Example 6 with SbmlException
use of org.vcell.sbml.SbmlException in project vcell by virtualcell.
the class BiomodelsDB_TestSuite method main.
public static void main(String[] args) {
try {
Logging.init();
/*sanity check -- we currently only have a copasi_java dll for 32-bit, so let's make sure
* we're running on the right JVM. (Note we can run this on 64 bit machine, just have to install
* a 32 bit JVM...)
*/
OperatingSystemInfo osi = OperatingSystemInfo.getInstance();
if (!osi.isWindows() || osi.is64bit()) {
System.err.println("run on 32 bit JVM");
System.exit(99);
}
// following are set in command line processing
SortedSet<BiomodelsNetEntry> modelIDs = new TreeSet<BiomodelsNetEntry>();
BioModelsWebServices service = null;
File outDir = null;
boolean isDetailed;
{
// scope for command line processing
Options commandOptions = new Options();
Option help = new Option("help", false, "show help");
commandOptions.addOption(help);
Option detailed = new Option("detailed", false, "record detailed information");
commandOptions.addOption(detailed);
Option output = new Option("output", true, "output directory");
output.setRequired(true);
commandOptions.addOption(output);
OptionGroup primary = new OptionGroup();
LOption min = new LOption("min", true, "minimum number of model to import", true);
min.setType(Number.class);
LOption only = new LOption("only", true, "run only this model", false);
only.setType(Number.class);
LOption include = new LOption("include", true, "run on models in specified file", false);
include.setType(String.class);
LOption exclude = new LOption("exclude", true, "exclude models in specified file", true);
exclude.setType(String.class);
primary.addOption(min).addOption(only).addOption(include).addOption(exclude);
for (Object obj : primary.getOptions()) {
// CLI old, non-generic API
commandOptions.addOption((Option) obj);
}
CommandLine cmdLine = null;
try {
CommandLineParser parser = new DefaultParser();
cmdLine = parser.parse(commandOptions, args);
} catch (ParseException e1) {
e1.printStackTrace();
HelpFormatter hf = new HelpFormatter();
hf.printHelp("BiomodelsDB_TestSuite", commandOptions);
System.exit(2);
}
Option[] present = cmdLine.getOptions();
Set<Option> optionSet = new HashSet<Option>(Arrays.asList(present));
if (optionSet.contains(help)) {
HelpFormatter hf = new HelpFormatter();
hf.printHelp("BiomodelsDB_TestSuite", commandOptions);
System.exit(0);
}
// placeholder, avoid messing with nulls
LOption primaryOpt = new LOption("", false, "", true);
@SuppressWarnings("unchecked") Collection<? extends Option> priOpts = primary.getOptions();
priOpts.retainAll(optionSet);
if (!priOpts.isEmpty()) {
assert (priOpts.size() == 1);
primaryOpt = (LOption) priOpts.iterator().next();
}
outDir = new File(cmdLine.getOptionValue(output.getOpt()));
if (!outDir.exists()) {
outDir.mkdirs();
}
isDetailed = optionSet.contains(detailed);
BioModelsWebServicesServiceLocator locator = new BioModelsWebServicesServiceLocator();
service = locator.getBioModelsWebServices();
if (primaryOpt.downloads) {
String[] modelStrings = service.getAllCuratedModelsId();
for (String s : modelStrings) {
modelIDs.add(new BiomodelsNetEntry(s));
}
}
if (primaryOpt == only) {
Long only1 = (Long) cmdLine.getParsedOptionValue(only.getOpt());
modelIDs.add(new BiomodelsNetEntry(only1.intValue()));
} else if (primaryOpt == min) {
Long lv = (Long) cmdLine.getParsedOptionValue(min.getOpt());
int minimumModel = lv.intValue();
for (int m = 0; m < minimumModel; m++) {
modelIDs.remove(new BiomodelsNetEntry(m));
}
} else if (primaryOpt == include) {
FileBaseFilter fbf = new FileBaseFilter(cmdLine.getOptionValue(include.getOpt()));
modelIDs.addAll(fbf.models);
} else if (primaryOpt == exclude) {
FileBaseFilter fbf = new FileBaseFilter(cmdLine.getOptionValue(exclude.getOpt()));
modelIDs.removeAll(fbf.models);
}
}
// end command line processing
WriterFlusher flusher = new WriterFlusher(10);
PrintWriter detailWriter;
PrintWriter bngWriter;
PrintWriter sbmlWriter;
SBMLExceptionSorter sbmlExceptions;
if (isDetailed) {
detailWriter = new PrintWriter(new File(outDir, "compareDetail.txt"));
bngWriter = new PrintWriter(new File(outDir, "bngErrors.txt"));
sbmlWriter = new PrintWriter(new File(outDir, "sbmlErrors.txt"));
sbmlExceptions = new LiveSorter();
flusher.add(detailWriter);
flusher.add(bngWriter);
flusher.add(sbmlWriter);
} else {
detailWriter = new PrintWriter(new NullWriter());
bngWriter = new PrintWriter(new NullWriter());
sbmlWriter = new PrintWriter(new NullWriter());
sbmlExceptions = new NullSorter();
}
PropertyLoader.loadProperties();
/**
* example properties
*
* vcell.COPASI.executable = "C:\\Program Files\\COPASI\\bin\\CopasiSE.exe"
* vcell.mathSBML.directory = "c:\\developer\\eclipse\\workspace\\mathsbml\\"
* vcell.mathematica.kernel.executable = "C:\\Program Files\\Wolfram Research\\Mathematica\\7.0\\MathKernel.exe"
*/
ResourceUtil.setNativeLibraryDirectory();
PrintWriter printWriter = new PrintWriter(new FileWriter(new File(outDir, "summary.log"), true));
flusher.add(printWriter);
listModels(printWriter, modelIDs);
// SBMLSolver copasiSBMLSolver = new CopasiSBMLSolver();
SBMLSolver copasiSBMLSolver = new SBMLSolver() {
@Override
public File solve(String filePrefix, File outDir, String sbmlText, SimSpec testSpec) throws IOException, SolverException, SbmlException {
throw new RuntimeException("COPASI SOLVER REMOVED, REIMPLEMENT");
}
@Override
public String getResultsFileColumnDelimiter() {
throw new RuntimeException("COPASI SOLVER REMOVED, REIMPLEMENT");
}
};
try {
printWriter.println(" | *BIOMODEL ID* | *BioModel name* | *PASS* | *Rel Error (VC/COP)(VC/MSBML)(COP/MSBML)* | *Exception* | ");
removeToxic(modelIDs, printWriter);
for (BiomodelsNetEntry modelID : modelIDs) {
String modelName = service.getModelNameById(modelID.toString());
String modelSBML = service.getModelById(modelID.toString());
Element bioModelInfo = new Element(BioModelsNetPanel.BIOMODELINFO_ELEMENT_NAME);
bioModelInfo.setAttribute(BioModelsNetPanel.ID_ATTRIBUTE_NAME, modelID.toString());
bioModelInfo.setAttribute(BioModelsNetPanel.SUPPORTED_ATTRIBUTE_NAME, "false");
bioModelInfo.setAttribute("vcell_ran", "false");
bioModelInfo.setAttribute("COPASI_ran", "false");
bioModelInfo.setAttribute("mSBML_ran", "false");
bioModelInfo.setAttribute(BioModelsNetPanel.MODELNAME_ATTRIBUTE_NAME, modelName);
boolean bUseUTF8 = true;
File sbmlFile = new File(outDir, modelID + ".sbml");
XmlUtil.writeXMLStringToFile(modelSBML, sbmlFile.getAbsolutePath(), bUseUTF8);
PrintStream saved_sysout = System.out;
PrintStream saved_syserr = System.err;
PrintStream new_sysout = null;
PrintStream new_syserr = null;
try {
String filePrefix = modelID.toString();
String sbmlText = modelSBML;
File logFile = new File(outDir, filePrefix + ".log");
new_sysout = new PrintStream(logFile);
new_syserr = new_sysout;
System.setOut(new_sysout);
System.setErr(new_syserr);
StringBuffer combinedErrorBuffer = new StringBuffer();
SimSpec simSpec = SimSpec.fromSBML(modelSBML);
String[] varsToTest = simSpec.getVarsList();
printWriter.print("ModelId: " + modelID + ": ");
// if a model crashes out the libSBML dll, we will terminate abruptly. Flush
// summary log before that happens
printWriter.flush();
try {
//
// get VCell solution with an embedded "ROUND TRIP" (time and species concentrations)
//
ODESolverResultSet vcellResults_RT = null;
try {
VCellSBMLSolver vcellSBMLSolver_RT = new VCellSBMLSolver();
vcellSBMLSolver_RT.setRoundTrip(false);
// TODO try with round-trip later.
String columnDelimiter = vcellSBMLSolver_RT.getResultsFileColumnDelimiter();
File resultFile = vcellSBMLSolver_RT.solve(filePrefix, outDir, sbmlFile.getAbsolutePath(), simSpec);
vcellResults_RT = readResultFile(resultFile, columnDelimiter);
bioModelInfo.setAttribute("vcell_ran", "true");
} catch (BNGException e) {
bngWriter.println(modelID + " " + e.getMessage());
throw e;
} catch (SBMLImportException e) {
ModelException me = new ModelException(modelID, e);
write(sbmlWriter, me);
sbmlExceptions.add(me);
throw e;
} catch (Exception e) {
printWriter.println("vcell solve(roundtrip=true) failed");
e.printStackTrace(printWriter);
System.out.println("vcell solve(roundtrip=true) failed");
e.printStackTrace(System.out);
combinedErrorBuffer.append(" *VCELL_RT* _" + e.getMessage() + "_ ");
Element vcellSolverReport = new Element("SolverReport");
vcellSolverReport.setAttribute("solverName", "vcell");
vcellSolverReport.setAttribute("errorMessage", e.getMessage());
bioModelInfo.addContent(vcellSolverReport);
bioModelInfo.setAttribute("vcell_ran", "false");
}
//
// get COPASI solution (time and species concentrations)
//
ODESolverResultSet copasiResults = null;
try {
String columnDelimiter = copasiSBMLSolver.getResultsFileColumnDelimiter();
File resultFile = copasiSBMLSolver.solve(filePrefix, outDir, sbmlText, simSpec);
copasiResults = readResultFile(resultFile, columnDelimiter);
bioModelInfo.setAttribute("COPASI_ran", "true");
} catch (Exception e) {
printWriter.println("Copasi solve() failed");
e.printStackTrace(printWriter);
System.out.println("Copasi solve() failed");
e.printStackTrace(System.out);
combinedErrorBuffer.append(" *COPASI* _" + e.getMessage() + "_ ");
Element copasiSolverReport = new Element("SolverReport");
copasiSolverReport.setAttribute("solverName", "COPASI");
copasiSolverReport.setAttribute("errorMessage", e.getMessage());
bioModelInfo.addContent(copasiSolverReport);
bioModelInfo.setAttribute("COPASI_ran", "false");
}
//
// get mSBML solution (time and species concentrations)
//
/*
ODESolverResultSet mSBMLResults = null;
if (idInt != 246 && idInt != 250 && idInt != 285 && idInt != 301) {
try {
MathSBMLSolver mSBMLSolver = new MathSBMLSolver();
String columnDelimiter = mSBMLSolver.getResultsFileColumnDelimiter();
org.sbml.libsbml.SBMLDocument sbmlDocument = new SBMLReader().readSBML(sbmlFile.getAbsolutePath());
long level = sbmlDocument.getLevel();
long version = sbmlDocument.getVersion();
String mathsbmlFilePrefix = filePrefix;
if (level!=2 || (level==2 && version>3)){
// sbmlDocument.setConsistencyChecksForConversion(libsbmlConstants.LIBSBML_CAT_MODELING_PRACTICE, false);
long numErrors = sbmlDocument.checkL2v3Compatibility();
if (numErrors==0){
boolean bConversionWorked = sbmlDocument.setLevelAndVersion(2, 3, false);
SBMLDocument doc = new SBMLDocument(sbmlDocument);
doc.setLevelAndVersion(2,3,false);
if (bConversionWorked){
mathsbmlFilePrefix = filePrefix+"_L2V3";
long newVersion = doc.getVersion();
SBMLWriter sbmlWriter = new SBMLWriter();
sbmlText = sbmlWriter.writeToString(doc);
try {
XmlUtil.writeXMLStringToFile(sbmlText, mathsbmlFilePrefix+".sbml", true);
} catch (IOException e1) {
e1.printStackTrace(System.out);
}
}else{
throw new RuntimeException("couldn't convert SBML from L"+level+"V"+version+" to L2V3");
}
}else{
throw new RuntimeException("couldn't convert SBML from L"+level+"V"+version+" to L2V3, not compatible: "+sbmlDocument.getError(0));
}
}
File resultFile = mSBMLSolver.solve(mathsbmlFilePrefix, outDir, sbmlText, simSpec);
mSBMLResults = readResultFile(resultFile, columnDelimiter);
bioModelInfo.setAttribute("mSBML_ran","true");
}catch (Exception e){
printWriter.println("mSBML solve() failed");
e.printStackTrace(printWriter);
System.out.println("mSBML solve() failed");
e.printStackTrace(System.out);
combinedErrorBuffer.append(" *mSBML* _"+e.getMessage()+"_ ");
Element mSBMLSolverReport = new Element("SolverReport");
mSBMLSolverReport.setAttribute("solverName","mSBML");
mSBMLSolverReport.setAttribute("errorMessage",e.getMessage());
bioModelInfo.addContent(mSBMLSolverReport);
bioModelInfo.setAttribute("mSBML_ran","false");
}
}
*/
//
// compare results from COPASI and VCELL_RT
//
Boolean bCOPASI_VCELL_matched = null;
if (copasiResults != null && vcellResults_RT != null) {
try {
SimulationComparisonSummary summary = MathTestingUtilities.compareResultSets(copasiResults, vcellResults_RT, varsToTest, TestCaseNew.REGRESSION, 1e-5, 1e-5);
double maxRelError = summary.getMaxRelativeError();
bioModelInfo.setAttribute("COPASI_VCELL_maxRelErr", Double.toString(maxRelError));
if (maxRelError < 1) {
bCOPASI_VCELL_matched = true;
} else {
detailWriter.println(modelID + " " + modelName);
bCOPASI_VCELL_matched = false;
Element solverComparison = new Element("SolverComparison");
solverComparison.setAttribute("solver1", "vcell");
solverComparison.setAttribute("solver2", "COPASI");
VariableComparisonSummary[] failedVCSummaries = summary.getFailingVariableComparisonSummaries(1e-5, 1e-5);
for (VariableComparisonSummary vcSummary : failedVCSummaries) {
Element failedVariableSummary = getVariableSummary(vcSummary);
solverComparison.addContent(failedVariableSummary);
String ss = vcSummary.toShortString();
detailWriter.print('\t');
detailWriter.println(ss);
System.out.println(ss);
}
detailWriter.println();
bioModelInfo.addContent(solverComparison);
}
} catch (Exception e) {
printWriter.println("COMPARE VC/COPASI failed");
e.printStackTrace(printWriter);
System.out.println("COMPARE VC/COPASI failed");
e.printStackTrace(System.out);
combinedErrorBuffer.append(" *COMPARE VC/COPASI* _" + e.getMessage() + "_ ");
Element solverComparison = new Element("SolverComparison");
solverComparison.setAttribute("solver1", "vcell");
solverComparison.setAttribute("solver2", "COPASI");
solverComparison.setAttribute("error", e.getMessage());
bioModelInfo.addContent(solverComparison);
}
}
/*
Boolean bmSBML_VCELL_matched = null;
if (mSBMLResults!=null && vcellResults_RT!=null){
try {
SimulationComparisonSummary summary = MathTestingUtilities.compareUnEqualResultSets(mSBMLResults, vcellResults_RT, varsToTest, 1e-5, 1e-5, 1);
double maxRelError = summary.getMaxRelativeError();
bioModelInfo.setAttribute("mSBML_VCELL_maxRelErr", Double.toString(maxRelError));
if (maxRelError<1){
bmSBML_VCELL_matched = true;
}else{
bmSBML_VCELL_matched = false;
Element solverComparison = new Element("SolverComparison");
solverComparison.setAttribute("solver1","vcell");
solverComparison.setAttribute("solver2","mSBML");
VariableComparisonSummary[] failedVCSummaries = summary.getFailingVariableComparisonSummaries(1e-5, 1e-5);
for (VariableComparisonSummary vcSummary : failedVCSummaries){
Element failedVariableSummary = getVariableSummary(vcSummary);
solverComparison.addContent(failedVariableSummary);
System.out.println(vcSummary.toShortString());
}
bioModelInfo.addContent(solverComparison);
}
} catch (Exception e) {
printWriter.println("COMPARE VCRT/mSBML failed");
e.printStackTrace(printWriter);
System.out.println("COMPARE VCRT/mSBML failed");
e.printStackTrace(System.out);
combinedErrorBuffer.append(" *COMPARE VCRT/mSBML* _"+e.getMessage()+"_ ");
Element solverComparison = new Element("SolverComparison");
solverComparison.setAttribute("solver1","vcell");
solverComparison.setAttribute("solver2","mSBML");
solverComparison.setAttribute("error",e.getMessage());
bioModelInfo.addContent(solverComparison);
}
}
//
// compare results from COPASI and mSBML
//
Boolean bCOPASI_mSBML_matched = null;
if (copasiResults!=null && mSBMLResults!=null){
try {
SimulationComparisonSummary summary = MathTestingUtilities.compareUnEqualResultSets(copasiResults, mSBMLResults, varsToTest, 1e-5, 1e-5, 1);
double maxRelError = summary.getMaxRelativeError();
bioModelInfo.setAttribute("COPASI_mSBML_maxRelErr", Double.toString(maxRelError));
if (maxRelError<1){
bCOPASI_mSBML_matched = true;
}else{
bCOPASI_mSBML_matched = false;
Element solverComparison = new Element("SolverComparison");
solverComparison.setAttribute("solver1","COPASI");
solverComparison.setAttribute("solver2","mSBML");
solverComparison.setAttribute("result","failed");
VariableComparisonSummary[] vcSummaries = summary.getVariableComparisonSummaries();
for (VariableComparisonSummary vcSummary : vcSummaries){
Element failedVariableSummary = getVariableSummary(vcSummary);
solverComparison.addContent(failedVariableSummary);
System.out.println(vcSummary.toShortString());
}
bioModelInfo.addContent(solverComparison);
}
} catch (Exception e) {
printWriter.println("COMPARE COPASI/mSBML failed");
e.printStackTrace(printWriter);
System.out.println("COMPARE COPASI/mSBML failed");
e.printStackTrace(System.out);
combinedErrorBuffer.append(" *COMPARE COPASI/mSBML* _"+e.getMessage()+"_ ");
Element solverComparison = new Element("SolverComparison");
solverComparison.setAttribute("solver1","COPASI");
solverComparison.setAttribute("solver2","mSBML");
solverComparison.setAttribute("error",e.getMessage());
}
}
*/
if ((bCOPASI_VCELL_matched != null && bCOPASI_VCELL_matched.booleanValue())) {
// || /*(bmSBML_VCELL_matched!=null && bmSBML_VCELL_matched.booleanValue()) */ )
bioModelInfo.setAttribute(BioModelsNetPanel.SUPPORTED_ATTRIBUTE_NAME, "true");
printWriter.println("PASS");
} else {
bioModelInfo.setAttribute(BioModelsNetPanel.SUPPORTED_ATTRIBUTE_NAME, "false");
printWriter.println("FAIL");
}
} catch (Exception e) {
e.printStackTrace(printWriter);
combinedErrorBuffer.append(" *UNKNOWN* _" + e.getMessage() + "_ ");
bioModelInfo.setAttribute(BioModelsNetPanel.SUPPORTED_ATTRIBUTE_NAME, "false");
bioModelInfo.setAttribute("exception", e.getMessage());
}
printWriter.flush();
// write for each model just in case files get corrupted (it happened).
write(bioModelInfo, new File(outDir, modelID + "_report.xml"));
} finally {
if (new_sysout != null) {
new_sysout.close();
new_sysout = null;
}
if (new_syserr != null) {
new_syserr.close();
new_syserr = null;
}
System.setOut(saved_sysout);
System.setOut(saved_syserr);
}
}
// this writes out the SBML import exceptions grouped by type
if (!sbmlExceptions.isEmpty()) {
Map<Category, Collection<ModelException>> map = sbmlExceptions.getMap();
try (PrintWriter pw = new PrintWriter(new File(outDir, "sbmlSorted.txt"))) {
// SBMLImportException.Category
for (Category c : Category.values()) {
Collection<ModelException> meCollection = map.get(c);
for (ModelException me : meCollection) {
write(pw, me);
}
}
}
}
} finally {
printWriter.close();
detailWriter.close();
bngWriter.close();
}
} catch (Throwable e) {
e.printStackTrace(System.out);
e.printStackTrace(System.err);
}
System.exit(0);
}
Also used :
BNGException(cbit.vcell.server.bionetgen.BNGException)
HelpFormatter(org.apache.commons.cli.HelpFormatter)
TreeSet(java.util.TreeSet)
SBMLSolver(org.vcell.sbml.SBMLSolver)
VariableComparisonSummary(cbit.vcell.solver.test.VariableComparisonSummary)
BioModelsWebServicesServiceLocator(uk.ac.ebi.www.biomodels_main.services.BioModelsWebServices.BioModelsWebServicesServiceLocator)
Collection(java.util.Collection)
Option(org.apache.commons.cli.Option)
File(java.io.File)
Options(org.apache.commons.cli.Options)
SortedSet(java.util.SortedSet)
Set(java.util.Set)
ODESolverResultSet(cbit.vcell.solver.ode.ODESolverResultSet)
TreeSet(java.util.TreeSet)
HashSet(java.util.HashSet)
Category(org.vcell.sbml.vcell.SBMLImportException.Category)
OperatingSystemInfo(cbit.vcell.resource.OperatingSystemInfo)
FileWriter(java.io.FileWriter)
Element(org.jdom.Element)
NullWriter(org.apache.commons.io.output.NullWriter)
OptionGroup(org.apache.commons.cli.OptionGroup)
ODESolverResultSet(cbit.vcell.solver.ode.ODESolverResultSet)
SimulationComparisonSummary(cbit.vcell.solver.test.SimulationComparisonSummary)
CommandLineParser(org.apache.commons.cli.CommandLineParser)
DefaultParser(org.apache.commons.cli.DefaultParser)
PrintWriter(java.io.PrintWriter)
PrintStream(java.io.PrintStream)
SBMLImportException(org.vcell.sbml.vcell.SBMLImportException)
SimSpec(org.vcell.sbml.SimSpec)
SbmlException(org.vcell.sbml.SbmlException)
FileNotFoundException(java.io.FileNotFoundException)
BNGException(cbit.vcell.server.bionetgen.BNGException)
SBMLImportException(org.vcell.sbml.vcell.SBMLImportException)
ParseException(org.apache.commons.cli.ParseException)
SolverException(cbit.vcell.solver.SolverException)
IOException(java.io.IOException)
BioModelsWebServices(uk.ac.ebi.www.biomodels_main.services.BioModelsWebServices.BioModelsWebServices)
CommandLine(org.apache.commons.cli.CommandLine)
ParseException(org.apache.commons.cli.ParseException)
Example 7 with SbmlException
use of org.vcell.sbml.SbmlException in project vcell by virtualcell.
the class VCellSBMLSolver method solve.
public File solve(String filePrefix, File outDir, String sbmlFileName, SimSpec testSpec) throws IOException, SolverException, SbmlException {
try {
cbit.util.xml.VCLogger sbmlImportLogger = new LocalLogger();
//
// Instantiate an SBMLImporter to get the speciesUnitsHash - to compute the conversion factor from VC->SB species units.
// and import SBML (sbml->bioModel)
BioModel bioModel = importSBML(sbmlFileName, sbmlImportLogger, false);
// Hashtable<String, SBMLImporter.SBVCConcentrationUnits> speciesUnitsHash = sbmlImporter.getSpeciesUnitsHash();
// double timeFactor = sbmlImporter.getSBMLTimeUnitsFactor();
String vcml_1 = XmlHelper.bioModelToXML(bioModel);
SBMLUtils.writeStringToFile(vcml_1, new File(outDir, filePrefix + ".vcml").getAbsolutePath(), true);
if (bRoundTrip) {
// Round trip the bioModel (bioModel->sbml->bioModel).
// save imported "bioModel" as VCML
// String vcml_1 = XmlHelper.bioModelToXML(bioModel);
// SBMLUtils.writeStringToFile(vcml_1, new File(outDir,filePrefix+".vcml").getAbsolutePath());
// export bioModel as sbml and save
// String vcml_sbml = cbit.vcell.xml.XmlHelper.exportSBML(bioModel, 2, 1, bioModel.getSimulationContexts(0).getName());
// SimulationJob simJob = new SimulationJob(bioModel.getSimulations(bioModel.getSimulationContexts(0))[0], null, 0);
String vcml_sbml = cbit.vcell.xml.XmlHelper.exportSBML(bioModel, 2, 1, 0, false, bioModel.getSimulationContext(0), null);
SBMLUtils.writeStringToFile(vcml_sbml, new File(outDir, filePrefix + ".vcml.sbml").getAbsolutePath(), true);
// re-import bioModel from exported sbml
XMLSource vcml_sbml_Src = new XMLSource(vcml_sbml);
BioModel newBioModel = (BioModel) XmlHelper.importSBML(sbmlImportLogger, vcml_sbml_Src, false);
String vcml_sbml_vcml = XmlHelper.bioModelToXML(newBioModel);
SBMLUtils.writeStringToFile(vcml_sbml_vcml, new File(outDir, filePrefix + ".vcml.sbml.vcml").getAbsolutePath(), true);
// have rest of code use the round-tripped biomodel
bioModel = newBioModel;
}
//
// select only Application, generate math, and create a single Simulation.
//
SimulationContext simContext = bioModel.getSimulationContext(0);
MathMapping mathMapping = simContext.createNewMathMapping();
MathDescription mathDesc = mathMapping.getMathDescription();
String vcml = mathDesc.getVCML();
try (PrintWriter pw = new PrintWriter("vcmlTrace.txt")) {
pw.println(vcml);
}
simContext.setMathDescription(mathDesc);
SimulationVersion simVersion = new SimulationVersion(new KeyValue("100"), "unnamed", null, null, null, null, null, null, null, null);
Simulation sim = new Simulation(simVersion, mathDesc);
sim.setName("unnamed");
// if time factor from SBML is not 1 (i.e., it is not in secs but in minutes or hours), convert endTime to min/hr as : endTime*timeFactor
// double endTime = testSpec.getEndTime()*timeFactor;
double endTime = testSpec.getEndTime();
sim.getSolverTaskDescription().setTimeBounds(new TimeBounds(0, endTime));
TimeStep timeStep = new TimeStep();
sim.getSolverTaskDescription().setTimeStep(new TimeStep(timeStep.getMinimumTimeStep(), timeStep.getDefaultTimeStep(), endTime / 10000));
sim.getSolverTaskDescription().setOutputTimeSpec(new UniformOutputTimeSpec((endTime - 0) / testSpec.getNumTimeSteps()));
sim.getSolverTaskDescription().setErrorTolerance(new ErrorTolerance(1e-10, 1e-12));
// sim.getSolverTaskDescription().setErrorTolerance(new cbit.vcell.solver.ErrorTolerance(1e-10, 1e-12));
// Generate .idaInput string
/* IDAFileWriter idaFileWriter = new IDAFileWriter(sim);
File idaInputFile = new File(filePathName.replace(".vcml", ".idaInput"));
PrintWriter idaPW = new java.io.PrintWriter(idaInputFile);
idaFileWriter.writeInputFile(idaPW);
idaPW.close();
// use the idastandalone solver
File idaOutputFile = new File(filePathName.replace(".vcml", ".ida"));
Executable executable = new Executable("IDAStandalone " + idaInputFile + " " + idaOutputFile);
executable.start();
*/
// Generate .cvodeInput string
File cvodeFile = new File(outDir, filePrefix + SimDataConstants.CVODEINPUT_DATA_EXTENSION);
PrintWriter cvodePW = new java.io.PrintWriter(cvodeFile);
SimulationJob simJob = new SimulationJob(sim, 0, null);
SimulationTask simTask = new SimulationTask(simJob, 0);
CVodeFileWriter cvodeFileWriter = new CVodeFileWriter(cvodePW, simTask);
cvodeFileWriter.write();
cvodePW.close();
// use the cvodeStandalone solver
File cvodeOutputFile = new File(outDir, filePrefix + SimDataConstants.IDA_DATA_EXTENSION);
String executableName = null;
try {
executableName = SolverUtilities.getExes(SolverDescription.CVODE)[0].getAbsolutePath();
} catch (IOException e) {
throw new RuntimeException("failed to get executable for solver " + SolverDescription.CVODE.getDisplayLabel() + ": " + e.getMessage(), e);
}
Executable executable = new Executable(new String[] { executableName, cvodeFile.getAbsolutePath(), cvodeOutputFile.getAbsolutePath() });
executable.start();
// get the result
ODESolverResultSet odeSolverResultSet = getODESolverResultSet(simJob, cvodeOutputFile.getPath());
//
// print header
//
File outputFile = new File(outDir, filePrefix + ".vcell.csv");
java.io.PrintStream outputStream = new java.io.PrintStream(new java.io.BufferedOutputStream(new java.io.FileOutputStream(outputFile)));
outputStream.print("time");
for (int i = 0; i < testSpec.getVarsList().length; i++) {
outputStream.print("," + testSpec.getVarsList()[i]);
}
outputStream.println();
//
// extract data for time and species
//
double[][] data = new double[testSpec.getVarsList().length + 1][];
int column = odeSolverResultSet.findColumn("t");
data[0] = odeSolverResultSet.extractColumn(column);
int origDataLength = data[0].length;
for (int i = 0; i < testSpec.getVarsList().length; i++) {
column = odeSolverResultSet.findColumn(testSpec.getVarsList()[i]);
if (column == -1) {
Variable var = simJob.getSimulationSymbolTable().getVariable(testSpec.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 " + testSpec.getVarsList()[i] + " in simulation");
}
} else {
data[i + 1] = odeSolverResultSet.extractColumn(column);
}
}
//
// for each time, print row
//
int index = 0;
double[] sampleTimes = new double[testSpec.getNumTimeSteps() + 1];
for (int i = 0; i <= testSpec.getNumTimeSteps(); i++) {
sampleTimes[i] = endTime * i / testSpec.getNumTimeSteps();
}
Model vcModel = bioModel.getModel();
ReservedSymbol kMole = vcModel.getKMOLE();
for (int i = 0; i < sampleTimes.length; i++) {
//
while (true) {
//
if (index == odeSolverResultSet.getRowCount() - 1) {
if (data[0][index] == sampleTimes[i]) {
break;
} else {
throw new RuntimeException("sampleTime does not match at last time point");
}
}
//
if (data[0][index + 1] > sampleTimes[i]) {
break;
}
//
// sampleTime must be later in our data list.
//
index++;
}
// if data[0][index] == sampleTime no need to interpolate
if (data[0][index] == sampleTimes[i]) {
// 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 (timeFactor != 1.0) {
// outputStream.print(data[0][index]/timeFactor);
// } else {
outputStream.print(data[0][index]);
// }
for (int j = 0; j < testSpec.getVarsList().length; j++) {
// SBMLImporter.SBVCConcentrationUnits spConcUnits = speciesUnitsHash.get(testSpec.getVarsList()[j]);
// if (spConcUnits != null) {
// VCUnitDefinition sbunits = spConcUnits.getSBConcentrationUnits();
// VCUnitDefinition vcunits = spConcUnits.getVCConcentrationUnits();
// SBMLUnitParameter unitFactor = SBMLUtils.getConcUnitFactor("spConcParam", vcunits, sbunits, kMole);
// 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]);
// }
}
// System.out.println("No interpolation needed!");
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 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 (timeFactor != 1.0) {
// outputStream.print(sampleTimes[i]/timeFactor);
// } else {
outputStream.print(sampleTimes[i]);
// }
for (int j = 0; j < testSpec.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);
}
// // Currently using 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 = taylorInterpolation(sampleTimes[i], times, speciesVals);
// interpolatedValue = interpolatedValue * unitFactor.getExpression().evaluateConstant(); //earlier, hack unitfactor = 0.000001
// System.out.println("Sample time: " + sampleTimes[i] + ", between time[" + index + "]=" + data[0][index]+" and time["+(index+1)+"]="+(data[0][index+1])+", interpolated = "+interpolatedValue);
outputStream.print("," + interpolatedValue);
}
outputStream.println();
}
}
outputStream.close();
return outputFile;
} catch (RuntimeException e) {
e.printStackTrace(System.out);
// rethrow without losing context
throw e;
} catch (Exception e) {
e.printStackTrace(System.out);
throw new SolverException(e.getMessage(), e);
}
}
Also used :
KeyValue(org.vcell.util.document.KeyValue)
SimulationTask(cbit.vcell.messaging.server.SimulationTask)
Variable(cbit.vcell.math.Variable)
MathDescription(cbit.vcell.math.MathDescription)
ReservedSymbol(cbit.vcell.model.Model.ReservedSymbol)
CVodeFileWriter(cbit.vcell.solver.ode.CVodeFileWriter)
TimeBounds(cbit.vcell.solver.TimeBounds)
TimeStep(cbit.vcell.solver.TimeStep)
SimulationVersion(org.vcell.util.document.SimulationVersion)
ErrorTolerance(cbit.vcell.solver.ErrorTolerance)
ODESolverResultSet(cbit.vcell.solver.ode.ODESolverResultSet)
Executable(org.vcell.util.exe.Executable)
SimulationJob(cbit.vcell.solver.SimulationJob)
PrintWriter(java.io.PrintWriter)
UniformOutputTimeSpec(cbit.vcell.solver.UniformOutputTimeSpec)
VCLogger(cbit.util.xml.VCLogger)
IOException(java.io.IOException)
SimulationContext(cbit.vcell.mapping.SimulationContext)
ExecutableException(org.vcell.util.exe.ExecutableException)
XMLStreamException(javax.xml.stream.XMLStreamException)
XmlParseException(cbit.vcell.xml.XmlParseException)
SolverException(cbit.vcell.solver.SolverException)
SbmlException(org.vcell.sbml.SbmlException)
IOException(java.io.IOException)
SBMLImportException(org.vcell.sbml.vcell.SBMLImportException)
Simulation(cbit.vcell.solver.Simulation)
BioModel(cbit.vcell.biomodel.BioModel)
MathMapping(cbit.vcell.mapping.MathMapping)
BioModel(cbit.vcell.biomodel.BioModel)
Model(cbit.vcell.model.Model)
SolverException(cbit.vcell.solver.SolverException)
File(java.io.File)
XMLSource(cbit.vcell.xml.XMLSource)
Example 8 with SbmlException
use of org.vcell.sbml.SbmlException in project vcell by virtualcell.
the class VCellSBMLSolver method solveVCell.
public File solveVCell(String filePrefix, File outDir, String sbmlFileName, SimSpec testSpec) throws IOException, SolverException, SbmlException {
try {
cbit.util.xml.VCLogger logger = new LocalLogger();
//
// Instantiate an SBMLImporter to get the speciesUnitsHash - to compute the conversion factor from VC->SB species units.
// and import SBML (sbml->bioModel)
org.vcell.sbml.vcell.SBMLImporter sbmlImporter = new org.vcell.sbml.vcell.SBMLImporter(sbmlFileName, logger, false);
BioModel bioModel = sbmlImporter.getBioModel();
if (bRoundTrip) {
// Round trip the bioModel (bioModel->sbml->bioModel).
// export bioModel as sbml and save
String vcml_sbml = cbit.vcell.xml.XmlHelper.exportSBML(bioModel, 2, 1, 0, false, bioModel.getSimulationContext(0), null);
// re-import bioModel from exported sbml
XMLSource vcml_sbml_Src = new XMLSource(vcml_sbml);
BioModel newBioModel = (BioModel) XmlHelper.importSBML(logger, vcml_sbml_Src, false);
// have rest of code use the round-tripped biomodel
bioModel = newBioModel;
}
//
// select only Application, generate math, and create a single Simulation.
//
SimulationContext simContext = bioModel.getSimulationContext(0);
MathMapping mathMapping = simContext.createNewMathMapping();
MathDescription mathDesc = mathMapping.getMathDescription();
simContext.setMathDescription(mathDesc);
SimulationVersion simVersion = new SimulationVersion(new KeyValue("100"), "unnamed", null, null, null, null, null, null, null, null);
Simulation sim = new Simulation(simVersion, mathDesc);
sim.setName("unnamed");
// if time factor from SBML is not 1 (i.e., it is not in secs but in minutes or hours), convert endTime to min/hr as : endTime*timeFactor
// double endTime = testSpec.getEndTime()*timeFactor;
double endTime = testSpec.getEndTime();
sim.getSolverTaskDescription().setTimeBounds(new TimeBounds(0, endTime));
TimeStep timeStep = new TimeStep();
sim.getSolverTaskDescription().setTimeStep(new TimeStep(timeStep.getMinimumTimeStep(), timeStep.getDefaultTimeStep(), endTime / 10000));
sim.getSolverTaskDescription().setOutputTimeSpec(new UniformOutputTimeSpec((endTime - 0) / testSpec.getNumTimeSteps()));
sim.getSolverTaskDescription().setErrorTolerance(new ErrorTolerance(testSpec.getAbsTolerance(), testSpec.getRelTolerance()));
// sim.getSolverTaskDescription().setErrorTolerance(new ErrorTolerance(1e-10, 1e-12));
// Generate .idaInput string
File idaInputFile = new File(outDir, filePrefix + SimDataConstants.IDAINPUT_DATA_EXTENSION);
PrintWriter idaPW = new java.io.PrintWriter(idaInputFile);
SimulationJob simJob = new SimulationJob(sim, 0, null);
SimulationTask simTask = new SimulationTask(simJob, 0);
IDAFileWriter idaFileWriter = new IDAFileWriter(idaPW, simTask);
idaFileWriter.write();
idaPW.close();
// use the idastandalone solver
File idaOutputFile = new File(outDir, filePrefix + SimDataConstants.IDA_DATA_EXTENSION);
// String sundialsSolverExecutable = "C:\\Developer\\Eclipse\\workspace\\VCell 4.8\\SundialsSolverStandalone_NoMessaging.exe";
String executableName = null;
try {
executableName = SolverUtilities.getExes(SolverDescription.IDA)[0].getAbsolutePath();
} catch (IOException e) {
throw new RuntimeException("failed to get executable for solver " + SolverDescription.IDA.getDisplayLabel() + ": " + e.getMessage(), e);
}
Executable executable = new Executable(new String[] { executableName, idaInputFile.getAbsolutePath(), idaOutputFile.getAbsolutePath() });
executable.start();
/* // Generate .cvodeInput string
File cvodeFile = new File(outDir,filePrefix+SimDataConstants.CVODEINPUT_DATA_EXTENSION);
PrintWriter cvodePW = new java.io.PrintWriter(cvodeFile);
SimulationJob simJob = new SimulationJob(sim, 0, null);
CVodeFileWriter cvodeFileWriter = new CVodeFileWriter(cvodePW, simJob);
cvodeFileWriter.write();
cvodePW.close();
// use the cvodeStandalone solver
File cvodeOutputFile = new File(outDir,filePrefix+SimDataConstants.IDA_DATA_EXTENSION);
String sundialsSolverExecutable = PropertyLoader.getRequiredProperty(PropertyLoader.sundialsSolverExecutableProperty);
Executable executable = new Executable(new String[]{sundialsSolverExecutable, cvodeFile.getAbsolutePath(), cvodeOutputFile.getAbsolutePath()});
executable.start();
*/
// get the result
ODESolverResultSet odeSolverResultSet = getODESolverResultSet(simJob, idaOutputFile.getPath());
// remove CVOde input and output files ??
idaInputFile.delete();
idaOutputFile.delete();
//
// print header
//
File outputFile = new File(outDir, "results" + filePrefix + ".csv");
java.io.PrintStream outputStream = new java.io.PrintStream(new java.io.BufferedOutputStream(new java.io.FileOutputStream(outputFile)));
outputStream.print("time");
for (int i = 0; i < testSpec.getVarsList().length; i++) {
outputStream.print("," + testSpec.getVarsList()[i]);
}
outputStream.println();
//
// extract data for time and species
//
double[][] data = new double[testSpec.getVarsList().length + 1][];
int column = odeSolverResultSet.findColumn("t");
data[0] = odeSolverResultSet.extractColumn(column);
int origDataLength = data[0].length;
for (int i = 0; i < testSpec.getVarsList().length; i++) {
column = odeSolverResultSet.findColumn(testSpec.getVarsList()[i]);
if (column == -1) {
Variable var = simJob.getSimulationSymbolTable().getVariable(testSpec.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 " + testSpec.getVarsList()[i] + " in simulation");
}
} else {
data[i + 1] = odeSolverResultSet.extractColumn(column);
}
}
//
// for each time, print row
//
int index = 0;
double[] sampleTimes = new double[testSpec.getNumTimeSteps() + 1];
for (int i = 0; i <= testSpec.getNumTimeSteps(); i++) {
sampleTimes[i] = endTime * i / testSpec.getNumTimeSteps();
}
Model vcModel = bioModel.getModel();
ReservedSymbol kMole = vcModel.getKMOLE();
for (int i = 0; i < sampleTimes.length; i++) {
//
while (true) {
//
if (index == odeSolverResultSet.getRowCount() - 1) {
if (data[0][index] == sampleTimes[i]) {
break;
} else {
throw new RuntimeException("sampleTime does not match at last time point");
}
}
//
if (data[0][index + 1] > sampleTimes[i]) {
break;
}
//
// sampleTime must be later in our data list.
//
index++;
}
// if data[0][index] == sampleTime no need to interpolate
if (data[0][index] == sampleTimes[i]) {
// 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 (timeFactor != 1.0) {
// outputStream.print(data[0][index]/timeFactor);
// } else {
outputStream.print(data[0][index]);
// }
for (int j = 0; j < testSpec.getVarsList().length; j++) {
// SBMLImporter.SBVCConcentrationUnits spConcUnits = speciesUnitsHash.get(testSpec.getVarsList()[j]);
// if (spConcUnits != null) {
// VCUnitDefinition sbunits = spConcUnits.getSBConcentrationUnits();
// VCUnitDefinition vcunits = spConcUnits.getVCConcentrationUnits();
// SBMLUnitParameter unitFactor = SBMLUtils.getConcUnitFactor("spConcParam", vcunits, sbunits, kMole);
// 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]);
// }
}
// System.out.println("No interpolation needed!");
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 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 (timeFactor != 1.0) {
// outputStream.print(sampleTimes[i]/timeFactor);
// } else {
outputStream.print(sampleTimes[i]);
// }
for (int j = 0; j < testSpec.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);
}
// // Currently using 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 = taylorInterpolation(sampleTimes[i], times, speciesVals);
// interpolatedValue = interpolatedValue * unitFactor.getExpression().evaluateConstant(); //earlier, hack unitfactor = 0.000001
// System.out.println("Sample time: " + sampleTimes[i] + ", between time[" + index + "]=" + data[0][index]+" and time["+(index+1)+"]="+(data[0][index+1])+", interpolated = "+interpolatedValue);
outputStream.print("," + interpolatedValue);
}
outputStream.println();
}
}
outputStream.close();
return outputFile;
} catch (Exception e) {
e.printStackTrace(System.out);
// File outputFile = new File(outDir,"results" + filePrefix + ".csv");
throw new SolverException(e.getMessage());
}
}
Also used :
KeyValue(org.vcell.util.document.KeyValue)
SimulationTask(cbit.vcell.messaging.server.SimulationTask)
Variable(cbit.vcell.math.Variable)
SBMLImporter(org.vcell.sbml.vcell.SBMLImporter)
MathDescription(cbit.vcell.math.MathDescription)
ReservedSymbol(cbit.vcell.model.Model.ReservedSymbol)
TimeBounds(cbit.vcell.solver.TimeBounds)
TimeStep(cbit.vcell.solver.TimeStep)
SimulationVersion(org.vcell.util.document.SimulationVersion)
ErrorTolerance(cbit.vcell.solver.ErrorTolerance)
ODESolverResultSet(cbit.vcell.solver.ode.ODESolverResultSet)
Executable(org.vcell.util.exe.Executable)
SimulationJob(cbit.vcell.solver.SimulationJob)
PrintWriter(java.io.PrintWriter)
UniformOutputTimeSpec(cbit.vcell.solver.UniformOutputTimeSpec)
VCLogger(cbit.util.xml.VCLogger)
SBMLImporter(org.vcell.sbml.vcell.SBMLImporter)
IOException(java.io.IOException)
SimulationContext(cbit.vcell.mapping.SimulationContext)
ExecutableException(org.vcell.util.exe.ExecutableException)
XMLStreamException(javax.xml.stream.XMLStreamException)
XmlParseException(cbit.vcell.xml.XmlParseException)
SolverException(cbit.vcell.solver.SolverException)
SbmlException(org.vcell.sbml.SbmlException)
IOException(java.io.IOException)
SBMLImportException(org.vcell.sbml.vcell.SBMLImportException)
IDAFileWriter(cbit.vcell.solver.ode.IDAFileWriter)
Simulation(cbit.vcell.solver.Simulation)
BioModel(cbit.vcell.biomodel.BioModel)
MathMapping(cbit.vcell.mapping.MathMapping)
BioModel(cbit.vcell.biomodel.BioModel)
Model(cbit.vcell.model.Model)
SolverException(cbit.vcell.solver.SolverException)
XMLSource(cbit.vcell.xml.XMLSource)
File(java.io.File)
Example 9 with SbmlException
use of org.vcell.sbml.SbmlException in project vcell by virtualcell.
the class SBMLExporter method addSpecies.
/**
* addSpecies comment.
* @throws XMLStreamException
* @throws SbmlException
*/
protected void addSpecies() throws XMLStreamException, SbmlException {
Model vcModel = vcBioModel.getModel();
SpeciesContext[] vcSpeciesContexts = vcModel.getSpeciesContexts();
for (int i = 0; i < vcSpeciesContexts.length; i++) {
org.sbml.jsbml.Species sbmlSpecies = sbmlModel.createSpecies();
sbmlSpecies.setId(vcSpeciesContexts[i].getName());
// Assuming that at this point, the compartment(s) for the model are already filled in.
Compartment compartment = sbmlModel.getCompartment(TokenMangler.mangleToSName(vcSpeciesContexts[i].getStructure().getName()));
if (compartment != null) {
sbmlSpecies.setCompartment(compartment.getId());
}
// 'hasSubstanceOnly' field will be 'false', since VC deals only with initial concentrations and not initial amounts.
sbmlSpecies.setHasOnlySubstanceUnits(false);
// Get (and set) the initial concentration value
if (getSelectedSimContext() == null) {
throw new RuntimeException("No simcontext (application) specified; Cannot proceed.");
}
// Get the speciesContextSpec in the simContext corresponding to the 'speciesContext'; and extract its initial concentration value.
SpeciesContextSpec vcSpeciesContextsSpec = getSelectedSimContext().getReactionContext().getSpeciesContextSpec(vcSpeciesContexts[i]);
// we need to convert concentration from uM -> molecules/um3; this can be achieved by dividing by KMOLE.
try {
sbmlSpecies.setInitialConcentration(vcSpeciesContextsSpec.getInitialConditionParameter().getExpression().evaluateConstant());
} catch (cbit.vcell.parser.ExpressionException e) {
// If exporting to L2V3, if species concentration is not an expr with x, y, z or other species, add as InitialAssignment, else complain.
if (vcSpeciesContextsSpec.getInitialConditionParameter().getExpression() != null) {
Expression initConcExpr = vcSpeciesContextsSpec.getInitialConditionParameter().getExpression();
if ((sbmlLevel == 2 && sbmlVersion >= 3) || (sbmlLevel > 2)) {
// L2V3 and above - add expression as init assignment
ASTNode initAssgnMathNode = getFormulaFromExpression(initConcExpr);
InitialAssignment initAssignment = sbmlModel.createInitialAssignment();
initAssignment.setSymbol(vcSpeciesContexts[i].getName());
initAssignment.setMath(initAssgnMathNode);
} else {
// L2V1 (or L1V2 also??)
// L2V1 (and L1V2?) and species is 'fixed' (constant), and not fn of x,y,z, other sp, add expr as assgn rule
ASTNode assgnRuleMathNode = getFormulaFromExpression(initConcExpr);
AssignmentRule assgnRule = sbmlModel.createAssignmentRule();
assgnRule.setVariable(vcSpeciesContexts[i].getName());
assgnRule.setMath(assgnRuleMathNode);
}
}
}
// Get (and set) the boundary condition value
boolean bBoundaryCondition = getBoundaryCondition(vcSpeciesContexts[i]);
sbmlSpecies.setBoundaryCondition(bBoundaryCondition);
// mandatory for L3, optional for L2
sbmlSpecies.setConstant(false);
// set species substance units as 'molecules' - same as defined in the model; irrespective of it is in surface or volume.
UnitDefinition unitDefn = getOrCreateSBMLUnit(sbmlExportSpec.getSubstanceUnits());
sbmlSpecies.setSubstanceUnits(unitDefn);
// need to do the following if exporting to SBML spatial
if (bSpatial) {
// Required for setting BoundaryConditions : structureMapping for vcSpeciesContext[i] & sbmlGeometry.coordinateComponents
StructureMapping sm = getSelectedSimContext().getGeometryContext().getStructureMapping(vcSpeciesContexts[i].getStructure());
SpatialModelPlugin mplugin = (SpatialModelPlugin) sbmlModel.getPlugin(SBMLUtils.SBML_SPATIAL_NS_PREFIX);
org.sbml.jsbml.ext.spatial.Geometry sbmlGeometry = mplugin.getGeometry();
CoordinateComponent ccX = sbmlGeometry.getListOfCoordinateComponents().get(vcModel.getX().getName());
CoordinateComponent ccY = sbmlGeometry.getListOfCoordinateComponents().get(vcModel.getY().getName());
CoordinateComponent ccZ = sbmlGeometry.getListOfCoordinateComponents().get(vcModel.getZ().getName());
// add diffusion, advection, boundary condition parameters for species, if they exist
Parameter[] scsParams = vcSpeciesContextsSpec.getParameters();
if (scsParams != null) {
for (int j = 0; j < scsParams.length; j++) {
if (scsParams[j] != null) {
SpeciesContextSpecParameter scsParam = (SpeciesContextSpecParameter) scsParams[j];
// no need to add parameters in SBML for init conc or init count
int role = scsParam.getRole();
switch(role) {
case SpeciesContextSpec.ROLE_BoundaryValueXm:
{
break;
}
case SpeciesContextSpec.ROLE_BoundaryValueXp:
{
break;
}
case SpeciesContextSpec.ROLE_BoundaryValueYm:
{
break;
}
case SpeciesContextSpec.ROLE_BoundaryValueYp:
{
break;
}
case SpeciesContextSpec.ROLE_BoundaryValueZm:
{
break;
}
case SpeciesContextSpec.ROLE_BoundaryValueZp:
{
break;
}
case SpeciesContextSpec.ROLE_DiffusionRate:
{
break;
}
case SpeciesContextSpec.ROLE_InitialConcentration:
{
// done elsewhere??
continue;
// break;
}
case SpeciesContextSpec.ROLE_InitialCount:
{
// done elsewhere??
continue;
// break;
}
case SpeciesContextSpec.ROLE_VelocityX:
{
break;
}
case SpeciesContextSpec.ROLE_VelocityY:
{
break;
}
case SpeciesContextSpec.ROLE_VelocityZ:
{
break;
}
default:
{
throw new RuntimeException("SpeciesContext Specification parameter with role " + SpeciesContextSpec.RoleNames[role] + " not yet supported for SBML export");
}
}
// if diffusion is 0 && vel terms are not specified, boundary condition not present
if (vcSpeciesContextsSpec.isAdvecting() || vcSpeciesContextsSpec.isDiffusing()) {
Expression diffExpr = vcSpeciesContextsSpec.getDiffusionParameter().getExpression();
boolean bDiffExprNull = (diffExpr == null);
boolean bDiffExprIsZero = false;
if (!bDiffExprNull && diffExpr.isNumeric()) {
try {
bDiffExprIsZero = (diffExpr.evaluateConstant() == 0.0);
} catch (Exception e) {
e.printStackTrace(System.out);
throw new RuntimeException("Unable to evalute numeric value of diffusion parameter for speciesContext '" + vcSpeciesContexts[i] + "'.");
}
}
boolean bDiffusionZero = (bDiffExprNull || bDiffExprIsZero);
Expression velX_Expr = vcSpeciesContextsSpec.getVelocityXParameter().getExpression();
SpatialQuantity[] velX_Quantities = vcSpeciesContextsSpec.getVelocityQuantities(QuantityComponent.X);
boolean bVelX_ExprIsNull = (velX_Expr == null && velX_Quantities.length == 0);
Expression velY_Expr = vcSpeciesContextsSpec.getVelocityYParameter().getExpression();
SpatialQuantity[] velY_Quantities = vcSpeciesContextsSpec.getVelocityQuantities(QuantityComponent.Y);
boolean bVelY_ExprIsNull = (velY_Expr == null && velY_Quantities.length == 0);
Expression velZ_Expr = vcSpeciesContextsSpec.getVelocityZParameter().getExpression();
SpatialQuantity[] velZ_Quantities = vcSpeciesContextsSpec.getVelocityQuantities(QuantityComponent.Z);
boolean bVelZ_ExprIsNull = (velZ_Expr == null && velZ_Quantities.length == 0);
boolean bAdvectionNull = (bVelX_ExprIsNull && bVelY_ExprIsNull && bVelZ_ExprIsNull);
if (bDiffusionZero && bAdvectionNull) {
continue;
}
}
// for example, if scsParam is BC_Zm and if coordinateComponent 'ccZ' is null, no SBML parameter should be created for BC_Zm
if ((((role == SpeciesContextSpec.ROLE_BoundaryValueXm) || (role == SpeciesContextSpec.ROLE_BoundaryValueXp)) && (ccX == null)) || (((role == SpeciesContextSpec.ROLE_BoundaryValueYm) || (role == SpeciesContextSpec.ROLE_BoundaryValueYp)) && (ccY == null)) || (((role == SpeciesContextSpec.ROLE_BoundaryValueZm) || (role == SpeciesContextSpec.ROLE_BoundaryValueZp)) && (ccZ == null))) {
continue;
}
org.sbml.jsbml.Parameter sbmlParam = createSBMLParamFromSpeciesParam(vcSpeciesContexts[i], (SpeciesContextSpecParameter) scsParams[j]);
if (sbmlParam != null) {
BoundaryConditionType vcBCType_Xm = vcSelectedSimContext.getGeometryContext().getStructureMapping(vcSpeciesContexts[i].getStructure()).getBoundaryConditionTypeXm();
BoundaryConditionType vcBCType_Xp = vcSelectedSimContext.getGeometryContext().getStructureMapping(vcSpeciesContexts[i].getStructure()).getBoundaryConditionTypeXp();
BoundaryConditionType vcBCType_Ym = vcSelectedSimContext.getGeometryContext().getStructureMapping(vcSpeciesContexts[i].getStructure()).getBoundaryConditionTypeYm();
BoundaryConditionType vcBCType_Yp = vcSelectedSimContext.getGeometryContext().getStructureMapping(vcSpeciesContexts[i].getStructure()).getBoundaryConditionTypeYp();
BoundaryConditionType vcBCType_Zm = vcSelectedSimContext.getGeometryContext().getStructureMapping(vcSpeciesContexts[i].getStructure()).getBoundaryConditionTypeZm();
BoundaryConditionType vcBCType_Zp = vcSelectedSimContext.getGeometryContext().getStructureMapping(vcSpeciesContexts[i].getStructure()).getBoundaryConditionTypeZp();
SpatialParameterPlugin spplugin = (SpatialParameterPlugin) sbmlParam.getPlugin(SBMLUtils.SBML_SPATIAL_NS_PREFIX);
if (role == SpeciesContextSpec.ROLE_DiffusionRate) {
// set diffusionCoefficient element in SpatialParameterPlugin for param
DiffusionCoefficient sbmlDiffCoeff = new DiffusionCoefficient();
sbmlDiffCoeff.setVariable(vcSpeciesContexts[i].getName());
sbmlDiffCoeff.setDiffusionKind(DiffusionKind.isotropic);
sbmlDiffCoeff.setSpeciesRef(vcSpeciesContexts[i].getName());
spplugin.setParamType(sbmlDiffCoeff);
}
if ((role == SpeciesContextSpec.ROLE_BoundaryValueXm) && (ccX != null)) {
// set BoundaryCondn Xm element in SpatialParameterPlugin for param
BoundaryCondition sbmlBCXm = new BoundaryCondition();
spplugin.setParamType(sbmlBCXm);
sbmlBCXm.setType(getBoundaryConditionKind(vcBCType_Xm));
sbmlBCXm.setVariable(vcSpeciesContexts[i].getName());
sbmlBCXm.setCoordinateBoundary(ccX.getBoundaryMinimum().getId());
}
if ((role == SpeciesContextSpec.ROLE_BoundaryValueXp) && (ccX != null)) {
// set BoundaryCondn Xp element in SpatialParameterPlugin for param
BoundaryCondition sbmlBCXp = new BoundaryCondition();
spplugin.setParamType(sbmlBCXp);
sbmlBCXp.setType(getBoundaryConditionKind(vcBCType_Xp));
sbmlBCXp.setVariable(vcSpeciesContexts[i].getName());
sbmlBCXp.setType(sm.getBoundaryConditionTypeXp().boundaryTypeStringValue());
sbmlBCXp.setCoordinateBoundary(ccX.getBoundaryMaximum().getId());
}
if ((role == SpeciesContextSpec.ROLE_BoundaryValueYm) && (ccY != null)) {
// set BoundaryCondn Ym element in SpatialParameterPlugin for param
BoundaryCondition sbmlBCYm = new BoundaryCondition();
spplugin.setParamType(sbmlBCYm);
sbmlBCYm.setType(getBoundaryConditionKind(vcBCType_Yp));
sbmlBCYm.setVariable(vcSpeciesContexts[i].getName());
sbmlBCYm.setType(sm.getBoundaryConditionTypeYm().boundaryTypeStringValue());
sbmlBCYm.setCoordinateBoundary(ccY.getBoundaryMinimum().getId());
}
if ((role == SpeciesContextSpec.ROLE_BoundaryValueYp) && (ccY != null)) {
// set BoundaryCondn Yp element in SpatialParameterPlugin for param
BoundaryCondition sbmlBCYp = new BoundaryCondition();
spplugin.setParamType(sbmlBCYp);
sbmlBCYp.setType(getBoundaryConditionKind(vcBCType_Yp));
sbmlBCYp.setVariable(vcSpeciesContexts[i].getName());
sbmlBCYp.setType(sm.getBoundaryConditionTypeYp().boundaryTypeStringValue());
sbmlBCYp.setCoordinateBoundary(ccY.getBoundaryMaximum().getId());
}
if ((role == SpeciesContextSpec.ROLE_BoundaryValueZm) && (ccZ != null)) {
// set BoundaryCondn Zm element in SpatialParameterPlugin for param
BoundaryCondition sbmlBCZm = new BoundaryCondition();
spplugin.setParamType(sbmlBCZm);
sbmlBCZm.setType(getBoundaryConditionKind(vcBCType_Zm));
sbmlBCZm.setVariable(vcSpeciesContexts[i].getName());
sbmlBCZm.setType(sm.getBoundaryConditionTypeZm().boundaryTypeStringValue());
sbmlBCZm.setCoordinateBoundary(ccZ.getBoundaryMinimum().getId());
}
if ((role == SpeciesContextSpec.ROLE_BoundaryValueZp) && (ccZ != null)) {
// set BoundaryCondn Zp element in SpatialParameterPlugin for param
BoundaryCondition sbmlBCZp = new BoundaryCondition();
spplugin.setParamType(sbmlBCZp);
sbmlBCZp.setType(getBoundaryConditionKind(vcBCType_Zp));
sbmlBCZp.setVariable(vcSpeciesContexts[i].getName());
sbmlBCZp.setType(sm.getBoundaryConditionTypeZp().boundaryTypeStringValue());
sbmlBCZp.setCoordinateBoundary(ccZ.getBoundaryMaximum().getId());
}
if (role == SpeciesContextSpec.ROLE_VelocityX) {
// set advectionCoeff X element in SpatialParameterPlugin for param
AdvectionCoefficient sbmlAdvCoeffX = new AdvectionCoefficient();
spplugin.setParamType(sbmlAdvCoeffX);
sbmlAdvCoeffX.setVariable(vcSpeciesContexts[i].getName());
sbmlAdvCoeffX.setCoordinate(CoordinateKind.cartesianX);
}
if (role == SpeciesContextSpec.ROLE_VelocityY) {
// set advectionCoeff Y element in SpatialParameterPlugin for param
AdvectionCoefficient sbmlAdvCoeffY = new AdvectionCoefficient();
spplugin.setParamType(sbmlAdvCoeffY);
sbmlAdvCoeffY.setVariable(vcSpeciesContexts[i].getName());
sbmlAdvCoeffY.setCoordinate(CoordinateKind.cartesianY);
}
if (role == SpeciesContextSpec.ROLE_VelocityZ) {
// set advectionCoeff Z element in SpatialParameterPlugin for param
AdvectionCoefficient sbmlAdvCoeffZ = new AdvectionCoefficient();
spplugin.setParamType(sbmlAdvCoeffZ);
sbmlAdvCoeffZ.setVariable(vcSpeciesContexts[i].getName());
sbmlAdvCoeffZ.setCoordinate(CoordinateKind.cartesianZ);
}
}
// if sbmlParam != null
}
// if scsParams[j] != null
}
// end for scsParams
}
// end scsParams != null
}
// end if (bSpatial)
// Add the common name of species to annotation, and add an annotation element to the species.
// This is required later while trying to read in fluxes ...
// new Element(XMLTags.VCellRelatedInfoTag, sbml_vcml_ns);
Element sbmlImportRelatedElement = null;
// Element speciesElement = new Element(XMLTags.SpeciesTag, sbml_vcml_ns);
// speciesElement.setAttribute(XMLTags.NameAttrTag, TokenMangler.mangleToSName(vcSpeciesContexts[i].getSpecies().getCommonName()));
// sbmlImportRelatedElement.addContent(speciesElement);
// Get RDF annotation for species from SBMLAnnotationUtils
sbmlAnnotationUtil.writeAnnotation(vcSpeciesContexts[i].getSpecies(), sbmlSpecies, sbmlImportRelatedElement);
// Now set notes,
sbmlAnnotationUtil.writeNotes(vcSpeciesContexts[i].getSpecies(), sbmlSpecies);
}
}
Also used :
Compartment(org.sbml.jsbml.Compartment)
Element(org.jdom.Element)
BoundaryConditionType(cbit.vcell.math.BoundaryConditionType)
SpatialParameterPlugin(org.sbml.jsbml.ext.spatial.SpatialParameterPlugin)
SpeciesContext(cbit.vcell.model.SpeciesContext)
SpeciesContextSpec(cbit.vcell.mapping.SpeciesContextSpec)
StructureMapping(cbit.vcell.mapping.StructureMapping)
ASTNode(org.sbml.jsbml.ASTNode)
SpatialQuantity(cbit.vcell.mapping.spatial.SpatialObject.SpatialQuantity)
VCUnitDefinition(cbit.vcell.units.VCUnitDefinition)
UnitDefinition(org.sbml.jsbml.UnitDefinition)
CoordinateComponent(org.sbml.jsbml.ext.spatial.CoordinateComponent)
SpeciesContextSpecParameter(cbit.vcell.mapping.SpeciesContextSpec.SpeciesContextSpecParameter)
AdvectionCoefficient(org.sbml.jsbml.ext.spatial.AdvectionCoefficient)
AssignmentRule(org.sbml.jsbml.AssignmentRule)
SpatialModelPlugin(org.sbml.jsbml.ext.spatial.SpatialModelPlugin)
ExpressionException(cbit.vcell.parser.ExpressionException)
DiffusionCoefficient(org.sbml.jsbml.ext.spatial.DiffusionCoefficient)
InteriorPoint(org.sbml.jsbml.ext.spatial.InteriorPoint)
XMLStreamException(javax.xml.stream.XMLStreamException)
SbmlException(org.vcell.sbml.SbmlException)
ImageException(cbit.image.ImageException)
SBMLException(org.sbml.jsbml.SBMLException)
ExpressionException(cbit.vcell.parser.ExpressionException)
InitialAssignment(org.sbml.jsbml.InitialAssignment)
Expression(cbit.vcell.parser.Expression)
BoundaryCondition(org.sbml.jsbml.ext.spatial.BoundaryCondition)
Model(cbit.vcell.model.Model)
BioModel(cbit.vcell.biomodel.BioModel)
StructureMappingParameter(cbit.vcell.mapping.StructureMapping.StructureMappingParameter)
Parameter(cbit.vcell.model.Parameter)
KineticsParameter(cbit.vcell.model.Kinetics.KineticsParameter)
ModelParameter(cbit.vcell.model.Model.ModelParameter)
SpeciesContextSpecParameter(cbit.vcell.mapping.SpeciesContextSpec.SpeciesContextSpecParameter)
LocalParameter(cbit.vcell.mapping.ParameterContext.LocalParameter)
Example 10 with SbmlException
use of org.vcell.sbml.SbmlException in project vcell by virtualcell.
the class SBMLExporter method addGeometry.
private void addGeometry() throws SbmlException {
SpatialModelPlugin mplugin = (SpatialModelPlugin) sbmlModel.getPlugin(SBMLUtils.SBML_SPATIAL_NS_PREFIX);
// Creates a geometry object via SpatialModelPlugin object.
org.sbml.jsbml.ext.spatial.Geometry sbmlGeometry = mplugin.createGeometry();
sbmlGeometry.setCoordinateSystem(GeometryKind.cartesian);
sbmlGeometry.setSpatialId("vcell");
Geometry vcGeometry = getSelectedSimContext().getGeometry();
Model vcModel = getSelectedSimContext().getModel();
//
// list of CoordinateComponents : 1 if geometry is 1-d, 2 if geometry is 2-d, 3 if geometry is 3-d
//
int dimension = vcGeometry.getDimension();
Extent vcExtent = vcGeometry.getExtent();
Origin vcOrigin = vcGeometry.getOrigin();
// add x coordinate component
CoordinateComponent xComp = sbmlGeometry.createCoordinateComponent();
xComp.setSpatialId(vcModel.getX().getName());
xComp.setType(CoordinateKind.cartesianX);
final UnitDefinition sbmlUnitDef_length = getOrCreateSBMLUnit(vcModel.getUnitSystem().getLengthUnit());
xComp.setUnits(sbmlUnitDef_length);
Boundary minX = new Boundary();
xComp.setBoundaryMinimum(minX);
minX.setSpatialId("Xmin");
minX.setValue(vcOrigin.getX());
Boundary maxX = new Boundary();
xComp.setBoundaryMaximum(maxX);
maxX.setSpatialId("Xmax");
maxX.setValue(vcOrigin.getX() + (vcExtent.getX()));
org.sbml.jsbml.Parameter pX = sbmlModel.createParameter();
pX.setId(vcModel.getX().getName());
pX.setValue(0.0);
pX.setConstant(false);
pX.setUnits(sbmlUnitDef_length);
SpatialParameterPlugin spPluginPx = (SpatialParameterPlugin) pX.getPlugin(SBMLUtils.SBML_SPATIAL_NS_PREFIX);
SpatialSymbolReference spSymRefPx = new SpatialSymbolReference();
spPluginPx.setParamType(spSymRefPx);
spSymRefPx.setSpatialRef(xComp.getSpatialId());
// add y coordinate component
if (dimension == 2 || dimension == 3) {
CoordinateComponent yComp = sbmlGeometry.createCoordinateComponent();
yComp.setSpatialId(vcModel.getY().getName());
yComp.setType(CoordinateKind.cartesianY);
yComp.setUnits(sbmlUnitDef_length);
Boundary minY = new Boundary();
yComp.setBoundaryMinimum(minY);
minY.setSpatialId("Ymin");
minY.setValue(vcOrigin.getY());
Boundary maxY = new Boundary();
yComp.setBoundaryMaximum(maxY);
maxY.setSpatialId("Ymax");
maxY.setValue(vcOrigin.getY() + (vcExtent.getY()));
org.sbml.jsbml.Parameter pY = sbmlModel.createParameter();
pY.setId(vcModel.getY().getName());
pY.setValue(0.0);
pY.setConstant(false);
pY.setUnits(sbmlUnitDef_length);
SpatialParameterPlugin spPluginPy = (SpatialParameterPlugin) pY.getPlugin(SBMLUtils.SBML_SPATIAL_NS_PREFIX);
SpatialSymbolReference spSymRefPy = new SpatialSymbolReference();
spPluginPy.setParamType(spSymRefPy);
spSymRefPy.setSpatialRef(yComp.getSpatialId());
}
// add z coordinate component
if (dimension == 3) {
CoordinateComponent zComp = sbmlGeometry.createCoordinateComponent();
zComp.setSpatialId(vcModel.getZ().getName());
zComp.setType(CoordinateKind.cartesianZ);
zComp.setUnits(sbmlUnitDef_length);
Boundary minZ = new Boundary();
zComp.setBoundaryMinimum(minZ);
minZ.setSpatialId("Zmin");
minZ.setValue(vcOrigin.getZ());
Boundary maxZ = new Boundary();
zComp.setBoundaryMaximum(maxZ);
maxZ.setSpatialId("Zmax");
maxZ.setValue(vcOrigin.getZ() + (vcExtent.getZ()));
org.sbml.jsbml.Parameter pZ = sbmlModel.createParameter();
pZ.setId(vcModel.getZ().getName());
pZ.setValue(0.0);
pZ.setConstant(false);
pZ.setUnits(sbmlUnitDef_length);
SpatialParameterPlugin spPluginPz = (SpatialParameterPlugin) pZ.getPlugin(SBMLUtils.SBML_SPATIAL_NS_PREFIX);
SpatialSymbolReference spSymRefPz = new SpatialSymbolReference();
spPluginPz.setParamType(spSymRefPz);
spSymRefPz.setSpatialRef(zComp.getSpatialId());
}
//
// list of compartmentMappings : VC structureMappings
//
GeometryContext vcGeoContext = getSelectedSimContext().getGeometryContext();
StructureMapping[] vcStrucMappings = vcGeoContext.getStructureMappings();
for (int i = 0; i < vcStrucMappings.length; i++) {
StructureMapping vcStructMapping = vcStrucMappings[i];
String structName = vcStructMapping.getStructure().getName();
Compartment comp = sbmlModel.getCompartment(TokenMangler.mangleToSName(structName));
SpatialCompartmentPlugin cplugin = (SpatialCompartmentPlugin) comp.getPlugin(SBMLUtils.SBML_SPATIAL_NS_PREFIX);
GeometryClass gc = vcStructMapping.getGeometryClass();
if (!goodPointer(gc, GeometryClass.class, structName)) {
continue;
}
CompartmentMapping compMapping = new CompartmentMapping();
cplugin.setCompartmentMapping(compMapping);
String geomClassName = gc.getName();
String id = TokenMangler.mangleToSName(geomClassName + structName);
compMapping.setSpatialId(id);
compMapping.setDomainType(TokenMangler.mangleToSName(DOMAIN_TYPE_PREFIX + geomClassName));
try {
StructureMappingParameter usp = vcStructMapping.getUnitSizeParameter();
Expression e = usp.getExpression();
if (goodPointer(e, Expression.class, id)) {
compMapping.setUnitSize(e.evaluateConstant());
}
} catch (ExpressionException e) {
e.printStackTrace(System.out);
throw new RuntimeException("Unable to create compartment mapping for structureMapping '" + compMapping.getId() + "' : " + e.getMessage());
}
}
//
// list of domain types : subvolumes and surface classes from VC
//
boolean bAnyAnalyticSubvolumes = false;
boolean bAnyImageSubvolumes = false;
boolean bAnyCSGSubvolumes = false;
GeometryClass[] vcGeomClasses = vcGeometry.getGeometryClasses();
int numSubVols = 0;
for (int i = 0; i < vcGeomClasses.length; i++) {
DomainType domainType = sbmlGeometry.createDomainType();
domainType.setSpatialId(DOMAIN_TYPE_PREFIX + vcGeomClasses[i].getName());
if (vcGeomClasses[i] instanceof SubVolume) {
if (((SubVolume) vcGeomClasses[i]) instanceof AnalyticSubVolume) {
bAnyAnalyticSubvolumes = true;
} else if (((SubVolume) vcGeomClasses[i]) instanceof ImageSubVolume) {
bAnyImageSubvolumes = true;
} else if (((SubVolume) vcGeomClasses[i]) instanceof CSGObject) {
bAnyCSGSubvolumes = true;
}
domainType.setSpatialDimensions(3);
numSubVols++;
} else if (vcGeomClasses[i] instanceof SurfaceClass) {
domainType.setSpatialDimensions(2);
}
}
//
// list of domains, adjacent domains : from VC geometricRegions
//
GeometrySurfaceDescription vcGSD = vcGeometry.getGeometrySurfaceDescription();
if (vcGSD.getRegionImage() == null) {
try {
vcGSD.updateAll();
} catch (Exception e) {
e.printStackTrace(System.out);
throw new RuntimeException("Unable to generate region images for geometry");
}
}
GeometricRegion[] vcGeometricRegions = vcGSD.getGeometricRegions();
ISize sampleSize = vcGSD.getVolumeSampleSize();
int numX = sampleSize.getX();
int numY = sampleSize.getY();
int numZ = sampleSize.getZ();
double ox = vcOrigin.getX();
double oy = vcOrigin.getY();
double oz = vcOrigin.getZ();
RegionInfo[] regionInfos = vcGSD.getRegionImage().getRegionInfos();
for (int i = 0; i < vcGeometricRegions.length; i++) {
// domains
Domain domain = sbmlGeometry.createDomain();
domain.setSpatialId(vcGeometricRegions[i].getName());
if (vcGeometricRegions[i] instanceof VolumeGeometricRegion) {
domain.setDomainType(DOMAIN_TYPE_PREFIX + ((VolumeGeometricRegion) vcGeometricRegions[i]).getSubVolume().getName());
//
// get a list of interior points ... should probably use the distance map to find a point
// furthest inside (or several points associated with the morphological skeleton).
//
InteriorPoint interiorPt = domain.createInteriorPoint();
int regionID = ((VolumeGeometricRegion) vcGeometricRegions[i]).getRegionID();
boolean bFound = false;
int regInfoIndx = 0;
for (int j = 0; j < regionInfos.length; j++) {
regInfoIndx = j;
if (regionInfos[j].getRegionIndex() == regionID) {
int volIndx = 0;
for (int z = 0; z < numZ && !bFound; z++) {
for (int y = 0; y < numY && !bFound; y++) {
for (int x = 0; x < numX && !bFound; x++) {
if (regionInfos[j].isIndexInRegion(volIndx)) {
bFound = true;
double unit_z = (numZ > 1) ? ((double) z) / (numZ - 1) : 0.5;
double coordZ = oz + vcExtent.getZ() * unit_z;
double unit_y = (numY > 1) ? ((double) y) / (numY - 1) : 0.5;
double coordY = oy + vcExtent.getY() * unit_y;
double unit_x = (numX > 1) ? ((double) x) / (numX - 1) : 0.5;
double coordX = ox + vcExtent.getX() * unit_x;
interiorPt.setCoord1(coordX);
interiorPt.setCoord2(coordY);
interiorPt.setCoord3(coordZ);
}
volIndx++;
}
// end - for x
}
// end - for y
}
// end - for z
}
// end if
}
// end for regionInfos
if (!bFound) {
throw new RuntimeException("Unable to find interior point for region '" + regionInfos[regInfoIndx].toString());
}
} else if (vcGeometricRegions[i] instanceof SurfaceGeometricRegion) {
SurfaceGeometricRegion vcSurfaceGeomReg = (SurfaceGeometricRegion) vcGeometricRegions[i];
GeometricRegion geomRegion0 = vcSurfaceGeomReg.getAdjacentGeometricRegions()[0];
GeometricRegion geomRegion1 = vcSurfaceGeomReg.getAdjacentGeometricRegions()[1];
SurfaceClass surfaceClass = vcGSD.getSurfaceClass(((VolumeGeometricRegion) geomRegion0).getSubVolume(), ((VolumeGeometricRegion) geomRegion1).getSubVolume());
domain.setDomainType(DOMAIN_TYPE_PREFIX + surfaceClass.getName());
// adjacent domains : 2 adjacent domain objects for each surfaceClass in VC.
// adjacent domain 1
GeometricRegion adjGeomRegion0 = vcSurfaceGeomReg.getAdjacentGeometricRegions()[0];
GeometricRegion adjGeomRegion1 = vcSurfaceGeomReg.getAdjacentGeometricRegions()[1];
AdjacentDomains adjDomain = new AdjacentDomains();
adjDomain.setSpatialId(TokenMangler.mangleToSName(vcSurfaceGeomReg.getName() + "_" + adjGeomRegion0.getName()));
adjDomain.setDomain1(vcSurfaceGeomReg.getName());
adjDomain.setDomain2(adjGeomRegion0.getName());
sbmlGeometry.addAdjacentDomain(adjDomain);
// adj domain 2
adjDomain = new AdjacentDomains();
adjDomain.setSpatialId(TokenMangler.mangleToSName(vcSurfaceGeomReg.getName() + "_" + adjGeomRegion1.getName()));
adjDomain.setDomain1(vcSurfaceGeomReg.getName());
adjDomain.setDomain2(adjGeomRegion1.getName());
sbmlGeometry.addAdjacentDomain(adjDomain);
}
}
//
if (bAnyAnalyticSubvolumes && !bAnyImageSubvolumes && !bAnyCSGSubvolumes) {
AnalyticGeometry sbmlAnalyticGeomDefinition = sbmlGeometry.createAnalyticGeometry();
sbmlAnalyticGeomDefinition.setSpatialId(TokenMangler.mangleToSName("Analytic_" + vcGeometry.getName()));
sbmlAnalyticGeomDefinition.setIsActive(true);
for (int i = 0; i < vcGeomClasses.length; i++) {
if (vcGeomClasses[i] instanceof AnalyticSubVolume) {
AnalyticVolume analyticVol = sbmlAnalyticGeomDefinition.createAnalyticVolume();
analyticVol.setSpatialId(vcGeomClasses[i].getName());
analyticVol.setDomainType(DOMAIN_TYPE_PREFIX + vcGeomClasses[i].getName());
analyticVol.setFunctionType(FunctionKind.layered);
analyticVol.setOrdinal(numSubVols - (i + 1));
Expression expr = ((AnalyticSubVolume) vcGeomClasses[i]).getExpression();
try {
String mathMLStr = ExpressionMathMLPrinter.getMathML(expr, true, MathType.BOOLEAN);
ASTNode mathMLNode = ASTNode.readMathMLFromString(mathMLStr);
analyticVol.setMath(mathMLNode);
} catch (Exception e) {
e.printStackTrace(System.out);
throw new RuntimeException("Error converting VC subvolume expression to mathML" + e.getMessage());
}
}
}
}
//
if (!bAnyAnalyticSubvolumes && !bAnyImageSubvolumes && bAnyCSGSubvolumes) {
CSGeometry sbmlCSGeomDefinition = new CSGeometry();
sbmlGeometry.addGeometryDefinition(sbmlCSGeomDefinition);
sbmlCSGeomDefinition.setSpatialId(TokenMangler.mangleToSName("CSG_" + vcGeometry.getName()));
for (int i = 0; i < vcGeomClasses.length; i++) {
if (vcGeomClasses[i] instanceof CSGObject) {
CSGObject vcellCSGObject = (CSGObject) vcGeomClasses[i];
org.sbml.jsbml.ext.spatial.CSGObject sbmlCSGObject = new org.sbml.jsbml.ext.spatial.CSGObject();
sbmlCSGeomDefinition.addCSGObject(sbmlCSGObject);
sbmlCSGObject.setSpatialId(vcellCSGObject.getName());
sbmlCSGObject.setDomainType(DOMAIN_TYPE_PREFIX + vcellCSGObject.getName());
// the ordinal should the the least for the default/background subVolume
sbmlCSGObject.setOrdinal(numSubVols - (i + 1));
org.sbml.jsbml.ext.spatial.CSGNode sbmlcsgNode = getSBMLCSGNode(vcellCSGObject.getRoot());
sbmlCSGObject.setCSGNode(sbmlcsgNode);
}
}
}
//
// add "Segmented" and "DistanceMap" SampledField Geometries
//
final boolean bVCGeometryIsImage = bAnyImageSubvolumes && !bAnyAnalyticSubvolumes && !bAnyCSGSubvolumes;
// 55if (bAnyAnalyticSubvolumes || bAnyImageSubvolumes || bAnyCSGSubvolumes){
if (bVCGeometryIsImage) {
//
// add "Segmented" SampledFieldGeometry
//
SampledFieldGeometry segmentedImageSampledFieldGeometry = sbmlGeometry.createSampledFieldGeometry();
segmentedImageSampledFieldGeometry.setSpatialId(TokenMangler.mangleToSName("SegmentedImage_" + vcGeometry.getName()));
segmentedImageSampledFieldGeometry.setIsActive(true);
// 55boolean bVCGeometryIsImage = bAnyImageSubvolumes && !bAnyAnalyticSubvolumes && !bAnyCSGSubvolumes;
Geometry vcImageGeometry = null;
{
if (bVCGeometryIsImage) {
// make a resampled image;
if (dimension == 3) {
try {
ISize imageSize = vcGeometry.getGeometrySpec().getDefaultSampledImageSize();
vcGeometry.precomputeAll(new GeometryThumbnailImageFactoryAWT());
vcImageGeometry = RayCaster.resampleGeometry(new GeometryThumbnailImageFactoryAWT(), vcGeometry, imageSize);
} catch (Throwable e) {
e.printStackTrace(System.out);
throw new RuntimeException("Unable to convert the original analytic or constructed solid geometry to image-based geometry : " + e.getMessage());
}
} else {
try {
vcGeometry.precomputeAll(new GeometryThumbnailImageFactoryAWT(), true, false);
GeometrySpec origGeometrySpec = vcGeometry.getGeometrySpec();
VCImage newVCImage = origGeometrySpec.getSampledImage().getCurrentValue();
//
// construct the new geometry with the sampled VCImage.
//
vcImageGeometry = new Geometry(vcGeometry.getName() + "_asImage", newVCImage);
vcImageGeometry.getGeometrySpec().setExtent(vcGeometry.getExtent());
vcImageGeometry.getGeometrySpec().setOrigin(vcGeometry.getOrigin());
vcImageGeometry.setDescription(vcGeometry.getDescription());
vcImageGeometry.getGeometrySurfaceDescription().setFilterCutoffFrequency(vcGeometry.getGeometrySurfaceDescription().getFilterCutoffFrequency());
vcImageGeometry.precomputeAll(new GeometryThumbnailImageFactoryAWT(), true, true);
} catch (Exception e) {
e.printStackTrace(System.out);
throw new RuntimeException("Unable to convert the original analytic or constructed solid geometry to image-based geometry : " + e.getMessage());
}
}
GeometryClass[] vcImageGeomClasses = vcImageGeometry.getGeometryClasses();
for (int j = 0; j < vcImageGeomClasses.length; j++) {
if (vcImageGeomClasses[j] instanceof ImageSubVolume) {
SampledVolume sampledVol = segmentedImageSampledFieldGeometry.createSampledVolume();
sampledVol.setSpatialId(vcGeomClasses[j].getName());
sampledVol.setDomainType(DOMAIN_TYPE_PREFIX + vcGeomClasses[j].getName());
sampledVol.setSampledValue(((ImageSubVolume) vcImageGeomClasses[j]).getPixelValue());
}
}
// add sampledField to sampledFieldGeometry
SampledField segmentedImageSampledField = sbmlGeometry.createSampledField();
VCImage vcImage = vcImageGeometry.getGeometrySpec().getImage();
segmentedImageSampledField.setSpatialId("SegmentedImageSampledField");
segmentedImageSampledField.setNumSamples1(vcImage.getNumX());
segmentedImageSampledField.setNumSamples2(vcImage.getNumY());
segmentedImageSampledField.setNumSamples3(vcImage.getNumZ());
segmentedImageSampledField.setInterpolationType(InterpolationKind.nearestneighbor);
segmentedImageSampledField.setCompression(CompressionKind.uncompressed);
segmentedImageSampledField.setDataType(DataKind.UINT8);
segmentedImageSampledFieldGeometry.setSampledField(segmentedImageSampledField.getId());
try {
byte[] vcImagePixelsBytes = vcImage.getPixels();
// imageData.setCompression("");
StringBuffer sb = new StringBuffer();
for (int i = 0; i < vcImagePixelsBytes.length; i++) {
int uint8_sample = ((int) vcImagePixelsBytes[i]) & 0xff;
sb.append(uint8_sample + " ");
}
segmentedImageSampledField.setSamplesLength(vcImage.getNumXYZ());
segmentedImageSampledField.setSamples(sb.toString().trim());
} catch (ImageException e) {
e.printStackTrace(System.out);
throw new RuntimeException("Unable to export image from VCell to SBML : " + e.getMessage());
}
}
}
/*
//
// add "DistanceMap" SampledFieldGeometry if there are exactly two subvolumes (else need more fields) and geometry is 3d.
//
if (numSubVols==2 && dimension == 3){
SignedDistanceMap[] distanceMaps = null;
try {
distanceMaps = DistanceMapGenerator.computeDistanceMaps(vcImageGeometry, vcImageGeometry.getGeometrySpec().getImage(), false, false);
} catch (ImageException e) {
e.printStackTrace(System.out);
System.err.println("Unable to export distance map sampled field from VCell to SBML : " + e.getMessage());
// throw new RuntimeException("Unable to export distance map sampled field from VCell to SBML : " + e.getMessage());
// don't want to throw an exception and stop export because distance map geometry couldn't be exported.
// just 'return' from method (since this is the last thing that is being done in this method).
return;
}
//
// the two distanceMaps should be redundant (one is negation of the other) ... so choose first one for field.
//
double[] signedDistances = distanceMaps[0].getSignedDistances();
SampledFieldGeometry distanceMapSampledFieldGeometry = sbmlGeometry.createSampledFieldGeometry();
distanceMapSampledFieldGeometry.setSpatialId(TokenMangler.mangleToSName("DistanceMap_"+vcGeometry.getName()));
SampledField distanceMapSampledField = distanceMapSampledFieldGeometry.createSampledField();
distanceMapSampledField.setSpatialId("DistanceMapSampledField");
distanceMapSampledField.setNumSamples1(distanceMaps[0].getSamplesX().length);
distanceMapSampledField.setNumSamples2(distanceMaps[0].getSamplesY().length);
distanceMapSampledField.setNumSamples3(distanceMaps[0].getSamplesZ().length);
distanceMapSampledField.setDataType("real");
System.err.println("do we need distanceMapSampleField.setDataType()?");
distanceMapSampledField.setInterpolationType("linear");
ImageData distanceMapImageData = distanceMapSampledField.createImageData();
distanceMapImageData.setDataType("int16");
System.err.println("should be:\n distanceMapImageData.setDataType(\"float32\")");
// distanceMapImageData.setCompression("");
double maxAbsValue = 0;
for (int i = 0; i < signedDistances.length; i++) {
maxAbsValue = Math.max(maxAbsValue,Math.abs(signedDistances[i]));
}
if (maxAbsValue==0.0){
throw new RuntimeException("computed distance map all zeros");
}
double scale = (Short.MAX_VALUE-1)/maxAbsValue;
int[] scaledIntegerDistanceMap = new int[signedDistances.length];
for (int i = 0; i < signedDistances.length; i++) {
scaledIntegerDistanceMap[i] = (int)(scale * signedDistances[i]);
}
distanceMapImageData.setSamples(scaledIntegerDistanceMap, signedDistances.length);
System.err.println("should be:\n distanceMapImageData.setSamples((float[])signedDistances,signedDistances.length)");
SampledVolume sampledVol = distanceMapSampledFieldGeometry.createSampledVolume();
sampledVol.setSpatialId(distanceMaps[0].getInsideSubvolumeName());
sampledVol.setDomainType(DOMAIN_TYPE_PREFIX+distanceMaps[0].getInsideSubvolumeName());
sampledVol.setSampledValue(255);
sampledVol = distanceMapSampledFieldGeometry.createSampledVolume();
sampledVol.setSpatialId(distanceMaps[1].getInsideSubvolumeName());
sampledVol.setDomainType(DOMAIN_TYPE_PREFIX+distanceMaps[1].getInsideSubvolumeName());
sampledVol.setSampledValue(1);
}
*/
}
//
// add "SurfaceMesh" ParametricGeometry
//
// if (bAnyAnalyticSubvolumes || bAnyImageSubvolumes || bAnyCSGSubvolumes){
// ParametricGeometry sbmlParametricGeomDefinition = sbmlGeometry.createParametricGeometry();
// sbmlParametricGeomDefinition.setSpatialId(TokenMangler.mangleToSName("SurfaceMesh_"+vcGeometry.getName()));
// xxxx
// }
}
Also used :
Origin(org.vcell.util.Origin)
CompartmentMapping(org.sbml.jsbml.ext.spatial.CompartmentMapping)
Compartment(org.sbml.jsbml.Compartment)
SpatialParameterPlugin(org.sbml.jsbml.ext.spatial.SpatialParameterPlugin)
StructureMappingParameter(cbit.vcell.mapping.StructureMapping.StructureMappingParameter)
AnalyticGeometry(org.sbml.jsbml.ext.spatial.AnalyticGeometry)
ExpressionException(cbit.vcell.parser.ExpressionException)
Boundary(org.sbml.jsbml.ext.spatial.Boundary)
GeometrySpec(cbit.vcell.geometry.GeometrySpec)
DomainType(org.sbml.jsbml.ext.spatial.DomainType)
SampledVolume(org.sbml.jsbml.ext.spatial.SampledVolume)
SubVolume(cbit.vcell.geometry.SubVolume)
ImageSubVolume(cbit.vcell.geometry.ImageSubVolume)
AnalyticSubVolume(cbit.vcell.geometry.AnalyticSubVolume)
GeometryContext(cbit.vcell.mapping.GeometryContext)
SpatialCompartmentPlugin(org.sbml.jsbml.ext.spatial.SpatialCompartmentPlugin)
CoordinateComponent(org.sbml.jsbml.ext.spatial.CoordinateComponent)
SimulationContext(cbit.vcell.mapping.SimulationContext)
SpeciesContext(cbit.vcell.model.SpeciesContext)
GeometryContext(cbit.vcell.mapping.GeometryContext)
VolumeGeometricRegion(cbit.vcell.geometry.surface.VolumeGeometricRegion)
SurfaceGeometricRegion(cbit.vcell.geometry.surface.SurfaceGeometricRegion)
VolumeGeometricRegion(cbit.vcell.geometry.surface.VolumeGeometricRegion)
GeometricRegion(cbit.vcell.geometry.surface.GeometricRegion)
SpatialSymbolReference(org.sbml.jsbml.ext.spatial.SpatialSymbolReference)
AnalyticVolume(org.sbml.jsbml.ext.spatial.AnalyticVolume)
InteriorPoint(org.sbml.jsbml.ext.spatial.InteriorPoint)
SampledField(org.sbml.jsbml.ext.spatial.SampledField)
Domain(org.sbml.jsbml.ext.spatial.Domain)
AnalyticSubVolume(cbit.vcell.geometry.AnalyticSubVolume)
GeometryClass(cbit.vcell.geometry.GeometryClass)
ImageException(cbit.image.ImageException)
GeometrySurfaceDescription(cbit.vcell.geometry.surface.GeometrySurfaceDescription)
Extent(org.vcell.util.Extent)
SurfaceClass(cbit.vcell.geometry.SurfaceClass)
ISize(org.vcell.util.ISize)
CSGeometry(org.sbml.jsbml.ext.spatial.CSGeometry)
RegionInfo(cbit.vcell.geometry.RegionImage.RegionInfo)
VCImage(cbit.image.VCImage)
StructureMapping(cbit.vcell.mapping.StructureMapping)
GeometryThumbnailImageFactoryAWT(cbit.vcell.geometry.GeometryThumbnailImageFactoryAWT)
ASTNode(org.sbml.jsbml.ASTNode)
CSGObject(cbit.vcell.geometry.CSGObject)
VCUnitDefinition(cbit.vcell.units.VCUnitDefinition)
UnitDefinition(org.sbml.jsbml.UnitDefinition)
ImageSubVolume(cbit.vcell.geometry.ImageSubVolume)
SurfaceGeometricRegion(cbit.vcell.geometry.surface.SurfaceGeometricRegion)
SampledFieldGeometry(org.sbml.jsbml.ext.spatial.SampledFieldGeometry)
SpatialModelPlugin(org.sbml.jsbml.ext.spatial.SpatialModelPlugin)
InteriorPoint(org.sbml.jsbml.ext.spatial.InteriorPoint)
XMLStreamException(javax.xml.stream.XMLStreamException)
SbmlException(org.vcell.sbml.SbmlException)
ImageException(cbit.image.ImageException)
SBMLException(org.sbml.jsbml.SBMLException)
ExpressionException(cbit.vcell.parser.ExpressionException)
AdjacentDomains(org.sbml.jsbml.ext.spatial.AdjacentDomains)
Geometry(cbit.vcell.geometry.Geometry)
SampledFieldGeometry(org.sbml.jsbml.ext.spatial.SampledFieldGeometry)
AnalyticGeometry(org.sbml.jsbml.ext.spatial.AnalyticGeometry)
CSGeometry(org.sbml.jsbml.ext.spatial.CSGeometry)
Expression(cbit.vcell.parser.Expression)
Model(cbit.vcell.model.Model)
BioModel(cbit.vcell.biomodel.BioModel)
Aggregations
SbmlException (org.vcell.sbml.SbmlException)11
XMLStreamException (javax.xml.stream.XMLStreamException)9
BioModel (cbit.vcell.biomodel.BioModel)8
SimulationContext (cbit.vcell.mapping.SimulationContext)7
ExpressionException (cbit.vcell.parser.ExpressionException)7
SBMLException (org.sbml.jsbml.SBMLException)7
IOException (java.io.IOException)6
StructureMapping (cbit.vcell.mapping.StructureMapping)5
Expression (cbit.vcell.parser.Expression)5
Model (cbit.vcell.model.Model)4
SpeciesContext (cbit.vcell.model.SpeciesContext)4
Simulation (cbit.vcell.solver.Simulation)4
SimulationJob (cbit.vcell.solver.SimulationJob)4
InteriorPoint (org.sbml.jsbml.ext.spatial.InteriorPoint)4
ImageException (cbit.image.ImageException)3
KineticsParameter (cbit.vcell.model.Kinetics.KineticsParameter)3
ModelUnitSystem (cbit.vcell.model.ModelUnitSystem)3
Structure (cbit.vcell.model.Structure)3
SolverException (cbit.vcell.solver.SolverException)3
ODESolverResultSet (cbit.vcell.solver.ode.ODESolverResultSet)3
