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

Example 41 with UShortImage

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

the class MicroscopyXmlReader method getImageDataset.

/**
 * This method returns a Biomodel object from a XML Element.
 * Creation date: (3/13/2001 12:35:00 PM)
 * @param param org.jdom.Element
 * @return cbit.vcell.biomodel.BioModel
 * @throws XmlParseException
 */
private ImageDataset getImageDataset(Element param, ClientTaskStatusSupport progressListener) throws XmlParseException {
    List<Element> ushortImageElementList = param.getChildren(MicroscopyXMLTags.UShortImageTag);
    Iterator<Element> imageElementIter = ushortImageElementList.iterator();
    UShortImage[] images = new UShortImage[ushortImageElementList.size()];
    // added in Feb 2008, for counting loading progress
    int imageSize = ushortImageElementList.size();
    int imageCount = 0;
    while (imageElementIter.hasNext()) {
        images[imageCount++] = getUShortImage(imageElementIter.next());
        if (progressListener != null) {
            progressListener.setProgress((int) ((imageCount * 100.0) / imageSize));
        }
    }
    Element timeStampListElement = param.getChild(MicroscopyXMLTags.TimeStampListTag);
    double[] timestamps = null;
    if (timeStampListElement != null) {
        String timeStampListText = timeStampListElement.getTextTrim();
        StringTokenizer tokens = new StringTokenizer(timeStampListText, ",\n\r\t ", false);
        ArrayList<Double> times = new ArrayList<Double>();
        while (tokens.hasMoreTokens()) {
            String token = tokens.nextToken();
            times.add(Double.parseDouble(token));
        }
        timestamps = new double[times.size()];
        for (int i = 0; i < timestamps.length; i++) {
            timestamps[i] = times.get(i);
        }
    }
    int numTimeSteps = (timestamps != null) ? (timestamps.length) : (1);
    int numZ = images.length / numTimeSteps;
    ImageDataset imageDataset = new ImageDataset(images, timestamps, numZ);
    return imageDataset;
}

Example 42 with UShortImage

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

the class ROIMultiPaintManager method smoothImageDataset.

private ImageDataset[] smoothImageDataset(ImageDataset[] origImageDatasetChannels, int enhanceImageAmount, ClientTaskStatusSupport clientTaskStatusSupport) throws Exception {
    if (enhanceImageAmount == ROIMultiPaintManager.ENHANCE_NONE) {
        return null;
    }
    ImageDataset[] smoothedImageDatasetChannels = new ImageDataset[origImageDatasetChannels.length];
    int allCount = origImageDatasetChannels.length * origImageDatasetChannels[0].getSizeZ();
    int progress = 0;
    for (int c = 0; c < origImageDatasetChannels.length; c++) {
        UShortImage[] smoothedZSections = new UShortImage[origImageDatasetChannels[c].getISize().getZ()];
        // *2+1;
        int radius = enhanceImageAmount;
        // int[] divideTable = BoxBlurFilter.createDivideTable(radius);
        short[] intermediateArr = new short[origImageDatasetChannels[c].getAllImages()[0].getPixels().length];
        for (int z = 0; z < origImageDatasetChannels[c].getAllImages().length; z++) {
            smoothedZSections[z] = new UShortImage(new short[origImageDatasetChannels[c].getISize().getX() * origImageDatasetChannels[c].getISize().getY()], ROIMultiPaintManager.DEFAULT_ORIGIN, ROIMultiPaintManager.DEFAULT_EXTENT, origImageDatasetChannels[c].getISize().getX(), origImageDatasetChannels[c].getISize().getY(), 1);
            short[] enhancedData = smoothedZSections[z].getPixels();
            short[] roiSourceData = origImageDatasetChannels[c].getAllImages()[z].getPixels();
            BoxBlurFilter.blur(roiSourceData, intermediateArr, origImageDatasetChannels[c].getISize().getX(), origImageDatasetChannels[c].getISize().getY(), radius);
            BoxBlurFilter.blur(intermediateArr, enhancedData, origImageDatasetChannels[c].getISize().getY(), origImageDatasetChannels[c].getISize().getX(), radius);
            if (clientTaskStatusSupport != null) {
                if (clientTaskStatusSupport.isInterrupted()) {
                    return null;
                }
                progress++;
                clientTaskStatusSupport.setProgress(progress * 100 / allCount);
            }
        }
        ImageDataset smoothedImageDataset = new ImageDataset(smoothedZSections, new double[] { 0 }, origImageDatasetChannels[c].getISize().getZ());
        smoothedImageDatasetChannels[c] = smoothedImageDataset;
    }
    return smoothedImageDatasetChannels;
}

Example 43 with UShortImage

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

the class ROIMultiPaintManager method applyHighlightToROI.

private void applyHighlightToROI(ROIMultiPaintManager.ComboboxROIName currentComboboxROIName, boolean bOverWrite) {
    UShortImage[] roiZ = overlayEditorPanelJAI.getHighliteInfo().getRoiImages();
    // Update composite ROI
    int roiColorIndex = currentComboboxROIName.getContrastColorIndex();
    for (int i = 0; i < roiZ.length; i++) {
        short[] pixels = roiZ[i].getPixels();
        byte[] compositePixels = ((DataBufferByte) roiComposite[i].getRaster().getDataBuffer()).getData();
        for (int j = 0; j < pixels.length; j++) {
            if (pixels[j] != 0) {
                compositePixels[j] = (bOverWrite ? (byte) roiColorIndex : (compositePixels[j] == 0 ? (byte) roiColorIndex : compositePixels[j]));
            }
        }
    }
    overlayEditorPanelJAI.setAllROICompositeImage(roiComposite, OverlayEditorPanelJAI.FRAP_DATA_UPDATEROI_WITHHIGHLIGHT_PROPERTY);
    overlayEditorPanelJAI.setHighliteInfo(null, OverlayEditorPanelJAI.FRAP_DATA_UPDATEROI_WITHHIGHLIGHT_PROPERTY);
}

Example 44 with UShortImage

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

the class ROIMultiPaintManager method resizeImpl.

private void resizeImpl(ResizeInfo resizeInfo, ClientTaskStatusSupport clientTaskStatusSupport) throws Exception {
    resizeImpl0(resizeInfo, (bHasOriginalData ? initImageDataSetChannels : null), roiComposite);
    ISize newISize = resizeInfo.getNewSize();
    ISize oldISize = resizeInfo.getOriginalSize();
    Extent resizeExtent = createResizeExtent(originalExtent, oldISize, newISize);
    if (bHasOriginalData) {
        for (int c = 0; c < initImageDataSetChannels.length; c++) {
            UShortImage[] zImageSet = new UShortImage[newISize.getZ()];
            for (int z = 0; z < zImageSet.length; z++) {
                zImageSet[z] = new UShortImage(resizeInfo.underlayC[c][z], originalOrigin, resizeExtent, newISize.getX(), newISize.getY(), 1);
            }
            initImageDataSetChannels[c] = new ImageDataset(zImageSet, new double[] { 0.0 }, newISize.getZ());
        }
    } else {
        initImageDataSet(null, newISize);
    }
    roiComposite = resizeInfo.roiComposite;
    updateAuxiliaryInfo(originalISize, clientTaskStatusSupport);
}

Example 45 with UShortImage

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

the class ROIMultiPaintManager method getNonZeroBoundingBox.

private ROIMultiPaintManager.Crop3D getNonZeroBoundingBox(boolean bUseROI) {
    Rectangle bounding2D = null;
    int lowZ = Integer.MAX_VALUE;
    int highZ = -1;
    if (bUseROI) {
        int lowX = Integer.MAX_VALUE;
        int lowY = Integer.MAX_VALUE;
        int highX = -1;
        int highY = -1;
        for (int z = 0; z < roiComposite.length; z++) {
            int xyIndex = 0;
            byte[] zSectData = ((DataBufferByte) roiComposite[z].getRaster().getDataBuffer()).getData();
            for (int y = 0; y < roiComposite[0].getHeight(); y++) {
                for (int x = 0; x < roiComposite[0].getWidth(); x++) {
                    if (zSectData[xyIndex] != 0) {
                        lowX = Math.min(lowX, x);
                        lowY = Math.min(lowY, y);
                        highX = Math.max(highX, x);
                        highY = Math.max(highY, y);
                        lowZ = Math.min(lowZ, z);
                        ;
                        highZ = Math.max(highZ, z);
                    }
                    xyIndex++;
                }
            }
        }
        if (lowX != Integer.MAX_VALUE) {
            bounding2D = new Rectangle(lowX, lowY, highX - lowX + 1, highY - lowY + 1);
        }
    } else {
        UShortImage[] images = getImageDataSetChannel().getAllImages();
        for (int z = 0; z < images.length; z++) {
            Rectangle boundingRect = images[z].getNonzeroBoundingBox();
            if (boundingRect != null) {
                lowZ = Math.min(lowZ, z);
                ;
                highZ = Math.max(highZ, z);
                if (bounding2D == null) {
                    bounding2D = boundingRect;
                } else {
                    bounding2D = bounding2D.union(boundingRect);
                }
            }
        }
    }
    if (bounding2D == null) {
        return null;
    }
    ROIMultiPaintManager.Crop3D bounding3D = new ROIMultiPaintManager.Crop3D();
    bounding3D.setBounds(bounding2D.x, bounding2D.y, lowZ, bounding2D.width, bounding2D.height, highZ - lowZ + 1);
    return bounding3D;
}