Examples with ReflectedUniverse loci.common.ReflectedUniverse used on opensource projects

Example 1 with ReflectedUniverse

use of loci.common.ReflectedUniverse in project bioformats by openmicroscopy.

the class FormatTools method openThumbBytes.

/**
 * Default implementation for {@link IFormatReader#openThumbBytes}.
 *
 * At the moment, it uses {@link java.awt.image.BufferedImage} objects
 * to resize thumbnails, so it is not safe for use in headless contexts.
 * In the future, we may reimplement the image scaling logic purely with
 * byte arrays, but handling every case would be substantial effort, so
 * doing so is currently a low priority item.
 */
public static byte[] openThumbBytes(IFormatReader reader, int no) throws FormatException, IOException {
    // NB: Dependency on AWT here is unfortunate, but very difficult to
    // eliminate in general. We use reflection to limit class loading
    // problems with AWT on Mac OS X.
    ReflectedUniverse r = new ReflectedUniverse();
    byte[][] bytes = null;
    try {
        r.exec("import loci.formats.gui.AWTImageTools");
        int planeSize = getPlaneSize(reader);
        byte[] plane = null;
        if (planeSize < 0) {
            int width = reader.getThumbSizeX() * 4;
            int height = reader.getThumbSizeY() * 4;
            int x = (reader.getSizeX() - width) / 2;
            int y = (reader.getSizeY() - height) / 2;
            plane = reader.openBytes(no, x, y, width, height);
        } else {
            plane = reader.openBytes(no);
        }
        r.setVar("plane", plane);
        r.setVar("reader", reader);
        r.setVar("sizeX", reader.getSizeX());
        r.setVar("sizeY", reader.getSizeY());
        r.setVar("thumbSizeX", reader.getThumbSizeX());
        r.setVar("thumbSizeY", reader.getThumbSizeY());
        r.setVar("little", reader.isLittleEndian());
        // always normalize floating point images, otherwise scaling will fail
        r.setVar("normal", true);
        r.exec("img = AWTImageTools.openImage(plane, reader, sizeX, sizeY, normal)");
        r.exec("img = AWTImageTools.makeUnsigned(img)");
        r.exec("thumb = AWTImageTools.scale(img, thumbSizeX, thumbSizeY, false)");
        bytes = (byte[][]) r.exec("AWTImageTools.getPixelBytes(thumb, little)");
    } catch (ReflectException exc) {
        throw new FormatException(exc);
    }
    if (bytes.length == 1)
        return bytes[0];
    int rgbChannelCount = reader.getRGBChannelCount();
    byte[] rtn = new byte[rgbChannelCount * bytes[0].length];
    if (!reader.isInterleaved()) {
        for (int i = 0; i < rgbChannelCount; i++) {
            System.arraycopy(bytes[i], 0, rtn, bytes[0].length * i, bytes[i].length);
        }
    } else {
        int bpp = FormatTools.getBytesPerPixel(reader.getPixelType());
        for (int i = 0; i < bytes[0].length; i += bpp) {
            for (int j = 0; j < rgbChannelCount; j++) {
                System.arraycopy(bytes[j], i, rtn, (i * rgbChannelCount) + j * bpp, bpp);
            }
        }
    }
    return rtn;
}

Example 2 with ReflectedUniverse

use of loci.common.ReflectedUniverse in project bioformats by openmicroscopy.

the class LegacyQTTools method initClass.

// -- LegacyQTTools API methods --
/**
 * Initializes the class.
 */
protected void initClass() {
    if (initialized)
        return;
    String arch = System.getProperty("os.arch");
    if (arch != null && arch.indexOf("64") >= 0) {
        // QTJava is not supported on 64-bit Java; don't even try
        noQT = true;
        jvm64Bit = true;
        initialized = true;
        return;
    }
    boolean needClose = false;
    r = new ReflectedUniverse(LOADER);
    try {
        r.exec("import quicktime.QTSession");
        r.exec("QTSession.open()");
        needClose = true;
        // for LegacyQTReader and LegacyQTWriter
        r.exec("import quicktime.io.QTFile");
        r.exec("import quicktime.std.movies.Movie");
        // for LegacyQTReader
        r.exec("import quicktime.app.view.MoviePlayer");
        r.exec("import quicktime.app.view.QTImageProducer");
        r.exec("import quicktime.io.OpenMovieFile");
        r.exec("import quicktime.qd.QDDimension");
        r.exec("import quicktime.std.StdQTConstants");
        r.exec("import quicktime.std.movies.TimeInfo");
        r.exec("import quicktime.std.movies.Track");
        // for LegacyQTWriter
        r.exec("import quicktime.qd.QDGraphics");
        r.exec("import quicktime.qd.QDRect");
        r.exec("import quicktime.std.image.CSequence");
        r.exec("import quicktime.std.image.CodecComponent");
        r.exec("import quicktime.std.image.ImageDescription");
        r.exec("import quicktime.std.movies.media.VideoMedia");
        r.exec("import quicktime.util.QTHandle");
        r.exec("import quicktime.util.RawEncodedImage");
        r.exec("import quicktime.util.EndianOrder");
    } catch (ExceptionInInitializerError err) {
        noQT = true;
        Throwable t = err.getException();
        if (t instanceof SecurityException) {
            SecurityException exc = (SecurityException) t;
            if (exc.getMessage().indexOf("expired") >= 0)
                expiredQT = true;
        }
    } catch (Throwable t) {
        noQT = true;
        LOGGER.debug("Could not find QuickTime for Java", t);
    } finally {
        if (needClose) {
            try {
                r.exec("QTSession.close()");
            } catch (Throwable t) {
                LOGGER.debug("Could not close QuickTime session", t);
            }
        }
        initialized = true;
    }
}

Example 3 with ReflectedUniverse

use of loci.common.ReflectedUniverse in project bioformats by openmicroscopy.

the class DisplayHandler method displayImage5D.

public void displayImage5D(ImagePlus imp) {
    WindowManager.setTempCurrentImage(imp);
    IFormatReader r = process.getReader();
    ReflectedUniverse ru = new ReflectedUniverse();
    try {
        ru.exec("import i5d.Image5D");
        ru.setVar("title", imp.getTitle());
        ru.setVar("stack", imp.getStack());
        ru.setVar("sizeC", imp.getNChannels());
        ru.setVar("sizeZ", imp.getNSlices());
        ru.setVar("sizeT", imp.getNFrames());
        ru.exec("i5d = new Image5D(title, stack, sizeC, sizeZ, sizeT)");
        ru.setVar("cal", imp.getCalibration());
        ru.setVar("fi", imp.getOriginalFileInfo());
        ru.exec("i5d.setCalibration(cal)");
        ru.exec("i5d.setFileInfo(fi)");
        // ru.exec("i5d.setDimensions(sizeC, sizeZ, sizeT)");
        ru.exec("i5d.show()");
    } catch (ReflectException exc) {
        WindowTools.reportException(exc, options.isQuiet(), "Sorry, there was a problem interfacing with Image5D");
    }
}

Example 4 with ReflectedUniverse

use of loci.common.ReflectedUniverse in project bioformats by openmicroscopy.

the class ImportProcess method createBaseReader.

/**
 * Initializes an {@link loci.formats.IFormatReader}
 * according to the current configuration.
 */
private void createBaseReader() throws FormatException, IOException {
    if (options.isLocal() || options.isHTTP()) {
        BF.status(options.isQuiet(), "Identifying " + idName);
        imageReader = LociPrefs.makeImageReader();
        baseReader = imageReader.getReader(options.isUsingPatternIds() ? new FilePattern(options.getId()).getFiles()[0] : options.getId());
    } else if (options.isOMERO()) {
        BF.status(options.isQuiet(), "Establishing server connection");
        try {
            ReflectedUniverse r = new ReflectedUniverse();
            r.exec("import loci.ome.io.OmeroReader");
            r.exec("baseReader = new OmeroReader()");
            ClassList<IFormatReader> classes = new ClassList<IFormatReader>(IFormatReader.class);
            r.setVar("classes", classes);
            r.exec("class = baseReader.getClass()");
            r.exec("classes.addClass(class)");
            imageReader = new ImageReader(classes);
            baseReader = imageReader.getReader(options.getId());
        } catch (Exception exc) {
            WindowTools.reportException(exc, options.isQuiet(), "Sorry, there was a problem communicating with the server.");
            cancel();
            return;
        }
    } else {
        WindowTools.reportException(null, options.isQuiet(), "Sorry, there has been an internal error: unknown data source");
        cancel();
        return;
    }
    // attach OME-XML metadata store
    Exception exc = null;
    try {
        ServiceFactory factory = new ServiceFactory();
        OMEXMLService service = factory.getInstance(OMEXMLService.class);
        meta = service.createOMEXMLMetadata();
        omeXML = null;
    } catch (DependencyException de) {
        exc = de;
    } catch (ServiceException se) {
        exc = se;
    }
    if (exc != null) {
        WindowTools.reportException(exc, options.isQuiet(), "Sorry, there was a problem constructing the OME-XML metadata store");
        throw new FormatException(exc);
    }
    baseReader.setMetadataStore(meta);
    BF.status(options.isQuiet(), "");
    DebugTools.enableIJLogging(IJ.debugMode);
}

Example 5 with ReflectedUniverse

use of loci.common.ReflectedUniverse in project bioformats by openmicroscopy.

the class MetaSupportList method format.

/**
 * Gets the name of the format for the current handler.
 */
public String format() {
    ReflectedUniverse r = new ReflectedUniverse();
    IFormatHandler handler;
    try {
        r.exec("import loci.formats.in." + handlerName);
    } catch (ReflectException exc) {
    }
    try {
        r.exec("import loci.formats.out." + handlerName);
    } catch (ReflectException exc) {
    }
    try {
        handler = (IFormatHandler) r.exec("new " + handlerName + "()");
        return handler.getFormat();
    } catch (ReflectException exc) {
    }
    return null;
}