Examples with ColorDeconvolutionStains qupath.lib.color.ColorDeconvolutionStains used on opensource projects

Example 11 with ColorDeconvolutionStains

use of qupath.lib.color.ColorDeconvolutionStains in project qupath by qupath.

the class ImageDetailsPane method getValue.

private Object getValue(ImageDetailRow rowType) {
    if (imageData == null)
        return null;
    ImageServer<BufferedImage> server = imageData.getServer();
    PixelCalibration cal = server.getPixelCalibration();
    switch(rowType) {
        case NAME:
            var project = QuPathGUI.getInstance().getProject();
            var entry = project == null ? null : project.getEntry(imageData);
            if (entry == null)
                return ServerTools.getDisplayableImageName(server);
            else
                return entry.getImageName();
        case URI:
            Collection<URI> uris = server.getURIs();
            if (uris.isEmpty())
                return "Not available";
            if (uris.size() == 1)
                return decodeURI(uris.iterator().next());
            return "[" + String.join(", ", uris.stream().map(ImageDetailsPane::decodeURI).collect(Collectors.toList())) + "]";
        case IMAGE_TYPE:
            return imageData.getImageType();
        case METADATA_CHANGED:
            return hasOriginalMetadata(imageData.getServer()) ? "No" : "Yes";
        case PIXEL_TYPE:
            String type = server.getPixelType().toString().toLowerCase();
            if (server.isRGB())
                type += " (rgb)";
            return type;
        case MAGNIFICATION:
            double mag = server.getMetadata().getMagnification();
            if (Double.isNaN(mag))
                return "Unknown";
            return mag;
        case WIDTH:
            if (cal.hasPixelSizeMicrons())
                return String.format("%s px (%.2f %s)", server.getWidth(), server.getWidth() * cal.getPixelWidthMicrons(), GeneralTools.micrometerSymbol());
            else
                return String.format("%s px", server.getWidth());
        case HEIGHT:
            if (cal.hasPixelSizeMicrons())
                return String.format("%s px (%.2f %s)", server.getHeight(), server.getHeight() * cal.getPixelHeightMicrons(), GeneralTools.micrometerSymbol());
            else
                return String.format("%s px", server.getHeight());
        case DIMENSIONS:
            return String.format("%d x %d x %d", server.nChannels(), server.nZSlices(), server.nTimepoints());
        case PIXEL_WIDTH:
            if (cal.hasPixelSizeMicrons())
                return String.format("%.4f %s", cal.getPixelWidthMicrons(), GeneralTools.micrometerSymbol());
            else
                return "Unknown";
        case PIXEL_HEIGHT:
            if (cal.hasPixelSizeMicrons())
                return String.format("%.4f %s", cal.getPixelHeightMicrons(), GeneralTools.micrometerSymbol());
            else
                return "Unknown";
        case Z_SPACING:
            if (cal.hasZSpacingMicrons())
                return String.format("%.4f %s", cal.getZSpacingMicrons(), GeneralTools.micrometerSymbol());
            else
                return "Unknown";
        case UNCOMPRESSED_SIZE:
            double size = server.getWidth() / 1024.0 * server.getHeight() / 1024.0 * server.getPixelType().getBytesPerPixel() * server.nChannels() * server.nZSlices() * server.nTimepoints();
            String units = " MB";
            if (size > 1000) {
                size /= 1024.0;
                units = " GB";
            }
            return GeneralTools.formatNumber(size, 1) + units;
        case SERVER_TYPE:
            return server.getServerType();
        case PYRAMID:
            if (server.nResolutions() == 1)
                return "No";
            return GeneralTools.arrayToString(Locale.getDefault(Locale.Category.FORMAT), server.getPreferredDownsamples(), 1);
        case STAIN_1:
            return imageData.getColorDeconvolutionStains().getStain(1);
        case STAIN_2:
            return imageData.getColorDeconvolutionStains().getStain(2);
        case STAIN_3:
            return imageData.getColorDeconvolutionStains().getStain(3);
        case BACKGROUND:
            ColorDeconvolutionStains stains = imageData.getColorDeconvolutionStains();
            double[] whitespace = new double[] { stains.getMaxRed(), stains.getMaxGreen(), stains.getMaxBlue() };
            return whitespace;
        default:
            return null;
    }
}

Example 12 with ColorDeconvolutionStains

use of qupath.lib.color.ColorDeconvolutionStains in project qupath by qupath.

the class QP method setColorDeconvolutionStains.

/**
 * Set the color deconvolution stains for hte current image data using a (JSON) String representation
 *
 * @param arg
 * @return
 */
public static boolean setColorDeconvolutionStains(final String arg) {
    ImageData<?> imageData = getCurrentImageData();
    if (imageData == null)
        return false;
    ColorDeconvolutionStains stains = ColorDeconvolutionStains.parseColorDeconvolutionStainsArg(arg);
    imageData.setColorDeconvolutionStains(stains);
    return true;
}