Examples with JPEGTurboServiceImpl loci.formats.services.JPEGTurboServiceImpl used on opensource projects

Example 1 with JPEGTurboServiceImpl

use of loci.formats.services.JPEGTurboServiceImpl in project bioformats by openmicroscopy.

the class HamamatsuVMSReader method openBytes.

/**
 * @see loci.formats.IFormatReader#openBytes(int, byte[], int, int, int, int)
 */
@Override
public byte[] openBytes(int no, byte[] buf, int x, int y, int w, int h) throws FormatException, IOException {
    FormatTools.checkPlaneParameters(this, no, buf.length, x, y, w, h);
    int startCol = x / MAX_JPEG_SIZE;
    int startRow = y / MAX_JPEG_SIZE;
    String file = null;
    switch(getCoreIndex()) {
        case 0:
            file = tileFiles[no][startRow][startCol];
            break;
        case 1:
            file = macroFile;
            break;
        case 2:
            file = mapFile;
            break;
    }
    if (getSizeX() <= MAX_SIZE || getSizeY() <= MAX_SIZE) {
        JPEGReader reader = new JPEGReader();
        reader.setId(file);
        reader.openBytes(0, buf, x, y, w, h);
        reader.close();
        return buf;
    }
    if (service == null) {
        service = new JPEGTurboServiceImpl();
    }
    try {
        Region image = new Region(x, y, w, h);
        for (int row = startRow; row < nRows; row++) {
            for (int col = startCol; col < nCols; col++) {
                Region tile = new Region(col * MAX_JPEG_SIZE, row * MAX_JPEG_SIZE, col == nCols - 1 ? getSizeX() % MAX_JPEG_SIZE : MAX_JPEG_SIZE, row == nRows - 1 ? getSizeY() % MAX_JPEG_SIZE : MAX_JPEG_SIZE);
                if (!tile.intersects(image)) {
                    continue;
                }
                file = tileFiles[no][row][col];
                if (initializedSeries != getCoreIndex() || initializedPlane != no || !file.equals(initializedFile)) {
                    service.close();
                    if (restartMarkers.containsKey(file)) {
                        service.setRestartMarkers(restartMarkers.get(file));
                    } else {
                        service.setRestartMarkers(null);
                    }
                    // closing the service will close this file
                    RandomAccessInputStream s = new RandomAccessInputStream(file);
                    service.initialize(s, tile.width, tile.height);
                    restartMarkers.put(file, service.getRestartMarkers());
                    initializedSeries = getCoreIndex();
                    initializedPlane = no;
                    initializedFile = file;
                }
                Region intersection = tile.intersection(image);
                int tileX = intersection.x % MAX_JPEG_SIZE;
                int tileY = intersection.y % MAX_JPEG_SIZE;
                int rowLen = intersection.width * getRGBChannelCount();
                byte[] b = new byte[rowLen * intersection.height];
                service.getTile(b, tileX, tileY, intersection.width, intersection.height);
                for (int tileRow = 0; tileRow < intersection.height; tileRow++) {
                    int src = tileRow * rowLen;
                    int dest = (((intersection.y + tileRow - y) * w) + (intersection.x - x)) * getRGBChannelCount();
                    System.arraycopy(b, src, buf, dest, rowLen);
                }
            }
        }
    } catch (ServiceException e) {
        throw new FormatException(e);
    }
    return buf;
}

Example 2 with JPEGTurboServiceImpl

use of loci.formats.services.JPEGTurboServiceImpl in project bioformats by openmicroscopy.

the class TileJPEGReader method reopenFile.

@Override
public void reopenFile() throws IOException {
    if (in != null) {
        in.close();
    }
    in = new RandomAccessInputStream(currentId);
    in.seek(0);
    service = new JPEGTurboServiceImpl();
    try {
        service.initialize(in, getSizeX(), getSizeY());
    } catch (ServiceException se) {
        service = null;
        throw new IOException("Could not initialize JPEG service", se);
    }
}