Basic ome.tif tile writer

TiledWriter.java

import java.io.IOException;

import loci.common.services.DependencyException;

import loci.common.services.ServiceException;
import loci.common.services.ServiceFactory;
import loci.formats.services.OMEXMLService;
import loci.formats.FormatException;
import loci.formats.FormatTools;
import loci.formats.meta.IMetadata;
import loci.formats.MetadataTools;
import loci.formats.in.FakeReader;
import loci.formats.out.OMETiffWriter;

public class TiledWriter {
    
    public static void writeImage(Integer sizeX, Integer sizeY, boolean bigTiff, boolean writeSequentially, String pixelType)
    
        throws DependencyException, ServiceException,
        FormatException, IOException
    {
    Integer sizeC = 4;
    Integer tileSizeX = 256;
    Integer tileSizeY = 256;
    Integer numberOfTilesX = sizeX / tileSizeX;
    Integer numberOfTilesY = sizeY / tileSizeY;

    String pref = "/tmp/";
    String imageName = "test";
    String fileName = imageName + "_tiled_" + sizeX + "_" + sizeY + "_" + bigTiff + "_" + writeSequentially + "_" + pixelType + ".ome.tif";

    ServiceFactory factory = new ServiceFactory();
    OMEXMLService service = factory.getInstance(OMEXMLService.class);
    IMetadata meta = service.createOMEXMLMetadata();
    MetadataTools.populateMetadata(
        meta, 0, null, true, "XYZCT", pixelType,
        sizeX, sizeY, 1, sizeC, 1, 1);
    OMETiffWriter writer = new OMETiffWriter();
    FakeReader reader = new FakeReader();
    writer.setMetadataRetrieve(meta);
    writer.setTileSizeX(tileSizeX);
    writer.setTileSizeY(tileSizeY);
    writer.setBigTiff(bigTiff);
    writer.setWriteSequentially(writeSequentially);
    writer.setId(pref + fileName);
    reader.setId("tiles&sizeX=" + sizeX + "&sizeY=" + sizeY  + "&sizeC=" + sizeC + "&pixelType=" + pixelType + ".fake");

    byte[] byteBuffer;
    for (int image=0; image<reader.getImageCount(); image++) {
        for (Integer tileY = 0; tileY < numberOfTilesY; tileY++) {
            Integer y = tileY * tileSizeY;
            for (Integer tileX = 0; tileX < numberOfTilesX; tileX++) {
                Integer x = tileX * tileSizeX;
                int writeSizeX =
                    (x + tileSizeX) < sizeX ? tileSizeX : sizeX - x;
                int writeSizeY =
                    (y + tileSizeY) < sizeY ? tileSizeY : sizeY - y;
                    byteBuffer = reader.openBytes(image, x, y, writeSizeX, writeSizeY);
                    writer.saveBytes(image, byteBuffer, x, y, writeSizeX, writeSizeY);
                }
            
            }
        }
    writer.close();
    reader.close();
    }

    public static void main(String[] args)
        throws DependencyException, ServiceException,
        FormatException, IOException
   {
       writeImage(1200, 1024, true, true, "uint8");
       writeImage(1200, 1024, true, false, "uint8");
       writeImage(1200, 1024, false, true, "uint8");
       writeImage(1200, 1024, false, false, "uint8");
       writeImage(1200, 1024, true, true, "uint16");
       writeImage(1200, 1024, true, false, "uint16");
       writeImage(1200, 1024, false, true, "uint16");
       writeImage(1200, 1024, false, false, "uint16");
   }  
}