use of cbit.vcell.math.VolumeRegionVariable in project vcell by virtualcell.
the class MathOverridesPanel method jMenuItemPaste_ActionPerformed.
/**
* Comment
*/
private void jMenuItemPaste_ActionPerformed(java.awt.event.ActionEvent actionEvent) {
java.util.Vector<String> pasteDescriptionsV = new java.util.Vector<String>();
java.util.Vector<Expression> newConstantsV = new java.util.Vector<Expression>();
java.util.Vector<String> changedParameterNamesV = new java.util.Vector<String>();
try {
if (actionEvent.getSource().equals(getJMenuItemPaste()) || actionEvent.getSource().equals(getJMenuItemPasteAll())) {
int[] rows = null;
if (actionEvent.getSource() == getJMenuItemPasteAll()) {
rows = new int[getJTableFixed().getRowCount()];
for (int i = 0; i < rows.length; i += 1) {
rows[i] = i;
}
} else {
rows = getJTableFixed().getSelectedRows();
}
Object pasteThis = VCellTransferable.getFromClipboard(VCellTransferable.OBJECT_FLAVOR);
for (int i = 0; i < rows.length; i += 1) {
if (pasteThis instanceof VCellTransferable.ResolvedValuesSelection) {
VCellTransferable.ResolvedValuesSelection rvs = (VCellTransferable.ResolvedValuesSelection) pasteThis;
for (int j = 0; j < rvs.getPrimarySymbolTableEntries().length; j += 1) {
Constant pastedConstant = null;
if (rvs.getPrimarySymbolTableEntries()[j] instanceof Constant) {
pastedConstant = (Constant) rvs.getPrimarySymbolTableEntries()[j];
} else if (rvs.getAlternateSymbolTableEntries() != null && rvs.getAlternateSymbolTableEntries()[j] instanceof Constant) {
pastedConstant = (Constant) rvs.getAlternateSymbolTableEntries()[j];
}
//
if (pastedConstant == null && (rvs.getPrimarySymbolTableEntries()[j] instanceof Function) || (rvs.getPrimarySymbolTableEntries()[j] instanceof VolVariable) || (rvs.getPrimarySymbolTableEntries()[j] instanceof VolumeRegionVariable) || (rvs.getPrimarySymbolTableEntries()[j] instanceof MemVariable) || (rvs.getPrimarySymbolTableEntries()[j] instanceof MembraneRegionVariable)) {
MathDescription mathDescription = getMathOverrides().getSimulation().getMathDescription();
Enumeration<Constant> constants = mathDescription.getConstants();
while (constants.hasMoreElements()) {
Constant constant = constants.nextElement();
if (constant.getName().startsWith(rvs.getPrimarySymbolTableEntries()[j].getName() + DiffEquMathMapping.MATH_FUNC_SUFFIX_SPECIES_INIT_CONC_UNIT_PREFIX)) {
pastedConstant = new Constant(constant.getName(), rvs.getExpressionValues()[j]);
}
}
}
//
// find row of math overrides table with the same name as the pastedConstant and propose to change that override to the pasted value
//
String rowName = (String) getJTableFixed().getValueAt(rows[i], MathOverridesTableModel.COLUMN_PARAMETER);
if (pastedConstant != null && pastedConstant.getName().equals(rowName)) {
changedParameterNamesV.add(rowName);
newConstantsV.add(rvs.getExpressionValues()[j]);
String originalValueDescription = null;
if (getMathOverrides().getConstantArraySpec(rowName) != null) {
originalValueDescription = getMathOverrides().getConstantArraySpec(rowName).toString();
} else if (getMathOverrides().getActualExpression(rowName, 0) != null) {
originalValueDescription = getMathOverrides().getActualExpression(rowName, 0).infix();
} else {
throw new Exception("MathOverridesPanel can't find value for '" + rowName + "'");
}
pasteDescriptionsV.add(VCellCopyPasteHelper.formatPasteList(rowName, pastedConstant.getName(), originalValueDescription, rvs.getExpressionValues()[j].infix() + ""));
}
}
}
}
}
} catch (Throwable e) {
PopupGenerator.showErrorDialog(this, "Paste failed during pre-check (no changes made).\n" + e.getClass().getName() + " " + e.getMessage(), e);
return;
}
// Do paste
try {
if (pasteDescriptionsV.size() > 0) {
String[] pasteDescriptionArr = new String[pasteDescriptionsV.size()];
pasteDescriptionsV.copyInto(pasteDescriptionArr);
String[] changedParameterNamesArr = new String[changedParameterNamesV.size()];
changedParameterNamesV.copyInto(changedParameterNamesArr);
VCellCopyPasteHelper.chooseApplyPaste(this, pasteDescriptionArr, getMathOverrides(), changedParameterNamesArr, newConstantsV);
} else {
PopupGenerator.showInfoDialog(this, "No paste items match the destination (no changes made).");
}
} catch (Throwable e) {
PopupGenerator.showErrorDialog(this, "Paste Error\n" + e.getClass().getName() + " " + e.getMessage(), e);
}
}
use of cbit.vcell.math.VolumeRegionVariable in project vcell by virtualcell.
the class XmlReader method getVolumeRegionEquation.
/**
* This method returns a VolumeRegionEquation from a XML Element.
* Creation date: (5/17/2001 3:52:40 PM)
* @return cbit.vcell.math.VolumeRegionEquation
* @param param org.jdom.Element
* @exception cbit.vcell.xml.XmlParseException The exception description.
*/
private VolumeRegionEquation getVolumeRegionEquation(Element param, MathDescription mathDesc) throws XmlParseException {
// get attributes
String varname = unMangle(param.getAttributeValue(XMLTags.NameAttrTag));
// try a VolumeRegionVariable
VolumeRegionVariable varref = (VolumeRegionVariable) mathDesc.getVariable(varname);
if (varref == null) {
throw new XmlParseException("The reference to the VolumeRegion variable " + varname + " could not be resolved!");
}
// get Initial condition
String temp = param.getChildText(XMLTags.InitialTag, vcNamespace);
Expression exp = unMangleExpression(temp);
// ** Create the Equation **
VolumeRegionEquation volRegEq = new VolumeRegionEquation(varref, exp);
// set the Uniform Rate
temp = param.getChildText(XMLTags.UniformRateTag, vcNamespace);
exp = unMangleExpression(temp);
volRegEq.setUniformRateExpression(exp);
// Set the Volume Rate
temp = param.getChildText(XMLTags.VolumeRateTag, vcNamespace);
exp = unMangleExpression(temp);
volRegEq.setVolumeRateExpression(exp);
return volRegEq;
}
use of cbit.vcell.math.VolumeRegionVariable in project vcell by virtualcell.
the class XmlReader method getComputeCentroid.
private ComputeCentroidComponentEquation getComputeCentroid(Element param, MathDescription mathDesc) throws XmlParseException {
// get attributes
String varname = unMangle(param.getAttributeValue(XMLTags.NameAttrTag));
// find reference in the dictionnary
// try a MembraneRegionVariable
VolumeRegionVariable varref = (VolumeRegionVariable) mathDesc.getVariable(varname);
if (varref == null) {
throw new XmlParseException("The reference to the Volume Region variable " + varname + " could not be resolved!");
}
CentroidComponent normalComponent = null;
String normalComponentString = param.getAttributeValue(XMLTags.ComputeCentroidComponentAttrTag);
if (normalComponentString.equals(XMLTags.ComputeCentroidComponentAttrTagValue_X)) {
normalComponent = CentroidComponent.X;
} else if (normalComponentString.equals(XMLTags.ComputeCentroidComponentAttrTagValue_Y)) {
normalComponent = CentroidComponent.Y;
} else if (normalComponentString.equals(XMLTags.ComputeCentroidComponentAttrTagValue_Z)) {
normalComponent = CentroidComponent.Z;
}
ComputeCentroidComponentEquation centroid = new ComputeCentroidComponentEquation(varref, normalComponent);
return centroid;
}
use of cbit.vcell.math.VolumeRegionVariable in project vcell by virtualcell.
the class MathTestingUtilities method substituteWithExactSolution.
/**
* Insert the method's description here.
* Creation date: (1/24/2003 10:18:14 AM)
* @return cbit.vcell.parser.Expression
* @param origExp cbit.vcell.parser.Expression
* @param subDomain cbit.vcell.math.SubDomain
*/
private static Expression substituteWithExactSolution(Expression origExp, CompartmentSubDomain subDomain, MathDescription exactMathDesc) throws ExpressionException {
Expression substitutedExp = new Expression(origExp);
substitutedExp.bindExpression(exactMathDesc);
substitutedExp = MathUtilities.substituteFunctions(substitutedExp, exactMathDesc);
substitutedExp.bindExpression(null);
substitutedExp = substitutedExp.flatten();
substitutedExp.bindExpression(exactMathDesc);
String[] symbols = substitutedExp.getSymbols();
for (int i = 0; i < symbols.length; i++) {
Variable var = (Variable) substitutedExp.getSymbolBinding(symbols[i]);
if (var instanceof VolVariable) {
String exactVarName = var.getName() + "_" + subDomain.getName() + "_exact";
substitutedExp.substituteInPlace(new Expression(var.getName()), new Expression(exactVarName));
} else if (var instanceof VolumeRegionVariable || var instanceof MemVariable || var instanceof MembraneRegionVariable || var instanceof FilamentVariable || var instanceof FilamentRegionVariable) {
throw new RuntimeException("variable substitution not yet implemented for Variable type " + var.getClass().getName() + "(" + var.getName() + ")");
}
}
substitutedExp.bindExpression(null);
return substitutedExp;
}
use of cbit.vcell.math.VolumeRegionVariable in project vcell by virtualcell.
the class FiniteVolumeFileWriter method writeVariables.
/**
*# Variables : type name unit time_dependent_flag advection_flag solve_whole_mesh_flag solve_regions
*VARIABLE_BEGIN
*VOLUME_ODE rB uM
*VOLUME_PDE rf uM false false
*VOLUME_PDE r uM false false
*VOLUME_ODE rfB uM
*VARIABLE_END
* @throws MathException
* @throws ExpressionException
* @throws IOException
*/
private void writeVariables() throws MathException, ExpressionException, IOException {
SimulationSymbolTable simSymbolTable = simTask.getSimulationJob().getSimulationSymbolTable();
printWriter.println("# Variables : type name domain time_dependent_flag advection_flag grad_flag solve_whole_mesh_flag solve_regions");
printWriter.println(FVInputFileKeyword.VARIABLE_BEGIN);
MathDescription mathDesc = simSymbolTable.getSimulation().getMathDescription();
Variable[] vars = simSymbolTable.getVariables();
ArrayList<RandomVariable> rvList = new ArrayList<RandomVariable>();
for (int i = 0; i < vars.length; i++) {
String varName = vars[i].getName();
String domainName = vars[i].getDomain() == null ? null : vars[i].getDomain().getName();
if (vars[i] instanceof VolumeRandomVariable || vars[i] instanceof MembraneRandomVariable) {
rvList.add((RandomVariable) vars[i]);
} else if (vars[i] instanceof VolVariable) {
if (bChomboSolver && domainName == null) {
throw new MathException(simTask.getSimulation().getSolverTaskDescription().getSolverDescription().getDisplayLabel() + " requires that every variable is defined in a single domain");
}
VolVariable volVar = (VolVariable) vars[i];
if (mathDesc.isPDE(volVar)) {
boolean hasTimeVaryingDiffusionOrAdvection = simSymbolTable.hasTimeVaryingDiffusionOrAdvection(volVar);
final boolean hasVelocity = mathDesc.hasVelocity(volVar);
final boolean hasGradient = mathDesc.hasGradient(volVar);
if (mathDesc.isPdeSteady(volVar)) {
printWriter.print("VOLUME_PDE_STEADY ");
} else {
printWriter.print("VOLUME_PDE ");
}
printWriter.print(varName + " " + domainName + " " + hasTimeVaryingDiffusionOrAdvection + " " + hasVelocity + " " + hasGradient);
} else {
printWriter.print("VOLUME_ODE " + varName + " " + domainName);
}
if (domainName == null) {
Vector<SubDomain> listOfSubDomains = new Vector<SubDomain>();
int totalNumCompartments = 0;
Enumeration<SubDomain> subDomainEnum = mathDesc.getSubDomains();
while (subDomainEnum.hasMoreElements()) {
SubDomain subDomain = subDomainEnum.nextElement();
if (subDomain instanceof CompartmentSubDomain) {
CompartmentSubDomain compartmentSubDomain = (CompartmentSubDomain) subDomain;
totalNumCompartments++;
Equation varEquation = subDomain.getEquation(vars[i]);
if (varEquation != null) {
if (!(varEquation instanceof PdeEquation) || !((PdeEquation) varEquation).isDummy(simSymbolTable, compartmentSubDomain)) {
listOfSubDomains.add(compartmentSubDomain);
}
}
}
}
if ((totalNumCompartments == listOfSubDomains.size()) || (listOfSubDomains.size() == 0 && simTask.getSimulation().getSolverTaskDescription().getSolverDescription().equals(SolverDescription.SundialsPDE))) {
printWriter.print(" true");
} else {
printWriter.print(" false");
for (int j = 0; j < listOfSubDomains.size(); j++) {
CompartmentSubDomain compartmentSubDomain = (CompartmentSubDomain) listOfSubDomains.elementAt(j);
printWriter.print(" " + compartmentSubDomain.getName());
}
}
printWriter.println();
} else {
printWriter.println(" false " + domainName);
}
} else if (vars[i] instanceof VolumeParticleVariable) {
printWriter.println(FVInputFileKeyword.VOLUME_PARTICLE + " " + varName + " " + domainName);
} else if (vars[i] instanceof MembraneParticleVariable) {
printWriter.println(FVInputFileKeyword.MEMBRANE_PARTICLE + " " + varName + " " + domainName);
} else if (vars[i] instanceof VolumeRegionVariable) {
printWriter.println("VOLUME_REGION " + varName + " " + domainName);
} else if (vars[i] instanceof MemVariable) {
if (bChomboSolver && domainName == null) {
throw new MathException(simTask.getSimulation().getSolverTaskDescription().getSolverDescription().getDisplayLabel() + " requires that every variable is defined in a single domain");
}
MemVariable memVar = (MemVariable) vars[i];
if (mathDesc.isPDE(memVar)) {
printWriter.println("MEMBRANE_PDE " + varName + " " + domainName + " " + simSymbolTable.hasTimeVaryingDiffusionOrAdvection(memVar));
} else {
printWriter.println("MEMBRANE_ODE " + varName + " " + domainName);
}
} else if (vars[i] instanceof MembraneRegionVariable) {
printWriter.println("MEMBRANE_REGION " + varName + " " + domainName);
} else if (vars[i] instanceof FilamentVariable) {
throw new RuntimeException("Filament application not supported yet");
}
}
int numRandomVariables = rvList.size();
if (numRandomVariables > 0) {
ISize samplingSize = simTask.getSimulation().getMeshSpecification().getSamplingSize();
String[] varNameArr = new String[numRandomVariables];
VariableType[] varTypeArr = new VariableType[numRandomVariables];
double[][] dataArr = new double[numRandomVariables][];
for (int i = 0; i < numRandomVariables; i++) {
RandomVariable rv = rvList.get(i);
varNameArr[i] = rv.getName();
int numRandomNumbers = 0;
if (rv instanceof VolumeRandomVariable) {
printWriter.print("VOLUME_RANDOM");
varTypeArr[i] = VariableType.VOLUME;
numRandomNumbers = samplingSize.getXYZ();
} else if (rv instanceof MembraneRandomVariable) {
printWriter.print("MEMBRANE_RANDOM");
varTypeArr[i] = VariableType.MEMBRANE;
numRandomNumbers = resampledGeometry.getGeometrySurfaceDescription().getSurfaceCollection().getTotalPolygonCount();
} else {
throw new RuntimeException("Unknown RandomVariable type");
}
printWriter.println(" " + varNameArr[i]);
dataArr[i] = generateRandomNumbers(rv, numRandomNumbers);
}
File rvFile = new File(workingDirectory, simTask.getSimulationJobID() + RANDOM_VARIABLE_FILE_EXTENSION);
DataSet.writeNew(rvFile, varNameArr, varTypeArr, samplingSize, dataArr);
}
printWriter.println(FVInputFileKeyword.VARIABLE_END);
printWriter.println();
}
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