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Example 1 with ImagePlaneManagerPanel

use of cbit.image.gui.ImagePlaneManagerPanel 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);
}
Also used : DisplayAdapterService(cbit.image.DisplayAdapterService) JPanel(javax.swing.JPanel) GridBagConstraints(java.awt.GridBagConstraints) GridBagLayout(java.awt.GridBagLayout) ActionEvent(java.awt.event.ActionEvent) ImagePlaneManagerPanel(cbit.image.gui.ImagePlaneManagerPanel) JButton(javax.swing.JButton) VCImage(cbit.image.VCImage) SourceDataInfo(cbit.image.SourceDataInfo) CoordinateIndex(org.vcell.util.CoordinateIndex) JFrame(javax.swing.JFrame) PlotData(cbit.plot.PlotData) DataSymbolMetadataResolver(cbit.vcell.solver.SimulationModelInfo.DataSymbolMetadataResolver) VariableType(cbit.vcell.math.VariableType) VolVariable(cbit.vcell.math.VolVariable) Curve(cbit.vcell.geometry.Curve) VCImageUncompressed(cbit.image.VCImageUncompressed) Range(org.vcell.util.Range) CartesianMesh(cbit.vcell.solvers.CartesianMesh) CurveValueProvider(cbit.vcell.simdata.gui.CurveValueProvider) ActionListener(java.awt.event.ActionListener) Coordinate(org.vcell.util.Coordinate) SpatialSelectionVolume(cbit.vcell.simdata.SpatialSelectionVolume) RegionImage(cbit.vcell.geometry.RegionImage) PlotPane(cbit.plot.gui.PlotPane) Plot2D(cbit.plot.Plot2D) CurveSelectionInfo(cbit.vcell.geometry.CurveSelectionInfo)

Example 2 with ImagePlaneManagerPanel

use of cbit.image.gui.ImagePlaneManagerPanel in project vcell by virtualcell.

the class PDEDataContextPanel method getImagePlaneManagerPanel.

/**
 * Return the ImagePlaneManagerPanel1 property value.
 * @return cbit.image.ImagePlaneManagerPanel
 */
/* WARNING: THIS METHOD WILL BE REGENERATED. */
private ImagePlaneManagerPanel getImagePlaneManagerPanel() {
    if (ivjImagePlaneManagerPanel == null) {
        try {
            ivjImagePlaneManagerPanel = new ImagePlaneManagerPanel();
            ivjImagePlaneManagerPanel.setName("ImagePlaneManagerPanel");
            ivjImagePlaneManagerPanel.setMode(1);
        // user code begin {1}
        // user code end
        } catch (java.lang.Throwable ivjExc) {
            // user code begin {2}
            // user code end
            handleException(ivjExc);
        }
    }
    return ivjImagePlaneManagerPanel;
}
Also used : ImagePlaneManagerPanel(cbit.image.gui.ImagePlaneManagerPanel)

Example 3 with ImagePlaneManagerPanel

use of cbit.image.gui.ImagePlaneManagerPanel in project vcell by virtualcell.

the class GeometryViewer method getImagePlaneManagerPanel1.

/**
 * Return the ImagePlaneManagerPanel1 property value.
 * @return cbit.image.ImagePlaneManagerPanel
 */
/* WARNING: THIS METHOD WILL BE REGENERATED. */
private ImagePlaneManagerPanel getImagePlaneManagerPanel1() {
    if (ivjImagePlaneManagerPanel1 == null) {
        try {
            ivjImagePlaneManagerPanel1 = new ImagePlaneManagerPanel();
            ivjImagePlaneManagerPanel1.setName("ImagePlaneManagerPanel1");
            ivjImagePlaneManagerPanel1.setDisplayAdapterServicePanelVisible(false);
        // user code begin {1}
        // user code end
        } catch (java.lang.Throwable ivjExc) {
            // user code begin {2}
            // user code end
            handleException(ivjExc);
        }
    }
    return ivjImagePlaneManagerPanel1;
}
Also used : ImagePlaneManagerPanel(cbit.image.gui.ImagePlaneManagerPanel)

Aggregations

ImagePlaneManagerPanel (cbit.image.gui.ImagePlaneManagerPanel)3 DisplayAdapterService (cbit.image.DisplayAdapterService)1 SourceDataInfo (cbit.image.SourceDataInfo)1 VCImage (cbit.image.VCImage)1 VCImageUncompressed (cbit.image.VCImageUncompressed)1 Plot2D (cbit.plot.Plot2D)1 PlotData (cbit.plot.PlotData)1 PlotPane (cbit.plot.gui.PlotPane)1 Curve (cbit.vcell.geometry.Curve)1 CurveSelectionInfo (cbit.vcell.geometry.CurveSelectionInfo)1 RegionImage (cbit.vcell.geometry.RegionImage)1 VariableType (cbit.vcell.math.VariableType)1 VolVariable (cbit.vcell.math.VolVariable)1 SpatialSelectionVolume (cbit.vcell.simdata.SpatialSelectionVolume)1 CurveValueProvider (cbit.vcell.simdata.gui.CurveValueProvider)1 DataSymbolMetadataResolver (cbit.vcell.solver.SimulationModelInfo.DataSymbolMetadataResolver)1 CartesianMesh (cbit.vcell.solvers.CartesianMesh)1 GridBagConstraints (java.awt.GridBagConstraints)1 GridBagLayout (java.awt.GridBagLayout)1 ActionEvent (java.awt.event.ActionEvent)1