Examples with UShortImage cbit.vcell.VirtualMicroscopy.UShortImage used on opensource projects

Example 51 with UShortImage

use of cbit.vcell.VirtualMicroscopy.UShortImage in project vcell by virtualcell.

the class ROIMultiPaintManager method duplicateROIData.

private void duplicateROIData(final int newZSize) {
    final AsynchClientTask extrudeTask = new AsynchClientTask("Extruding...", AsynchClientTask.TASKTYPE_NONSWING_BLOCKING) {

        @Override
        public void run(Hashtable<String, Object> hashTable) throws Exception {
            ISize origSize = getImageDataSetChannel().getISize();
            if (origSize.getZ() != 1 || newZSize < 1) {
                throw new IllegalArgumentException("Extrude assumes starting with 2D and new Z size >= 1.");
            }
            UShortImage[][] newUnderLayImageArr = new UShortImage[initImageDataSetChannels.length][newZSize];
            BufferedImage[] newROICompositeArr = new BufferedImage[newZSize];
            for (int i = 0; i < newZSize; i++) {
                for (int c = 0; c < initImageDataSetChannels.length; c++) {
                    // short[] zslice = new short[initImageDataSetChannels[c].getAllImages()[0].getPixels().length];
                    // System.arraycopy(initImageDataSetChannels[c].getAllImages()[0].getPixels(), 0, zslice, 0, zslice.length);
                    newUnderLayImageArr[c][i] = new UShortImage(// zslice,
                    initImageDataSetChannels[c].getAllImages()[0].getPixels().clone(), DEFAULT_ORIGIN, DEFAULT_EXTENT, initImageDataSetChannels[c].getAllImages()[0].getNumX(), initImageDataSetChannels[c].getAllImages()[0].getNumY(), 1);
                }
                newROICompositeArr[i] = new BufferedImage(roiComposite[0].getWidth(), roiComposite[0].getHeight(), BufferedImage.TYPE_BYTE_INDEXED, getContrastIndexColorModel());
                System.arraycopy((byte[]) ((DataBufferByte) roiComposite[0].getRaster().getDataBuffer()).getData(), 0, (byte[]) ((DataBufferByte) newROICompositeArr[i].getRaster().getDataBuffer()).getData(), 0, origSize.getX() * origSize.getY());
            }
            for (int c = 0; c < initImageDataSetChannels.length; c++) {
                initImageDataSetChannels[c] = new ImageDataset(newUnderLayImageArr[c], null, newZSize);
            }
            roiComposite = newROICompositeArr;
            if (!(enhanceImageAmount == ROIMultiPaintManager.ENHANCE_NONE)) {
                getClientTaskStatusSupport().setMessage("smoothing...");
            }
            updateAuxiliaryInfo(origSize, getClientTaskStatusSupport());
        }
    };
    final AsynchClientTask updatePanelTask = getUpdateDisplayAfterCropTask();
    ClientTaskDispatcher.dispatch(overlayEditorPanelJAI, new Hashtable<String, Object>(), new AsynchClientTask[] { extrudeTask, updatePanelTask }, false, false, null, true);
}

Example 52 with UShortImage

use of cbit.vcell.VirtualMicroscopy.UShortImage in project vcell by virtualcell.

the class OverlayEditorPanelJAI method displaySpecialData.

public void displaySpecialData(short[] specialData, int width, int height) throws Exception {
    if (specialData == null) {
        forceImage();
        return;
    }
    UShortImage specialUShortImage = new UShortImage(specialData, null, null, width, height, 1);
    BufferedImage specialBufferedImage = createUnderlyingImage(specialUShortImage);
    imagePane.setUnderlyingImage(specialBufferedImage, /* false,*/
    null);
}

Example 53 with UShortImage

use of cbit.vcell.VirtualMicroscopy.UShortImage in project vcell by virtualcell.

the class VFrap_OverlayEditorPanelJAI method getImportROIMaskButton.

public JButton getImportROIMaskButton() {
    if (importROIMaskButton == null) {
        importROIMaskButton = new JButton(new ImageIcon(getClass().getResource("/images/importROI.gif")));
        importROIMaskButton.setPreferredSize(new Dimension(32, 32));
        importROIMaskButton.setMargin(new Insets(2, 2, 2, 2));
        importROIMaskButton.setToolTipText("Import ROI mask from file");
        importROIMaskButton.addActionListener(new ActionListener() {

            public void actionPerformed(final ActionEvent e) {
                File inputFile = null;
                try {
                    int option = openJFileChooser.showOpenDialog(VFrap_OverlayEditorPanelJAI.this);
                    if (option == JFileChooser.APPROVE_OPTION) {
                        inputFile = openJFileChooser.getSelectedFile();
                    } else {
                        throw UserCancelException.CANCEL_GENERIC;
                    }
                    if (!customROIImport.importROI(inputFile)) {
                        ImageDataset importImageDataset = ImageDatasetReaderService.getInstance().getImageDatasetReader().readImageDataset(inputFile.getAbsolutePath(), null);
                        if (importImageDataset.getISize().getX() * importImageDataset.getISize().getY() != getImagePane().getHighlightImage().getWidth() * getImagePane().getHighlightImage().getHeight()) {
                            throw new Exception("Imported ROI mask size (" + importImageDataset.getISize().getX() + "," + importImageDataset.getISize().getY() + ")" + " does not match current Frap DataSet size (" + getImagePane().getHighlightImage().getWidth() + "," + getImagePane().getHighlightImage().getHeight() + ")");
                        }
                        // BufferedImage roiMaskImage = BufferedImageReader.makeBufferedImageReader(iFormatReader).openImage(0);
                        UShortImage roiMaskImage = importImageDataset.getImage(0, 0, 0);
                        int maskColor = highlightColor.getRGB();
                        for (int y = 0; y < importImageDataset.getISize().getY(); y++) {
                            for (int x = 0; x < importImageDataset.getISize().getX(); x++) {
                                if ((roiMaskImage.getPixel(x, y, 0) & 0xFFFF) != 0) {
                                    getImagePane().getHighlightImage().setRGB(x, y, maskColor);
                                }
                            }
                        }
                        getImagePane().refreshImage();
                    }
                } catch (UserCancelException uce) {
                // Do Nothing
                } catch (Exception e1) {
                    e1.printStackTrace();
                    DialogUtils.showErrorDialog(VFrap_OverlayEditorPanelJAI.this, "Error importing ROI" + e1.getMessage());
                }
            }
        });
    }
    return importROIMaskButton;
}

Example 54 with UShortImage

use of cbit.vcell.VirtualMicroscopy.UShortImage in project vcell by virtualcell.

the class VFrap_OverlayEditorPanelJAI method createHighlightImageFromROI.

/**
 * Method createHighlightImageFromROI.
 * @return BufferedImage
 */
private BufferedImage createHighlightImageFromROI() {
    int[] cmap = new int[256];
    // colormap (grayscale)
    for (int i = 0; i < 256; i += 1) {
        if (i != 0) {
            cmap[i] = 0xFF000000 | highlightColor.getRGB();
        } else {
            cmap[1] = 0xFF000000;
        }
    }
    IndexColorModel indexColorModel = new java.awt.image.IndexColorModel(8, cmap.length, cmap, 0, false, /*false means NOT USE alpha*/
    -1, /*NO transparent single pixel*/
    java.awt.image.DataBuffer.TYPE_BYTE);
    UShortImage roiImage = roi.getRoiImages()[getRoiImageIndex()];
    int width = roiImage.getNumX();
    int height = roiImage.getNumY();
    BufferedImage hiLiteImage = new BufferedImage(width, height, BufferedImage.TYPE_BYTE_INDEXED, indexColorModel);
    byte[] hiLiteArr = ((DataBufferByte) hiLiteImage.getRaster().getDataBuffer()).getData();
    for (int i = 0; i < roiImage.getPixels().length; i++) {
        hiLiteArr[i] = (roiImage.getPixels()[i] != 0 ? (byte) highlightColor.getRed() : 0);
    }
    return hiLiteImage;
}

Example 55 with UShortImage

use of cbit.vcell.VirtualMicroscopy.UShortImage in project vcell by virtualcell.

the class VFrap_OverlayEditorPanelJAI method calcMinMaxPixelValueRange.

private Range calcMinMaxPixelValueRange(ImageDataset argImageDataset) {
    UShortImage[] allImages = argImageDataset.getAllImages();
    double min = 0;
    double max = min;
    for (int i = 0; i < allImages.length; i++) {
        ImageStatistics imageStats = allImages[i].getImageStatistics();
        if (i == 0 || imageStats.minValue < min) {
            min = imageStats.minValue;
        }
        if (i == 0 || imageStats.maxValue > max) {
            max = imageStats.maxValue;
        }
    }
    if (max < SHORT_TO_BYTE_FACTOR) {
        return new Range(min, max);
    }
    return new Range(min / SHORT_TO_BYTE_FACTOR, max / SHORT_TO_BYTE_FACTOR);
}