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

Example 6 with Plot2D

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

the class ODESolverPlotSpecificationPanel method setPlot2D.

private void setPlot2D(Plot2D plot2D) {
    // amended March 29, 2007. To fire event to ODEDataViewer.
    Plot2D oldValue = this.fieldPlot2D;
    this.fieldPlot2D = plot2D;
    firePropertyChange("Plot2D", oldValue, plot2D);
}

Example 7 with Plot2D

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

the class DisplayImageOp method displayImage.

public void displayImage(final Image image, String title, WindowListener listener) {
    final ImagePlaneManagerPanel imagePanel = new ImagePlaneManagerPanel();
    double[] doublePixels = image.getDoublePixels();
    double minPixel = Double.MAX_VALUE;
    double maxPixel = -Double.MAX_VALUE;
    for (int i = 0; i < doublePixels.length; i++) {
        double pixel = doublePixels[i];
        doublePixels[i] = pixel;
        minPixel = Math.min(minPixel, pixel);
        maxPixel = Math.max(maxPixel, pixel);
    }
    Range newRange = new Range(minPixel, maxPixel);
    SourceDataInfo source = new SourceDataInfo(SourceDataInfo.RAW_VALUE_TYPE, doublePixels, image.getExtent(), image.getOrigin(), newRange, 0, image.getNumX(), 1, image.getNumY(), image.getNumX(), image.getNumZ(), image.getNumX() * image.getNumY());
    imagePanel.setDisplayAdapterServicePanelVisible(true);
    imagePanel.setCurveValueProvider(new CurveValueProvider() {

        @Override
        public void curveAdded(Curve curve) {
            System.out.println("called curveAdded(" + curve + "), do nothing for now");
        }

        @Override
        public void curveRemoved(Curve curve) {
            System.out.println("called curveRemoved(" + curve + ")");
        }

        @Override
        public String getCurveValue(CurveSelectionInfo csi) {
            System.out.println("called getCurveValue(CurveSelectionInfo " + csi);
            return null;
        }

        @Override
        public CurveSelectionInfo getInitalCurveSelection(int tool, Coordinate wc) {
            System.out.println("called getInitialCurveSelection(tool=" + tool + ", coord=" + wc + ")");
            return null;
        }

        @Override
        public boolean isAddControlPointOK(int tool, Coordinate wc, Curve addedToThisCurve) {
            System.out.println("called isAddControlPointOK");
            return true;
        }

        @Override
        public boolean providesInitalCurve(int tool, Coordinate wc) {
            System.out.println("called providesInitialCurve(tool=" + tool + " (TOOL_LINE=" + CurveEditorTool.TOOL_LINE + "), coord=" + wc);
            return false;
        }

        @Override
        public void setDescription(Curve curve) {
            System.out.println("called setDescription(" + curve + ")");
            curve.setDescription(CurveValueProvider.DESCRIPTION_VOLUME);
        }

        @Override
        public CurveSelectionInfo findChomboCurveSelectionInfoForPoint(CoordinateIndex ci) {
            System.out.println("called find ChomboCurveSelectionInfoForPoint(coord=" + ci + ")");
            return null;
        }
    });
    DisplayAdapterService das = imagePanel.getDisplayAdapterServicePanel().getDisplayAdapterService();
    das.setValueDomain(null);
    das.addColorModelForValues(DisplayAdapterService.createGrayColorModel(), DisplayAdapterService.createGraySpecialColors(), DisplayAdapterService.GRAY);
    das.addColorModelForValues(DisplayAdapterService.createBlueRedColorModel(), DisplayAdapterService.createBlueRedSpecialColors(), DisplayAdapterService.BLUERED);
    das.setActiveColorModelID(DisplayAdapterService.BLUERED);
    final JFrame jframe = new JFrame();
    jframe.setTitle(title);
    JPanel panel = new JPanel();
    panel.setLayout(new GridBagLayout());
    GridBagConstraints imageConstraints = new GridBagConstraints();
    imageConstraints.gridx = 0;
    imageConstraints.gridy = 0;
    imageConstraints.weightx = 1.0;
    imageConstraints.weighty = 1.0;
    imageConstraints.fill = GridBagConstraints.BOTH;
    panel.add(imagePanel, imageConstraints);
    JButton plotButton = new JButton("plot");
    plotButton.addActionListener(new ActionListener() {

        @Override
        public void actionPerformed(ActionEvent e) {
            try {
                Curve curve = imagePanel.getCurveRenderer().getSelection().getCurve();
                VariableType variableType = VariableType.VOLUME;
                Curve samplerCurve = curve.getSampledCurve();
                samplerCurve.setDescription(curve.getDescription());
                VCImage vcImage = new VCImageUncompressed(null, new byte[image.getISize().getXYZ()], image.getExtent(), image.getISize().getX(), image.getISize().getY(), image.getISize().getZ());
                int dimension = 1 + (image.getISize().getY() > 0 ? 1 : 0) + (image.getISize().getZ() > 0 ? 1 : 0);
                RegionImage regionImage = new RegionImage(vcImage, dimension, image.getExtent(), image.getOrigin(), RegionImage.NO_SMOOTHING);
                CartesianMesh mesh = CartesianMesh.createSimpleCartesianMesh(image.getOrigin(), image.getExtent(), image.getISize(), regionImage);
                SpatialSelectionVolume ssVolume = new SpatialSelectionVolume(new CurveSelectionInfo(samplerCurve), variableType, mesh);
                String varName = "var";
                SymbolTableEntry[] symbolTableEntries = new SymbolTableEntry[] { new VolVariable(varName, null) };
                PlotData plotData = getLineScan(ssVolume, image, mesh);
                PlotPane plotPane = new PlotPane();
                DataSymbolMetadataResolver resolver = null;
                Plot2D plot2D = new Plot2D(symbolTableEntries, resolver, new String[] { varName }, new PlotData[] { plotData }, new String[] { "Values along curve", "Distance (\u00b5m)", "[" + varName + "]" });
                plotPane.setPlot2D(plot2D);
                DialogUtils.showComponentCloseDialog(jframe, plotPane, "plot");
            } catch (ImageException | IOException | DataAccessException | MathException e1) {
                e1.printStackTrace();
            }
        }
    });
    GridBagConstraints plotButtonConstraints = new GridBagConstraints();
    plotButtonConstraints.gridx = 0;
    plotButtonConstraints.gridy = 1;
    panel.add(plotButton, plotButtonConstraints);
    jframe.getContentPane().add(panel);
    jframe.setSize(500, 500);
    jframe.addWindowListener(listener);
    jframe.setVisible(true);
    imagePanel.setSourceDataInfo(source);
}

Example 8 with Plot2D

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

the class DisplayPlotOp method displayPlot.

public void displayPlot(RowColumnResultSet rowColumnResultSet, String title, WindowListener listener) throws ExpressionException {
    JFrame frame = new javax.swing.JFrame();
    PlotPane aPlotPane;
    aPlotPane = new PlotPane();
    frame.setContentPane(aPlotPane);
    frame.setSize(aPlotPane.getSize());
    if (listener != null) {
        frame.addWindowListener(listener);
    }
    frame.setTitle(title);
    frame.setVisible(true);
    java.awt.Insets insets = frame.getInsets();
    frame.setSize(frame.getWidth() + insets.left + insets.right, frame.getHeight() + insets.top + insets.bottom);
    frame.setVisible(true);
    int dataColumnCount = rowColumnResultSet.getDataColumnCount();
    PlotData[] plotDatas = new PlotData[dataColumnCount - 1];
    String[] labels = new String[dataColumnCount - 1];
    double[] time = rowColumnResultSet.extractColumn(0);
    for (int i = 0; i < dataColumnCount - 1; i++) {
        double[] yArray = rowColumnResultSet.extractColumn(i + 1);
        plotDatas[i] = new PlotData(time, yArray);
        labels[i] = rowColumnResultSet.getColumnDescriptions(i + 1).getName();
    }
    Plot2D plot2D = new Plot2D(null, null, labels, plotDatas);
    aPlotPane.setPlot2D(plot2D);
}

Example 9 with Plot2D

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

the class BNGDataPlotPanel method selectionModel1_ValueChanged.

/**
 * Comment
 */
private void selectionModel1_ValueChanged(javax.swing.event.ListSelectionEvent listSelectionEvent) throws Exception {
    int firstIndex = listSelectionEvent.getFirstIndex();
    int lastIndex = listSelectionEvent.getLastIndex();
    if (firstIndex < 0 || lastIndex < 0) {
        return;
    }
    Object[] selectedValues = getJList1().getSelectedValues();
    int numSelected = selectedValues.length;
    if (numSelected == 0) {
        return;
    }
    double[][] dataValues = new double[1 + numSelected][];
    String[] names = new String[numSelected];
    int t_index = fieldOdeSolverResultSet.findColumn("t");
    dataValues[0] = fieldOdeSolverResultSet.extractColumn(t_index);
    for (int i = 0; i < numSelected; i++) {
        names[i] = (String) selectedValues[i];
        int index = fieldOdeSolverResultSet.findColumn(names[i]);
        dataValues[i + 1] = fieldOdeSolverResultSet.extractColumn(index);
    }
    boolean[] visibleFlags = new boolean[dataValues.length];
    Arrays.fill(visibleFlags, true);
    String[] labels = { "", "t", "" };
    Plot2D plot2D = new SingleXPlot2D(null, null, "Time", names, dataValues, labels, visibleFlags);
    getplotPane().setPlot2D(plot2D);
    return;
}

Example 10 with Plot2D

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

the class DataProcessingResultsPanel method onVariablesChange.

private void onVariablesChange() {
    try {
        // keep old indices
        lastSelectedIdxArray = varJList.getSelectedIndices();
        Object[] selectedObjects = varJList.getSelectedValues();
        int numSelectedVars = selectedObjects.length;
        int totalColumns = 1;
        for (int v = 0; v < numSelectedVars; v++) {
            totalColumns++;
        // String varName = (String)selectedObjects[v];
        // ucar.nc2.Variable volVar = ncfile.findVariable(varName);
        // int[] shape = volVar.getShape();
        // int numColumns = shape[1];
        // 
        // totalColumns += numColumns;
        }
        if (dataProcessingOutputInfo == null) {
            throw new RuntimeException("dataProcessingOutInfo null, thread = " + Thread.currentThread().getName());
        }
        final double[] vtp = dataProcessingOutputInfo.getVariableTimePoints();
        if (vtp == null) {
            throw new RuntimeException("getVariableTimePoints( ) null, thread = " + Thread.currentThread().getName());
        }
        final int numTimes = vtp.length;
        double[][] plotDatas = new double[totalColumns][numTimes];
        // assumes all times same
        plotDatas[0] = dataProcessingOutputInfo.getVariableTimePoints();
        String[] plotNames = new String[totalColumns - 1];
        int columnCount = 0;
        for (int v = 0; v < numSelectedVars; v++) {
            String varName = ((String) selectedObjects[v]);
            // remove the unit from name if exist
            if (// "_(" doesn't suppose to be the first char
            varName.indexOf("_(") > 0) {
                varName = varName.substring(0, varName.indexOf("_("));
            }
            // }
            for (int i = 0; i < /*numColumns*/
            1; i++) {
                String plotName = varName;
                if (i > 0) {
                    plotName += ": region " + (i - 1);
                }
                plotNames[columnCount] = plotName;
                if (columnCount >= plotDatas.length) {
                    throw new RuntimeException("invalid columnCount " + columnCount + " >= " + plotDatas.length);
                }
                for (int j = 0; j < numTimes; j++) {
                    // data.get(j, i);
                    double[] vars = dataProcessingOutputInfo.getVariableStatValues().get(varName);
                    if (j >= vars.length) {
                        throw new RuntimeException("invalid index " + j + " on " + varName + ", greater than " + vars.length);
                    }
                    plotDatas[columnCount + 1][j] = vars[j];
                }
                columnCount++;
            }
        }
        Plot2D plot2D = new SingleXPlot2D(null, null, ReservedVariable.TIME.getName(), plotNames, plotDatas, new String[] { "Time Plot", ReservedVariable.TIME.getName(), "" });
        plotPane.setPlot2D(plot2D);
    } catch (Exception e1) {
        VCDataIdentifier id = dataProcessingOutputInfo.getVCDataIdentifier();
        DialogUtils.ErrorContext ec = new DialogUtils.ErrorContext(VerboseDataIdentifier.parse(id));
        DialogUtils.showErrorDialog(this, e1.getMessage(), e1, ec);
        e1.printStackTrace();
    }
}