Examples with ServiceFactory loci.common.services.ServiceFactory used on opensource projects

Example 16 with ServiceFactory

use of loci.common.services.ServiceFactory in project bioformats by openmicroscopy.

the class ZeissZVIReader method initPOIService.

private void initPOIService() throws FormatException, IOException {
    try {
        ServiceFactory factory = new ServiceFactory();
        poi = factory.getInstance(POIService.class);
    } catch (DependencyException de) {
        throw new FormatException("POI library not found", de);
    }
    poi.initialize(Location.getMappedId(getCurrentFile()));
}

Example 17 with ServiceFactory

use of loci.common.services.ServiceFactory 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 18 with ServiceFactory

use of loci.common.services.ServiceFactory 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 19 with ServiceFactory

use of loci.common.services.ServiceFactory 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();
    }
}

Example 20 with ServiceFactory

use of loci.common.services.ServiceFactory in project bioformats by openmicroscopy.

the class PrintROIs method main.

public static void main(String[] args) throws Exception {
    ImageReader reader = new ImageReader();
    IMetadata omexml;
    try {
        ServiceFactory factory = new ServiceFactory();
        OMEXMLService service = factory.getInstance(OMEXMLService.class);
        omexml = service.createOMEXMLMetadata();
    } catch (DependencyException exc) {
        throw new FormatException("Could not create OME-XML store.", exc);
    } catch (ServiceException exc) {
        throw new FormatException("Could not create OME-XML store.", exc);
    }
    reader.setMetadataStore(omexml);
    reader.setId(args[0]);
    printAllROIs(omexml);
    System.out.println();
    for (int series = 0; series < reader.getSeriesCount(); series++) {
        printSeriesROIs(omexml, series);
    }
    reader.close();
}