use of cbit.vcell.math.Constant in project vcell by virtualcell.
the class MathOverridesTableModel method setValueAt.
/**
* getValueAt method comment.
*/
public void setValueAt(Object object, int r, int c) {
try {
String name = (String) getValueAt(r, 0);
if (c == COLUMN_ACTUAL) {
if (object instanceof ConstantArraySpec) {
editScanValues(name, r);
} else if (object instanceof ScopedExpression) {
throw new RuntimeException("unexpected value type ScopedExpression");
} else if (object instanceof String) {
String inputValue = (String) object;
Expression expression = null;
if (inputValue == null || inputValue.trim().length() == 0) {
expression = new Expression((String) getValueAt(r, COLUMN_DEFAULT));
} else {
expression = new Expression(inputValue);
}
Constant constant = new Constant(name, expression);
getMathOverrides().putConstant(constant);
fireTableCellUpdated(r, c);
this.fireTableDataChanged();
setModified(true);
}
} else if (c == COLUMN_SCAN) {
if (((Boolean) object).booleanValue()) {
// setting scan values
editScanValues(name, r);
} else {
// resetting to default
setValueAt(getValueAt(r, COLUMN_DEFAULT), r, COLUMN_ACTUAL);
}
}
} catch (Throwable exc) {
PopupGenerator.showErrorDialog(ownerTable, exc.getMessage() + "\nOld value was restored.", exc);
}
}
use of cbit.vcell.math.Constant in project vcell by virtualcell.
the class ODESolverPlotSpecificationPanel method regeneratePlot2D.
/**
* Comment
*/
private void regeneratePlot2D() throws ExpressionException, ObjectNotFoundException {
if (getMyDataInterface() == null) {
return;
}
if (!getMyDataInterface().isMultiTrialData()) {
if (getXAxisComboBox_frm().getSelectedIndex() < 0) {
return;
} else {
// double[] xData = getOdeSolverResultSet().extractColumn(getPlottableColumnIndices()[getXIndex()]);
// getUnfilteredSortedXAxisNames
double[] xData = getMyDataInterface().extractColumn((String) getXAxisComboBox_frm().getSelectedItem());
double[][] allData = new double[((DefaultListModel) getYAxisChoice().getModel()).size() + 1][xData.length];
String[] yNames = new String[((DefaultListModel) getYAxisChoice().getModel()).size()];
allData[0] = xData;
double[] yData = new double[xData.length];
double currParamValue = 0.0;
double deltaParamValue = 0.0;
// Extrapolation calculations!
if (getSensitivityParameter() != null) {
int val = getSensitivityParameterSlider().getValue();
double nominalParamValue = getSensitivityParameter().getConstantValue();
double pMax = nominalParamValue * 1.1;
double pMin = nominalParamValue * 0.9;
int iMax = getSensitivityParameterSlider().getMaximum();
int iMin = getSensitivityParameterSlider().getMinimum();
double slope = (pMax - pMin) / (iMax - iMin);
currParamValue = slope * val + pMin;
deltaParamValue = currParamValue - nominalParamValue;
getMaxLabel().setText(Double.toString(pMax));
getMinLabel().setText(Double.toString(pMin));
getCurLabel().setText(Double.toString(currParamValue));
}
if (!getLogSensCheckbox().getModel().isSelected()) {
// When log sensitivity check box is not selected.
for (int i = 0; i < allData.length - 1; i++) {
// If sensitivity analysis is enabled, extrapolate values for State vars and non-sensitivity functions
if (getSensitivityParameter() != null) {
ColumnDescription cd = getMyDataInterface().getColumnDescription((String) ((DefaultListModel) getYAxisChoice().getModel()).elementAt(i));
double[] sens = getSensValues(cd);
yData = getMyDataInterface().extractColumn(cd.getName());
// sens array != null for non-sensitivity state vars and functions, so extrapolate
if (sens != null) {
for (int j = 0; j < sens.length; j++) {
if (Math.abs(yData[j]) > 1e-6) {
// away from zero, exponential extrapolation
allData[i + 1][j] = yData[j] * Math.exp(deltaParamValue * sens[j] / yData[j]);
} else {
// around zero - linear extrapolation
allData[i + 1][j] = yData[j] + sens[j] * deltaParamValue;
}
}
// sens array == null for sensitivity state vars and functions, so don't change their original values
} else {
allData[i + 1] = getMyDataInterface().extractColumn((String) ((DefaultListModel) getYAxisChoice().getModel()).elementAt(i));
}
} else {
// No sensitivity analysis case, so do not alter the original values for any variable or function
allData[i + 1] = getMyDataInterface().extractColumn((String) ((DefaultListModel) getYAxisChoice().getModel()).elementAt(i));
}
yNames[i] = (String) ((DefaultListModel) getYAxisChoice().getModel()).elementAt(i);
}
} else {
// When log sensitivity checkbox is selected.
// Get sensitivity parameter and its value to compute log sensitivity
Constant sensParam = getSensitivityParameter();
double sensParamValue = sensParam.getConstantValue();
getJLabelSensitivityParameter().setText("Sensitivity wrt Parameter " + sensParam.getName());
//
for (int i = 0; i < allData.length - 1; i++) {
// Finding sensitivity var column for each column in result set.
ColumnDescription cd = getMyDataInterface().getColumnDescription((String) ((DefaultListModel) getYAxisChoice().getModel()).elementAt(i));
String sensVarName = null;
ColumnDescription[] allColumnDescriptions = getMyDataInterface().getAllColumnDescriptions();
for (int j = 0; j < allColumnDescriptions.length; j++) {
String obj = "sens_" + cd.getName() + "_wrt_" + sensParam.getName();
if (allColumnDescriptions[j].getName().equals(obj)) {
sensVarName = obj;
break;
}
}
int sensIndex = -1;
if (sensVarName != null) {
for (int j = 0; j < ((DefaultListModel) getYAxisChoice().getModel()).getSize(); j++) {
if (((String) ((DefaultListModel) getYAxisChoice().getModel()).get(j)).equals(sensVarName)) {
sensIndex = j;
break;
}
}
}
yData = getMyDataInterface().extractColumn(cd.getName());
// If sensitivity var exists, compute log sensitivity
if (sensVarName != null) {
double[] sens = getMyDataInterface().extractColumn(sensVarName);
for (int k = 0; k < yData.length; k++) {
// Extrapolated statevars and functions
if (Math.abs(yData[k]) > 1e-6) {
// away from zero, exponential extrapolation
allData[i + 1][k] = yData[k] * Math.exp(deltaParamValue * sens[k] / yData[k]);
} else {
// around zero - linear extrapolation
allData[i + 1][k] = yData[k] + sens[k] * deltaParamValue;
}
// Log sensitivity for the state variables and functions
// default if floating point problems
double logSens = 0.0;
if (Math.abs(yData[k]) > 0) {
double tempLogSens = sens[k] * sensParamValue / yData[k];
if (tempLogSens != Double.NEGATIVE_INFINITY && tempLogSens != Double.POSITIVE_INFINITY && tempLogSens != Double.NaN) {
logSens = tempLogSens;
}
}
if (sensIndex > -1) {
allData[sensIndex + 1][k] = logSens;
}
}
// If sensitivity var does not exist, retain original value of column (var or function).
} else {
if (!cd.getName().startsWith("sens_")) {
allData[i + 1] = yData;
}
}
yNames[i] = (String) ((DefaultListModel) getYAxisChoice().getModel()).elementAt(i);
}
}
String title = "";
String xLabel = (String) getXAxisComboBox_frm().getSelectedItem();
String yLabel = "";
if (yNames.length == 1) {
yLabel = yNames[0];
}
// Update Sensitivity parameter label depending on whether Log sensitivity check box is checked or not.
if (!getLogSensCheckbox().getModel().isSelected()) {
getJLabelSensitivityParameter().setText("");
}
SymbolTableEntry[] symbolTableEntries = null;
if (getSymbolTable() != null && yNames != null && yNames.length > 0) {
symbolTableEntries = new SymbolTableEntry[yNames.length];
for (int i = 0; i < yNames.length; i += 1) {
SymbolTableEntry ste = getSymbolTable().getEntry(yNames[i]);
symbolTableEntries[i] = ste;
}
}
SingleXPlot2D plot2D = new SingleXPlot2D(symbolTableEntries, getMyDataInterface().getDataSymbolMetadataResolver(), xLabel, yNames, allData, new String[] { title, xLabel, yLabel });
refreshVisiblePlots(plot2D);
// here fire "singleXPlot2D" event, ODEDataViewer's event handler listens to it.
setPlot2D(plot2D);
}
} else // end of none MultitrialData
// multitrial data
{
// a column of data get from ODESolverRestultSet, which is actually the results for a specific variable during multiple trials
double[] rowData = new double[getMyDataInterface().getRowCount()];
PlotData[] plotData = new PlotData[((DefaultListModel) getYAxisChoice().getModel()).size()];
for (int i = 0; i < plotData.length; i++) {
ColumnDescription cd = getMyDataInterface().getColumnDescription((String) ((DefaultListModel) getYAxisChoice().getModel()).elementAt(i));
rowData = getMyDataInterface().extractColumn(cd.getName());
Point2D[] histogram = generateHistogram(rowData);
double[] x = new double[histogram.length];
double[] y = new double[histogram.length];
for (int j = 0; j < histogram.length; j++) {
x[j] = histogram[j].getX();
y[j] = histogram[j].getY();
}
plotData[i] = new PlotData(x, y);
}
SymbolTableEntry[] symbolTableEntries = null;
if (getSymbolTable() != null && ((DefaultListModel) getYAxisChoice().getModel()).size() > 0) {
symbolTableEntries = new SymbolTableEntry[((DefaultListModel) getYAxisChoice().getModel()).size()];
for (int i = 0; i < symbolTableEntries.length; i += 1) {
symbolTableEntries[i] = getSymbolTable().getEntry((String) ((DefaultListModel) getYAxisChoice().getModel()).elementAt(i));
}
}
String title = "Probability Distribution of Species";
String xLabel = "Number of Particles";
String yLabel = "";
String[] yNames = new String[((DefaultListModel) getYAxisChoice().getModel()).size()];
((DefaultListModel) getYAxisChoice().getModel()).copyInto(yNames);
Plot2D plot2D = new Plot2D(symbolTableEntries, getMyDataInterface().getDataSymbolMetadataResolver(), yNames, plotData, new String[] { title, xLabel, yLabel });
refreshVisiblePlots(plot2D);
setPlot2D(plot2D);
}
}
use of cbit.vcell.math.Constant in project vcell by virtualcell.
the class SimulationSummaryPanel method displayTask.
/**
* Comment
*/
private void displayTask() {
SolverTaskDescription solverTaskDescription = getSimulation().getSolverTaskDescription();
try {
NonspatialStochSimOptions stochOpt = solverTaskDescription.getStochOpt();
if (stochOpt != null && stochOpt.getNumOfTrials() > 1) {
getJLabelOutput().setText("Histogram with " + stochOpt.getNumOfTrials() + " Trials(@last time point)");
} else {
// gcwtodo
String text = solverTaskDescription.getOutputTimeSpec().getShortDescription();
if (solverTaskDescription.getSolverDescription().isChomboSolver()) {
text = "Variable";
if (solverTaskDescription.getChomboSolverSpec().getTimeIntervalList().size() == 1) {
text = "Every " + solverTaskDescription.getChomboSolverSpec().getLastTimeInterval().getOutputTimeStep() + "s";
}
} else if (solverTaskDescription.getOutputTimeSpec().isDefault() && !solverTaskDescription.getSolverDescription().isSemiImplicitPdeSolver() && !solverTaskDescription.getSolverDescription().equals(SolverDescription.StochGibson)) {
text += ", at most " + ((DefaultOutputTimeSpec) solverTaskDescription.getOutputTimeSpec()).getKeepAtMost();
}
getJLabelOutput().setText(text);
}
} catch (Exception exc) {
exc.printStackTrace(System.out);
getJLabelOutput().setText("");
}
SolverDescription solverDescription = solverTaskDescription.getSolverDescription();
try {
ErrorTolerance errorTolerance = solverTaskDescription.getErrorTolerance();
TimeStep timeStep = solverTaskDescription.getTimeStep();
getJLabelRelTol().setText("Rel tol");
getJLabelAbsTol().setText("Abs tol");
getJLabel12().setText("Timestep");
getJLabelRelTol().setEnabled(false);
getJLabelAbsTol().setEnabled(false);
getJLabel12().setEnabled(false);
getJLabel10().setText("Sensitivity Analysis");
getJLabel10().setEnabled(true);
if (solverDescription.equals(SolverDescription.StochGibson)) {
getJLabel12().setEnabled(false);
getJLabelTimestep().setText("");
} else if (solverDescription.equals(SolverDescription.NFSim)) {
TimeBounds tb = solverTaskDescription.getTimeBounds();
double dtime = tb.getEndingTime() - tb.getStartingTime();
if (solverTaskDescription.getOutputTimeSpec() instanceof UniformOutputTimeSpec) {
UniformOutputTimeSpec uots = (UniformOutputTimeSpec) solverTaskDescription.getOutputTimeSpec();
double interval = uots.getOutputTimeStep();
int steps = (int) Math.round(dtime / interval);
getJLabel12().setEnabled(true);
getJLabel12().setText("Timepoints");
getJLabelTimestep().setText(steps + "");
} else if (solverTaskDescription.getOutputTimeSpec() instanceof DefaultOutputTimeSpec) {
DefaultOutputTimeSpec uots = (DefaultOutputTimeSpec) solverTaskDescription.getOutputTimeSpec();
getJLabel12().setEnabled(true);
getJLabel12().setText("End Time");
getJLabelTimestep().setText(solverTaskDescription.getTimeBounds().getEndingTime() + "");
} else {
getJLabel12().setEnabled(false);
getJLabel12().setText("End Time");
getJLabelTimestep().setText("na");
}
NFsimSimulationOptions nfsso = solverTaskDescription.getNFSimSimulationOptions();
String utl = "default";
Integer moleculeDistance = nfsso.getMoleculeDistance();
if (moleculeDistance != null) {
utl = moleculeDistance + "";
}
getJLabelRelTol().setEnabled(true);
getJLabelRelTol().setText("Universal Transversal Limit");
getJLabelRelTolValue().setText(utl);
String gml = "default";
Integer maxMoleculesPerType = nfsso.getMaxMoleculesPerType();
if (maxMoleculesPerType != null) {
gml = maxMoleculesPerType + "";
}
getJLabelAbsTol().setEnabled(true);
getJLabelAbsTol().setText("Max # of each " + MolecularType.typeName);
getJLabelAbsTolValue().setText(gml);
} else if (solverDescription.isNonSpatialStochasticSolver()) {
getJLabel12().setEnabled(true);
getJLabel12().setText("Timestep");
getJLabelTimestep().setText(timeStep.getDefaultTimeStep() + "s");
} else if (solverDescription.hasVariableTimestep()) {
getJLabel12().setEnabled(true);
getJLabel12().setText("Max timestep");
getJLabelTimestep().setText(timeStep.getMaximumTimeStep() + "s");
getJLabelRelTol().setEnabled(true);
getJLabelRelTolValue().setText("" + errorTolerance.getRelativeErrorTolerance());
getJLabelAbsTol().setEnabled(true);
getJLabelAbsTolValue().setText("" + errorTolerance.getAbsoluteErrorTolerance());
} else {
getJLabel12().setEnabled(true);
getJLabel12().setText("Timestep");
if (solverDescription.isChomboSolver()) {
String text = "Variable";
if (solverTaskDescription.getChomboSolverSpec().getTimeIntervalList().size() == 1) {
text = solverTaskDescription.getChomboSolverSpec().getLastTimeInterval().getTimeStep() + "s";
}
getJLabelTimestep().setText(text);
} else {
getJLabelTimestep().setText(timeStep.getDefaultTimeStep() + "s");
}
if (solverDescription.isSemiImplicitPdeSolver()) {
getJLabelRelTol().setEnabled(true);
getJLabelRelTolValue().setText("" + errorTolerance.getRelativeErrorTolerance());
} else {
getJLabelRelTol().setEnabled(false);
getJLabelRelTolValue().setText("");
}
getJLabelAbsTol().setEnabled(false);
getJLabelAbsTolValue().setText("");
}
} catch (Exception exc) {
exc.printStackTrace(System.out);
getJLabelTimestep().setText("");
getJLabelRelTolValue().setText("");
getJLabelAbsTolValue().setText("");
}
try {
boolean bChomboSolver = solverDescription.isChomboSolver();
getJLabelTitleNumProcessors().setVisible(bChomboSolver);
getJLabelNumProcessors().setVisible(bChomboSolver);
if (bChomboSolver) {
getJLabelNumProcessors().setText(String.valueOf(solverTaskDescription.getNumProcessors()));
}
if (getSimulation().isSpatial() || solverDescription.isNonSpatialStochasticSolver()) {
getJLabelSensitivity().setVisible(false);
getJLabel10().setVisible(false);
} else if (solverDescription.equals(SolverDescription.NFSim)) {
getJLabel10().setText("On-the-fly observ comp.");
NFsimSimulationOptions nfsso = solverTaskDescription.getNFSimSimulationOptions();
boolean goc = nfsso.getObservableComputationOff();
getJLabelSensitivity().setText(goc + "");
} else {
getJLabelSensitivity().setVisible(true);
getJLabel10().setVisible(true);
Constant param = solverTaskDescription.getSensitivityParameter();
if (param == null) {
getJLabelSensitivity().setText("no");
} else {
getJLabelSensitivity().setText(param.getName());
}
}
} catch (Exception exc) {
exc.printStackTrace(System.out);
getJLabelSensitivity().setText("");
}
if (solverDescription.isNonSpatialStochasticSolver()) {
getJLabelRelTol().setVisible(false);
getJLabelAbsTol().setVisible(false);
getJLabelRelTolValue().setVisible(false);
getJLabelAbsTolValue().setVisible(false);
} else {
getJLabelRelTol().setVisible(true);
getJLabelAbsTol().setVisible(true);
}
}
use of cbit.vcell.math.Constant in project vcell by virtualcell.
the class SolverTaskDescriptionAdvancedPanel method updateSensitivityAnalysisComboBox.
private void updateSensitivityAnalysisComboBox() {
// Inhibit actionEvents from ComboBox during comboBoxModel update.
sensitivityAnalysisComboBox.removeActionListener(ivjEventHandler);
//
try {
// clear comboBoxModel
((javax.swing.DefaultComboBoxModel) (sensitivityAnalysisComboBox.getModel())).removeAllElements();
//
if (getSolverTaskDescription() != null && getSolverTaskDescription().getSimulation() != null) {
MathDescription mathDescription = getSolverTaskDescription().getSimulation().getMathDescription();
if (mathDescription != null) {
Enumeration<Constant> enum1 = mathDescription.getConstants();
if (enum1.hasMoreElements()) {
((javax.swing.DefaultComboBoxModel) (sensitivityAnalysisComboBox.getModel())).addElement(SELECT_PARAMETER);
}
// Sort Constants, ignore case
TreeSet<String> sortedConstants = new TreeSet<String>(new Comparator<String>() {
public int compare(String o1, String o2) {
int ignoreCaseB = o1.compareToIgnoreCase(o2);
if (ignoreCaseB == 0) {
return o1.compareTo(o2);
}
return ignoreCaseB;
}
});
while (enum1.hasMoreElements()) {
Constant constant = (Constant) enum1.nextElement();
sortedConstants.add(constant.getName());
}
String[] sortedConstantsArr = new String[sortedConstants.size()];
sortedConstants.toArray(sortedConstantsArr);
for (int i = 0; i < sortedConstantsArr.length; i += 1) {
((javax.swing.DefaultComboBoxModel) (sensitivityAnalysisComboBox.getModel())).addElement(sortedConstantsArr[i]);
}
}
}
} finally {
updateSensitivityParameterDisplay((getSolverTaskDescription() != null ? getSolverTaskDescription().getSensitivityParameter() : null));
// Re-activate actionEvents on ComboBox
sensitivityAnalysisComboBox.addActionListener(ivjEventHandler);
}
}
use of cbit.vcell.math.Constant in project vcell by virtualcell.
the class DiffEquMathMapping method refreshMathDescription.
/**
* This method was created in VisualAge.
*/
@SuppressWarnings("deprecation")
private void refreshMathDescription() throws MappingException, MatrixException, MathException, ExpressionException, ModelException {
// All sizes must be set for new ODE models and ratios must be set for old ones.
simContext.checkValidity();
//
// temporarily place all variables in a hashtable (before binding) and discarding duplicates (check for equality)
//
VariableHash varHash = new VariableHash();
StructureMapping[] structureMappings = simContext.getGeometryContext().getStructureMappings();
//
// verify that all structures are mapped to subvolumes and all subvolumes are mapped to a structure
//
// Structure structures[] =
simContext.getGeometryContext().getModel().getStructures();
// for (int i = 0; i < structures.length; i++){
// StructureMapping sm = simContext.getGeometryContext().getStructureMapping(structures[i]);
// if (sm==null || (sm.getGeometryClass() == null)){
// localIssueList.add(new Issue(structures[i], IssueCategory.StructureNotMapped,"In Application '" + simContext.getName() + "', model structure '"+structures[i].getName()+"' not mapped to a geometry subdomain",Issue.SEVERITY_WARNING));
// }
// }
// SubVolume subVolumes[] = simContext.getGeometryContext().getGeometry().getGeometrySpec().getSubVolumes();
// for (int i = 0; i < subVolumes.length; i++){
// Structure[] mappedStructures = simContext.getGeometryContext().getStructuresFromGeometryClass(subVolumes[i]);
// if (mappedStructures==null || mappedStructures.length==0){
// localIssueList.add(new Issue(subVolumes[i], IssueCategory.GeometryClassNotMapped,"In Application '" + simContext.getName() + "', geometry subVolume '"+subVolumes[i].getName()+"' not mapped from a model structure",Issue.SEVERITY_WARNING));
// }
// }
// deals with model parameters
HashMap<VolVariable, EventAssignmentOrRateRuleInitParameter> eventOrRateRuleVolVarHash = new HashMap<VolVariable, EventAssignmentOrRateRuleInitParameter>();
HashMap<VolVariable, RateRuleRateParameter> rateRuleRateParamHash = new HashMap<VolVariable, RateRuleRateParameter>();
ArrayList<SymbolTableEntry> rateRuleVarTargets = new ArrayList<SymbolTableEntry>();
Model model = simContext.getModel();
ModelUnitSystem modelUnitSystem = model.getUnitSystem();
VCUnitDefinition timeUnit = modelUnitSystem.getTimeUnit();
ModelParameter[] modelParameters = model.getModelParameters();
if (simContext.getGeometry().getDimension() == 0) {
//
// global parameters from model (that presently are constants)
//
BioEvent[] bioEvents = simContext.getBioEvents();
ArrayList<SymbolTableEntry> eventAssignTargets = new ArrayList<SymbolTableEntry>();
if (bioEvents != null && bioEvents.length > 0) {
for (BioEvent be : bioEvents) {
ArrayList<EventAssignment> eventAssignments = be.getEventAssignments();
if (eventAssignments != null) {
for (EventAssignment ea : eventAssignments) {
if (!eventAssignTargets.contains(ea.getTarget())) {
eventAssignTargets.add(ea.getTarget());
}
}
}
}
}
/**
* @author anu : RATE RULES
*/
RateRule[] rateRules = simContext.getRateRules();
if (rateRules != null && rateRules.length > 0) {
for (RateRule rr : rateRules) {
SymbolTableEntry rateRuleVar = rr.getRateRuleVar();
if (!rateRuleVarTargets.contains(rateRuleVar)) {
rateRuleVarTargets.add(rateRuleVar);
}
}
}
for (int j = 0; j < modelParameters.length; j++) {
Expression modelParamExpr = modelParameters[j].getExpression();
GeometryClass geometryClass = getDefaultGeometryClass(modelParamExpr);
VCUnitDefinition paramUnit = modelParameters[j].getUnitDefinition();
modelParamExpr = getIdentifierSubstitutions(modelParamExpr, paramUnit, geometryClass);
if (eventAssignTargets.contains(modelParameters[j]) || rateRuleVarTargets.contains(modelParameters[j])) {
EventAssignmentOrRateRuleInitParameter eap = null;
try {
eap = addEventAssignmentOrRateRuleInitParameter(modelParameters[j], modelParamExpr, PARAMETER_ROLE_EVENTASSIGN_OR_RATERULE_INITCONDN, paramUnit);
} catch (PropertyVetoException e) {
e.printStackTrace(System.out);
throw new MappingException(e.getMessage());
}
VolVariable volVar = new VolVariable(modelParameters[j].getName(), null);
varHash.addVariable(volVar);
eventOrRateRuleVolVarHash.put(volVar, eap);
/**
* RATE RULES
*/
if (rateRuleVarTargets.contains(modelParameters[j])) {
RateRuleRateParameter rateParam = null;
try {
Expression origExp = simContext.getRateRule(modelParameters[j]).getRateRuleExpression();
VCUnitDefinition rateUnit = modelUnitSystem.getInstance_TBD();
if (paramUnit != null && !paramUnit.equals(modelUnitSystem.getInstance_TBD())) {
rateUnit = paramUnit.divideBy(timeUnit);
}
Expression rateExpr = getIdentifierSubstitutions(origExp, rateUnit, geometryClass);
rateParam = addRateRuleRateParameter(modelParameters[j], rateExpr, PARAMETER_ROLE_RATERULE_RATE, rateUnit);
} catch (PropertyVetoException e) {
e.printStackTrace(System.out);
throw new MappingException(e.getMessage());
}
rateRuleRateParamHash.put(volVar, rateParam);
}
} else {
varHash.addVariable(newFunctionOrConstant(getMathSymbol(modelParameters[j], geometryClass), modelParamExpr, geometryClass));
}
}
} else {
for (int j = 0; j < modelParameters.length; j++) {
Expression modelParamExpr = modelParameters[j].getExpression();
GeometryClass geometryClass = getDefaultGeometryClass(modelParamExpr);
modelParamExpr = getIdentifierSubstitutions(modelParamExpr, modelParameters[j].getUnitDefinition(), geometryClass);
varHash.addVariable(newFunctionOrConstant(getMathSymbol(modelParameters[j], geometryClass), modelParamExpr, geometryClass));
}
}
//
for (SimulationContextParameter scParameter : simContext.getSimulationContextParameters()) {
Expression scParameterExpression = scParameter.getExpression();
GeometryClass gc = getDefaultGeometryClass(scParameterExpression);
varHash.addVariable(newFunctionOrConstant(getMathSymbol(scParameter, gc), getIdentifierSubstitutions(scParameter.getExpression(), scParameter.getUnitDefinition(), gc), gc));
}
//
for (DataSymbol dataSymbol : simContext.getDataContext().getDataSymbols()) {
if (dataSymbol instanceof FieldDataSymbol) {
FieldDataSymbol fieldDataSymbol = (FieldDataSymbol) dataSymbol;
GeometryClass geometryClass = null;
FieldFunctionArguments ffs = new FieldFunctionArguments(fieldDataSymbol.getExternalDataIdentifier().getName(), fieldDataSymbol.getFieldDataVarName(), new Expression(fieldDataSymbol.getFieldDataVarTime()), VariableType.getVariableTypeFromVariableTypeName(fieldDataSymbol.getFieldDataVarType()));
Expression exp = new Expression(ffs.infix());
varHash.addVariable(newFunctionOrConstant(getMathSymbol(dataSymbol, geometryClass), getIdentifierSubstitutions(exp, dataSymbol.getUnitDefinition(), geometryClass), geometryClass));
} else {
throw new RuntimeException("In Application '" + simContext.getName() + "', dataSymbol type '" + dataSymbol.getClass().getName() + "' not yet supported for math generation");
}
}
//
// gather only those reactionSteps that are not "excluded"
//
ReactionSpec[] reactionSpecs = simContext.getReactionContext().getReactionSpecs();
Vector<ReactionStep> rsList = new Vector<ReactionStep>();
for (int i = 0; i < reactionSpecs.length; i++) {
if (reactionSpecs[i].isExcluded() == false) {
rsList.add(reactionSpecs[i].getReactionStep());
}
}
ReactionStep[] reactionSteps = new ReactionStep[rsList.size()];
rsList.copyInto(reactionSteps);
//
for (int i = 0; i < reactionSteps.length; i++) {
Kinetics.UnresolvedParameter[] unresolvedParameters = reactionSteps[i].getKinetics().getUnresolvedParameters();
if (unresolvedParameters != null && unresolvedParameters.length > 0) {
StringBuffer buffer = new StringBuffer();
for (int j = 0; j < unresolvedParameters.length; j++) {
if (j > 0) {
buffer.append(", ");
}
buffer.append(unresolvedParameters[j].getName());
}
throw new MappingException("In Application '" + simContext.getName() + "', " + reactionSteps[i].getDisplayType() + " '" + reactionSteps[i].getName() + "' contains unresolved identifier(s): " + buffer);
}
}
//
// create new MathDescription (based on simContext's previous MathDescription if possible)
//
MathDescription oldMathDesc = simContext.getMathDescription();
mathDesc = null;
if (oldMathDesc != null) {
if (oldMathDesc.getVersion() != null) {
mathDesc = new MathDescription(oldMathDesc.getVersion());
} else {
mathDesc = new MathDescription(oldMathDesc.getName());
}
} else {
mathDesc = new MathDescription(simContext.getName() + "_generated");
}
//
// volume variables
//
Enumeration<SpeciesContextMapping> enum1 = getSpeciesContextMappings();
while (enum1.hasMoreElements()) {
SpeciesContextMapping scm = enum1.nextElement();
if (scm.getVariable() instanceof VolVariable) {
if (!(mathDesc.getVariable(scm.getVariable().getName()) instanceof VolVariable)) {
varHash.addVariable(scm.getVariable());
}
}
}
//
// membrane variables
//
enum1 = getSpeciesContextMappings();
while (enum1.hasMoreElements()) {
SpeciesContextMapping scm = (SpeciesContextMapping) enum1.nextElement();
if (scm.getVariable() instanceof MemVariable) {
varHash.addVariable(scm.getVariable());
}
}
//
// volume region variables
//
enum1 = getSpeciesContextMappings();
while (enum1.hasMoreElements()) {
SpeciesContextMapping scm = (SpeciesContextMapping) enum1.nextElement();
if (scm.getVariable() instanceof VolumeRegionVariable) {
varHash.addVariable(scm.getVariable());
}
}
//
// membrane region variables
//
enum1 = getSpeciesContextMappings();
while (enum1.hasMoreElements()) {
SpeciesContextMapping scm = (SpeciesContextMapping) enum1.nextElement();
if (scm.getVariable() instanceof MembraneRegionVariable) {
varHash.addVariable(scm.getVariable());
}
}
//
// add compartment and membrane subdomains
//
ArrayList<CompartmentSubdomainContext> compartmentSubdomainContexts = new ArrayList<CompartmentSubdomainContext>();
ArrayList<MembraneSubdomainContext> membraneSubdomainContexts = new ArrayList<MembraneSubdomainContext>();
addSubdomains(model, compartmentSubdomainContexts, membraneSubdomainContexts);
// membrane velocities set on MembraneSubdomains later.
addSpatialProcesses(varHash, compartmentSubdomainContexts, membraneSubdomainContexts);
varHash.addVariable(new Constant(getMathSymbol(model.getPI_CONSTANT(), null), getIdentifierSubstitutions(model.getPI_CONSTANT().getExpression(), model.getPI_CONSTANT().getUnitDefinition(), null)));
varHash.addVariable(new Constant(getMathSymbol(model.getFARADAY_CONSTANT(), null), getIdentifierSubstitutions(model.getFARADAY_CONSTANT().getExpression(), model.getFARADAY_CONSTANT().getUnitDefinition(), null)));
varHash.addVariable(new Constant(getMathSymbol(model.getFARADAY_CONSTANT_NMOLE(), null), getIdentifierSubstitutions(model.getFARADAY_CONSTANT_NMOLE().getExpression(), model.getFARADAY_CONSTANT_NMOLE().getUnitDefinition(), null)));
varHash.addVariable(new Constant(getMathSymbol(model.getGAS_CONSTANT(), null), getIdentifierSubstitutions(model.getGAS_CONSTANT().getExpression(), model.getGAS_CONSTANT().getUnitDefinition(), null)));
varHash.addVariable(new Constant(getMathSymbol(model.getTEMPERATURE(), null), getIdentifierSubstitutions(new Expression(simContext.getTemperatureKelvin()), model.getTEMPERATURE().getUnitDefinition(), null)));
//
// only calculate potential if at least one MembraneMapping has CalculateVoltage == true
//
boolean bCalculatePotential = false;
for (int i = 0; i < structureMappings.length; i++) {
if (structureMappings[i] instanceof MembraneMapping) {
if (((MembraneMapping) structureMappings[i]).getCalculateVoltage()) {
bCalculatePotential = true;
}
}
}
potentialMapping = new PotentialMapping(simContext, this);
if (bCalculatePotential) {
potentialMapping.computeMath();
//
// copy functions for currents and constants for capacitances
//
ElectricalDevice[] devices = potentialMapping.getElectricalDevices();
for (int j = 0; j < devices.length; j++) {
if (devices[j] instanceof MembraneElectricalDevice) {
MembraneElectricalDevice membraneElectricalDevice = (MembraneElectricalDevice) devices[j];
MembraneMapping memMapping = membraneElectricalDevice.getMembraneMapping();
Parameter specificCapacitanceParm = memMapping.getParameterFromRole(MembraneMapping.ROLE_SpecificCapacitance);
varHash.addVariable(new Constant(getMathSymbol(specificCapacitanceParm, memMapping.getGeometryClass()), getIdentifierSubstitutions(specificCapacitanceParm.getExpression(), specificCapacitanceParm.getUnitDefinition(), memMapping.getGeometryClass())));
ElectricalDevice.ElectricalDeviceParameter transmembraneCurrentParm = membraneElectricalDevice.getParameterFromRole(ElectricalDevice.ROLE_TransmembraneCurrent);
ElectricalDevice.ElectricalDeviceParameter totalCurrentParm = membraneElectricalDevice.getParameterFromRole(ElectricalDevice.ROLE_TotalCurrent);
ElectricalDevice.ElectricalDeviceParameter capacitanceParm = membraneElectricalDevice.getParameterFromRole(ElectricalDevice.ROLE_Capacitance);
GeometryClass geometryClass = membraneElectricalDevice.getMembraneMapping().getGeometryClass();
if (totalCurrentParm != null && /* totalCurrentDensityParm.getExpression()!=null && */
memMapping.getCalculateVoltage()) {
Expression totalCurrentDensityExp = (totalCurrentParm.getExpression() != null) ? (totalCurrentParm.getExpression()) : (new Expression(0.0));
varHash.addVariable(newFunctionOrConstant(getMathSymbol(totalCurrentParm, geometryClass), getIdentifierSubstitutions(totalCurrentDensityExp, totalCurrentParm.getUnitDefinition(), geometryClass), geometryClass));
}
if (transmembraneCurrentParm != null && transmembraneCurrentParm.getExpression() != null && memMapping.getCalculateVoltage()) {
varHash.addVariable(newFunctionOrConstant(getMathSymbol(transmembraneCurrentParm, geometryClass), getIdentifierSubstitutions(transmembraneCurrentParm.getExpression(), transmembraneCurrentParm.getUnitDefinition(), geometryClass), geometryClass));
}
if (capacitanceParm != null && capacitanceParm.getExpression() != null && memMapping.getCalculateVoltage()) {
StructureMappingParameter sizeParameter = membraneElectricalDevice.getMembraneMapping().getSizeParameter();
if (simContext.getGeometry().getDimension() == 0 && (sizeParameter.getExpression() == null || sizeParameter.getExpression().isZero())) {
varHash.addVariable(newFunctionOrConstant(getMathSymbol(capacitanceParm, geometryClass), getIdentifierSubstitutions(Expression.mult(memMapping.getNullSizeParameterValue(), specificCapacitanceParm.getExpression()), capacitanceParm.getUnitDefinition(), geometryClass), geometryClass));
} else {
varHash.addVariable(newFunctionOrConstant(getMathSymbol(capacitanceParm, geometryClass), getIdentifierSubstitutions(capacitanceParm.getExpression(), capacitanceParm.getUnitDefinition(), geometryClass), geometryClass));
}
}
//
if (membraneElectricalDevice.getDependentVoltageExpression() == null) {
// is Voltage Independent?
StructureMapping.StructureMappingParameter initialVoltageParm = memMapping.getInitialVoltageParameter();
varHash.addVariable(newFunctionOrConstant(getMathSymbol(initialVoltageParm, memMapping.getGeometryClass()), getIdentifierSubstitutions(initialVoltageParm.getExpression(), initialVoltageParm.getUnitDefinition(), memMapping.getGeometryClass()), memMapping.getGeometryClass()));
} else //
// membrane forced potential
//
{
varHash.addVariable(newFunctionOrConstant(getMathSymbol(memMapping.getMembrane().getMembraneVoltage(), memMapping.getGeometryClass()), getIdentifierSubstitutions(membraneElectricalDevice.getDependentVoltageExpression(), memMapping.getMembrane().getMembraneVoltage().getUnitDefinition(), memMapping.getGeometryClass()), memMapping.getGeometryClass()));
}
} else if (devices[j] instanceof CurrentClampElectricalDevice) {
CurrentClampElectricalDevice currentClampDevice = (CurrentClampElectricalDevice) devices[j];
// total current = current source (no capacitance)
Parameter totalCurrentParm = currentClampDevice.getParameterFromRole(CurrentClampElectricalDevice.ROLE_TotalCurrent);
Parameter currentParm = currentClampDevice.getParameterFromRole(CurrentClampElectricalDevice.ROLE_TransmembraneCurrent);
// Parameter dependentVoltage = currentClampDevice.getCurrentClampStimulus().getVoltageParameter();
Feature deviceElectrodeFeature = currentClampDevice.getCurrentClampStimulus().getElectrode().getFeature();
Feature groundElectrodeFeature = simContext.getGroundElectrode().getFeature();
Membrane membrane = model.getStructureTopology().getMembrane(deviceElectrodeFeature, groundElectrodeFeature);
GeometryClass geometryClass = null;
if (membrane != null) {
StructureMapping membraneStructureMapping = simContext.getGeometryContext().getStructureMapping(membrane);
geometryClass = membraneStructureMapping.getGeometryClass();
}
varHash.addVariable(newFunctionOrConstant(getMathSymbol(totalCurrentParm, geometryClass), getIdentifierSubstitutions(totalCurrentParm.getExpression(), totalCurrentParm.getUnitDefinition(), geometryClass), geometryClass));
varHash.addVariable(newFunctionOrConstant(getMathSymbol(currentParm, geometryClass), getIdentifierSubstitutions(currentParm.getExpression(), currentParm.getUnitDefinition(), geometryClass), geometryClass));
// varHash.addVariable(newFunctionOrConstant(getMathSymbol(dependentVoltage,null),getIdentifierSubstitutions(currentClampDevice.getDependentVoltageExpression(),dependentVoltage.getUnitDefinition(),null)));
//
// add user-defined parameters
//
ElectricalDevice.ElectricalDeviceParameter[] parameters = currentClampDevice.getParameters();
for (int k = 0; k < parameters.length; k++) {
if (parameters[k].getExpression() != null) {
// guards against voltage parameters that are "variable".
varHash.addVariable(newFunctionOrConstant(getMathSymbol(parameters[k], null), getIdentifierSubstitutions(parameters[k].getExpression(), parameters[k].getUnitDefinition(), geometryClass), geometryClass));
}
}
} else if (devices[j] instanceof VoltageClampElectricalDevice) {
VoltageClampElectricalDevice voltageClampDevice = (VoltageClampElectricalDevice) devices[j];
Feature deviceElectrodeFeature = voltageClampDevice.getVoltageClampStimulus().getElectrode().getFeature();
Feature groundElectrodeFeature = simContext.getGroundElectrode().getFeature();
Membrane membrane = model.getStructureTopology().getMembrane(deviceElectrodeFeature, groundElectrodeFeature);
GeometryClass geometryClass = null;
if (membrane != null) {
StructureMapping membraneStructureMapping = simContext.getGeometryContext().getStructureMapping(membrane);
geometryClass = membraneStructureMapping.getGeometryClass();
}
// total current = current source (no capacitance)
Parameter totalCurrent = voltageClampDevice.getParameterFromRole(VoltageClampElectricalDevice.ROLE_TotalCurrent);
Parameter totalCurrentParm = voltageClampDevice.getParameterFromRole(VoltageClampElectricalDevice.ROLE_TotalCurrent);
Parameter voltageParm = voltageClampDevice.getParameterFromRole(VoltageClampElectricalDevice.ROLE_Voltage);
varHash.addVariable(newFunctionOrConstant(getMathSymbol(totalCurrent, geometryClass), getIdentifierSubstitutions(totalCurrent.getExpression(), totalCurrent.getUnitDefinition(), geometryClass), geometryClass));
varHash.addVariable(newFunctionOrConstant(getMathSymbol(totalCurrentParm, geometryClass), getIdentifierSubstitutions(totalCurrentParm.getExpression(), totalCurrentParm.getUnitDefinition(), geometryClass), geometryClass));
varHash.addVariable(newFunctionOrConstant(getMathSymbol(voltageParm, geometryClass), getIdentifierSubstitutions(voltageParm.getExpression(), voltageParm.getUnitDefinition(), geometryClass), geometryClass));
//
// add user-defined parameters
//
ElectricalDevice.ElectricalDeviceParameter[] parameters = voltageClampDevice.getParameters();
for (int k = 0; k < parameters.length; k++) {
if (parameters[k].getRole() == ElectricalDevice.ROLE_UserDefined) {
varHash.addVariable(newFunctionOrConstant(getMathSymbol(parameters[k], geometryClass), getIdentifierSubstitutions(parameters[k].getExpression(), parameters[k].getUnitDefinition(), geometryClass), geometryClass));
}
}
}
}
} else {
//
for (int j = 0; j < structureMappings.length; j++) {
if (structureMappings[j] instanceof MembraneMapping) {
MembraneMapping memMapping = (MembraneMapping) structureMappings[j];
varHash.addVariable(newFunctionOrConstant(getMathSymbol(memMapping.getMembrane().getMembraneVoltage(), memMapping.getGeometryClass()), getIdentifierSubstitutions(memMapping.getInitialVoltageParameter().getExpression(), memMapping.getInitialVoltageParameter().getUnitDefinition(), memMapping.getGeometryClass()), memMapping.getGeometryClass()));
}
}
}
//
for (int j = 0; j < structureMappings.length; j++) {
if (structureMappings[j] instanceof MembraneMapping) {
MembraneMapping membraneMapping = (MembraneMapping) structureMappings[j];
Membrane.MembraneVoltage membraneVoltage = membraneMapping.getMembrane().getMembraneVoltage();
ElectricalDevice[] membraneDevices = potentialMapping.getElectricalDevices(membraneMapping.getMembrane());
// ElectricalDevice membraneDevice = null;
for (int i = 0; i < membraneDevices.length; i++) {
if (membraneDevices[i].hasCapacitance() && membraneDevices[i].getDependentVoltageExpression() == null) {
GeometryClass geometryClass = membraneMapping.getGeometryClass();
if (geometryClass == null) {
throw new MappingException("Application '" + getSimulationContext().getName() + "'\nGeometry->StructureMapping->(" + structureMappings[j].getStructure().getTypeName() + ")'" + structureMappings[j].getStructure().getName() + "' must be mapped to geometry domain.\n(see 'Problems' tab)");
}
Domain domain = new Domain(geometryClass);
if (membraneMapping.getCalculateVoltage() && bCalculatePotential) {
if (geometryClass instanceof SurfaceClass) {
//
if (mathDesc.getVariable(Membrane.MEMBRANE_VOLTAGE_REGION_NAME) == null) {
// varHash.addVariable(new MembraneRegionVariable(MembraneVoltage.MEMBRANE_VOLTAGE_REGION_NAME));
varHash.addVariable(new MembraneRegionVariable(getMathSymbol(membraneVoltage, geometryClass), domain));
}
} else {
//
// spatially unresolved membrane, and must solve for potential ... make VolVariable for this compartment
//
varHash.addVariable(new VolVariable(getMathSymbol(membraneVoltage, geometryClass), domain));
}
Parameter initialVoltageParm = membraneMapping.getInitialVoltageParameter();
Variable initVoltageFunction = newFunctionOrConstant(getMathSymbol(initialVoltageParm, geometryClass), getIdentifierSubstitutions(initialVoltageParm.getExpression(), initialVoltageParm.getUnitDefinition(), geometryClass), geometryClass);
varHash.addVariable(initVoltageFunction);
} else {
//
// don't calculate voltage, still may need it though
//
Parameter initialVoltageParm = membraneMapping.getInitialVoltageParameter();
Variable voltageFunction = newFunctionOrConstant(getMathSymbol(membraneMapping.getMembrane().getMembraneVoltage(), geometryClass), getIdentifierSubstitutions(initialVoltageParm.getExpression(), initialVoltageParm.getUnitDefinition(), geometryClass), geometryClass);
varHash.addVariable(voltageFunction);
}
}
}
}
}
//
for (int j = 0; j < reactionSteps.length; j++) {
ReactionStep rs = reactionSteps[j];
if (simContext.getReactionContext().getReactionSpec(rs).isExcluded()) {
continue;
}
Kinetics.KineticsParameter[] parameters = rs.getKinetics().getKineticsParameters();
GeometryClass geometryClass = null;
if (rs.getStructure() != null) {
geometryClass = simContext.getGeometryContext().getStructureMapping(rs.getStructure()).getGeometryClass();
}
if (parameters != null) {
for (int i = 0; i < parameters.length; i++) {
if (((parameters[i].getRole() == Kinetics.ROLE_CurrentDensity) || (parameters[i].getRole() == Kinetics.ROLE_LumpedCurrent)) && (parameters[i].getExpression() == null || parameters[i].getExpression().isZero())) {
continue;
}
varHash.addVariable(newFunctionOrConstant(getMathSymbol(parameters[i], geometryClass), getIdentifierSubstitutions(parameters[i].getExpression(), parameters[i].getUnitDefinition(), geometryClass), geometryClass));
}
}
}
//
// initial constants (either function or constant)
//
SpeciesContextSpec[] speciesContextSpecs = simContext.getReactionContext().getSpeciesContextSpecs();
for (int i = 0; i < speciesContextSpecs.length; i++) {
// add initial count if present (!= null)
SpeciesContextSpecParameter initCountParm = speciesContextSpecs[i].getParameterFromRole(SpeciesContextSpec.ROLE_InitialCount);
SpeciesContext speciesContext = speciesContextSpecs[i].getSpeciesContext();
if (initCountParm != null && initCountParm.getExpression() != null) {
Expression initCountExpr = new Expression(initCountParm.getExpression());
StructureMapping sm = simContext.getGeometryContext().getStructureMapping(speciesContext.getStructure());
String[] symbols = initCountExpr.getSymbols();
// Check if 'initExpr' has other speciesContexts in its expression, need to replace it with 'spContext_init'
for (int j = 0; symbols != null && j < symbols.length; j++) {
// if symbol is a speciesContext, replacing it with a reference to initial condition for that speciesContext.
SpeciesContext spC = null;
SymbolTableEntry ste = initCountExpr.getSymbolBinding(symbols[j]);
if (ste instanceof SpeciesContextSpecProxyParameter) {
SpeciesContextSpecProxyParameter spspp = (SpeciesContextSpecProxyParameter) ste;
if (spspp.getTarget() instanceof SpeciesContext) {
spC = (SpeciesContext) spspp.getTarget();
SpeciesContextSpec spcspec = simContext.getReactionContext().getSpeciesContextSpec(spC);
SpeciesContextSpecParameter spCInitParm = spcspec.getParameterFromRole(SpeciesContextSpec.ROLE_InitialCount);
// need to get init condn expression, but can't get it from getMathSymbol() (mapping between bio and math), hence get it as below.
Expression scsInitExpr = new Expression(spCInitParm, getNameScope());
// scsInitExpr.bindExpression(this);
initCountExpr.substituteInPlace(new Expression(spC.getName()), scsInitExpr);
}
}
}
// now create the appropriate function for the current speciesContextSpec.
varHash.addVariable(newFunctionOrConstant(getMathSymbol(initCountParm, sm.getGeometryClass()), getIdentifierSubstitutions(initCountExpr, initCountParm.getUnitDefinition(), sm.getGeometryClass()), sm.getGeometryClass()));
}
// add initial concentration (may be derived from initial count if necessary)
SpeciesContextSpecParameter initConcParm = speciesContextSpecs[i].getParameterFromRole(SpeciesContextSpec.ROLE_InitialConcentration);
if (initConcParm != null) {
Expression initConcExpr = null;
if (initConcParm.getExpression() != null) {
initConcExpr = new Expression(initConcParm.getExpression());
} else if (initCountParm != null && initCountParm.getExpression() != null) {
Expression structureSizeExpr = new Expression(speciesContext.getStructure().getStructureSize(), getNameScope());
VCUnitDefinition concUnit = initConcParm.getUnitDefinition();
VCUnitDefinition countDensityUnit = initCountParm.getUnitDefinition().divideBy(speciesContext.getStructure().getStructureSize().getUnitDefinition());
Expression unitFactor = getUnitFactor(concUnit.divideBy(countDensityUnit));
initConcExpr = Expression.mult(Expression.div(new Expression(initCountParm, getNameScope()), structureSizeExpr), unitFactor);
}
StructureMapping sm = simContext.getGeometryContext().getStructureMapping(speciesContext.getStructure());
String[] symbols = initConcExpr.getSymbols();
// Check if 'initExpr' has other speciesContexts in its expression, need to replace it with 'spContext_init'
for (int j = 0; symbols != null && j < symbols.length; j++) {
// if symbol is a speciesContext, replacing it with a reference to initial condition for that speciesContext.
SpeciesContext spC = null;
SymbolTableEntry ste = initConcExpr.getSymbolBinding(symbols[j]);
if (ste instanceof SpeciesContextSpecProxyParameter) {
SpeciesContextSpecProxyParameter spspp = (SpeciesContextSpecProxyParameter) ste;
if (spspp.getTarget() instanceof SpeciesContext) {
spC = (SpeciesContext) spspp.getTarget();
SpeciesContextSpec spcspec = simContext.getReactionContext().getSpeciesContextSpec(spC);
SpeciesContextSpecParameter spCInitParm = spcspec.getParameterFromRole(SpeciesContextSpec.ROLE_InitialConcentration);
// if initConc param expression is null, try initCount
if (spCInitParm.getExpression() == null) {
spCInitParm = spcspec.getParameterFromRole(SpeciesContextSpec.ROLE_InitialCount);
}
// need to get init condn expression, but can't get it from getMathSymbol() (mapping between bio and math), hence get it as below.
Expression scsInitExpr = new Expression(spCInitParm, getNameScope());
// scsInitExpr.bindExpression(this);
initConcExpr.substituteInPlace(new Expression(spC.getName()), scsInitExpr);
}
}
}
// now create the appropriate function for the current speciesContextSpec.
varHash.addVariable(newFunctionOrConstant(getMathSymbol(initConcParm, sm.getGeometryClass()), getIdentifierSubstitutions(initConcExpr, initConcParm.getUnitDefinition(), sm.getGeometryClass()), sm.getGeometryClass()));
}
}
//
for (int i = 0; i < speciesContextSpecs.length; i++) {
SpeciesContextMapping scm = getSpeciesContextMapping(speciesContextSpecs[i].getSpeciesContext());
SpeciesContextSpec.SpeciesContextSpecParameter diffParm = speciesContextSpecs[i].getParameterFromRole(SpeciesContextSpec.ROLE_DiffusionRate);
if (diffParm != null && (scm.isPDERequired())) {
StructureMapping sm = simContext.getGeometryContext().getStructureMapping(speciesContextSpecs[i].getSpeciesContext().getStructure());
varHash.addVariable(newFunctionOrConstant(getMathSymbol(diffParm, sm.getGeometryClass()), getIdentifierSubstitutions(diffParm.getExpression(), diffParm.getUnitDefinition(), sm.getGeometryClass()), sm.getGeometryClass()));
}
}
//
for (int i = 0; i < speciesContextSpecs.length; i++) {
SpeciesContextSpec.SpeciesContextSpecParameter bc_xm = speciesContextSpecs[i].getParameterFromRole(SpeciesContextSpec.ROLE_BoundaryValueXm);
StructureMapping sm = simContext.getGeometryContext().getStructureMapping(speciesContextSpecs[i].getSpeciesContext().getStructure());
if (bc_xm != null && (bc_xm.getExpression() != null)) {
varHash.addVariable(newFunctionOrConstant(getMathSymbol(bc_xm, sm.getGeometryClass()), getIdentifierSubstitutions(bc_xm.getExpression(), bc_xm.getUnitDefinition(), sm.getGeometryClass()), sm.getGeometryClass()));
}
SpeciesContextSpec.SpeciesContextSpecParameter bc_xp = speciesContextSpecs[i].getParameterFromRole(SpeciesContextSpec.ROLE_BoundaryValueXp);
if (bc_xp != null && (bc_xp.getExpression() != null)) {
varHash.addVariable(newFunctionOrConstant(getMathSymbol(bc_xp, sm.getGeometryClass()), getIdentifierSubstitutions(bc_xp.getExpression(), bc_xp.getUnitDefinition(), sm.getGeometryClass()), sm.getGeometryClass()));
}
SpeciesContextSpec.SpeciesContextSpecParameter bc_ym = speciesContextSpecs[i].getParameterFromRole(SpeciesContextSpec.ROLE_BoundaryValueYm);
if (bc_ym != null && (bc_ym.getExpression() != null)) {
varHash.addVariable(newFunctionOrConstant(getMathSymbol(bc_ym, sm.getGeometryClass()), getIdentifierSubstitutions(bc_ym.getExpression(), bc_ym.getUnitDefinition(), sm.getGeometryClass()), sm.getGeometryClass()));
}
SpeciesContextSpec.SpeciesContextSpecParameter bc_yp = speciesContextSpecs[i].getParameterFromRole(SpeciesContextSpec.ROLE_BoundaryValueYp);
if (bc_yp != null && (bc_yp.getExpression() != null)) {
varHash.addVariable(newFunctionOrConstant(getMathSymbol(bc_yp, sm.getGeometryClass()), getIdentifierSubstitutions(bc_yp.getExpression(), bc_yp.getUnitDefinition(), sm.getGeometryClass()), sm.getGeometryClass()));
}
SpeciesContextSpec.SpeciesContextSpecParameter bc_zm = speciesContextSpecs[i].getParameterFromRole(SpeciesContextSpec.ROLE_BoundaryValueZm);
if (bc_zm != null && (bc_zm.getExpression() != null)) {
varHash.addVariable(newFunctionOrConstant(getMathSymbol(bc_zm, sm.getGeometryClass()), getIdentifierSubstitutions(bc_zm.getExpression(), bc_zm.getUnitDefinition(), sm.getGeometryClass()), sm.getGeometryClass()));
}
SpeciesContextSpec.SpeciesContextSpecParameter bc_zp = speciesContextSpecs[i].getParameterFromRole(SpeciesContextSpec.ROLE_BoundaryValueZp);
if (bc_zp != null && (bc_zp.getExpression() != null)) {
varHash.addVariable(newFunctionOrConstant(getMathSymbol(bc_zp, sm.getGeometryClass()), getIdentifierSubstitutions(bc_zp.getExpression(), bc_zp.getUnitDefinition(), sm.getGeometryClass()), sm.getGeometryClass()));
}
}
//
for (int i = 0; i < speciesContextSpecs.length; i++) {
SpeciesContextSpec.SpeciesContextSpecParameter advection_velX = speciesContextSpecs[i].getParameterFromRole(SpeciesContextSpec.ROLE_VelocityX);
StructureMapping sm = simContext.getGeometryContext().getStructureMapping(speciesContextSpecs[i].getSpeciesContext().getStructure());
GeometryClass geometryClass = sm.getGeometryClass();
if (advection_velX != null && (advection_velX.getExpression() != null)) {
varHash.addVariable(newFunctionOrConstant(getMathSymbol(advection_velX, geometryClass), getIdentifierSubstitutions(advection_velX.getExpression(), advection_velX.getUnitDefinition(), geometryClass), geometryClass));
}
SpeciesContextSpec.SpeciesContextSpecParameter advection_velY = speciesContextSpecs[i].getParameterFromRole(SpeciesContextSpec.ROLE_VelocityY);
if (advection_velY != null && (advection_velY.getExpression() != null)) {
varHash.addVariable(newFunctionOrConstant(getMathSymbol(advection_velY, geometryClass), getIdentifierSubstitutions(advection_velY.getExpression(), advection_velY.getUnitDefinition(), geometryClass), geometryClass));
}
SpeciesContextSpec.SpeciesContextSpecParameter advection_velZ = speciesContextSpecs[i].getParameterFromRole(SpeciesContextSpec.ROLE_VelocityZ);
if (advection_velZ != null && (advection_velZ.getExpression() != null)) {
varHash.addVariable(newFunctionOrConstant(getMathSymbol(advection_velZ, geometryClass), getIdentifierSubstitutions(advection_velZ.getExpression(), advection_velZ.getUnitDefinition(), geometryClass), geometryClass));
}
}
//
// constant species (either function or constant)
//
enum1 = getSpeciesContextMappings();
while (enum1.hasMoreElements()) {
SpeciesContextMapping scm = (SpeciesContextMapping) enum1.nextElement();
if (scm.getVariable() instanceof Constant) {
varHash.addVariable(scm.getVariable());
}
}
//
// conversion factors
//
varHash.addVariable(new Constant(model.getKMOLE().getName(), getIdentifierSubstitutions(model.getKMOLE().getExpression(), model.getKMOLE().getUnitDefinition(), null)));
varHash.addVariable(new Constant(model.getN_PMOLE().getName(), getIdentifierSubstitutions(model.getN_PMOLE().getExpression(), model.getN_PMOLE().getUnitDefinition(), null)));
varHash.addVariable(new Constant(model.getKMILLIVOLTS().getName(), getIdentifierSubstitutions(model.getKMILLIVOLTS().getExpression(), model.getKMILLIVOLTS().getUnitDefinition(), null)));
varHash.addVariable(new Constant(model.getK_GHK().getName(), getIdentifierSubstitutions(model.getK_GHK().getExpression(), model.getK_GHK().getUnitDefinition(), null)));
//
for (int i = 0; i < structureMappings.length; i++) {
StructureMapping sm = structureMappings[i];
if (simContext.getGeometry().getDimension() == 0) {
StructureMappingParameter sizeParm = sm.getSizeParameter();
if (sizeParm != null && sizeParm.getExpression() != null) {
varHash.addVariable(newFunctionOrConstant(getMathSymbol(sizeParm, sm.getGeometryClass()), getIdentifierSubstitutions(sizeParm.getExpression(), sizeParm.getUnitDefinition(), sm.getGeometryClass()), sm.getGeometryClass()));
} else {
if (sm instanceof MembraneMapping) {
MembraneMapping mm = (MembraneMapping) sm;
StructureMappingParameter volFrac = mm.getVolumeFractionParameter();
if (volFrac != null && volFrac.getExpression() != null) {
varHash.addVariable(newFunctionOrConstant(getMathSymbol(volFrac, sm.getGeometryClass()), getIdentifierSubstitutions(volFrac.getExpression(), volFrac.getUnitDefinition(), sm.getGeometryClass()), sm.getGeometryClass()));
}
StructureMappingParameter surfToVol = mm.getSurfaceToVolumeParameter();
if (surfToVol != null && surfToVol.getExpression() != null) {
varHash.addVariable(newFunctionOrConstant(getMathSymbol(surfToVol, sm.getGeometryClass()), getIdentifierSubstitutions(surfToVol.getExpression(), surfToVol.getUnitDefinition(), sm.getGeometryClass()), sm.getGeometryClass()));
}
}
}
} else {
Parameter parm = sm.getParameterFromRole(StructureMapping.ROLE_AreaPerUnitArea);
if (parm != null && parm.getExpression() != null && sm.getGeometryClass() instanceof SurfaceClass) {
varHash.addVariable(newFunctionOrConstant(getMathSymbol(parm, sm.getGeometryClass()), getIdentifierSubstitutions(parm.getExpression(), parm.getUnitDefinition(), sm.getGeometryClass()), sm.getGeometryClass()));
}
parm = sm.getParameterFromRole(StructureMapping.ROLE_AreaPerUnitVolume);
if (parm != null && parm.getExpression() != null && sm.getGeometryClass() instanceof SubVolume) {
varHash.addVariable(newFunctionOrConstant(getMathSymbol(parm, sm.getGeometryClass()), getIdentifierSubstitutions(parm.getExpression(), parm.getUnitDefinition(), sm.getGeometryClass()), sm.getGeometryClass()));
}
parm = sm.getParameterFromRole(StructureMapping.ROLE_VolumePerUnitArea);
if (parm != null && parm.getExpression() != null && sm.getGeometryClass() instanceof SurfaceClass) {
varHash.addVariable(newFunctionOrConstant(getMathSymbol(parm, sm.getGeometryClass()), getIdentifierSubstitutions(parm.getExpression(), parm.getUnitDefinition(), sm.getGeometryClass()), sm.getGeometryClass()));
}
parm = sm.getParameterFromRole(StructureMapping.ROLE_VolumePerUnitVolume);
if (parm != null && parm.getExpression() != null && sm.getGeometryClass() instanceof SubVolume) {
varHash.addVariable(newFunctionOrConstant(getMathSymbol(parm, sm.getGeometryClass()), getIdentifierSubstitutions(parm.getExpression(), parm.getUnitDefinition(), sm.getGeometryClass()), sm.getGeometryClass()));
}
}
StructureMappingParameter sizeParm = sm.getSizeParameter();
if (sm.getGeometryClass() != null && sizeParm != null) {
if (simContext.getGeometry().getDimension() == 0) {
if (sizeParm.getExpression() != null) {
varHash.addVariable(newFunctionOrConstant(getMathSymbol(sizeParm, sm.getGeometryClass()), getIdentifierSubstitutions(sizeParm.getExpression(), sizeParm.getUnitDefinition(), sm.getGeometryClass()), sm.getGeometryClass()));
}
} else {
String compartmentName = sm.getGeometryClass().getName();
VCUnitDefinition sizeUnit = sm.getSizeParameter().getUnitDefinition();
String sizeFunctionName = null;
if (sm instanceof MembraneMapping) {
MembraneMapping mm = (MembraneMapping) sm;
if (mm.getGeometryClass() instanceof SurfaceClass) {
sizeFunctionName = MathFunctionDefinitions.Function_regionArea_current.getFunctionName();
} else if (mm.getGeometryClass() instanceof SubVolume) {
sizeFunctionName = MathFunctionDefinitions.Function_regionVolume_current.getFunctionName();
}
} else if (sm instanceof FeatureMapping) {
sizeFunctionName = MathFunctionDefinitions.Function_regionVolume_current.getFunctionName();
} else {
throw new RuntimeException("structure mapping " + sm.getClass().getName() + " not yet supported");
}
Expression totalVolumeCorrection = sm.getStructureSizeCorrection(simContext, this);
Expression sizeFunctionExpression = Expression.function(sizeFunctionName, new Expression[] { new Expression("'" + compartmentName + "'") });
// sizeFunctionExpression.bindExpression(mathDesc);
varHash.addVariable(newFunctionOrConstant(getMathSymbol(sizeParm, sm.getGeometryClass()), getIdentifierSubstitutions(Expression.mult(totalVolumeCorrection, sizeFunctionExpression), sizeUnit, sm.getGeometryClass()), sm.getGeometryClass()));
}
}
}
//
for (SymbolTableEntry rrvSTE : rateRuleVarTargets) {
if (rrvSTE instanceof SpeciesContext) {
SpeciesContext rateRuleSpContext = (SpeciesContext) rrvSTE;
// check if speciesContext has already been added as a vol/membrane var
SpeciesContextMapping scm = getSpeciesContextMapping(rateRuleSpContext);
if (scm.getVariable() instanceof VolVariable || scm.getVariable() instanceof MemVariable) {
throw new RuntimeException("SpeciesContext '" + rrvSTE.getName() + "' has an equation and is also a rate rule variable, which is not allowed.");
}
// get the initial condition expression of the speciesContext.
SpeciesContextSpec speciesContextSpec = simContext.getReactionContext().getSpeciesContextSpec(rateRuleSpContext);
SpeciesContextSpecParameter scsInitParam = speciesContextSpec.getInitialConditionParameter();
Expression scInitExpr = scsInitParam.getExpression();
GeometryClass geometryClass = getDefaultGeometryClass(scInitExpr);
VCUnitDefinition scsInitParamUnit = scsInitParam.getUnitDefinition();
scInitExpr = getIdentifierSubstitutions(scInitExpr, scsInitParamUnit, geometryClass);
EventAssignmentOrRateRuleInitParameter eap = null;
try {
// create an eventAssgnmentOrRateRuleInitParameter for the rate rule variable
eap = addEventAssignmentOrRateRuleInitParameter(rateRuleSpContext, scInitExpr, PARAMETER_ROLE_EVENTASSIGN_OR_RATERULE_INITCONDN, scsInitParamUnit);
} catch (PropertyVetoException e) {
e.printStackTrace(System.out);
throw new MappingException(e.getMessage());
}
// create a volVariable for this speciesContext (shouldn't have one already - since a speciesContext that has a rate rule should not participate in a reaction.
VolVariable volVar = new VolVariable(rateRuleSpContext.getName(), null);
varHash.addVariable(volVar);
eventOrRateRuleVolVarHash.put(volVar, eap);
// create the rate parameter
RateRuleRateParameter rateParam = null;
try {
Expression origExp = simContext.getRateRule(rateRuleSpContext).getRateRuleExpression();
VCUnitDefinition rateUnit = modelUnitSystem.getInstance_TBD();
if (scsInitParamUnit != null && !scsInitParamUnit.equals(modelUnitSystem.getInstance_TBD())) {
rateUnit = scsInitParamUnit.divideBy(timeUnit);
}
Expression rateExpr = getIdentifierSubstitutions(origExp, rateUnit, geometryClass);
rateParam = addRateRuleRateParameter(rateRuleSpContext, rateExpr, PARAMETER_ROLE_RATERULE_RATE, rateUnit);
} catch (PropertyVetoException e) {
e.printStackTrace(System.out);
throw new MappingException(e.getMessage());
}
rateRuleRateParamHash.put(volVar, rateParam);
}
// end if (ste instanceof SC)
}
//
for (int i = 0; i < fieldMathMappingParameters.length; i++) {
GeometryClass geometryClass = fieldMathMappingParameters[i].getGeometryClass();
varHash.addVariable(newFunctionOrConstant(getMathSymbol(fieldMathMappingParameters[i], geometryClass), getIdentifierSubstitutions(fieldMathMappingParameters[i].getExpression(), fieldMathMappingParameters[i].getUnitDefinition(), geometryClass), fieldMathMappingParameters[i].getGeometryClass()));
}
//
// functions
//
enum1 = getSpeciesContextMappings();
RateRule[] rateRules = simContext.getRateRules();
while (enum1.hasMoreElements()) {
SpeciesContextMapping scm = (SpeciesContextMapping) enum1.nextElement();
if (scm.getVariable() == null && scm.getDependencyExpression() != null) {
// check if speciesContext has a rateRule; then the speciesContext should not be added as a constant
if (rateRules == null) {
if (simContext.getRateRule(scm.getSpeciesContext()) == null) {
StructureMapping sm = simContext.getGeometryContext().getStructureMapping(scm.getSpeciesContext().getStructure());
if (sm.getGeometryClass() == null) {
Structure s = sm.getStructure();
if (s != null) {
throw new RuntimeException("unmapped structure " + s.getName());
}
throw new RuntimeException("structure mapping with no structure or mapping");
}
Variable dependentVariable = newFunctionOrConstant(getMathSymbol(scm.getSpeciesContext(), sm.getGeometryClass()), getIdentifierSubstitutions(scm.getDependencyExpression(), scm.getSpeciesContext().getUnitDefinition(), sm.getGeometryClass()), sm.getGeometryClass());
dependentVariable.setDomain(new Domain(sm.getGeometryClass()));
varHash.addVariable(dependentVariable);
}
}
}
}
BioEvent[] bioevents = simContext.getBioEvents();
if (bioevents != null && bioevents.length > 0) {
for (BioEvent be : bioevents) {
// transform the bioEvent trigger/delay to math Event
for (LocalParameter p : be.getEventParameters()) {
if (p.getExpression() != null) {
varHash.addVariable(newFunctionOrConstant(getMathSymbol(p, null), getIdentifierSubstitutions(p.getExpression(), p.getUnitDefinition(), null), null));
} else if (be.getParameter(BioEventParameterType.GeneralTriggerFunction) == p) {
//
// use generated function here.
//
varHash.addVariable(newFunctionOrConstant(getMathSymbol(p, null), getIdentifierSubstitutions(be.generateTriggerExpression(), p.getUnitDefinition(), null), null));
}
}
}
}
//
// set Variables to MathDescription all at once with the order resolved by "VariableHash"
//
mathDesc.setAllVariables(varHash.getAlphabeticallyOrderedVariables());
//
if (simContext.getGeometryContext().getGeometry() != null) {
try {
mathDesc.setGeometry(simContext.getGeometryContext().getGeometry());
} catch (java.beans.PropertyVetoException e) {
e.printStackTrace(System.out);
throw new MappingException("failure setting geometry " + e.getMessage());
}
} else {
throw new MappingException("geometry must be defined");
}
//
for (CompartmentSubdomainContext compartmentSubDomainContext : compartmentSubdomainContexts) {
SubVolume subVolume = compartmentSubDomainContext.subvolume;
CompartmentSubDomain subDomain = mathDesc.getCompartmentSubDomain(subVolume.getName());
//
// assign boundary condition types
//
StructureMapping[] mappedSMs = simContext.getGeometryContext().getStructureMappings(subVolume);
FeatureMapping mappedFM = null;
for (int i = 0; i < mappedSMs.length; i++) {
if (mappedSMs[i] instanceof FeatureMapping) {
if (mappedFM != null) {
lg.warn("WARNING:::: MathMapping.refreshMathDescription() ... assigning boundary condition types not unique");
}
mappedFM = (FeatureMapping) mappedSMs[i];
}
}
if (mappedFM != null) {
if (simContext.getGeometry().getDimension() > 0) {
subDomain.setBoundaryConditionXm(mappedFM.getBoundaryConditionTypeXm());
subDomain.setBoundaryConditionXp(mappedFM.getBoundaryConditionTypeXp());
}
if (simContext.getGeometry().getDimension() > 1) {
subDomain.setBoundaryConditionYm(mappedFM.getBoundaryConditionTypeYm());
subDomain.setBoundaryConditionYp(mappedFM.getBoundaryConditionTypeYp());
}
if (simContext.getGeometry().getDimension() > 2) {
subDomain.setBoundaryConditionZm(mappedFM.getBoundaryConditionTypeZm());
subDomain.setBoundaryConditionZp(mappedFM.getBoundaryConditionTypeZp());
}
}
//
// create equations
//
VolumeStructureAnalyzer structureAnalyzer = getVolumeStructureAnalyzer(subVolume);
Enumeration<SpeciesContextMapping> enumSCM = getSpeciesContextMappings();
while (enumSCM.hasMoreElements()) {
SpeciesContextMapping scm = enumSCM.nextElement();
SpeciesContext sc = scm.getSpeciesContext();
StructureMapping sm = simContext.getGeometryContext().getStructureMapping(sc.getStructure());
SpeciesContextSpec scs = simContext.getReactionContext().getSpeciesContextSpec(sc);
//
// if an independent volume variable, then create equation for it (if mapped to this subDomain)
//
final GeometryClass gc = sm.getGeometryClass();
if (gc == null || !gc.getName().equals(subDomain.getName())) {
continue;
}
SpeciesContextSpecParameter initConcParameter = scs.getParameterFromRole(SpeciesContextSpec.ROLE_InitialConcentration);
if ((scm.getVariable() instanceof VolumeRegionVariable) && scm.getDependencyExpression() == null) {
VolumeRegionVariable volumeRegionVariable = (VolumeRegionVariable) scm.getVariable();
Expression initial = getIdentifierSubstitutions(new Expression(initConcParameter, getNameScope()), initConcParameter.getUnitDefinition(), sm.getGeometryClass());
Expression rate = getIdentifierSubstitutions(scm.getRate(), scm.getSpeciesContext().getUnitDefinition().divideBy(timeUnit), simContext.getGeometryContext().getStructureMapping(sc.getStructure()).getGeometryClass());
VolumeRegionEquation volumeRegionEquation = new VolumeRegionEquation(volumeRegionVariable, initial);
volumeRegionEquation.setVolumeRateExpression(rate);
subDomain.addEquation(volumeRegionEquation);
} else if (scm.getVariable() instanceof VolVariable && scm.getDependencyExpression() == null) {
VolVariable variable = (VolVariable) scm.getVariable();
Equation equation = null;
if (sm.getGeometryClass() == subVolume) {
if (scm.isPDERequired()) {
//
// species context belongs to this subDomain
//
Expression initial = getIdentifierSubstitutions(new Expression(initConcParameter, getNameScope()), initConcParameter.getUnitDefinition(), sm.getGeometryClass());
Expression rate = getIdentifierSubstitutions(scm.getRate(), scm.getSpeciesContext().getUnitDefinition().divideBy(timeUnit), simContext.getGeometryContext().getStructureMapping(sc.getStructure()).getGeometryClass());
SpeciesContextSpecParameter diffusionParameter = scs.getDiffusionParameter();
Expression diffusion = getIdentifierSubstitutions(new Expression(diffusionParameter, getNameScope()), diffusionParameter.getUnitDefinition(), sm.getGeometryClass());
equation = new PdeEquation(variable, initial, rate, diffusion);
((PdeEquation) equation).setBoundaryXm((scs.getBoundaryXmParameter().getExpression() == null) ? (null) : new Expression(getMathSymbol(scs.getBoundaryXmParameter(), sm.getGeometryClass())));
((PdeEquation) equation).setBoundaryXp((scs.getBoundaryXpParameter().getExpression() == null) ? (null) : new Expression(getMathSymbol(scs.getBoundaryXpParameter(), sm.getGeometryClass())));
((PdeEquation) equation).setBoundaryYm((scs.getBoundaryYmParameter().getExpression() == null) ? (null) : new Expression(getMathSymbol(scs.getBoundaryYmParameter(), sm.getGeometryClass())));
((PdeEquation) equation).setBoundaryYp((scs.getBoundaryYpParameter().getExpression() == null) ? (null) : new Expression(getMathSymbol(scs.getBoundaryYpParameter(), sm.getGeometryClass())));
((PdeEquation) equation).setBoundaryZm((scs.getBoundaryZmParameter().getExpression() == null) ? (null) : new Expression(getMathSymbol(scs.getBoundaryZmParameter(), sm.getGeometryClass())));
((PdeEquation) equation).setBoundaryZp((scs.getBoundaryZpParameter().getExpression() == null) ? (null) : new Expression(getMathSymbol(scs.getBoundaryZpParameter(), sm.getGeometryClass())));
if (simContext.getGeometry().getDimension() >= 1) {
Expression velXExp = null;
if (scs.getVelocityXParameter().getExpression() != null) {
velXExp = new Expression(getMathSymbol(scs.getVelocityXParameter(), sm.getGeometryClass()));
} else {
SpatialQuantity[] velX_quantities = scs.getVelocityQuantities(QuantityComponent.X);
if (velX_quantities.length > 0) {
int numRegions = simContext.getGeometry().getGeometrySurfaceDescription().getGeometricRegions(subVolume).length;
if (velX_quantities.length == 1 && numRegions == 1) {
velXExp = new Expression(getMathSymbol(velX_quantities[0], sm.getGeometryClass()));
} else {
throw new MappingException("multiple advection velocities enabled set for multiple volume domains ");
}
}
}
((PdeEquation) equation).setVelocityX(velXExp);
}
if (simContext.getGeometry().getDimension() >= 2) {
Expression velYExp = null;
if (scs.getVelocityYParameter().getExpression() != null) {
velYExp = new Expression(getMathSymbol(scs.getVelocityYParameter(), sm.getGeometryClass()));
} else {
SpatialQuantity[] velY_quantities = scs.getVelocityQuantities(QuantityComponent.Y);
if (velY_quantities.length > 0) {
int numRegions = simContext.getGeometry().getGeometrySurfaceDescription().getGeometricRegions(subVolume).length;
if (velY_quantities.length == 1 && numRegions == 1) {
velYExp = new Expression(getMathSymbol(velY_quantities[0], sm.getGeometryClass()));
} else {
throw new MappingException("multiple advection velocities enabled set for multiple volume domains ");
}
}
}
((PdeEquation) equation).setVelocityY(velYExp);
}
if (simContext.getGeometry().getDimension() == 3) {
Expression velZExp = null;
if (scs.getVelocityZParameter().getExpression() != null) {
velZExp = new Expression(getMathSymbol(scs.getVelocityZParameter(), sm.getGeometryClass()));
} else {
SpatialQuantity[] velZ_quantities = scs.getVelocityQuantities(QuantityComponent.Z);
if (velZ_quantities.length > 0) {
int numRegions = simContext.getGeometry().getGeometrySurfaceDescription().getGeometricRegions(subVolume).length;
if (velZ_quantities.length == 1 && numRegions == 1) {
velZExp = new Expression(getMathSymbol(velZ_quantities[0], sm.getGeometryClass()));
} else {
throw new MappingException("multiple advection velocities enabled set for multiple volume domains ");
}
}
}
((PdeEquation) equation).setVelocityZ(velZExp);
}
subDomain.replaceEquation(equation);
} else {
//
// ODE - species context belongs to this subDomain
//
Expression initial = new Expression(getMathSymbol(initConcParameter, null));
Expression rate = (scm.getRate() == null) ? new Expression(0.0) : getIdentifierSubstitutions(scm.getRate(), scm.getSpeciesContext().getUnitDefinition().divideBy(timeUnit), simContext.getGeometryContext().getStructureMapping(sc.getStructure()).getGeometryClass());
equation = new OdeEquation(variable, initial, rate);
subDomain.replaceEquation(equation);
}
}
}
}
//
// create fast system (if neccessary)
//
SpeciesContextMapping[] fastSpeciesContextMappings = structureAnalyzer.getFastSpeciesContextMappings();
if (fastSpeciesContextMappings != null) {
FastSystem fastSystem = new FastSystem(mathDesc);
for (int i = 0; i < fastSpeciesContextMappings.length; i++) {
SpeciesContextMapping scm = fastSpeciesContextMappings[i];
if (scm.getFastInvariant() == null) {
//
// independant-fast variable, create a fastRate object
//
Expression rate = getIdentifierSubstitutions(scm.getFastRate(), scm.getSpeciesContext().getUnitDefinition().divideBy(timeUnit), subVolume);
FastRate fastRate = new FastRate(rate);
fastSystem.addFastRate(fastRate);
} else {
//
// dependant-fast variable, create a fastInvariant object
//
Expression rate = getIdentifierSubstitutions(scm.getFastInvariant(), modelUnitSystem.getVolumeConcentrationUnit(), subVolume);
FastInvariant fastInvariant = new FastInvariant(rate);
fastSystem.addFastInvariant(fastInvariant);
}
}
subDomain.setFastSystem(fastSystem);
// constructor calls the 'refresh' method which constructs depemdency matrix, dependent/independent vars and pseudoconstants, etc.
// FastSystemAnalyzer fs_analyzer =
new FastSystemAnalyzer(fastSystem, mathDesc);
}
//
// create ode's for voltages to be calculated on unresolved membranes mapped to this subVolume
//
Structure[] localStructures = simContext.getGeometryContext().getStructuresFromGeometryClass(subVolume);
for (int sIndex = 0; sIndex < localStructures.length; sIndex++) {
if (localStructures[sIndex] instanceof Membrane) {
Membrane membrane = (Membrane) localStructures[sIndex];
MembraneMapping membraneMapping = (MembraneMapping) simContext.getGeometryContext().getStructureMapping(membrane);
if ((membraneMapping.getGeometryClass() instanceof SubVolume) && membraneMapping.getCalculateVoltage()) {
MembraneElectricalDevice capacitiveDevice = potentialMapping.getCapacitiveDevice(membrane);
if (capacitiveDevice.getDependentVoltageExpression() == null) {
VolVariable vVar = (VolVariable) mathDesc.getVariable(getMathSymbol(capacitiveDevice.getVoltageSymbol(), membraneMapping.getGeometryClass()));
Expression initExp = new Expression(getMathSymbol(capacitiveDevice.getMembraneMapping().getInitialVoltageParameter(), membraneMapping.getGeometryClass()));
subDomain.addEquation(new OdeEquation(vVar, initExp, getIdentifierSubstitutions(potentialMapping.getOdeRHS(capacitiveDevice, this), membrane.getMembraneVoltage().getUnitDefinition().divideBy(timeUnit), membraneMapping.getGeometryClass())));
} else {
//
//
//
}
}
}
}
}
//
for (MembraneSubdomainContext memSubdomainContext : membraneSubdomainContexts) {
MembraneSubDomain memSubDomain = memSubdomainContext.membraneSubdomain;
SurfaceClass surfaceClass = memSubdomainContext.surfaceClass;
for (SurfaceRegionObject surfaceRegionObject : memSubdomainContext.surfaceRegionObjects) {
if (surfaceRegionObject.isQuantityCategoryEnabled(QuantityCategory.SurfaceVelocity)) {
int dim = simContext.getGeometry().getDimension();
if (dim != 2) {
throw new MappingException("Membrane Velocity only supported for 2D geometries");
}
if (simContext.getGeometry().getDimension() >= 1) {
SpatialQuantity velXQuantity = surfaceRegionObject.getSpatialQuantity(QuantityCategory.SurfaceVelocity, QuantityComponent.X);
Expression velXExp = new Expression(velXQuantity, simContext.getNameScope());
memSubDomain.setVelocityX(getIdentifierSubstitutions(velXExp, velXQuantity.getUnitDefinition(), surfaceClass));
}
if (simContext.getGeometry().getDimension() >= 2) {
SpatialQuantity velYQuantity = surfaceRegionObject.getSpatialQuantity(QuantityCategory.SurfaceVelocity, QuantityComponent.Y);
Expression velYExp = new Expression(velYQuantity, simContext.getNameScope());
memSubDomain.setVelocityY(getIdentifierSubstitutions(velYExp, velYQuantity.getUnitDefinition(), surfaceClass));
}
if (simContext.getGeometry().getDimension() == 3) {
SpatialQuantity velZQuantity = surfaceRegionObject.getSpatialQuantity(QuantityCategory.SurfaceVelocity, QuantityComponent.Z);
Expression velZExp = new Expression(velZQuantity, simContext.getNameScope());
// memSubDomain.setVelocityZ(getIdentifierSubstitutions(velZExp, velZQuantity.getUnitDefinition(), surfaceClass));
throw new MappingException("Membrane Velocity not supported for 2D problems");
}
}
}
//
// create equations for membrane-bound molecular species
//
MembraneStructureAnalyzer membraneStructureAnalyzer = getMembraneStructureAnalyzer(surfaceClass);
Enumeration<SpeciesContextMapping> enumSCM = getSpeciesContextMappings();
while (enumSCM.hasMoreElements()) {
SpeciesContextMapping scm = enumSCM.nextElement();
SpeciesContext sc = scm.getSpeciesContext();
SpeciesContextSpec scs = simContext.getReactionContext().getSpeciesContextSpec(sc);
StructureMapping sm = simContext.getGeometryContext().getStructureMapping(sc.getStructure());
//
if ((scm.getVariable() instanceof MembraneRegionVariable) && scm.getDependencyExpression() == null) {
MembraneRegionEquation equation = null;
MembraneRegionVariable memRegionVar = (MembraneRegionVariable) scm.getVariable();
if (sm.getGeometryClass() == surfaceClass) {
//
// species context belongs to this subDomain
//
Expression initial = new Expression(getMathSymbol(scs.getParameterFromRole(SpeciesContextSpec.ROLE_InitialConcentration), sm.getGeometryClass()));
Expression rate = getIdentifierSubstitutions(scm.getRate(), scm.getSpeciesContext().getUnitDefinition().divideBy(timeUnit), simContext.getGeometryContext().getStructureMapping(sc.getStructure()).getGeometryClass());
equation = new MembraneRegionEquation(memRegionVar, initial);
equation.setMembraneRateExpression(rate);
// equation.setUniformRateExpression(newUniformRateExpression);
memSubDomain.replaceEquation(equation);
}
} else if ((scm.getVariable() instanceof MemVariable) && scm.getDependencyExpression() == null) {
//
if (sm.getGeometryClass() == surfaceClass) {
Equation equation = null;
MemVariable variable = (MemVariable) scm.getVariable();
if (scm.isPDERequired()) {
//
// PDE
//
//
// species context belongs to this subDomain
//
Expression initial = new Expression(getMathSymbol(scs.getParameterFromRole(SpeciesContextSpec.ROLE_InitialConcentration), sm.getGeometryClass()));
Expression rate = getIdentifierSubstitutions(scm.getRate(), scm.getSpeciesContext().getUnitDefinition().divideBy(timeUnit), simContext.getGeometryContext().getStructureMapping(sc.getStructure()).getGeometryClass());
Expression diffusion = new Expression(getMathSymbol(scs.getDiffusionParameter(), sm.getGeometryClass()));
equation = new PdeEquation(variable, initial, rate, diffusion);
((PdeEquation) equation).setBoundaryXm((scs.getBoundaryXmParameter().getExpression() == null) ? (null) : new Expression(getMathSymbol(scs.getBoundaryXmParameter(), sm.getGeometryClass())));
((PdeEquation) equation).setBoundaryXp((scs.getBoundaryXpParameter().getExpression() == null) ? (null) : new Expression(getMathSymbol(scs.getBoundaryXpParameter(), sm.getGeometryClass())));
((PdeEquation) equation).setBoundaryYm((scs.getBoundaryYmParameter().getExpression() == null) ? (null) : new Expression(getMathSymbol(scs.getBoundaryYmParameter(), sm.getGeometryClass())));
((PdeEquation) equation).setBoundaryYp((scs.getBoundaryYpParameter().getExpression() == null) ? (null) : new Expression(getMathSymbol(scs.getBoundaryYpParameter(), sm.getGeometryClass())));
((PdeEquation) equation).setBoundaryZm((scs.getBoundaryZmParameter().getExpression() == null) ? (null) : new Expression(getMathSymbol(scs.getBoundaryZmParameter(), sm.getGeometryClass())));
((PdeEquation) equation).setBoundaryZp((scs.getBoundaryZpParameter().getExpression() == null) ? (null) : new Expression(getMathSymbol(scs.getBoundaryZpParameter(), sm.getGeometryClass())));
memSubDomain.replaceEquation(equation);
} else {
//
// ODE
//
//
// species context belongs to this subDomain
//
Expression initial = new Expression(getMathSymbol(scs.getParameterFromRole(SpeciesContextSpec.ROLE_InitialConcentration), null));
Expression rate = getIdentifierSubstitutions(scm.getRate(), scm.getSpeciesContext().getUnitDefinition().divideBy(timeUnit), simContext.getGeometryContext().getStructureMapping(sc.getStructure()).getGeometryClass());
equation = new OdeEquation(variable, initial, rate);
memSubDomain.replaceEquation(equation);
}
}
}
}
Enumeration<SpeciesContextMapping> enum_scm = getSpeciesContextMappings();
while (enum_scm.hasMoreElements()) {
SpeciesContextMapping scm = enum_scm.nextElement();
if (scm.isPDERequired() || scm.getVariable() instanceof VolumeRegionVariable) {
// Species species = scm.getSpeciesContext().getSpecies();
Variable var = scm.getVariable();
final Domain dm = var.getDomain();
if (dm != null) {
final String domainName = dm.getName();
if (sameName(domainName, memSubDomain.getInsideCompartment()) || sameName(domainName, memSubDomain.getOutsideCompartment())) {
JumpCondition jc = memSubDomain.getJumpCondition(var);
if (jc == null) {
// System.out.println("MathMapping.refreshMathDescription(), adding jump condition for diffusing variable "+var.getName()+" on membrane "+membraneStructureAnalyzer.getMembrane().getName());
if (var instanceof VolVariable) {
jc = new JumpCondition((VolVariable) var);
} else if (var instanceof VolumeRegionVariable) {
jc = new JumpCondition((VolumeRegionVariable) var);
} else {
throw new RuntimeException("unexpected Variable type " + var.getClass().getName());
}
memSubDomain.addJumpCondition(jc);
}
}
}
}
}
//
// set jump conditions for any volume variables or volume region variables that have explicitly defined fluxes
//
ResolvedFlux[] resolvedFluxes = membraneStructureAnalyzer.getResolvedFluxes();
if (resolvedFluxes != null) {
for (int i = 0; i < resolvedFluxes.length; i++) {
SpeciesContext sc = resolvedFluxes[i].getSpeciesContext();
SpeciesContextMapping scm = getSpeciesContextMapping(sc);
StructureMapping sm = getSimulationContext().getGeometryContext().getStructureMapping(sc.getStructure());
if (scm.getVariable() instanceof VolVariable && scm.isPDERequired()) {
VolVariable volVar = (VolVariable) scm.getVariable();
JumpCondition jc = memSubDomain.getJumpCondition(volVar);
if (jc == null) {
jc = new JumpCondition(volVar);
memSubDomain.addJumpCondition(jc);
}
Expression flux = getIdentifierSubstitutions(resolvedFluxes[i].getFluxExpression(), resolvedFluxes[i].getUnitDefinition(), membraneStructureAnalyzer.getSurfaceClass());
if (memSubDomain.getInsideCompartment().getName().equals(sm.getGeometryClass().getName())) {
jc.setInFlux(flux);
} else if (memSubDomain.getOutsideCompartment().getName().equals(sm.getGeometryClass().getName())) {
jc.setOutFlux(flux);
} else {
throw new RuntimeException("Application " + simContext.getName() + " : " + scm.getSpeciesContext().getName() + " has spatially resolved flux at membrane " + scm.getSpeciesContext().getStructure().getName() + " with a non-local flux species " + scm.getSpeciesContext().getName());
}
} else if (scm.getVariable() instanceof VolumeRegionVariable) {
VolumeRegionVariable volRegionVar = (VolumeRegionVariable) scm.getVariable();
JumpCondition jc = memSubDomain.getJumpCondition(volRegionVar);
if (jc == null) {
jc = new JumpCondition(volRegionVar);
memSubDomain.addJumpCondition(jc);
}
Expression flux = getIdentifierSubstitutions(resolvedFluxes[i].getFluxExpression(), resolvedFluxes[i].getUnitDefinition(), membraneStructureAnalyzer.getSurfaceClass());
if (memSubDomain.getInsideCompartment().getName().equals(sm.getGeometryClass().getName())) {
jc.setInFlux(flux);
} else if (memSubDomain.getOutsideCompartment().getName().equals(sm.getGeometryClass().getName())) {
jc.setOutFlux(flux);
} else {
throw new RuntimeException("Application " + simContext.getName() + " : " + scm.getSpeciesContext().getName() + " has spatially resolved flux at membrane " + scm.getSpeciesContext().getStructure().getName() + " with a non-local flux species " + scm.getSpeciesContext().getName());
}
} else {
throw new MappingException("Application " + simContext.getName() + " : " + scm.getSpeciesContext().getName() + " has spatially resolved flux at membrane " + scm.getSpeciesContext().getStructure().getName() + ", but doesn't diffuse in compartment " + scm.getSpeciesContext().getStructure().getName());
}
}
}
//
// create fast system (if neccessary)
//
SpeciesContextMapping[] fastSpeciesContextMappings = membraneStructureAnalyzer.getFastSpeciesContextMappings();
if (fastSpeciesContextMappings != null) {
FastSystem fastSystem = new FastSystem(mathDesc);
for (int i = 0; i < fastSpeciesContextMappings.length; i++) {
SpeciesContextMapping scm = fastSpeciesContextMappings[i];
if (scm.getFastInvariant() == null) {
//
// independant-fast variable, create a fastRate object
//
VCUnitDefinition rateUnit = scm.getSpeciesContext().getUnitDefinition().divideBy(timeUnit);
FastRate fastRate = new FastRate(getIdentifierSubstitutions(scm.getFastRate(), rateUnit, surfaceClass));
fastSystem.addFastRate(fastRate);
} else {
//
// dependant-fast variable, create a fastInvariant object
//
VCUnitDefinition invariantUnit = scm.getSpeciesContext().getUnitDefinition();
FastInvariant fastInvariant = new FastInvariant(getIdentifierSubstitutions(scm.getFastInvariant(), invariantUnit, surfaceClass));
fastSystem.addFastInvariant(fastInvariant);
}
}
memSubDomain.setFastSystem(fastSystem);
// constructor calls the 'refresh' method which constructs depemdency matrix, dependent/independent vars and pseudoconstants, etc.
// FastSystemAnalyzer fs_analyzer =
new FastSystemAnalyzer(fastSystem, mathDesc);
}
//
// create Membrane-region equations for potential of this resolved membrane
//
Structure[] resolvedSurfaceStructures = membraneStructureAnalyzer.getStructures();
for (int m = 0; m < resolvedSurfaceStructures.length; m++) {
if (resolvedSurfaceStructures[m] instanceof Membrane) {
Membrane membrane = (Membrane) resolvedSurfaceStructures[m];
MembraneMapping membraneMapping = (MembraneMapping) simContext.getGeometryContext().getStructureMapping(membrane);
if (membraneMapping.getCalculateVoltage()) {
ElectricalDevice[] membraneDevices = potentialMapping.getElectricalDevices(membrane);
int numCapacitiveDevices = 0;
MembraneElectricalDevice capacitiveDevice = null;
for (int i = 0; i < membraneDevices.length; i++) {
if (membraneDevices[i] instanceof MembraneElectricalDevice) {
numCapacitiveDevices++;
capacitiveDevice = (MembraneElectricalDevice) membraneDevices[i];
}
}
if (numCapacitiveDevices != 1) {
throw new MappingException("expecting 1 capacitive electrical device on graph edge for membrane " + membrane.getName() + ", found '" + numCapacitiveDevices + "'");
}
if (mathDesc.getVariable(getMathSymbol(capacitiveDevice.getVoltageSymbol(), membraneMapping.getGeometryClass())) instanceof MembraneRegionVariable) {
MembraneRegionVariable vVar = (MembraneRegionVariable) mathDesc.getVariable(getMathSymbol(capacitiveDevice.getVoltageSymbol(), membraneMapping.getGeometryClass()));
Parameter initialVoltageParm = capacitiveDevice.getMembraneMapping().getInitialVoltageParameter();
Expression initExp = getIdentifierSubstitutions(initialVoltageParm.getExpression(), initialVoltageParm.getUnitDefinition(), capacitiveDevice.getMembraneMapping().getGeometryClass());
MembraneRegionEquation vEquation = new MembraneRegionEquation(vVar, initExp);
vEquation.setMembraneRateExpression(getIdentifierSubstitutions(potentialMapping.getOdeRHS(capacitiveDevice, this), membrane.getMembraneVoltage().getUnitDefinition().divideBy(timeUnit), capacitiveDevice.getMembraneMapping().getGeometryClass()));
memSubDomain.addEquation(vEquation);
}
}
}
}
}
// create equations for event assignment or rate rule targets that are model params/species, etc.
Set<VolVariable> hashKeySet = eventOrRateRuleVolVarHash.keySet();
Iterator<VolVariable> volVarsIter = hashKeySet.iterator();
// working under the assumption that we are dealing with non-spatial math, hence only one compartment domain!
SubDomain subDomain = mathDesc.getSubDomains().nextElement();
while (volVarsIter.hasNext()) {
VolVariable volVar = volVarsIter.next();
EventAssignmentOrRateRuleInitParameter initParam = eventOrRateRuleVolVarHash.get(volVar);
// check event initial condition, it shouldn't contain vars, we have to do it here, coz we want to substitute functions...etc.
Expression eapExp = MathUtilities.substituteFunctions(initParam.getExpression(), mathDesc);
if (eapExp.getSymbols() != null) {
for (String symbol : eapExp.getSymbols()) {
SymbolTableEntry ste = eapExp.getSymbolBinding(symbol);
if (ste instanceof VolVariable || ste instanceof MemVariable) {
throw new MathException("Variables are not allowed in Event assignment initial condition.\nEvent assignment target: " + volVar.getName() + " has variable (" + symbol + ") in its expression.");
}
}
}
Expression rateExpr = new Expression(0.0);
RateRuleRateParameter rateParam = rateRuleRateParamHash.get(volVar);
if (rateParam != null) {
// this is a rate rule, get its expression.
rateExpr = new Expression(getMathSymbol(rateParam, null));
}
Equation equation = new OdeEquation(volVar, new Expression(getMathSymbol(initParam, null)), rateExpr);
subDomain.addEquation(equation);
}
// events - add events to math desc for event assignments that have parameters as target variables
if (bioevents != null && bioevents.length > 0) {
for (BioEvent be : bioevents) {
// transform the bioEvent trigger/delay to math Event
LocalParameter genTriggerParam = be.getParameter(BioEventParameterType.GeneralTriggerFunction);
Expression mathTriggerExpr = getIdentifierSubstitutions(new Expression(genTriggerParam, be.getNameScope()), modelUnitSystem.getInstance_DIMENSIONLESS(), null);
Delay mathDelay = null;
LocalParameter delayParam = be.getParameter(BioEventParameterType.TriggerDelay);
if (delayParam != null && delayParam.getExpression() != null && !delayParam.getExpression().compareEqual(new Expression(0.0))) {
boolean bUseValsFromTriggerTime = be.getUseValuesFromTriggerTime();
Expression mathDelayExpr = getIdentifierSubstitutions(new Expression(delayParam, be.getNameScope()), timeUnit, null);
mathDelay = new Delay(bUseValsFromTriggerTime, mathDelayExpr);
}
// now deal with (bio)event Assignment translation to math EventAssignment
ArrayList<EventAssignment> eventAssignments = be.getEventAssignments();
ArrayList<Event.EventAssignment> mathEventAssignmentsList = new ArrayList<Event.EventAssignment>();
if (eventAssignments != null) {
for (EventAssignment ea : eventAssignments) {
SymbolTableEntry ste = simContext.getEntry(ea.getTarget().getName());
if (ste instanceof StructureSize) {
throw new RuntimeException("Event Assignment Variable for compartment size is not supported yet");
}
VCUnitDefinition eventAssignVarUnit = ste.getUnitDefinition();
Variable variable = varHash.getVariable(ste.getName());
Event.EventAssignment mathEA = new Event.EventAssignment(variable, getIdentifierSubstitutions(ea.getAssignmentExpression(), eventAssignVarUnit, null));
mathEventAssignmentsList.add(mathEA);
}
}
// use the translated trigger, delay and event assignments to create (math) event
Event mathEvent = new Event(be.getName(), mathTriggerExpr, mathDelay, mathEventAssignmentsList);
mathDesc.addEvent(mathEvent);
}
}
if (simContext.getMicroscopeMeasurement() != null && simContext.getMicroscopeMeasurement().getFluorescentSpecies().size() > 0) {
MicroscopeMeasurement measurement = simContext.getMicroscopeMeasurement();
Expression volumeConcExp = new Expression(0.0);
Expression membraneDensityExp = new Expression(0.0);
for (SpeciesContext speciesContext : measurement.getFluorescentSpecies()) {
GeometryClass geometryClass = simContext.getGeometryContext().getStructureMapping(speciesContext.getStructure()).getGeometryClass();
StructureMapping structureMapping = simContext.getGeometryContext().getStructureMapping(speciesContext.getStructure());
StructureMappingParameter unitSizeParameter = structureMapping.getUnitSizeParameter();
Expression mappedSpeciesContextExpression = Expression.mult(unitSizeParameter.getExpression(), new Expression(getMathSymbol(speciesContext, geometryClass)));
VCUnitDefinition mappedSpeciesContextUnit = unitSizeParameter.getUnitDefinition().multiplyBy(speciesContext.getUnitDefinition());
if (geometryClass instanceof SubVolume) {
// volume function
int dimension = 3;
VCUnitDefinition desiredConcUnits = model.getUnitSystem().getInstance("molecules").divideBy(model.getUnitSystem().getLengthUnit().raiseTo(new ucar.units_vcell.RationalNumber(dimension)));
Expression unitFactor = getUnitFactor(desiredConcUnits.divideBy(mappedSpeciesContextUnit));
volumeConcExp = Expression.add(volumeConcExp, Expression.mult(unitFactor, mappedSpeciesContextExpression)).flatten();
} else if (geometryClass instanceof SurfaceClass) {
// membrane function
int dimension = 2;
VCUnitDefinition desiredSurfaceDensityUnits = model.getUnitSystem().getInstance("molecules").divideBy(model.getUnitSystem().getLengthUnit().raiseTo(new ucar.units_vcell.RationalNumber(dimension)));
Expression unitFactor = getUnitFactor(desiredSurfaceDensityUnits.divideBy(mappedSpeciesContextUnit));
membraneDensityExp = Expression.add(membraneDensityExp, Expression.mult(unitFactor, mappedSpeciesContextExpression)).flatten();
} else {
throw new MathException("unsupported geometry mapping for microscopy measurement");
}
}
ConvolutionKernel kernel = measurement.getConvolutionKernel();
if (kernel instanceof ExperimentalPSF) {
if (!membraneDensityExp.isZero()) {
throw new MappingException("membrane variables and functions not yet supported for Z projection in Microcopy Measurements");
}
ExperimentalPSF psf = (ExperimentalPSF) kernel;
DataSymbol psfDataSymbol = psf.getPSFDataSymbol();
if (psfDataSymbol instanceof FieldDataSymbol) {
FieldDataSymbol fieldDataSymbol = (FieldDataSymbol) psfDataSymbol;
String fieldDataName = ((FieldDataSymbol) psfDataSymbol).getExternalDataIdentifier().getName();
Expression psfExp = Expression.function(FieldFunctionDefinition.FUNCTION_name, new Expression("'" + fieldDataName + "'"), new Expression("'" + fieldDataSymbol.getFieldDataVarName() + "'"), new Expression(fieldDataSymbol.getFieldDataVarTime()), new Expression("'" + fieldDataSymbol.getFieldDataVarType() + "'"));
varHash.addVariable(new Function("__PSF__", psfExp, null));
}
Expression convExp = Expression.function(ConvFunctionDefinition.FUNCTION_name, volumeConcExp, new Expression("__PSF__"));
varHash.addVariable(newFunctionOrConstant(measurement.getName(), convExp, null));
} else if (kernel instanceof GaussianConvolutionKernel) {
GaussianConvolutionKernel gaussianConvolutionKernel = (GaussianConvolutionKernel) kernel;
GaussianConvolutionDataGeneratorKernel mathKernel = new GaussianConvolutionDataGeneratorKernel(gaussianConvolutionKernel.getSigmaXY_um(), gaussianConvolutionKernel.getSigmaZ_um());
ConvolutionDataGenerator dataGenerator = new ConvolutionDataGenerator(measurement.getName(), mathKernel, volumeConcExp, membraneDensityExp);
mathDesc.getPostProcessingBlock().addDataGenerator(dataGenerator);
} else if (kernel instanceof ProjectionZKernel) {
if (mathDesc.getGeometry().getDimension() == 3) {
if (!membraneDensityExp.isZero()) {
throw new MappingException("membrane variables and functions not yet supported for Z projection in Microcopy Measurements");
}
ProjectionDataGenerator dataGenerator = new ProjectionDataGenerator(measurement.getName(), null, ProjectionDataGenerator.Axis.z, ProjectionDataGenerator.Operation.sum, volumeConcExp);
mathDesc.getPostProcessingBlock().addDataGenerator(dataGenerator);
} else {
throw new MappingException("Z Projection is only supported in 3D spatial applications.");
}
}
}
//
for (int i = 0; i < fieldMathMappingParameters.length; i++) {
if (fieldMathMappingParameters[i] instanceof UnitFactorParameter) {
GeometryClass geometryClass = fieldMathMappingParameters[i].getGeometryClass();
Variable variable = newFunctionOrConstant(getMathSymbol(fieldMathMappingParameters[i], geometryClass), getIdentifierSubstitutions(fieldMathMappingParameters[i].getExpression(), fieldMathMappingParameters[i].getUnitDefinition(), geometryClass), fieldMathMappingParameters[i].getGeometryClass());
if (mathDesc.getVariable(variable.getName()) == null) {
mathDesc.addVariable(variable);
}
}
}
if (!mathDesc.isValid()) {
System.out.println(mathDesc.getVCML_database());
throw new MappingException("generated an invalid mathDescription: " + mathDesc.getWarning());
}
// System.out.println("]]]]]]]]]]]]]]]]]]]]]] VCML string begin ]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]");
// System.out.println(mathDesc.getVCML());
// System.out.println("]]]]]]]]]]]]]]]]]]]]]] VCML string end ]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]");
}
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