use of cbit.vcell.modelopt.ModelOptimizationSpec in project vcell by virtualcell.
the class ParameterEstimationRunTaskPanel method plot.
private void plot() {
try {
java.util.Vector<DataSource> dataSourceList = new java.util.Vector<DataSource>();
java.util.Vector<String> nameVector = new java.util.Vector<String>();
ModelOptimizationSpec modelOptimizationSpec = parameterEstimationTask.getModelOptimizationSpec();
final ReferenceDataMappingSpec[] mappingSpecs = modelOptimizationSpec.getReferenceDataMappingSpecs();
int timeIndex = modelOptimizationSpec.getReferenceDataTimeColumnIndex();
ReferenceData referenceData = modelOptimizationSpec.getReferenceData();
if (referenceData != null) {
dataSourceList.add(new DataSource.DataSourceReferenceData("EXPT", timeIndex, referenceData));
String[] refColumnNames = referenceData.getColumnNames();
for (int i = 0; i < refColumnNames.length; i++) {
if (i == timeIndex) {
continue;
}
nameVector.add(refColumnNames[i]);
break;
}
}
ParameterEstimationTaskSimulatorIDA parestSimulator = new ParameterEstimationTaskSimulatorIDA();
ODESolverResultSet odeSolverResultSet = parestSimulator.getOdeSolverResultSet(parameterEstimationTask);
if (odeSolverResultSet != null) {
dataSourceList.add(new DataSource.DataSourceRowColumnResultSet("EST", odeSolverResultSet));
if (mappingSpecs != null) {
for (int i = 0; i < mappingSpecs.length; i++) {
if (i == timeIndex) {
continue;
}
Variable var = parameterEstimationTask.getMathSymbolMapping().getVariable(mappingSpecs[i].getModelObject());
nameVector.add(var.getName());
break;
}
}
}
DataSource[] dataSources = (DataSource[]) BeanUtils.getArray(dataSourceList, DataSource.class);
MultisourcePlotPane multisourcePlotPane = new MultisourcePlotPane();
multisourcePlotPane.setGroupingListSorter(new Comparator<SortDataReferenceHelper>() {
@Override
public int compare(SortDataReferenceHelper o1, SortDataReferenceHelper o2) {
DataSource ds01 = o1.dataReference.getDataSource();
DataSource ds02 = o2.dataReference.getDataSource();
// System.out.println(ds01.getClass().getSimpleName()+" "+o1.dataReference.getIdentifier()+" "+ds02.getClass().getSimpleName()+" "+o2.dataReference.getIdentifier());
if (ds01 instanceof DataSource.DataSourceReferenceData) {
if (ds02 instanceof DataSource.DataSourceReferenceData) {
// both reference data, sort names
ReferenceDataMappingSpec mspec01 = null;
ReferenceDataMappingSpec mspec02 = null;
for (ReferenceDataMappingSpec rdMappingSpec : mappingSpecs) {
// Variable var = parameterEstimationTask.getMathSymbolMapping().getVariable(rdMappingSpec.getModelObject());
if (rdMappingSpec.getModelObject() instanceof ReservedSymbol) {
continue;
}
if (o1.dataReference.getIdentifier().equals(rdMappingSpec.getReferenceDataColumnName())) {
mspec01 = rdMappingSpec;
o1.setReferenceDataMappingSpec(rdMappingSpec);
} else if (o2.dataReference.getIdentifier().equals(rdMappingSpec.getReferenceDataColumnName())) {
mspec02 = rdMappingSpec;
o2.setReferenceDataMappingSpec(rdMappingSpec);
}
}
if (mspec01 == null && mspec02 == null) {
return o1.dataReference.getIdentifier().compareToIgnoreCase(o2.dataReference.getIdentifier());
} else if (mspec01 != null && mspec02 != null) {
return mspec01.getReferenceDataColumnName().compareToIgnoreCase(mspec02.getReferenceDataColumnName());
} else if (mspec01 != null && mspec02 == null) {
return -1;
} else {
return 1;
}
} else {
// compare ref to ode
ReferenceDataMappingSpec mspec01 = null;
ReferenceDataMappingSpec mspec02 = null;
for (ReferenceDataMappingSpec rdMappingSpec : mappingSpecs) {
Variable var = parameterEstimationTask.getMathSymbolMapping().getVariable(rdMappingSpec.getModelObject());
if (rdMappingSpec.getModelObject() instanceof ReservedSymbol) {
continue;
}
if (o1.dataReference.getIdentifier().equals(rdMappingSpec.getReferenceDataColumnName())) {
mspec01 = rdMappingSpec;
o1.setReferenceDataMappingSpec(rdMappingSpec);
} else if (o2.dataReference.getIdentifier().equals(var.getName())) {
mspec02 = rdMappingSpec;
o2.setReferenceDataMappingSpec(rdMappingSpec);
}
}
if (mspec01 == null && mspec02 == null) {
return -1;
} else if (mspec01 != null && mspec02 == null) {
return -1;
} else if (mspec02 != null && mspec01 == null) {
return 1;
} else {
// BeanUtils.forceStringSize(mspec02.getReferenceDataColumnName(), 25, " ", true));
return mspec01.getReferenceDataColumnName().compareToIgnoreCase(mspec02.getReferenceDataColumnName());
}
}
} else {
if (ds02 instanceof DataSource.DataSourceRowColumnResultSet) {
// both OdeSolverResultSet data, sort names
ReferenceDataMappingSpec mspec01 = null;
ReferenceDataMappingSpec mspec02 = null;
for (ReferenceDataMappingSpec rdMappingSpec : mappingSpecs) {
Variable var = parameterEstimationTask.getMathSymbolMapping().getVariable(rdMappingSpec.getModelObject());
if (rdMappingSpec.getModelObject() instanceof ReservedSymbol) {
continue;
}
if (o1.dataReference.getIdentifier().equals(var.getName())) {
mspec01 = rdMappingSpec;
o1.setReferenceDataMappingSpec(rdMappingSpec);
} else if (o2.dataReference.getIdentifier().equals(var.getName())) {
mspec02 = rdMappingSpec;
o2.setReferenceDataMappingSpec(rdMappingSpec);
}
}
if (mspec01 == null && mspec02 == null) {
return o1.dataReference.getIdentifier().compareToIgnoreCase(o2.dataReference.getIdentifier());
} else if (mspec01 != null && mspec02 != null) {
return mspec01.getReferenceDataColumnName().compareToIgnoreCase(mspec02.getReferenceDataColumnName());
} else if (mspec01 != null && mspec02 == null) {
return -1;
} else {
return 1;
}
} else {
// compare ode to ref
ReferenceDataMappingSpec mspec01 = null;
ReferenceDataMappingSpec mspec02 = null;
for (ReferenceDataMappingSpec rdMappingSpec : mappingSpecs) {
Variable var = parameterEstimationTask.getMathSymbolMapping().getVariable(rdMappingSpec.getModelObject());
if (rdMappingSpec.getModelObject() instanceof ReservedSymbol) {
continue;
}
if (o2.dataReference.getIdentifier().equals(rdMappingSpec.getReferenceDataColumnName())) {
mspec02 = rdMappingSpec;
o2.setReferenceDataMappingSpec(rdMappingSpec);
} else if (o1.dataReference.getIdentifier().equals(var.getName())) {
mspec01 = rdMappingSpec;
o1.setReferenceDataMappingSpec(rdMappingSpec);
}
}
if (mspec01 == null && mspec02 == null) {
return 1;
} else if (mspec01 != null && mspec02 == null) {
return -1;
} else if (mspec02 != null && mspec01 == null) {
return 1;
} else {
// BeanUtils.forceStringSize(mspec02.getReferenceDataColumnName(), 25, " ", true));
return mspec01.getReferenceDataColumnName().compareToIgnoreCase(mspec02.getReferenceDataColumnName());
}
}
}
}
});
multisourcePlotPane.setDataSources(dataSources);
String[] nameArray = new String[nameVector.size()];
nameArray = (String[]) BeanUtils.getArray(nameVector, String.class);
multisourcePlotPane.select(nameArray);
DialogUtils.showComponentCloseDialog(JOptionPane.getFrameForComponent(this), multisourcePlotPane, "Data Plot");
} catch (Exception e) {
e.printStackTrace(System.out);
}
}
use of cbit.vcell.modelopt.ModelOptimizationSpec in project vcell by virtualcell.
the class IssueTableModel method getSourceObjectPathDescription.
private String getSourceObjectPathDescription(VCDocument vcDocument, Issue issue) {
VCAssert.assertValid(issue);
Object source = issue.getSource();
{
IssueOrigin io = BeanUtils.downcast(IssueOrigin.class, source);
if (io != null) {
return io.getDescription();
}
}
if (vcDocument instanceof BioModel) {
BioModel bioModel = (BioModel) vcDocument;
String description = "";
if (source instanceof SymbolTableEntry) {
if (source instanceof SpeciesContext) {
description = "Model / Species";
} else if (source instanceof RbmObservable) {
description = "Model / Observables";
} else {
description = ((SymbolTableEntry) source).getNameScope().getPathDescription();
}
} else if (source instanceof MolecularType) {
description = "Model / Molecules";
} else if (source instanceof ReactionStep) {
ReactionStep reactionStep = (ReactionStep) source;
description = ((ReactionNameScope) reactionStep.getNameScope()).getPathDescription();
} else if (source instanceof ReactionRule) {
ReactionRule reactionRule = (ReactionRule) source;
description = ((ReactionRuleNameScope) reactionRule.getNameScope()).getPathDescription();
} else if (source instanceof SpeciesPattern) {
// if (issue.getIssueContext().hasContextType(ContextType.SpeciesContext)){
// description = "Model / Species";
// }else if(issue.getIssueContext().hasContextType(ContextType.ReactionRule)) {
// ReactionRule thing = (ReactionRule)issue.getIssueContext().getContextObject(ContextType.ReactionRule);
// description = ((ReactionRuleNameScope)thing.getNameScope()).getPathDescription();
// }else if(issue.getIssueContext().hasContextType(ContextType.RbmObservable)) {
// description = "Model / Observables";
// } else {
System.err.println("Bad issue context for " + ((SpeciesPattern) source).toString());
description = ((SpeciesPattern) source).toString();
// }
} else if (source instanceof Structure) {
Structure structure = (Structure) source;
description = "Model / " + structure.getTypeName() + "(" + structure.getName() + ")";
} else if (source instanceof StructureMapping) {
StructureMapping structureMapping = (StructureMapping) source;
description = ((StructureMappingNameScope) structureMapping.getNameScope()).getPathDescription();
} else if (source instanceof OutputFunctionIssueSource) {
SimulationContext simulationContext = (SimulationContext) ((OutputFunctionIssueSource) source).getOutputFunctionContext().getSimulationOwner();
description = "App(" + simulationContext.getName() + ") / " + "Simulations" + " / " + "Output Functions";
} else if (source instanceof Simulation) {
Simulation simulation = (Simulation) source;
try {
SimulationContext simulationContext = bioModel.getSimulationContext(simulation);
description = "App(" + simulationContext.getName() + ") / Simulations";
} catch (ObjectNotFoundException e) {
e.printStackTrace();
description = "App(" + "unknown" + ") / Simulations";
}
} else if (source instanceof UnmappedGeometryClass) {
UnmappedGeometryClass unmappedGC = (UnmappedGeometryClass) source;
description = "App(" + unmappedGC.getSimulationContext().getName() + ") / Subdomain(" + unmappedGC.getGeometryClass().getName() + ")";
} else if (source instanceof GeometryContext) {
description = "App(" + ((GeometryContext) source).getSimulationContext().getName() + ")";
} else if (source instanceof ModelOptimizationSpec) {
description = "App(" + ((ModelOptimizationSpec) source).getSimulationContext().getName() + ") / Parameter Estimation";
} else if (source instanceof MicroscopeMeasurement) {
description = "App(" + ((MicroscopeMeasurement) source).getSimulationContext().getName() + ") / Microscope Measurements";
} else if (source instanceof SpatialObject) {
description = "App(" + ((SpatialObject) source).getSimulationContext().getName() + ") / Spatial Objects";
} else if (source instanceof SpatialProcess) {
description = "App(" + ((SpatialProcess) source).getSimulationContext().getName() + ") / Spatial Processes";
} else if (source instanceof SpeciesContextSpec) {
SpeciesContextSpec scs = (SpeciesContextSpec) source;
description = "App(" + scs.getSimulationContext().getName() + ") / Specifications / Species";
} else if (source instanceof ReactionCombo) {
ReactionCombo rc = (ReactionCombo) source;
description = "App(" + rc.getReactionContext().getSimulationContext().getName() + ") / Specifications / Reactions";
} else if (source instanceof RbmModelContainer) {
IssueCategory ic = issue.getCategory();
switch(ic) {
case RbmMolecularTypesTableBad:
description = "Model / " + MolecularType.typeName + "s";
break;
case RbmReactionRulesTableBad:
description = "Model / Reactions";
break;
case RbmObservablesTableBad:
description = "Model / Observables";
break;
case RbmNetworkConstraintsBad:
description = "Network Constrains";
break;
default:
description = "Model";
break;
}
} else if (source instanceof SimulationContext) {
SimulationContext sc = (SimulationContext) source;
IssueCategory ic = issue.getCategory();
switch(ic) {
case RbmNetworkConstraintsBad:
description = "Specifications / Network";
break;
default:
description = "Application";
break;
}
} else if (source instanceof Model) {
description = "Model";
} else if (source instanceof BioEvent) {
return "Protocols / Events";
} else if (source instanceof MathDescription) {
return "Math Description";
} else {
System.err.println("unknown source type in IssueTableModel.getSourceObjectPathDescription(): " + source.getClass());
}
return description;
} else if (vcDocument instanceof MathModel) {
if (source instanceof Geometry) {
return GuiConstants.DOCUMENT_EDITOR_FOLDERNAME_MATH_GEOMETRY;
} else if (source instanceof OutputFunctionIssueSource) {
return GuiConstants.DOCUMENT_EDITOR_FOLDERNAME_MATH_OUTPUTFUNCTIONS;
} else if (source instanceof Simulation) {
return "Simulation(" + ((Simulation) source).getName() + ")";
} else {
return GuiConstants.DOCUMENT_EDITOR_FOLDERNAME_MATH_VCML;
}
} else {
System.err.println("unknown document type in IssueTableModel.getSourceObjectPathDescription()");
return "";
}
}
use of cbit.vcell.modelopt.ModelOptimizationSpec in project vcell by virtualcell.
the class IssueTableModel method getSourceObjectDescription.
private String getSourceObjectDescription(VCDocument vcDocument, Issue issue) {
if (vcDocument instanceof BioModel) {
Object object = issue.getSource();
{
DecoratedIssueSource dis = BeanUtils.downcast(DecoratedIssueSource.class, object);
if (dis != null) {
return dis.getSourcePath();
}
}
String description = "";
if (object instanceof SymbolTableEntry) {
description = ((SymbolTableEntry) object).getName();
} else if (object instanceof ReactionStep) {
description = ((ReactionStep) object).getName();
} else if (object instanceof ReactionRule) {
description = ((ReactionRule) object).getName();
} else if (object instanceof SpeciesPattern) {
// Object parent = issue.getIssueContext().getContextObject();
// if (parent instanceof SpeciesContext){
// description = ((SpeciesContext)parent).getName();
// }
// if (issue.getIssueContext().hasContextType(ContextType.SpeciesContext)){
// SpeciesContext thing = (SpeciesContext)issue.getIssueContext().getContextObject(ContextType.SpeciesContext);
// description = thing.getName();
// }else if(issue.getIssueContext().hasContextType(ContextType.ReactionRule)) {
// ReactionRule thing = (ReactionRule)issue.getIssueContext().getContextObject(ContextType.ReactionRule);
// description = thing.getName();
// }else if(issue.getIssueContext().hasContextType(ContextType.RbmObservable)) {
// RbmObservable thing = (RbmObservable)issue.getIssueContext().getContextObject(ContextType.RbmObservable);
// description = thing.getName();
// } else {
System.err.println("Bad issue context for " + ((SpeciesPattern) object).toString());
description = ((SpeciesPattern) object).toString();
// }
} else if (object instanceof MolecularType) {
description = ((MolecularType) object).getName();
} else if (object instanceof MolecularComponent) {
description = ((MolecularComponent) object).getName();
} else if (object instanceof ComponentStateDefinition) {
description = ((ComponentStateDefinition) object).getName();
} else if (object instanceof Structure) {
description = ((Structure) object).getName();
} else if (object instanceof SubDomain) {
description = ((SubDomain) object).getName();
} else if (object instanceof Geometry) {
description = ((Geometry) object).getName();
} else if (object instanceof StructureMapping) {
description = ((StructureMapping) object).getStructure().getName();
} else if (object instanceof OutputFunctionIssueSource) {
description = ((OutputFunctionIssueSource) object).getAnnotatedFunction().getName();
} else if (object instanceof UnmappedGeometryClass) {
description = ((UnmappedGeometryClass) object).getGeometryClass().getName();
} else if (object instanceof MicroscopeMeasurement) {
description = ((MicroscopeMeasurement) object).getName();
} else if (object instanceof SpatialObject) {
description = ((SpatialObject) object).getName();
} else if (object instanceof SpatialProcess) {
description = ((SpatialProcess) object).getName();
} else if (object instanceof GeometryContext) {
description = "Geometry";
} else if (object instanceof ModelOptimizationSpec) {
description = ((ModelOptimizationSpec) object).getParameterEstimationTask().getName();
} else if (object instanceof Simulation) {
description = ((Simulation) object).getName();
} else if (object instanceof SpeciesContextSpec) {
SpeciesContextSpec scs = (SpeciesContextSpec) object;
description = scs.getSpeciesContext().getName();
} else if (object instanceof ReactionCombo) {
ReactionSpec rs = ((ReactionCombo) object).getReactionSpec();
description = rs.getReactionStep().getName();
} else if (object instanceof RbmModelContainer) {
// RbmModelContainer mc = (RbmModelContainer)object;
description = "Rules validator";
} else if (object instanceof SimulationContext) {
SimulationContext sc = (SimulationContext) object;
description = sc.getName();
} else if (object instanceof Model) {
Model m = (Model) object;
description = m.getName();
} else if (object instanceof BioEvent) {
return ((BioEvent) object).getName() + "";
} else if (object instanceof MathDescription) {
return ((MathDescription) object).getName() + "";
} else {
System.err.println("unknown object type in IssueTableModel.getSourceObjectDescription(): " + object.getClass());
}
return description;
} else if (vcDocument instanceof MathModel) {
Object object = issue.getSource();
String description = "";
if (object instanceof Variable) {
description = ((Variable) object).getName();
} else if (object instanceof SubDomain) {
description = ((SubDomain) object).getName();
} else if (object instanceof Geometry) {
description = "Geometry";
} else if (object instanceof OutputFunctionIssueSource) {
description = ((OutputFunctionIssueSource) object).getAnnotatedFunction().getName();
} else if (object instanceof MathDescription) {
return "math";
} else if (object instanceof Simulation) {
return "Simulation " + ((Simulation) object).getName() + "";
}
return description;
} else {
System.err.println("unknown document type in IssueTableModel.getSourceObjectDescription()");
return "";
}
}
use of cbit.vcell.modelopt.ModelOptimizationSpec in project vcell by virtualcell.
the class ReferenceDataMappingSpecTableModel method setModelOptimizationSpec.
/**
* Sets the modelOptimizationSpec property (cbit.vcell.modelopt.ModelOptimizationSpec) value.
* @param modelOptimizationSpec The new value for the property.
* @see #getModelOptimizationSpec
*/
public void setModelOptimizationSpec(ModelOptimizationSpec newValue) {
ModelOptimizationSpec oldValue = fieldModelOptimizationSpec;
if (oldValue != null) {
oldValue.removePropertyChangeListener(this);
ReferenceDataMappingSpec[] refDataMappingSpecs = oldValue.getReferenceDataMappingSpecs();
for (int i = 0; refDataMappingSpecs != null && i < refDataMappingSpecs.length; i++) {
refDataMappingSpecs[i].removePropertyChangeListener(this);
}
}
fieldModelOptimizationSpec = newValue;
if (newValue != null) {
newValue.addPropertyChangeListener(this);
ReferenceDataMappingSpec[] refDataMappingSpecs = newValue.getReferenceDataMappingSpecs();
for (int i = 0; refDataMappingSpecs != null && i < refDataMappingSpecs.length; i++) {
refDataMappingSpecs[i].addPropertyChangeListener(this);
}
}
fireTableDataChanged();
}
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