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

Example 1 with OMEXMLService

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

the class ImportProcess method getOMEXML.

/**
 * Valid only after {@link ImportStep#READER}.
 */
public String getOMEXML() {
    if (omeXML == null) {
        // NB: Extract the OME-XML once, then keep it cached.
        try {
            ServiceFactory factory = new ServiceFactory();
            OMEXMLService service = factory.getInstance(OMEXMLService.class);
            omeXML = service.getOMEXML(getOMEMetadata());
        } catch (DependencyException de) {
        } catch (ServiceException se) {
        }
    }
    return omeXML;
}

Example 2 with OMEXMLService

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

the class Memoizer method getService.

// Copied from OMETiffReader.
protected OMEXMLService getService() throws MissingLibraryException {
    if (service == null) {
        try {
            ServiceFactory factory = new ServiceFactory();
            service = factory.getInstance(OMEXMLService.class);
        } catch (DependencyException de) {
            throw new MissingLibraryException(OMEXMLServiceImpl.NO_OME_XML_MSG, de);
        }
    }
    return service;
}

Example 3 with OMEXMLService

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

the class GetPhysicalMetadata method main.

public static void main(String[] args) throws Exception {
    // parse command line arguments
    if (args.length < 1) {
        System.err.println("Usage: java GetMetadata imageFile [seriesNo]");
        System.exit(1);
    }
    String id = args[0];
    int series = args.length > 1 ? Integer.parseInt(args[1]) : 0;
    // create OME-XML metadata store
    ServiceFactory factory = new ServiceFactory();
    OMEXMLService service = factory.getInstance(OMEXMLService.class);
    IMetadata meta = service.createOMEXMLMetadata();
    // create format reader
    IFormatReader reader = new ImageReader();
    reader.setMetadataStore(meta);
    // initialize file
    System.out.println("Initializing " + id);
    reader.setId(id);
    int seriesCount = reader.getSeriesCount();
    if (series < seriesCount)
        reader.setSeries(series);
    series = reader.getSeries();
    System.out.println("\tImage series = " + series + " of " + seriesCount);
    printPixelDimensions(reader);
    printPhysicalDimensions(meta, series);
}

Example 4 with OMEXMLService

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

the class MinimumWriter method main.

public static void main(String[] args) throws Exception {
    if (args.length < 1) {
        System.out.println("Please specify an output file name.");
        System.exit(1);
    }
    String id = args[0];
    // create blank 512x512 image
    System.out.println("Creating random image...");
    int w = 512, h = 512, c = 1;
    int pixelType = FormatTools.UINT16;
    byte[] img = new byte[w * h * c * FormatTools.getBytesPerPixel(pixelType)];
    // fill with random data
    for (int i = 0; i < img.length; i++) img[i] = (byte) (256 * Math.random());
    // create metadata object with minimum required metadata fields
    System.out.println("Populating metadata...");
    ServiceFactory factory = new ServiceFactory();
    OMEXMLService service = factory.getInstance(OMEXMLService.class);
    IMetadata meta = service.createOMEXMLMetadata();
    MetadataTools.populateMetadata(meta, 0, null, false, "XYZCT", FormatTools.getPixelTypeString(pixelType), w, h, 1, c, 1, c);
    // write image plane to disk
    System.out.println("Writing image to '" + id + "'...");
    IFormatWriter writer = new ImageWriter();
    writer.setMetadataRetrieve(meta);
    writer.setId(id);
    writer.saveBytes(0, img);
    writer.close();
    System.out.println("Done.");
}

Example 5 with OMEXMLService

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

the class ParallelRead method run.

public void run() {
    try {
        ImageReader r = new ImageReader();
        ServiceFactory factory = new ServiceFactory();
        OMEXMLService service = factory.getInstance(OMEXMLService.class);
        IMetadata meta = service.createOMEXMLMetadata();
        r.setMetadataStore(meta);
        r.setId(id);
        System.out.println(Thread.currentThread().getName() + ": id=" + id + ", sizeX=" + r.getSizeX() + ", sizeY=" + r.getSizeY() + ", sizeZ=" + r.getSizeZ() + ", sizeT=" + r.getSizeT() + ", sizeC=" + r.getSizeC() + ", imageName=" + meta.getImageName(0));
        r.close();
    } catch (Exception exc) {
        exc.printStackTrace();
    }
}