Example 6 with SpeciesContextSpec
use of cbit.vcell.mapping.SpeciesContextSpec 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 SpeciesContextSpec
use of cbit.vcell.mapping.SpeciesContextSpec in project vcell by virtualcell.
the class MathMapping_4_8 method getMathSymbol0.
/**
* Substitutes appropriate variables for speciesContext bindings
*
* @return cbit.vcell.parser.Expression
* @param origExp cbit.vcell.parser.Expression
* @param structureMapping cbit.vcell.mapping.StructureMapping
*/
private String getMathSymbol0(SymbolTableEntry ste, StructureMapping structureMapping) throws MappingException {
String steName = ste.getName();
if (ste instanceof Kinetics.KineticsParameter) {
Integer count = localNameCountHash.get(steName);
if (count == null) {
throw new MappingException("KineticsParameter " + steName + " not found in local name count");
}
if (count > 1 || steName.equals("J")) {
return steName + "_" + ste.getNameScope().getName();
// return getNameScope().getSymbolName(ste);
} else {
return steName;
}
}
if (ste instanceof MathMapping_4_8.ProbabilityParameter) {
// be careful here, to see if we need mangle the reaction name
MathMapping_4_8.ProbabilityParameter probParm = (MathMapping_4_8.ProbabilityParameter) ste;
return probParm.getName();
}
if (ste instanceof MathMapping_4_8.SpeciesConcentrationParameter) {
MathMapping_4_8.SpeciesConcentrationParameter concParm = (MathMapping_4_8.SpeciesConcentrationParameter) ste;
return concParm.getSpeciesContextSpec().getSpeciesContext().getName() + MATH_FUNC_SUFFIX_SPECIES_CONCENTRATION;
}
if (ste instanceof MathMapping_4_8.SpeciesCountParameter) {
MathMapping_4_8.SpeciesCountParameter countParm = (MathMapping_4_8.SpeciesCountParameter) ste;
return countParm.getSpeciesContextSpec().getSpeciesContext().getName() + MATH_VAR_SUFFIX_SPECIES_COUNT;
}
if (ste instanceof MathMapping_4_8.EventAssignmentInitParameter) {
MathMapping_4_8.EventAssignmentInitParameter eventInitParm = (MathMapping_4_8.EventAssignmentInitParameter) ste;
return eventInitParm.getName() + MATH_FUNC_SUFFIX_EVENTASSIGN_INIT;
}
if (ste instanceof Model.ReservedSymbol) {
return steName;
}
if (ste instanceof Membrane.MembraneVoltage) {
return steName;
}
if (ste instanceof Structure.StructureSize) {
Structure structure = ((Structure.StructureSize) ste).getStructure();
StructureMapping.StructureMappingParameter sizeParameter = simContext.getGeometryContext().getStructureMapping(structure).getSizeParameter();
return getMathSymbol(sizeParameter, structureMapping);
}
if (ste instanceof ProxyParameter) {
ProxyParameter pp = (ProxyParameter) ste;
return getMathSymbol0(pp.getTarget(), structureMapping);
}
//
Model model = simContext.getModel();
if (ste instanceof ModelParameter) {
ModelParameter mp = (ModelParameter) ste;
if (simContext.getGeometry().getDimension() == 0) {
return mp.getName();
} else {
if (mp.getExpression().getSymbols() == null) {
return mp.getName();
}
// check if global param variant name exists in globalVarsHash. If so, return it, else, throw exception.
Hashtable<String, Expression> smVariantsHash = globalParamVariantsHash.get(mp);
String variantName = mp.getName() + "_" + TokenMangler.fixTokenStrict(structureMapping.getStructure().getName());
if (smVariantsHash.get(variantName) != null) {
return variantName;
} else {
// global param variant doesn't exist in the hash, so get the substituted expression for global param and
// gather all symbols (speciesContexts) that do not match with arg 'structureMapping' to display a proper error message.
Expression expr = null;
try {
expr = substituteGlobalParameters(mp.getExpression());
} catch (ExpressionException e) {
e.printStackTrace(System.out);
throw new RuntimeException("Could not substitute expression for global parameter '" + mp.getName() + "' with expression '" + "'" + e.getMessage());
}
// find symbols (typically speciesContexts) in 'exp' that do not match with the arg 'structureMapping'
String[] symbols = expr.getSymbols();
String msg = "";
if (symbols != null) {
Vector<String> spContextNamesVector = new Vector<String>();
for (int j = 0; j < symbols.length; j++) {
SpeciesContext sc = model.getSpeciesContext(symbols[j]);
if (sc != null) {
if (!sc.getStructure().compareEqual(structureMapping.getStructure())) {
spContextNamesVector.addElement(sc.getName());
}
}
}
for (int i = 0; (spContextNamesVector != null && i < spContextNamesVector.size()); i++) {
if (i == 0) {
msg += "'" + spContextNamesVector.elementAt(i) + ", ";
} else if (i == spContextNamesVector.size() - 1) {
msg += spContextNamesVector.elementAt(i) + "'";
} else {
msg += spContextNamesVector.elementAt(i) + ", ";
}
}
}
throw new RuntimeException("Global parameter '" + mp.getName() + "' is not defined in compartment '" + structureMapping.getStructure().getName() + "', but was referenced in that compartment." + "\n\nExpression '" + mp.getExpression().infix() + "' for global parameter '" + mp.getName() + "' expands to '" + expr.infix() + "' " + "and contains species " + msg + " that is/are not in adjacent compartments.");
}
// return (mp.getName()+"_"+TokenMangler.fixTokenStrict(structureMapping.getStructure().getName()));
}
}
if (ste instanceof SpeciesContextSpec.SpeciesContextSpecParameter) {
SpeciesContextSpec.SpeciesContextSpecParameter scsParm = (SpeciesContextSpec.SpeciesContextSpecParameter) ste;
if (scsParm.getRole() == SpeciesContextSpec.ROLE_InitialConcentration) {
return ((SpeciesContextSpec) (scsParm.getNameScope().getScopedSymbolTable())).getSpeciesContext().getName() + MATH_FUNC_SUFFIX_SPECIES_INIT_CONCENTRATION;
}
if (scsParm.getRole() == SpeciesContextSpec.ROLE_InitialCount) {
return ((SpeciesContextSpec) (scsParm.getNameScope().getScopedSymbolTable())).getSpeciesContext().getName() + MATH_FUNC_SUFFIX_SPECIES_INIT_COUNT;
}
if (scsParm.getRole() == SpeciesContextSpec.ROLE_DiffusionRate) {
return ((SpeciesContextSpec) (scsParm.getNameScope().getScopedSymbolTable())).getSpeciesContext().getName() + "_diffusionRate";
}
if (scsParm.getRole() == SpeciesContextSpec.ROLE_BoundaryValueXm) {
return ((SpeciesContextSpec) (scsParm.getNameScope().getScopedSymbolTable())).getSpeciesContext().getName() + "_boundaryXm";
}
if (scsParm.getRole() == SpeciesContextSpec.ROLE_BoundaryValueXp) {
return ((SpeciesContextSpec) (scsParm.getNameScope().getScopedSymbolTable())).getSpeciesContext().getName() + "_boundaryXp";
}
if (scsParm.getRole() == SpeciesContextSpec.ROLE_BoundaryValueYm) {
return ((SpeciesContextSpec) (scsParm.getNameScope().getScopedSymbolTable())).getSpeciesContext().getName() + "_boundaryYm";
}
if (scsParm.getRole() == SpeciesContextSpec.ROLE_BoundaryValueYp) {
return ((SpeciesContextSpec) (scsParm.getNameScope().getScopedSymbolTable())).getSpeciesContext().getName() + "_boundaryYp";
}
if (scsParm.getRole() == SpeciesContextSpec.ROLE_BoundaryValueZm) {
return ((SpeciesContextSpec) (scsParm.getNameScope().getScopedSymbolTable())).getSpeciesContext().getName() + "_boundaryZm";
}
if (scsParm.getRole() == SpeciesContextSpec.ROLE_BoundaryValueZp) {
return ((SpeciesContextSpec) (scsParm.getNameScope().getScopedSymbolTable())).getSpeciesContext().getName() + "_boundaryZp";
}
if (scsParm.getRole() == SpeciesContextSpec.ROLE_VelocityX) {
return ((SpeciesContextSpec) (scsParm.getNameScope().getScopedSymbolTable())).getSpeciesContext().getName() + "_velocityX";
}
if (scsParm.getRole() == SpeciesContextSpec.ROLE_VelocityY) {
return ((SpeciesContextSpec) (scsParm.getNameScope().getScopedSymbolTable())).getSpeciesContext().getName() + "_velocityY";
}
if (scsParm.getRole() == SpeciesContextSpec.ROLE_VelocityZ) {
return ((SpeciesContextSpec) (scsParm.getNameScope().getScopedSymbolTable())).getSpeciesContext().getName() + "_velocityZ";
}
}
if (ste instanceof ElectricalDevice.ElectricalDeviceParameter) {
ElectricalDevice.ElectricalDeviceParameter edParm = (ElectricalDevice.ElectricalDeviceParameter) ste;
ElectricalDevice electricalDevice = (ElectricalDevice) edParm.getNameScope().getScopedSymbolTable();
if (electricalDevice instanceof MembraneElectricalDevice) {
String nameWithScope = ((MembraneElectricalDevice) electricalDevice).getMembraneMapping().getMembrane().getNameScope().getName();
if (edParm.getRole() == ElectricalDevice.ROLE_TotalCurrent) {
return "I_" + nameWithScope;
}
if (edParm.getRole() == ElectricalDevice.ROLE_TransmembraneCurrent) {
return "F_" + nameWithScope;
}
// }else if (electricalDevice instanceof CurrentClampElectricalDevice) {
// if (edParm.getRole()==ElectricalDevice.ROLE_TotalCurrentDensity){
// return "I_"+((CurrentClampElectricalDevice)electricalDevice).getCurrentClampStimulus().getNameScope().getName();
// }
// if (edParm.getRole()==ElectricalDevice.ROLE_TransmembraneCurrentDensity){
// return "F_"+((CurrentClampElectricalDevice)electricalDevice).getCurrentClampStimulus().getNameScope().getName();
// }
// }else if (electricalDevice instanceof VoltageClampElectricalDevice) {
// if (edParm.getRole()==ElectricalDevice.ROLE_TotalCurrentDensity){
// return "I_"+((VoltageClampElectricalDevice)electricalDevice).getVoltageClampStimulus().getNameScope().getName();
// }
// if (edParm.getRole()==ElectricalDevice.ROLE_TransmembraneCurrentDensity){
// return "F_"+((VoltageClampElectricalDevice)electricalDevice).getVoltageClampStimulus().getNameScope().getName();
// }
}
}
if (ste instanceof LocalParameter && ((LocalParameter) ste).getNameScope() instanceof ElectricalStimulus.ElectricalStimulusNameScope) {
LocalParameter esParm = (LocalParameter) ste;
String nameWithScope = esParm.getNameScope().getName();
if (esParm.getRole() == ElectricalStimulusParameterType.TotalCurrent) {
return "I_" + nameWithScope;
} else if (esParm.getRole() == ElectricalStimulusParameterType.Voltage) {
return "V_" + nameWithScope;
}
}
StructureTopology structTopology = model.getStructureTopology();
if (ste instanceof StructureMapping.StructureMappingParameter) {
StructureMapping.StructureMappingParameter smParm = (StructureMapping.StructureMappingParameter) ste;
Structure structure = ((StructureMapping) (smParm.getNameScope().getScopedSymbolTable())).getStructure();
int role = smParm.getRole();
if (role == StructureMapping.ROLE_VolumeFraction) {
return "VolFract_" + (structTopology.getInsideFeature((Membrane) structure)).getNameScope().getName();
} else {
String nameWithScope = structure.getNameScope().getName();
if (role == StructureMapping.ROLE_SurfaceToVolumeRatio) {
return "SurfToVol_" + nameWithScope;
} else if (role == StructureMapping.ROLE_InitialVoltage) {
return smParm.getName();
} else if (role == StructureMapping.ROLE_SpecificCapacitance) {
return "C_" + nameWithScope;
} else if (role == StructureMapping.ROLE_AreaPerUnitArea) {
return "AreaPerUnitArea_" + nameWithScope;
} else if (role == StructureMapping.ROLE_AreaPerUnitVolume) {
return "AreaPerUnitVolume_" + nameWithScope;
} else if (role == StructureMapping.ROLE_VolumePerUnitArea) {
return "VolumePerUnitArea_" + nameWithScope;
} else if (role == StructureMapping.ROLE_VolumePerUnitVolume) {
return "VolumePerUnitVolume_" + nameWithScope;
} else if (role == StructureMapping.ROLE_Size) {
if (simContext.getGeometry().getDimension() == 0) {
// if geometry is compartmental, make sure compartment sizes are set if referenced in model.
if (smParm.getExpression() == null || smParm.getExpression().isZero()) {
throw new MappingException("\nIn non-spatial application '" + getSimulationContext().getName() + "', " + "size of structure '" + structure.getName() + "' must be assigned a " + "positive value if referenced in the model.\n\nPlease go to 'Structure Mapping' tab to check the size.");
}
}
return "Size_" + nameWithScope;
}
}
}
//
if (ste instanceof SpeciesContext) {
SpeciesContext sc = (SpeciesContext) ste;
SpeciesContextMapping scm = getSpeciesContextMapping(sc);
//
if (structureMapping instanceof FeatureMapping) {
//
if (scm.getVariable() != null && !scm.getVariable().getName().equals(steName)) {
return scm.getVariable().getName();
}
//
// for reactions within a spatially resolved membrane, may need "_INSIDE" or "_OUTSIDE" for jump condition
//
// if the membrane is distributed, then always use the plain variable.
//
} else if (structureMapping instanceof MembraneMapping) {
Membrane membrane = ((MembraneMapping) structureMapping).getMembrane();
//
if (sc.getStructure() instanceof Membrane || getResolved(structureMapping) == false) {
if (scm.getVariable() != null && !(scm.getVariable().getName().equals(steName))) {
return scm.getVariable().getName();
}
//
// if the speciesContext is outside the membrane
//
} else {
SpeciesContextSpec scs = simContext.getReactionContext().getSpeciesContextSpec(sc);
if (sc.getStructure() == structTopology.getInsideFeature(membrane) || sc.getStructure() == structTopology.getOutsideFeature(membrane)) {
if (getResolved(structureMapping) && !scs.isConstant()) {
if (!scs.isDiffusing()) {
throw new MappingException("Enable diffusion in Application '" + simContext.getName() + "'. This must be done for any species (e.g '" + sc.getName() + "') in flux reactions.\n\n" + "To save or run simulations, set the diffusion rate to a non-zero " + "value in Initial Conditions or disable those reactions in Specifications->Reactions.");
}
return scm.getVariable().getName() + (sc.getStructure() == structTopology.getInsideFeature(membrane) ? "_INSIDE" : "_OUTSIDE");
} else {
return scm.getSpeciesContext().getName();
}
} else {
throw new MappingException(sc.getName() + " shouldn't be involved with structure " + structureMapping.getStructure().getName());
}
}
}
}
return getNameScope().getSymbolName(ste);
}
Also used :
MembraneMapping(cbit.vcell.mapping.MembraneMapping)
SpeciesContextMapping(cbit.vcell.mapping.SpeciesContextMapping)
SpeciesContext(cbit.vcell.model.SpeciesContext)
StructureMappingParameter(cbit.vcell.mapping.StructureMapping.StructureMappingParameter)
SpeciesContextSpec(cbit.vcell.mapping.SpeciesContextSpec)
StructureMapping(cbit.vcell.mapping.StructureMapping)
ExpressionException(cbit.vcell.parser.ExpressionException)
MappingException(cbit.vcell.mapping.MappingException)
KineticsParameter(cbit.vcell.model.Kinetics.KineticsParameter)
FeatureMapping(cbit.vcell.mapping.FeatureMapping)
Membrane(cbit.vcell.model.Membrane)
Structure(cbit.vcell.model.Structure)
Vector(java.util.Vector)
SpeciesContextSpecParameter(cbit.vcell.mapping.SpeciesContextSpec.SpeciesContextSpecParameter)
SpeciesContextSpecParameter(cbit.vcell.mapping.SpeciesContextSpec.SpeciesContextSpecParameter)
StructureTopology(cbit.vcell.model.Model.StructureTopology)
LocalParameter(cbit.vcell.mapping.ParameterContext.LocalParameter)
ModelParameter(cbit.vcell.model.Model.ModelParameter)
ElectricalStimulus(cbit.vcell.mapping.ElectricalStimulus)
ProxyParameter(cbit.vcell.model.ProxyParameter)
SpeciesContextSpecProxyParameter(cbit.vcell.mapping.SpeciesContextSpec.SpeciesContextSpecProxyParameter)
StructureMappingParameter(cbit.vcell.mapping.StructureMapping.StructureMappingParameter)
Expression(cbit.vcell.parser.Expression)
Model(cbit.vcell.model.Model)
Example 8 with SpeciesContextSpec
use of cbit.vcell.mapping.SpeciesContextSpec in project vcell by virtualcell.
the class MathMapping_4_8 method refreshMathDescription.
/**
* This method was created in VisualAge.
*/
private void refreshMathDescription() throws MappingException, MatrixException, MathException, ExpressionException, ModelException {
// All sizes must be set for new ODE models and ratios must be set for old ones.
simContext.checkValidity();
//
// temporarily place all variables in a hashtable (before binding) and discarding duplicates (check for equality)
//
VariableHash varHash = new VariableHash();
StructureMapping[] structureMappings = simContext.getGeometryContext().getStructureMappings();
Model model = simContext.getModel();
StructureTopology structTopology = model.getStructureTopology();
//
// verify that all structures are mapped to subvolumes and all subvolumes are mapped to a structure
//
Structure[] structures = simContext.getGeometryContext().getModel().getStructures();
for (int i = 0; i < structures.length; i++) {
StructureMapping sm = simContext.getGeometryContext().getStructureMapping(structures[i]);
if (sm == null || (sm instanceof FeatureMapping && getSubVolume((FeatureMapping) sm) == null)) {
throw new MappingException("model structure '" + structures[i].getName() + "' not mapped to a geometry subdomain");
}
if (sm != null && (sm instanceof MembraneMapping) && ((MembraneMapping) sm).getVolumeFractionParameter() != null) {
Expression volFractExp = ((MembraneMapping) sm).getVolumeFractionParameter().getExpression();
if (volFractExp != null) {
try {
double volFract = volFractExp.evaluateConstant();
if (volFract >= 1.0) {
throw new MappingException("model structure '" + structTopology.getInsideFeature(((MembraneMapping) sm).getMembrane()).getName() + "' has volume fraction >= 1.0");
}
} catch (ExpressionException e) {
}
}
}
}
SubVolume[] subVolumes = simContext.getGeometryContext().getGeometry().getGeometrySpec().getSubVolumes();
for (int i = 0; i < subVolumes.length; i++) {
if (getStructures(subVolumes[i]) == null || getStructures(subVolumes[i]).length == 0) {
throw new MappingException("geometry subdomain '" + subVolumes[i].getName() + "' not mapped from a model structure");
}
}
// deals with model parameters
Hashtable<VolVariable, EventAssignmentInitParameter> eventVolVarHash = new Hashtable<VolVariable, EventAssignmentInitParameter>();
ModelParameter[] modelParameters = model.getModelParameters();
if (simContext.getGeometry().getDimension() == 0) {
//
// global parameters from model (that presently are constants)
//
BioEvent[] bioEvents = simContext.getBioEvents();
ArrayList<SymbolTableEntry> eventAssignTargets = new ArrayList<SymbolTableEntry>();
if (bioEvents != null && bioEvents.length > 0) {
for (BioEvent be : bioEvents) {
for (EventAssignment ea : be.getEventAssignments()) {
if (!eventAssignTargets.contains(ea.getTarget())) {
eventAssignTargets.add(ea.getTarget());
}
}
}
}
for (int j = 0; j < modelParameters.length; j++) {
Expression modelParamExpr = getIdentifierSubstitutions(modelParameters[j].getExpression(), modelParameters[j].getUnitDefinition(), null);
if (eventAssignTargets.contains(modelParameters[j])) {
EventAssignmentInitParameter eap = null;
try {
eap = addEventAssignmentInitParameter(modelParameters[j].getName(), modelParameters[j].getExpression(), PARAMETER_ROLE_EVENTASSIGN_INITCONDN, modelParameters[j].getUnitDefinition());
} catch (PropertyVetoException e) {
e.printStackTrace(System.out);
throw new MappingException(e.getMessage());
}
// varHash.addVariable(newFunctionOrConstant(getMathSymbol(eap, null), modelParamExpr));
VolVariable volVar = new VolVariable(modelParameters[j].getName(), nullDomain);
varHash.addVariable(volVar);
eventVolVarHash.put(volVar, eap);
} else {
varHash.addVariable(newFunctionOrConstant(getMathSymbol(modelParameters[j], null), modelParamExpr));
}
}
} else {
//
for (int pass = 0; pass < 2; pass++) {
for (int j = 0; j < modelParameters.length; j++) {
Hashtable<String, Expression> structMappingVariantsHash = new Hashtable<String, Expression>();
for (int k = 0; k < structureMappings.length; k++) {
String paramVariantName = null;
Expression paramVariantExpr = null;
if (modelParameters[j].getExpression().getSymbols() == null) {
paramVariantName = modelParameters[j].getName();
paramVariantExpr = getIdentifierSubstitutions(modelParameters[j].getExpression(), modelParameters[j].getUnitDefinition(), null);
} else {
paramVariantName = modelParameters[j].getName() + "_" + TokenMangler.fixTokenStrict(structureMappings[k].getStructure().getName());
// if the expression has symbols that do not belong in that structureMapping, do not create the variant.
Expression exp1 = modelParameters[j].getExpression();
Expression flattenedModelParamExpr = substituteGlobalParameters(exp1);
String[] symbols = flattenedModelParamExpr.getSymbols();
boolean bValid = true;
Structure sm_struct = structureMappings[k].getStructure();
if (symbols != null) {
for (int ii = 0; ii < symbols.length; ii++) {
SpeciesContext sc = model.getSpeciesContext(symbols[ii]);
if (sc != null) {
// symbol[ii] is a speciesContext, check its structure with structureMapping[k].structure. If they are the same or
// if it is the adjacent membrane(s), allow variant expression to be created. Else, continue.
Structure sp_struct = sc.getStructure();
if (sp_struct.compareEqual(sm_struct)) {
bValid = bValid && true;
} else {
// if the 2 structures are not the same, are they adjacent? then 'bValid' is true, else false.
if ((sm_struct instanceof Feature) && (sp_struct instanceof Membrane)) {
Feature sm_feature = (Feature) sm_struct;
Membrane sp_mem = (Membrane) sp_struct;
if (sp_mem.compareEqual(structTopology.getParentStructure(sm_feature)) || (structTopology.getInsideFeature(sp_mem).compareEqual(sm_feature) || structTopology.getOutsideFeature(sp_mem).compareEqual(sm_feature))) {
bValid = bValid && true;
} else {
bValid = bValid && false;
break;
}
} else if ((sm_struct instanceof Membrane) && (sp_struct instanceof Feature)) {
Feature sp_feature = (Feature) sp_struct;
Membrane sm_mem = (Membrane) sm_struct;
if (sm_mem.compareEqual(structTopology.getParentStructure(sp_feature)) || (structTopology.getInsideFeature(sm_mem).compareEqual(sp_feature) || structTopology.getOutsideFeature(sm_mem).compareEqual(sp_feature))) {
bValid = bValid && true;
} else {
bValid = bValid && false;
break;
}
} else {
bValid = bValid && false;
break;
}
}
}
}
}
if (bValid) {
if (pass == 0) {
paramVariantExpr = new Expression("VCELL_TEMPORARY_EXPRESSION_PLACEHOLDER");
} else {
paramVariantExpr = getIdentifierSubstitutions(modelParameters[j].getExpression(), modelParameters[j].getUnitDefinition(), structureMappings[k]);
}
}
}
if (paramVariantExpr != null) {
structMappingVariantsHash.put(paramVariantName, paramVariantExpr);
}
}
globalParamVariantsHash.put(modelParameters[j], structMappingVariantsHash);
}
}
//
for (int j = 0; j < modelParameters.length; j++) {
if (modelParameters[j].getExpression().getSymbols() == null) {
varHash.addVariable(newFunctionOrConstant(getMathSymbol(modelParameters[j], null), getIdentifierSubstitutions(modelParameters[j].getExpression(), modelParameters[j].getUnitDefinition(), null)));
} else {
Hashtable<String, Expression> smVariantsHash = globalParamVariantsHash.get(modelParameters[j]);
for (int k = 0; k < structureMappings.length; k++) {
String variantName = modelParameters[j].getName() + "_" + TokenMangler.fixTokenStrict(structureMappings[k].getStructure().getName());
Expression variantExpr = smVariantsHash.get(variantName);
if (variantExpr != null) {
varHash.addVariable(newFunctionOrConstant(variantName, variantExpr));
}
}
}
}
}
//
// gather only those reactionSteps that are not "excluded"
//
ReactionSpec[] reactionSpecs = simContext.getReactionContext().getReactionSpecs();
Vector<ReactionStep> rsList = new Vector<ReactionStep>();
for (int i = 0; i < reactionSpecs.length; i++) {
if (reactionSpecs[i].isExcluded() == false) {
rsList.add(reactionSpecs[i].getReactionStep());
}
}
ReactionStep[] reactionSteps = new ReactionStep[rsList.size()];
rsList.copyInto(reactionSteps);
//
for (int i = 0; i < reactionSteps.length; i++) {
Kinetics.UnresolvedParameter[] unresolvedParameters = reactionSteps[i].getKinetics().getUnresolvedParameters();
if (unresolvedParameters != null && unresolvedParameters.length > 0) {
StringBuffer buffer = new StringBuffer();
for (int j = 0; j < unresolvedParameters.length; j++) {
if (j > 0) {
buffer.append(", ");
}
buffer.append(unresolvedParameters[j].getName());
}
throw new MappingException(reactionSteps[i].getDisplayType() + " '" + reactionSteps[i].getName() + "' contains unresolved identifier(s): " + buffer);
}
}
//
// create new MathDescription (based on simContext's previous MathDescription if possible)
//
MathDescription oldMathDesc = simContext.getMathDescription();
mathDesc = null;
if (oldMathDesc != null) {
if (oldMathDesc.getVersion() != null) {
mathDesc = new MathDescription(oldMathDesc.getVersion());
} else {
mathDesc = new MathDescription(oldMathDesc.getName());
}
} else {
mathDesc = new MathDescription(simContext.getName() + "_generated");
}
//
// volume variables
//
Enumeration<SpeciesContextMapping> enum1 = getSpeciesContextMappings();
while (enum1.hasMoreElements()) {
SpeciesContextMapping scm = enum1.nextElement();
if (scm.getVariable() instanceof VolVariable) {
if (!(mathDesc.getVariable(scm.getVariable().getName()) instanceof VolVariable)) {
varHash.addVariable(scm.getVariable());
}
}
}
//
// membrane variables
//
enum1 = getSpeciesContextMappings();
while (enum1.hasMoreElements()) {
SpeciesContextMapping scm = (SpeciesContextMapping) enum1.nextElement();
if (scm.getVariable() instanceof MemVariable) {
varHash.addVariable(scm.getVariable());
}
}
varHash.addVariable(new Constant(getMathSymbol(model.getFARADAY_CONSTANT(), null), getIdentifierSubstitutions(model.getFARADAY_CONSTANT().getExpression(), model.getFARADAY_CONSTANT().getUnitDefinition(), null)));
varHash.addVariable(new Constant(getMathSymbol(model.getFARADAY_CONSTANT_NMOLE(), null), getIdentifierSubstitutions(model.getFARADAY_CONSTANT_NMOLE().getExpression(), model.getFARADAY_CONSTANT_NMOLE().getUnitDefinition(), null)));
varHash.addVariable(new Constant(getMathSymbol(model.getGAS_CONSTANT(), null), getIdentifierSubstitutions(model.getGAS_CONSTANT().getExpression(), model.getGAS_CONSTANT().getUnitDefinition(), null)));
varHash.addVariable(new Constant(getMathSymbol(model.getTEMPERATURE(), null), getIdentifierSubstitutions(new Expression(simContext.getTemperatureKelvin()), model.getTEMPERATURE().getUnitDefinition(), null)));
//
// only calculate potential if at least one MembraneMapping has CalculateVoltage == true
//
boolean bCalculatePotential = false;
for (int i = 0; i < structureMappings.length; i++) {
if (structureMappings[i] instanceof MembraneMapping) {
if (((MembraneMapping) structureMappings[i]).getCalculateVoltage()) {
bCalculatePotential = true;
}
}
}
// (simContext.getGeometry().getDimension() == 0);
potentialMapping = new PotentialMapping(simContext, this);
potentialMapping.computeMath();
if (bCalculatePotential) {
//
// copy functions for currents and constants for capacitances
//
ElectricalDevice[] devices = potentialMapping.getElectricalDevices();
for (int j = 0; j < devices.length; j++) {
if (devices[j] instanceof MembraneElectricalDevice) {
MembraneElectricalDevice membraneElectricalDevice = (MembraneElectricalDevice) devices[j];
MembraneMapping memMapping = membraneElectricalDevice.getMembraneMapping();
Parameter specificCapacitanceParm = memMapping.getParameterFromRole(MembraneMapping.ROLE_SpecificCapacitance);
varHash.addVariable(new Constant(getMathSymbol(specificCapacitanceParm, memMapping), getIdentifierSubstitutions(specificCapacitanceParm.getExpression(), specificCapacitanceParm.getUnitDefinition(), memMapping)));
ElectricalDevice.ElectricalDeviceParameter transmembraneCurrentParm = membraneElectricalDevice.getParameterFromRole(ElectricalDevice.ROLE_TransmembraneCurrent);
ElectricalDevice.ElectricalDeviceParameter totalCurrentParm = membraneElectricalDevice.getParameterFromRole(ElectricalDevice.ROLE_TotalCurrent);
ElectricalDevice.ElectricalDeviceParameter capacitanceParm = membraneElectricalDevice.getParameterFromRole(ElectricalDevice.ROLE_Capacitance);
if (totalCurrentParm != null && /* totalCurrentDensityParm.getExpression()!=null && */
memMapping.getCalculateVoltage()) {
Expression totalCurrentDensityExp = (totalCurrentParm.getExpression() != null) ? (totalCurrentParm.getExpression()) : (new Expression(0.0));
varHash.addVariable(newFunctionOrConstant(getMathSymbol(totalCurrentParm, membraneElectricalDevice.getMembraneMapping()), getIdentifierSubstitutions(totalCurrentDensityExp, totalCurrentParm.getUnitDefinition(), membraneElectricalDevice.getMembraneMapping())));
}
if (transmembraneCurrentParm != null && transmembraneCurrentParm.getExpression() != null && memMapping.getCalculateVoltage()) {
varHash.addVariable(newFunctionOrConstant(getMathSymbol(transmembraneCurrentParm, membraneElectricalDevice.getMembraneMapping()), getIdentifierSubstitutions(transmembraneCurrentParm.getExpression(), transmembraneCurrentParm.getUnitDefinition(), membraneElectricalDevice.getMembraneMapping())));
}
if (capacitanceParm != null && capacitanceParm.getExpression() != null && memMapping.getCalculateVoltage()) {
StructureMappingParameter sizeParameter = membraneElectricalDevice.getMembraneMapping().getSizeParameter();
if (simContext.getGeometry().getDimension() == 0 && (sizeParameter.getExpression() == null || sizeParameter.getExpression().isZero())) {
varHash.addVariable(newFunctionOrConstant(getMathSymbol(capacitanceParm, membraneElectricalDevice.getMembraneMapping()), getIdentifierSubstitutions(Expression.mult(memMapping.getNullSizeParameterValue(), specificCapacitanceParm.getExpression()), capacitanceParm.getUnitDefinition(), membraneElectricalDevice.getMembraneMapping())));
} else {
varHash.addVariable(newFunctionOrConstant(getMathSymbol(capacitanceParm, membraneElectricalDevice.getMembraneMapping()), getIdentifierSubstitutions(capacitanceParm.getExpression(), capacitanceParm.getUnitDefinition(), membraneElectricalDevice.getMembraneMapping())));
}
}
//
if (membraneElectricalDevice.getDependentVoltageExpression() == null) {
// is Voltage Independent?
StructureMapping.StructureMappingParameter initialVoltageParm = memMapping.getInitialVoltageParameter();
varHash.addVariable(newFunctionOrConstant(getMathSymbol(initialVoltageParm, memMapping), getIdentifierSubstitutions(initialVoltageParm.getExpression(), initialVoltageParm.getUnitDefinition(), memMapping)));
} else //
// membrane forced potential
//
{
varHash.addVariable(newFunctionOrConstant(getMathSymbol(memMapping.getMembrane().getMembraneVoltage(), memMapping), getIdentifierSubstitutions(membraneElectricalDevice.getDependentVoltageExpression(), memMapping.getMembrane().getMembraneVoltage().getUnitDefinition(), memMapping)));
}
} else if (devices[j] instanceof CurrentClampElectricalDevice) {
CurrentClampElectricalDevice currentClampDevice = (CurrentClampElectricalDevice) devices[j];
// total current = current source (no capacitance)
Parameter totalCurrentParm = currentClampDevice.getParameterFromRole(CurrentClampElectricalDevice.ROLE_TotalCurrent);
Parameter currentParm = currentClampDevice.getParameterFromRole(CurrentClampElectricalDevice.ROLE_TransmembraneCurrent);
// Parameter dependentVoltage = currentClampDevice.getCurrentClampStimulus().getVoltageParameter();
varHash.addVariable(newFunctionOrConstant(getMathSymbol(totalCurrentParm, null), getIdentifierSubstitutions(totalCurrentParm.getExpression(), totalCurrentParm.getUnitDefinition(), null)));
varHash.addVariable(newFunctionOrConstant(getMathSymbol(currentParm, null), getIdentifierSubstitutions(currentParm.getExpression(), currentParm.getUnitDefinition(), null)));
// varHash.addVariable(newFunctionOrConstant(getMathSymbol(dependentVoltage,null),getIdentifierSubstitutions(currentClampDevice.getDependentVoltageExpression(),dependentVoltage.getUnitDefinition(),null)));
//
// add user-defined parameters
//
ElectricalDevice.ElectricalDeviceParameter[] parameters = currentClampDevice.getParameters();
for (int k = 0; k < parameters.length; k++) {
if (parameters[k].getExpression() != null) {
// guards against voltage parameters that are "variable".
varHash.addVariable(newFunctionOrConstant(getMathSymbol(parameters[k], null), getIdentifierSubstitutions(parameters[k].getExpression(), parameters[k].getUnitDefinition(), null)));
}
}
} else if (devices[j] instanceof VoltageClampElectricalDevice) {
VoltageClampElectricalDevice voltageClampDevice = (VoltageClampElectricalDevice) devices[j];
// total current = current source (no capacitance)
Parameter totalCurrent = voltageClampDevice.getParameterFromRole(VoltageClampElectricalDevice.ROLE_TotalCurrent);
Parameter totalCurrentParm = voltageClampDevice.getParameterFromRole(VoltageClampElectricalDevice.ROLE_TotalCurrent);
Parameter voltageParm = voltageClampDevice.getParameterFromRole(VoltageClampElectricalDevice.ROLE_Voltage);
varHash.addVariable(newFunctionOrConstant(getMathSymbol(totalCurrent, null), getIdentifierSubstitutions(totalCurrent.getExpression(), totalCurrent.getUnitDefinition(), null)));
varHash.addVariable(newFunctionOrConstant(getMathSymbol(totalCurrentParm, null), getIdentifierSubstitutions(totalCurrentParm.getExpression(), totalCurrentParm.getUnitDefinition(), null)));
varHash.addVariable(newFunctionOrConstant(getMathSymbol(voltageParm, null), getIdentifierSubstitutions(voltageParm.getExpression(), voltageParm.getUnitDefinition(), null)));
//
// add user-defined parameters
//
ElectricalDevice.ElectricalDeviceParameter[] parameters = voltageClampDevice.getParameters();
for (int k = 0; k < parameters.length; k++) {
if (parameters[k].getRole() == ElectricalDevice.ROLE_UserDefined) {
varHash.addVariable(newFunctionOrConstant(getMathSymbol(parameters[k], null), getIdentifierSubstitutions(parameters[k].getExpression(), parameters[k].getUnitDefinition(), null)));
}
}
}
}
} else {
//
for (int j = 0; j < structureMappings.length; j++) {
if (structureMappings[j] instanceof MembraneMapping) {
MembraneMapping memMapping = (MembraneMapping) structureMappings[j];
varHash.addVariable(newFunctionOrConstant(getMathSymbol(memMapping.getMembrane().getMembraneVoltage(), memMapping), getIdentifierSubstitutions(memMapping.getInitialVoltageParameter().getExpression(), memMapping.getInitialVoltageParameter().getUnitDefinition(), memMapping)));
}
}
}
//
for (int j = 0; j < structureMappings.length; j++) {
if (structureMappings[j] instanceof MembraneMapping) {
MembraneMapping membraneMapping = (MembraneMapping) structureMappings[j];
Membrane.MembraneVoltage membraneVoltage = membraneMapping.getMembrane().getMembraneVoltage();
ElectricalDevice[] membraneDevices = potentialMapping.getElectricalDevices(membraneMapping.getMembrane());
// ElectricalDevice membraneDevice = null;
for (int i = 0; i < membraneDevices.length; i++) {
if (membraneDevices[i].hasCapacitance() && membraneDevices[i].getDependentVoltageExpression() == null) {
if (membraneMapping.getCalculateVoltage() && bCalculatePotential) {
if (getResolved(membraneMapping)) {
//
if (mathDesc.getVariable(Membrane.MEMBRANE_VOLTAGE_REGION_NAME) == null) {
// varHash.addVariable(new MembraneRegionVariable(MembraneVoltage.MEMBRANE_VOLTAGE_REGION_NAME));
varHash.addVariable(new MembraneRegionVariable(getMathSymbol(membraneVoltage, membraneMapping), nullDomain));
}
} else {
//
// spatially unresolved membrane, and must solve for potential ... make VolVariable for this compartment
//
varHash.addVariable(new VolVariable(getMathSymbol(membraneVoltage, membraneMapping), nullDomain));
}
Parameter initialVoltageParm = membraneMapping.getInitialVoltageParameter();
Variable initVoltageFunction = newFunctionOrConstant(getMathSymbol(initialVoltageParm, membraneMapping), getIdentifierSubstitutions(initialVoltageParm.getExpression(), initialVoltageParm.getUnitDefinition(), membraneMapping));
varHash.addVariable(initVoltageFunction);
} else {
//
// don't calculate voltage, still may need it though
//
Parameter initialVoltageParm = membraneMapping.getInitialVoltageParameter();
Variable voltageFunction = newFunctionOrConstant(getMathSymbol(membraneMapping.getMembrane().getMembraneVoltage(), membraneMapping), getIdentifierSubstitutions(initialVoltageParm.getExpression(), initialVoltageParm.getUnitDefinition(), membraneMapping));
varHash.addVariable(voltageFunction);
}
}
}
}
}
//
for (int j = 0; j < reactionSteps.length; j++) {
ReactionStep rs = reactionSteps[j];
if (simContext.getReactionContext().getReactionSpec(rs).isExcluded()) {
continue;
}
Kinetics.KineticsParameter[] parameters = rs.getKinetics().getKineticsParameters();
StructureMapping sm = simContext.getGeometryContext().getStructureMapping(rs.getStructure());
if (parameters != null) {
for (int i = 0; i < parameters.length; i++) {
if (((parameters[i].getRole() == Kinetics.ROLE_CurrentDensity) || (parameters[i].getRole() == Kinetics.ROLE_LumpedCurrent)) && (parameters[i].getExpression() == null || parameters[i].getExpression().isZero())) {
continue;
}
varHash.addVariable(newFunctionOrConstant(getMathSymbol(parameters[i], sm), getIdentifierSubstitutions(parameters[i].getExpression(), parameters[i].getUnitDefinition(), sm)));
}
}
}
//
// initial constants (either function or constant)
//
SpeciesContextSpec[] speciesContextSpecs = simContext.getReactionContext().getSpeciesContextSpecs();
for (int i = 0; i < speciesContextSpecs.length; i++) {
SpeciesContextSpecParameter initParm = speciesContextSpecs[i].getParameterFromRole(SpeciesContextSpec.ROLE_InitialConcentration);
if (initParm != null) {
Expression initExpr = new Expression(initParm.getExpression());
StructureMapping sm = simContext.getGeometryContext().getStructureMapping(speciesContextSpecs[i].getSpeciesContext().getStructure());
String[] symbols = initExpr.getSymbols();
// Check if 'initExpr' has other speciesContexts in its expression, need to replace it with 'spContext_init'
for (int j = 0; symbols != null && j < symbols.length; j++) {
// if symbol is a speciesContext, replacing it with a reference to initial condition for that speciesContext.
SpeciesContext spC = null;
SymbolTableEntry ste = initExpr.getSymbolBinding(symbols[j]);
if (ste instanceof SpeciesContextSpecProxyParameter) {
SpeciesContextSpecProxyParameter spspp = (SpeciesContextSpecProxyParameter) ste;
if (spspp.getTarget() instanceof SpeciesContext) {
spC = (SpeciesContext) spspp.getTarget();
SpeciesContextSpec spcspec = simContext.getReactionContext().getSpeciesContextSpec(spC);
SpeciesContextSpecParameter spCInitParm = spcspec.getParameterFromRole(SpeciesContextSpec.ROLE_InitialConcentration);
// if initConc param expression is null, try initCount
if (spCInitParm.getExpression() == null) {
spCInitParm = spcspec.getParameterFromRole(SpeciesContextSpec.ROLE_InitialCount);
}
// need to get init condn expression, but can't get it from getMathSymbol() (mapping between bio and math), hence get it as below.
Expression scsInitExpr = new Expression(spCInitParm, getNameScope());
// scsInitExpr.bindExpression(this);
initExpr.substituteInPlace(new Expression(spC.getName()), scsInitExpr);
}
}
}
// now create the appropriate function for the current speciesContextSpec.
varHash.addVariable(newFunctionOrConstant(getMathSymbol(initParm, sm), getIdentifierSubstitutions(initExpr, initParm.getUnitDefinition(), sm)));
}
}
//
for (int i = 0; i < speciesContextSpecs.length; i++) {
SpeciesContextMapping scm = getSpeciesContextMapping(speciesContextSpecs[i].getSpeciesContext());
SpeciesContextSpec.SpeciesContextSpecParameter diffParm = speciesContextSpecs[i].getParameterFromRole(SpeciesContextSpec.ROLE_DiffusionRate);
if (diffParm != null && (scm.isPDERequired())) {
StructureMapping sm = simContext.getGeometryContext().getStructureMapping(speciesContextSpecs[i].getSpeciesContext().getStructure());
varHash.addVariable(newFunctionOrConstant(getMathSymbol(diffParm, sm), getIdentifierSubstitutions(diffParm.getExpression(), diffParm.getUnitDefinition(), sm)));
}
}
//
for (int i = 0; i < speciesContextSpecs.length; i++) {
SpeciesContextSpec.SpeciesContextSpecParameter bc_xm = speciesContextSpecs[i].getParameterFromRole(SpeciesContextSpec.ROLE_BoundaryValueXm);
StructureMapping sm = simContext.getGeometryContext().getStructureMapping(speciesContextSpecs[i].getSpeciesContext().getStructure());
if (bc_xm != null && (bc_xm.getExpression() != null)) {
varHash.addVariable(newFunctionOrConstant(getMathSymbol(bc_xm, sm), getIdentifierSubstitutions(bc_xm.getExpression(), bc_xm.getUnitDefinition(), sm)));
}
SpeciesContextSpec.SpeciesContextSpecParameter bc_xp = speciesContextSpecs[i].getParameterFromRole(SpeciesContextSpec.ROLE_BoundaryValueXp);
if (bc_xp != null && (bc_xp.getExpression() != null)) {
varHash.addVariable(newFunctionOrConstant(getMathSymbol(bc_xp, sm), getIdentifierSubstitutions(bc_xp.getExpression(), bc_xp.getUnitDefinition(), sm)));
}
SpeciesContextSpec.SpeciesContextSpecParameter bc_ym = speciesContextSpecs[i].getParameterFromRole(SpeciesContextSpec.ROLE_BoundaryValueYm);
if (bc_ym != null && (bc_ym.getExpression() != null)) {
varHash.addVariable(newFunctionOrConstant(getMathSymbol(bc_ym, sm), getIdentifierSubstitutions(bc_ym.getExpression(), bc_ym.getUnitDefinition(), sm)));
}
SpeciesContextSpec.SpeciesContextSpecParameter bc_yp = speciesContextSpecs[i].getParameterFromRole(SpeciesContextSpec.ROLE_BoundaryValueYp);
if (bc_yp != null && (bc_yp.getExpression() != null)) {
varHash.addVariable(newFunctionOrConstant(getMathSymbol(bc_yp, sm), getIdentifierSubstitutions(bc_yp.getExpression(), bc_yp.getUnitDefinition(), sm)));
}
SpeciesContextSpec.SpeciesContextSpecParameter bc_zm = speciesContextSpecs[i].getParameterFromRole(SpeciesContextSpec.ROLE_BoundaryValueZm);
if (bc_zm != null && (bc_zm.getExpression() != null)) {
varHash.addVariable(newFunctionOrConstant(getMathSymbol(bc_zm, sm), getIdentifierSubstitutions(bc_zm.getExpression(), bc_zm.getUnitDefinition(), sm)));
}
SpeciesContextSpec.SpeciesContextSpecParameter bc_zp = speciesContextSpecs[i].getParameterFromRole(SpeciesContextSpec.ROLE_BoundaryValueZp);
if (bc_zp != null && (bc_zp.getExpression() != null)) {
varHash.addVariable(newFunctionOrConstant(getMathSymbol(bc_zp, sm), getIdentifierSubstitutions(bc_zp.getExpression(), bc_zp.getUnitDefinition(), sm)));
}
}
//
for (int i = 0; i < speciesContextSpecs.length; i++) {
SpeciesContextSpec.SpeciesContextSpecParameter advection_velX = speciesContextSpecs[i].getParameterFromRole(SpeciesContextSpec.ROLE_VelocityX);
StructureMapping sm = simContext.getGeometryContext().getStructureMapping(speciesContextSpecs[i].getSpeciesContext().getStructure());
if (advection_velX != null && (advection_velX.getExpression() != null)) {
varHash.addVariable(newFunctionOrConstant(getMathSymbol(advection_velX, sm), getIdentifierSubstitutions(advection_velX.getExpression(), advection_velX.getUnitDefinition(), sm)));
}
SpeciesContextSpec.SpeciesContextSpecParameter advection_velY = speciesContextSpecs[i].getParameterFromRole(SpeciesContextSpec.ROLE_VelocityY);
if (advection_velY != null && (advection_velY.getExpression() != null)) {
varHash.addVariable(newFunctionOrConstant(getMathSymbol(advection_velY, sm), getIdentifierSubstitutions(advection_velY.getExpression(), advection_velY.getUnitDefinition(), sm)));
}
SpeciesContextSpec.SpeciesContextSpecParameter advection_velZ = speciesContextSpecs[i].getParameterFromRole(SpeciesContextSpec.ROLE_VelocityZ);
if (advection_velZ != null && (advection_velZ.getExpression() != null)) {
varHash.addVariable(newFunctionOrConstant(getMathSymbol(advection_velZ, sm), getIdentifierSubstitutions(advection_velZ.getExpression(), advection_velZ.getUnitDefinition(), sm)));
}
}
//
// constant species (either function or constant)
//
enum1 = getSpeciesContextMappings();
while (enum1.hasMoreElements()) {
SpeciesContextMapping scm = (SpeciesContextMapping) enum1.nextElement();
if (scm.getVariable() instanceof Constant) {
varHash.addVariable(scm.getVariable());
}
}
//
// conversion factors
//
varHash.addVariable(new Constant(getMathSymbol(model.getKMOLE(), null), getIdentifierSubstitutions(model.getKMOLE().getExpression(), model.getKMOLE().getUnitDefinition(), null)));
varHash.addVariable(new Constant(model.getN_PMOLE().getName(), getIdentifierSubstitutions(model.getN_PMOLE().getExpression(), model.getN_PMOLE().getUnitDefinition(), null)));
varHash.addVariable(new Constant(model.getKMILLIVOLTS().getName(), getIdentifierSubstitutions(model.getKMILLIVOLTS().getExpression(), model.getKMILLIVOLTS().getUnitDefinition(), null)));
varHash.addVariable(new Constant(model.getK_GHK().getName(), getIdentifierSubstitutions(model.getK_GHK().getExpression(), model.getK_GHK().getUnitDefinition(), null)));
//
// geometric functions
//
ModelUnitSystem modelUnitSystem = simContext.getModel().getUnitSystem();
VCUnitDefinition lengthInverseUnit = modelUnitSystem.getLengthUnit().getInverse();
for (int i = 0; i < structureMappings.length; i++) {
StructureMapping sm = structureMappings[i];
Parameter parm = sm.getParameterFromRole(StructureMapping.ROLE_VolumeFraction);
if (parm != null && parm.getExpression() != null && sm.getGeometryClass() instanceof SubVolume) {
varHash.addVariable(newFunctionOrConstant(getMathSymbol(parm, sm), getIdentifierSubstitutions(parm.getExpression(), parm.getUnitDefinition(), sm)));
}
parm = sm.getParameterFromRole(StructureMapping.ROLE_SurfaceToVolumeRatio);
if (parm != null && parm.getExpression() != null && sm.getGeometryClass() instanceof SubVolume) {
varHash.addVariable(newFunctionOrConstant(getMathSymbol(parm, sm), getIdentifierSubstitutions(parm.getExpression(), parm.getUnitDefinition(), sm)));
}
if (sm instanceof MembraneMapping && !getResolved(sm)) {
MembraneMapping mm = (MembraneMapping) sm;
parm = ((MembraneMapping) sm).getVolumeFractionParameter();
if (parm.getExpression() == null) {
throw new MappingException("volume fraction not specified for feature '" + structTopology.getInsideFeature(mm.getMembrane()).getName() + "', please refer to Structure Mapping in Application '" + simContext.getName() + "'");
}
varHash.addVariable(newFunctionOrConstant(getMathSymbol(parm, sm), getIdentifierSubstitutions(parm.getExpression(), modelUnitSystem.getInstance_DIMENSIONLESS(), sm)));
parm = mm.getSurfaceToVolumeParameter();
if (parm.getExpression() == null) {
throw new MappingException("surface to volume ratio not specified for membrane '" + mm.getMembrane().getName() + "', please refer to Structure Mapping in Application '" + simContext.getName() + "'");
}
varHash.addVariable(newFunctionOrConstant(getMathSymbol(parm, sm), getIdentifierSubstitutions(parm.getExpression(), lengthInverseUnit, sm)));
}
StructureMappingParameter sizeParm = sm.getSizeParameter();
if (sizeParm != null) {
if (simContext.getGeometry().getDimension() == 0) {
if (sizeParm.getExpression() != null) {
try {
double value = sizeParm.getExpression().evaluateConstant();
varHash.addVariable(new Constant(getMathSymbol(sizeParm, sm), new Expression(value)));
} catch (ExpressionException e) {
// varHash.addVariable(new Function(getMathSymbol(parm,sm),getIdentifierSubstitutions(parm.getExpression(),parm.getUnitDefinition(),sm)));
e.printStackTrace(System.out);
throw new MappingException("Size of structure:" + sm.getNameScope().getName() + " cannot be evaluated as constant.");
}
}
} else {
String compartmentName = null;
VCUnitDefinition sizeUnit = sm.getSizeParameter().getUnitDefinition();
String sizeFunctionName = null;
if (sm instanceof MembraneMapping) {
MembraneMapping mm = (MembraneMapping) sm;
if (getResolved(mm)) {
FeatureMapping fm_inside = (FeatureMapping) simContext.getGeometryContext().getStructureMapping(structTopology.getInsideFeature(mm.getMembrane()));
FeatureMapping fm_outside = (FeatureMapping) simContext.getGeometryContext().getStructureMapping(structTopology.getOutsideFeature(mm.getMembrane()));
compartmentName = getSubVolume(fm_inside).getName() + "_" + getSubVolume(fm_outside).getName();
sizeFunctionName = MathFunctionDefinitions.Function_regionArea_current.getFunctionName();
} else {
FeatureMapping fm_inside = (FeatureMapping) simContext.getGeometryContext().getStructureMapping(structTopology.getInsideFeature(mm.getMembrane()));
FeatureMapping fm_outside = (FeatureMapping) simContext.getGeometryContext().getStructureMapping(structTopology.getOutsideFeature(mm.getMembrane()));
if (getSubVolume(fm_inside) == getSubVolume(fm_outside)) {
compartmentName = getSubVolume(fm_inside).getName();
sizeFunctionName = MathFunctionDefinitions.Function_regionVolume_current.getFunctionName();
} else {
throw new RuntimeException("unexpected structure mapping for membrane '" + mm.getMembrane().getName() + "'");
}
}
} else if (sm instanceof FeatureMapping) {
FeatureMapping fm = (FeatureMapping) sm;
compartmentName = getSubVolume(fm).getName();
sizeFunctionName = MathFunctionDefinitions.Function_regionVolume_current.getFunctionName();
} else {
throw new RuntimeException("structure mapping " + sm.getClass().getName() + " not yet supported");
}
Expression totalVolumeCorrection = sm.getStructureSizeCorrection(simContext, this);
Expression sizeFunctionExpression = Expression.function(sizeFunctionName, new Expression[] { new Expression("'" + compartmentName + "'") });
sizeFunctionExpression.bindExpression(mathDesc);
varHash.addVariable(newFunctionOrConstant(getMathSymbol(sizeParm, sm), getIdentifierSubstitutions(Expression.mult(totalVolumeCorrection, sizeFunctionExpression), sizeUnit, sm)));
parm = sm.getParameterFromRole(StructureMapping.ROLE_AreaPerUnitArea);
if (parm != null && parm.getExpression() != null && sm.getGeometryClass() instanceof SurfaceClass) {
varHash.addVariable(newFunctionOrConstant(getMathSymbol(parm, sm), getIdentifierSubstitutions(parm.getExpression(), parm.getUnitDefinition(), sm)));
}
parm = sm.getParameterFromRole(StructureMapping.ROLE_AreaPerUnitVolume);
if (parm != null && parm.getExpression() != null && sm.getGeometryClass() instanceof SubVolume) {
varHash.addVariable(newFunctionOrConstant(getMathSymbol(parm, sm), getIdentifierSubstitutions(parm.getExpression(), parm.getUnitDefinition(), sm)));
}
parm = sm.getParameterFromRole(StructureMapping.ROLE_VolumePerUnitArea);
if (parm != null && parm.getExpression() != null && sm.getGeometryClass() instanceof SurfaceClass) {
varHash.addVariable(newFunctionOrConstant(getMathSymbol(parm, sm), getIdentifierSubstitutions(parm.getExpression(), parm.getUnitDefinition(), sm)));
}
parm = sm.getParameterFromRole(StructureMapping.ROLE_VolumePerUnitVolume);
if (parm != null && parm.getExpression() != null && sm.getGeometryClass() instanceof SubVolume) {
varHash.addVariable(newFunctionOrConstant(getMathSymbol(parm, sm), getIdentifierSubstitutions(parm.getExpression(), parm.getUnitDefinition(), sm)));
}
}
}
}
//
for (int i = 0; i < fieldMathMappingParameters.length; i++) {
varHash.addVariable(newFunctionOrConstant(getMathSymbol(fieldMathMappingParameters[i], null), getIdentifierSubstitutions(fieldMathMappingParameters[i].getExpression(), fieldMathMappingParameters[i].getUnitDefinition(), null)));
}
//
// functions
//
enum1 = getSpeciesContextMappings();
while (enum1.hasMoreElements()) {
SpeciesContextMapping scm = (SpeciesContextMapping) enum1.nextElement();
if (scm.getVariable() == null && scm.getDependencyExpression() != null) {
StructureMapping sm = simContext.getGeometryContext().getStructureMapping(scm.getSpeciesContext().getStructure());
varHash.addVariable(newFunctionOrConstant(getMathSymbol(scm.getSpeciesContext(), sm), getIdentifierSubstitutions(scm.getDependencyExpression(), scm.getSpeciesContext().getUnitDefinition(), sm)));
}
}
//
// set Variables to MathDescription all at once with the order resolved by "VariableHash"
//
mathDesc.setAllVariables(varHash.getAlphabeticallyOrderedVariables());
//
if (simContext.getGeometryContext().getGeometry() != null) {
try {
mathDesc.setGeometry(simContext.getGeometryContext().getGeometry());
} catch (java.beans.PropertyVetoException e) {
e.printStackTrace(System.out);
throw new MappingException("failure setting geometry " + e.getMessage());
}
} else {
throw new MappingException("geometry must be defined");
}
//
// volume subdomains
//
subVolumes = simContext.getGeometryContext().getGeometry().getGeometrySpec().getSubVolumes();
VCUnitDefinition timeUnit = modelUnitSystem.getTimeUnit();
for (int j = 0; j < subVolumes.length; j++) {
SubVolume subVolume = (SubVolume) subVolumes[j];
//
// get priority of subDomain
//
int priority;
Feature spatialFeature = getResolvedFeature(subVolume);
if (spatialFeature == null) {
if (simContext.getGeometryContext().getGeometry().getDimension() > 0) {
throw new MappingException("no compartment (in Physiology) is mapped to subdomain '" + subVolume.getName() + "' (in Geometry)");
} else {
priority = CompartmentSubDomain.NON_SPATIAL_PRIORITY;
}
} else {
// now does not have to match spatial feature, *BUT* needs to be unique
priority = j;
}
//
// create subDomain
//
CompartmentSubDomain subDomain = new CompartmentSubDomain(subVolume.getName(), priority);
mathDesc.addSubDomain(subDomain);
//
if (spatialFeature != null) {
FeatureMapping fm = (FeatureMapping) simContext.getGeometryContext().getStructureMapping(spatialFeature);
subDomain.setBoundaryConditionXm(fm.getBoundaryConditionTypeXm());
subDomain.setBoundaryConditionXp(fm.getBoundaryConditionTypeXp());
if (simContext.getGeometry().getDimension() > 1) {
subDomain.setBoundaryConditionYm(fm.getBoundaryConditionTypeYm());
subDomain.setBoundaryConditionYp(fm.getBoundaryConditionTypeYp());
}
if (simContext.getGeometry().getDimension() > 2) {
subDomain.setBoundaryConditionZm(fm.getBoundaryConditionTypeZm());
subDomain.setBoundaryConditionZp(fm.getBoundaryConditionTypeZp());
}
}
//
// create equations
//
VolumeStructureAnalyzer structureAnalyzer = getVolumeStructureAnalyzer(subVolume);
Enumeration<SpeciesContextMapping> enumSCM = getSpeciesContextMappings();
while (enumSCM.hasMoreElements()) {
SpeciesContextMapping scm = enumSCM.nextElement();
//
if (scm.getVariable() instanceof VolVariable && scm.getDependencyExpression() == null) {
SpeciesContext sc = scm.getSpeciesContext();
StructureMapping sm = simContext.getGeometryContext().getStructureMapping(sc.getStructure());
SpeciesContextSpec scs = simContext.getReactionContext().getSpeciesContextSpec(sc);
VolVariable variable = (VolVariable) scm.getVariable();
Equation equation = null;
if ((scm.isPDERequired()) && sm instanceof FeatureMapping) {
//
if (getSubVolume((FeatureMapping) sm) == subVolume) {
//
// species context belongs to this subDomain
//
Expression initial = new Expression(getMathSymbol(scs.getParameterFromRole(SpeciesContextSpec.ROLE_InitialConcentration), sm));
Expression rate = getIdentifierSubstitutions(scm.getRate(), scm.getSpeciesContext().getUnitDefinition().divideBy(timeUnit), simContext.getGeometryContext().getStructureMapping(sc.getStructure()));
Expression diffusion = new Expression(getMathSymbol(scs.getDiffusionParameter(), sm));
equation = new PdeEquation(variable, initial, rate, diffusion);
((PdeEquation) equation).setBoundaryXm((scs.getBoundaryXmParameter().getExpression() == null) ? (null) : new Expression(getMathSymbol(scs.getBoundaryXmParameter(), sm)));
((PdeEquation) equation).setBoundaryXp((scs.getBoundaryXpParameter().getExpression() == null) ? (null) : new Expression(getMathSymbol(scs.getBoundaryXpParameter(), sm)));
((PdeEquation) equation).setBoundaryYm((scs.getBoundaryYmParameter().getExpression() == null) ? (null) : new Expression(getMathSymbol(scs.getBoundaryYmParameter(), sm)));
((PdeEquation) equation).setBoundaryYp((scs.getBoundaryYpParameter().getExpression() == null) ? (null) : new Expression(getMathSymbol(scs.getBoundaryYpParameter(), sm)));
((PdeEquation) equation).setBoundaryZm((scs.getBoundaryZmParameter().getExpression() == null) ? (null) : new Expression(getMathSymbol(scs.getBoundaryZmParameter(), sm)));
((PdeEquation) equation).setBoundaryZp((scs.getBoundaryZpParameter().getExpression() == null) ? (null) : new Expression(getMathSymbol(scs.getBoundaryZpParameter(), sm)));
((PdeEquation) equation).setVelocityX((scs.getVelocityXParameter().getExpression() == null) ? (null) : new Expression(getMathSymbol(scs.getVelocityXParameter(), sm)));
((PdeEquation) equation).setVelocityY((scs.getVelocityYParameter().getExpression() == null) ? (null) : new Expression(getMathSymbol(scs.getVelocityYParameter(), sm)));
((PdeEquation) equation).setVelocityZ((scs.getVelocityZParameter().getExpression() == null) ? (null) : new Expression(getMathSymbol(scs.getVelocityZParameter(), sm)));
subDomain.replaceEquation(equation);
} else {
Expression initial = new Expression(0.0);
Expression rate = new Expression(0.0);
Expression diffusion = new Expression(getMathSymbol(scs.getDiffusionParameter(), sm));
equation = new PdeEquation(variable, initial, rate, diffusion);
if (subDomain.getEquation(variable) == null) {
subDomain.addEquation(equation);
}
}
} else {
//
// ODE
//
SubVolume mappedSubVolume = null;
if (sm instanceof FeatureMapping) {
mappedSubVolume = getSubVolume((FeatureMapping) sm);
} else if (sm instanceof MembraneMapping) {
// membrane is mapped to that of the inside feature
FeatureMapping featureMapping = (FeatureMapping) simContext.getGeometryContext().getStructureMapping(structTopology.getInsideFeature((Membrane) sm.getStructure()));
mappedSubVolume = getSubVolume(featureMapping);
}
if (mappedSubVolume == subVolume) {
//
// species context belongs to this subDomain
//
Expression initial = new Expression(getMathSymbol(scs.getParameterFromRole(SpeciesContextSpec.ROLE_InitialConcentration), null));
Expression rate = (scm.getRate() == null) ? new Expression(0.0) : getIdentifierSubstitutions(scm.getRate(), scm.getSpeciesContext().getUnitDefinition().divideBy(timeUnit), simContext.getGeometryContext().getStructureMapping(sc.getStructure()));
equation = new OdeEquation(variable, initial, rate);
subDomain.replaceEquation(equation);
} else {
Expression initial = new Expression(0.0);
Expression rate = new Expression(0.0);
equation = new OdeEquation(variable, initial, rate);
if (subDomain.getEquation(variable) == null) {
subDomain.addEquation(equation);
}
}
}
}
}
//
// create fast system (if neccessary)
//
SpeciesContextMapping[] fastSpeciesContextMappings = structureAnalyzer.getFastSpeciesContextMappings();
VCUnitDefinition subDomainUnit = modelUnitSystem.getVolumeConcentrationUnit();
if (fastSpeciesContextMappings != null) {
FastSystem fastSystem = new FastSystem(mathDesc);
for (int i = 0; i < fastSpeciesContextMappings.length; i++) {
SpeciesContextMapping scm = fastSpeciesContextMappings[i];
if (scm.getFastInvariant() == null) {
//
// independant-fast variable, create a fastRate object
//
Expression rate = getIdentifierSubstitutions(scm.getFastRate(), scm.getSpeciesContext().getUnitDefinition().divideBy(timeUnit), simContext.getGeometryContext().getStructureMapping(getResolvedFeature(subVolume)));
FastRate fastRate = new FastRate(rate);
fastSystem.addFastRate(fastRate);
} else {
//
// dependant-fast variable, create a fastInvariant object
//
Expression rate = getIdentifierSubstitutions(scm.getFastInvariant(), subDomainUnit, simContext.getGeometryContext().getStructureMapping(getResolvedFeature(subVolume)));
FastInvariant fastInvariant = new FastInvariant(rate);
fastSystem.addFastInvariant(fastInvariant);
}
}
subDomain.setFastSystem(fastSystem);
// constructor calls the 'refresh' method which constructs depemdency matrix, dependent/independent vars and pseudoconstants, etc.
FastSystemAnalyzer fs_analyzer = new FastSystemAnalyzer(fastSystem, mathDesc);
}
//
// create ode's for voltages to be calculated on unresolved membranes mapped to this subVolume
//
Structure[] localStructures = getStructures(subVolume);
for (int sIndex = 0; sIndex < localStructures.length; sIndex++) {
if (localStructures[sIndex] instanceof Membrane) {
Membrane membrane = (Membrane) localStructures[sIndex];
MembraneMapping membraneMapping = (MembraneMapping) simContext.getGeometryContext().getStructureMapping(membrane);
if (!getResolved(membraneMapping) && membraneMapping.getCalculateVoltage()) {
MembraneElectricalDevice capacitiveDevice = potentialMapping.getCapacitiveDevice(membrane);
if (capacitiveDevice.getDependentVoltageExpression() == null) {
VolVariable vVar = (VolVariable) mathDesc.getVariable(getMathSymbol(capacitiveDevice.getVoltageSymbol(), membraneMapping));
Expression initExp = new Expression(getMathSymbol(capacitiveDevice.getMembraneMapping().getInitialVoltageParameter(), membraneMapping));
subDomain.addEquation(new OdeEquation(vVar, initExp, getIdentifierSubstitutions(potentialMapping.getOdeRHS(capacitiveDevice, this), membrane.getMembraneVoltage().getUnitDefinition().divideBy(timeUnit), membraneMapping)));
} else {
//
//
//
}
}
}
}
}
//
for (int k = 0; k < subVolumes.length; k++) {
SubVolume subVolume = (SubVolume) subVolumes[k];
//
// if there is a spatially resolved membrane surrounding this subVolume, then create a membraneSubDomain
//
structures = getStructures(subVolume);
Membrane membrane = null;
if (structures != null) {
for (int j = 0; j < structures.length; j++) {
if (structures[j] instanceof Membrane && getResolved(simContext.getGeometryContext().getStructureMapping(structures[j]))) {
membrane = (Membrane) structures[j];
}
}
}
if (membrane == null) {
continue;
}
SubVolume outerSubVolume = getSubVolume(((FeatureMapping) simContext.getGeometryContext().getStructureMapping(structTopology.getOutsideFeature(membrane))));
SubVolume innerSubVolume = getSubVolume(((FeatureMapping) simContext.getGeometryContext().getStructureMapping(structTopology.getInsideFeature(membrane))));
if (innerSubVolume != subVolume) {
throw new MappingException("membrane " + membrane.getName() + " improperly mapped to inner subVolume " + innerSubVolume.getName());
}
//
// get priority of subDomain
//
// Feature spatialFeature = simContext.getGeometryContext().getResolvedFeature(subVolume);
// int priority = spatialFeature.getPriority();
//
// create subDomain
//
CompartmentSubDomain outerCompartment = mathDesc.getCompartmentSubDomain(outerSubVolume.getName());
CompartmentSubDomain innerCompartment = mathDesc.getCompartmentSubDomain(innerSubVolume.getName());
SurfaceClass surfaceClass = simContext.getGeometry().getGeometrySurfaceDescription().getSurfaceClass(innerSubVolume, outerSubVolume);
MembraneSubDomain memSubDomain = new MembraneSubDomain(innerCompartment, outerCompartment, surfaceClass.getName());
mathDesc.addSubDomain(memSubDomain);
//
// create equations for membrane-bound molecular species
//
MembraneStructureAnalyzer membraneStructureAnalyzer = getMembraneStructureAnalyzer(membrane);
Enumeration<SpeciesContextMapping> enumSCM = getSpeciesContextMappings();
while (enumSCM.hasMoreElements()) {
SpeciesContextMapping scm = enumSCM.nextElement();
SpeciesContext sc = scm.getSpeciesContext();
SpeciesContextSpec scs = simContext.getReactionContext().getSpeciesContextSpec(sc);
//
if ((scm.getVariable() instanceof MemVariable) && scm.getDependencyExpression() == null) {
//
// independant variable, create an equation object
//
Equation equation = null;
MemVariable variable = (MemVariable) scm.getVariable();
MembraneMapping mm = (MembraneMapping) simContext.getGeometryContext().getStructureMapping(sc.getStructure());
if (scm.isPDERequired()) {
//
if (mm.getMembrane() == membrane) {
//
// species context belongs to this subDomain
//
Expression initial = new Expression(getMathSymbol(scs.getParameterFromRole(SpeciesContextSpec.ROLE_InitialConcentration), mm));
Expression rate = getIdentifierSubstitutions(scm.getRate(), scm.getSpeciesContext().getUnitDefinition().divideBy(timeUnit), simContext.getGeometryContext().getStructureMapping(sc.getStructure()));
Expression diffusion = new Expression(getMathSymbol(scs.getDiffusionParameter(), mm));
equation = new PdeEquation(variable, initial, rate, diffusion);
((PdeEquation) equation).setBoundaryXm((scs.getBoundaryXmParameter().getExpression() == null) ? (null) : new Expression(getMathSymbol(scs.getBoundaryXmParameter(), mm)));
((PdeEquation) equation).setBoundaryXp((scs.getBoundaryXpParameter().getExpression() == null) ? (null) : new Expression(getMathSymbol(scs.getBoundaryXpParameter(), mm)));
((PdeEquation) equation).setBoundaryYm((scs.getBoundaryYmParameter().getExpression() == null) ? (null) : new Expression(getMathSymbol(scs.getBoundaryYmParameter(), mm)));
((PdeEquation) equation).setBoundaryYp((scs.getBoundaryYpParameter().getExpression() == null) ? (null) : new Expression(getMathSymbol(scs.getBoundaryYpParameter(), mm)));
((PdeEquation) equation).setBoundaryZm((scs.getBoundaryZmParameter().getExpression() == null) ? (null) : new Expression(getMathSymbol(scs.getBoundaryZmParameter(), mm)));
((PdeEquation) equation).setBoundaryZp((scs.getBoundaryZpParameter().getExpression() == null) ? (null) : new Expression(getMathSymbol(scs.getBoundaryZpParameter(), mm)));
memSubDomain.replaceEquation(equation);
} else {
Expression initial = new Expression(0.0);
Expression rate = new Expression(0.0);
Expression diffusion = new Expression(getMathSymbol(scs.getDiffusionParameter(), mm));
equation = new PdeEquation(variable, initial, rate, diffusion);
if (memSubDomain.getEquation(variable) == null) {
memSubDomain.addEquation(equation);
}
}
} else {
//
if (mm.getMembrane() == membrane) {
//
// species context belongs to this subDomain
//
Expression initial = new Expression(getMathSymbol(scs.getParameterFromRole(SpeciesContextSpec.ROLE_InitialConcentration), null));
Expression rate = getIdentifierSubstitutions(scm.getRate(), scm.getSpeciesContext().getUnitDefinition().divideBy(timeUnit), simContext.getGeometryContext().getStructureMapping(sc.getStructure()));
equation = new OdeEquation(variable, initial, rate);
memSubDomain.replaceEquation(equation);
} else {
Expression initial = new Expression(0.0);
Expression rate = new Expression(0.0);
equation = new OdeEquation(variable, initial, rate);
if (memSubDomain.getEquation(variable) == null) {
memSubDomain.addEquation(equation);
}
}
}
}
}
//
// create dummy jump conditions for all volume variables that diffuse and/or advect
//
Enumeration<SpeciesContextMapping> enum_scm = getSpeciesContextMappings();
while (enum_scm.hasMoreElements()) {
SpeciesContextMapping scm = enum_scm.nextElement();
if (scm.isPDERequired()) {
// Species species = scm.getSpeciesContext().getSpecies();
Variable var = scm.getVariable();
if (var instanceof VolVariable && (scm.isPDERequired())) {
JumpCondition jc = memSubDomain.getJumpCondition((VolVariable) var);
if (jc == null) {
// System.out.println("MathMapping.refreshMathDescription(), adding jump condition for diffusing variable "+var.getName()+" on membrane "+membraneStructureAnalyzer.getMembrane().getName());
jc = new JumpCondition((VolVariable) var);
memSubDomain.addJumpCondition(jc);
}
}
}
}
//
// create jump conditions for any volume variables that bind to membrane or have explicitly defined fluxes
//
ResolvedFlux[] resolvedFluxes = membraneStructureAnalyzer.getResolvedFluxes();
if (resolvedFluxes != null) {
for (int i = 0; i < resolvedFluxes.length; i++) {
Species species = resolvedFluxes[i].getSpecies();
SpeciesContext sc = simContext.getReactionContext().getModel().getSpeciesContext(species, structTopology.getInsideFeature(membraneStructureAnalyzer.getMembrane()));
if (sc == null) {
sc = simContext.getReactionContext().getModel().getSpeciesContext(species, structTopology.getOutsideFeature(membraneStructureAnalyzer.getMembrane()));
}
SpeciesContextMapping scm = getSpeciesContextMapping(sc);
// if (scm.getVariable() instanceof VolVariable && scm.isDiffusing()){
if (scm.getVariable() instanceof VolVariable && ((MembraneStructureAnalyzer.bNoFluxIfFixed || (scm.isPDERequired())))) {
if (MembraneStructureAnalyzer.bNoFluxIfFixed && !scm.isPDERequired()) {
MembraneStructureAnalyzer.bNoFluxIfFixedExercised = true;
}
JumpCondition jc = memSubDomain.getJumpCondition((VolVariable) scm.getVariable());
if (jc == null) {
jc = new JumpCondition((VolVariable) scm.getVariable());
memSubDomain.addJumpCondition(jc);
}
Expression inFlux = getIdentifierSubstitutions(resolvedFluxes[i].inFluxExpression, resolvedFluxes[i].getUnitDefinition(), simContext.getGeometryContext().getStructureMapping(membraneStructureAnalyzer.getMembrane()));
jc.setInFlux(inFlux);
Expression outFlux = getIdentifierSubstitutions(resolvedFluxes[i].outFluxExpression, resolvedFluxes[i].getUnitDefinition(), simContext.getGeometryContext().getStructureMapping(membraneStructureAnalyzer.getMembrane()));
jc.setOutFlux(outFlux);
} else {
throw new MappingException("APPLICATION " + simContext.getName() + " : " + scm.getSpeciesContext().getName() + " has spatially resolved flux at membrane " + membrane.getName() + ", but doesn't diffuse in compartment " + scm.getSpeciesContext().getStructure().getName());
}
}
}
//
// create fast system (if neccessary)
//
SpeciesContextMapping[] fastSpeciesContextMappings = membraneStructureAnalyzer.getFastSpeciesContextMappings();
if (fastSpeciesContextMappings != null) {
FastSystem fastSystem = new FastSystem(mathDesc);
for (int i = 0; i < fastSpeciesContextMappings.length; i++) {
SpeciesContextMapping scm = fastSpeciesContextMappings[i];
if (scm.getFastInvariant() == null) {
//
// independant-fast variable, create a fastRate object
//
VCUnitDefinition rateUnit = scm.getSpeciesContext().getUnitDefinition().divideBy(timeUnit);
MembraneMapping membraneMapping = (MembraneMapping) simContext.getGeometryContext().getStructureMapping(membraneStructureAnalyzer.getMembrane());
FastRate fastRate = new FastRate(getIdentifierSubstitutions(scm.getFastRate(), rateUnit, membraneMapping));
fastSystem.addFastRate(fastRate);
} else {
//
// dependant-fast variable, create a fastInvariant object
//
VCUnitDefinition invariantUnit = scm.getSpeciesContext().getUnitDefinition();
MembraneMapping membraneMapping = (MembraneMapping) simContext.getGeometryContext().getStructureMapping(membraneStructureAnalyzer.getMembrane());
FastInvariant fastInvariant = new FastInvariant(getIdentifierSubstitutions(scm.getFastInvariant(), invariantUnit, membraneMapping));
fastSystem.addFastInvariant(fastInvariant);
}
}
memSubDomain.setFastSystem(fastSystem);
// constructor calls the 'refresh' method which constructs depemdency matrix, dependent/independent vars and pseudoconstants, etc.
FastSystemAnalyzer fs_analyzer = new FastSystemAnalyzer(fastSystem, mathDesc);
}
//
// create Membrane-region equations for potential of this resolved membrane
//
MembraneMapping membraneMapping = (MembraneMapping) simContext.getGeometryContext().getStructureMapping(membrane);
if (membraneMapping.getCalculateVoltage()) {
ElectricalDevice[] membraneDevices = potentialMapping.getElectricalDevices(membrane);
int numCapacitiveDevices = 0;
MembraneElectricalDevice capacitiveDevice = null;
for (int i = 0; i < membraneDevices.length; i++) {
if (membraneDevices[i] instanceof MembraneElectricalDevice) {
numCapacitiveDevices++;
capacitiveDevice = (MembraneElectricalDevice) membraneDevices[i];
}
}
if (numCapacitiveDevices != 1) {
throw new MappingException("expecting 1 capacitive electrical device on graph edge for membrane " + membrane.getName() + ", found '" + numCapacitiveDevices + "'");
}
if (mathDesc.getVariable(getMathSymbol(capacitiveDevice.getVoltageSymbol(), membraneMapping)) instanceof MembraneRegionVariable) {
MembraneRegionVariable vVar = (MembraneRegionVariable) mathDesc.getVariable(getMathSymbol(capacitiveDevice.getVoltageSymbol(), membraneMapping));
Parameter initialVoltageParm = capacitiveDevice.getMembraneMapping().getInitialVoltageParameter();
Expression initExp = getIdentifierSubstitutions(initialVoltageParm.getExpression(), initialVoltageParm.getUnitDefinition(), capacitiveDevice.getMembraneMapping());
MembraneRegionEquation vEquation = new MembraneRegionEquation(vVar, initExp);
vEquation.setMembraneRateExpression(getIdentifierSubstitutions(potentialMapping.getOdeRHS(capacitiveDevice, this), membrane.getMembraneVoltage().getUnitDefinition().divideBy(timeUnit), capacitiveDevice.getMembraneMapping()));
memSubDomain.addEquation(vEquation);
}
}
}
// create equations for event assign targets that are model params/strutureSize, etc.
Set<VolVariable> hashKeySet = eventVolVarHash.keySet();
Iterator<VolVariable> volVarsIter = hashKeySet.iterator();
// working under teh assumption that we are dealing with non-spatial math, hence only one compartment domain!
SubDomain subDomain = mathDesc.getSubDomains().nextElement();
while (volVarsIter.hasNext()) {
VolVariable volVar = volVarsIter.next();
EventAssignmentInitParameter eap = eventVolVarHash.get(volVar);
Expression rateExpr = new Expression(0.0);
Equation equation = new OdeEquation(volVar, new Expression(getMathSymbol(eap, null)), rateExpr);
subDomain.addEquation(equation);
}
// events - add events to math desc and odes for event assignments that have parameters as target variables
BioEvent[] bioevents = simContext.getBioEvents();
if (bioevents != null && bioevents.length > 0) {
for (BioEvent be : bioevents) {
// transform the bioEvent trigger/delay to math Event
Expression mathTriggerExpr = getIdentifierSubstitutions(be.generateTriggerExpression(), modelUnitSystem.getInstance_DIMENSIONLESS(), null);
Delay mathDelay = null;
if (be.getParameter(BioEventParameterType.TriggerDelay) != null) {
boolean bUseValsFromTriggerTime = be.getUseValuesFromTriggerTime();
Expression mathDelayExpr = getIdentifierSubstitutions(be.getParameter(BioEventParameterType.TriggerDelay).getExpression(), timeUnit, null);
mathDelay = new Delay(bUseValsFromTriggerTime, mathDelayExpr);
}
// now deal with (bio)event Assignment translation to math EventAssignment
ArrayList<EventAssignment> eventAssignments = be.getEventAssignments();
ArrayList<Event.EventAssignment> mathEventAssignmentsList = new ArrayList<Event.EventAssignment>();
for (EventAssignment ea : eventAssignments) {
SymbolTableEntry ste = simContext.getEntry(ea.getTarget().getName());
VCUnitDefinition eventAssignVarUnit = ste.getUnitDefinition();
Variable variable = varHash.getVariable(ste.getName());
Event.EventAssignment mathEA = new Event.EventAssignment(variable, getIdentifierSubstitutions(ea.getAssignmentExpression(), eventAssignVarUnit, null));
mathEventAssignmentsList.add(mathEA);
}
// use the translated trigger, delay and event assignments to create (math) event
Event mathEvent = new Event(be.getName(), mathTriggerExpr, mathDelay, mathEventAssignmentsList);
mathDesc.addEvent(mathEvent);
}
}
if (!mathDesc.isValid()) {
throw new MappingException("generated an invalid mathDescription: " + mathDesc.getWarning());
}
// System.out.println("]]]]]]]]]]]]]]]]]]]]]] VCML string begin ]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]");
// System.out.println(mathDesc.getVCML());
// System.out.println("]]]]]]]]]]]]]]]]]]]]]] VCML string end ]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]");
}
Also used :
MembraneMapping(cbit.vcell.mapping.MembraneMapping)
MembraneSubDomain(cbit.vcell.math.MembraneSubDomain)
ArrayList(java.util.ArrayList)
SpeciesContext(cbit.vcell.model.SpeciesContext)
StructureMappingParameter(cbit.vcell.mapping.StructureMapping.StructureMappingParameter)
Feature(cbit.vcell.model.Feature)
MemVariable(cbit.vcell.math.MemVariable)
KineticsParameter(cbit.vcell.model.Kinetics.KineticsParameter)
SubVolume(cbit.vcell.geometry.SubVolume)
Vector(java.util.Vector)
SpeciesContextSpecParameter(cbit.vcell.mapping.SpeciesContextSpec.SpeciesContextSpecParameter)
StructureTopology(cbit.vcell.model.Model.StructureTopology)
ReactionSpec(cbit.vcell.mapping.ReactionSpec)
FastInvariant(cbit.vcell.math.FastInvariant)
PropertyVetoException(java.beans.PropertyVetoException)
VCUnitDefinition(cbit.vcell.units.VCUnitDefinition)
FastSystem(cbit.vcell.math.FastSystem)
CompartmentSubDomain(cbit.vcell.math.CompartmentSubDomain)
ReactionStep(cbit.vcell.model.ReactionStep)
MembraneRegionEquation(cbit.vcell.math.MembraneRegionEquation)
SurfaceClass(cbit.vcell.geometry.SurfaceClass)
VariableHash(cbit.vcell.math.VariableHash)
StructureMapping(cbit.vcell.mapping.StructureMapping)
FeatureMapping(cbit.vcell.mapping.FeatureMapping)
Structure(cbit.vcell.model.Structure)
ModelUnitSystem(cbit.vcell.model.ModelUnitSystem)
Hashtable(java.util.Hashtable)
StructureMappingParameter(cbit.vcell.mapping.StructureMapping.StructureMappingParameter)
Expression(cbit.vcell.parser.Expression)
Model(cbit.vcell.model.Model)
ProxyParameter(cbit.vcell.model.ProxyParameter)
StructureMappingParameter(cbit.vcell.mapping.StructureMapping.StructureMappingParameter)
Parameter(cbit.vcell.model.Parameter)
KineticsParameter(cbit.vcell.model.Kinetics.KineticsParameter)
SpeciesContextSpecProxyParameter(cbit.vcell.mapping.SpeciesContextSpec.SpeciesContextSpecProxyParameter)
LocalParameter(cbit.vcell.mapping.ParameterContext.LocalParameter)
ModelParameter(cbit.vcell.model.Model.ModelParameter)
SpeciesContextSpecParameter(cbit.vcell.mapping.SpeciesContextSpec.SpeciesContextSpecParameter)
BioEvent(cbit.vcell.mapping.BioEvent)
Event(cbit.vcell.math.Event)
BioEvent(cbit.vcell.mapping.BioEvent)
MembraneRegionVariable(cbit.vcell.math.MembraneRegionVariable)
MathDescription(cbit.vcell.math.MathDescription)
SpeciesContextMapping(cbit.vcell.mapping.SpeciesContextMapping)
SpeciesContextSpec(cbit.vcell.mapping.SpeciesContextSpec)
ExpressionException(cbit.vcell.parser.ExpressionException)
Delay(cbit.vcell.math.Event.Delay)
MappingException(cbit.vcell.mapping.MappingException)
PropertyVetoException(java.beans.PropertyVetoException)
PdeEquation(cbit.vcell.math.PdeEquation)
CompartmentSubDomain(cbit.vcell.math.CompartmentSubDomain)
SubDomain(cbit.vcell.math.SubDomain)
MembraneSubDomain(cbit.vcell.math.MembraneSubDomain)
Species(cbit.vcell.model.Species)
SpeciesContextSpecParameter(cbit.vcell.mapping.SpeciesContextSpec.SpeciesContextSpecParameter)
EventAssignment(cbit.vcell.mapping.BioEvent.EventAssignment)
VolVariable(cbit.vcell.math.VolVariable)
ModelParameter(cbit.vcell.model.Model.ModelParameter)
OdeEquation(cbit.vcell.math.OdeEquation)
JumpCondition(cbit.vcell.math.JumpCondition)
MembraneRegionVariable(cbit.vcell.math.MembraneRegionVariable)
VolVariable(cbit.vcell.math.VolVariable)
MemVariable(cbit.vcell.math.MemVariable)
Variable(cbit.vcell.math.Variable)
SpeciesContextSpecProxyParameter(cbit.vcell.mapping.SpeciesContextSpec.SpeciesContextSpecProxyParameter)
Constant(cbit.vcell.math.Constant)
SymbolTableEntry(cbit.vcell.parser.SymbolTableEntry)
Membrane(cbit.vcell.model.Membrane)
EventAssignment(cbit.vcell.mapping.BioEvent.EventAssignment)
OdeEquation(cbit.vcell.math.OdeEquation)
MembraneRegionEquation(cbit.vcell.math.MembraneRegionEquation)
PdeEquation(cbit.vcell.math.PdeEquation)
Equation(cbit.vcell.math.Equation)
FastRate(cbit.vcell.math.FastRate)
Example 9 with SpeciesContextSpec
use of cbit.vcell.mapping.SpeciesContextSpec 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 10 with SpeciesContextSpec
use of cbit.vcell.mapping.SpeciesContextSpec in project vcell by virtualcell.
the class StochMathMapping_4_8 method refreshSpeciesContextMappings.
/**
* Insert the method's description here.
* Creation date: (10/26/2006 11:47:26 AM)
* @exception cbit.vcell.parser.ExpressionException The exception description.
* @exception cbit.vcell.mapping.MappingException The exception description.
* @exception cbit.vcell.math.MathException The exception description.
*/
private void refreshSpeciesContextMappings() throws cbit.vcell.parser.ExpressionException, MappingException, cbit.vcell.math.MathException {
//
// create a SpeciesContextMapping for each speciesContextSpec.
//
// set initialExpression from SpeciesContextSpec.
// set diffusing5
// set variable (only if "Constant" or "Function", else leave it as null)-----why commented?
//
//
// have to put geometric paras into mathsymbolmapping, since species initial condition needs the volume size symbol.
// and the parameters later on were added into contants or functions in refreshMathDescription()
//
StructureMapping[] structureMappings = getSimulationContext().getGeometryContext().getStructureMappings();
for (int i = 0; i < structureMappings.length; i++) {
StructureMapping sm = structureMappings[i];
StructureMapping.StructureMappingParameter parm = sm.getParameterFromRole(StructureMapping.ROLE_Size);
getMathSymbol(parm, sm);
}
getSpeciesContextMappingList().removeAllElements();
SpeciesContextSpec[] speciesContextSpecs = getSimulationContext().getReactionContext().getSpeciesContextSpecs();
for (int i = 0; i < speciesContextSpecs.length; i++) {
SpeciesContextSpec scs = speciesContextSpecs[i];
SpeciesContextMapping scm = new SpeciesContextMapping(scs.getSpeciesContext());
scm.setPDERequired(getSimulationContext().isPDERequired(scs.getSpeciesContext()));
scm.setHasEventAssignment(getSimulationContext().hasEventAssignment(scs.getSpeciesContext()));
scm.setHasHybridReaction(false);
for (ReactionSpec reactionSpec : getSimulationContext().getReactionContext().getReactionSpecs()) {
if (!reactionSpec.isExcluded() && reactionSpec.hasHybrid(getSimulationContext(), scs.getSpeciesContext())) {
scm.setHasHybridReaction(true);
}
}
// scm.setAdvecting(isAdvectionRequired(scs.getSpeciesContext()));
if (scs.isConstant()) {
SpeciesContextSpec.SpeciesContextSpecParameter initCountParm = scs.getInitialCountParameter();
SpeciesContextSpec.SpeciesContextSpecParameter initConcParm = scs.getInitialConcentrationParameter();
Expression initCondInCount = null;
// initial condition is concentration
if (initConcParm != null && initConcParm.getExpression() != null) {
initCondInCount = getExpressionConcToAmt(new Expression(initConcParm, getNameScope()), speciesContextSpecs[i].getSpeciesContext());
} else {
initCondInCount = new Expression(initCountParm, getNameScope());
}
// initCondInCount.bindExpression(this);
initCondInCount = getSubstitutedExpr(initCondInCount, true, true);
scm.setDependencyExpression(initCondInCount);
}
//
// test if participant in fast reaction step, request elimination if possible
//
scm.setFastParticipant(false);
ReactionSpec[] reactionSpecs = getSimulationContext().getReactionContext().getReactionSpecs();
for (int j = 0; j < reactionSpecs.length; j++) {
ReactionSpec reactionSpec = reactionSpecs[j];
if (reactionSpec.isExcluded()) {
continue;
}
ReactionStep rs = reactionSpec.getReactionStep();
if (rs instanceof SimpleReaction && rs.countNumReactionParticipants(scs.getSpeciesContext()) > 0) {
if (reactionSpec.isFast()) {
scm.setFastParticipant(true);
}
}
}
getSpeciesContextMappingList().addElement(scm);
}
}
Also used :
SimpleReaction(cbit.vcell.model.SimpleReaction)
SpeciesContextMapping(cbit.vcell.mapping.SpeciesContextMapping)
ReactionSpec(cbit.vcell.mapping.ReactionSpec)
SpeciesContextSpec(cbit.vcell.mapping.SpeciesContextSpec)
StructureMapping(cbit.vcell.mapping.StructureMapping)
Expression(cbit.vcell.parser.Expression)
ReactionStep(cbit.vcell.model.ReactionStep)
Aggregations
SpeciesContextSpec (cbit.vcell.mapping.SpeciesContextSpec)58
Expression (cbit.vcell.parser.Expression)33
SpeciesContext (cbit.vcell.model.SpeciesContext)28
SimulationContext (cbit.vcell.mapping.SimulationContext)23
Model (cbit.vcell.model.Model)21
BioModel (cbit.vcell.biomodel.BioModel)19
StructureMapping (cbit.vcell.mapping.StructureMapping)17
ReactionStep (cbit.vcell.model.ReactionStep)16
Simulation (cbit.vcell.solver.Simulation)13
ReactionSpec (cbit.vcell.mapping.ReactionSpec)12
SpeciesContextSpecParameter (cbit.vcell.mapping.SpeciesContextSpec.SpeciesContextSpecParameter)12
KineticsParameter (cbit.vcell.model.Kinetics.KineticsParameter)12
Structure (cbit.vcell.model.Structure)12
ExpressionException (cbit.vcell.parser.ExpressionException)12
MathDescription (cbit.vcell.math.MathDescription)11
ModelParameter (cbit.vcell.model.Model.ModelParameter)11
FeatureMapping (cbit.vcell.mapping.FeatureMapping)10
SpeciesContextMapping (cbit.vcell.mapping.SpeciesContextMapping)10
Feature (cbit.vcell.model.Feature)10
Parameter (cbit.vcell.model.Parameter)10
