Example 1 with SimpleSymbolTable
use of cbit.vcell.parser.SimpleSymbolTable in project vcell by virtualcell.
the class RefinementLevel method setRoiExpression.
public void setRoiExpression(String roiExp) throws ExpressionException {
Expression exp = null;
if (roiExp != null) {
roiExp = roiExp.trim();
if (roiExp.length() > 0) {
exp = new Expression(roiExp);
exp.bindExpression(new SimpleSymbolTable(new String[] { "x", "y", "z" }));
}
}
this.roiExpression = exp;
}
Also used :
SimpleSymbolTable(cbit.vcell.parser.SimpleSymbolTable)
Expression(cbit.vcell.parser.Expression)
Example 2 with SimpleSymbolTable
use of cbit.vcell.parser.SimpleSymbolTable in project vcell by virtualcell.
the class CurveFitting method bindExpressionToParametersAndTime.
private static void bindExpressionToParametersAndTime(Expression modelExp, Parameter[] parameters) throws ExpressionBindingException {
ArrayList<String> symbols = new ArrayList<String>();
symbols.add("t");
for (Parameter p : parameters) {
symbols.add(p.getName());
}
modelExp.bindExpression(new SimpleSymbolTable(symbols.toArray(new String[0])));
}
Also used :
SimpleSymbolTable(cbit.vcell.parser.SimpleSymbolTable)
ArrayList(java.util.ArrayList)
Parameter(cbit.vcell.opt.Parameter)
Example 3 with SimpleSymbolTable
use of cbit.vcell.parser.SimpleSymbolTable in project vcell by virtualcell.
the class MathDescription method compareEquivalentCanonicalMath.
/**
* This method was created in VisualAge.
* @return boolean
* @param mathDesc cbit.vcell.math.MathDescription
*/
private MathCompareResults compareEquivalentCanonicalMath(MathDescription newMathDesc) {
try {
MathDescription oldMathDesc = this;
if (oldMathDesc.compareEqual(newMathDesc)) {
return new MathCompareResults(Decision.MathEquivalent_FLATTENED);
} else {
// if (!bSilent) System.out.println("------NATIVE MATHS ARE DIFFERENT----------------------");
if (!oldMathDesc.postProcessingBlock.compareEqual(newMathDesc.postProcessingBlock)) {
return new MathCompareResults(Decision.MathDifferent_DIFFERENT_PostProcessingBlock, "Post processing block does not match");
}
Variable[] oldVars = (Variable[]) BeanUtils.getArray(oldMathDesc.getVariables(), Variable.class);
Variable[] newVars = (Variable[]) BeanUtils.getArray(newMathDesc.getVariables(), Variable.class);
if (oldVars.length != newVars.length) {
//
return new MathCompareResults(Decision.MathDifferent_DIFFERENT_NUMBER_OF_VARIABLES);
}
if (!Compare.isEqual(oldVars, newVars)) {
//
// variables are not strictly equal - must try to ignore domains and try again
//
boolean bIgnoreMissingDomains = true;
for (Variable oldVar : oldVars) {
boolean bFound = false;
for (Variable newVar : newVars) {
if (oldVar.compareEqual(newVar, bIgnoreMissingDomains)) {
bFound = true;
break;
}
}
if (!bFound) {
//
return new MathCompareResults(Decision.MathDifferent_VARIABLES_DONT_MATCH, "variable '" + oldVar.getQualifiedName() + "' not matched");
}
}
for (Variable newVar : newVars) {
boolean bFound = false;
for (Variable oldVar : oldVars) {
if (newVar.compareEqual(oldVar, bIgnoreMissingDomains)) {
bFound = true;
break;
}
}
if (!bFound) {
//
return new MathCompareResults(Decision.MathDifferent_VARIABLES_DONT_MATCH, "variable '" + newVar.getQualifiedName() + "' not matched");
}
}
}
//
// go through the list of SubDomains, and compare equations one by one and "correct" new one if possible
//
SubDomain[] subDomainsOld = (SubDomain[]) BeanUtils.getArray(oldMathDesc.getSubDomains(), SubDomain.class);
SubDomain[] subDomainsNew = (SubDomain[]) BeanUtils.getArray(newMathDesc.getSubDomains(), SubDomain.class);
if (subDomainsOld.length != subDomainsNew.length) {
return new MathCompareResults(Decision.MathDifferent_DIFFERENT_NUMBER_OF_SUBDOMAINS);
}
for (int i = 0; i < subDomainsOld.length; i++) {
// compare boundary type
if (getGeometry().getDimension() > 0) {
if (subDomainsOld[i] instanceof CompartmentSubDomain && subDomainsNew[i] instanceof CompartmentSubDomain) {
CompartmentSubDomain csdOld = (CompartmentSubDomain) subDomainsOld[i];
CompartmentSubDomain csdNew = (CompartmentSubDomain) subDomainsNew[i];
if (!Compare.isEqualOrNull(csdOld.getBoundaryConditionXm(), csdNew.getBoundaryConditionXm()) || !Compare.isEqualOrNull(csdOld.getBoundaryConditionXp(), csdNew.getBoundaryConditionXp()) || !Compare.isEqualOrNull(csdOld.getBoundaryConditionYm(), csdNew.getBoundaryConditionYm()) || !Compare.isEqualOrNull(csdOld.getBoundaryConditionYp(), csdNew.getBoundaryConditionYp()) || !Compare.isEqualOrNull(csdOld.getBoundaryConditionZm(), csdNew.getBoundaryConditionZm()) || !Compare.isEqualOrNull(csdOld.getBoundaryConditionZp(), csdNew.getBoundaryConditionZp())) {
return new MathCompareResults(Decision.MathDifferent_DIFFERENT_BC_TYPE);
}
} else if (subDomainsOld[i] instanceof MembraneSubDomain && subDomainsNew[i] instanceof MembraneSubDomain) {
MembraneSubDomain msdOld = (MembraneSubDomain) subDomainsOld[i];
MembraneSubDomain msdNew = (MembraneSubDomain) subDomainsNew[i];
if (!Compare.isEqualOrNull(msdOld.getBoundaryConditionXm(), msdNew.getBoundaryConditionXm()) || !Compare.isEqualOrNull(msdOld.getBoundaryConditionXp(), msdNew.getBoundaryConditionXp()) || !Compare.isEqualOrNull(msdOld.getBoundaryConditionYm(), msdNew.getBoundaryConditionYm()) || !Compare.isEqualOrNull(msdOld.getBoundaryConditionYp(), msdNew.getBoundaryConditionYp()) || !Compare.isEqualOrNull(msdOld.getBoundaryConditionZm(), msdNew.getBoundaryConditionZm()) || !Compare.isEqualOrNull(msdOld.getBoundaryConditionZp(), msdNew.getBoundaryConditionZp())) {
return new MathCompareResults(Decision.MathDifferent_DIFFERENT_BC_TYPE);
}
if (!compareUpdate(msdNew.getVelocityX(), msdOld.getVelocityX(), msdNew::setVelocityX)) {
return new MathCompareResults(Decision.MathDifferent_DIFFERENT_VELOCITY, "x");
}
if (!compareUpdate(msdNew.getVelocityY(), msdOld.getVelocityY(), msdNew::setVelocityY)) {
return new MathCompareResults(Decision.MathDifferent_DIFFERENT_VELOCITY, "y");
}
}
}
for (int j = 0; j < oldVars.length; j++) {
//
// test equation for this subdomain and variable
//
{
Equation oldEqu = subDomainsOld[i].getEquation(oldVars[j]);
Equation newEqu = subDomainsNew[i].getEquation(oldVars[j]);
if (!Compare.isEqualOrNull(oldEqu, newEqu)) {
boolean bFoundDifference = false;
//
if (oldEqu == null) {
//
return new MathCompareResults(Decision.MathDifferent_EQUATION_ADDED, "only one mathDescription had equation for '" + oldVars[j].getQualifiedName() + "' in SubDomain '" + subDomainsOld[i].getName() + "'");
}
if (newEqu == null) {
//
return new MathCompareResults(Decision.MathDifferent_EQUATION_REMOVED, "only one mathDescription had equation for '" + oldVars[j].getQualifiedName() + "' in SubDomain '" + subDomainsOld[i].getName() + "'");
}
ArrayList<Expression> oldExps = new ArrayList<Expression>();
ArrayList<Expression> newExps = new ArrayList<Expression>();
boolean bOdePdeMismatch = false;
if (oldEqu instanceof PdeEquation && newEqu instanceof OdeEquation && oldEqu.getExpressions(newMathDesc).size() == 3 && ((PdeEquation) oldEqu).getDiffusionExpression().isZero()) {
oldExps.add(oldEqu.getRateExpression());
oldExps.add(oldEqu.getInitialExpression());
newExps.add(newEqu.getRateExpression());
newExps.add(newEqu.getInitialExpression());
bOdePdeMismatch = true;
} else if (oldEqu instanceof OdeEquation && newEqu instanceof PdeEquation && newEqu.getExpressions(newMathDesc).size() == 3 && ((PdeEquation) newEqu).getDiffusionExpression().isZero()) {
oldExps.add(oldEqu.getRateExpression());
oldExps.add(oldEqu.getInitialExpression());
newExps.add(newEqu.getRateExpression());
newExps.add(newEqu.getInitialExpression());
bOdePdeMismatch = true;
} else {
oldExps.addAll(oldEqu.getExpressions(oldMathDesc));
newExps.addAll(newEqu.getExpressions(newMathDesc));
}
if (oldExps.size() != newExps.size()) {
return new MathCompareResults(Decision.MathDifferent_DIFFERENT_NUMBER_OF_EXPRESSIONS, "equations have different number of expressions");
}
for (int k = 0; k < oldExps.size(); k++) {
if (!oldExps.get(k).compareEqual(newExps.get(k))) {
bFoundDifference = true;
if (!ExpressionUtils.functionallyEquivalent(oldExps.get(k), newExps.get(k))) {
//
return new MathCompareResults(Decision.MathDifferent_DIFFERENT_EXPRESSION, "expressions are different Old: '" + oldExps.get(k) + "'\n" + "expressions are different New: '" + newExps.get(k) + "'");
} else {
// if (!bSilent) System.out.println("expressions are equivalent Old: '"+oldExps[k]+"'\n"+
// "expressions are equivalent New: '"+newExps[k]+"'");
}
}
}
if (!oldEqu.getVariable().compareEqual(newEqu.getVariable())) {
bFoundDifference = true;
boolean bIgnoreMissingDomains = true;
if (!oldEqu.getVariable().compareEqual(newEqu.getVariable(), bIgnoreMissingDomains)) {
return new MathCompareResults(Decision.MathDifferent_DIFFERENT_VARIABLE_IN_EQUATION, "var1='" + oldEqu.getVariable().getQualifiedName() + "', var2='" + newEqu.getVariable().getQualifiedName() + "'");
}
}
//
if (bFoundDifference || bOdePdeMismatch) {
subDomainsNew[i].replaceEquation(oldEqu);
} else {
//
return new MathCompareResults(Decision.MathDifferent_UNKNOWN_DIFFERENCE_IN_EQUATION, "couldn't find problem with equation for " + oldVars[j].getName() + " in compartment " + subDomainsOld[i].getName());
}
}
}
{
ParticleProperties oldPP = subDomainsOld[i].getParticleProperties(oldVars[j]);
ParticleProperties newPP = subDomainsNew[i].getParticleProperties(oldVars[j]);
if (!Compare.isEqualOrNull(oldPP, newPP)) {
return new MathCompareResults(Decision.MathDifferent_DIFFERENT_PARTICLE_PROPERTIES);
}
}
//
if (subDomainsOld[i] instanceof MembraneSubDomain && oldVars[j] instanceof VolVariable) {
JumpCondition oldJumpCondition = ((MembraneSubDomain) subDomainsOld[i]).getJumpCondition((VolVariable) oldVars[j]);
JumpCondition newJumpCondition = ((MembraneSubDomain) subDomainsNew[i]).getJumpCondition((VolVariable) oldVars[j]);
if (!Compare.isEqualOrNull(oldJumpCondition, newJumpCondition)) {
boolean bFoundDifference = false;
//
if (oldJumpCondition == null) {
//
return new MathCompareResults(Decision.MathDifferent_EQUATION_ADDED);
}
if (newJumpCondition == null) {
//
return new MathCompareResults(Decision.MathDifferent_EQUATION_REMOVED);
}
final Vector<Expression> oldJC = oldJumpCondition.getExpressions(oldMathDesc);
Expression[] oldExps = oldJC.toArray(new Expression[oldJC.size()]);
final Vector<Expression> newJC = newJumpCondition.getExpressions(newMathDesc);
Expression[] newExps = newJC.toArray(new Expression[newJC.size()]);
if (oldExps.length != newExps.length) {
return new MathCompareResults(Decision.MathDifferent_DIFFERENT_NUMBER_OF_EXPRESSIONS, "jump condition has different number of expressions");
}
for (int k = 0; k < oldExps.length; k++) {
if (!oldExps[k].compareEqual(newExps[k])) {
bFoundDifference = true;
if (!ExpressionUtils.functionallyEquivalent(oldExps[k], newExps[k])) {
//
return new MathCompareResults(Decision.MathDifferent_DIFFERENT_EXPRESSION, "expressions are different Old: '" + oldExps[k] + "'\n" + "expressions are different New: '" + newExps[k] + "'");
} else {
// if (!bSilent) System.out.println("expressions are equivalent Old: '"+oldExps[k]+"'\n"+
// "expressions are equivalent New: '"+newExps[k]+"'");
}
}
}
//
if (bFoundDifference) {
((MembraneSubDomain) subDomainsNew[i]).replaceJumpCondition(oldJumpCondition);
} else {
//
return new MathCompareResults(Decision.MathDifferent_UNKNOWN_DIFFERENCE_IN_EQUATION, "couldn't find problem with jumpCondition for " + oldVars[j].getName() + " in compartment " + subDomainsOld[i].getName());
}
}
}
}
//
// test fast system for subdomain
//
FastSystem oldFastSystem = subDomainsOld[i].getFastSystem();
FastSystem newFastSystem = subDomainsNew[i].getFastSystem();
if (!Compare.isEqualOrNull(oldFastSystem, newFastSystem)) {
boolean bFoundDifference = false;
//
if (oldFastSystem == null) {
//
return new MathCompareResults(Decision.MathDifferent_EQUATION_ADDED);
}
if (newFastSystem == null) {
//
return new MathCompareResults(Decision.MathDifferent_EQUATION_REMOVED);
}
Enumeration<Expression> oldFastInvExpEnum = oldFastSystem.getFastInvariantExpressions();
Enumeration<Expression> newFastInvExpEnum = newFastSystem.getFastInvariantExpressions();
Expression[] oldFastInvariantExps = (Expression[]) BeanUtils.getArray(oldFastInvExpEnum, Expression.class);
Expression[] newFastInvariantExps = (Expression[]) BeanUtils.getArray(newFastInvExpEnum, Expression.class);
if (oldFastInvariantExps.length != newFastInvariantExps.length) {
return new MathCompareResults(Decision.MathDifferent_DIFFERENT_NUMBER_OF_EXPRESSIONS, "fast invariants have different number of expressions");
}
for (int k = 0; k < oldFastInvariantExps.length; k++) {
if (!oldFastInvariantExps[k].compareEqual(newFastInvariantExps[k])) {
bFoundDifference = true;
if (!ExpressionUtils.functionallyEquivalent(oldFastInvariantExps[k], newFastInvariantExps[k])) {
//
// difference couldn't be reconciled
// ... for fast invariants, it is ok if the two equations are different by a scale factor (e.g. if X+Y is conserved, so is 2*X+2*Y, or 2*(X+Y))
//
// estimate proportionality factor (average of 5 evaluations)
//
// ratio = old/new
//
// then compare old with ratio*new.
//
Expression ratioExp = Expression.mult(oldFastInvariantExps[k], Expression.invert(newFastInvariantExps[k]));
String[] symbols = ratioExp.getSymbols();
SimpleSymbolTable symbolTable = new SimpleSymbolTable(symbols);
double[] values = new double[symbols.length];
ratioExp.bindExpression(symbolTable);
Random random = new Random(0);
double ratioAccum = 0.0;
final int NUM_TRIALS = 5;
for (int m = 0; m < NUM_TRIALS; m++) {
for (int j = 0; j < values.length; j++) {
values[j] = random.nextDouble() + 1.0;
}
ratioAccum += ratioExp.evaluateVector(values);
}
double estimatedRatio = ratioAccum / NUM_TRIALS;
Expression scaled_newFastInvariantExp = Expression.mult(new Expression(estimatedRatio), newFastInvariantExps[k]);
System.out.println("MathDescription.compareEquivalent(): comparing " + oldFastInvariantExps[k].infix() + " with " + scaled_newFastInvariantExp.infix());
if (!ExpressionUtils.functionallyEquivalent(oldFastInvariantExps[k], scaled_newFastInvariantExp)) {
return new MathCompareResults(Decision.MathDifferent_DIFFERENT_FASTINV_EXPRESSION, "fast invariant expressions are different Old: '" + oldFastInvariantExps[k] + "'\n" + "fast invariant expressions are different New: '" + newFastInvariantExps[k] + "'");
}
// if (!bSilent) System.out.println("fast invariant expressions are proportional Old: '"+oldFastInvariantExps[k]+"'\n"+
// "fast invariant expressions are proportional New: '"+newFastInvariantExps[k]+"'");
} else {
// if (!bSilent) System.out.println("expressions are equivalent Old: '"+oldExps[k]+"'\n"+
// "expressions are equivalent New: '"+newExps[k]+"'");
}
}
}
Enumeration<Expression> oldFastRateExpEnum = oldFastSystem.getFastRateExpressions();
Enumeration<Expression> newFastRateExpEnum = newFastSystem.getFastRateExpressions();
Expression[] oldFastRateExps = (Expression[]) BeanUtils.getArray(oldFastRateExpEnum, Expression.class);
Expression[] newFastRateExps = (Expression[]) BeanUtils.getArray(newFastRateExpEnum, Expression.class);
if (oldFastRateExps.length != newFastRateExps.length) {
return new MathCompareResults(Decision.MathDifferent_DIFFERENT_NUMBER_OF_EXPRESSIONS, "fast rates have different number of expressions");
}
for (int k = 0; k < oldFastRateExps.length; k++) {
if (!oldFastRateExps[k].compareEqual(newFastRateExps[k])) {
bFoundDifference = true;
if (!ExpressionUtils.functionallyEquivalent(oldFastRateExps[k], newFastRateExps[k])) {
//
return new MathCompareResults(Decision.MathDifferent_DIFFERENT_FASTRATE_EXPRESSION, "fast rate expressions are different Old: '" + oldFastRateExps[k] + "'\n" + "fast rate expressions are different New: '" + newFastRateExps[k] + "'");
} else {
// if (!bSilent) System.out.println("expressions are equivalent Old: '"+oldExps[k]+"'\n"+
// "expressions are equivalent New: '"+newExps[k]+"'");
}
}
}
//
if (bFoundDifference) {
subDomainsNew[i].setFastSystem(oldFastSystem);
} else {
//
return new MathCompareResults(Decision.MathDifferent_UNKNOWN_DIFFERENCE_IN_EQUATION, "couldn't find problem with FastSystem for compartment " + subDomainsOld[i].getName());
}
}
List<ParticleJumpProcess> oldPjpList = subDomainsOld[i].getParticleJumpProcesses();
List<ParticleJumpProcess> newPjpList = subDomainsNew[i].getParticleJumpProcesses();
if (oldPjpList.size() != newPjpList.size()) {
return new MathCompareResults(Decision.MathDifferent_DIFFERENT_NUMBER_OF_PARTICLE_JUMP_PROCESS);
}
for (ParticleJumpProcess oldPjp : oldPjpList) {
boolean bEqual = false;
for (ParticleJumpProcess newPjp : newPjpList) {
if (oldPjp.getName().equals(newPjp.getName())) {
if (oldPjp.compareEqual(newPjp)) {
bEqual = true;
}
break;
}
}
if (!bEqual) {
return new MathCompareResults(Decision.MathDifferent_DIFFERENT_PARTICLE_JUMP_PROCESS);
}
}
}
//
return oldMathDesc.compareInvariantAttributes(newMathDesc, true);
}
} catch (Throwable e) {
e.printStackTrace(System.out);
return new MathCompareResults(Decision.MathDifferent_FAILURE_UNKNOWN);
}
}
Also used :
ArrayList(java.util.ArrayList)
Random(java.util.Random)
SimpleSymbolTable(cbit.vcell.parser.SimpleSymbolTable)
Expression(cbit.vcell.parser.Expression)
Example 4 with SimpleSymbolTable
use of cbit.vcell.parser.SimpleSymbolTable in project vcell by virtualcell.
the class PdeTimePlotMultipleVariablesPanel method initialize.
private void initialize() {
VariableType varType = multiTimePlotHelper.getPdeDatacontext().getDataIdentifier().getVariableType();
String varName = multiTimePlotHelper.getPdeDatacontext().getVariableName();
String[] plotNames = new String[pointVector.size()];
final SymbolTableEntry[] symbolTableEntries = new SymbolTableEntry[plotNames.length];
DefaultListModel<String> pointListModel = new DefaultListModel<String>();
for (int i = 0; i < pointVector.size(); i++) {
Coordinate tp = null;
if (varType.equals(VariableType.VOLUME) || varType.equals(VariableType.VOLUME_REGION) || varType.equals(VariableType.POSTPROCESSING)) {
SpatialSelectionVolume ssv = (SpatialSelectionVolume) pointVector.get(i);
tp = ssv.getCurveSelectionInfo().getCurve().getBeginningCoordinate();
} else if (varType.equals(VariableType.MEMBRANE) || varType.equals(VariableType.MEMBRANE_REGION)) {
SpatialSelectionMembrane ssm = (SpatialSelectionMembrane) pointVector.get(i);
double midU = ssm.getCurveSelectionInfo().getCurveUfromSelectionU(.5);
tp = ((SampledCurve) ssm.getCurveSelectionInfo().getCurve()).coordinateFromNormalizedU(midU);
}
plotNames[i] = varName + " at P[" + i + "]";
String point = "P[" + i + "] (" + niceCoordinateString(tp) + ")";
pointListModel.addElement(point);
if (multiTimePlotHelper.getsimulation() != null) {
symbolTableEntries[0] = multiTimePlotHelper.getsimulation().getMathDescription().getEntry(varName);
} else {
System.out.println("PdeTimePlotMultipleVariablesPanel.initialize() adding artificial symbol table entries for field data");
SimpleSymbolTable simpleSymbolTable = new SimpleSymbolTable(new String[] { varName });
symbolTableEntries[0] = simpleSymbolTable.getEntry(varName);
}
}
pointJList.setModel(pointListModel);
pointJList.setForeground(variableJList.getForeground());
pointJList.setVisibleRowCount(3);
pointJList.setBackground(getBackground());
pointJList.setSelectionBackground(getBackground());
pointJList.setSelectionForeground(Color.black);
plotPane = new PlotPane();
double[][] plotDatas = tsJobResultsNoStats.getTimesAndValuesForVariable(varName);
Plot2D plot2D = new SingleXPlot2D(symbolTableEntries, multiTimePlotHelper.getDataSymbolMetadataResolver(), ReservedVariable.TIME.getName(), plotNames, plotDatas, new String[] { "Time Plot", ReservedVariable.TIME.getName(), "" });
plotPane.setPlot2D(plot2D);
DataIdentifier[] dis = (multiTimePlotHelper.getCopyOfDisplayedDataIdentifiers() != null ? multiTimePlotHelper.getCopyOfDisplayedDataIdentifiers() : DataIdentifier.collectSortedSimilarDataTypes(multiTimePlotHelper.getVariableType(), multiTimePlotHelper.getPdeDatacontext().getDataIdentifiers()));
Arrays.sort(dis, new Comparator<DataIdentifier>() {
public int compare(DataIdentifier o1, DataIdentifier o2) {
int bEqualIgnoreCase = o1.getDisplayName().compareToIgnoreCase(o2.getDisplayName());
if (bEqualIgnoreCase == 0) {
return o1.getDisplayName().compareTo(o2.getDisplayName());
}
return bEqualIgnoreCase;
}
});
variableJList.setListData(dis);
initVariableListSelected(variableJList, multiTimePlotHelper.getPdeDatacontext().getDataIdentifier());
variableJList.setCellRenderer(multiTimePlotHelper.getListCellRenderer());
setLayout(new GridBagLayout());
JLabel label = new JLabel("Selected Points");
label.setFont(label.getFont().deriveFont(Font.BOLD));
GridBagConstraints gbc = new GridBagConstraints();
gbc.gridx = 0;
gbc.gridy = 0;
gbc.anchor = GridBagConstraints.WEST;
gbc.insets = new java.awt.Insets(15, 10, 4, 4);
add(label, gbc);
gbc = new GridBagConstraints();
gbc.gridx = 1;
gbc.gridy = 0;
gbc.fill = java.awt.GridBagConstraints.BOTH;
gbc.gridheight = 4;
gbc.weightx = 1;
gbc.weighty = 1;
gbc.fill = GridBagConstraints.BOTH;
gbc.insets = new java.awt.Insets(0, 4, 0, 0);
add(plotPane, gbc);
JScrollPane sp = new JScrollPane(pointJList);
sp.setVerticalScrollBarPolicy(JScrollPane.VERTICAL_SCROLLBAR_ALWAYS);
sp.setHorizontalScrollBarPolicy(JScrollPane.HORIZONTAL_SCROLLBAR_ALWAYS);
gbc = new GridBagConstraints();
gbc.gridx = 0;
gbc.gridy = 1;
gbc.anchor = GridBagConstraints.WEST;
gbc.weighty = 0.5;
gbc.fill = java.awt.GridBagConstraints.BOTH;
gbc.insets = new java.awt.Insets(4, 10, 4, 4);
add(sp, gbc);
label = new JLabel("Y Axis");
label.setFont(label.getFont().deriveFont(Font.BOLD));
gbc = new GridBagConstraints();
gbc.gridx = 0;
gbc.gridy = 2;
gbc.anchor = GridBagConstraints.WEST;
gbc.insets = new java.awt.Insets(4, 10, 4, 4);
add(label, gbc);
sp = new JScrollPane(variableJList);
sp.setVerticalScrollBarPolicy(JScrollPane.VERTICAL_SCROLLBAR_ALWAYS);
sp.setHorizontalScrollBarPolicy(JScrollPane.HORIZONTAL_SCROLLBAR_ALWAYS);
gbc = new GridBagConstraints();
gbc.gridx = 0;
gbc.gridy = 3;
gbc.weightx = 0.2;
gbc.weighty = 1;
gbc.insets = new java.awt.Insets(4, 10, 50, 4);
gbc.fill = java.awt.GridBagConstraints.BOTH;
add(sp, gbc);
variableJList.addListSelectionListener(eventHandler);
multiTimePlotHelper.addPropertyChangeListener(eventHandler);
}
Also used :
GridBagConstraints(java.awt.GridBagConstraints)
DataIdentifier(cbit.vcell.simdata.DataIdentifier)
GridBagLayout(java.awt.GridBagLayout)
SpatialSelectionMembrane(cbit.vcell.simdata.SpatialSelectionMembrane)
DefaultListModel(javax.swing.DefaultListModel)
SymbolTableEntry(cbit.vcell.parser.SymbolTableEntry)
JScrollPane(javax.swing.JScrollPane)
SampledCurve(cbit.vcell.geometry.SampledCurve)
VariableType(cbit.vcell.math.VariableType)
JLabel(javax.swing.JLabel)
SingleXPlot2D(cbit.plot.SingleXPlot2D)
SimpleSymbolTable(cbit.vcell.parser.SimpleSymbolTable)
Coordinate(org.vcell.util.Coordinate)
SpatialSelectionVolume(cbit.vcell.simdata.SpatialSelectionVolume)
PlotPane(cbit.plot.gui.PlotPane)
SingleXPlot2D(cbit.plot.SingleXPlot2D)
Plot2D(cbit.plot.Plot2D)
Example 5 with SimpleSymbolTable
use of cbit.vcell.parser.SimpleSymbolTable in project vcell by virtualcell.
the class MathTestingUtilities method comparePDEResultsWithExact.
/**
* Insert the method's description here.
* Creation date: (8/20/2003 12:58:10 PM)
*/
public static SimulationComparisonSummary comparePDEResultsWithExact(SimulationSymbolTable simSymbolTable, PDEDataManager dataManager, String type, double absErrorThreshold, double relErrorThreshold) throws DataAccessException, ExpressionException {
java.util.Hashtable<String, DataErrorSummary> tempVarHash = new java.util.Hashtable<String, DataErrorSummary>();
double[] timeArray = dataManager.getDataSetTimes();
Variable[] vars = simSymbolTable.getVariables();
CartesianMesh mesh = dataManager.getMesh();
MathDescription mathDesc = simSymbolTable.getSimulation().getMathDescription();
// Get volumeSubdomains from mathDesc/mesh and store in lookupTable
int numVol = mesh.getSizeX() * mesh.getSizeY() * mesh.getSizeZ();
CompartmentSubDomain[] volSubDomainLookup = new CompartmentSubDomain[numVol];
for (int i = 0; i < numVol; i++) {
int subVolumeIndex = mesh.getSubVolumeFromVolumeIndex(i);
SubVolume subVolume = mathDesc.getGeometry().getGeometrySpec().getSubVolume(subVolumeIndex);
CompartmentSubDomain compSubDomain = mathDesc.getCompartmentSubDomain(subVolume.getName());
volSubDomainLookup[i] = compSubDomain;
}
// Get membraneSubdomains from mathDesc/mesh and store in lookupTable
int numMem = mesh.getMembraneElements().length;
MembraneSubDomain[] memSubDomainLookup = new MembraneSubDomain[numMem];
for (int i = 0; i < numMem; i++) {
int insideVolIndex = mesh.getMembraneElements()[i].getInsideVolumeIndex();
int outsideVolIndex = mesh.getMembraneElements()[i].getOutsideVolumeIndex();
MembraneSubDomain memSubDomain = mathDesc.getMembraneSubDomain(volSubDomainLookup[insideVolIndex], volSubDomainLookup[outsideVolIndex]);
memSubDomainLookup[i] = memSubDomain;
}
double[] valueArray = new double[4];
SimpleSymbolTable symbolTable = new SimpleSymbolTable(new String[] { "t", "x", "y", "z" });
int tIndex = symbolTable.getEntry("t").getIndex();
int xIndex = symbolTable.getEntry("x").getIndex();
int yIndex = symbolTable.getEntry("y").getIndex();
int zIndex = symbolTable.getEntry("z").getIndex();
SimulationComparisonSummary simComparisonSummary = new SimulationComparisonSummary();
String hashKey = new String("");
long dataLength = 0;
// for each var, do the following :
for (int i = 0; i < vars.length; i++) {
if (vars[i] instanceof VolVariable || vars[i] instanceof MemVariable || vars[i] instanceof FilamentVariable || vars[i] instanceof VolumeRegionVariable || vars[i] instanceof MembraneRegionVariable || vars[i] instanceof FilamentRegionVariable) {
// for each time in timeArray,
for (int j = 0; j < timeArray.length; j++) {
if (type.equals(TestCaseNew.EXACT_STEADY)) {
if (j != (timeArray.length - 1)) {
continue;
}
}
// get data block from varName, data from datablock
SimDataBlock simDataBlock = dataManager.getSimDataBlock(vars[i].getName(), timeArray[j]);
double[] data = simDataBlock.getData();
dataLength = data.length;
SubDomain subDomain = null;
Coordinate subDomainCoord = null;
// for each point in data block ...
for (int k = 0; k < dataLength; k++) {
// Get subdomain from mesh (from the lookupTable), get coordinates (x,y,z) from mesh, evaluate EXACT SOLN at that coord
if (vars[i] instanceof VolVariable) {
subDomain = volSubDomainLookup[k];
subDomainCoord = mesh.getCoordinateFromVolumeIndex(k);
} else if (vars[i] instanceof MemVariable) {
subDomain = memSubDomainLookup[k];
subDomainCoord = mesh.getCoordinateFromMembraneIndex(k);
} else {
throw new RuntimeException("Var " + vars[i].getName() + " not supported yet!");
}
hashKey = vars[i].getName() + ":" + subDomain.getName();
DataErrorSummary tempVar = (DataErrorSummary) tempVarHash.get(hashKey);
if (tempVar == null) {
Expression exp = new Expression(subDomain.getEquation(vars[i]).getExactSolution());
exp.bindExpression(simSymbolTable);
exp = MathUtilities.substituteFunctions(exp, simSymbolTable);
exp = exp.flatten();
exp.bindExpression(symbolTable);
tempVar = new DataErrorSummary(exp);
tempVarHash.put(hashKey, tempVar);
}
// time
valueArray[tIndex] = timeArray[j];
// x
valueArray[xIndex] = subDomainCoord.getX();
// y
valueArray[yIndex] = subDomainCoord.getY();
// z
valueArray[zIndex] = subDomainCoord.getZ();
// EXACT soln at coord subDomainCoord
double value = tempVar.getExactExp().evaluateVector(valueArray);
tempVar.addDataValues(value, data[k], timeArray[j], k, absErrorThreshold, relErrorThreshold);
}
// end for (k)
}
// end for (j)
}
// end - if (var)
}
// end for (i)
Enumeration<String> enumKeys = tempVarHash.keys();
while (enumKeys.hasMoreElements()) {
String key = enumKeys.nextElement();
DataErrorSummary tempVarSummary = tempVarHash.get(key);
simComparisonSummary.addVariableComparisonSummary(new VariableComparisonSummary(key, tempVarSummary.getMinRef(), tempVarSummary.getMaxRef(), tempVarSummary.getMaxAbsoluteError(), tempVarSummary.getMaxRelativeError(), tempVarSummary.getL2Norm(), tempVarSummary.getTimeAtMaxAbsoluteError(), tempVarSummary.getIndexAtMaxAbsoluteError(), tempVarSummary.getTimeAtMaxRelativeError(), tempVarSummary.getIndexAtMaxRelativeError()));
}
return simComparisonSummary;
}
Also used :
MembraneSubDomain(cbit.vcell.math.MembraneSubDomain)
MembraneRegionVariable(cbit.vcell.math.MembraneRegionVariable)
InsideVariable(cbit.vcell.math.InsideVariable)
SensVariable(cbit.vcell.solver.ode.SensVariable)
FilamentVariable(cbit.vcell.math.FilamentVariable)
VolVariable(cbit.vcell.math.VolVariable)
VolumeRegionVariable(cbit.vcell.math.VolumeRegionVariable)
ReservedVariable(cbit.vcell.math.ReservedVariable)
MemVariable(cbit.vcell.math.MemVariable)
OutsideVariable(cbit.vcell.math.OutsideVariable)
FilamentRegionVariable(cbit.vcell.math.FilamentRegionVariable)
Variable(cbit.vcell.math.Variable)
MembraneRegionVariable(cbit.vcell.math.MembraneRegionVariable)
MathDescription(cbit.vcell.math.MathDescription)
VolumeRegionVariable(cbit.vcell.math.VolumeRegionVariable)
CompartmentSubDomain(cbit.vcell.math.CompartmentSubDomain)
SubDomain(cbit.vcell.math.SubDomain)
MembraneSubDomain(cbit.vcell.math.MembraneSubDomain)
MemVariable(cbit.vcell.math.MemVariable)
SimDataBlock(cbit.vcell.simdata.SimDataBlock)
SubVolume(cbit.vcell.geometry.SubVolume)
AnalyticSubVolume(cbit.vcell.geometry.AnalyticSubVolume)
VolVariable(cbit.vcell.math.VolVariable)
FilamentRegionVariable(cbit.vcell.math.FilamentRegionVariable)
CartesianMesh(cbit.vcell.solvers.CartesianMesh)
SimpleSymbolTable(cbit.vcell.parser.SimpleSymbolTable)
Coordinate(org.vcell.util.Coordinate)
Expression(cbit.vcell.parser.Expression)
CompartmentSubDomain(cbit.vcell.math.CompartmentSubDomain)
FilamentVariable(cbit.vcell.math.FilamentVariable)
Aggregations
SimpleSymbolTable (cbit.vcell.parser.SimpleSymbolTable)16
Expression (cbit.vcell.parser.Expression)11
ArrayList (java.util.ArrayList)6
Coordinate (org.vcell.util.Coordinate)3
ImageException (cbit.image.ImageException)2
Plot2D (cbit.plot.Plot2D)2
SingleXPlot2D (cbit.plot.SingleXPlot2D)2
PlotPane (cbit.plot.gui.PlotPane)2
ChildWindowManager (cbit.vcell.client.ChildWindowManager)2
ChildWindow (cbit.vcell.client.ChildWindowManager.ChildWindow)2
SinglePoint (cbit.vcell.geometry.SinglePoint)2
CompartmentSubDomain (cbit.vcell.math.CompartmentSubDomain)2
MathException (cbit.vcell.math.MathException)2
MembraneSubDomain (cbit.vcell.math.MembraneSubDomain)2
VariableType (cbit.vcell.math.VariableType)2
ExpressionBindingException (cbit.vcell.parser.ExpressionBindingException)2
ExpressionException (cbit.vcell.parser.ExpressionException)2
SymbolTableEntry (cbit.vcell.parser.SymbolTableEntry)2
DataIdentifier (cbit.vcell.simdata.DataIdentifier)2
SpatialSelectionMembrane (cbit.vcell.simdata.SpatialSelectionMembrane)2
