Examples with OMETiffWriter loci.formats.out.OMETiffWriter used on opensource projects

Example 11 with OMETiffWriter

use of loci.formats.out.OMETiffWriter in project bioformats by openmicroscopy.

the class OrthogonalReader method readOrthogonalPlanes.

private void readOrthogonalPlanes() throws Exception {
    // Setup logger
    ch.qos.logback.classic.Logger root = (ch.qos.logback.classic.Logger) LoggerFactory.getLogger(Logger.ROOT_LOGGER_NAME);
    if (debug) {
        root.setLevel(Level.DEBUG);
    } else {
        root.setLevel(Level.INFO);
    }
    ImageReader reader = this.initialiseReader(this.input);
    reader.setSeries(0);
    OMETiffWriter writer = this.initialiseWriter(this.output, reader);
    int index;
    // Write XZ planes
    writer.setSeries(0);
    for (int y = 0; y < reader.getSizeY(); y++) {
        ByteBuffer bufferXZ = ByteBuffer.allocate((int) (0.125 * reader.getBitsPerPixel()) * reader.getSizeX() * reader.getSizeZ());
        for (int z = 0; z < reader.getSizeZ(); z++) {
            index = reader.getIndex(z, 0, 0);
            byte[] line = reader.openBytes(index, 0, y, reader.getSizeX(), 1);
            bufferXZ.put(line);
        }
        log.debug("y: {}, {}", y, bufferXZ.array().length);
        writer.saveBytes(y, bufferXZ.array());
    }
    // Write YZ planes
    writer.setSeries(1);
    for (int x = 0; x < reader.getSizeX(); x++) {
        ByteBuffer bufferYZ = ByteBuffer.allocate((int) (0.125 * reader.getBitsPerPixel()) * reader.getSizeY() * reader.getSizeZ());
        for (int z = 0; z < reader.getSizeZ(); z++) {
            index = reader.getIndex(z, 0, 0);
            byte[] line = reader.openBytes(index, x, 0, 1, reader.getSizeY());
            bufferYZ.put(line);
        }
        log.debug("x: {}, {}", x, bufferYZ.array().length);
        writer.saveBytes(x, bufferYZ.array());
    }
    reader.close();
    writer.close();
}