Examples with SourceDataInfo cbit.image.SourceDataInfo used on opensource projects

Example 6 with SourceDataInfo

use of cbit.image.SourceDataInfo in project vcell by virtualcell.

the class GeometrySummaryPanel method initGeometry.

/**
 * Comment
 */
private void initGeometry(Geometry arg1) {
    final boolean bSpatial = getGeometry() != null && getGeometry().getDimension() > 0;
    getImagePlaneManagerPanel1().setVisible(bSpatial);
    getJPanelOrigin().setVisible(bSpatial);
    getJPanelSize().setVisible(bSpatial);
    if (getGeometry() != null) {
        try {
            if (getGeometry().getGeometrySpec().getSampledImage().isDirty()) {
                return;
            }
            VCImage vcImage = getGeometry().getGeometrySpec().getSampledImage().getCurrentValue();
            byte[] pixels = vcImage.getPixels();
            DisplayAdapterService das = new DisplayAdapterService();
            das.setActiveScaleRange(new org.vcell.util.Range(0, 255));
            das.setValueDomain(new org.vcell.util.Range(0, 255));
            das.addColorModelForValues(DisplayAdapterService.createContrastColorModel(), DisplayAdapterService.createGraySpecialColors(), "Contrast");
            das.setActiveColorModelID("Contrast");
            int[] rgb = new int[pixels.length];
            for (int i = 0; i < rgb.length; i += 1) {
                rgb[i] = das.getColorFromIndex(pixels[i]);
            }
            SourceDataInfo sdi = new SourceDataInfo(SourceDataInfo.INT_RGB_TYPE, rgb, getGeometry().getExtent(), getGeometry().getOrigin(), new org.vcell.util.Range(0, 255), 0, vcImage.getNumX(), 1, vcImage.getNumY(), vcImage.getNumX(), vcImage.getNumZ(), vcImage.getNumX() * vcImage.getNumY());
            getImagePlaneManagerPanel1().setSourceDataInfo(sdi);
        } catch (Exception e) {
            PopupGenerator.showErrorDialog(GeometrySummaryPanel.this, e.getMessage(), e);
        }
    } else {
        getImagePlaneManagerPanel1().setSourceDataInfo(null);
    }
}

Example 7 with SourceDataInfo

use of cbit.image.SourceDataInfo in project vcell by virtualcell.

the class GeometryViewer method refreshSourceDataInfo.

/**
 * connEtoM2:  (Geometry.this --> ImagePlaneManagerPanel1.sourceDataInfo)
 * @param value cbit.vcell.geometry.Geometry
 */
/* WARNING: THIS METHOD WILL BE REGENERATED. */
private void refreshSourceDataInfo() {
    if (getGeometry() == null) {
        return;
    }
    GeometrySpec geometrySpec = getGeometry().getGeometrySpec();
    if (geometrySpec.getSampledImage().isDirty()) {
        return;
    }
    VCImage sampledImage = geometrySpec.getSampledImage().getCurrentValue();
    try {
        SourceDataInfo sdi = new SourceDataInfo(SourceDataInfo.INDEX_TYPE, sampledImage.getPixels(), geometrySpec.getExtent(), geometrySpec.getOrigin(), null, 0, sampledImage.getNumX(), 1, sampledImage.getNumY(), sampledImage.getNumX(), sampledImage.getNumZ(), sampledImage.getNumX() * sampledImage.getNumY());
        getImagePlaneManagerPanel1().setSourceDataInfo(sdi);
    } catch (ImageException e) {
        e.printStackTrace();
        DialogUtils.showErrorDialog(this, e.getMessage());
    } catch (Exception e) {
        e.printStackTrace();
        DialogUtils.showErrorDialog(this, e.getMessage(), e);
    }
}

Example 8 with SourceDataInfo

use of cbit.image.SourceDataInfo 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 9 with SourceDataInfo

use of cbit.image.SourceDataInfo in project vcell by virtualcell.

the class DataSymbolsSpecPanel method setDataSymbol.

// public void createDataSymbol() throws Exception, UserCancelException{
// final int VFRAP_DATASET = 0;
// final int VFRAP_SPECIALS = 1;
// final int ASSOCIATE_EXISTING_FD = 2;
// final int POINT_SPREAD_FUNCTION = 3;
// final int IMAGE_FILE = 4;
// final int COPY_FROM_BIOMODEL = 5;
// int[] dataSymbolSource = null;
// 
// String[][] choices = new String[][] {{ADD_VFRAP_DATASET_MENU},{ADD_VFRAP_SPECIALS_MENU},{ADD_ASSOCIATE_EXISTING_FD_MENU},
// {ADD_PSF_MENU},{ADD_IMAGE_FILE_MENU},{ADD_COPY_FROM_BIOMODEL_MENU} };
// 
// dataSymbolSource = DialogUtils.showComponentOKCancelTableList(
// getComponent(),
// "Choose a source for the data symbol.",
// new String[] {"Available Sources:"},
// choices, ListSelectionModel.SINGLE_SELECTION);
// 
// if(dataSymbolSource[0] == VFRAP_DATASET){
// getDataSymbolsPanel().addVFrapOriginalImages();
// }else if(dataSymbolSource[0] == VFRAP_SPECIALS){
// getDataSymbolsPanel().addVFrapDerivedImages();
// }else if(dataSymbolSource[0] == ASSOCIATE_EXISTING_FD){
// Component requesterComponent = DataSymbolsSpecPanel.this;
// DocumentWindow documentWindow = (DocumentWindow)BeanUtils.findTypeParentOfComponent(requesterComponent, DocumentWindow.class);
// documentWindow.getTopLevelWindowManager().getRequestManager().showFieldDataWindow(new FieldDataWindowManager.DataSymbolCallBack() {
// public void createDataSymbol(ExternalDataIdentifier dataSetID,
// String fieldDataVarName, VariableType fieldDataVarType,
// double fieldDataVarTime) {
// 
// System.out.println(dataSetID+" "+fieldDataVarName+" "+fieldDataVarType+" "+fieldDataVarTime);
// // ex: incomplete 51780592 danv(26766043)      fluor     Volume_VariableType     23.680419921875
// 
// DecimalFormat df = new  DecimalFormat("###000.00");		// max time interval we can display is about 11 days
// String fluorName = fieldDataVarName + "_" + df.format(fieldDataVarTime).substring(0, df.format(fieldDataVarTime).indexOf(".")) + "s" + df.format(fieldDataVarTime).substring(1+df.format(fieldDataVarTime).indexOf(".")) + "_" + dataSetID.getName();
// // TODO:  symbol names may not be unique, must check for unicity and prompt the user
// FieldDataSymbol dataSymbol = new FieldDataSymbol(fluorName, DataSymbolType.GENERIC_SYMBOL,
// getSimulationContext().getDataContext(), VCUnitDefinition.UNIT_TBD,
// dataSetID,
// fieldDataVarName, fieldDataVarType.getTypeName(), fieldDataVarTime);
// getSimulationContext().getDataContext().addDataSymbol(dataSymbol);
// 
// }
// });
// }else if(dataSymbolSource[0] == POINT_SPREAD_FUNCTION){
// PointSpreadFunctionManagement psfManager = new PointSpreadFunctionManagement(DataSymbolsSpecPanel.this,
// getSimulationContext());
// psfManager.importPointSpreadFunction();
// }else if(dataSymbolSource[0] == IMAGE_FILE){
// throw new RuntimeException("Option not yet implemented.");
// }else if(dataSymbolSource[0] == COPY_FROM_BIOMODEL){
// throw new RuntimeException("Option not yet implemented.");
// }else{
// throw new IllegalArgumentException("Error selecting data symbol, Unknown Source type " + dataSymbolSource[0]);
// }
// }
public void setDataSymbol(Object object) {
    if (object == null) {
        // TODO: display empty image
        return;
    }
    if (((DataSymbol) object).equals(ivjCurrentSymbol)) {
        return;
    } else {
        ivjCurrentSymbol = (DataSymbol) object;
    }
    // manage checkbox status depending on type of current data symbol
    DataSymbolType dsType = ivjCurrentSymbol.getDataSymbolType();
    switch(dsType) {
        case GENERIC_SYMBOL:
            getChckbxPointSpreadFunction().setEnabled(true);
            getChckbxPointSpreadFunction().setSelected(false);
            break;
        case POINT_SPREAD_FUNCTION:
            getChckbxPointSpreadFunction().setEnabled(true);
            getChckbxPointSpreadFunction().setSelected(true);
            break;
        default:
            getChckbxPointSpreadFunction().setEnabled(false);
            getChckbxPointSpreadFunction().setSelected(false);
            break;
    }
    // displays iconized image for the current (field?) data symbol
    getImagePlaneManagerPanel().setMode(ImagePaneModel.MESH_MODE);
    int w = Integer.valueOf(30).intValue() + 5 * (countW % 5);
    int h = Integer.valueOf(20).intValue() + 3 * (countH % 7);
    String type = "double";
    System.out.println("  " + w + ", " + h);
    SourceDataInfo sdi = ImagePaneScrollerTest.getExampleSDI(type, w, h);
    getImagePlaneManagerPanel().setSourceDataInfo(sdi);
    countW++;
    countH++;
}

Example 10 with SourceDataInfo

use of cbit.image.SourceDataInfo in project vcell by virtualcell.

the class PDEOffscreenRenderer method getScaledRGBVolume.

private BufferedImage getScaledRGBVolume(CartesianMesh mesh, int meshMode, int imageScale, boolean bBackground) {
    Dimension dim = FormatSpecificSpecs.getMeshDimensionUnscaled(getNormalAxis(), getServerPDEDataContext().getCartesianMesh());
    int width = (int) dim.getWidth();
    int height = (int) dim.getHeight();
    double[] volumeData = new double[width * height];
    if (!bBackground) {
        // if(bNeedsDefaultScaling){setDefaultScaling();}
        double notInDomainValue = getDisplayAdapterService().getValueDomain().getMin() - 1.0;
        double[] values = getServerPDEDataContext().getDataValues();
        int[] dataIndices = getServerPDEDataContext().getCartesianMesh().getVolumeSliceIndices(getNormalAxis(), getSlice());
        for (int i = 0; i < dataIndices.length; i++) {
            double value = values[dataIndices[i]];
            if (domainValid != null) {
                if (domainValid.get(dataIndices[i]) || domainValid.isEmpty()) {
                    volumeData[i] = value;
                } else {
                    volumeData[i] = notInDomainValue;
                }
            } else {
                volumeData[i] = value;
            }
        }
    }
    SourceDataInfo sourceDataInfo = new SourceDataInfo(SourceDataInfo.RAW_VALUE_TYPE, volumeData, mesh.getExtent(), mesh.getOrigin(), new Range(0, 1), 0, width, 1, height, width, 1, 0);
    ImagePaneModel imagePaneModel = new ImagePaneModel();
    imagePaneModel.setSourceData(sourceDataInfo);
    imagePaneModel.setBackgroundColor(Color.black);
    imagePaneModel.setDisplayAdapterService(getDisplayAdapterService());
    // getDisplayAdapterService().setActiveScaleRange(new Range(0,1));
    imagePaneModel.setMode(meshMode);
    imagePaneModel.setZoom(imageScale);
    imagePaneModel.setViewport(new Rectangle(imagePaneModel.getScaledLength(width), imagePaneModel.getScaledLength(height)));
    imagePaneModel.updateViewPortImage();
    if (bBackground) {
        int[] internalBuffer = ((DataBufferInt) (imagePaneModel.getViewPortImage().getRaster().getDataBuffer())).getData();
        Arrays.fill(internalBuffer, getDisplayAdapterService().getSpecialColors()[DisplayAdapterService.NULL_COLOR_OFFSET]);
    }
    BufferedImage bufferedImage = imagePaneModel.getViewPortImage();
    imagePaneModel.setDisplayAdapterService(null);
    return bufferedImage;
}