Examples with VolVariable cbit.vcell.math.VolVariable used on opensource projects

Example 31 with VolVariable

use of cbit.vcell.math.VolVariable in project vcell by virtualcell.

the class PDEDataViewer method showSpatialPlot.

/**
 * Comment
 */
private void showSpatialPlot() {
    // check selections
    final SpatialSelection[] sl = getPDEDataContextPanel1().fetchSpatialSelections(false, true);
    if (sl == null) {
        PopupGenerator.showErrorDialog(this, "Nothing selected!");
        return;
    }
    for (int i = 0; i < sl.length; i++) {
        if (sl[i].isPoint()) {
            PopupGenerator.showErrorDialog(this, "One or more selections are single points - no spatial plot will be produced for those selections");
            break;
        }
    }
    final String varName = getPdeDataContext().getVariableName();
    final double timePoint = getPdeDataContext().getTimePoint();
    final SymbolTableEntry[] symbolTableEntries = new SymbolTableEntry[1];
    if (getSimulation() != null && getSimulation().getMathDescription() != null) {
        symbolTableEntries[0] = getSimulation().getMathDescription().getEntry(varName);
    }
    if (symbolTableEntries[0] == null) {
        // TODO domain
        Domain domain = null;
        symbolTableEntries[0] = new VolVariable(varName, domain);
    }
    AsynchClientTask task1 = new AsynchClientTask("Retrieving spatial series for variable '" + varName, AsynchClientTask.TASKTYPE_NONSWING_BLOCKING) {

        @Override
        public void run(Hashtable<String, Object> hashTable) throws Exception {
            // get plots, ignoring points
            PlotData[] plotDatas = new PlotData[sl.length];
            for (int i = 0; i < sl.length; i++) {
                PlotData plotData = null;
                if (getPdeDataContext() instanceof PDEDataViewerPostProcess.PostProcessDataPDEDataContext) {
                    SpatialSelectionVolume ssVolume = (SpatialSelectionVolume) sl[i];
                    SpatialSelection.SSHelper ssvHelper = ssVolume.getIndexSamples(0.0, 1.0);
                    ssvHelper.initializeValues_VOLUME(getPdeDataContext().getDataValues());
                    double[] values = ssvHelper.getSampledValues();
                    plotData = new PlotData(ssvHelper.getWorldCoordinateLengths(), values);
                } else {
                    plotData = getPdeDataContext().getLineScan(varName, timePoint, sl[i]);
                }
                plotDatas[i] = plotData;
            }
            hashTable.put("plotDatas", plotDatas);
        }
    };
    AsynchClientTask task2 = new AsynchClientTask("Showing spatial plot for variable" + varName, AsynchClientTask.TASKTYPE_SWING_BLOCKING) {

        @Override
        public void run(Hashtable<String, Object> hashTable) throws Exception {
            PlotData[] plotDatas = (PlotData[]) hashTable.get("plotDatas");
            for (PlotData plotData : plotDatas) {
                if (plotData != null) {
                    PlotPane plotPane = new PlotPane();
                    Plot2D plot2D = new Plot2D(symbolTableEntries, getSimulationModelInfo().getDataSymbolMetadataResolver(), new String[] { varName }, new PlotData[] { plotData }, new String[] { "Values along curve", "Distance (\u00b5m)", "[" + varName + "]" });
                    plotPane.setPlot2D(plot2D);
                    String title = createContextTitle(PDEDataViewer.this.isPostProcess(), "Spatial Plot:'" + varName + "' ", getPdeDataContext(), getSimulationModelInfo(), getSimulation());
                    ChildWindowManager childWindowManager = ChildWindowManager.findChildWindowManager(PDEDataViewer.this);
                    ChildWindow childWindow = childWindowManager.addChildWindow(plotPane, plotPane, title);
                    childWindow.setIsCenteredOnParent();
                    childWindow.pack();
                    childWindow.show();
                // System.out.println("Spatial plot requesting focus.  Result is: "+childWindow.requestFocusInWindow());
                }
            }
        }
    };
    ClientTaskDispatcher.dispatch(this, new Hashtable<String, Object>(), new AsynchClientTask[] { task1, task2 }, false);
}

Example 32 with VolVariable

use of cbit.vcell.math.VolVariable in project vcell by virtualcell.

the class XmlReader method getComputeMembraneMetric.

private ComputeMembraneMetricEquation getComputeMembraneMetric(Element param, MathDescription mathDesc) throws XmlParseException {
    // get attributes
    String varname = unMangle(param.getAttributeValue(XMLTags.NameAttrTag));
    // find reference in the dictionnary
    // try a MembraneRegionVariable
    VolVariable varref = (VolVariable) mathDesc.getVariable(varname);
    if (varref == null) {
        throw new XmlParseException("The reference to the Volume variable " + varname + " could not be resolved!");
    }
    MembraneMetricComponent normalComponent = null;
    String normalComponentString = param.getAttributeValue(XMLTags.ComputeMembraneMetricComponentAttrTag);
    if (normalComponentString.equals(XMLTags.ComputeMembraneMetricComponentAttrTagValue_directionX)) {
        normalComponent = MembraneMetricComponent.directionToMembraneX;
    } else if (normalComponentString.equals(XMLTags.ComputeMembraneMetricComponentAttrTagValue_directionY)) {
        normalComponent = MembraneMetricComponent.directionToMembraneY;
    } else if (normalComponentString.equals(XMLTags.ComputeMembraneMetricComponentAttrTagValue_directionZ)) {
        normalComponent = MembraneMetricComponent.directionToMembraneZ;
    } else if (normalComponentString.equals(XMLTags.ComputeMembraneMetricComponentAttrTagValue_distance)) {
        normalComponent = MembraneMetricComponent.distanceToMembrane;
    }
    ComputeMembraneMetricEquation computeMembraneMetric = new ComputeMembraneMetricEquation(varref, normalComponent);
    String membraneName = param.getAttributeValue(XMLTags.ComputeMembraneMetricTargetMembraneAttrTag);
    computeMembraneMetric.setTargetMembraneName(membraneName);
    return computeMembraneMetric;
}

Example 33 with VolVariable

use of cbit.vcell.math.VolVariable in project vcell by virtualcell.

the class XmlReader method getOdeEquation.

/**
 * This method returns an OdeEquation from a XML Element.
 * Creation date: (5/17/2001 3:52:40 PM)
 * @return cbit.vcell.math.OdeEquation
 * @param param org.jdom.Element
 * @exception cbit.vcell.xml.XmlParseException The exception description.
 */
private OdeEquation getOdeEquation(Element param, MathDescription mathDesc) throws XmlParseException {
    // get attributes
    String varname = unMangle(param.getAttributeValue(XMLTags.NameAttrTag));
    // find reference in the dictionnary
    // try as a VolVariable
    Variable varref = mathDesc.getVariable(varname);
    // Make sure that the reference is not empty!!!
    if (varref == null) {
        throw new XmlParseException("The reference to the variable " + varname + " in a OdeEquation could not be resolved!");
    }
    // get Initial condition
    String temp = param.getChildText(XMLTags.InitialTag, vcNamespace);
    Expression initialexp = null;
    if (temp != null && temp.length() > 0) {
        initialexp = unMangleExpression(temp);
    }
    // Get Rate condition
    temp = param.getChildText(XMLTags.RateTag, vcNamespace);
    Expression rateexp = null;
    if (temp != null && temp.length() > 0) {
        rateexp = unMangleExpression((temp));
    }
    // --- Create the OdeEquation object ---
    OdeEquation odeEquation = new OdeEquation(varref, initialexp, rateexp);
    // add specific solutions expressions
    String solType = param.getAttributeValue(XMLTags.SolutionTypeTag);
    if (solType.equalsIgnoreCase(XMLTags.ExactTypeTag)) {
        String solutionExp = param.getChildText(XMLTags.SolutionExpressionTag, vcNamespace);
        if (solutionExp != null && solutionExp.length() > 0) {
            Expression expression = unMangleExpression(solutionExp);
            odeEquation.setExactSolution(expression);
        }
    }
    return odeEquation;
}

Example 34 with VolVariable

use of cbit.vcell.math.VolVariable in project vcell by virtualcell.

the class XmlReader method getVolVariable.

/**
 * This method returns a VolVariable object from a XML Element.
 * Creation date: (5/16/2001 2:56:34 PM)
 * @return cbit.vcell.math.VolVariable
 * @param param org.jdom.Element
 */
private VolVariable getVolVariable(Element param) {
    String name = unMangle(param.getAttributeValue(XMLTags.NameAttrTag));
    String domainStr = unMangle(param.getAttributeValue(XMLTags.DomainAttrTag));
    Domain domain = null;
    if (domainStr != null) {
        domain = new Domain(domainStr);
    }
    // -- create new VolVariable object
    VolVariable volVariable = new VolVariable(name, domain);
    transcribeComments(param, volVariable);
    return volVariable;
}

Example 35 with VolVariable

use of cbit.vcell.math.VolVariable in project vcell by virtualcell.

the class MathTestingUtilities method substituteWithExactSolution.

/**
 * Insert the method's description here.
 * Creation date: (1/24/2003 10:18:14 AM)
 * @return cbit.vcell.parser.Expression
 * @param origExp cbit.vcell.parser.Expression
 * @param subDomain cbit.vcell.math.SubDomain
 */
private static Expression substituteWithExactSolution(Expression origExp, CompartmentSubDomain subDomain, MathDescription exactMathDesc) throws ExpressionException {
    Expression substitutedExp = new Expression(origExp);
    substitutedExp.bindExpression(exactMathDesc);
    substitutedExp = MathUtilities.substituteFunctions(substitutedExp, exactMathDesc);
    substitutedExp.bindExpression(null);
    substitutedExp = substitutedExp.flatten();
    substitutedExp.bindExpression(exactMathDesc);
    String[] symbols = substitutedExp.getSymbols();
    for (int i = 0; i < symbols.length; i++) {
        Variable var = (Variable) substitutedExp.getSymbolBinding(symbols[i]);
        if (var instanceof VolVariable) {
            String exactVarName = var.getName() + "_" + subDomain.getName() + "_exact";
            substitutedExp.substituteInPlace(new Expression(var.getName()), new Expression(exactVarName));
        } else if (var instanceof VolumeRegionVariable || var instanceof MemVariable || var instanceof MembraneRegionVariable || var instanceof FilamentVariable || var instanceof FilamentRegionVariable) {
            throw new RuntimeException("variable substitution not yet implemented for Variable type " + var.getClass().getName() + "(" + var.getName() + ")");
        }
    }
    substitutedExp.bindExpression(null);
    return substitutedExp;
}