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

Example 6 with ReflectException

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

the class LegacyQTReader method initFile.

// -- Internal FormatReader API methods --
/* @see loci.formats.FormatReader#initFile(String) */
@Override
protected void initFile(String id) throws FormatException, IOException {
    LOGGER.info("Checking for QuickTime Java");
    if (tools == null) {
        tools = new LegacyQTTools();
        r = tools.getUniverse();
    }
    tools.checkQTLibrary();
    super.initFile(id);
    LOGGER.info("Reading movie dimensions");
    try {
        r.exec("QTSession.open()");
        // open movie file
        Location file = new Location(id);
        r.setVar("path", file.getAbsolutePath());
        r.exec("qtf = new QTFile(path)");
        r.exec("openMovieFile = OpenMovieFile.asRead(qtf)");
        r.exec("m = Movie.fromFile(openMovieFile)");
        int numTracks = ((Integer) r.exec("m.getTrackCount()")).intValue();
        int trackMostLikely = 0;
        int trackNum = 0;
        while (++trackNum <= numTracks && trackMostLikely == 0) {
            r.setVar("trackNum", trackNum);
            r.exec("imageTrack = m.getTrack(trackNum)");
            r.exec("d = imageTrack.getSize()");
            Integer w = (Integer) r.exec("d.getWidth()");
            if (w.intValue() > 0)
                trackMostLikely = trackNum;
        }
        r.setVar("trackMostLikely", trackMostLikely);
        r.exec("imageTrack = m.getTrack(trackMostLikely)");
        r.exec("d = imageTrack.getSize()");
        Integer w = (Integer) r.exec("d.getWidth()");
        Integer h = (Integer) r.exec("d.getHeight()");
        r.exec("moviePlayer = new MoviePlayer(m)");
        r.setVar("dim", new Dimension(w.intValue(), h.intValue()));
        ImageProducer qtip = (ImageProducer) r.exec("qtip = new QTImageProducer(moviePlayer, dim)");
        image = Toolkit.getDefaultToolkit().createImage(qtip);
        r.setVar("zero", 0);
        r.setVar("one", 1f);
        r.exec("timeInfo = new TimeInfo(zero, zero)");
        r.exec("moviePlayer.setTime(zero)");
        Vector<Integer> v = new Vector<Integer>();
        int time = 0;
        Integer q = new Integer(time);
        do {
            v.add(q);
            r.exec("timeInfo = imageTrack.getNextInterestingTime(" + "StdQTConstants.nextTimeMediaSample, timeInfo.time, one)");
            q = (Integer) r.getVar("timeInfo.time");
            time = q.intValue();
        } while (time >= 0);
        CoreMetadata m = core.get(0);
        m.imageCount = v.size();
        times = new int[getImageCount()];
        for (int i = 0; i < times.length; i++) {
            q = v.elementAt(i);
            times[i] = q.intValue();
        }
        LOGGER.info("Populating metadata");
        BufferedImage img = AWTImageTools.makeBuffered(image);
        m.sizeX = img.getWidth();
        m.sizeY = img.getHeight();
        m.sizeZ = 1;
        m.sizeC = img.getRaster().getNumBands();
        m.sizeT = getImageCount();
        m.pixelType = AWTImageTools.getPixelType(img);
        m.dimensionOrder = "XYCTZ";
        m.rgb = true;
        m.interleaved = false;
        m.littleEndian = false;
        m.indexed = false;
        m.falseColor = false;
        MetadataStore store = makeFilterMetadata();
        MetadataTools.populatePixels(store, this);
    } catch (ReflectException e) {
        throw new FormatException("Open movie failed", e);
    }
}

Example 7 with ReflectException

use of loci.common.ReflectException 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 8 with ReflectException

use of loci.common.ReflectException 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;
}

Example 9 with ReflectException

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

the class TiffJAIReader method initFile.

// -- Internal FormatReader API methods --
/* @see loci.formats.FormatReader#initFile(String) */
@Override
protected void initFile(String id) throws FormatException, IOException {
    LOGGER.info("Checking for JAI");
    try {
        r = new ReflectedUniverse();
        r.exec("import javax.media.jai.NullOpImage");
        r.exec("import javax.media.jai.OpImage");
        r.exec("import com.sun.media.jai.codec.FileSeekableStream");
        r.exec("import com.sun.media.jai.codec.ImageDecoder");
        r.exec("import com.sun.media.jai.codec.ImageCodec");
    } catch (ReflectException exc) {
        throw new MissingLibraryException(NO_JAI_MSG, exc);
    }
    super.initFile(id);
    LOGGER.info("Reading movie dimensions");
    // map Location to File or RandomAccessFile, if possible
    IRandomAccess ira = Location.getMappedFile(id);
    if (ira != null) {
        if (ira instanceof FileHandle) {
            FileHandle fh = (FileHandle) ira;
            r.setVar("file", fh.getRandomAccessFile());
        } else {
            throw new FormatException("Unsupported handle type" + ira.getClass().getName());
        }
    } else {
        String mapId = Location.getMappedId(id);
        File file = new File(mapId);
        if (file.exists()) {
            r.setVar("file", file);
        } else
            throw new FileNotFoundException(id);
    }
    r.setVar("tiff", "tiff");
    r.setVar("param", null);
    // create TIFF decoder
    int numPages;
    try {
        r.exec("s = new FileSeekableStream(file)");
        r.exec("dec = ImageCodec.createImageDecoder(tiff, s, param)");
        numPages = ((Integer) r.exec("dec.getNumPages()")).intValue();
    } catch (ReflectException exc) {
        throw new FormatException(exc);
    }
    if (numPages < 0) {
        throw new FormatException("Invalid page count: " + numPages);
    }
    // decode first image plane
    BufferedImage img = openBufferedImage(0);
    if (img == null)
        throw new FormatException("Invalid image stream");
    LOGGER.info("Populating metadata");
    CoreMetadata m = core.get(0);
    m.imageCount = numPages;
    m.sizeX = img.getWidth();
    m.sizeY = img.getHeight();
    m.sizeZ = 1;
    m.sizeC = img.getSampleModel().getNumBands();
    m.sizeT = numPages;
    m.rgb = m.sizeC > 1;
    m.dimensionOrder = "XYCZT";
    m.pixelType = AWTImageTools.getPixelType(img);
    m.interleaved = true;
    m.littleEndian = false;
    m.metadataComplete = true;
    m.indexed = false;
    m.falseColor = false;
    // populate the metadata store
    MetadataStore store = makeFilterMetadata();
    MetadataTools.populatePixels(store, this);
}

Example 10 with ReflectException

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

the class TiffJAIReader method openBufferedImage.

/**
 * Obtains a BufferedImage from the given data source using JAI.
 */
protected BufferedImage openBufferedImage(int no) throws FormatException {
    r.setVar("no", no);
    RenderedImage img;
    try {
        r.exec("img = dec.decodeAsRenderedImage(no)");
        img = (RenderedImage) r.exec("new NullOpImage(img, null, OpImage.OP_IO_BOUND, null)");
    } catch (ReflectException exc) {
        throw new FormatException(exc);
    }
    return AWTImageTools.convertRenderedImage(img);
}