use of cbit.vcell.math.FilamentSubDomain in project vcell by virtualcell.
the class Xmlproducer method getXML.
/**
* This method returns a XML representation of a SubDomain object type.
* Creation date: (3/2/2001 1:13:30 PM)
* @return Element
* @param param cbit.vcell.math.SubDomain
*/
private Element getXML(SubDomain param) throws XmlParseException {
Element e = null;
if (param instanceof CompartmentSubDomain) {
e = getXML((CompartmentSubDomain) param);
} else if (param instanceof FilamentSubDomain) {
e = getXML((FilamentSubDomain) param);
} else if (param instanceof MembraneSubDomain) {
e = getXML((MembraneSubDomain) param);
} else if (param instanceof PointSubDomain) {
e = getXML((PointSubDomain) param);
}
transcribeComments(param, e);
return e;
}
use of cbit.vcell.math.FilamentSubDomain in project vcell by virtualcell.
the class ITextWriter method writeSubDomainsEquationsAsText.
protected void writeSubDomainsEquationsAsText(Section mathDescSection, MathDescription mathDesc) throws DocumentException {
Enumeration<SubDomain> subDomains = mathDesc.getSubDomains();
Section volDomains = mathDescSection.addSection("Volume Domains", mathDescSection.depth() + 1);
Section memDomains = mathDescSection.addSection("Membrane Domains", mathDescSection.depth() + 1);
Section filDomains = mathDescSection.addSection("Filament Domains", mathDescSection.depth() + 1);
while (subDomains.hasMoreElements()) {
Section tempSection = null;
SubDomain subDomain = subDomains.nextElement();
if (subDomain instanceof CompartmentSubDomain) {
tempSection = volDomains.addSection(subDomain.getName(), volDomains.depth() + 1);
} else if (subDomain instanceof MembraneSubDomain) {
tempSection = memDomains.addSection(subDomain.getName(), memDomains.depth() + 1);
} else if (subDomain instanceof FilamentSubDomain) {
tempSection = filDomains.addSection(subDomain.getName(), filDomains.depth() + 1);
}
Enumeration<Equation> equationsList = subDomain.getEquations();
while (equationsList.hasMoreElements()) {
Equation equ = equationsList.nextElement();
writeEquation(tempSection, equ);
}
if (subDomain.getFastSystem() != null) {
writeFastSystem(tempSection, subDomain.getFastSystem());
}
if (subDomain instanceof MembraneSubDomain) {
Enumeration<JumpCondition> jcList = ((MembraneSubDomain) subDomain).getJumpConditions();
while (jcList.hasMoreElements()) {
JumpCondition jc = jcList.nextElement();
writeJumpCondition(tempSection, jc);
}
}
}
if (volDomains.isEmpty()) {
mathDescSection.remove(volDomains);
}
if (memDomains.isEmpty()) {
mathDescSection.remove(memDomains);
}
if (filDomains.isEmpty()) {
mathDescSection.remove(filDomains);
}
}
use of cbit.vcell.math.FilamentSubDomain in project vcell by virtualcell.
the class SimulationData method getVarAndFunctionDataIdentifiers.
/**
* This method was created in VisualAge.
* @return java.lang.String[]
*/
public synchronized DataIdentifier[] getVarAndFunctionDataIdentifiers(OutputContext outputContext) throws IOException, DataAccessException {
// Is this zip format?
boolean bIsChombo = false;
try {
bIsChombo = isChombo();
} catch (FileNotFoundException e) {
e.printStackTrace(System.out);
}
File zipFile1 = getZipFile(bIsChombo, null);
File zipFile2 = getZipFile(bIsChombo, 0);
bZipFormat1 = false;
bZipFormat2 = false;
if (zipFile1.exists()) {
bZipFormat1 = true;
} else if (zipFile2.exists()) {
bZipFormat2 = true;
}
refreshLogFile();
if (!isComsol()) {
try {
refreshMeshFile();
} catch (MathException e) {
e.printStackTrace(System.out);
throw new DataAccessException(e.getMessage());
}
}
if (!isRulesData && !getIsODEData() && !isComsol() && dataFilenames != null) {
// read variables only when I have never read the file since variables don't change
if (dataSetIdentifierList.size() == 0) {
File file = getPDEDataFile(0.0);
DataSet dataSet = getPDEDataSet(file, 0.0);
String[] varNames = dataSet.getDataNames();
int[] varTypeInts = dataSet.getVariableTypeIntegers();
if (varNames == null) {
return null;
}
dataSetIdentifierList.clear();
for (int i = 0; i < varNames.length; i++) {
VariableType varType = null;
try {
varType = VariableType.getVariableTypeFromInteger(varTypeInts[i]);
} catch (IllegalArgumentException e) {
if (LG.isEnabledFor(Level.WARN)) {
LG.warn("Exception typing " + varNames[i] + " has unsupported type " + varTypeInts[i] + ": " + e.getMessage());
}
varType = SimulationData.getVariableTypeFromLength(mesh, dataSet.getDataLength(varNames[i]));
}
Domain domain = Variable.getDomainFromCombinedIdentifier(varNames[i]);
String varName = Variable.getNameFromCombinedIdentifier(varNames[i]);
dataSetIdentifierList.addElement(new DataSetIdentifier(varName, varType, domain));
}
refreshDataProcessingOutputInfo(outputContext);
if (dataProcessingOutputInfo != null) {
for (int i = 0; i < dataProcessingOutputInfo.getVariableNames().length; i++) {
if (dataProcessingOutputInfo.getPostProcessDataType(dataProcessingOutputInfo.getVariableNames()[i]).equals(DataProcessingOutputInfo.PostProcessDataType.image)) {
dataSetIdentifierList.addElement(new DataSetIdentifier(dataProcessingOutputInfo.getVariableNames()[i], VariableType.POSTPROCESSING, null));
}
}
}
}
// always read functions file since functions might change
getFunctionDataIdentifiers(outputContext);
}
if ((isRulesData || getIsODEData()) && dataSetIdentifierList.size() == 0) {
ODEDataBlock odeDataBlock = getODEDataBlock();
if (odeDataBlock == null) {
throw new DataAccessException("Results are not availabe yet. Please try again later.");
}
ODESimData odeSimData = odeDataBlock.getODESimData();
int colCount = odeSimData.getColumnDescriptionsCount();
// assume index=0 is time "t"
int DATA_OFFSET = 1;
dataSetIdentifierList.clear();
for (int i = 0; i < (colCount - DATA_OFFSET); i++) {
String varName = odeSimData.getColumnDescriptions(i + DATA_OFFSET).getDisplayName();
// TODO domain
Domain domain = null;
dataSetIdentifierList.addElement(new DataSetIdentifier(varName, VariableType.NONSPATIAL, domain));
}
}
if (isComsol() && dataSetIdentifierList.size() == 0) {
ComsolSimFiles comsolSimFiles = getComsolSimFiles();
if (comsolSimFiles.simTaskXMLFile != null) {
try {
String xmlString = FileUtils.readFileToString(comsolSimFiles.simTaskXMLFile);
SimulationTask simTask = XmlHelper.XMLToSimTask(xmlString);
Enumeration<Variable> variablesEnum = simTask.getSimulation().getMathDescription().getVariables();
while (variablesEnum.hasMoreElements()) {
Variable var = variablesEnum.nextElement();
if (var instanceof VolVariable) {
dataSetIdentifierList.addElement(new DataSetIdentifier(var.getName(), VariableType.VOLUME, var.getDomain()));
} else if (var instanceof MemVariable) {
dataSetIdentifierList.addElement(new DataSetIdentifier(var.getName(), VariableType.MEMBRANE, var.getDomain()));
} else if (var instanceof Function) {
VariableType varType = VariableType.UNKNOWN;
if (var.getDomain() != null && var.getDomain().getName() != null) {
SubDomain subDomain = simTask.getSimulation().getMathDescription().getSubDomain(var.getDomain().getName());
if (subDomain instanceof CompartmentSubDomain) {
varType = VariableType.VOLUME;
} else if (subDomain instanceof MembraneSubDomain) {
varType = VariableType.MEMBRANE;
} else if (subDomain instanceof FilamentSubDomain) {
throw new RuntimeException("filament subdomains not supported");
} else if (subDomain instanceof PointSubDomain) {
varType = VariableType.POINT_VARIABLE;
}
}
dataSetIdentifierList.addElement(new DataSetIdentifier(var.getName(), varType, var.getDomain()));
} else if (var instanceof Constant) {
System.out.println("ignoring Constant " + var.getName());
} else if (var instanceof InsideVariable) {
System.out.println("ignoring InsideVariable " + var.getName());
} else if (var instanceof OutsideVariable) {
System.out.println("ignoring OutsideVariable " + var.getName());
} else {
throw new RuntimeException("unexpected variable " + var.getName() + " of type " + var.getClass().getName());
}
}
} catch (XmlParseException | ExpressionException e) {
e.printStackTrace();
throw new RuntimeException("failed to read sim task file, msg: " + e.getMessage(), e);
}
}
}
DataIdentifier[] dis = new DataIdentifier[dataSetIdentifierList.size()];
for (int i = 0; i < dataSetIdentifierList.size(); i++) {
DataSetIdentifier dsi = (DataSetIdentifier) dataSetIdentifierList.elementAt(i);
String displayName = dsi.getName();
if (dsi.isFunction()) {
AnnotatedFunction f = null;
for (int j = 0; j < annotatedFunctionList.size(); j++) {
AnnotatedFunction function = (AnnotatedFunction) annotatedFunctionList.elementAt(j);
if (function.getName().equals(dsi.getName())) {
f = function;
break;
}
}
if (f != null) {
displayName = f.getDisplayName();
}
}
dis[i] = new DataIdentifier(dsi.getName(), dsi.getVariableType(), dsi.getDomain(), dsi.isFunction(), displayName);
}
return dis;
}
use of cbit.vcell.math.FilamentSubDomain in project vcell by virtualcell.
the class XmlReader method getFilamentSubDomain.
/**
* This method returns a FilamentSubDomain object from a XMl element.
* Creation date: (5/18/2001 4:27:22 PM)
* @return cbit.vcell.math.FilamentSubDomain
* @param param org.jdom.Element
* @exception cbit.vcell.xml.XmlParseException The exception description.
*/
private FilamentSubDomain getFilamentSubDomain(Element param, MathDescription mathDesc) throws XmlParseException {
// get name
String name = unMangle(param.getAttributeValue(XMLTags.NameAttrTag));
// get outside Compartment ref
String outsideName = unMangle(param.getAttributeValue(XMLTags.OutsideCompartmentTag));
CompartmentSubDomain outsideRef = (CompartmentSubDomain) mathDesc.getCompartmentSubDomain(outsideName);
if (outsideRef == null) {
throw new XmlParseException("The reference to the CompartmentSubDomain " + outsideName + ", could not be resolved!");
}
// *** create new filamentSubDomain object ***
FilamentSubDomain filDomain = new FilamentSubDomain(name, outsideRef);
// add OdeEquations
Iterator<Element> iterator = param.getChildren(XMLTags.OdeEquationTag, vcNamespace).iterator();
while (iterator.hasNext()) {
Element tempElement = (Element) iterator.next();
try {
filDomain.addEquation(getOdeEquation(tempElement, mathDesc));
} catch (MathException e) {
e.printStackTrace(System.out);
throw new XmlParseException("A MathException was fired when adding an OdeEquation to the FilamentSubDomain " + name, e);
}
}
// Add the FastSytem
filDomain.setFastSystem(getFastSystem(param.getChild(XMLTags.FastSystemTag, vcNamespace), mathDesc));
return filDomain;
}
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