Examples with Plot2D cbit.plot.Plot2D used on opensource projects

Example 1 with Plot2D

use of cbit.plot.Plot2D in project vcell by virtualcell.

the class ODETimePlotMultipleScansPanel method updateScanParamChoices.

/**
 * Insert the method's description here.
 * Creation date: (10/18/2005 12:44:06 AM)
 */
private void updateScanParamChoices() {
    AsynchClientTask task1 = new AsynchClientTask("get ode results", AsynchClientTask.TASKTYPE_NONSWING_BLOCKING) {

        @Override
        public void run(Hashtable<String, Object> hashTable) throws Exception {
            int[] jobIndexes = scanChoiceTable.getSelectedRows();
            VCSimulationIdentifier vcSimulationIdentifier = simulation.getSimulationInfo().getAuthoritativeVCSimulationIdentifier();
            int plotCount = jobIndexes.length * variableNames.length;
            SymbolTableEntry[] symbolTableEntries = new SymbolTableEntry[plotCount];
            double[][] dataValues = new double[plotCount + 1][];
            PlotData[] plotDatas = new PlotData[plotCount];
            String[] plotNames = new String[plotCount];
            int plotIndex = 0;
            dataValues[0] = null;
            for (int ji = 0; ji < jobIndexes.length; ji++) {
                int jobIndex = jobIndexes[ji];
                final VCDataIdentifier vcdid = new VCSimulationDataIdentifier(vcSimulationIdentifier, jobIndex);
                ODEDataManager odeDatamanager = ((ODEDataManager) dataManager).createNewODEDataManager(vcdid);
                ODESolverResultSet odeSolverResultSet = odeDatamanager.getODESolverResultSet();
                if (ji == 0) {
                    plotPane.setStepViewVisible(simulation.getSolverTaskDescription().getSolverDescription().isNonSpatialStochasticSolver(), odeSolverResultSet.isMultiTrialData());
                    hashTable.put("bMultiTrial", new Boolean(odeSolverResultSet.isMultiTrialData()));
                }
                double[] tdata = null;
                if (!odeSolverResultSet.isMultiTrialData()) {
                    int tcol = odeSolverResultSet.findColumn(ReservedVariable.TIME.getName());
                    tdata = odeSolverResultSet.extractColumn(tcol);
                    if (dataValues[0] == null) {
                        dataValues[0] = tdata;
                    }
                }
                for (int v = 0; v < variableNames.length; v++) {
                    String varname = variableNames[v];
                    int varcol = odeSolverResultSet.findColumn(varname);
                    double[] vdata = odeSolverResultSet.extractColumn(varcol);
                    if (!odeSolverResultSet.isMultiTrialData()) {
                        dataValues[plotIndex + 1] = vdata;
                        // plotNames[plotIndex] = varname + " -- " + JOB_PLOT_NAME + " " + jobIndex;
                        plotDatas[plotIndex] = new PlotData(tdata, vdata);
                    // symbolTableEntries[plotIndex] = simulation.getMathDescription().getVariable(varname);
                    } else {
                        Point2D[] histogram = ODESolverPlotSpecificationPanel.generateHistogram(vdata);
                        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();
                        }
                        plotDatas[plotIndex] = new PlotData(x, y);
                    }
                    plotNames[plotIndex] = varname + " -- " + JOB_PLOT_NAME + " " + jobIndex;
                    symbolTableEntries[plotIndex] = simulation.getMathDescription().getVariable(varname);
                    plotIndex++;
                }
            }
            hashTable.put("dataValues", dataValues);
            hashTable.put("plotDatas", plotDatas);
            hashTable.put("plotNames", plotNames);
            hashTable.put("symbolTableEntries", symbolTableEntries);
        }
    };
    AsynchClientTask task2 = new AsynchClientTask("show results", AsynchClientTask.TASKTYPE_SWING_BLOCKING) {

        @Override
        public void run(Hashtable<String, Object> hashTable) throws Exception {
            double[][] dataValues = (double[][]) hashTable.get("dataValues");
            PlotData[] plotDatas = (PlotData[]) hashTable.get("plotDatas");
            String[] plotNames = (String[]) hashTable.get("plotNames");
            SymbolTableEntry[] symbolTableEntries = (SymbolTableEntry[]) hashTable.get("symbolTableEntries");
            if (plotDatas == null || plotDatas.length == 0 || (plotDatas.length == 1 && plotDatas[0] == null) || plotNames == null) {
                plotPane.setPlot2D(null);
                return;
            }
            Plot2D plot2D = null;
            if (hashTable.get("bMultiTrial") instanceof Boolean && (Boolean) hashTable.get("bMultiTrial")) {
                plot2D = new Plot2D(symbolTableEntries, null, plotNames, plotDatas, new String[] { "Probability Distribution of Species", "Number of Particles", "" });
            } else if (simulation.getSolverTaskDescription().getOutputTimeSpec() instanceof DefaultOutputTimeSpec) {
                plot2D = new Plot2D(symbolTableEntries, null, plotNames, plotDatas, new String[] { "Time Plot", ReservedVariable.TIME.getName(), "" });
            } else {
                plot2D = new SingleXPlot2D(symbolTableEntries, null, ReservedVariable.TIME.getName(), plotNames, dataValues);
            }
            plotPane.setPlot2D(plot2D);
        }
    };
    ClientTaskDispatcher.dispatch(this, new Hashtable<String, Object>(), new AsynchClientTask[] { task1, task2 });
}

Example 2 with Plot2D

use of cbit.plot.Plot2D in project vcell by virtualcell.

the class Plot2DPanel method setplot2D1.

/**
 * Set the plot2D1 to a new value.
 * @param newValue cbit.plot.Plot2D
 */
/* WARNING: THIS METHOD WILL BE REGENERATED. */
private void setplot2D1(Plot2D newValue) {
    if (ivjplot2D1 != newValue) {
        try {
            cbit.plot.Plot2D oldValue = getplot2D1();
            /* Stop listening for events from the current object */
            if (ivjplot2D1 != null) {
                ivjplot2D1.removeChangeListener(ivjEventHandler);
            }
            ivjplot2D1 = newValue;
            /* Listen for events from the new object */
            if (ivjplot2D1 != null) {
                ivjplot2D1.addChangeListener(ivjEventHandler);
            }
            connPtoP1SetSource();
            connEtoC16(ivjplot2D1);
            connEtoC3(ivjplot2D1);
            firePropertyChange("plot2D", oldValue, newValue);
        // user code begin {1}
        // user code end
        } catch (java.lang.Throwable ivjExc) {
            // user code begin {2}
            // user code end
            handleException(ivjExc);
        }
    }
    ;
// user code begin {3}
// user code end
}

Example 3 with Plot2D

use of cbit.plot.Plot2D in project vcell by virtualcell.

the class PdeTimePlotMultipleVariablesPanel method initialize.

private void initialize() {
    VariableType varType = multiTimePlotHelper.getPdeDatacontext().getDataIdentifier().getVariableType();
    String varName = multiTimePlotHelper.getPdeDatacontext().getVariableName();
    String[] plotNames = new String[pointVector.size()];
    final SymbolTableEntry[] symbolTableEntries = new SymbolTableEntry[plotNames.length];
    DefaultListModel<String> pointListModel = new DefaultListModel<String>();
    for (int i = 0; i < pointVector.size(); i++) {
        Coordinate tp = null;
        if (varType.equals(VariableType.VOLUME) || varType.equals(VariableType.VOLUME_REGION) || varType.equals(VariableType.POSTPROCESSING)) {
            SpatialSelectionVolume ssv = (SpatialSelectionVolume) pointVector.get(i);
            tp = ssv.getCurveSelectionInfo().getCurve().getBeginningCoordinate();
        } else if (varType.equals(VariableType.MEMBRANE) || varType.equals(VariableType.MEMBRANE_REGION)) {
            SpatialSelectionMembrane ssm = (SpatialSelectionMembrane) pointVector.get(i);
            double midU = ssm.getCurveSelectionInfo().getCurveUfromSelectionU(.5);
            tp = ((SampledCurve) ssm.getCurveSelectionInfo().getCurve()).coordinateFromNormalizedU(midU);
        }
        plotNames[i] = varName + " at P[" + i + "]";
        String point = "P[" + i + "]  (" + niceCoordinateString(tp) + ")";
        pointListModel.addElement(point);
        if (multiTimePlotHelper.getsimulation() != null) {
            symbolTableEntries[0] = multiTimePlotHelper.getsimulation().getMathDescription().getEntry(varName);
        } else {
            System.out.println("PdeTimePlotMultipleVariablesPanel.initialize() adding artificial symbol table entries for field data");
            SimpleSymbolTable simpleSymbolTable = new SimpleSymbolTable(new String[] { varName });
            symbolTableEntries[0] = simpleSymbolTable.getEntry(varName);
        }
    }
    pointJList.setModel(pointListModel);
    pointJList.setForeground(variableJList.getForeground());
    pointJList.setVisibleRowCount(3);
    pointJList.setBackground(getBackground());
    pointJList.setSelectionBackground(getBackground());
    pointJList.setSelectionForeground(Color.black);
    plotPane = new PlotPane();
    double[][] plotDatas = tsJobResultsNoStats.getTimesAndValuesForVariable(varName);
    Plot2D plot2D = new SingleXPlot2D(symbolTableEntries, multiTimePlotHelper.getDataSymbolMetadataResolver(), ReservedVariable.TIME.getName(), plotNames, plotDatas, new String[] { "Time Plot", ReservedVariable.TIME.getName(), "" });
    plotPane.setPlot2D(plot2D);
    DataIdentifier[] dis = (multiTimePlotHelper.getCopyOfDisplayedDataIdentifiers() != null ? multiTimePlotHelper.getCopyOfDisplayedDataIdentifiers() : DataIdentifier.collectSortedSimilarDataTypes(multiTimePlotHelper.getVariableType(), multiTimePlotHelper.getPdeDatacontext().getDataIdentifiers()));
    Arrays.sort(dis, new Comparator<DataIdentifier>() {

        public int compare(DataIdentifier o1, DataIdentifier o2) {
            int bEqualIgnoreCase = o1.getDisplayName().compareToIgnoreCase(o2.getDisplayName());
            if (bEqualIgnoreCase == 0) {
                return o1.getDisplayName().compareTo(o2.getDisplayName());
            }
            return bEqualIgnoreCase;
        }
    });
    variableJList.setListData(dis);
    initVariableListSelected(variableJList, multiTimePlotHelper.getPdeDatacontext().getDataIdentifier());
    variableJList.setCellRenderer(multiTimePlotHelper.getListCellRenderer());
    setLayout(new GridBagLayout());
    JLabel label = new JLabel("Selected Points");
    label.setFont(label.getFont().deriveFont(Font.BOLD));
    GridBagConstraints gbc = new GridBagConstraints();
    gbc.gridx = 0;
    gbc.gridy = 0;
    gbc.anchor = GridBagConstraints.WEST;
    gbc.insets = new java.awt.Insets(15, 10, 4, 4);
    add(label, gbc);
    gbc = new GridBagConstraints();
    gbc.gridx = 1;
    gbc.gridy = 0;
    gbc.fill = java.awt.GridBagConstraints.BOTH;
    gbc.gridheight = 4;
    gbc.weightx = 1;
    gbc.weighty = 1;
    gbc.fill = GridBagConstraints.BOTH;
    gbc.insets = new java.awt.Insets(0, 4, 0, 0);
    add(plotPane, gbc);
    JScrollPane sp = new JScrollPane(pointJList);
    sp.setVerticalScrollBarPolicy(JScrollPane.VERTICAL_SCROLLBAR_ALWAYS);
    sp.setHorizontalScrollBarPolicy(JScrollPane.HORIZONTAL_SCROLLBAR_ALWAYS);
    gbc = new GridBagConstraints();
    gbc.gridx = 0;
    gbc.gridy = 1;
    gbc.anchor = GridBagConstraints.WEST;
    gbc.weighty = 0.5;
    gbc.fill = java.awt.GridBagConstraints.BOTH;
    gbc.insets = new java.awt.Insets(4, 10, 4, 4);
    add(sp, gbc);
    label = new JLabel("Y Axis");
    label.setFont(label.getFont().deriveFont(Font.BOLD));
    gbc = new GridBagConstraints();
    gbc.gridx = 0;
    gbc.gridy = 2;
    gbc.anchor = GridBagConstraints.WEST;
    gbc.insets = new java.awt.Insets(4, 10, 4, 4);
    add(label, gbc);
    sp = new JScrollPane(variableJList);
    sp.setVerticalScrollBarPolicy(JScrollPane.VERTICAL_SCROLLBAR_ALWAYS);
    sp.setHorizontalScrollBarPolicy(JScrollPane.HORIZONTAL_SCROLLBAR_ALWAYS);
    gbc = new GridBagConstraints();
    gbc.gridx = 0;
    gbc.gridy = 3;
    gbc.weightx = 0.2;
    gbc.weighty = 1;
    gbc.insets = new java.awt.Insets(4, 10, 50, 4);
    gbc.fill = java.awt.GridBagConstraints.BOTH;
    add(sp, gbc);
    variableJList.addListSelectionListener(eventHandler);
    multiTimePlotHelper.addPropertyChangeListener(eventHandler);
}

Example 4 with Plot2D

use of cbit.plot.Plot2D in project vcell by virtualcell.

the class PdeTimePlotMultipleVariablesPanel method showTimePlot.

public void showTimePlot() {
    if ((plotChangeTimer = ClientTaskDispatcher.getBlockingTimer(this, multiTimePlotHelper.getPdeDatacontext(), null, plotChangeTimer, new ActionListener() {

        @Override
        public void actionPerformed(ActionEvent e2) {
            showTimePlot();
        }
    }, "PdeTimePlotMultipleVariablesPanel update...")) != null) {
        return;
    }
    VariableType varType = multiTimePlotHelper.getVariableType();
    Object[] selectedValues = variableJList.getSelectedValues();
    DataIdentifier[] selectedDataIdentifiers = new DataIdentifier[selectedValues.length];
    System.arraycopy(selectedValues, 0, selectedDataIdentifiers, 0, selectedValues.length);
    if (selectedDataIdentifiers.length > 1) {
        for (DataIdentifier selectedDataIdentifier : selectedDataIdentifiers) {
            if (!selectedDataIdentifier.getVariableType().getVariableDomain().equals(varType.getVariableDomain())) {
                PopupGenerator.showErrorDialog(this, "Please choose VOLUME variables or MEMBRANE variables only");
                variableJList.clearSelection();
                variableJList.setSelectedValue(multiTimePlotHelper.getPdeDatacontext().getVariableName(), true);
                return;
            }
        }
    }
    try {
        final int numSelectedVariables = selectedDataIdentifiers.length;
        final int numSelectedSpatialPoints = pointVector.size();
        int[][] indices = new int[numSelectedVariables][numSelectedSpatialPoints];
        // 
        for (int i = 0; i < numSelectedSpatialPoints; i++) {
            for (int v = 0; v < numSelectedVariables; v++) {
                if (selectedDataIdentifiers[v].getVariableType().equals(varType)) {
                    if (varType.equals(VariableType.VOLUME) || varType.equals(VariableType.VOLUME_REGION) || varType.equals(VariableType.POSTPROCESSING)) {
                        SpatialSelectionVolume ssv = (SpatialSelectionVolume) pointVector.get(i);
                        indices[v][i] = ssv.getIndex(0);
                    } else if (varType.equals(VariableType.MEMBRANE) || varType.equals(VariableType.MEMBRANE_REGION)) {
                        SpatialSelectionMembrane ssm = (SpatialSelectionMembrane) pointVector.get(i);
                        indices[v][i] = ssm.getIndex(0);
                    }
                } else {
                    if (varType.equals(VariableType.VOLUME) || varType.equals(VariableType.VOLUME_REGION) || varType.equals(VariableType.POSTPROCESSING)) {
                        SpatialSelectionVolume ssv = (SpatialSelectionVolume) pointVector2.get(i);
                        indices[v][i] = ssv.getIndex(0);
                    } else if (varType.equals(VariableType.MEMBRANE) || varType.equals(VariableType.MEMBRANE_REGION)) {
                        SpatialSelectionMembrane ssm = (SpatialSelectionMembrane) pointVector2.get(i);
                        indices[v][i] = ssm.getIndex(0);
                    }
                }
            }
        }
        final String[] selectedVarNames = new String[numSelectedVariables];
        for (int i = 0; i < selectedVarNames.length; i++) {
            selectedVarNames[i] = selectedDataIdentifiers[i].getName();
        }
        final double[] timePoints = multiTimePlotHelper.getPdeDatacontext().getTimePoints();
        TimeSeriesJobSpec tsjs = new TimeSeriesJobSpec(selectedVarNames, indices, null, timePoints[0], 1, timePoints[timePoints.length - 1], VCDataJobID.createVCDataJobID(multiTimePlotHelper.getUser(), true));
        if (!tsjs.getVcDataJobID().isBackgroundTask()) {
            throw new RuntimeException("Use getTimeSeries(...) if not a background job");
        }
        Hashtable<String, Object> hash = new Hashtable<String, Object>();
        hash.put(PDEDataViewer.StringKey_timeSeriesJobSpec, tsjs);
        AsynchClientTask task1 = new PDEDataViewer.TimeSeriesDataRetrievalTask("Retrieving Data", multiTimePlotHelper, multiTimePlotHelper.getPdeDatacontext());
        AsynchClientTask task2 = new AsynchClientTask("showing time plot", AsynchClientTask.TASKTYPE_SWING_BLOCKING) {

            @Override
            public void run(Hashtable<String, Object> hashTable) throws Exception {
                TSJobResultsNoStats tsJobResultsNoStats = (TSJobResultsNoStats) hashTable.get(PDEDataViewer.StringKey_timeSeriesJobResults);
                int plotCount = numSelectedVariables * numSelectedSpatialPoints;
                SymbolTableEntry[] symbolTableEntries = new SymbolTableEntry[plotCount];
                String[] plotNames = new String[plotCount];
                double[][] plotDatas = new double[1 + plotCount][];
                plotDatas[0] = timePoints;
                int plotIndex = 0;
                for (int v = 0; v < numSelectedVariables; v++) {
                    String varName = selectedVarNames[v];
                    double[][] data = tsJobResultsNoStats.getTimesAndValuesForVariable(varName);
                    for (int i = 1; i < data.length; i++) {
                        symbolTableEntries[plotIndex] = multiTimePlotHelper.getsimulation().getMathDescription().getEntry(varName);
                        plotNames[plotIndex] = varName + " at P[" + (i - 1) + "]";
                        plotDatas[plotIndex + 1] = data[i];
                        plotIndex++;
                    }
                }
                Plot2D plot2D = new SingleXPlot2D(symbolTableEntries, multiTimePlotHelper.getDataSymbolMetadataResolver(), ReservedVariable.TIME.getName(), plotNames, plotDatas, new String[] { "Time Plot", ReservedVariable.TIME.getName(), "" });
                plotPane.setPlot2D(plot2D);
            }
        };
        ClientTaskDispatcher.dispatch(this, hash, new AsynchClientTask[] { task1, task2 }, false, true, true, null, false);
    } catch (Exception e) {
        e.printStackTrace(System.out);
    }
}

Example 5 with Plot2D

use of cbit.plot.Plot2D 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);
    }
}