Examples with IMetadata loci.formats.meta.IMetadata used on opensource projects

Example 26 with IMetadata

use of loci.formats.meta.IMetadata in project bioformats by openmicroscopy.

the class TiffWriterTest method initializeWriter.

/**
 * Initializes the writer.
 * @param output The file where to write the compressed data.
 * @param compression The compression to use.
 * @param bigTiff Pass <code>true</code> to set the <code>bigTiff</code> flag,
 *                <code>false</code> otherwise.
 * @return See above.
 * @throws Exception Thrown if an error occurred.
 */
private TiffWriter initializeWriter(String output, String compression, boolean bigTiff) throws Exception {
    IMetadata newMetadata = service.createOMEXMLMetadata();
    MetadataConverter.convertMetadata(metadata, newMetadata);
    TiffWriter writer = new TiffWriter();
    writer.setMetadataRetrieve(newMetadata);
    writer.setCompression(compression);
    writer.setWriteSequentially(true);
    writer.setInterleaved(false);
    writer.setBigTiff(bigTiff);
    writer.setId(output);
    return writer;
}

Example 27 with IMetadata

use of loci.formats.meta.IMetadata in project bioformats by openmicroscopy.

the class FileConvert method initialize.

/**
 * Set up the file reader and writer, ensuring that the input file is
 * associated with the reader and the output file is associated with the
 * writer.
 *
 * @return true if the reader and writer were successfully set up, or false
 *   if an error occurred
 */
private boolean initialize() {
    Exception exception = null;
    try {
        // construct the object that stores OME-XML metadata
        ServiceFactory factory = new ServiceFactory();
        OMEXMLService service = factory.getInstance(OMEXMLService.class);
        IMetadata omexml = service.createOMEXMLMetadata();
        // set up the reader and associate it with the input file
        reader = new ImageReader();
        reader.setMetadataStore(omexml);
        reader.setId(inputFile);
        // set up the writer and associate it with the output file
        writer = new ImageWriter();
        writer.setMetadataRetrieve(omexml);
        writer.setInterleaved(reader.isInterleaved());
        writer.setId(outputFile);
    } catch (FormatException e) {
        exception = e;
    } catch (IOException e) {
        exception = e;
    } catch (DependencyException e) {
        exception = e;
    } catch (ServiceException e) {
        exception = e;
    }
    if (exception != null) {
        System.err.println("Failed to initialize files.");
        exception.printStackTrace();
    }
    return exception == null;
}

Example 28 with IMetadata

use of loci.formats.meta.IMetadata in project bioformats by openmicroscopy.

the class FileExportSPW method export.

/**
 * Save a single uint16 plane of data.
 */
public void export() {
    int width = 4, height = 4;
    int pixelType = FormatTools.UINT16;
    Exception exception = null;
    IMetadata omexml = initializeMetadata(width, height, pixelType);
    int series = 0;
    int nSeries = rows * cols * fovPerWell;
    // only save data if the file writer was initialized successfully
    boolean initializationSuccess = initializeWriter(omexml);
    if (initializationSuccess) {
        while (series < nSeries) {
            for (int p = 0; p < sizeT; p++) {
                savePlane(width, height, pixelType, p, series);
            }
            series++;
            if (series < nSeries) {
                try {
                    writer.setSeries(series);
                } catch (FormatException e) {
                    System.err.println("Fatal error unable to select correct image in series! " + e.getMessage());
                    break;
                }
            }
        }
    // endwhile
    }
    // endif
    cleanup();
}

Example 29 with IMetadata

use of loci.formats.meta.IMetadata in project bioformats by openmicroscopy.

the class OverlappedTiledWriter method initialize.

/**
 * Set up the file reader and writer, ensuring that the input file is
 * associated with the reader and the output file is associated with the
 * writer.
 *
 * @return true if the reader and writer were successfully set up, or false
 *   if an error occurred
 * @throws DependencyException thrown if failed to create an OMEXMLService
 * @throws IOException thrown if unable to setup input or output stream for reader or writer
 * @throws FormatException thrown if invalid ID set for reader or writer or invalid tile size set
 * @throws ServiceException thrown if unable to create OME-XML meta data
 */
private void initialize() throws DependencyException, FormatException, IOException, ServiceException {
    // construct the object that stores OME-XML metadata
    ServiceFactory factory = new ServiceFactory();
    OMEXMLService service = factory.getInstance(OMEXMLService.class);
    IMetadata omexml = service.createOMEXMLMetadata();
    // set up the reader and associate it with the input file
    reader = new ImageReader();
    reader.setMetadataStore(omexml);
    reader.setId(inputFile);
    // set up the writer and associate it with the output file
    writer = new OMETiffWriter();
    writer.setMetadataRetrieve(omexml);
    writer.setInterleaved(reader.isInterleaved());
    // set the tile size height and width for writing
    this.tileSizeX = writer.setTileSizeX(tileSizeX);
    this.tileSizeY = writer.setTileSizeY(tileSizeY);
    writer.setId(outputFile);
}

Example 30 with IMetadata

use of loci.formats.meta.IMetadata in project bioformats by openmicroscopy.

the class writeMapAnnotationsExample 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 MapPair Object and add to List
    List<MapPair> mapList = new ArrayList<MapPair>();
    mapList.add(new MapPair("Example Key", "Example Value"));
    mapList.add(new MapPair("Bio-Formats Version", FormatTools.VERSION));
    // create metadata object with minimum required metadata fields
    System.out.println("Populating metadata...");
    // add (minimum+Map)Annotations to the metadata object
    ServiceFactory factory = new ServiceFactory();
    OMEXMLService service = factory.getInstance(OMEXMLService.class);
    IMetadata metadata = service.createOMEXMLMetadata();
    metadata.createRoot();
    MetadataTools.populateMetadata(metadata, 0, null, false, "XYZCT", FormatTools.getPixelTypeString(pixelType), w, h, 1, c, 1, c);
    int mapAnnotationIndex = 0;
    int annotationRefIndex = 0;
    String mapAnnotationID = MetadataTools.createLSID("MapAnnotation", 0, mapAnnotationIndex);
    metadata.setMapAnnotationID(mapAnnotationID, mapAnnotationIndex);
    metadata.setMapAnnotationValue(mapList, mapAnnotationIndex);
    metadata.setMapAnnotationAnnotator("Example Map Annotation", mapAnnotationIndex);
    metadata.setMapAnnotationDescription("Example Description", mapAnnotationIndex);
    metadata.setMapAnnotationNamespace("Example NameSpace", mapAnnotationIndex);
    metadata.setImageAnnotationRef(mapAnnotationID, 0, annotationRefIndex);
    mapAnnotationIndex = 1;
    annotationRefIndex = 1;
    mapAnnotationID = MetadataTools.createLSID("MapAnnotation", 0, mapAnnotationIndex);
    metadata.setMapAnnotationID(mapAnnotationID, mapAnnotationIndex);
    metadata.setMapAnnotationValue(mapList, mapAnnotationIndex);
    metadata.setMapAnnotationAnnotator("Example Map Annotation 1", mapAnnotationIndex);
    metadata.setMapAnnotationDescription("Example Description 1", mapAnnotationIndex);
    metadata.setMapAnnotationNamespace("Example NameSpace 1", mapAnnotationIndex);
    metadata.setImageAnnotationRef(mapAnnotationID, 0, annotationRefIndex);
    // Initialize writer and save file
    ImageWriter writer = new ImageWriter();
    writer.setMetadataRetrieve(metadata);
    writer.setId(id);
    writer.saveBytes(0, img);
    writer.close();
    System.out.println("Done.");
}