Example 6 with Variable
use of cbit.vcell.math.Variable in project vcell by virtualcell.
the class ParameterMappingPanel method jMenuItemPaste_ActionPerformed.
/**
* Comment
*/
private void jMenuItemPaste_ActionPerformed(java.awt.event.ActionEvent actionEvent) {
java.util.Vector<String> pasteDescriptionsV = new java.util.Vector<String>();
java.util.Vector<Expression> newExpressionsV = new java.util.Vector<Expression>();
java.util.Vector<ParameterMappingSpec> changedParametersV = new java.util.Vector<ParameterMappingSpec>();
try {
if (actionEvent.getSource() == getJMenuItemPaste() || actionEvent.getSource() == getJMenuItemPasteAll()) {
Object pasteThis = VCellTransferable.getFromClipboard(VCellTransferable.OBJECT_FLAVOR);
SimulationContext sc = getParameterEstimationTask().getModelOptimizationSpec().getSimulationContext();
MathSymbolMapping msm = null;
Exception mathMappingException = null;
try {
MathMapping mm = sc.createNewMathMapping();
msm = mm.getMathSymbolMapping();
} catch (Exception e) {
mathMappingException = e;
e.printStackTrace(System.out);
}
// if(msm == null){
// try{
// getParameterEstimationTask().refreshMappings();
// msm = getParameterEstimationTask().getMathSymbolMapping();
// }catch(Exception e){
// e.printStackTrace();
// }
// }
int[] rows = null;
if (actionEvent.getSource() == getJMenuItemPasteAll()) {
rows = new int[getScrollPaneTable().getRowCount()];
for (int i = 0; i < rows.length; i += 1) {
rows[i] = i;
}
} else {
rows = getScrollPaneTable().getSelectedRows();
}
//
// Check paste
//
StringBuffer errors = null;
for (int i = 0; i < rows.length; i += 1) {
ParameterMappingSpec pms = parameterMappingTableModel.getValueAt(rows[i]);
try {
if (pasteThis instanceof VCellTransferable.ResolvedValuesSelection) {
VCellTransferable.ResolvedValuesSelection rvs = (VCellTransferable.ResolvedValuesSelection) pasteThis;
for (int j = 0; j < rvs.getPrimarySymbolTableEntries().length; j += 1) {
ParameterMappingSpec pasteDestination = null;
Parameter clipboardBiologicalParameter = null;
if (rvs.getPrimarySymbolTableEntries()[j] instanceof Parameter) {
clipboardBiologicalParameter = (Parameter) rvs.getPrimarySymbolTableEntries()[j];
} else if (rvs.getAlternateSymbolTableEntries() != null && rvs.getAlternateSymbolTableEntries()[j] instanceof Parameter) {
clipboardBiologicalParameter = (Parameter) rvs.getAlternateSymbolTableEntries()[j];
}
if (clipboardBiologicalParameter == null) {
Variable pastedMathVariable = null;
if (rvs.getPrimarySymbolTableEntries()[j] instanceof Variable) {
pastedMathVariable = (Variable) rvs.getPrimarySymbolTableEntries()[j];
} else if (rvs.getAlternateSymbolTableEntries() != null && rvs.getAlternateSymbolTableEntries()[j] instanceof Variable) {
pastedMathVariable = (Variable) rvs.getAlternateSymbolTableEntries()[j];
}
if (pastedMathVariable != null) {
if (msm == null) {
throw mathMappingException;
}
Variable localMathVariable = msm.findVariableByName(pastedMathVariable.getName());
if (localMathVariable != null) {
SymbolTableEntry[] localBiologicalSymbolArr = msm.getBiologicalSymbol(localMathVariable);
for (int k = 0; k < localBiologicalSymbolArr.length; k += 1) {
if (localBiologicalSymbolArr[k] == pms.getModelParameter()) {
pasteDestination = pms;
break;
}
}
}
}
} else {
if (pms.getModelParameter().getName().equals(clipboardBiologicalParameter.getName()) && pms.getModelParameter().getClass().equals(clipboardBiologicalParameter.getClass()) && pms.getModelParameter().getNameScope().getName().equals(clipboardBiologicalParameter.getNameScope().getName())) {
pasteDestination = pms;
}
}
if (pasteDestination != null) {
changedParametersV.add(pasteDestination);
newExpressionsV.add(rvs.getExpressionValues()[j]);
pasteDescriptionsV.add(VCellCopyPasteHelper.formatPasteList(pms.getModelParameter().getNameScope().getName(), pms.getModelParameter().getName(), pasteDestination.getCurrent() + "", rvs.getExpressionValues()[j].infix()));
}
}
}
} catch (Throwable e) {
if (errors == null) {
errors = new StringBuffer();
}
errors.append(pms.getModelParameter().getName() + " (" + e.getClass().getName() + ") " + e.getMessage() + "\n");
}
}
if (errors != null) {
throw new Exception(errors.toString());
}
}
} catch (Throwable e) {
PopupGenerator.showErrorDialog(this, "Paste failed during pre-check (no changes made).\n" + e.getMessage(), e);
return;
}
// Do paste
try {
if (pasteDescriptionsV.size() > 0) {
String[] pasteDescriptionArr = new String[pasteDescriptionsV.size()];
pasteDescriptionsV.copyInto(pasteDescriptionArr);
ParameterMappingSpec[] changedParametersArr = new ParameterMappingSpec[changedParametersV.size()];
changedParametersV.copyInto(changedParametersArr);
Expression[] newExpressionsArr = new Expression[newExpressionsV.size()];
newExpressionsV.copyInto(newExpressionsArr);
VCellCopyPasteHelper.chooseApplyPaste(this, pasteDescriptionArr, changedParametersArr, newExpressionsArr);
} else {
PopupGenerator.showInfoDialog(this, "No paste items match the destination (no changes made).");
}
} catch (Throwable e) {
PopupGenerator.showErrorDialog(this, "Paste Error\n" + e.getMessage(), e);
}
}
Also used :
Variable(cbit.vcell.math.Variable)
VCellTransferable(cbit.vcell.desktop.VCellTransferable)
SymbolTableEntry(cbit.vcell.parser.SymbolTableEntry)
ParameterMappingSpec(cbit.vcell.modelopt.ParameterMappingSpec)
SimulationContext(cbit.vcell.mapping.SimulationContext)
MathSymbolMapping(cbit.vcell.mapping.MathSymbolMapping)
Expression(cbit.vcell.parser.Expression)
MathMapping(cbit.vcell.mapping.MathMapping)
ModelParameter(cbit.vcell.model.Model.ModelParameter)
Parameter(cbit.vcell.model.Parameter)
UnresolvedParameter(cbit.vcell.model.Kinetics.UnresolvedParameter)
Example 7 with Variable
use of cbit.vcell.math.Variable in project vcell by virtualcell.
the class SbmlVcmlConverter method solveSimulation.
/**
* solves the simulation that is passed in throught the simulation job.
*/
private static void solveSimulation(SimulationJob simJob, String filePathName, SimSpec argSimSpec) /* Hashtable argSpUnitsHash, double argTimeFactor, Model.ReservedSymbol kMoleSymbol*/
{
ODESolverResultSet odeSolverResultSet = null;
try {
/* // Generate .idaInput string
File idaInputFile = new File(filePathName.replace(".vcml", ".idaInput"));
PrintWriter idaPW = new java.io.PrintWriter(idaInputFile);
IDAFileWriter idaFileWriter = new IDAFileWriter(idaPW, simJob);
idaFileWriter.write();
idaPW.close();
// use the SundialsStandaloneSolver
File idaOutputFile = new File(filePathName.replace(".vcml", ".ida"));
Executable executable = new Executable(new String[]{"SundialsSolverStandalone", idaInputFile.getAbsolutePath(), idaOutputFile.getAbsolutePath()});
executable.start();
*/
// Generate .cvodeInput string
File cvodeInputFile = new File(filePathName.replace(".vcml", ".cvodeInput"));
PrintWriter cvodePW = new java.io.PrintWriter(cvodeInputFile);
SimulationTask simTask = new SimulationTask(simJob, 0);
CVodeFileWriter cvodeFileWriter = new CVodeFileWriter(cvodePW, simTask);
cvodeFileWriter.write();
cvodePW.close();
// use the cvodeStandalone solver
// use the SundialsStandaloneSolver
File cvodeOutputFile = new File(filePathName.replace(".vcml", ".ida"));
/*
Executable executable = new Executable(new String[]{"d:/workspace/VCell_5.3_VCell/SundialsSolverStandalone_x64", cvodeInputFile.getAbsolutePath(), cvodeOutputFile.getAbsolutePath()});
executable.start();
*/
// use the cvodeStandalone solver
// use the SundialsStandaloneSolver
File[] exes = SolverUtilities.getExes(SolverDescription.CombinedSundials);
assert exes.length == 1 : "one and only one smoldyn solver expected";
File sundialsExe = exes[0];
Executable executable = new Executable(new String[] { sundialsExe.getAbsolutePath(), cvodeInputFile.getAbsolutePath(), cvodeOutputFile.getAbsolutePath() });
executable.start();
// get the result
odeSolverResultSet = VCellSBMLSolver.getODESolverResultSet(simJob, cvodeOutputFile.getPath());
} catch (Exception e) {
e.printStackTrace(System.out);
throw new RuntimeException("Error running NativeIDA solver : " + e.getMessage());
}
// now write out the results into CSV file
try {
if (odeSolverResultSet != null) {
File csvFile = new File(filePathName.replace(".vcml", ".csv"));
PrintStream outputStream = new PrintStream(new BufferedOutputStream(new FileOutputStream(csvFile)));
outputStream.print("time");
for (int i = 0; i < argSimSpec.getVarsList().length; i++) {
outputStream.print("," + argSimSpec.getVarsList()[i]);
}
outputStream.println();
// extract data for time and species
double[][] data = new double[argSimSpec.getVarsList().length + 1][];
int column = odeSolverResultSet.findColumn("t");
data[0] = odeSolverResultSet.extractColumn(column);
int origDataLength = data[0].length;
for (int i = 0; i < argSimSpec.getVarsList().length; i++) {
column = odeSolverResultSet.findColumn(argSimSpec.getVarsList()[i]);
if (column == -1) {
Variable var = simJob.getSimulationSymbolTable().getVariable(argSimSpec.getVarsList()[i]);
data[i + 1] = new double[data[0].length];
if (var instanceof cbit.vcell.math.Constant) {
double value = ((cbit.vcell.math.Constant) var).getExpression().evaluateConstant();
for (int j = 0; j < data[i + 1].length; j++) {
data[i + 1][j] = value;
}
} else {
throw new RuntimeException("Did not find " + argSimSpec.getVarsList()[i] + " in simulation");
}
} else {
data[i + 1] = odeSolverResultSet.extractColumn(column);
}
}
double endTime = (simJob.getSimulation().getSolverTaskDescription().getTimeBounds().getEndingTime());
// for each time, print row
int index = 0;
double[] sampleTimes = new double[numTimeSteps + 1];
for (int i = 0; i <= numTimeSteps; i++) {
sampleTimes[i] = endTime * i / numTimeSteps;
}
for (int i = 0; i < sampleTimes.length; i++) {
// find largest index whose time is not past sample time
while (true) {
// if already at last time point, then if it equals the sampleTime, we're done if it doesn't then we don't have this time point.
if (index == odeSolverResultSet.getRowCount() - 1) {
if (data[0][index] == sampleTimes[i]) {
break;
} else {
throw new RuntimeException("sampleTime does not match at last time point");
}
}
// haven't gotten to last time point yet, stop when next time step is past sampleTime.
if (data[0][index + 1] > sampleTimes[i]) {
break;
}
// sampleTime must be later in our data list.
index++;
}
// if (data[0][index] == sampleTimes[i]) {
if (Math.abs(data[0][index] - sampleTimes[i]) < 1e-12) {
// if timeFactor is not 1.0, time is not in seconds (mins or hrs); if timeFactor is 60, divide sampleTime/60; if it is 3600, divide sampleTime/3600.
// if (argTimeFactor != 1.0) {
// outputStream.print(data[0][index]/argTimeFactor);
// } else {
outputStream.print(data[0][index]);
// }
for (int j = 0; j < argSimSpec.getVarsList().length; j++) {
// SBMLImporter.SBVCConcentrationUnits spConcUnits = (SBMLImporter.SBVCConcentrationUnits)argSpUnitsHash.get(argSimSpec.getVarsList()[j]);
// if (spConcUnits != null) {
// VCUnitDefinition sbunits = spConcUnits.getSBConcentrationUnits();
// VCUnitDefinition vcunits = spConcUnits.getVCConcentrationUnits();
// SBMLUnitParameter unitFactor = SBMLUtils.getConcUnitFactor("spConcParam", vcunits, sbunits, kMoleSymbol);
// outputStream.print("," + data[j + 1][index] * unitFactor.getExpression().evaluateConstant()); //earlier, hack unitfactor = 0.000001
// earlier, hack unitfactor = 0.000001
outputStream.print("," + data[j + 1][index]);
}
// }
outputStream.println();
} else {
// if data[0][index] < sampleTime, must interpolate
double fraction = (sampleTimes[i] - data[0][index]) / (data[0][index + 1] - data[0][index]);
// if argTimeFactor is not 1.0, time is not in seconds (mins or hrs); if argTimeFactor is 60, divide sampleTime/60; if it is 3600, divide sampleTime/3600.
// if (argTimeFactor != 1.0) {
// outputStream.print(sampleTimes[i]/argTimeFactor);
// } else {
outputStream.print(sampleTimes[i]);
// }
for (int j = 0; j < argSimSpec.getVarsList().length; j++) {
double interpolatedValue = 0.0;
double[] speciesVals = null;
double[] times = null;
// Currently using 2nd order interpolation
if (index == 0) {
// can only do 1st order interpolation
times = new double[] { data[0][index], data[0][index + 1] };
speciesVals = new double[] { data[j + 1][index], data[j + 1][index + 1] };
interpolatedValue = MathTestingUtilities.taylorInterpolation(sampleTimes[i], times, speciesVals);
} else {
if (index >= 1 && index <= origDataLength - 3) {
double val_1 = Math.abs(sampleTimes[i] - data[0][index - 1]);
double val_2 = Math.abs(sampleTimes[i] - data[0][index + 2]);
if (val_1 < val_2) {
times = new double[] { data[0][index - 1], data[0][index], data[0][index + 1] };
speciesVals = new double[] { data[j + 1][index - 1], data[j + 1][index], data[j + 1][index + 1] };
} else {
times = new double[] { data[0][index], data[0][index + 1], data[0][index + 2] };
speciesVals = new double[] { data[j + 1][index], data[j + 1][index + 1], data[j + 1][index + 2] };
}
interpolatedValue = MathTestingUtilities.taylorInterpolation(sampleTimes[i], times, speciesVals);
} else {
times = new double[] { data[0][index - 1], data[0][index], data[0][index + 1] };
speciesVals = new double[] { data[j + 1][index - 1], data[j + 1][index], data[j + 1][index + 1] };
interpolatedValue = MathTestingUtilities.taylorInterpolation(sampleTimes[i], times, speciesVals);
}
}
// end if-else - calc of interpolated value
// interpolatedValue = interpolatedValue * unitFactor.getExpression().evaluateConstant();
outputStream.print("," + interpolatedValue);
}
// end for - sp values for each time point (row)
outputStream.println();
}
}
outputStream.close();
} else {
throw new RuntimeException("Result set was null, could not write to CSV file");
}
} catch (Exception e) {
e.printStackTrace(System.out);
throw new RuntimeException("Errors saving results to CSV file" + e.getMessage());
}
}
Also used :
PrintStream(java.io.PrintStream)
SimulationTask(cbit.vcell.messaging.server.SimulationTask)
Variable(cbit.vcell.math.Variable)
CVodeFileWriter(cbit.vcell.solver.ode.CVodeFileWriter)
IOException(java.io.IOException)
FileOutputStream(java.io.FileOutputStream)
ODESolverResultSet(cbit.vcell.solver.ode.ODESolverResultSet)
Executable(org.vcell.util.exe.Executable)
File(java.io.File)
BufferedOutputStream(java.io.BufferedOutputStream)
PrintWriter(java.io.PrintWriter)
Example 8 with Variable
use of cbit.vcell.math.Variable in project vcell by virtualcell.
the class VcmlOmexConverter method vcmlToOmexConversion.
public static boolean vcmlToOmexConversion(String outputBaseDir) throws XmlParseException, IOException, DataAccessException, SQLException {
// Get VCML file path from -i flag
int sedmlLevel = 1;
int sedmlVersion = 2;
String inputVcmlFile = cliHandler.getInputFilePath();
// Get directory file path from -o flag
String outputDir = cliHandler.getOutputDirPath();
// get VCML name from VCML path
// String vcmlName = inputVcmlFile.split(File.separator, 10)[inputVcmlFile.split(File.separator, 10).length - 1].split("\\.", 5)[0];
// platform independent, strips extension too
String vcmlName = FilenameUtils.getBaseName(inputVcmlFile);
File vcmlFilePath = new File(inputVcmlFile);
// Create biomodel
BioModel bioModel = XmlHelper.XMLToBioModel(new XMLSource(vcmlFilePath));
bioModel.refreshDependencies();
int numSimulations = bioModel.getNumSimulations();
if (outputBaseDir != null && numSimulations == 0) {
CLIStandalone.writeSimErrorList(outputBaseDir, vcmlName + " has no simulations.");
return false;
}
// we extract the simulations with field data from the list of simulations since they are not supported
List<Simulation> simulationsToRemove = new ArrayList<>();
for (Simulation simulation : bioModel.getSimulations()) {
boolean bFieldDataFound = false;
Enumeration<Variable> variables = simulation.getMathDescription().getVariables();
while (variables.hasMoreElements()) {
Variable var = variables.nextElement();
Expression exp = var.getExpression();
FieldFunctionArguments[] ffas = FieldUtilities.getFieldFunctionArguments(exp);
if (ffas != null && ffas.length > 0) {
bFieldDataFound = true;
// we are done with this simulation if we know it has at least one variable with a field data in its expression
break;
}
}
if (bFieldDataFound) {
simulationsToRemove.add(simulation);
CLIStandalone.writeSimErrorList(outputBaseDir, vcmlName + " excluded: FieldData not supported at this time.");
SolverDescription solverDescription = simulation.getSolverTaskDescription().getSolverDescription();
String solverName = solverDescription.getShortDisplayLabel();
CLIStandalone.writeSimErrorList(outputBaseDir, " " + solverName);
}
}
for (Simulation simulation : simulationsToRemove) {
try {
bioModel.removeSimulation(simulation);
} catch (PropertyVetoException e) {
System.out.println("Failed to remove simulation with field data");
e.printStackTrace();
}
}
// we replace the obsolete solver with the fully supported equivalent
for (Simulation simulation : bioModel.getSimulations()) {
if (simulation.getSolverTaskDescription().getSolverDescription().equals(SolverDescription.FiniteVolume)) {
try {
simulation.getSolverTaskDescription().setSolverDescription(SolverDescription.SundialsPDE);
} catch (PropertyVetoException e) {
System.out.println("Failed to replace obsolete solver");
e.printStackTrace();
}
}
}
// NOTE: SEDML exporter exports both SEDML as well as required SBML
List<Simulation> simsToExport = null;
Set<String> solverNames = new LinkedHashSet<>();
if (bHasDataOnly) {
// make list of simulations to export with only sims that have data on the server
simsToExport = new ArrayList<Simulation>();
for (Simulation simulation : bioModel.getSimulations()) {
SolverDescription solverDescription = simulation.getSolverTaskDescription().getSolverDescription();
String solverName = solverDescription.getShortDisplayLabel();
solverNames.add(solverName);
// check server status
KeyValue parentKey = simulation.getSimulationVersion().getParentSimulationReference();
SimulationJobStatusPersistent[] statuses = adminDbTopLevel.getSimulationJobStatusArray(parentKey == null ? simulation.getKey() : parentKey, false);
if (statuses == null)
continue;
if (statuses.length == 0)
continue;
for (int i = 0; i < statuses.length; i++) {
if (statuses[i].hasData()) {
simsToExport.add(simulation);
continue;
}
}
// String dbDriverName = PropertyLoader.getProperty(PropertyLoader.dbDriverName, null);
// String dbConnectURL = PropertyLoader.getProperty(PropertyLoader.dbConnectURL, null);
// String dbSchemaUser = PropertyLoader.getProperty(PropertyLoader.dbUserid, null);
// String dbPassword = PropertyLoader.getSecretValue(PropertyLoader.dbPasswordValue, PropertyLoader.dbPasswordFile);
// DataSetControllerImpl dsControllerImpl = new DataSetControllerImpl(null, new File(outputBaseDir), null);
//
// code used to recover field data
//
// HashMap<User, Vector<ExternalDataIdentifier>> allExternalDataIdentifiers = FieldDataDBOperationDriver.getAllExternalDataIdentifiers();
// Enumeration<Variable> variables = simulation.getMathDescription().getVariables();
// while(variables.hasMoreElements()) {
// Variable var = variables.nextElement();
// Expression exp = var.getExpression();
// FieldFunctionArguments[] ffas = FieldUtilities.getFieldFunctionArguments( exp);
//
// if(ffas != null && ffas.length > 0) {
// FieldDataIdentifierSpec[] aaa = DataSetControllerImpl.getFieldDataIdentifierSpecs_private(
// ffas, simulation.getVersion().getOwner(), true, allExternalDataIdentifiers);
//
// System.out.println((ffas == null) ? "null" : exp.infix() + ", not null:" + ffas.length);
// }
// }
}
}
if (outputBaseDir != null && bHasDataOnly == true && simsToExport.size() == 0) {
CLIStandalone.writeSimErrorList(outputBaseDir, vcmlName + " has no simulations with any results.");
for (String solverName : solverNames) {
CLIStandalone.writeSimErrorList(outputBaseDir, " " + solverName);
}
return false;
}
String rdfString = getMetadata(vcmlName, bioModel);
XmlUtil.writeXMLStringToFile(rdfString, String.valueOf(Paths.get(outputDir, "metadata.rdf")), true);
if (bMakeLogsOnly) {
return false;
}
SEDMLExporter sedmlExporter = new SEDMLExporter(bioModel, sedmlLevel, sedmlVersion, simsToExport);
String sedmlString = sedmlExporter.getSEDMLFile(outputDir, vcmlName, bForceVCML, bHasDataOnly, true);
XmlUtil.writeXMLStringToFile(sedmlString, String.valueOf(Paths.get(outputDir, vcmlName + ".sedml")), true);
// libCombine needs native lib
ResourceUtil.setNativeLibraryDirectory();
NativeLoader.load("combinej");
boolean isDeleted = false;
boolean isCreated;
try {
CombineArchive archive = new CombineArchive();
String[] files;
// TODO: try-catch if no files
File dir = new File(outputDir);
files = dir.list();
for (String sd : files) {
if (sd.endsWith(".sedml")) {
archive.addFile(Paths.get(outputDir, sd).toString(), // target file name
"./" + sd, KnownFormats.lookupFormat("sedml"), // mark file as master
true);
} else if (sd.endsWith(".sbml") || sd.endsWith(".xml")) {
archive.addFile(Paths.get(outputDir, sd).toString(), "./" + sd, KnownFormats.lookupFormat("sbml"), // mark file as master
false);
} else if (sd.endsWith(".rdf")) {
archive.addFile(Paths.get(outputDir, sd).toString(), "./" + sd, "http://identifiers.org/combine.specifications/omex-metadata", // KnownFormats.lookupFormat("xml"),
false);
}
}
archive.addFile(Paths.get(String.valueOf(vcmlFilePath)).toString(), "./" + vcmlName + ".vcml", "http://purl.org/NET/mediatypes/application/vcml+xml", false);
// writing into combine archive
String omexPath = Paths.get(outputDir, vcmlName + ".omex").toString();
File omexFile = new File(omexPath);
// Deleting file if already exists with same name
if (omexFile.exists()) {
omexFile.delete();
}
isCreated = archive.writeToFile(omexPath);
// Removing all other files(like SEDML, XML, SBML) after archiving
for (String sd : files) {
// removing
if (sd.endsWith(".sedml") || sd.endsWith(".sbml") || sd.endsWith("xml") || sd.endsWith("vcml") || sd.endsWith("rdf")) {
isDeleted = Paths.get(outputDir, sd).toFile().delete();
}
}
if (isDeleted)
System.out.println("Removed intermediary files");
} catch (Exception e) {
throw new RuntimeException("createZipArchive threw exception: " + e.getMessage());
}
return isCreated;
}
Also used :
LinkedHashSet(java.util.LinkedHashSet)
Variable(cbit.vcell.math.Variable)
SolverDescription(cbit.vcell.solver.SolverDescription)
KeyValue(org.vcell.util.document.KeyValue)
SEDMLExporter(org.vcell.sedml.SEDMLExporter)
ArrayList(java.util.ArrayList)
SimulationJobStatusPersistent(cbit.vcell.server.SimulationJobStatusPersistent)
FieldFunctionArguments(cbit.vcell.field.FieldFunctionArguments)
CombineArchive(org.sbml.libcombine.CombineArchive)
PropertyVetoException(java.beans.PropertyVetoException)
FileNotFoundException(java.io.FileNotFoundException)
SQLException(java.sql.SQLException)
XmlParseException(cbit.vcell.xml.XmlParseException)
RDFHandlerException(org.openrdf.rio.RDFHandlerException)
IOException(java.io.IOException)
DataAccessException(org.vcell.util.DataAccessException)
PropertyVetoException(java.beans.PropertyVetoException)
Simulation(cbit.vcell.solver.Simulation)
Expression(cbit.vcell.parser.Expression)
BioModel(cbit.vcell.biomodel.BioModel)
File(java.io.File)
XMLSource(cbit.vcell.xml.XMLSource)
Example 9 with Variable
use of cbit.vcell.math.Variable 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 if (object instanceof AssignmentRule) {
return ((AssignmentRule) object).getDisplayName() + "";
} else if (object instanceof RateRule) {
return ((RateRule) object).getDisplayName() + "";
} else {
System.err.println("unknown object type in IssueTableModel.getSourceObjectDescription(): " + object.getClass());
}
return description;
} else if (vcDocument instanceof MathModel) {
Object object = issue.getSource();
String description = "";
if (object instanceof Variable) {
description = ((Variable) object).getName();
} else if (object instanceof SubDomain) {
description = ((SubDomain) object).getName();
} else if (object instanceof Geometry) {
description = "Geometry";
} else if (object instanceof OutputFunctionIssueSource) {
description = ((OutputFunctionIssueSource) object).getAnnotatedFunction().getName();
} else if (object instanceof MathDescription) {
return "math";
} else if (object instanceof Simulation) {
return "Simulation " + ((Simulation) object).getName() + "";
}
return description;
} else {
System.err.println("unknown document type in IssueTableModel.getSourceObjectDescription()");
return "";
}
}
Also used :
MathModel(cbit.vcell.mathmodel.MathModel)
Variable(cbit.vcell.math.Variable)
MathDescription(cbit.vcell.math.MathDescription)
SpeciesContextSpec(cbit.vcell.mapping.SpeciesContextSpec)
StructureMapping(cbit.vcell.mapping.StructureMapping)
SpeciesPattern(org.vcell.model.rbm.SpeciesPattern)
ComponentStateDefinition(org.vcell.model.rbm.ComponentStateDefinition)
SpatialObject(cbit.vcell.mapping.spatial.SpatialObject)
SubDomain(cbit.vcell.math.SubDomain)
SymbolTableEntry(cbit.vcell.parser.SymbolTableEntry)
OutputFunctionIssueSource(cbit.vcell.solver.OutputFunctionContext.OutputFunctionIssueSource)
MolecularComponent(org.vcell.model.rbm.MolecularComponent)
RbmModelContainer(cbit.vcell.model.Model.RbmModelContainer)
SpatialProcess(cbit.vcell.mapping.spatial.processes.SpatialProcess)
ModelOptimizationSpec(cbit.vcell.modelopt.ModelOptimizationSpec)
UnmappedGeometryClass(cbit.vcell.mapping.GeometryContext.UnmappedGeometryClass)
MicroscopeMeasurement(cbit.vcell.mapping.MicroscopeMeasurement)
RateRule(cbit.vcell.mapping.RateRule)
GeometryContext(cbit.vcell.mapping.GeometryContext)
Structure(cbit.vcell.model.Structure)
ReactionCombo(cbit.vcell.mapping.ReactionSpec.ReactionCombo)
ReactionRule(cbit.vcell.model.ReactionRule)
DecoratedIssueSource(cbit.vcell.client.desktop.DecoratedIssueSource)
ReactionSpec(cbit.vcell.mapping.ReactionSpec)
AssignmentRule(cbit.vcell.mapping.AssignmentRule)
SimulationContext(cbit.vcell.mapping.SimulationContext)
MolecularType(org.vcell.model.rbm.MolecularType)
Geometry(cbit.vcell.geometry.Geometry)
Simulation(cbit.vcell.solver.Simulation)
BioModel(cbit.vcell.biomodel.BioModel)
ReactionStep(cbit.vcell.model.ReactionStep)
MathModel(cbit.vcell.mathmodel.MathModel)
Model(cbit.vcell.model.Model)
BioModel(cbit.vcell.biomodel.BioModel)
SpatialObject(cbit.vcell.mapping.spatial.SpatialObject)
BioEvent(cbit.vcell.mapping.BioEvent)
Example 10 with Variable
use of cbit.vcell.math.Variable in project vcell by virtualcell.
the class DiffEquMathMapping method refreshMathDescription.
/**
* This method was created in VisualAge.
*/
@SuppressWarnings("deprecation")
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();
//
// 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.getGeometryClass() == null)){
// localIssueList.add(new Issue(structures[i], IssueCategory.StructureNotMapped,"In Application '" + simContext.getName() + "', model structure '"+structures[i].getName()+"' not mapped to a geometry subdomain",Issue.SEVERITY_WARNING));
// }
// }
// SubVolume subVolumes[] = simContext.getGeometryContext().getGeometry().getGeometrySpec().getSubVolumes();
// for (int i = 0; i < subVolumes.length; i++){
// Structure[] mappedStructures = simContext.getGeometryContext().getStructuresFromGeometryClass(subVolumes[i]);
// if (mappedStructures==null || mappedStructures.length==0){
// localIssueList.add(new Issue(subVolumes[i], IssueCategory.GeometryClassNotMapped,"In Application '" + simContext.getName() + "', geometry subVolume '"+subVolumes[i].getName()+"' not mapped from a model structure",Issue.SEVERITY_WARNING));
// }
// }
// deals with model parameters
HashMap<VolVariable, EventAssignmentOrRateRuleInitParameter> eventVolVarHash = new HashMap<VolVariable, EventAssignmentOrRateRuleInitParameter>();
HashMap<Variable, RateRuleRateParameter> rateRuleRateParamHash = new HashMap<Variable, RateRuleRateParameter>();
ArrayList<SymbolTableEntry> rateRuleVarTargets = new ArrayList<SymbolTableEntry>();
ArrayList<SymbolTableEntry> assignmentRuleVarTargets = new ArrayList<SymbolTableEntry>();
ArrayList<SymbolTableEntry> eventAssignTargets = new ArrayList<SymbolTableEntry>();
Model model = simContext.getModel();
ModelUnitSystem modelUnitSystem = model.getUnitSystem();
VCUnitDefinition timeUnit = modelUnitSystem.getTimeUnit();
ModelParameter[] modelParameters = model.getModelParameters();
if (simContext.getGeometry().getDimension() == 0) {
//
// global parameters from model (that presently are constants)
//
BioEvent[] bioEvents = simContext.getBioEvents();
if (bioEvents != null && bioEvents.length > 0) {
for (BioEvent be : bioEvents) {
ArrayList<EventAssignment> eventAssignments = be.getEventAssignments();
if (eventAssignments != null) {
for (EventAssignment ea : eventAssignments) {
if (!eventAssignTargets.contains(ea.getTarget())) {
eventAssignTargets.add(ea.getTarget());
}
}
}
}
}
RateRule[] rrs = simContext.getRateRules();
if (rrs != null && rrs.length > 0) {
for (RateRule rr : rrs) {
SymbolTableEntry rrVar = rr.getRateRuleVar();
if (!rateRuleVarTargets.contains(rrVar)) {
rateRuleVarTargets.add(rrVar);
}
}
}
AssignmentRule[] ars = simContext.getAssignmentRules();
if (ars != null && ars.length > 0) {
for (AssignmentRule ar : ars) {
SymbolTableEntry arVar = ar.getAssignmentRuleVar();
if (!assignmentRuleVarTargets.contains(arVar)) {
assignmentRuleVarTargets.add(arVar);
}
}
}
for (int j = 0; j < modelParameters.length; j++) {
Expression modelParamExpr = modelParameters[j].getExpression();
GeometryClass geometryClass = getDefaultGeometryClass(modelParamExpr);
VCUnitDefinition paramUnit = modelParameters[j].getUnitDefinition();
modelParamExpr = getIdentifierSubstitutions(modelParamExpr, paramUnit, geometryClass);
// if (eventAssignTargets.contains(modelParameters[j]) || rateRuleVarTargets.contains(modelParameters[j])) {
if (eventAssignTargets.contains(modelParameters[j])) {
EventAssignmentOrRateRuleInitParameter eap = null;
try {
eap = addEventAssignmentOrRateRuleInitParameter(modelParameters[j], modelParamExpr, PARAMETER_ROLE_EVENTASSIGN_OR_RATERULE_INITCONDN, paramUnit);
} catch (PropertyVetoException e) {
e.printStackTrace(System.out);
throw new MappingException(e.getMessage());
}
if (geometryClass == null) {
GeometryClass[] geometryClasses = simContext.getGeometryContext().getGeometry().getGeometryClasses();
geometryClass = geometryClasses[0];
}
Domain domain = null;
if (geometryClass != null) {
// the volume variable will look like Compartment::g0 rather than just g0
domain = new Domain(geometryClass);
}
VolVariable volVar = new VolVariable(modelParameters[j].getName(), domain);
varHash.addVariable(volVar);
eventVolVarHash.put(volVar, eap);
} else if (rateRuleVarTargets.contains(modelParameters[j])) {
// do nothing, will do elsewhere
;
} else if (assignmentRuleVarTargets.contains(modelParameters[j])) {
// do nothing, will do elsewhere
;
} else {
Variable variable = newFunctionOrConstant(getMathSymbol(modelParameters[j], geometryClass), modelParamExpr, geometryClass);
varHash.addVariable(variable);
}
}
} else {
for (int j = 0; j < modelParameters.length; j++) {
Expression modelParamExpr = modelParameters[j].getExpression();
GeometryClass geometryClass = getDefaultGeometryClass(modelParamExpr);
modelParamExpr = getIdentifierSubstitutions(modelParamExpr, modelParameters[j].getUnitDefinition(), geometryClass);
varHash.addVariable(newFunctionOrConstant(getMathSymbol(modelParameters[j], geometryClass), modelParamExpr, geometryClass));
}
}
//
for (SimulationContextParameter scParameter : simContext.getSimulationContextParameters()) {
Expression scParameterExpression = scParameter.getExpression();
GeometryClass gc = getDefaultGeometryClass(scParameterExpression);
varHash.addVariable(newFunctionOrConstant(getMathSymbol(scParameter, gc), getIdentifierSubstitutions(scParameter.getExpression(), scParameter.getUnitDefinition(), gc), gc));
}
//
for (DataSymbol dataSymbol : simContext.getDataContext().getDataSymbols()) {
if (dataSymbol instanceof FieldDataSymbol) {
FieldDataSymbol fieldDataSymbol = (FieldDataSymbol) dataSymbol;
GeometryClass geometryClass = null;
FieldFunctionArguments ffs = new FieldFunctionArguments(fieldDataSymbol.getExternalDataIdentifier().getName(), fieldDataSymbol.getFieldDataVarName(), new Expression(fieldDataSymbol.getFieldDataVarTime()), VariableType.getVariableTypeFromVariableTypeName(fieldDataSymbol.getFieldDataVarType()));
Expression exp = new Expression(ffs.infix());
varHash.addVariable(newFunctionOrConstant(getMathSymbol(dataSymbol, geometryClass), getIdentifierSubstitutions(exp, dataSymbol.getUnitDefinition(), geometryClass), geometryClass));
} else {
throw new RuntimeException("In Application '" + simContext.getName() + "', dataSymbol type '" + dataSymbol.getClass().getName() + "' not yet supported for math generation");
}
}
//
// 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("In Application '" + simContext.getName() + "', " + 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());
}
}
//
// volume region variables
//
enum1 = getSpeciesContextMappings();
while (enum1.hasMoreElements()) {
SpeciesContextMapping scm = (SpeciesContextMapping) enum1.nextElement();
if (scm.getVariable() instanceof VolumeRegionVariable) {
varHash.addVariable(scm.getVariable());
}
}
//
// membrane region variables
//
enum1 = getSpeciesContextMappings();
while (enum1.hasMoreElements()) {
SpeciesContextMapping scm = (SpeciesContextMapping) enum1.nextElement();
if (scm.getVariable() instanceof MembraneRegionVariable) {
varHash.addVariable(scm.getVariable());
}
}
//
// add compartment and membrane subdomains
//
ArrayList<CompartmentSubdomainContext> compartmentSubdomainContexts = new ArrayList<CompartmentSubdomainContext>();
ArrayList<MembraneSubdomainContext> membraneSubdomainContexts = new ArrayList<MembraneSubdomainContext>();
addSubdomains(model, compartmentSubdomainContexts, membraneSubdomainContexts);
// membrane velocities set on MembraneSubdomains later.
addSpatialProcesses(varHash, compartmentSubdomainContexts, membraneSubdomainContexts);
varHash.addVariable(new Constant(getMathSymbol(model.getPI_CONSTANT(), null), getIdentifierSubstitutions(model.getPI_CONSTANT().getExpression(), model.getPI_CONSTANT().getUnitDefinition(), null)));
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;
}
}
}
potentialMapping = new PotentialMapping(simContext, this);
if (bCalculatePotential) {
potentialMapping.computeMath();
//
// 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.getGeometryClass()), getIdentifierSubstitutions(specificCapacitanceParm.getExpression(), specificCapacitanceParm.getUnitDefinition(), memMapping.getGeometryClass())));
ElectricalDevice.ElectricalDeviceParameter transmembraneCurrentParm = membraneElectricalDevice.getParameterFromRole(ElectricalDevice.ROLE_TransmembraneCurrent);
ElectricalDevice.ElectricalDeviceParameter totalCurrentParm = membraneElectricalDevice.getParameterFromRole(ElectricalDevice.ROLE_TotalCurrent);
ElectricalDevice.ElectricalDeviceParameter capacitanceParm = membraneElectricalDevice.getParameterFromRole(ElectricalDevice.ROLE_Capacitance);
GeometryClass geometryClass = membraneElectricalDevice.getMembraneMapping().getGeometryClass();
if (totalCurrentParm != null && /* totalCurrentDensityParm.getExpression()!=null && */
memMapping.getCalculateVoltage()) {
Expression totalCurrentDensityExp = (totalCurrentParm.getExpression() != null) ? (totalCurrentParm.getExpression()) : (new Expression(0.0));
varHash.addVariable(newFunctionOrConstant(getMathSymbol(totalCurrentParm, geometryClass), getIdentifierSubstitutions(totalCurrentDensityExp, totalCurrentParm.getUnitDefinition(), geometryClass), geometryClass));
}
if (transmembraneCurrentParm != null && transmembraneCurrentParm.getExpression() != null && memMapping.getCalculateVoltage()) {
varHash.addVariable(newFunctionOrConstant(getMathSymbol(transmembraneCurrentParm, geometryClass), getIdentifierSubstitutions(transmembraneCurrentParm.getExpression(), transmembraneCurrentParm.getUnitDefinition(), geometryClass), geometryClass));
}
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, geometryClass), getIdentifierSubstitutions(Expression.mult(memMapping.getNullSizeParameterValue(), specificCapacitanceParm.getExpression()), capacitanceParm.getUnitDefinition(), geometryClass), geometryClass));
} else {
varHash.addVariable(newFunctionOrConstant(getMathSymbol(capacitanceParm, geometryClass), getIdentifierSubstitutions(capacitanceParm.getExpression(), capacitanceParm.getUnitDefinition(), geometryClass), geometryClass));
}
}
//
if (membraneElectricalDevice.getDependentVoltageExpression() == null) {
// is Voltage Independent?
StructureMapping.StructureMappingParameter initialVoltageParm = memMapping.getInitialVoltageParameter();
varHash.addVariable(newFunctionOrConstant(getMathSymbol(initialVoltageParm, memMapping.getGeometryClass()), getIdentifierSubstitutions(initialVoltageParm.getExpression(), initialVoltageParm.getUnitDefinition(), memMapping.getGeometryClass()), memMapping.getGeometryClass()));
} else //
// membrane forced potential
//
{
varHash.addVariable(newFunctionOrConstant(getMathSymbol(memMapping.getMembrane().getMembraneVoltage(), memMapping.getGeometryClass()), getIdentifierSubstitutions(membraneElectricalDevice.getDependentVoltageExpression(), memMapping.getMembrane().getMembraneVoltage().getUnitDefinition(), memMapping.getGeometryClass()), memMapping.getGeometryClass()));
}
} 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();
Feature deviceElectrodeFeature = currentClampDevice.getCurrentClampStimulus().getElectrode().getFeature();
Feature groundElectrodeFeature = simContext.getGroundElectrode().getFeature();
Membrane membrane = model.getStructureTopology().getMembrane(deviceElectrodeFeature, groundElectrodeFeature);
GeometryClass geometryClass = null;
if (membrane != null) {
StructureMapping membraneStructureMapping = simContext.getGeometryContext().getStructureMapping(membrane);
geometryClass = membraneStructureMapping.getGeometryClass();
}
varHash.addVariable(newFunctionOrConstant(getMathSymbol(totalCurrentParm, geometryClass), getIdentifierSubstitutions(totalCurrentParm.getExpression(), totalCurrentParm.getUnitDefinition(), geometryClass), geometryClass));
varHash.addVariable(newFunctionOrConstant(getMathSymbol(currentParm, geometryClass), getIdentifierSubstitutions(currentParm.getExpression(), currentParm.getUnitDefinition(), geometryClass), geometryClass));
// 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(), geometryClass), geometryClass));
}
}
} else if (devices[j] instanceof VoltageClampElectricalDevice) {
VoltageClampElectricalDevice voltageClampDevice = (VoltageClampElectricalDevice) devices[j];
Feature deviceElectrodeFeature = voltageClampDevice.getVoltageClampStimulus().getElectrode().getFeature();
Feature groundElectrodeFeature = simContext.getGroundElectrode().getFeature();
Membrane membrane = model.getStructureTopology().getMembrane(deviceElectrodeFeature, groundElectrodeFeature);
GeometryClass geometryClass = null;
if (membrane != null) {
StructureMapping membraneStructureMapping = simContext.getGeometryContext().getStructureMapping(membrane);
geometryClass = membraneStructureMapping.getGeometryClass();
}
// 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, geometryClass), getIdentifierSubstitutions(totalCurrent.getExpression(), totalCurrent.getUnitDefinition(), geometryClass), geometryClass));
varHash.addVariable(newFunctionOrConstant(getMathSymbol(totalCurrentParm, geometryClass), getIdentifierSubstitutions(totalCurrentParm.getExpression(), totalCurrentParm.getUnitDefinition(), geometryClass), geometryClass));
varHash.addVariable(newFunctionOrConstant(getMathSymbol(voltageParm, geometryClass), getIdentifierSubstitutions(voltageParm.getExpression(), voltageParm.getUnitDefinition(), geometryClass), geometryClass));
//
// 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], geometryClass), getIdentifierSubstitutions(parameters[k].getExpression(), parameters[k].getUnitDefinition(), geometryClass), geometryClass));
}
}
}
}
} 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.getGeometryClass()), getIdentifierSubstitutions(memMapping.getInitialVoltageParameter().getExpression(), memMapping.getInitialVoltageParameter().getUnitDefinition(), memMapping.getGeometryClass()), memMapping.getGeometryClass()));
}
}
}
//
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) {
GeometryClass geometryClass = membraneMapping.getGeometryClass();
if (geometryClass == null) {
throw new MappingException("Application '" + getSimulationContext().getName() + "'\nGeometry->StructureMapping->(" + structureMappings[j].getStructure().getTypeName() + ")'" + structureMappings[j].getStructure().getName() + "' must be mapped to geometry domain.\n(see 'Problems' tab)");
}
Domain domain = new Domain(geometryClass);
if (membraneMapping.getCalculateVoltage() && bCalculatePotential) {
if (geometryClass instanceof SurfaceClass) {
//
if (mathDesc.getVariable(Membrane.MEMBRANE_VOLTAGE_REGION_NAME) == null) {
// varHash.addVariable(new MembraneRegionVariable(MembraneVoltage.MEMBRANE_VOLTAGE_REGION_NAME));
varHash.addVariable(new MembraneRegionVariable(getMathSymbol(membraneVoltage, geometryClass), domain));
}
} else {
//
// spatially unresolved membrane, and must solve for potential ... make VolVariable for this compartment
//
varHash.addVariable(new VolVariable(getMathSymbol(membraneVoltage, geometryClass), domain));
}
Parameter initialVoltageParm = membraneMapping.getInitialVoltageParameter();
Variable initVoltageFunction = newFunctionOrConstant(getMathSymbol(initialVoltageParm, geometryClass), getIdentifierSubstitutions(initialVoltageParm.getExpression(), initialVoltageParm.getUnitDefinition(), geometryClass), geometryClass);
varHash.addVariable(initVoltageFunction);
} else {
//
// don't calculate voltage, still may need it though
//
Parameter initialVoltageParm = membraneMapping.getInitialVoltageParameter();
Variable voltageFunction = newFunctionOrConstant(getMathSymbol(membraneMapping.getMembrane().getMembraneVoltage(), geometryClass), getIdentifierSubstitutions(initialVoltageParm.getExpression(), initialVoltageParm.getUnitDefinition(), geometryClass), geometryClass);
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();
GeometryClass geometryClass = null;
if (rs.getStructure() != null) {
geometryClass = simContext.getGeometryContext().getStructureMapping(rs.getStructure()).getGeometryClass();
}
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;
}
String mathSymbol = getMathSymbol(parameters[i], geometryClass);
Expression expr = getIdentifierSubstitutions(parameters[i].getExpression(), parameters[i].getUnitDefinition(), geometryClass);
varHash.addVariable(newFunctionOrConstant(mathSymbol, expr, geometryClass));
}
}
}
//
// initial conditions (either function or constant) for rate rule variables that are model parameters
//
// the init variables with expressions still containing variables
Map<ModelParameter, Variable> initModelParameterHashTmp = new HashMap<>();
// here we store the init parameter of the model parameter
Map<EventAssignmentOrRateRuleInitParameter, ModelParameter> rateRuleInitToModelParamMapping = new HashMap<>();
// here we store the init parameter of the model parameter
Map<ModelParameter, EventAssignmentOrRateRuleInitParameter> modelParamTorateRuleInitMapping = new HashMap<>();
for (ModelParameter mp : modelParameters) {
// initial assignment for global parameter used as rate rule variable
RateRule rr = simContext.getRateRule(mp);
if (rr == null) {
// we only care about global parameters that are rate rule variables
continue;
}
Variable var = varHash.getVariable(mp.getName());
if (var != null) {
if (eventVolVarHash.containsKey(var)) {
System.out.println("Global Parameters that are rate rule Variables should be unmapped at this point, unless they are EventAssignments too.");
} else {
throw new MappingException("Global Parameters that are rate rule Variables should be unmapped at this point.");
}
}
Expression modelParamExpr = mp.getExpression();
if (modelParamExpr == null) {
continue;
}
GeometryClass gc = getDefaultGeometryClass(modelParamExpr);
VCUnitDefinition paramUnit = modelUnitSystem.getInstance_TBD();
if (mp.getUnitDefinition() != null && !mp.getUnitDefinition().equals(modelUnitSystem.getInstance_TBD())) {
paramUnit = mp.getUnitDefinition();
}
// TODO: is this really needed? or could I directly use modelParamExpr in addEventAssignmentOrRateRuleInitParameter()
Expression mpInitExpr = getIdentifierSubstitutions(modelParamExpr, paramUnit, gc);
EventAssignmentOrRateRuleInitParameter mpInitParam;
try {
mpInitParam = addEventAssignmentOrRateRuleInitParameter(mp, mpInitExpr, PARAMETER_ROLE_EVENTASSIGN_OR_RATERULE_INITCONDN, paramUnit);
} catch (PropertyVetoException e) {
e.printStackTrace(System.out);
throw new MappingException(e.getMessage());
}
rateRuleInitToModelParamMapping.put(mpInitParam, mp);
modelParamTorateRuleInitMapping.put(mp, mpInitParam);
}
//
for (int i = 0; i < fieldMathMappingParameters.length; i++) {
GeometryClass geometryClass = fieldMathMappingParameters[i].getGeometryClass();
fieldMathMappingParameters[i].getExpression().bindExpression(this);
Expression exp = getIdentifierSubstitutions(fieldMathMappingParameters[i].getExpression(), fieldMathMappingParameters[i].getUnitDefinition(), geometryClass);
Variable var = newFunctionOrConstant(getMathSymbol(fieldMathMappingParameters[i], geometryClass), exp, geometryClass);
varHash.addVariable(var);
ModelParameter mp = rateRuleInitToModelParamMapping.get(fieldMathMappingParameters[i]);
if (mp != null) {
initModelParameterHashTmp.put(mp, var);
}
}
//
// initial conditions (either function or constant) for species variables
//
SpeciesContextSpec[] speciesContextSpecs = simContext.getReactionContext().getSpeciesContextSpecs();
for (int i = 0; i < speciesContextSpecs.length; i++) {
// add initial count if present (!= null)
SpeciesContextSpecParameter initCountParm = speciesContextSpecs[i].getParameterFromRole(SpeciesContextSpec.ROLE_InitialCount);
SpeciesContext speciesContext = speciesContextSpecs[i].getSpeciesContext();
if (initCountParm != null && initCountParm.getExpression() != null) {
Expression initCountExpr = new Expression(initCountParm.getExpression());
StructureMapping sm = simContext.getGeometryContext().getStructureMapping(speciesContext.getStructure());
String[] symbols = initCountExpr.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 = initCountExpr.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_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());
initCountExpr.substituteInPlace(new Expression(spC.getName()), scsInitExpr);
}
}
}
// now create the appropriate function for the current speciesContextSpec.
varHash.addVariable(newFunctionOrConstant(getMathSymbol(initCountParm, sm.getGeometryClass()), getIdentifierSubstitutions(initCountExpr, initCountParm.getUnitDefinition(), sm.getGeometryClass()), sm.getGeometryClass()));
}
// add initial concentration (may be derived from initial count if necessary)
SpeciesContextSpecParameter initConcParm = speciesContextSpecs[i].getParameterFromRole(SpeciesContextSpec.ROLE_InitialConcentration);
if (initConcParm != null) {
Expression initConcExpr = null;
if (initConcParm.getExpression() != null) {
initConcExpr = new Expression(initConcParm.getExpression());
} else if (initCountParm != null && initCountParm.getExpression() != null) {
Expression structureSizeExpr = new Expression(speciesContext.getStructure().getStructureSize(), getNameScope());
VCUnitDefinition concUnit = initConcParm.getUnitDefinition();
VCUnitDefinition countDensityUnit = initCountParm.getUnitDefinition().divideBy(speciesContext.getStructure().getStructureSize().getUnitDefinition());
Expression unitFactor = getUnitFactor(concUnit.divideBy(countDensityUnit));
initConcExpr = Expression.mult(Expression.div(new Expression(initCountParm, getNameScope()), structureSizeExpr), unitFactor);
}
StructureMapping sm = simContext.getGeometryContext().getStructureMapping(speciesContext.getStructure());
String[] symbols = initConcExpr.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 = initConcExpr.getSymbolBinding(symbols[j]);
if (ste == null) {
String msg = initConcParm.getName() == null ? "??" : initConcParm.getName();
System.out.println("Unexpected NULL symbol in the initial expression of " + msg);
} else 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());
initConcExpr.substituteInPlace(new Expression(spC.getName()), scsInitExpr);
}
} else if (ste instanceof ModelParameter) {
ModelParameter mpArg = (ModelParameter) ste;
System.out.println(mpArg.getName());
if (simContext.getRateRule(mpArg) == null) {
// only globals that are RateRule variables need to be replaced with their _init variable
continue;
}
EventAssignmentOrRateRuleInitParameter mpInitParam = modelParamTorateRuleInitMapping.get(mpArg);
if (mpInitParam != null) {
// we already made it, we only need to use it
Expression mpArgInitExpr = new Expression(mpInitParam, getNameScope());
initConcExpr.substituteInPlace(new Expression(ste.getName()), mpArgInitExpr);
}
} else {
String msg = ste.getName() == null ? "??" : ste.getName();
String msg2 = initConcParm.getName() == null ? "??" : initConcParm.getName();
System.out.println("Unexpected symbol type for " + msg + " in the initial expression of " + msg2);
}
}
// now create the appropriate function for the current speciesContextSpec.
varHash.addVariable(newFunctionOrConstant(getMathSymbol(initConcParm, sm.getGeometryClass()), getIdentifierSubstitutions(initConcExpr, initConcParm.getUnitDefinition(), sm.getGeometryClass()), sm.getGeometryClass()));
}
}
//
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.getGeometryClass()), getIdentifierSubstitutions(diffParm.getExpression(), diffParm.getUnitDefinition(), sm.getGeometryClass()), sm.getGeometryClass()));
}
}
//
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.getGeometryClass()), getIdentifierSubstitutions(bc_xm.getExpression(), bc_xm.getUnitDefinition(), sm.getGeometryClass()), sm.getGeometryClass()));
}
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.getGeometryClass()), getIdentifierSubstitutions(bc_xp.getExpression(), bc_xp.getUnitDefinition(), sm.getGeometryClass()), sm.getGeometryClass()));
}
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.getGeometryClass()), getIdentifierSubstitutions(bc_ym.getExpression(), bc_ym.getUnitDefinition(), sm.getGeometryClass()), sm.getGeometryClass()));
}
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.getGeometryClass()), getIdentifierSubstitutions(bc_yp.getExpression(), bc_yp.getUnitDefinition(), sm.getGeometryClass()), sm.getGeometryClass()));
}
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.getGeometryClass()), getIdentifierSubstitutions(bc_zm.getExpression(), bc_zm.getUnitDefinition(), sm.getGeometryClass()), sm.getGeometryClass()));
}
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.getGeometryClass()), getIdentifierSubstitutions(bc_zp.getExpression(), bc_zp.getUnitDefinition(), sm.getGeometryClass()), sm.getGeometryClass()));
}
}
//
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());
GeometryClass geometryClass = sm.getGeometryClass();
if (advection_velX != null && (advection_velX.getExpression() != null)) {
varHash.addVariable(newFunctionOrConstant(getMathSymbol(advection_velX, geometryClass), getIdentifierSubstitutions(advection_velX.getExpression(), advection_velX.getUnitDefinition(), geometryClass), geometryClass));
}
SpeciesContextSpec.SpeciesContextSpecParameter advection_velY = speciesContextSpecs[i].getParameterFromRole(SpeciesContextSpec.ROLE_VelocityY);
if (advection_velY != null && (advection_velY.getExpression() != null)) {
varHash.addVariable(newFunctionOrConstant(getMathSymbol(advection_velY, geometryClass), getIdentifierSubstitutions(advection_velY.getExpression(), advection_velY.getUnitDefinition(), geometryClass), geometryClass));
}
SpeciesContextSpec.SpeciesContextSpecParameter advection_velZ = speciesContextSpecs[i].getParameterFromRole(SpeciesContextSpec.ROLE_VelocityZ);
if (advection_velZ != null && (advection_velZ.getExpression() != null)) {
varHash.addVariable(newFunctionOrConstant(getMathSymbol(advection_velZ, geometryClass), getIdentifierSubstitutions(advection_velZ.getExpression(), advection_velZ.getUnitDefinition(), geometryClass), geometryClass));
}
}
//
// 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(model.getKMOLE().getName(), 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)));
//
for (int i = 0; i < structureMappings.length; i++) {
StructureMapping sm = structureMappings[i];
if (simContext.getGeometry().getDimension() == 0) {
StructureMappingParameter sizeParm = sm.getSizeParameter();
if (sizeParm != null && sizeParm.getExpression() != null) {
varHash.addVariable(newFunctionOrConstant(getMathSymbol(sizeParm, sm.getGeometryClass()), getIdentifierSubstitutions(sizeParm.getExpression(), sizeParm.getUnitDefinition(), sm.getGeometryClass()), sm.getGeometryClass()));
} else {
if (sm instanceof MembraneMapping) {
MembraneMapping mm = (MembraneMapping) sm;
StructureMappingParameter volFrac = mm.getVolumeFractionParameter();
if (volFrac != null && volFrac.getExpression() != null) {
varHash.addVariable(newFunctionOrConstant(getMathSymbol(volFrac, sm.getGeometryClass()), getIdentifierSubstitutions(volFrac.getExpression(), volFrac.getUnitDefinition(), sm.getGeometryClass()), sm.getGeometryClass()));
}
StructureMappingParameter surfToVol = mm.getSurfaceToVolumeParameter();
if (surfToVol != null && surfToVol.getExpression() != null) {
varHash.addVariable(newFunctionOrConstant(getMathSymbol(surfToVol, sm.getGeometryClass()), getIdentifierSubstitutions(surfToVol.getExpression(), surfToVol.getUnitDefinition(), sm.getGeometryClass()), sm.getGeometryClass()));
}
}
}
} else {
Parameter parm = sm.getParameterFromRole(StructureMapping.ROLE_AreaPerUnitArea);
if (parm != null && parm.getExpression() != null && sm.getGeometryClass() instanceof SurfaceClass) {
varHash.addVariable(newFunctionOrConstant(getMathSymbol(parm, sm.getGeometryClass()), getIdentifierSubstitutions(parm.getExpression(), parm.getUnitDefinition(), sm.getGeometryClass()), sm.getGeometryClass()));
}
parm = sm.getParameterFromRole(StructureMapping.ROLE_AreaPerUnitVolume);
if (parm != null && parm.getExpression() != null && sm.getGeometryClass() instanceof SubVolume) {
varHash.addVariable(newFunctionOrConstant(getMathSymbol(parm, sm.getGeometryClass()), getIdentifierSubstitutions(parm.getExpression(), parm.getUnitDefinition(), sm.getGeometryClass()), sm.getGeometryClass()));
}
parm = sm.getParameterFromRole(StructureMapping.ROLE_VolumePerUnitArea);
if (parm != null && parm.getExpression() != null && sm.getGeometryClass() instanceof SurfaceClass) {
varHash.addVariable(newFunctionOrConstant(getMathSymbol(parm, sm.getGeometryClass()), getIdentifierSubstitutions(parm.getExpression(), parm.getUnitDefinition(), sm.getGeometryClass()), sm.getGeometryClass()));
}
parm = sm.getParameterFromRole(StructureMapping.ROLE_VolumePerUnitVolume);
if (parm != null && parm.getExpression() != null && sm.getGeometryClass() instanceof SubVolume) {
varHash.addVariable(newFunctionOrConstant(getMathSymbol(parm, sm.getGeometryClass()), getIdentifierSubstitutions(parm.getExpression(), parm.getUnitDefinition(), sm.getGeometryClass()), sm.getGeometryClass()));
}
}
StructureMappingParameter sizeParm = sm.getSizeParameter();
if (sm.getGeometryClass() != null && sizeParm != null) {
if (simContext.getGeometry().getDimension() == 0) {
if (sizeParm.getExpression() != null) {
varHash.addVariable(newFunctionOrConstant(getMathSymbol(sizeParm, sm.getGeometryClass()), getIdentifierSubstitutions(sizeParm.getExpression(), sizeParm.getUnitDefinition(), sm.getGeometryClass()), sm.getGeometryClass()));
}
} else {
String compartmentName = sm.getGeometryClass().getName();
VCUnitDefinition sizeUnit = sm.getSizeParameter().getUnitDefinition();
String sizeFunctionName = null;
if (sm instanceof MembraneMapping) {
MembraneMapping mm = (MembraneMapping) sm;
if (mm.getGeometryClass() instanceof SurfaceClass) {
sizeFunctionName = MathFunctionDefinitions.Function_regionArea_current.getFunctionName();
} else if (mm.getGeometryClass() instanceof SubVolume) {
sizeFunctionName = MathFunctionDefinitions.Function_regionVolume_current.getFunctionName();
}
} else if (sm instanceof FeatureMapping) {
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.getGeometryClass()), getIdentifierSubstitutions(Expression.mult(totalVolumeCorrection, sizeFunctionExpression), sizeUnit, sm.getGeometryClass()), sm.getGeometryClass()));
}
}
}
//
// functions
//
enum1 = getSpeciesContextMappings();
while (enum1.hasMoreElements()) {
SpeciesContextMapping scm = (SpeciesContextMapping) enum1.nextElement();
if (scm.getVariable() == null && scm.getDependencyExpression() != null) {
// check if speciesContext has a rateRule; then the speciesContext should not be added as a constant
if (simContext.getRateRule(scm.getSpeciesContext()) == null) {
StructureMapping sm = simContext.getGeometryContext().getStructureMapping(scm.getSpeciesContext().getStructure());
if (sm.getGeometryClass() == null) {
Structure s = sm.getStructure();
if (s != null) {
throw new RuntimeException("unmapped structure " + s.getName());
}
throw new RuntimeException("structure mapping with no structure or mapping");
}
Variable dependentVariable = newFunctionOrConstant(getMathSymbol(scm.getSpeciesContext(), sm.getGeometryClass()), getIdentifierSubstitutions(scm.getDependencyExpression(), scm.getSpeciesContext().getUnitDefinition(), sm.getGeometryClass()), sm.getGeometryClass());
dependentVariable.setDomain(new Domain(sm.getGeometryClass()));
varHash.addVariable(dependentVariable);
}
}
}
BioEvent[] bioevents = simContext.getBioEvents();
if (bioevents != null && bioevents.length > 0) {
for (BioEvent be : bioevents) {
// transform the bioEvent trigger/delay to math Event
for (LocalParameter p : be.getEventParameters()) {
if (p.getExpression() != null) {
// ex: eventName.delay and eventName.triggerFunction
String name = getMathSymbol(p, null);
Expression exp = getIdentifierSubstitutions(p.getExpression(), p.getUnitDefinition(), null);
Variable var = newFunctionOrConstant(name, exp, null);
varHash.addVariable(var);
} else if (be.getParameter(BioEventParameterType.GeneralTriggerFunction) == p) {
//
// use generated function here.
//
String name = getMathSymbol(p, null);
Expression exp = getIdentifierSubstitutions(be.generateTriggerExpression(), p.getUnitDefinition(), null);
Variable var = newFunctionOrConstant(name, exp, null);
varHash.addVariable(var);
}
}
}
}
//
// substitute init functions for event assignment variables
//
// for (Map.Entry<VolVariable,EventAssignmentOrRateRuleInitParameter> entry : eventVolVarHash.entrySet()) {
// EventAssignmentOrRateRuleInitParameter eap = entry.getValue();
//
// String argName = eap.getName();
// Expression modelParamExpr = eap.getExpression();
// GeometryClass gc = getDefaultGeometryClass(modelParamExpr);
// VCUnitDefinition paramUnit = eap.getUnitDefinition();
// Expression mpInitExpr = new Expression(modelParamExpr);
// String[] symbols = mpInitExpr.getSymbols();
// if(symbols == null || symbols.length == 0) {
// continue;
// }
// // TODO: this is still not working well
// // check if 'initExpr' has other speciesContexts or rate rule global parameter variables in its expression
// // need to replace it with 'spContext_init', modelParameter_init
// for (String symbol : symbols) {
// // if symbol is a speciesContext, replacing it with a reference to initial condition for that speciesContext.
// SymbolTableEntry ste = mpInitExpr.getSymbolBinding(symbol);
// if (ste == null) {
// System.out.println("Unexpected NULL symbol in the initial expression of " + argName);
// } else if (ste instanceof SpeciesContext) {
// SpeciesContextSpec scs = simContext.getReactionContext().getSpeciesContextSpec((SpeciesContext)ste);
// // TODO: what if initial count???
// SpeciesContextSpecParameter spCInitParm = scs.getParameterFromRole(SpeciesContextSpec.ROLE_InitialConcentration);
// // 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());
// mpInitExpr.substituteInPlace(new Expression(ste.getName()), scsInitExpr);
// } else if(ste instanceof ModelParameter) {
// ModelParameter mpArg = (ModelParameter)ste;
// System.out.println(mpArg.getName());
// if(simContext.getRateRule(mpArg) == null) {
// continue; // only globals that are RateRule variables need to be replaced with their _init variable
// }
// Variable mpArgVar = initModelParameterHashTmp.get(mpArg);
// if(mpArgVar != null && eventVolVarHash.get(mpArgVar) != null) {
// EventAssignmentOrRateRuleInitParameter mpInitParam = eventVolVarHash.get(mpArgVar);
// Expression mpArgInitExpr = new Expression(mpInitParam, getNameScope());
// mpInitExpr.substituteInPlace(new Expression(ste.getName()), mpArgInitExpr);
//
// }
// } else {
// String msg = ste.getName() == null ? "??" : ste.getName();
// System.out.println("Unexpected symbol type for " + msg + " in the initial expression of " + argName);
// }
// }
// varHash.removeVariable(argName);
// Expression exp = getIdentifierSubstitutions(mpInitExpr, paramUnit, gc);
// Variable varInit = newFunctionOrConstant(argName, exp, gc);
// varHash.addVariable(varInit);
// }
//
// deal with rate rules
//
// first, substitute the init functions for rate rule variables that are model parameters
// we'll need this init variable (function or constant) for the ODE Equation
//
// here we store the init variable with the final substitutions within their expressions
Map<ModelParameter, Variable> initModelParameterHash = new HashMap<>();
Map<String, SymbolTableEntry> entryMap = new HashMap<String, SymbolTableEntry>();
simContext.getEntries(entryMap);
for (Map.Entry<ModelParameter, Variable> entry : initModelParameterHashTmp.entrySet()) {
ModelParameter mp = entry.getKey();
Variable mpInitVariable = entry.getValue();
String argName = mpInitVariable.getName();
Expression modelParamExpr = mp.getExpression();
GeometryClass gc = getDefaultGeometryClass(modelParamExpr);
Expression mpInitExpr = new Expression(modelParamExpr);
String[] symbols = mpInitExpr.getSymbols();
if (symbols == null || symbols.length == 0) {
// stays as it is in variable hash
// we just move it into the initModelParameterHash
initModelParameterHash.put(mp, mpInitVariable);
continue;
}
// need to replace it with 'spContext_init', modelParameter_init
for (String symbol : symbols) {
// if symbol is a speciesContext, replacing it with a reference to initial condition for that speciesContext.
SymbolTableEntry ste = mpInitExpr.getSymbolBinding(symbol);
if (ste == null) {
System.out.println("Unexpected NULL symbol in the initial expression of " + argName);
} else if (ste instanceof SpeciesContext) {
SpeciesContextSpec scs = simContext.getReactionContext().getSpeciesContextSpec((SpeciesContext) ste);
// TODO: what if initial count???
SpeciesContextSpecParameter spCInitParm = scs.getParameterFromRole(SpeciesContextSpec.ROLE_InitialConcentration);
// 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());
mpInitExpr.substituteInPlace(new Expression(ste.getName()), scsInitExpr);
} else if (ste instanceof ModelParameter) {
ModelParameter mpArg = (ModelParameter) ste;
System.out.println(mpArg.getName());
if (simContext.getRateRule(mpArg) == null) {
// only globals that are RateRule variables need to be replaced with their _init variable
continue;
}
EventAssignmentOrRateRuleInitParameter mpInitParam = modelParamTorateRuleInitMapping.get(mpArg);
if (mpInitParam != null) {
// we already made it, we only need to use it
Expression mpArgInitExpr = new Expression(mpInitParam, getNameScope());
mpInitExpr.substituteInPlace(new Expression(ste.getName()), mpArgInitExpr);
}
} else {
String msg = ste.getName() == null ? "??" : ste.getName();
System.out.println("Unexpected symbol type for " + msg + " in the initial expression of " + argName);
}
}
VCUnitDefinition paramUnit = modelUnitSystem.getInstance_TBD();
if (mp.getUnitDefinition() != null && !mp.getUnitDefinition().equals(modelUnitSystem.getInstance_TBD())) {
paramUnit = mp.getUnitDefinition();
}
varHash.removeVariable(mpInitVariable);
Expression exp = getIdentifierSubstitutions(mpInitExpr, paramUnit, gc);
mpInitVariable = newFunctionOrConstant(argName, exp, gc);
varHash.addVariable(mpInitVariable);
initModelParameterHash.put(mp, mpInitVariable);
}
//
// create the VolVariable for the species context used as rate rule variable
// create the Variable (function or constant) for its rate (need it for the ODE Equation)
//
enum1 = getSpeciesContextMappings();
while (enum1.hasMoreElements()) {
// species context used as rate rule variable
SpeciesContextMapping scm = (SpeciesContextMapping) enum1.nextElement();
Variable var = scm.getVariable();
Expression exp = scm.getDependencyExpression();
if (var == null && exp != null) {
RateRule rr = simContext.getRateRule(scm.getSpeciesContext());
if (rr != null && (rr.getRateRuleVar() instanceof SpeciesContext)) {
SpeciesContext sc = scm.getSpeciesContext();
StructureMapping sm = simContext.getGeometryContext().getStructureMapping(sc.getStructure());
if (sm.getGeometryClass() == null) {
Structure s = sm.getStructure();
if (s != null) {
throw new RuntimeException("unmapped structure " + s.getName());
}
throw new RuntimeException("structure mapping with no structure or mapping");
}
String name = getMathSymbol(scm.getSpeciesContext(), sm.getGeometryClass());
Expression orig = rr.getRateRuleExpression();
Expression ex = getIdentifierSubstitutions(orig, scm.getSpeciesContext().getUnitDefinition(), sm.getGeometryClass());
GeometryClass gc = sm.getGeometryClass();
Domain domain = null;
if (gc != null) {
domain = new Domain(gc);
}
if (gc instanceof SurfaceClass) {
scm.setVariable(new MemVariable(scm.getSpeciesContext().getName(), domain));
} else {
scm.setVariable(new VolVariable(scm.getSpeciesContext().getName(), domain));
}
Variable oldVariablre = varHash.getVariable(name);
if (oldVariablre != null) {
// should always be null
varHash.removeVariable(name);
}
varHash.addVariable(scm.getVariable());
// // create the rate parameter
SpeciesContextSpec scs = simContext.getReactionContext().getSpeciesContextSpec(sc);
SpeciesContextSpecParameter scsInitParam = scs.getInitialConditionParameter();
VCUnitDefinition scsInitParamUnit = scsInitParam.getUnitDefinition();
RateRuleRateParameter rateParam = null;
try {
Expression origExp = simContext.getRateRule(sc).getRateRuleExpression();
VCUnitDefinition rateUnit = modelUnitSystem.getInstance_TBD();
if (scsInitParamUnit != null && !scsInitParamUnit.equals(modelUnitSystem.getInstance_TBD())) {
rateUnit = scsInitParamUnit;
}
Expression rateExpr = getIdentifierSubstitutions(origExp, rateUnit, gc);
String argName = sc.getName() + MATH_FUNC_SUFFIX_RATERULE_RATE;
Variable param = newFunctionOrConstant(argName, rateExpr, gc);
varHash.addVariable(param);
rateParam = addRateRuleRateParameter(sc, rateExpr, PARAMETER_ROLE_RATERULE_RATE, rateUnit);
} catch (PropertyVetoException e) {
e.printStackTrace(System.out);
throw new MappingException(e.getMessage());
}
// we generate the ODE equation elsewhere (later)
rateRuleRateParamHash.put(scm.getVariable(), rateParam);
}
} else if (var != null && exp == null) {
// could be an event variable AND a rate rule variable - in which case we need a rate parameter for the event ODE equation
SpeciesContext sc = scm.getSpeciesContext();
boolean isRateRuleVar = rateRuleVarTargets.contains(sc);
boolean isEventAssignVar = eventAssignTargets.contains(sc);
if (isRateRuleVar && isEventAssignVar) {
// is both, so we make a rate parameter, like above
SpeciesContextSpec scs = simContext.getReactionContext().getSpeciesContextSpec(sc);
SpeciesContextSpecParameter scsInitParam = scs.getInitialConditionParameter();
VCUnitDefinition scsInitParamUnit = scsInitParam.getUnitDefinition();
StructureMapping sm = simContext.getGeometryContext().getStructureMapping(sc.getStructure());
GeometryClass gc = sm.getGeometryClass();
RateRuleRateParameter rateParam = null;
try {
Expression origExp = simContext.getRateRule(sc).getRateRuleExpression();
VCUnitDefinition rateUnit = modelUnitSystem.getInstance_TBD();
if (scsInitParamUnit != null && !scsInitParamUnit.equals(modelUnitSystem.getInstance_TBD())) {
rateUnit = scsInitParamUnit;
}
Expression rateExpr = getIdentifierSubstitutions(origExp, rateUnit, gc);
String argName = sc.getName() + MATH_FUNC_SUFFIX_RATERULE_RATE;
Variable param = newFunctionOrConstant(argName, rateExpr, gc);
varHash.addVariable(param);
rateParam = addRateRuleRateParameter(sc, rateExpr, PARAMETER_ROLE_RATERULE_RATE, rateUnit);
} catch (PropertyVetoException e) {
e.printStackTrace(System.out);
throw new MappingException(e.getMessage());
}
// we generate the ODE equation elsewhere (later)
rateRuleRateParamHash.put(var, rateParam);
}
}
}
//
for (ModelParameter mp : modelParameters) {
// global parameter used as rate rule variable
Variable var = varHash.getVariable(mp.getName());
RateRule rr = simContext.getRateRule(mp);
Expression modelParamExpr = mp.getExpression();
if (var == null && rr != null) {
// at this point var should be a constant
// we're under the assumption that it's non-spatial
GeometryClass[] geometryClasses = simContext.getGeometryContext().getGeometry().getGeometryClasses();
GeometryClass gc = geometryClasses[0];
// SubDomain subDomain = mathDesc.getSubDomains().nextElement();
// GeometryClass gc = getDefaultGeometryClass(modelParamExpr);
Domain domain = null;
if (gc != null) {
domain = new Domain(gc);
}
Variable variable;
if (gc instanceof SurfaceClass) {
variable = new MemVariable(mp.getName(), domain);
} else {
variable = new VolVariable(mp.getName(), domain);
}
varHash.addVariable(variable);
RateRuleRateParameter rateParam = null;
try {
Expression origExp = rr.getRateRuleExpression();
VCUnitDefinition rateUnit = modelUnitSystem.getInstance_TBD();
if (mp.getUnitDefinition() != null && !mp.getUnitDefinition().equals(modelUnitSystem.getInstance_TBD())) {
rateUnit = mp.getUnitDefinition().divideBy(timeUnit);
}
Expression rateExpr = getIdentifierSubstitutions(origExp, rateUnit, gc);
String argName = mp.getName() + MATH_FUNC_SUFFIX_RATERULE_RATE;
Variable param = newFunctionOrConstant(argName, rateExpr, gc);
varHash.addVariable(param);
rateParam = addRateRuleRateParameter(mp, rateExpr, PARAMETER_ROLE_RATERULE_RATE, rateUnit);
} catch (PropertyVetoException e) {
e.printStackTrace(System.out);
throw new MappingException(e.getMessage());
}
// no need to put it in the hash, we make the ODE Equation right here
// rateRuleRateParamHash.put(variable, rateParam);
// we know it's non-spatial
SubDomain subDomain = mathDesc.getSubDomains().nextElement();
Equation equation = null;
// TODO: replace the expression with the variable ex: "g0_protocol_init" computed above
Expression initial = new Expression(mp.getExpression());
// TODO: can it be null? should check and maybe try mp.getConstantValue() too ???
Variable mpInitVariable = initModelParameterHash.get(mp);
if (mpInitVariable != null) {
initial = new Expression(mpInitVariable.getName());
}
Expression rateExpr = new Expression(0.0);
// RateRuleRateParameter rateParam = rateRuleRateParamHash.get(variable);
if (rateParam != null) {
// ex: g0_rate
rateExpr = new Expression(getMathSymbol(rateParam, gc));
}
// ODE Equation for rate rule variable being a global parameter
equation = new OdeEquation(variable, initial, rateExpr);
subDomain.addEquation(equation);
}
}
//
// deal with assignment rules
//
enum1 = getSpeciesContextMappings();
while (enum1.hasMoreElements()) {
// species context used as assignment rule variable
SpeciesContextMapping scm = (SpeciesContextMapping) enum1.nextElement();
if (scm.getVariable() == null && scm.getDependencyExpression() != null) {
AssignmentRule ar = simContext.getAssignmentRule(scm.getSpeciesContext());
if (ar != null && (ar.getAssignmentRuleVar() instanceof SpeciesContext)) {
// TODO: we limit assignment rules to SpeciesContext for now
StructureMapping sm = simContext.getGeometryContext().getStructureMapping(scm.getSpeciesContext().getStructure());
if (sm.getGeometryClass() == null) {
Structure s = sm.getStructure();
if (s != null) {
throw new RuntimeException("unmapped structure " + s.getName());
}
throw new RuntimeException("structure mapping with no structure or mapping");
}
String name = getMathSymbol(scm.getSpeciesContext(), sm.getGeometryClass());
Expression orig = ar.getAssignmentRuleExpression();
Expression ex = getIdentifierSubstitutions(orig, scm.getSpeciesContext().getUnitDefinition(), sm.getGeometryClass());
GeometryClass gc = sm.getGeometryClass();
Variable dependentVariable = newFunctionOrConstant(name, ex, gc);
dependentVariable.setDomain(new Domain(sm.getGeometryClass()));
varHash.removeVariable(name);
varHash.addVariable(dependentVariable);
}
}
}
for (ModelParameter mp : modelParameters) {
// global parameter used as assignment rule variable
Variable var = varHash.getVariable(mp.getName());
AssignmentRule ar = simContext.getAssignmentRule(mp);
Expression modelParamExpr = mp.getExpression();
if (var == null && ar != null) {
// at this point var (global parameter used as assignment rule variable) should be null
// we're under the assumption that it's non-spatial
GeometryClass[] geometryClasses = simContext.getGeometryContext().getGeometry().getGeometryClasses();
GeometryClass gc = geometryClasses[0];
SubDomain subDomain = mathDesc.getSubDomains().nextElement();
Expression origExp = ar.getAssignmentRuleExpression();
VCUnitDefinition rateUnit = modelUnitSystem.getInstance_TBD();
if (mp.getUnitDefinition() != null && !mp.getUnitDefinition().equals(modelUnitSystem.getInstance_TBD())) {
rateUnit = mp.getUnitDefinition();
}
Expression rateExpr = getIdentifierSubstitutions(origExp, rateUnit, gc);
String argName = mp.getName();
Variable param = newFunctionOrConstant(argName, rateExpr, gc);
varHash.addVariable(param);
}
}
//
// 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");
}
//
for (CompartmentSubdomainContext compartmentSubDomainContext : compartmentSubdomainContexts) {
SubVolume subVolume = compartmentSubDomainContext.subvolume;
CompartmentSubDomain subDomain = mathDesc.getCompartmentSubDomain(subVolume.getName());
//
// assign boundary condition types
//
StructureMapping[] mappedSMs = simContext.getGeometryContext().getStructureMappings(subVolume);
FeatureMapping mappedFM = null;
for (int i = 0; i < mappedSMs.length; i++) {
if (mappedSMs[i] instanceof FeatureMapping) {
if (mappedFM != null) {
lg.warn("WARNING:::: MathMapping.refreshMathDescription() ... assigning boundary condition types not unique");
}
mappedFM = (FeatureMapping) mappedSMs[i];
}
}
if (mappedFM != null) {
if (simContext.getGeometry().getDimension() > 0) {
subDomain.setBoundaryConditionXm(mappedFM.getBoundaryConditionTypeXm());
subDomain.setBoundaryConditionXp(mappedFM.getBoundaryConditionTypeXp());
}
if (simContext.getGeometry().getDimension() > 1) {
subDomain.setBoundaryConditionYm(mappedFM.getBoundaryConditionTypeYm());
subDomain.setBoundaryConditionYp(mappedFM.getBoundaryConditionTypeYp());
}
if (simContext.getGeometry().getDimension() > 2) {
subDomain.setBoundaryConditionZm(mappedFM.getBoundaryConditionTypeZm());
subDomain.setBoundaryConditionZp(mappedFM.getBoundaryConditionTypeZp());
}
}
//
// create equations
//
VolumeStructureAnalyzer structureAnalyzer = getVolumeStructureAnalyzer(subVolume);
Enumeration<SpeciesContextMapping> enumSCM = getSpeciesContextMappings();
while (enumSCM.hasMoreElements()) {
SpeciesContextMapping scm = enumSCM.nextElement();
SpeciesContext sc = scm.getSpeciesContext();
StructureMapping sm = simContext.getGeometryContext().getStructureMapping(sc.getStructure());
SpeciesContextSpec scs = simContext.getReactionContext().getSpeciesContextSpec(sc);
//
// if an independent volume variable, then create equation for it (if mapped to this subDomain)
//
final GeometryClass gc = sm.getGeometryClass();
if (gc == null || !gc.getName().equals(subDomain.getName())) {
continue;
}
SpeciesContextSpecParameter initConcParameter = scs.getParameterFromRole(SpeciesContextSpec.ROLE_InitialConcentration);
if ((scm.getVariable() instanceof VolumeRegionVariable) && scm.getDependencyExpression() == null) {
VolumeRegionVariable volumeRegionVariable = (VolumeRegionVariable) scm.getVariable();
Expression initial = getIdentifierSubstitutions(new Expression(initConcParameter, getNameScope()), initConcParameter.getUnitDefinition(), sm.getGeometryClass());
Expression rate = getIdentifierSubstitutions(scm.getRate(), scm.getSpeciesContext().getUnitDefinition().divideBy(timeUnit), simContext.getGeometryContext().getStructureMapping(sc.getStructure()).getGeometryClass());
VolumeRegionEquation volumeRegionEquation = new VolumeRegionEquation(volumeRegionVariable, initial);
volumeRegionEquation.setVolumeRateExpression(rate);
subDomain.addEquation(volumeRegionEquation);
} else if (scm.getVariable() instanceof VolVariable && scm.getDependencyExpression() == null) {
VolVariable variable = (VolVariable) scm.getVariable();
Equation equation = null;
if (sm.getGeometryClass() == subVolume) {
if (scm.isPDERequired()) {
//
// species context belongs to this subDomain
//
Expression initial = getIdentifierSubstitutions(new Expression(initConcParameter, getNameScope()), initConcParameter.getUnitDefinition(), sm.getGeometryClass());
Expression rate = getIdentifierSubstitutions(scm.getRate(), scm.getSpeciesContext().getUnitDefinition().divideBy(timeUnit), simContext.getGeometryContext().getStructureMapping(sc.getStructure()).getGeometryClass());
SpeciesContextSpecParameter diffusionParameter = scs.getDiffusionParameter();
Expression diffusion = getIdentifierSubstitutions(new Expression(diffusionParameter, getNameScope()), diffusionParameter.getUnitDefinition(), sm.getGeometryClass());
equation = new PdeEquation(variable, initial, rate, diffusion);
((PdeEquation) equation).setBoundaryXm((scs.getBoundaryXmParameter().getExpression() == null) ? (null) : new Expression(getMathSymbol(scs.getBoundaryXmParameter(), sm.getGeometryClass())));
((PdeEquation) equation).setBoundaryXp((scs.getBoundaryXpParameter().getExpression() == null) ? (null) : new Expression(getMathSymbol(scs.getBoundaryXpParameter(), sm.getGeometryClass())));
((PdeEquation) equation).setBoundaryYm((scs.getBoundaryYmParameter().getExpression() == null) ? (null) : new Expression(getMathSymbol(scs.getBoundaryYmParameter(), sm.getGeometryClass())));
((PdeEquation) equation).setBoundaryYp((scs.getBoundaryYpParameter().getExpression() == null) ? (null) : new Expression(getMathSymbol(scs.getBoundaryYpParameter(), sm.getGeometryClass())));
((PdeEquation) equation).setBoundaryZm((scs.getBoundaryZmParameter().getExpression() == null) ? (null) : new Expression(getMathSymbol(scs.getBoundaryZmParameter(), sm.getGeometryClass())));
((PdeEquation) equation).setBoundaryZp((scs.getBoundaryZpParameter().getExpression() == null) ? (null) : new Expression(getMathSymbol(scs.getBoundaryZpParameter(), sm.getGeometryClass())));
if (simContext.getGeometry().getDimension() >= 1) {
Expression velXExp = null;
if (scs.getVelocityXParameter().getExpression() != null) {
velXExp = new Expression(getMathSymbol(scs.getVelocityXParameter(), sm.getGeometryClass()));
} else {
SpatialQuantity[] velX_quantities = scs.getVelocityQuantities(QuantityComponent.X);
if (velX_quantities.length > 0) {
int numRegions = simContext.getGeometry().getGeometrySurfaceDescription().getGeometricRegions(subVolume).length;
if (velX_quantities.length == 1 && numRegions == 1) {
velXExp = new Expression(getMathSymbol(velX_quantities[0], sm.getGeometryClass()));
} else {
throw new MappingException("multiple advection velocities enabled set for multiple volume domains ");
}
}
}
((PdeEquation) equation).setVelocityX(velXExp);
}
if (simContext.getGeometry().getDimension() >= 2) {
Expression velYExp = null;
if (scs.getVelocityYParameter().getExpression() != null) {
velYExp = new Expression(getMathSymbol(scs.getVelocityYParameter(), sm.getGeometryClass()));
} else {
SpatialQuantity[] velY_quantities = scs.getVelocityQuantities(QuantityComponent.Y);
if (velY_quantities.length > 0) {
int numRegions = simContext.getGeometry().getGeometrySurfaceDescription().getGeometricRegions(subVolume).length;
if (velY_quantities.length == 1 && numRegions == 1) {
velYExp = new Expression(getMathSymbol(velY_quantities[0], sm.getGeometryClass()));
} else {
throw new MappingException("multiple advection velocities enabled set for multiple volume domains ");
}
}
}
((PdeEquation) equation).setVelocityY(velYExp);
}
if (simContext.getGeometry().getDimension() == 3) {
Expression velZExp = null;
if (scs.getVelocityZParameter().getExpression() != null) {
velZExp = new Expression(getMathSymbol(scs.getVelocityZParameter(), sm.getGeometryClass()));
} else {
SpatialQuantity[] velZ_quantities = scs.getVelocityQuantities(QuantityComponent.Z);
if (velZ_quantities.length > 0) {
int numRegions = simContext.getGeometry().getGeometrySurfaceDescription().getGeometricRegions(subVolume).length;
if (velZ_quantities.length == 1 && numRegions == 1) {
velZExp = new Expression(getMathSymbol(velZ_quantities[0], sm.getGeometryClass()));
} else {
throw new MappingException("multiple advection velocities enabled set for multiple volume domains ");
}
}
}
((PdeEquation) equation).setVelocityZ(velZExp);
}
subDomain.replaceEquation(equation);
} else {
//
// ODE - species context belongs to this subDomain
//
Expression initial = new Expression(getMathSymbol(initConcParameter, null));
Expression rate = (scm.getRate() == null) ? new Expression(0.0) : getIdentifierSubstitutions(scm.getRate(), scm.getSpeciesContext().getUnitDefinition().divideBy(timeUnit), simContext.getGeometryContext().getStructureMapping(sc.getStructure()).getGeometryClass());
//
// if it's an event assignment variable AND a rate rule variable
// we replace the event rate computed above (which should be zero) with the RateRuleParameter expression
//
RateRuleRateParameter rateParam = rateRuleRateParamHash.get(variable);
if (rateParam != null) {
rate = new Expression(getMathSymbol(rateParam, null));
}
equation = new OdeEquation(variable, initial, rate);
subDomain.replaceEquation(equation);
}
}
} else if (scm.getVariable() instanceof VolVariable && scm.getDependencyExpression() != null) {
// rate rule variables are like this
RateRule rr = simContext.getRateRule(scm.getSpeciesContext());
if (rr != null && (rr.getRateRuleVar() instanceof SpeciesContext)) {
//
// we generate rate rule ODE equation only for species variable that are NOT event assignment variable (see right above)
// for global parameters variable we do it elsewhere
//
VolVariable variable = (VolVariable) scm.getVariable();
Equation equation = null;
if (sm.getGeometryClass() == subVolume) {
Expression initial = new Expression(getMathSymbol(initConcParameter, null));
Expression rateExpr = new Expression(0.0);
RateRuleRateParameter rateParam = rateRuleRateParamHash.get(variable);
if (rateParam != null) {
rateExpr = new Expression(getMathSymbol(rateParam, null));
}
equation = new OdeEquation(variable, initial, rateExpr);
subDomain.addEquation(equation);
}
}
}
}
//
// create fast system (if neccessary)
//
SpeciesContextMapping[] fastSpeciesContextMappings = structureAnalyzer.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
//
Expression rate = getIdentifierSubstitutions(scm.getFastRate(), scm.getSpeciesContext().getUnitDefinition().divideBy(timeUnit), subVolume);
FastRate fastRate = new FastRate(rate);
fastSystem.addFastRate(fastRate);
} else {
//
// dependant-fast variable, create a fastInvariant object
//
Expression rate = getIdentifierSubstitutions(scm.getFastInvariant(), modelUnitSystem.getVolumeConcentrationUnit(), 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 = simContext.getGeometryContext().getStructuresFromGeometryClass(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 ((membraneMapping.getGeometryClass() instanceof SubVolume) && membraneMapping.getCalculateVoltage()) {
MembraneElectricalDevice capacitiveDevice = potentialMapping.getCapacitiveDevice(membrane);
if (capacitiveDevice.getDependentVoltageExpression() == null) {
VolVariable vVar = (VolVariable) mathDesc.getVariable(getMathSymbol(capacitiveDevice.getVoltageSymbol(), membraneMapping.getGeometryClass()));
Expression initExp = new Expression(getMathSymbol(capacitiveDevice.getMembraneMapping().getInitialVoltageParameter(), membraneMapping.getGeometryClass()));
subDomain.addEquation(new OdeEquation(vVar, initExp, getIdentifierSubstitutions(potentialMapping.getOdeRHS(capacitiveDevice, this), membrane.getMembraneVoltage().getUnitDefinition().divideBy(timeUnit), membraneMapping.getGeometryClass())));
} else {
//
//
//
}
}
}
}
}
//
for (MembraneSubdomainContext memSubdomainContext : membraneSubdomainContexts) {
MembraneSubDomain memSubDomain = memSubdomainContext.membraneSubdomain;
SurfaceClass surfaceClass = memSubdomainContext.surfaceClass;
for (SurfaceRegionObject surfaceRegionObject : memSubdomainContext.surfaceRegionObjects) {
if (surfaceRegionObject.isQuantityCategoryEnabled(QuantityCategory.SurfaceVelocity)) {
int dim = simContext.getGeometry().getDimension();
if (dim != 2) {
throw new MappingException("Membrane Velocity only supported for 2D geometries");
}
if (simContext.getGeometry().getDimension() >= 1) {
SpatialQuantity velXQuantity = surfaceRegionObject.getSpatialQuantity(QuantityCategory.SurfaceVelocity, QuantityComponent.X);
Expression velXExp = new Expression(velXQuantity, simContext.getNameScope());
memSubDomain.setVelocityX(getIdentifierSubstitutions(velXExp, velXQuantity.getUnitDefinition(), surfaceClass));
}
if (simContext.getGeometry().getDimension() >= 2) {
SpatialQuantity velYQuantity = surfaceRegionObject.getSpatialQuantity(QuantityCategory.SurfaceVelocity, QuantityComponent.Y);
Expression velYExp = new Expression(velYQuantity, simContext.getNameScope());
memSubDomain.setVelocityY(getIdentifierSubstitutions(velYExp, velYQuantity.getUnitDefinition(), surfaceClass));
}
if (simContext.getGeometry().getDimension() == 3) {
SpatialQuantity velZQuantity = surfaceRegionObject.getSpatialQuantity(QuantityCategory.SurfaceVelocity, QuantityComponent.Z);
Expression velZExp = new Expression(velZQuantity, simContext.getNameScope());
// memSubDomain.setVelocityZ(getIdentifierSubstitutions(velZExp, velZQuantity.getUnitDefinition(), surfaceClass));
throw new MappingException("Membrane Velocity not supported for 2D problems");
}
}
}
//
// create equations for membrane-bound molecular species
//
MembraneStructureAnalyzer membraneStructureAnalyzer = getMembraneStructureAnalyzer(surfaceClass);
Enumeration<SpeciesContextMapping> enumSCM = getSpeciesContextMappings();
while (enumSCM.hasMoreElements()) {
SpeciesContextMapping scm = enumSCM.nextElement();
SpeciesContext sc = scm.getSpeciesContext();
SpeciesContextSpec scs = simContext.getReactionContext().getSpeciesContextSpec(sc);
StructureMapping sm = simContext.getGeometryContext().getStructureMapping(sc.getStructure());
//
if ((scm.getVariable() instanceof MembraneRegionVariable) && scm.getDependencyExpression() == null) {
MembraneRegionEquation equation = null;
MembraneRegionVariable memRegionVar = (MembraneRegionVariable) scm.getVariable();
if (sm.getGeometryClass() == surfaceClass) {
//
// species context belongs to this subDomain
//
Expression initial = new Expression(getMathSymbol(scs.getParameterFromRole(SpeciesContextSpec.ROLE_InitialConcentration), sm.getGeometryClass()));
Expression rate = getIdentifierSubstitutions(scm.getRate(), scm.getSpeciesContext().getUnitDefinition().divideBy(timeUnit), simContext.getGeometryContext().getStructureMapping(sc.getStructure()).getGeometryClass());
equation = new MembraneRegionEquation(memRegionVar, initial);
equation.setMembraneRateExpression(rate);
// equation.setUniformRateExpression(newUniformRateExpression);
memSubDomain.replaceEquation(equation);
}
} else if ((scm.getVariable() instanceof MemVariable) && scm.getDependencyExpression() == null) {
//
if (sm.getGeometryClass() == surfaceClass) {
Equation equation = null;
MemVariable variable = (MemVariable) scm.getVariable();
if (scm.isPDERequired()) {
//
// PDE
//
//
// species context belongs to this subDomain
//
Expression initial = new Expression(getMathSymbol(scs.getParameterFromRole(SpeciesContextSpec.ROLE_InitialConcentration), sm.getGeometryClass()));
Expression rate = getIdentifierSubstitutions(scm.getRate(), scm.getSpeciesContext().getUnitDefinition().divideBy(timeUnit), simContext.getGeometryContext().getStructureMapping(sc.getStructure()).getGeometryClass());
Expression diffusion = new Expression(getMathSymbol(scs.getDiffusionParameter(), sm.getGeometryClass()));
equation = new PdeEquation(variable, initial, rate, diffusion);
((PdeEquation) equation).setBoundaryXm((scs.getBoundaryXmParameter().getExpression() == null) ? (null) : new Expression(getMathSymbol(scs.getBoundaryXmParameter(), sm.getGeometryClass())));
((PdeEquation) equation).setBoundaryXp((scs.getBoundaryXpParameter().getExpression() == null) ? (null) : new Expression(getMathSymbol(scs.getBoundaryXpParameter(), sm.getGeometryClass())));
((PdeEquation) equation).setBoundaryYm((scs.getBoundaryYmParameter().getExpression() == null) ? (null) : new Expression(getMathSymbol(scs.getBoundaryYmParameter(), sm.getGeometryClass())));
((PdeEquation) equation).setBoundaryYp((scs.getBoundaryYpParameter().getExpression() == null) ? (null) : new Expression(getMathSymbol(scs.getBoundaryYpParameter(), sm.getGeometryClass())));
((PdeEquation) equation).setBoundaryZm((scs.getBoundaryZmParameter().getExpression() == null) ? (null) : new Expression(getMathSymbol(scs.getBoundaryZmParameter(), sm.getGeometryClass())));
((PdeEquation) equation).setBoundaryZp((scs.getBoundaryZpParameter().getExpression() == null) ? (null) : new Expression(getMathSymbol(scs.getBoundaryZpParameter(), sm.getGeometryClass())));
memSubDomain.replaceEquation(equation);
} else {
//
// ODE
//
//
// 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()).getGeometryClass());
equation = new OdeEquation(variable, initial, rate);
memSubDomain.replaceEquation(equation);
}
}
}
}
Enumeration<SpeciesContextMapping> enum_scm = getSpeciesContextMappings();
while (enum_scm.hasMoreElements()) {
SpeciesContextMapping scm = enum_scm.nextElement();
if (scm.isPDERequired() || scm.getVariable() instanceof VolumeRegionVariable) {
// Species species = scm.getSpeciesContext().getSpecies();
Variable var = scm.getVariable();
final Domain dm = var.getDomain();
if (dm != null) {
final String domainName = dm.getName();
if (sameName(domainName, memSubDomain.getInsideCompartment()) || sameName(domainName, memSubDomain.getOutsideCompartment())) {
JumpCondition jc = memSubDomain.getJumpCondition(var);
if (jc == null) {
// System.out.println("MathMapping.refreshMathDescription(), adding jump condition for diffusing variable "+var.getName()+" on membrane "+membraneStructureAnalyzer.getMembrane().getName());
if (var instanceof VolVariable) {
jc = new JumpCondition((VolVariable) var);
} else if (var instanceof VolumeRegionVariable) {
jc = new JumpCondition((VolumeRegionVariable) var);
} else {
throw new RuntimeException("unexpected Variable type " + var.getClass().getName());
}
memSubDomain.addJumpCondition(jc);
}
}
}
}
}
//
// set jump conditions for any volume variables or volume region variables that have explicitly defined fluxes
//
ResolvedFlux[] resolvedFluxes = membraneStructureAnalyzer.getResolvedFluxes();
if (resolvedFluxes != null) {
for (int i = 0; i < resolvedFluxes.length; i++) {
SpeciesContext sc = resolvedFluxes[i].getSpeciesContext();
SpeciesContextMapping scm = getSpeciesContextMapping(sc);
StructureMapping sm = getSimulationContext().getGeometryContext().getStructureMapping(sc.getStructure());
if (scm.getVariable() instanceof VolVariable && scm.isPDERequired()) {
VolVariable volVar = (VolVariable) scm.getVariable();
JumpCondition jc = memSubDomain.getJumpCondition(volVar);
if (jc == null) {
jc = new JumpCondition(volVar);
memSubDomain.addJumpCondition(jc);
}
Expression flux = getIdentifierSubstitutions(resolvedFluxes[i].getFluxExpression(), resolvedFluxes[i].getUnitDefinition(), membraneStructureAnalyzer.getSurfaceClass());
if (memSubDomain.getInsideCompartment().getName().equals(sm.getGeometryClass().getName())) {
jc.setInFlux(flux);
} else if (memSubDomain.getOutsideCompartment().getName().equals(sm.getGeometryClass().getName())) {
jc.setOutFlux(flux);
} else {
throw new RuntimeException("Application " + simContext.getName() + " : " + scm.getSpeciesContext().getName() + " has spatially resolved flux at membrane " + scm.getSpeciesContext().getStructure().getName() + " with a non-local flux species " + scm.getSpeciesContext().getName());
}
} else if (scm.getVariable() instanceof VolumeRegionVariable) {
VolumeRegionVariable volRegionVar = (VolumeRegionVariable) scm.getVariable();
JumpCondition jc = memSubDomain.getJumpCondition(volRegionVar);
if (jc == null) {
jc = new JumpCondition(volRegionVar);
memSubDomain.addJumpCondition(jc);
}
Expression flux = getIdentifierSubstitutions(resolvedFluxes[i].getFluxExpression(), resolvedFluxes[i].getUnitDefinition(), membraneStructureAnalyzer.getSurfaceClass());
if (memSubDomain.getInsideCompartment().getName().equals(sm.getGeometryClass().getName())) {
jc.setInFlux(flux);
} else if (memSubDomain.getOutsideCompartment().getName().equals(sm.getGeometryClass().getName())) {
jc.setOutFlux(flux);
} else {
throw new RuntimeException("Application " + simContext.getName() + " : " + scm.getSpeciesContext().getName() + " has spatially resolved flux at membrane " + scm.getSpeciesContext().getStructure().getName() + " with a non-local flux species " + scm.getSpeciesContext().getName());
}
} else {
throw new MappingException("Application " + simContext.getName() + " : " + scm.getSpeciesContext().getName() + " has spatially resolved flux at membrane " + scm.getSpeciesContext().getStructure().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);
FastRate fastRate = new FastRate(getIdentifierSubstitutions(scm.getFastRate(), rateUnit, surfaceClass));
fastSystem.addFastRate(fastRate);
} else {
//
// dependant-fast variable, create a fastInvariant object
//
VCUnitDefinition invariantUnit = scm.getSpeciesContext().getUnitDefinition();
FastInvariant fastInvariant = new FastInvariant(getIdentifierSubstitutions(scm.getFastInvariant(), invariantUnit, surfaceClass));
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
//
Structure[] resolvedSurfaceStructures = membraneStructureAnalyzer.getStructures();
for (int m = 0; m < resolvedSurfaceStructures.length; m++) {
if (resolvedSurfaceStructures[m] instanceof Membrane) {
Membrane membrane = (Membrane) resolvedSurfaceStructures[m];
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.getGeometryClass())) instanceof MembraneRegionVariable) {
MembraneRegionVariable vVar = (MembraneRegionVariable) mathDesc.getVariable(getMathSymbol(capacitiveDevice.getVoltageSymbol(), membraneMapping.getGeometryClass()));
Parameter initialVoltageParm = capacitiveDevice.getMembraneMapping().getInitialVoltageParameter();
Expression initExp = getIdentifierSubstitutions(initialVoltageParm.getExpression(), initialVoltageParm.getUnitDefinition(), capacitiveDevice.getMembraneMapping().getGeometryClass());
MembraneRegionEquation vEquation = new MembraneRegionEquation(vVar, initExp);
vEquation.setMembraneRateExpression(getIdentifierSubstitutions(potentialMapping.getOdeRHS(capacitiveDevice, this), membrane.getMembraneVoltage().getUnitDefinition().divideBy(timeUnit), capacitiveDevice.getMembraneMapping().getGeometryClass()));
memSubDomain.addEquation(vEquation);
}
}
}
}
}
// create equations for event assignment or rate rule targets that are model params/species, etc.
Set<VolVariable> hashKeySet = eventVolVarHash.keySet();
Iterator<VolVariable> volVarsIter = hashKeySet.iterator();
// working under the 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();
EventAssignmentOrRateRuleInitParameter initParam = eventVolVarHash.get(volVar);
// check event initial condition, it shouldn't contain vars, we have to do it here, coz we want to substitute functions...etc.
Expression eapExp = MathUtilities.substituteFunctions(initParam.getExpression(), mathDesc);
if (eapExp.getSymbols() != null) {
for (String symbol : eapExp.getSymbols()) {
SymbolTableEntry ste = eapExp.getSymbolBinding(symbol);
if (ste instanceof VolVariable || ste instanceof MemVariable) {
throw new MathException("Variables are not allowed in Event assignment initial condition.\nEvent assignment target: " + volVar.getName() + " has variable (" + symbol + ") in its expression.");
}
}
}
Expression rateExpr = new Expression(0.0);
RateRuleRateParameter rateParam = rateRuleRateParamHash.get(volVar);
if (rateParam != null) {
// this is a rate rule, get its expression.
rateExpr = new Expression(getMathSymbol(rateParam, null));
}
Equation equation = new OdeEquation(volVar, new Expression(getMathSymbol(initParam, null)), rateExpr);
subDomain.addEquation(equation);
}
// events - add events to math desc for event assignments that have parameters as target variables
if (bioevents != null && bioevents.length > 0) {
for (BioEvent be : bioevents) {
// transform the bioEvent trigger/delay to math Event
LocalParameter genTriggerParam = be.getParameter(BioEventParameterType.GeneralTriggerFunction);
Expression mathTriggerExpr = getIdentifierSubstitutions(new Expression(genTriggerParam, be.getNameScope()), modelUnitSystem.getInstance_DIMENSIONLESS(), null);
Delay mathDelay = null;
LocalParameter delayParam = be.getParameter(BioEventParameterType.TriggerDelay);
if (delayParam != null && delayParam.getExpression() != null && !delayParam.getExpression().compareEqual(new Expression(0.0))) {
boolean bUseValsFromTriggerTime = be.getUseValuesFromTriggerTime();
Expression mathDelayExpr = getIdentifierSubstitutions(new Expression(delayParam, be.getNameScope()), 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>();
if (eventAssignments != null) {
for (EventAssignment ea : eventAssignments) {
SymbolTableEntry ste = simContext.getEntry(ea.getTarget().getName());
if (ste instanceof StructureSize) {
throw new RuntimeException("Event Assignment Variable for compartment size is not supported yet");
}
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 (simContext.getMicroscopeMeasurement() != null && simContext.getMicroscopeMeasurement().getFluorescentSpecies().size() > 0) {
MicroscopeMeasurement measurement = simContext.getMicroscopeMeasurement();
Expression volumeConcExp = new Expression(0.0);
Expression membraneDensityExp = new Expression(0.0);
for (SpeciesContext speciesContext : measurement.getFluorescentSpecies()) {
GeometryClass geometryClass = simContext.getGeometryContext().getStructureMapping(speciesContext.getStructure()).getGeometryClass();
StructureMapping structureMapping = simContext.getGeometryContext().getStructureMapping(speciesContext.getStructure());
StructureMappingParameter unitSizeParameter = structureMapping.getUnitSizeParameter();
Expression mappedSpeciesContextExpression = Expression.mult(unitSizeParameter.getExpression(), new Expression(getMathSymbol(speciesContext, geometryClass)));
VCUnitDefinition mappedSpeciesContextUnit = unitSizeParameter.getUnitDefinition().multiplyBy(speciesContext.getUnitDefinition());
if (geometryClass instanceof SubVolume) {
// volume function
int dimension = 3;
VCUnitDefinition desiredConcUnits = model.getUnitSystem().getInstance("molecules").divideBy(model.getUnitSystem().getLengthUnit().raiseTo(new ucar.units_vcell.RationalNumber(dimension)));
Expression unitFactor = getUnitFactor(desiredConcUnits.divideBy(mappedSpeciesContextUnit));
volumeConcExp = Expression.add(volumeConcExp, Expression.mult(unitFactor, mappedSpeciesContextExpression)).flatten();
} else if (geometryClass instanceof SurfaceClass) {
// membrane function
int dimension = 2;
VCUnitDefinition desiredSurfaceDensityUnits = model.getUnitSystem().getInstance("molecules").divideBy(model.getUnitSystem().getLengthUnit().raiseTo(new ucar.units_vcell.RationalNumber(dimension)));
Expression unitFactor = getUnitFactor(desiredSurfaceDensityUnits.divideBy(mappedSpeciesContextUnit));
membraneDensityExp = Expression.add(membraneDensityExp, Expression.mult(unitFactor, mappedSpeciesContextExpression)).flatten();
} else {
throw new MathException("unsupported geometry mapping for microscopy measurement");
}
}
ConvolutionKernel kernel = measurement.getConvolutionKernel();
if (kernel instanceof ExperimentalPSF) {
if (!membraneDensityExp.isZero()) {
throw new MappingException("membrane variables and functions not yet supported for Z projection in Microcopy Measurements");
}
ExperimentalPSF psf = (ExperimentalPSF) kernel;
DataSymbol psfDataSymbol = psf.getPSFDataSymbol();
if (psfDataSymbol instanceof FieldDataSymbol) {
FieldDataSymbol fieldDataSymbol = (FieldDataSymbol) psfDataSymbol;
String fieldDataName = ((FieldDataSymbol) psfDataSymbol).getExternalDataIdentifier().getName();
Expression psfExp = Expression.function(FieldFunctionDefinition.FUNCTION_name, new Expression("'" + fieldDataName + "'"), new Expression("'" + fieldDataSymbol.getFieldDataVarName() + "'"), new Expression(fieldDataSymbol.getFieldDataVarTime()), new Expression("'" + fieldDataSymbol.getFieldDataVarType() + "'"));
varHash.addVariable(new Function("__PSF__", psfExp, null));
}
Expression convExp = Expression.function(ConvFunctionDefinition.FUNCTION_name, volumeConcExp, new Expression("__PSF__"));
varHash.addVariable(newFunctionOrConstant(measurement.getName(), convExp, null));
} else if (kernel instanceof GaussianConvolutionKernel) {
GaussianConvolutionKernel gaussianConvolutionKernel = (GaussianConvolutionKernel) kernel;
GaussianConvolutionDataGeneratorKernel mathKernel = new GaussianConvolutionDataGeneratorKernel(gaussianConvolutionKernel.getSigmaXY_um(), gaussianConvolutionKernel.getSigmaZ_um());
ConvolutionDataGenerator dataGenerator = new ConvolutionDataGenerator(measurement.getName(), mathKernel, volumeConcExp, membraneDensityExp);
mathDesc.getPostProcessingBlock().addDataGenerator(dataGenerator);
} else if (kernel instanceof ProjectionZKernel) {
if (mathDesc.getGeometry().getDimension() == 3) {
if (!membraneDensityExp.isZero()) {
throw new MappingException("membrane variables and functions not yet supported for Z projection in Microcopy Measurements");
}
ProjectionDataGenerator dataGenerator = new ProjectionDataGenerator(measurement.getName(), null, ProjectionDataGenerator.Axis.z, ProjectionDataGenerator.Operation.sum, volumeConcExp);
mathDesc.getPostProcessingBlock().addDataGenerator(dataGenerator);
} else {
throw new MappingException("Z Projection is only supported in 3D spatial applications.");
}
}
}
//
for (int i = 0; i < fieldMathMappingParameters.length; i++) {
if (fieldMathMappingParameters[i] instanceof UnitFactorParameter) {
GeometryClass geometryClass = fieldMathMappingParameters[i].getGeometryClass();
Variable variable = newFunctionOrConstant(getMathSymbol(fieldMathMappingParameters[i], geometryClass), getIdentifierSubstitutions(fieldMathMappingParameters[i].getExpression(), fieldMathMappingParameters[i].getUnitDefinition(), geometryClass), fieldMathMappingParameters[i].getGeometryClass());
if (mathDesc.getVariable(variable.getName()) == null) {
mathDesc.addVariable(variable);
}
}
}
if (!mathDesc.isValid()) {
System.out.println(mathDesc.getVCML_database());
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 :
MembraneSubDomain(cbit.vcell.math.MembraneSubDomain)
ArrayList(java.util.ArrayList)
StructureMappingParameter(cbit.vcell.mapping.StructureMapping.StructureMappingParameter)
SpeciesContext(cbit.vcell.model.SpeciesContext)
Feature(cbit.vcell.model.Feature)
MemVariable(cbit.vcell.math.MemVariable)
SubVolume(cbit.vcell.geometry.SubVolume)
Vector(java.util.Vector)
SpeciesContextSpecParameter(cbit.vcell.mapping.SpeciesContextSpec.SpeciesContextSpecParameter)
FastInvariant(cbit.vcell.math.FastInvariant)
GaussianConvolutionKernel(cbit.vcell.mapping.MicroscopeMeasurement.GaussianConvolutionKernel)
PropertyVetoException(java.beans.PropertyVetoException)
FieldDataSymbol(cbit.vcell.data.FieldDataSymbol)
DataSymbol(cbit.vcell.data.DataSymbol)
VCUnitDefinition(cbit.vcell.units.VCUnitDefinition)
FastSystem(cbit.vcell.math.FastSystem)
CompartmentSubDomain(cbit.vcell.math.CompartmentSubDomain)
ReactionStep(cbit.vcell.model.ReactionStep)
Map(java.util.Map)
HashMap(java.util.HashMap)
MembraneRegionEquation(cbit.vcell.math.MembraneRegionEquation)
SurfaceClass(cbit.vcell.geometry.SurfaceClass)
VariableHash(cbit.vcell.math.VariableHash)
ExperimentalPSF(cbit.vcell.mapping.MicroscopeMeasurement.ExperimentalPSF)
ConvolutionDataGenerator(cbit.vcell.math.ConvolutionDataGenerator)
GaussianConvolutionDataGeneratorKernel(cbit.vcell.math.ConvolutionDataGenerator.GaussianConvolutionDataGeneratorKernel)
Structure(cbit.vcell.model.Structure)
ModelUnitSystem(cbit.vcell.model.ModelUnitSystem)
LocalParameter(cbit.vcell.mapping.ParameterContext.LocalParameter)
VoltageClampElectricalDevice(cbit.vcell.mapping.potential.VoltageClampElectricalDevice)
StructureMappingParameter(cbit.vcell.mapping.StructureMapping.StructureMappingParameter)
Expression(cbit.vcell.parser.Expression)
Model(cbit.vcell.model.Model)
StructureMappingParameter(cbit.vcell.mapping.StructureMapping.StructureMappingParameter)
Parameter(cbit.vcell.model.Parameter)
SpeciesContextSpecProxyParameter(cbit.vcell.mapping.SpeciesContextSpec.SpeciesContextSpecProxyParameter)
SimulationContextParameter(cbit.vcell.mapping.SimulationContext.SimulationContextParameter)
ModelParameter(cbit.vcell.model.Model.ModelParameter)
SpeciesContextSpecParameter(cbit.vcell.mapping.SpeciesContextSpec.SpeciesContextSpecParameter)
LocalParameter(cbit.vcell.mapping.ParameterContext.LocalParameter)
Event(cbit.vcell.math.Event)
ProjectionDataGenerator(cbit.vcell.math.ProjectionDataGenerator)
SurfaceRegionObject(cbit.vcell.mapping.spatial.SurfaceRegionObject)
FieldDataSymbol(cbit.vcell.data.FieldDataSymbol)
MembraneRegionVariable(cbit.vcell.math.MembraneRegionVariable)
HashMap(java.util.HashMap)
MathDescription(cbit.vcell.math.MathDescription)
MembraneElectricalDevice(cbit.vcell.mapping.potential.MembraneElectricalDevice)
Delay(cbit.vcell.math.Event.Delay)
CompartmentSubDomain(cbit.vcell.math.CompartmentSubDomain)
SubDomain(cbit.vcell.math.SubDomain)
PointSubDomain(cbit.vcell.math.PointSubDomain)
MembraneSubDomain(cbit.vcell.math.MembraneSubDomain)
PropertyVetoException(java.beans.PropertyVetoException)
PdeEquation(cbit.vcell.math.PdeEquation)
CurrentClampElectricalDevice(cbit.vcell.mapping.potential.CurrentClampElectricalDevice)
SpatialQuantity(cbit.vcell.mapping.spatial.SpatialObject.SpatialQuantity)
SpeciesContextSpecParameter(cbit.vcell.mapping.SpeciesContextSpec.SpeciesContextSpecParameter)
EventAssignment(cbit.vcell.mapping.BioEvent.EventAssignment)
CurrentClampElectricalDevice(cbit.vcell.mapping.potential.CurrentClampElectricalDevice)
MembraneElectricalDevice(cbit.vcell.mapping.potential.MembraneElectricalDevice)
ElectricalDevice(cbit.vcell.mapping.potential.ElectricalDevice)
VoltageClampElectricalDevice(cbit.vcell.mapping.potential.VoltageClampElectricalDevice)
VolVariable(cbit.vcell.math.VolVariable)
StructureSize(cbit.vcell.model.Structure.StructureSize)
ProjectionZKernel(cbit.vcell.mapping.MicroscopeMeasurement.ProjectionZKernel)
ModelParameter(cbit.vcell.model.Model.ModelParameter)
OdeEquation(cbit.vcell.math.OdeEquation)
CompartmentSubDomain(cbit.vcell.math.CompartmentSubDomain)
SubDomain(cbit.vcell.math.SubDomain)
PointSubDomain(cbit.vcell.math.PointSubDomain)
Domain(cbit.vcell.math.Variable.Domain)
MembraneSubDomain(cbit.vcell.math.MembraneSubDomain)
JumpCondition(cbit.vcell.math.JumpCondition)
GeometryClass(cbit.vcell.geometry.GeometryClass)
VolVariable(cbit.vcell.math.VolVariable)
MembraneRegionVariable(cbit.vcell.math.MembraneRegionVariable)
PointVariable(cbit.vcell.math.PointVariable)
VolumeRegionVariable(cbit.vcell.math.VolumeRegionVariable)
MemVariable(cbit.vcell.math.MemVariable)
Variable(cbit.vcell.math.Variable)
SpeciesContextSpecProxyParameter(cbit.vcell.mapping.SpeciesContextSpec.SpeciesContextSpecProxyParameter)
Constant(cbit.vcell.math.Constant)
VolumeRegionVariable(cbit.vcell.math.VolumeRegionVariable)
Function(cbit.vcell.math.Function)
SymbolTableEntry(cbit.vcell.parser.SymbolTableEntry)
Membrane(cbit.vcell.model.Membrane)
VolumeRegionEquation(cbit.vcell.math.VolumeRegionEquation)
PotentialMapping(cbit.vcell.mapping.potential.PotentialMapping)
EventAssignment(cbit.vcell.mapping.BioEvent.EventAssignment)
FieldFunctionArguments(cbit.vcell.field.FieldFunctionArguments)
PdeEquation(cbit.vcell.math.PdeEquation)
ComputeMembraneMetricEquation(cbit.vcell.math.ComputeMembraneMetricEquation)
VolumeRegionEquation(cbit.vcell.math.VolumeRegionEquation)
OdeEquation(cbit.vcell.math.OdeEquation)
MembraneRegionEquation(cbit.vcell.math.MembraneRegionEquation)
Equation(cbit.vcell.math.Equation)
FastRate(cbit.vcell.math.FastRate)
SimulationContextParameter(cbit.vcell.mapping.SimulationContext.SimulationContextParameter)
ConvolutionKernel(cbit.vcell.mapping.MicroscopeMeasurement.ConvolutionKernel)
GaussianConvolutionKernel(cbit.vcell.mapping.MicroscopeMeasurement.GaussianConvolutionKernel)
MathException(cbit.vcell.math.MathException)
Aggregations
Variable (cbit.vcell.math.Variable)110
Expression (cbit.vcell.parser.Expression)71
VolVariable (cbit.vcell.math.VolVariable)64
MemVariable (cbit.vcell.math.MemVariable)48
ReservedVariable (cbit.vcell.math.ReservedVariable)43
MathException (cbit.vcell.math.MathException)38
MembraneRegionVariable (cbit.vcell.math.MembraneRegionVariable)38
VolumeRegionVariable (cbit.vcell.math.VolumeRegionVariable)36
ExpressionException (cbit.vcell.parser.ExpressionException)36
FilamentVariable (cbit.vcell.math.FilamentVariable)35
InsideVariable (cbit.vcell.math.InsideVariable)34
OutsideVariable (cbit.vcell.math.OutsideVariable)34
Function (cbit.vcell.math.Function)33
MathDescription (cbit.vcell.math.MathDescription)33
Constant (cbit.vcell.math.Constant)32
FilamentRegionVariable (cbit.vcell.math.FilamentRegionVariable)29
VolumeParticleVariable (cbit.vcell.math.VolumeParticleVariable)25
MembraneParticleVariable (cbit.vcell.math.MembraneParticleVariable)24
ParticleVariable (cbit.vcell.math.ParticleVariable)24
Vector (java.util.Vector)24
