Create a companion XML file associated to a plain TIFF file

CreateCompanion.java

import java.util.UUID;
import java.io.PrintWriter;

import loci.formats.ImageReader;
import loci.formats.FormatTools;
import loci.formats.ome.OMEXMLMetadata;
import loci.formats.services.OMEXMLService;
import loci.common.Constants;
import loci.common.Location;
import loci.common.xml.XMLTools;
import loci.common.services.ServiceFactory;

import ome.xml.meta.OMEXMLMetadataRoot;
import ome.xml.model.primitives.NonNegativeInteger;

import org.slf4j.LoggerFactory;
import ch.qos.logback.classic.Level;
import ch.qos.logback.classic.Logger;


public final class CreateCompanion {

  public static void main(String[] args) throws Exception {
    Logger root = (Logger)LoggerFactory.getLogger(Logger.ROOT_LOGGER_NAME);
    root.setLevel(Level.INFO);
    //--
    String id = args[0];

    ImageReader reader = new ImageReader();
    ServiceFactory factory = new ServiceFactory();
    OMEXMLService service = factory.getInstance(OMEXMLService.class);
    OMEXMLMetadata meta = service.createOMEXMLMetadata();
    reader.setOriginalMetadataPopulated(true);  // should be optional
    reader.setMetadataStore(meta);
    reader.setId(id);

    meta.resolveReferences();
    service.removeBinData(meta);
    service.removeTiffData(meta);

    String filename = new Location(id).getName();
    String uuid = "urn:uuid:" + UUID.randomUUID().toString();
    String targetUuid = "urn:uuid:" + UUID.randomUUID().toString();
    meta.setUUID(uuid);
    OMEXMLMetadataRoot metaroot = (OMEXMLMetadataRoot) meta.getRoot();
    metaroot.setCreator(FormatTools.CREATOR);
    for (int series = 0; series < meta.getImageCount(); series++) {
      reader.setSeries(series);
      int imageCount = reader.getImageCount();
      if (imageCount == 0) {
        meta.setTiffDataPlaneCount(new NonNegativeInteger(0), series, 0);
        continue;
      }
      for (int plane = 0; plane < imageCount; plane++) {
        int[] zct = reader.getZCTCoords(plane);
        int ifd = plane;  // Single file
        meta.setUUIDFileName(filename, series, plane);
        meta.setUUIDValue(targetUuid, series, plane);
        meta.setTiffDataFirstZ(new NonNegativeInteger(zct[0]), series, plane);
        meta.setTiffDataFirstC(new NonNegativeInteger(zct[1]), series, plane);
        meta.setTiffDataFirstT(new NonNegativeInteger(zct[2]), series, plane);
        meta.setTiffDataIFD(new NonNegativeInteger(ifd), series, plane);
        meta.setTiffDataPlaneCount(new NonNegativeInteger(1), series, plane);
      }
    }

    String xml = service.getOMEXML(meta);
    String companion = "test.companion.ome";
    PrintWriter out = new PrintWriter(companion, Constants.ENCODING);
    out.println(XMLTools.indentXML(xml, true));
    out.close();

    reader.close();
  }
}