Bio-Formats fun: messing with OME-XML, etc.

BioFormatsFun.java

import ij.ImagePlus;

import java.io.IOException;

import loci.common.xml.XMLTools;
import loci.formats.FormatException;
import loci.formats.ome.OMEXMLMetadata;
import loci.plugins.in.ImagePlusReader;
import loci.plugins.in.ImportProcess;
import loci.plugins.in.ImporterOptions;
import loci.plugins.util.ImageProcessorReader;
import ome.xml.meta.MetadataStore;
import ome.xml.meta.OMEXMLMetadataRoot;

import org.w3c.dom.Element;

public class BioFormatsFun {

	public static void main(final String... args) throws IOException,
		FormatException
	{
		final String id = args[0];

		// initialize Bio-Formats Importer
		final ImporterOptions options = new ImporterOptions();
		options.setId(id);
		final ImportProcess process = new ImportProcess(options);
		if (!process.execute()) throw new IllegalStateException("Process failed");
		final ImagePlusReader reader = new ImagePlusReader(process);
		final ImagePlus[] imps = reader.openImagePlus();

		// extract 0th series sizeX, sizeY from Bio-Formats reader
		final ImageProcessorReader r = process.getReader();
		r.setSeries(0); // query the 0th series
		final int sizeX = r.getSizeX();
		final int sizeY = r.getSizeY();
		System.out.println("From the reader: " + sizeX + " x " + sizeY);

		// extract OME-XML
		final MetadataStore store = process.getReader().getMetadataStore();
		if (!(store instanceof OMEXMLMetadata)) {
			throw new IllegalStateException("Not OME-XML");
		}
		final OMEXMLMetadata omexmlMeta = (OMEXMLMetadata) store;
		final OMEXMLMetadataRoot root = (OMEXMLMetadataRoot) omexmlMeta.getRoot();
		final int omeSizeX = root.getImage(0).getPixels().getSizeX().getValue();
		final int omeSizeY = root.getImage(0).getPixels().getSizeY().getValue();
		System.out.println("From the OME-XML: " + omeSizeX + " x " + omeSizeY);

		// let's have the OME-XML as a DOM (untested!)
		final Element rootElement = root.asXMLElement(XMLTools.createDocument());
		System.out.println("DOM root = " + rootElement);

		// let's have all the OME-XML as a string
		final String xml = omexmlMeta.dumpXML();
		System.out.println("Have some XML: " + xml);

		// needed to close open files
		if (!options.isVirtual()) process.getReader().close();
	}

}