Examples with SymbolTableEntry cbit.vcell.parser.SymbolTableEntry used on opensource projects

Example 91 with SymbolTableEntry

use of cbit.vcell.parser.SymbolTableEntry in project vcell by virtualcell.

the class PDEDataViewer method plotSpaceStats.

void plotSpaceStats(TSJobResultsSpaceStats tsjrss) {
    // Determine if Volume or Membrane
    DataIdentifier[] diArr = getPdeDataContext().getDataIdentifiers();
    boolean bVolume = true;
    for (int i = 0; i < diArr.length; i += 1) {
        if (diArr[i].getName().equals(tsjrss.getVariableNames()[0])) {
            if (diArr[i].getVariableType().equals(VariableType.MEMBRANE) || diArr[i].getVariableType().equals(VariableType.MEMBRANE_REGION)) {
                bVolume = false;
                break;
            }
        }
    }
    SymbolTableEntry[] symbolTableEntries = null;
    if (tsjrss.getVariableNames().length == 1) {
        // max.mean.min,sum
        symbolTableEntries = new SymbolTableEntry[3];
        if (getSimulation() != null && getSimulation().getMathDescription() != null) {
            symbolTableEntries[0] = getSimulation().getMathDescription().getEntry(tsjrss.getVariableNames()[0]);
        } else {
            symbolTableEntries[0] = new SimpleSymbolTable(tsjrss.getVariableNames()).getEntry(tsjrss.getVariableNames()[0]);
        }
        symbolTableEntries[1] = symbolTableEntries[0];
        symbolTableEntries[2] = symbolTableEntries[0];
    }
    SymbolTableEntry[] finalSymbolTableEntries = symbolTableEntries;
    boolean finalBVolume = bVolume;
    PlotPane plotPane = new cbit.plot.gui.PlotPane();
    plotPane.setPlot2D(new SingleXPlot2D(finalSymbolTableEntries, getSimulationModelInfo().getDataSymbolMetadataResolver(), "Time", new String[] { "Max", (tsjrss.getWeightedMean() != null ? "WeightedMean" : "UnweightedMean"), "Min" /*,
				(tsjrss.getWeightedSum() != null?"WeightedSum":"UnweightedSum")*/
    }, new double[][] { tsjrss.getTimes(), tsjrss.getMaximums()[0], (tsjrss.getWeightedMean() != null ? tsjrss.getWeightedMean()[0] : tsjrss.getUnweightedMean()[0]), tsjrss.getMinimums()[0] /*,
				(tsjrss.getWeightedSum() != null?tsjrss.getWeightedSum()[0]:tsjrss.getUnweightedSum()[0])*/
    }, new String[] { "Statistics Plot for " + tsjrss.getVariableNames()[0] + (tsjrss.getTotalSpace() != null ? " (ROI " + (finalBVolume ? "volume" : "area") + "=" + tsjrss.getTotalSpace()[0] + ")" : ""), ReservedVariable.TIME.getName(), "[" + tsjrss.getVariableNames()[0] + "]" }));
    String title = "Statistics: (" + tsjrss.getVariableNames()[0] + ") ";
    if (getSimulationModelInfo() != null) {
        title += getSimulationModelInfo().getContextName() + " " + getSimulationModelInfo().getSimulationName();
    }
    ChildWindowManager childWindowManager = ChildWindowManager.findChildWindowManager(PDEDataViewer.this);
    ChildWindow childWindow = childWindowManager.addChildWindow(plotPane, plotPane, title);
    childWindow.setIsCenteredOnParent();
    childWindow.pack();
    childWindow.show();
}

Example 92 with SymbolTableEntry

use of cbit.vcell.parser.SymbolTableEntry 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 93 with SymbolTableEntry

use of cbit.vcell.parser.SymbolTableEntry in project vcell by virtualcell.

the class XmlReader method getRateRules.

public RateRule[] getRateRules(SimulationContext simContext, Element rateRulesElement) throws XmlParseException {
    Iterator<Element> rateRulesIterator = rateRulesElement.getChildren(XMLTags.RateRuleTag, vcNamespace).iterator();
    Vector<RateRule> rateRulesVector = new Vector<RateRule>();
    while (rateRulesIterator.hasNext()) {
        Element rrElement = (Element) rateRulesIterator.next();
        RateRule newRateRule = null;
        try {
            String rrName = unMangle(rrElement.getAttributeValue(XMLTags.NameAttrTag));
            String varname = rrElement.getAttributeValue(XMLTags.RateRuleVariableAttrTag);
            SymbolTableEntry rrVar = simContext.getEntry(varname);
            Expression rrExp = unMangleExpression(rrElement.getText());
            newRateRule = new RateRule(rrName, rrVar, rrExp, simContext);
            newRateRule.bind();
        } catch (ExpressionBindingException e) {
            e.printStackTrace(System.out);
            throw new XmlParseException(e.getMessage());
        }
        if (newRateRule != null) {
            rateRulesVector.add(newRateRule);
        }
    }
    return ((RateRule[]) BeanUtils.getArray(rateRulesVector, RateRule.class));
}

Example 94 with SymbolTableEntry

use of cbit.vcell.parser.SymbolTableEntry in project vcell by virtualcell.

the class TriggerTemplatePanel method init.

public void init(SimulationContext simulationContext, AutoCompleteSymbolFilter autoCompleteSymbolFilter, BioEvent existingBioEvent) {
    if (simulationContext != null) {
        // mathOpComboBox.removeAllItems();
        // mathOpComboBox.addItem(BioEvent.TriggerComparison.greaterThan);
        // mathOpComboBox.addItem(BioEvent.TriggerComparison.lessThan);
        // mathOpComboBox.addItem(BioEvent.TriggerComparison.greaterThanOrEqual);
        // mathOpComboBox.addItem(BioEvent.TriggerComparison.lessThanOrEqual);
        varAboveComboBox.removeAllItems();
        varBelowComboBox.removeAllItems();
        SymbolTableEntry[] triggerExprSymbols = ModelOptimizationSpec.calculateTimeDependentModelObjects(simulationContext);
        Arrays.sort(triggerExprSymbols, new Comparator<SymbolTableEntry>() {

            @Override
            public int compare(SymbolTableEntry o1, SymbolTableEntry o2) {
                return o1.getName().compareToIgnoreCase(o2.getName());
            }
        });
        for (SymbolTableEntry ste : triggerExprSymbols) {
            if (!(ste instanceof ReservedSymbol)) {
                varAboveComboBox.addItem(ste);
                varBelowComboBox.addItem(ste);
            }
        }
        // setVerifier(simulationContext);
        Map<String, SymbolTableEntry> entryMap = new HashMap<String, SymbolTableEntry>();
        simulationContext.getEntries(entryMap);
        textFieldAboveVarVal.setAutoCompleteSymbolFilter(autoCompleteSymbolFilter);
        textFieldAboveVarVal.setAutoCompletionWords(entryMap.keySet());
        textFieldBelowVarVal.setAutoCompleteSymbolFilter(autoCompleteSymbolFilter);
        textFieldBelowVarVal.setAutoCompletionWords(entryMap.keySet());
        textFieldSingleTime.setAutoCompleteSymbolFilter(autoCompleteSymbolFilter);
        textFieldSingleTime.setAutoCompletionWords(entryMap.keySet());
        textFieldGeneral.setAutoCompleteSymbolFilter(autoCompleteSymbolFilter);
        textFieldGeneral.setAutoCompletionWords(entryMap.keySet());
        if (existingBioEvent != null) {
            // Edit Trigger mode
            switch(existingBioEvent.getTriggerType()) {
                case GeneralTrigger:
                    {
                        textFieldGeneral.setText(existingBioEvent.getParameter(BioEventParameterType.GeneralTriggerFunction).getExpression().infix());
                        rdbtnGeneral.setSelected(true);
                        break;
                    }
                case LogRangeTimes:
                    {
                        LocalParameter rangeMinParam = existingBioEvent.getParameter(BioEventParameterType.RangeMinTime);
                        if (rangeMinParam != null && rangeMinParam.getExpression() != null) {
                            textFieldLogMin.setText(rangeMinParam.getExpression().infix());
                        } else {
                            textFieldLogMin.setText("");
                        }
                        LocalParameter rangeMaxParam = existingBioEvent.getParameter(BioEventParameterType.RangeMaxTime);
                        if (rangeMaxParam != null && rangeMaxParam.getExpression() != null) {
                            textFieldLogMax.setText(rangeMaxParam.getExpression().infix());
                        } else {
                            textFieldLogMax.setText("");
                        }
                        LocalParameter rangeNumParam = existingBioEvent.getParameter(BioEventParameterType.RangeNumTimes);
                        if (rangeNumParam != null && rangeNumParam.getExpression() != null) {
                            textFieldLogNum.setText(rangeNumParam.getExpression().infix());
                        } else {
                            textFieldLogNum.setText("");
                        }
                        rdbtnLogTimeRange.setSelected(true);
                        break;
                    }
                case LinearRangeTimes:
                    {
                        LocalParameter rangeMinParam = existingBioEvent.getParameter(BioEventParameterType.RangeMinTime);
                        if (rangeMinParam != null && rangeMinParam.getExpression() != null) {
                            textFieldLinearMin.setText(rangeMinParam.getExpression().infix());
                        } else {
                            textFieldLinearMin.setText("");
                        }
                        LocalParameter rangeMaxParam = existingBioEvent.getParameter(BioEventParameterType.RangeMaxTime);
                        if (rangeMaxParam != null && rangeMaxParam.getExpression() != null) {
                            textFieldLinearMax.setText(rangeMaxParam.getExpression().infix());
                        } else {
                            textFieldLinearMax.setText("");
                        }
                        LocalParameter rangeNumParam = existingBioEvent.getParameter(BioEventParameterType.RangeNumTimes);
                        if (rangeNumParam != null && rangeNumParam.getExpression() != null) {
                            textFieldLinearNum.setText(rangeNumParam.getExpression().infix());
                        } else {
                            textFieldLinearNum.setText("");
                        }
                        rdbtnLinearTimeRange.setSelected(true);
                        break;
                    }
                case ListOfTimes:
                    {
                        StringBuffer sb = new StringBuffer();
                        for (LocalParameter p : existingBioEvent.getEventParameters()) {
                            if (p.getRole() == BioEventParameterType.TimeListItem) {
                                if (sb.length() > 0) {
                                    sb.append(",");
                                }
                                sb.append(p.getExpression().infix());
                            }
                        }
                        textFieldListTimes.setText(sb.toString());
                        rdbtnListTimes.setSelected(true);
                        break;
                    }
                case ObservableAboveThreshold:
                    {
                        LocalParameter observableParameter = existingBioEvent.getParameter(BioEventParameterType.Observable);
                        SymbolTableEntry ste = null;
                        if (observableParameter != null && observableParameter.getExpression() != null && observableParameter.getExpression().isIdentifier()) {
                            ste = observableParameter.getExpression().getSymbolBinding(observableParameter.getExpression().getSymbols()[0]);
                            varAboveComboBox.setSelectedItem(ste);
                        }
                        textFieldAboveVarVal.setText(existingBioEvent.getParameter(BioEventParameterType.Threshold).getExpression().infix());
                        rdbtnVarAboveThreshold.setSelected(true);
                        break;
                    }
                case ObservableBelowThreshold:
                    {
                        LocalParameter observableParameter = existingBioEvent.getParameter(BioEventParameterType.Observable);
                        SymbolTableEntry ste = null;
                        if (observableParameter != null && observableParameter.getExpression() != null && observableParameter.getExpression().isIdentifier()) {
                            ste = observableParameter.getExpression().getSymbolBinding(observableParameter.getExpression().getSymbols()[0]);
                            varBelowComboBox.setSelectedItem(ste);
                        }
                        textFieldBelowVarVal.setText(existingBioEvent.getParameter(BioEventParameterType.Threshold).getExpression().infix());
                        rdbtnVarBelowThreshold.setSelected(true);
                        break;
                    }
                case SingleTriggerTime:
                    {
                        LocalParameter parameter = existingBioEvent.getParameter(BioEventParameterType.SingleTriggerTime);
                        textFieldSingleTime.setText(parameter.getExpression().infix());
                        rdbtnSingleTime.setSelected(true);
                        break;
                    }
            }
        }
    }
}

Example 95 with SymbolTableEntry

use of cbit.vcell.parser.SymbolTableEntry in project vcell by virtualcell.

the class TriggerTemplatePanel method setTrigger.

// private void setVerifier(final SimulationContext simulationContext){
// textFieldGeneral.setInputVerifier(new InputVerifier() {
// @Override
// public boolean verify(JComponent input) {
// boolean bValid = true;
// if (textFieldGeneral.isEnabled()) {
// String text = textFieldGeneral.getText();
// String errorText = null;
// if (text == null || text.trim().length() == 0) {
// bValid = false;
// errorText = "Trigger expression cannot be empty";
// }else{
// Expression expr = null;
// try{
// expr = EventPanel.bindTriggerExpression(textFieldGeneral.getText(),simulationContext);
// }catch(Exception e){
// bValid = false;
// errorText = e.getMessage();
// }
// }
// if (bValid) {
// textFieldGeneral.setBorder(UIManager.getBorder("TextField.border"));
// //						getBtnPlotTrigger().setEnabled(true);
// textFieldGeneral.setToolTipText(null);
// } else {
// textFieldGeneral.setBorder(GuiConstants.ProblematicTextFieldBorder);
// //						getBtnPlotTrigger().setEnabled(false);
// textFieldGeneral.setToolTipText(errorText);
// //						SwingUtilities.invokeLater(new Runnable() {
// //						    public void run() {
// //						    	getTriggerTextField().requestFocus();
// //						    }
// //						});
// }
// }
// return bValid;
// }
// });
// 
// }
public void setTrigger(BioEvent bioEvent) throws Exception {
    LocalParameter delayParam = bioEvent.getParameter(BioEventParameterType.TriggerDelay);
    if (rdbtnGeneral.isSelected()) {
        bioEvent.setTriggerType(TriggerType.GeneralTrigger);
        bioEvent.setParameterValue(BioEventParameterType.GeneralTriggerFunction, new Expression(textFieldGeneral.getText()));
    } else if (rdbtnListTimes.isSelected()) {
        bioEvent.setTriggerType(TriggerType.ListOfTimes);
        Expression[] listExps = new Expression("myFunc(" + textFieldListTimes.getText() + ")").getFunctionInvocations(null)[0].getArguments();
        bioEvent.setTimeList(listExps);
    } else if (rdbtnLinearTimeRange.isSelected()) {
        bioEvent.setTriggerType(TriggerType.LinearRangeTimes);
        bioEvent.setParameterValue(BioEventParameterType.RangeMinTime, new Expression(textFieldLinearMin.getText()));
        bioEvent.setParameterValue(BioEventParameterType.RangeMaxTime, new Expression(textFieldLinearMax.getText()));
        bioEvent.setParameterValue(BioEventParameterType.RangeNumTimes, new Expression(textFieldLinearNum.getText()));
    } else if (rdbtnLogTimeRange.isSelected()) {
        bioEvent.setTriggerType(TriggerType.LogRangeTimes);
        bioEvent.setParameterValue(BioEventParameterType.RangeMinTime, new Expression(textFieldLogMin.getText()));
        bioEvent.setParameterValue(BioEventParameterType.RangeMaxTime, new Expression(textFieldLogMax.getText()));
        bioEvent.setParameterValue(BioEventParameterType.RangeNumTimes, new Expression(textFieldLogNum.getText()));
    } else if (rdbtnSingleTime.isSelected()) {
        bioEvent.setTriggerType(TriggerType.SingleTriggerTime);
        bioEvent.setParameterValue(BioEventParameterType.SingleTriggerTime, new Expression(textFieldSingleTime.getText()));
    } else if (rdbtnVarAboveThreshold.isSelected()) {
        bioEvent.setTriggerType(TriggerType.ObservableAboveThreshold);
        bioEvent.setParameterValue(BioEventParameterType.Observable, new Expression(((SymbolTableEntry) varAboveComboBox.getSelectedItem()).getName()));
        bioEvent.setParameterValue(BioEventParameterType.Threshold, new Expression(textFieldAboveVarVal.getText()));
    } else if (rdbtnVarBelowThreshold.isSelected()) {
        bioEvent.setTriggerType(TriggerType.ObservableBelowThreshold);
        bioEvent.setParameterValue(BioEventParameterType.Observable, new Expression(((SymbolTableEntry) varBelowComboBox.getSelectedItem()).getName()));
        bioEvent.setParameterValue(BioEventParameterType.Threshold, new Expression(textFieldBelowVarVal.getText()));
    }
    if (delayParam.getExpression() != null) {
        bioEvent.setParameterValue(BioEventParameterType.TriggerDelay, delayParam.getExpression());
    }
}