));
}
}
getReactionContext().gatherIssues(issueContext, issueVector);
getGeometryContext().gatherIssues(issueContext, issueVector);
if (fieldAnalysisTasks != null) {
for (AnalysisTask analysisTask : fieldAnalysisTasks) {
analysisTask.gatherIssues(issueContext, issueVector);
}
}
getOutputFunctionContext().gatherIssues(issueContext, issueVector);
getMicroscopeMeasurement().gatherIssues(issueContext, issueVector);
if (getMathDescription() != null && !bIgnoreMathDescription) {
getMathDescription().gatherIssues(issueContext, issueVector);
}
if (networkConstraints == null) {
// issueVector.add(new Issue(this, issueContext, IssueCategory.RbmNetworkConstraintsBad, "Network Constraints is null", Issue.Severity.ERROR));
} else {
networkConstraints.gatherIssues(issueContext, issueVector);
}
}
Also used :
Issue(org.vcell.util.Issue)
ReactionRule(cbit.vcell.model.ReactionRule)
Product(cbit.vcell.model.Product)
Reactant(cbit.vcell.model.Reactant)
SpatialObject(cbit.vcell.mapping.spatial.SpatialObject)
SpatialProcess(cbit.vcell.mapping.spatial.processes.SpatialProcess)
ReactionStep(cbit.vcell.model.ReactionStep)
AnalysisTask(cbit.vcell.modelopt.AnalysisTask)
Structure(cbit.vcell.model.Structure)
Example 8 with SpatialProcess
use of cbit.vcell.mapping.spatial.processes.SpatialProcess in project vcell by virtualcell.
the class IssueTableModel method getSourceObjectPathDescription.
private String getSourceObjectPathDescription(VCDocument vcDocument, Issue issue) {
VCAssert.assertValid(issue);
Object source = issue.getSource();
{
IssueOrigin io = BeanUtils.downcast(IssueOrigin.class, source);
if (io != null) {
return io.getDescription();
}
}
if (vcDocument instanceof BioModel) {
BioModel bioModel = (BioModel) vcDocument;
String description = "";
if (source instanceof SymbolTableEntry) {
if (source instanceof SpeciesContext) {
description = "Model / Species";
} else if (source instanceof RbmObservable) {
description = "Model / Observables";
} else {
description = ((SymbolTableEntry) source).getNameScope().getPathDescription();
}
} else if (source instanceof MolecularType) {
description = "Model / Molecules";
} else if (source instanceof ReactionStep) {
ReactionStep reactionStep = (ReactionStep) source;
description = ((ReactionNameScope) reactionStep.getNameScope()).getPathDescription();
} else if (source instanceof ReactionRule) {
ReactionRule reactionRule = (ReactionRule) source;
description = ((ReactionRuleNameScope) reactionRule.getNameScope()).getPathDescription();
} else if (source instanceof SpeciesPattern) {
// if (issue.getIssueContext().hasContextType(ContextType.SpeciesContext)){
// description = "Model / Species";
// }else if(issue.getIssueContext().hasContextType(ContextType.ReactionRule)) {
// ReactionRule thing = (ReactionRule)issue.getIssueContext().getContextObject(ContextType.ReactionRule);
// description = ((ReactionRuleNameScope)thing.getNameScope()).getPathDescription();
// }else if(issue.getIssueContext().hasContextType(ContextType.RbmObservable)) {
// description = "Model / Observables";
// } else {
System.err.println("Bad issue context for " + ((SpeciesPattern) source).toString());
description = ((SpeciesPattern) source).toString();
// }
} else if (source instanceof Structure) {
Structure structure = (Structure) source;
description = "Model / " + structure.getTypeName() + "(" + structure.getName() + ")";
} else if (source instanceof StructureMapping) {
StructureMapping structureMapping = (StructureMapping) source;
description = ((StructureMappingNameScope) structureMapping.getNameScope()).getPathDescription();
} else if (source instanceof OutputFunctionIssueSource) {
SimulationContext simulationContext = (SimulationContext) ((OutputFunctionIssueSource) source).getOutputFunctionContext().getSimulationOwner();
description = "App(" + simulationContext.getName() + ") / " + "Simulations" + " / " + "Output Functions";
} else if (source instanceof Simulation) {
Simulation simulation = (Simulation) source;
try {
SimulationContext simulationContext = bioModel.getSimulationContext(simulation);
description = "App(" + simulationContext.getName() + ") / Simulations";
} catch (ObjectNotFoundException e) {
e.printStackTrace();
description = "App(" + "unknown" + ") / Simulations";
}
} else if (source instanceof UnmappedGeometryClass) {
UnmappedGeometryClass unmappedGC = (UnmappedGeometryClass) source;
description = "App(" + unmappedGC.getSimulationContext().getName() + ") / Subdomain(" + unmappedGC.getGeometryClass().getName() + ")";
} else if (source instanceof GeometryContext) {
description = "App(" + ((GeometryContext) source).getSimulationContext().getName() + ")";
} else if (source instanceof ModelOptimizationSpec) {
description = "App(" + ((ModelOptimizationSpec) source).getSimulationContext().getName() + ") / Parameter Estimation";
} else if (source instanceof MicroscopeMeasurement) {
description = "App(" + ((MicroscopeMeasurement) source).getSimulationContext().getName() + ") / Microscope Measurements";
} else if (source instanceof SpatialObject) {
description = "App(" + ((SpatialObject) source).getSimulationContext().getName() + ") / Spatial Objects";
} else if (source instanceof SpatialProcess) {
description = "App(" + ((SpatialProcess) source).getSimulationContext().getName() + ") / Spatial Processes";
} else if (source instanceof SpeciesContextSpec) {
SpeciesContextSpec scs = (SpeciesContextSpec) source;
description = "App(" + scs.getSimulationContext().getName() + ") / Specifications / Species";
} else if (source instanceof ReactionCombo) {
ReactionCombo rc = (ReactionCombo) source;
description = "App(" + rc.getReactionContext().getSimulationContext().getName() + ") / Specifications / Reactions";
} else if (source instanceof RbmModelContainer) {
IssueCategory ic = issue.getCategory();
switch(ic) {
case RbmMolecularTypesTableBad:
description = "Model / " + MolecularType.typeName + "s";
break;
case RbmReactionRulesTableBad:
description = "Model / Reactions";
break;
case RbmObservablesTableBad:
description = "Model / Observables";
break;
case RbmNetworkConstraintsBad:
description = "Network Constrains";
break;
default:
description = "Model";
break;
}
} else if (source instanceof SimulationContext) {
SimulationContext sc = (SimulationContext) source;
IssueCategory ic = issue.getCategory();
switch(ic) {
case RbmNetworkConstraintsBad:
description = "Specifications / Network";
break;
default:
description = "Application";
break;
}
} else if (source instanceof Model) {
description = "Model";
} else if (source instanceof BioEvent) {
return "Protocols / Events";
} else if (source instanceof MathDescription) {
return "Math Description";
} else {
System.err.println("unknown source type in IssueTableModel.getSourceObjectPathDescription(): " + source.getClass());
}
return description;
} else if (vcDocument instanceof MathModel) {
if (source instanceof Geometry) {
return GuiConstants.DOCUMENT_EDITOR_FOLDERNAME_MATH_GEOMETRY;
} else if (source instanceof OutputFunctionIssueSource) {
return GuiConstants.DOCUMENT_EDITOR_FOLDERNAME_MATH_OUTPUTFUNCTIONS;
} else if (source instanceof Simulation) {
return "Simulation(" + ((Simulation) source).getName() + ")";
} else {
return GuiConstants.DOCUMENT_EDITOR_FOLDERNAME_MATH_VCML;
}
} else {
System.err.println("unknown document type in IssueTableModel.getSourceObjectPathDescription()");
return "";
}
}
Also used :
MathModel(cbit.vcell.mathmodel.MathModel)
IssueCategory(org.vcell.util.Issue.IssueCategory)
MathDescription(cbit.vcell.math.MathDescription)
IssueOrigin(org.vcell.util.Issue.IssueOrigin)
SpeciesContext(cbit.vcell.model.SpeciesContext)
SpeciesContextSpec(cbit.vcell.mapping.SpeciesContextSpec)
StructureMapping(cbit.vcell.mapping.StructureMapping)
SpeciesPattern(org.vcell.model.rbm.SpeciesPattern)
SpatialObject(cbit.vcell.mapping.spatial.SpatialObject)
SymbolTableEntry(cbit.vcell.parser.SymbolTableEntry)
OutputFunctionIssueSource(cbit.vcell.solver.OutputFunctionContext.OutputFunctionIssueSource)
RbmModelContainer(cbit.vcell.model.Model.RbmModelContainer)
ModelOptimizationSpec(cbit.vcell.modelopt.ModelOptimizationSpec)
SpatialProcess(cbit.vcell.mapping.spatial.processes.SpatialProcess)
UnmappedGeometryClass(cbit.vcell.mapping.GeometryContext.UnmappedGeometryClass)
MicroscopeMeasurement(cbit.vcell.mapping.MicroscopeMeasurement)
GeometryContext(cbit.vcell.mapping.GeometryContext)
ReactionRuleNameScope(cbit.vcell.model.ReactionRule.ReactionRuleNameScope)
Structure(cbit.vcell.model.Structure)
ReactionCombo(cbit.vcell.mapping.ReactionSpec.ReactionCombo)
ReactionRule(cbit.vcell.model.ReactionRule)
RbmObservable(cbit.vcell.model.RbmObservable)
SimulationContext(cbit.vcell.mapping.SimulationContext)
MolecularType(org.vcell.model.rbm.MolecularType)
Geometry(cbit.vcell.geometry.Geometry)
Simulation(cbit.vcell.solver.Simulation)
BioModel(cbit.vcell.biomodel.BioModel)
ReactionStep(cbit.vcell.model.ReactionStep)
ObjectNotFoundException(org.vcell.util.ObjectNotFoundException)
MathModel(cbit.vcell.mathmodel.MathModel)
Model(cbit.vcell.model.Model)
BioModel(cbit.vcell.biomodel.BioModel)
SpatialObject(cbit.vcell.mapping.spatial.SpatialObject)
BioEvent(cbit.vcell.mapping.BioEvent)
Example 9 with SpatialProcess
use of cbit.vcell.mapping.spatial.processes.SpatialProcess in project vcell by virtualcell.
the class IssueTableModel method getSourceObjectDescription.
private String getSourceObjectDescription(VCDocument vcDocument, Issue issue) {
if (vcDocument instanceof BioModel) {
Object object = issue.getSource();
{
DecoratedIssueSource dis = BeanUtils.downcast(DecoratedIssueSource.class, object);
if (dis != null) {
return dis.getSourcePath();
}
}
String description = "";
if (object instanceof SymbolTableEntry) {
description = ((SymbolTableEntry) object).getName();
} else if (object instanceof ReactionStep) {
description = ((ReactionStep) object).getName();
} else if (object instanceof ReactionRule) {
description = ((ReactionRule) object).getName();
} else if (object instanceof SpeciesPattern) {
// Object parent = issue.getIssueContext().getContextObject();
// if (parent instanceof SpeciesContext){
// description = ((SpeciesContext)parent).getName();
// }
// if (issue.getIssueContext().hasContextType(ContextType.SpeciesContext)){
// SpeciesContext thing = (SpeciesContext)issue.getIssueContext().getContextObject(ContextType.SpeciesContext);
// description = thing.getName();
// }else if(issue.getIssueContext().hasContextType(ContextType.ReactionRule)) {
// ReactionRule thing = (ReactionRule)issue.getIssueContext().getContextObject(ContextType.ReactionRule);
// description = thing.getName();
// }else if(issue.getIssueContext().hasContextType(ContextType.RbmObservable)) {
// RbmObservable thing = (RbmObservable)issue.getIssueContext().getContextObject(ContextType.RbmObservable);
// description = thing.getName();
// } else {
System.err.println("Bad issue context for " + ((SpeciesPattern) object).toString());
description = ((SpeciesPattern) object).toString();
// }
} else if (object instanceof MolecularType) {
description = ((MolecularType) object).getName();
} else if (object instanceof MolecularComponent) {
description = ((MolecularComponent) object).getName();
} else if (object instanceof ComponentStateDefinition) {
description = ((ComponentStateDefinition) object).getName();
} else if (object instanceof Structure) {
description = ((Structure) object).getName();
} else if (object instanceof SubDomain) {
description = ((SubDomain) object).getName();
} else if (object instanceof Geometry) {
description = ((Geometry) object).getName();
} else if (object instanceof StructureMapping) {
description = ((StructureMapping) object).getStructure().getName();
} else if (object instanceof OutputFunctionIssueSource) {
description = ((OutputFunctionIssueSource) object).getAnnotatedFunction().getName();
} else if (object instanceof UnmappedGeometryClass) {
description = ((UnmappedGeometryClass) object).getGeometryClass().getName();
} else if (object instanceof MicroscopeMeasurement) {
description = ((MicroscopeMeasurement) object).getName();
} else if (object instanceof SpatialObject) {
description = ((SpatialObject) object).getName();
} else if (object instanceof SpatialProcess) {
description = ((SpatialProcess) object).getName();
} else if (object instanceof GeometryContext) {
description = "Geometry";
} else if (object instanceof ModelOptimizationSpec) {
description = ((ModelOptimizationSpec) object).getParameterEstimationTask().getName();
} else if (object instanceof Simulation) {
description = ((Simulation) object).getName();
} else if (object instanceof SpeciesContextSpec) {
SpeciesContextSpec scs = (SpeciesContextSpec) object;
description = scs.getSpeciesContext().getName();
} else if (object instanceof ReactionCombo) {
ReactionSpec rs = ((ReactionCombo) object).getReactionSpec();
description = rs.getReactionStep().getName();
} else if (object instanceof RbmModelContainer) {
// RbmModelContainer mc = (RbmModelContainer)object;
description = "Rules validator";
} else if (object instanceof SimulationContext) {
SimulationContext sc = (SimulationContext) object;
description = sc.getName();
} else if (object instanceof Model) {
Model m = (Model) object;
description = m.getName();
} else if (object instanceof BioEvent) {
return ((BioEvent) object).getName() + "";
} else if (object instanceof MathDescription) {
return ((MathDescription) object).getName() + "";
} else {
System.err.println("unknown object type in IssueTableModel.getSourceObjectDescription(): " + object.getClass());
}
return description;
} else if (vcDocument instanceof MathModel) {
Object object = issue.getSource();
String description = "";
if (object instanceof Variable) {
description = ((Variable) object).getName();
} else if (object instanceof SubDomain) {
description = ((SubDomain) object).getName();
} else if (object instanceof Geometry) {
description = "Geometry";
} else if (object instanceof OutputFunctionIssueSource) {
description = ((OutputFunctionIssueSource) object).getAnnotatedFunction().getName();
} else if (object instanceof MathDescription) {
return "math";
} else if (object instanceof Simulation) {
return "Simulation " + ((Simulation) object).getName() + "";
}
return description;
} else {
System.err.println("unknown document type in IssueTableModel.getSourceObjectDescription()");
return "";
}
}
Also used :
MathModel(cbit.vcell.mathmodel.MathModel)
Variable(cbit.vcell.math.Variable)
MathDescription(cbit.vcell.math.MathDescription)
SpeciesContextSpec(cbit.vcell.mapping.SpeciesContextSpec)
StructureMapping(cbit.vcell.mapping.StructureMapping)
SpeciesPattern(org.vcell.model.rbm.SpeciesPattern)
ComponentStateDefinition(org.vcell.model.rbm.ComponentStateDefinition)
SpatialObject(cbit.vcell.mapping.spatial.SpatialObject)
SubDomain(cbit.vcell.math.SubDomain)
SymbolTableEntry(cbit.vcell.parser.SymbolTableEntry)
OutputFunctionIssueSource(cbit.vcell.solver.OutputFunctionContext.OutputFunctionIssueSource)
MolecularComponent(org.vcell.model.rbm.MolecularComponent)
RbmModelContainer(cbit.vcell.model.Model.RbmModelContainer)
SpatialProcess(cbit.vcell.mapping.spatial.processes.SpatialProcess)
ModelOptimizationSpec(cbit.vcell.modelopt.ModelOptimizationSpec)
UnmappedGeometryClass(cbit.vcell.mapping.GeometryContext.UnmappedGeometryClass)
MicroscopeMeasurement(cbit.vcell.mapping.MicroscopeMeasurement)
GeometryContext(cbit.vcell.mapping.GeometryContext)
Structure(cbit.vcell.model.Structure)
ReactionCombo(cbit.vcell.mapping.ReactionSpec.ReactionCombo)
ReactionRule(cbit.vcell.model.ReactionRule)
DecoratedIssueSource(cbit.vcell.client.desktop.DecoratedIssueSource)
ReactionSpec(cbit.vcell.mapping.ReactionSpec)
SimulationContext(cbit.vcell.mapping.SimulationContext)
MolecularType(org.vcell.model.rbm.MolecularType)
Geometry(cbit.vcell.geometry.Geometry)
Simulation(cbit.vcell.solver.Simulation)
BioModel(cbit.vcell.biomodel.BioModel)
ReactionStep(cbit.vcell.model.ReactionStep)
MathModel(cbit.vcell.mathmodel.MathModel)
Model(cbit.vcell.model.Model)
BioModel(cbit.vcell.biomodel.BioModel)
SpatialObject(cbit.vcell.mapping.spatial.SpatialObject)
BioEvent(cbit.vcell.mapping.BioEvent)
Example 10 with SpatialProcess
use of cbit.vcell.mapping.spatial.processes.SpatialProcess in project vcell by virtualcell.
the class DiffEquMathMapping method addSpatialProcesses.
private void addSpatialProcesses(VariableHash varHash, ArrayList<CompartmentSubdomainContext> compartmentSubdomainContexts, ArrayList<MembraneSubdomainContext> membraneSubdomainContexts) throws MathException, MappingException, ExpressionException {
if (simContext.getGeometry().getDimension() == 0) {
return;
}
//
for (SpatialObject spatialObject : simContext.getSpatialObjects()) {
if (spatialObject instanceof PointObject) {
PointObject pointObject = (PointObject) spatialObject;
//
// if true, have to solve for this category
//
boolean bPosition = pointObject.isQuantityCategoryEnabled(QuantityCategory.PointPosition);
boolean bVelocity = pointObject.isQuantityCategoryEnabled(QuantityCategory.PointVelocity);
boolean bDirection = pointObject.isQuantityCategoryEnabled(QuantityCategory.DirectionToPoint);
boolean bDistance = pointObject.isQuantityCategoryEnabled(QuantityCategory.PointDistanceMap);
//
// either make a point subdomain, or just define functions.
//
ArrayList<PointLocation> pointLocationProcesses = new ArrayList<PointLocation>();
ArrayList<PointKinematics> pointKinematicsProcesses = new ArrayList<PointKinematics>();
for (SpatialProcess spatialProcess : simContext.getSpatialProcesses()) {
if (spatialProcess instanceof PointLocation && ((PointLocation) spatialProcess).getPointObject() == pointObject) {
pointLocationProcesses.add((PointLocation) spatialProcess);
}
if (spatialProcess instanceof PointKinematics && ((PointKinematics) spatialProcess).getPointObject() == pointObject) {
pointKinematicsProcesses.add((PointKinematics) spatialProcess);
}
}
if (pointLocationProcesses.size() == 1 && pointKinematicsProcesses.size() == 0 && !bVelocity) {
GeometryClass gc = null;
PointLocation pointLocation = pointLocationProcesses.get(0);
if (bPosition) {
if (simContext.getGeometry().getDimension() == 1) {
SpatialQuantity posXQuantity = pointObject.getSpatialQuantity(QuantityCategory.PointPosition, QuantityComponent.X);
LocalParameter posXParam = pointLocation.getParameter(SpatialProcessParameterType.PointPositionX);
varHash.addVariable(newFunctionOrConstant(getMathSymbol(posXParam, gc), getIdentifierSubstitutions(posXParam.getExpression(), posXParam.getUnitDefinition(), gc), gc));
Expression posXExp = new Expression(posXParam, pointLocation.getNameScope());
Expression xExp = new Expression(simContext.getModel().getReservedSymbolByRole(ReservedSymbolRole.X), simContext.getModel().getNameScope());
varHash.addVariable(newFunctionOrConstant(getMathSymbol(posXQuantity, gc), getIdentifierSubstitutions(posXExp, posXQuantity.getUnitDefinition(), gc), gc));
Expression posX_minus_X = Expression.add(posXExp, Expression.negate(xExp));
Expression signum_posX_minus_X = Expression.function(FunctionType.MIN, new Expression(1.0), Expression.function(FunctionType.MAX, Expression.mult(new Expression(1e10), posX_minus_X), new Expression(-1)));
if (bDirection) {
SpatialQuantity dirXQuantity = pointObject.getSpatialQuantity(QuantityCategory.DirectionToPoint, QuantityComponent.X);
varHash.addVariable(newFunctionOrConstant(getMathSymbol(dirXQuantity, gc), getIdentifierSubstitutions(signum_posX_minus_X, dirXQuantity.getUnitDefinition(), gc), gc));
}
if (bDistance) {
Expression abs_X_minux_posX = Expression.function(FunctionType.ABS, posX_minus_X);
SpatialQuantity distanceQuantity = pointObject.getSpatialQuantity(QuantityCategory.PointDistanceMap, QuantityComponent.Scalar);
varHash.addVariable(newFunctionOrConstant(getMathSymbol(distanceQuantity, gc), getIdentifierSubstitutions(abs_X_minux_posX, distanceQuantity.getUnitDefinition(), gc), gc));
}
}
if (simContext.getGeometry().getDimension() == 2) {
SpatialQuantity posXQuantity = pointObject.getSpatialQuantity(QuantityCategory.PointPosition, QuantityComponent.X);
LocalParameter posXParam = pointLocation.getParameter(SpatialProcessParameterType.PointPositionX);
varHash.addVariable(newFunctionOrConstant(getMathSymbol(posXParam, gc), getIdentifierSubstitutions(posXParam.getExpression(), posXParam.getUnitDefinition(), gc), gc));
Expression posXExp = new Expression(posXParam, pointLocation.getNameScope());
Expression xExp = new Expression(simContext.getModel().getReservedSymbolByRole(ReservedSymbolRole.X), simContext.getModel().getNameScope());
varHash.addVariable(newFunctionOrConstant(getMathSymbol(posXQuantity, gc), getIdentifierSubstitutions(new Expression(posXParam, pointLocation.getNameScope()), posXQuantity.getUnitDefinition(), gc), gc));
SpatialQuantity posYQuantity = pointObject.getSpatialQuantity(QuantityCategory.PointPosition, QuantityComponent.Y);
LocalParameter posYParam = pointLocation.getParameter(SpatialProcessParameterType.PointPositionY);
varHash.addVariable(newFunctionOrConstant(getMathSymbol(posYParam, gc), getIdentifierSubstitutions(posYParam.getExpression(), posYParam.getUnitDefinition(), gc), gc));
Expression posYExp = new Expression(posYParam, pointLocation.getNameScope());
Expression yExp = new Expression(simContext.getModel().getReservedSymbolByRole(ReservedSymbolRole.Y), simContext.getModel().getNameScope());
varHash.addVariable(newFunctionOrConstant(getMathSymbol(posYQuantity, gc), getIdentifierSubstitutions(new Expression(posYParam, pointLocation.getNameScope()), posYQuantity.getUnitDefinition(), gc), gc));
Expression posX_minux_X = Expression.add(posXExp, Expression.negate(xExp));
Expression posY_minux_Y = Expression.add(posYExp, Expression.negate(yExp));
Expression DX2 = Expression.mult(posX_minux_X, posX_minux_X);
Expression DY2 = Expression.mult(posY_minux_Y, posY_minux_Y);
Expression sqrt_DX2_DY2 = Expression.function(FunctionType.SQRT, Expression.add(DX2, DY2));
Expression dirX = Expression.div(posX_minux_X, Expression.add(sqrt_DX2_DY2, new Expression(1e-8)));
Expression dirY = Expression.div(posY_minux_Y, Expression.add(sqrt_DX2_DY2, new Expression(1e-8)));
if (bDirection) {
SpatialQuantity dirXQuantity = pointObject.getSpatialQuantity(QuantityCategory.DirectionToPoint, QuantityComponent.X);
varHash.addVariable(newFunctionOrConstant(getMathSymbol(dirXQuantity, gc), getIdentifierSubstitutions(dirX, dirXQuantity.getUnitDefinition(), gc), gc));
SpatialQuantity dirYQuantity = pointObject.getSpatialQuantity(QuantityCategory.DirectionToPoint, QuantityComponent.Y);
varHash.addVariable(newFunctionOrConstant(getMathSymbol(dirYQuantity, gc), getIdentifierSubstitutions(dirY, dirYQuantity.getUnitDefinition(), gc), gc));
}
if (bDistance) {
SpatialQuantity distanceQuantity = pointObject.getSpatialQuantity(QuantityCategory.PointDistanceMap, QuantityComponent.Scalar);
varHash.addVariable(newFunctionOrConstant(getMathSymbol(distanceQuantity, gc), getIdentifierSubstitutions(sqrt_DX2_DY2, distanceQuantity.getUnitDefinition(), gc), gc));
}
}
if (simContext.getGeometry().getDimension() == 3) {
SpatialQuantity posXQuantity = pointObject.getSpatialQuantity(QuantityCategory.PointPosition, QuantityComponent.X);
LocalParameter posXParam = pointLocation.getParameter(SpatialProcessParameterType.PointPositionX);
varHash.addVariable(newFunctionOrConstant(getMathSymbol(posXParam, gc), getIdentifierSubstitutions(posXParam.getExpression(), posXParam.getUnitDefinition(), gc), gc));
Expression posXExp = new Expression(posXParam, pointLocation.getNameScope());
Expression xExp = new Expression(simContext.getModel().getReservedSymbolByRole(ReservedSymbolRole.X), simContext.getModel().getNameScope());
varHash.addVariable(newFunctionOrConstant(getMathSymbol(posXQuantity, gc), getIdentifierSubstitutions(new Expression(posXParam, pointLocation.getNameScope()), posXQuantity.getUnitDefinition(), gc), gc));
SpatialQuantity posYQuantity = pointObject.getSpatialQuantity(QuantityCategory.PointPosition, QuantityComponent.Y);
LocalParameter posYParam = pointLocation.getParameter(SpatialProcessParameterType.PointPositionY);
varHash.addVariable(newFunctionOrConstant(getMathSymbol(posYParam, gc), getIdentifierSubstitutions(posYParam.getExpression(), posYParam.getUnitDefinition(), gc), gc));
Expression posYExp = new Expression(posYParam, pointLocation.getNameScope());
Expression yExp = new Expression(simContext.getModel().getReservedSymbolByRole(ReservedSymbolRole.Y), simContext.getModel().getNameScope());
varHash.addVariable(newFunctionOrConstant(getMathSymbol(posYQuantity, gc), getIdentifierSubstitutions(new Expression(posYParam, pointLocation.getNameScope()), posYQuantity.getUnitDefinition(), gc), gc));
SpatialQuantity posZQuantity = pointObject.getSpatialQuantity(QuantityCategory.PointPosition, QuantityComponent.Z);
LocalParameter posZParam = pointLocation.getParameter(SpatialProcessParameterType.PointPositionZ);
varHash.addVariable(newFunctionOrConstant(getMathSymbol(posZParam, gc), getIdentifierSubstitutions(posZParam.getExpression(), posZParam.getUnitDefinition(), gc), gc));
Expression posZExp = new Expression(posZParam, pointLocation.getNameScope());
Expression zExp = new Expression(simContext.getModel().getReservedSymbolByRole(ReservedSymbolRole.Z), simContext.getModel().getNameScope());
varHash.addVariable(newFunctionOrConstant(getMathSymbol(posZQuantity, gc), getIdentifierSubstitutions(new Expression(posZParam, pointLocation.getNameScope()), posZQuantity.getUnitDefinition(), gc), gc));
Expression posX_minux_X = Expression.add(posXExp, Expression.negate(xExp));
Expression posY_minux_Y = Expression.add(posYExp, Expression.negate(yExp));
Expression posZ_minux_Z = Expression.add(posZExp, Expression.negate(zExp));
Expression DX2 = Expression.mult(posX_minux_X, posX_minux_X);
Expression DY2 = Expression.mult(posY_minux_Y, posY_minux_Y);
Expression DZ2 = Expression.mult(posZ_minux_Z, posZ_minux_Z);
Expression sqrt_DX2_DY2_DZ2 = Expression.function(FunctionType.SQRT, Expression.add(DX2, DY2, DZ2));
Expression dirX = Expression.div(posX_minux_X, Expression.add(sqrt_DX2_DY2_DZ2, new Expression(1e-8)));
Expression dirY = Expression.div(posY_minux_Y, Expression.add(sqrt_DX2_DY2_DZ2, new Expression(1e-8)));
Expression dirZ = Expression.div(posZ_minux_Z, Expression.add(sqrt_DX2_DY2_DZ2, new Expression(1e-8)));
if (bDirection) {
SpatialQuantity dirXQuantity = pointObject.getSpatialQuantity(QuantityCategory.DirectionToPoint, QuantityComponent.X);
varHash.addVariable(newFunctionOrConstant(getMathSymbol(dirXQuantity, gc), getIdentifierSubstitutions(dirX, dirXQuantity.getUnitDefinition(), gc), gc));
SpatialQuantity dirYQuantity = pointObject.getSpatialQuantity(QuantityCategory.DirectionToPoint, QuantityComponent.Y);
varHash.addVariable(newFunctionOrConstant(getMathSymbol(dirYQuantity, gc), getIdentifierSubstitutions(dirY, dirYQuantity.getUnitDefinition(), gc), gc));
SpatialQuantity dirZQuantity = pointObject.getSpatialQuantity(QuantityCategory.DirectionToPoint, QuantityComponent.Z);
varHash.addVariable(newFunctionOrConstant(getMathSymbol(dirZQuantity, gc), getIdentifierSubstitutions(dirZ, dirZQuantity.getUnitDefinition(), gc), gc));
}
if (bDistance) {
SpatialQuantity distanceQuantity = pointObject.getSpatialQuantity(QuantityCategory.PointDistanceMap, QuantityComponent.Scalar);
varHash.addVariable(newFunctionOrConstant(getMathSymbol(distanceQuantity, gc), getIdentifierSubstitutions(sqrt_DX2_DY2_DZ2, distanceQuantity.getUnitDefinition(), gc), gc));
}
}
} else {
throw new MappingException("PointLocation process defined for pointObject '" + pointObject.getName() + "' but Position not enabled");
}
} else if (pointLocationProcesses.size() == 0 && pointKinematicsProcesses.size() == 1) {
GeometryClass gc = null;
PointKinematics pointKinematics = pointKinematicsProcesses.get(0);
if (bPosition && bVelocity) {
LocalParameter velXParam = pointKinematics.getParameter(SpatialProcessParameterType.PointVelocityX);
LocalParameter iniPosXParam = pointKinematics.getParameter(SpatialProcessParameterType.PointInitialPositionX);
SpatialQuantity posXQuantity = pointObject.getSpatialQuantity(QuantityCategory.PointPosition, QuantityComponent.X);
SpatialQuantity velXQuantity = pointObject.getSpatialQuantity(QuantityCategory.PointVelocity, QuantityComponent.X);
Expression posXExp = new Expression(posXQuantity, simContext.getNameScope());
Expression xExp = new Expression(simContext.getModel().getReservedSymbolByRole(ReservedSymbolRole.X), simContext.getModel().getNameScope());
Expression posX_minux_X = Expression.add(posXExp, Expression.negate(xExp));
LocalParameter velYParam = pointKinematics.getParameter(SpatialProcessParameterType.PointVelocityY);
LocalParameter iniPosYParam = pointKinematics.getParameter(SpatialProcessParameterType.PointInitialPositionY);
SpatialQuantity posYQuantity = pointObject.getSpatialQuantity(QuantityCategory.PointPosition, QuantityComponent.Y);
SpatialQuantity velYQuantity = pointObject.getSpatialQuantity(QuantityCategory.PointVelocity, QuantityComponent.Y);
Expression posYExp = new Expression(posYQuantity, simContext.getNameScope());
Expression yExp = new Expression(simContext.getModel().getReservedSymbolByRole(ReservedSymbolRole.Y), simContext.getModel().getNameScope());
Expression posY_minux_Y = Expression.add(posYExp, Expression.negate(yExp));
LocalParameter velZParam = pointKinematics.getParameter(SpatialProcessParameterType.PointVelocityZ);
LocalParameter iniPosZParam = pointKinematics.getParameter(SpatialProcessParameterType.PointInitialPositionZ);
SpatialQuantity posZQuantity = pointObject.getSpatialQuantity(QuantityCategory.PointPosition, QuantityComponent.Z);
SpatialQuantity velZQuantity = pointObject.getSpatialQuantity(QuantityCategory.PointVelocity, QuantityComponent.Z);
Expression posZExp = new Expression(posZQuantity, simContext.getNameScope());
Expression zExp = new Expression(simContext.getModel().getReservedSymbolByRole(ReservedSymbolRole.Z), simContext.getModel().getNameScope());
Expression posZ_minux_Z = Expression.add(posZExp, Expression.negate(zExp));
String pointSubdomainName = pointObject.getName();
Domain domain = new Domain(pointSubdomainName);
PointSubDomain pointSubdomain = new PointSubDomain(pointSubdomainName);
mathDesc.addSubDomain(pointSubdomain);
if (simContext.getGeometry().getDimension() >= 1) {
PointVariable posXVar = new PointVariable(getMathSymbol(posXQuantity, gc), domain);
varHash.addVariable(posXVar);
Expression initXExp = getIdentifierSubstitutions(new Expression(iniPosXParam, pointKinematics.getNameScope()), iniPosXParam.getUnitDefinition(), gc);
Expression rateXExp = getIdentifierSubstitutions(new Expression(velXParam, pointKinematics.getNameScope()), velXParam.getUnitDefinition(), gc);
OdeEquation odeX = new OdeEquation(posXVar, initXExp, rateXExp);
pointSubdomain.addEquation(odeX);
varHash.addVariable(newFunctionOrConstant(getMathSymbol(iniPosXParam, gc), getIdentifierSubstitutions(new Expression(iniPosXParam.getExpression()), iniPosXParam.getUnitDefinition(), gc), gc));
varHash.addVariable(newFunctionOrConstant(getMathSymbol(velXParam, gc), getIdentifierSubstitutions(new Expression(velXParam.getExpression()), velXParam.getUnitDefinition(), gc), gc));
varHash.addVariable(newFunctionOrConstant(getMathSymbol(velXQuantity, gc), getIdentifierSubstitutions(new Expression(velXParam, pointKinematics.getNameScope()), velXQuantity.getUnitDefinition(), gc), gc));
pointSubdomain.setPositionX(getIdentifierSubstitutions(new Expression(posXQuantity, simContext.getNameScope()), posXQuantity.getUnitDefinition(), gc));
}
if (simContext.getGeometry().getDimension() >= 2) {
PointVariable posYVar = new PointVariable(getMathSymbol(posYQuantity, gc), domain);
varHash.addVariable(posYVar);
Expression initYExp = getIdentifierSubstitutions(new Expression(iniPosYParam, pointKinematics.getNameScope()), iniPosYParam.getUnitDefinition(), gc);
Expression rateYExp = getIdentifierSubstitutions(new Expression(velYParam, pointKinematics.getNameScope()), velYParam.getUnitDefinition(), gc);
OdeEquation odeY = new OdeEquation(posYVar, initYExp, rateYExp);
pointSubdomain.addEquation(odeY);
varHash.addVariable(newFunctionOrConstant(getMathSymbol(iniPosYParam, gc), getIdentifierSubstitutions(new Expression(iniPosYParam.getExpression()), iniPosYParam.getUnitDefinition(), gc), gc));
varHash.addVariable(newFunctionOrConstant(getMathSymbol(velYParam, gc), getIdentifierSubstitutions(new Expression(velYParam.getExpression()), velYParam.getUnitDefinition(), gc), gc));
varHash.addVariable(newFunctionOrConstant(getMathSymbol(velYQuantity, gc), getIdentifierSubstitutions(new Expression(velYParam, pointKinematics.getNameScope()), velYQuantity.getUnitDefinition(), gc), gc));
pointSubdomain.setPositionY(getIdentifierSubstitutions(new Expression(posYQuantity, simContext.getNameScope()), posYQuantity.getUnitDefinition(), gc));
}
if (simContext.getGeometry().getDimension() == 3) {
PointVariable posZVar = new PointVariable(getMathSymbol(posZQuantity, gc), domain);
varHash.addVariable(posZVar);
Expression initZExp = getIdentifierSubstitutions(new Expression(iniPosZParam, pointKinematics.getNameScope()), iniPosZParam.getUnitDefinition(), gc);
Expression rateZExp = getIdentifierSubstitutions(new Expression(velZParam, pointKinematics.getNameScope()), velZParam.getUnitDefinition(), gc);
OdeEquation odeZ = new OdeEquation(posZVar, initZExp, rateZExp);
pointSubdomain.addEquation(odeZ);
varHash.addVariable(newFunctionOrConstant(getMathSymbol(iniPosZParam, gc), getIdentifierSubstitutions(new Expression(iniPosZParam.getExpression()), iniPosZParam.getUnitDefinition(), gc), gc));
varHash.addVariable(newFunctionOrConstant(getMathSymbol(velZParam, gc), getIdentifierSubstitutions(new Expression(velZParam.getExpression()), velZParam.getUnitDefinition(), gc), gc));
varHash.addVariable(newFunctionOrConstant(getMathSymbol(velZQuantity, gc), getIdentifierSubstitutions(new Expression(velZParam, pointKinematics.getNameScope()), velZQuantity.getUnitDefinition(), gc), gc));
pointSubdomain.setPositionZ(getIdentifierSubstitutions(new Expression(posZQuantity, simContext.getNameScope()), posZQuantity.getUnitDefinition(), gc));
}
if (simContext.getGeometry().getDimension() == 1) {
Expression signum_posX_minus_X = Expression.function(FunctionType.MIN, new Expression(1.0), Expression.function(FunctionType.MAX, Expression.mult(new Expression(1e10), posX_minux_X), new Expression(-1)));
if (bDirection) {
SpatialQuantity dirXQuantity = pointObject.getSpatialQuantity(QuantityCategory.DirectionToPoint, QuantityComponent.X);
varHash.addVariable(newFunctionOrConstant(getMathSymbol(dirXQuantity, gc), getIdentifierSubstitutions(signum_posX_minus_X, dirXQuantity.getUnitDefinition(), gc), gc));
}
if (bDistance) {
Expression abs_X_minux_posX = Expression.function(FunctionType.ABS, posX_minux_X);
SpatialQuantity distanceQuantity = pointObject.getSpatialQuantity(QuantityCategory.PointDistanceMap, QuantityComponent.Scalar);
varHash.addVariable(newFunctionOrConstant(getMathSymbol(distanceQuantity, gc), getIdentifierSubstitutions(abs_X_minux_posX, distanceQuantity.getUnitDefinition(), gc), gc));
}
}
if (simContext.getGeometry().getDimension() == 2) {
Expression DX2 = Expression.mult(posX_minux_X, posX_minux_X);
Expression DY2 = Expression.mult(posY_minux_Y, posY_minux_Y);
Expression sqrt_DX2_DY2 = Expression.function(FunctionType.SQRT, Expression.add(DX2, DY2));
Expression dirX = Expression.div(posX_minux_X, Expression.add(sqrt_DX2_DY2, new Expression(1e-8)));
Expression dirY = Expression.div(posY_minux_Y, Expression.add(sqrt_DX2_DY2, new Expression(1e-8)));
if (bDirection) {
SpatialQuantity dirXQuantity = pointObject.getSpatialQuantity(QuantityCategory.DirectionToPoint, QuantityComponent.X);
varHash.addVariable(newFunctionOrConstant(getMathSymbol(dirXQuantity, gc), getIdentifierSubstitutions(dirX, dirXQuantity.getUnitDefinition(), gc), gc));
SpatialQuantity dirYQuantity = pointObject.getSpatialQuantity(QuantityCategory.DirectionToPoint, QuantityComponent.Y);
varHash.addVariable(newFunctionOrConstant(getMathSymbol(dirYQuantity, gc), getIdentifierSubstitutions(dirY, dirYQuantity.getUnitDefinition(), gc), gc));
}
if (bDistance) {
SpatialQuantity distanceQuantity = pointObject.getSpatialQuantity(QuantityCategory.PointDistanceMap, QuantityComponent.Scalar);
varHash.addVariable(newFunctionOrConstant(getMathSymbol(distanceQuantity, gc), getIdentifierSubstitutions(sqrt_DX2_DY2, distanceQuantity.getUnitDefinition(), gc), gc));
}
}
if (simContext.getGeometry().getDimension() == 3) {
Expression DX2 = Expression.mult(posX_minux_X, posX_minux_X);
Expression DY2 = Expression.mult(posY_minux_Y, posY_minux_Y);
Expression DZ2 = Expression.mult(posZ_minux_Z, posZ_minux_Z);
Expression sqrt_DX2_DY2_DZ2 = Expression.function(FunctionType.SQRT, Expression.add(DX2, DY2, DZ2));
Expression dirX = Expression.div(posX_minux_X, Expression.add(sqrt_DX2_DY2_DZ2, new Expression(1e-8)));
Expression dirY = Expression.div(posY_minux_Y, Expression.add(sqrt_DX2_DY2_DZ2, new Expression(1e-8)));
Expression dirZ = Expression.div(posZ_minux_Z, Expression.add(sqrt_DX2_DY2_DZ2, new Expression(1e-8)));
if (bDirection) {
SpatialQuantity dirXQuantity = pointObject.getSpatialQuantity(QuantityCategory.DirectionToPoint, QuantityComponent.X);
varHash.addVariable(newFunctionOrConstant(getMathSymbol(dirXQuantity, gc), getIdentifierSubstitutions(dirX, dirXQuantity.getUnitDefinition(), gc), gc));
SpatialQuantity dirYQuantity = pointObject.getSpatialQuantity(QuantityCategory.DirectionToPoint, QuantityComponent.Y);
varHash.addVariable(newFunctionOrConstant(getMathSymbol(dirYQuantity, gc), getIdentifierSubstitutions(dirY, dirYQuantity.getUnitDefinition(), gc), gc));
SpatialQuantity dirZQuantity = pointObject.getSpatialQuantity(QuantityCategory.DirectionToPoint, QuantityComponent.Z);
varHash.addVariable(newFunctionOrConstant(getMathSymbol(dirZQuantity, gc), getIdentifierSubstitutions(dirZ, dirZQuantity.getUnitDefinition(), gc), gc));
}
if (bDistance) {
SpatialQuantity distanceQuantity = pointObject.getSpatialQuantity(QuantityCategory.PointDistanceMap, QuantityComponent.Scalar);
varHash.addVariable(newFunctionOrConstant(getMathSymbol(distanceQuantity, gc), getIdentifierSubstitutions(sqrt_DX2_DY2_DZ2, distanceQuantity.getUnitDefinition(), gc), gc));
}
}
} else {
throw new MappingException(pointKinematics.getDescription() + " process defined for pointObject '" + pointObject.getName() + "' but Position and Velocity not enabled");
}
} else {
throw new MappingException("expecting 1 location or kinematics process for point '" + pointObject.getName() + "'");
}
} else if (spatialObject instanceof SurfaceRegionObject) {
SurfaceRegionObject surfaceRegionObject = (SurfaceRegionObject) spatialObject;
SubVolume insideSubvolume = surfaceRegionObject.getInsideSubVolume();
SubVolume outsideSubvolume = surfaceRegionObject.getOutsideSubVolume();
SurfaceClass surfaceClass = simContext.getGeometry().getGeometrySurfaceDescription().getSurfaceClass(insideSubvolume, outsideSubvolume);
MembraneSubdomainContext memSubdomainContext = null;
for (MembraneSubdomainContext context : membraneSubdomainContexts) {
if (context.surfaceClass == surfaceClass) {
memSubdomainContext = context;
}
}
//
// if true, have to solve for this category
//
boolean bNormal = surfaceRegionObject.isQuantityCategoryEnabled(QuantityCategory.Normal);
boolean bVelocity = surfaceRegionObject.isQuantityCategoryEnabled(QuantityCategory.SurfaceVelocity);
boolean bDistance = surfaceRegionObject.isQuantityCategoryEnabled(QuantityCategory.SurfaceDistanceMap);
boolean bDirection = surfaceRegionObject.isQuantityCategoryEnabled(QuantityCategory.DirectionToSurface);
boolean bSize = surfaceRegionObject.isQuantityCategoryEnabled(QuantityCategory.SurfaceSize);
if (bVelocity) {
ArrayList<SurfaceKinematics> surfaceKinematicsList = new ArrayList<SurfaceKinematics>();
for (SpatialProcess spatialProcess : simContext.getSpatialProcesses()) {
if (spatialProcess instanceof SurfaceKinematics && ((SurfaceKinematics) spatialProcess).getSurfaceRegionObject() == surfaceRegionObject) {
surfaceKinematicsList.add((SurfaceKinematics) spatialProcess);
}
}
if (surfaceKinematicsList.size() == 1) {
SurfaceKinematics surfaceKinematics = surfaceKinematicsList.get(0);
if (simContext.getGeometry().getDimension() >= 1) {
SpatialQuantity velXQuantity = surfaceRegionObject.getSpatialQuantity(QuantityCategory.SurfaceVelocity, QuantityComponent.X);
LocalParameter velXParam = surfaceKinematics.getParameter(SpatialProcessParameterType.SurfaceVelocityX);
varHash.addVariable(newFunctionOrConstant(getMathSymbol(velXParam, surfaceClass), getIdentifierSubstitutions(velXParam.getExpression(), velXParam.getUnitDefinition(), surfaceClass), surfaceClass));
Expression velXExp = new Expression(velXParam, surfaceKinematics.getNameScope());
varHash.addVariable(newFunctionOrConstant(getMathSymbol(velXQuantity, surfaceClass), getIdentifierSubstitutions(velXExp, velXQuantity.getUnitDefinition(), surfaceClass), surfaceClass));
if (bNormal) {
SpatialQuantity normXQuantity = surfaceRegionObject.getSpatialQuantity(QuantityCategory.Normal, QuantityComponent.X);
Expression normXExp = new Expression(MathFunctionDefinitions.FUNCTION_normalX);
varHash.addVariable(newFunctionOrConstant(getMathSymbol(normXQuantity, surfaceClass), getIdentifierSubstitutions(normXExp, normXQuantity.getUnitDefinition(), surfaceClass), surfaceClass));
}
}
if (simContext.getGeometry().getDimension() >= 2) {
SpatialQuantity velYQuantity = surfaceRegionObject.getSpatialQuantity(QuantityCategory.SurfaceVelocity, QuantityComponent.Y);
LocalParameter velYParam = surfaceKinematics.getParameter(SpatialProcessParameterType.SurfaceVelocityY);
varHash.addVariable(newFunctionOrConstant(getMathSymbol(velYParam, surfaceClass), getIdentifierSubstitutions(velYParam.getExpression(), velYParam.getUnitDefinition(), surfaceClass), surfaceClass));
Expression velYExp = new Expression(velYParam, surfaceKinematics.getNameScope());
varHash.addVariable(newFunctionOrConstant(getMathSymbol(velYQuantity, surfaceClass), getIdentifierSubstitutions(velYExp, velYQuantity.getUnitDefinition(), surfaceClass), surfaceClass));
if (bNormal) {
SpatialQuantity normYQuantity = surfaceRegionObject.getSpatialQuantity(QuantityCategory.Normal, QuantityComponent.Y);
Expression normYExp = new Expression(MathFunctionDefinitions.FUNCTION_normalY);
varHash.addVariable(newFunctionOrConstant(getMathSymbol(normYQuantity, surfaceClass), getIdentifierSubstitutions(normYExp, normYQuantity.getUnitDefinition(), surfaceClass), surfaceClass));
}
}
if (simContext.getGeometry().getDimension() >= 3) {
SpatialQuantity velZQuantity = surfaceRegionObject.getSpatialQuantity(QuantityCategory.SurfaceVelocity, QuantityComponent.Z);
LocalParameter velZParam = surfaceKinematics.getParameter(SpatialProcessParameterType.SurfaceVelocityZ);
varHash.addVariable(newFunctionOrConstant(getMathSymbol(velZParam, surfaceClass), getIdentifierSubstitutions(velZParam.getExpression(), velZParam.getUnitDefinition(), surfaceClass), surfaceClass));
Expression velYExp = new Expression(velZParam, surfaceKinematics.getNameScope());
varHash.addVariable(newFunctionOrConstant(getMathSymbol(velZQuantity, surfaceClass), getIdentifierSubstitutions(velYExp, velZQuantity.getUnitDefinition(), surfaceClass), surfaceClass));
if (bNormal) {
SpatialQuantity normZQuantity = surfaceRegionObject.getSpatialQuantity(QuantityCategory.Normal, QuantityComponent.Z);
// MathFunctionDefinitions.FUNCTION_normalZ);
Expression normZExp = new Expression("normalZ_not_implemented()");
varHash.addVariable(newFunctionOrConstant(getMathSymbol(normZQuantity, surfaceClass), getIdentifierSubstitutions(normZExp, normZQuantity.getUnitDefinition(), surfaceClass), surfaceClass));
}
}
} else {
throw new MappingException("expecting 1 Surface Kinematics process for Surface Object '" + surfaceRegionObject.getName() + "'");
}
}
if (bSize) {
SpatialQuantity sizeQuantity = surfaceRegionObject.getSpatialQuantity(QuantityCategory.SurfaceSize, QuantityComponent.Scalar);
String funcName = MathFunctionDefinitions.Function_regionArea_current.getFunctionName();
Expression sizeExp = Expression.function(funcName, new Expression[] { new Expression("'" + surfaceClass.getName() + "'") });
varHash.addVariable(newFunctionOrConstant(getMathSymbol(sizeQuantity, surfaceClass), getIdentifierSubstitutions(sizeExp, sizeQuantity.getUnitDefinition(), surfaceClass), surfaceClass));
}
if (bDirection) {
SpatialQuantity directionXQuantity = surfaceRegionObject.getSpatialQuantity(QuantityCategory.DirectionToSurface, QuantityComponent.X);
SpatialQuantity directionYQuantity = surfaceRegionObject.getSpatialQuantity(QuantityCategory.DirectionToSurface, QuantityComponent.Y);
SpatialQuantity directionZQuantity = surfaceRegionObject.getSpatialQuantity(QuantityCategory.DirectionToSurface, QuantityComponent.Z);
for (SubVolume adjacentSubvolume : surfaceClass.getAdjacentSubvolumes()) {
Domain domain = new Domain(adjacentSubvolume);
CompartmentSubDomain compSubdomain = mathDesc.getCompartmentSubDomain(adjacentSubvolume.getName());
if (simContext.getGeometry().getDimension() >= 1) {
String name = adjacentSubvolume.getName() + "_dirX_" + memSubdomainContext.membraneSubdomain.getName();
LocalizedDirectionToMembraneQuantity localDirectionXQuantity = addLocalizedDirectionToMembraneQuantity(name, surfaceClass, adjacentSubvolume, QuantityComponent.X);
VolVariable distanceVar = new VolVariable(getMathSymbol(localDirectionXQuantity, adjacentSubvolume), domain);
varHash.addVariable(distanceVar);
ComputeMembraneMetricEquation membraneMetricEquation = new ComputeMembraneMetricEquation(distanceVar, MembraneMetricComponent.directionToMembraneX);
membraneMetricEquation.setTargetMembraneName(memSubdomainContext.membraneSubdomain.getName());
compSubdomain.addEquation(membraneMetricEquation);
}
if (simContext.getGeometry().getDimension() >= 2) {
String name = adjacentSubvolume.getName() + "_dirY_" + memSubdomainContext.membraneSubdomain.getName();
LocalizedDirectionToMembraneQuantity localDirectionYQuantity = addLocalizedDirectionToMembraneQuantity(name, surfaceClass, adjacentSubvolume, QuantityComponent.Y);
VolVariable distanceVar = new VolVariable(getMathSymbol(localDirectionYQuantity, adjacentSubvolume), domain);
varHash.addVariable(distanceVar);
ComputeMembraneMetricEquation membraneMetricEquation = new ComputeMembraneMetricEquation(distanceVar, MembraneMetricComponent.directionToMembraneY);
membraneMetricEquation.setTargetMembraneName(memSubdomainContext.membraneSubdomain.getName());
compSubdomain.addEquation(membraneMetricEquation);
}
if (simContext.getGeometry().getDimension() == 3) {
String name = adjacentSubvolume.getName() + "_dirZ_" + memSubdomainContext.membraneSubdomain.getName();
LocalizedDirectionToMembraneQuantity localDirectionZQuantity = addLocalizedDirectionToMembraneQuantity(name, surfaceClass, adjacentSubvolume, QuantityComponent.Z);
VolVariable distanceVar = new VolVariable(getMathSymbol(localDirectionZQuantity, adjacentSubvolume), domain);
varHash.addVariable(distanceVar);
ComputeMembraneMetricEquation membraneMetricEquation = new ComputeMembraneMetricEquation(distanceVar, MembraneMetricComponent.directionToMembraneZ);
membraneMetricEquation.setTargetMembraneName(memSubdomainContext.membraneSubdomain.getName());
compSubdomain.addEquation(membraneMetricEquation);
}
}
}
if (bDistance) {
SpatialQuantity distanceQuantity = surfaceRegionObject.getSpatialQuantity(QuantityCategory.SurfaceDistanceMap, QuantityComponent.Scalar);
for (SubVolume adjacentSubvolume : surfaceClass.getAdjacentSubvolumes()) {
String name = adjacentSubvolume.getName() + "_distanceTo_" + memSubdomainContext.membraneSubdomain.getName();
LocalizedDistanceToMembraneQuantity localDistanceQuantity = addLocalizedDistanceToMembraneQuantity(name, surfaceClass, adjacentSubvolume);
CompartmentSubDomain compSubdomain = mathDesc.getCompartmentSubDomain(adjacentSubvolume.getName());
Domain domain = new Domain(adjacentSubvolume);
VolVariable distanceVar = new VolVariable(getMathSymbol(localDistanceQuantity, adjacentSubvolume), domain);
varHash.addVariable(distanceVar);
ComputeMembraneMetricEquation membraneMetricEquation = new ComputeMembraneMetricEquation(distanceVar, MembraneMetricComponent.distanceToMembrane);
membraneMetricEquation.setTargetMembraneName(memSubdomainContext.membraneSubdomain.getName());
compSubdomain.addEquation(membraneMetricEquation);
}
}
} else if (spatialObject instanceof VolumeRegionObject) {
VolumeRegionObject volumeRegionObject = (VolumeRegionObject) spatialObject;
SubVolume subvolume = volumeRegionObject.getSubVolume();
boolean bCentroid = volumeRegionObject.isQuantityCategoryEnabled(QuantityCategory.DirectionToSurface);
boolean bSize = volumeRegionObject.isQuantityCategoryEnabled(QuantityCategory.VolumeSize);
boolean bVelocity = volumeRegionObject.isQuantityCategoryEnabled(QuantityCategory.InteriorVelocity);
if (bVelocity) {
ArrayList<VolumeKinematics> volumeKinematicsList = new ArrayList<VolumeKinematics>();
for (SpatialProcess spatialProcess : simContext.getSpatialProcesses()) {
if (spatialProcess instanceof VolumeKinematics && ((VolumeKinematics) spatialProcess).getVolumeRegionObject() == volumeRegionObject) {
volumeKinematicsList.add((VolumeKinematics) spatialProcess);
}
}
if (volumeKinematicsList.size() == 1) {
VolumeKinematics volumeKinematics = volumeKinematicsList.get(0);
if (simContext.getGeometry().getDimension() >= 1) {
SpatialQuantity velXQuantity = volumeRegionObject.getSpatialQuantity(QuantityCategory.InteriorVelocity, QuantityComponent.X);
LocalParameter velXParam = volumeKinematics.getParameter(SpatialProcessParameterType.InternalVelocityX);
varHash.addVariable(newFunctionOrConstant(getMathSymbol(velXParam, subvolume), getIdentifierSubstitutions(velXParam.getExpression(), velXParam.getUnitDefinition(), subvolume), subvolume));
Expression velXExp = new Expression(velXParam, volumeKinematics.getNameScope());
varHash.addVariable(newFunctionOrConstant(getMathSymbol(velXQuantity, subvolume), getIdentifierSubstitutions(velXExp, velXQuantity.getUnitDefinition(), subvolume), subvolume));
}
if (simContext.getGeometry().getDimension() >= 2) {
SpatialQuantity velYQuantity = volumeRegionObject.getSpatialQuantity(QuantityCategory.InteriorVelocity, QuantityComponent.Y);
LocalParameter velYParam = volumeKinematics.getParameter(SpatialProcessParameterType.InternalVelocityY);
varHash.addVariable(newFunctionOrConstant(getMathSymbol(velYParam, subvolume), getIdentifierSubstitutions(velYParam.getExpression(), velYParam.getUnitDefinition(), subvolume), subvolume));
Expression velYExp = new Expression(velYParam, volumeKinematics.getNameScope());
varHash.addVariable(newFunctionOrConstant(getMathSymbol(velYQuantity, subvolume), getIdentifierSubstitutions(velYExp, velYQuantity.getUnitDefinition(), subvolume), subvolume));
}
if (simContext.getGeometry().getDimension() == 3) {
SpatialQuantity velZQuantity = volumeRegionObject.getSpatialQuantity(QuantityCategory.InteriorVelocity, QuantityComponent.Z);
LocalParameter velZParam = volumeKinematics.getParameter(SpatialProcessParameterType.InternalVelocityZ);
varHash.addVariable(newFunctionOrConstant(getMathSymbol(velZParam, subvolume), getIdentifierSubstitutions(velZParam.getExpression(), velZParam.getUnitDefinition(), subvolume), subvolume));
Expression velZExp = new Expression(velZParam, volumeKinematics.getNameScope());
varHash.addVariable(newFunctionOrConstant(getMathSymbol(velZQuantity, subvolume), getIdentifierSubstitutions(velZExp, velZQuantity.getUnitDefinition(), subvolume), subvolume));
}
} else {
throw new MappingException("expecting 1 Volume Kinematics process for Volume Object '" + volumeRegionObject.getName() + "'");
}
}
if (bSize) {
SpatialQuantity sizeQuantity = volumeRegionObject.getSpatialQuantity(QuantityCategory.VolumeSize, QuantityComponent.Scalar);
String funcName = MathFunctionDefinitions.Function_regionVolume_current.getFunctionName();
Expression sizeExp = Expression.function(funcName, new Expression[] { new Expression("'" + subvolume.getName() + "'") });
varHash.addVariable(newFunctionOrConstant(getMathSymbol(sizeQuantity, subvolume), getIdentifierSubstitutions(sizeExp, sizeQuantity.getUnitDefinition(), subvolume), subvolume));
}
if (bCentroid) {
throw new MappingException(QuantityCategory.Centroid.description + " not yet implemented in math generation");
}
}
}
}
Also used :
GeometryClass(cbit.vcell.geometry.GeometryClass)
PointLocation(cbit.vcell.mapping.spatial.processes.PointLocation)
SurfaceClass(cbit.vcell.geometry.SurfaceClass)
VolumeKinematics(cbit.vcell.mapping.spatial.processes.VolumeKinematics)
ArrayList(java.util.ArrayList)
PointSubDomain(cbit.vcell.math.PointSubDomain)
SpatialObject(cbit.vcell.mapping.spatial.SpatialObject)
PointObject(cbit.vcell.mapping.spatial.PointObject)
SpatialProcess(cbit.vcell.mapping.spatial.processes.SpatialProcess)
SubVolume(cbit.vcell.geometry.SubVolume)
ComputeMembraneMetricEquation(cbit.vcell.math.ComputeMembraneMetricEquation)
SpatialQuantity(cbit.vcell.mapping.spatial.SpatialObject.SpatialQuantity)
VolumeRegionObject(cbit.vcell.mapping.spatial.VolumeRegionObject)
VolVariable(cbit.vcell.math.VolVariable)
SurfaceKinematics(cbit.vcell.mapping.spatial.processes.SurfaceKinematics)
LocalParameter(cbit.vcell.mapping.ParameterContext.LocalParameter)
OdeEquation(cbit.vcell.math.OdeEquation)
Expression(cbit.vcell.parser.Expression)
CompartmentSubDomain(cbit.vcell.math.CompartmentSubDomain)
PointKinematics(cbit.vcell.mapping.spatial.processes.PointKinematics)
PointVariable(cbit.vcell.math.PointVariable)
CompartmentSubDomain(cbit.vcell.math.CompartmentSubDomain)
SubDomain(cbit.vcell.math.SubDomain)
PointSubDomain(cbit.vcell.math.PointSubDomain)
Domain(cbit.vcell.math.Variable.Domain)
MembraneSubDomain(cbit.vcell.math.MembraneSubDomain)
SurfaceRegionObject(cbit.vcell.mapping.spatial.SurfaceRegionObject)
Aggregations
SpatialProcess (cbit.vcell.mapping.spatial.processes.SpatialProcess)28
SpatialObject (cbit.vcell.mapping.spatial.SpatialObject)18
SimulationContext (cbit.vcell.mapping.SimulationContext)9
BioEvent (cbit.vcell.mapping.BioEvent)8
SpeciesContextSpec (cbit.vcell.mapping.SpeciesContextSpec)7
StructureMapping (cbit.vcell.mapping.StructureMapping)7
ReactionStep (cbit.vcell.model.ReactionStep)7
LocalParameter (cbit.vcell.mapping.ParameterContext.LocalParameter)6
SimulationContextParameter (cbit.vcell.mapping.SimulationContext.SimulationContextParameter)6
PointObject (cbit.vcell.mapping.spatial.PointObject)6
SurfaceRegionObject (cbit.vcell.mapping.spatial.SurfaceRegionObject)6
VolumeRegionObject (cbit.vcell.mapping.spatial.VolumeRegionObject)6
Element (org.jdom.Element)6
PointKinematics (cbit.vcell.mapping.spatial.processes.PointKinematics)5
PointLocation (cbit.vcell.mapping.spatial.processes.PointLocation)5
ReactionRule (cbit.vcell.model.ReactionRule)5
SpeciesContext (cbit.vcell.model.SpeciesContext)5
NetworkConstraints (org.vcell.model.rbm.NetworkConstraints)5
BioModel (cbit.vcell.biomodel.BioModel)4
Geometry (cbit.vcell.geometry.Geometry)4
