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

Example 6 with ReflectedUniverse

use of loci.common.ReflectedUniverse 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);
}