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

Example 1 with IMetadata

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

the class ImagePlusReader method readPlanes.

private ImageStack readPlanes(ImportProcess process, int s, List<LUT> luts, boolean thumbnail) throws FormatException, IOException {
    final ImageProcessorReader reader = process.getReader();
    reader.setSeries(s);
    final int zCount = process.getZCount(s);
    final int cCount = process.getCCount(s);
    final int tCount = process.getTCount(s);
    final IMetadata meta = process.getOMEMetadata();
    // get list of planes to load
    final boolean[] load = getPlanesToLoad(s);
    int current = 0, total = 0;
    for (int j = 0; j < load.length; j++) if (load[j])
        total++;
    final List<ImageProcessor> procs = new ArrayList<ImageProcessor>();
    final List<String> labels = new ArrayList<String>();
    // read applicable image planes
    final Region region = process.getCropRegion(s);
    for (int i = 0; i < load.length; i++) {
        if (!load[i])
            continue;
        // limit message update rate
        updateTiming(s, current, current++, total);
        // get image processor for ith plane
        final ImageProcessor[] p = readProcessors(process, i, region, thumbnail);
        if (p == null || p.length == 0) {
            throw new FormatException("Cannot read plane #" + i);
        }
        // generate a label for ith plane
        String label = constructSliceLabel(i, reader, meta, s, zCount, cCount, tCount);
        for (ImageProcessor ip : p) {
            procs.add(ip);
            labels.add(label);
        }
    }
    return createStack(procs, labels, luts);
}

Example 2 with IMetadata

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

the class ImagePlusReader method createVirtualStack.

private ImageStack createVirtualStack(ImportProcess process, int s, List<LUT> luts) throws FormatException, IOException {
    final ImporterOptions options = process.getOptions();
    final ImageProcessorReader reader = process.getReader();
    reader.setSeries(s);
    final int zCount = process.getZCount(s);
    final int cCount = process.getCCount(s);
    final int tCount = process.getTCount(s);
    final IMetadata meta = process.getOMEMetadata();
    final int imageCount = reader.getImageCount();
    // CTR FIXME: Make virtual stack work with different color modes?
    final BFVirtualStack virtualStack = new BFVirtualStack(options.getId(), reader, false, false, false);
    for (int i = 0; i < imageCount; i++) {
        String label = constructSliceLabel(i, reader, meta, s, zCount, cCount, tCount);
        virtualStack.addSlice(label);
    }
    if (luts != null) {
        for (int c = 0; c < cCount; c++) {
            int index = reader.getIndex(0, c, 0);
            ImageProcessor ip = reader.openProcessors(index)[0];
            final ColorModel cm = ip.getColorModel();
            final LUT lut = cm instanceof LUT ? (LUT) cm : null;
            luts.add(lut);
        }
    }
    return virtualStack;
}

Example 3 with IMetadata

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

the class ImageViewer method open.

/**
 * Opens the given data source using the current format reader.
 */
public void open(String id) {
    wait(true);
    try {
        // Location f = new Location(id);
        // id = f.getAbsolutePath();
        IMetadata meta = null;
        if (omexmlService != null) {
            try {
                meta = omexmlService.createOMEXMLMetadata();
                myReader.setMetadataStore(meta);
            } catch (ServiceException exc) {
                LOGGER.debug("Could not create OME-XML metadata", exc);
            }
        }
        if (meta == null) {
            LOGGER.info("OME metadata unavailable");
        }
        myReader.setId(id);
        int num = myReader.getImageCount();
        ProgressMonitor progress = new ProgressMonitor(this, "Reading " + id, null, 0, num + 1);
        sizeZ = myReader.getSizeZ();
        sizeT = myReader.getSizeT();
        sizeC = myReader.getEffectiveSizeC();
        // if (myReader.isRGB(id)) sizeC = (sizeC + 2) / 3; // adjust for RGB
        progress.setProgress(1);
        BufferedImage[] img = new BufferedImage[num];
        for (int i = 0; i < num; i++) {
            if (progress.isCanceled())
                break;
            img[i] = myReader.openImage(i);
            if (i == 0)
                setImages(myReader, img);
            progress.setProgress(i + 2);
        }
        myReader.close(true);
    } catch (FormatException exc) {
        LOGGER.info("", exc);
        wait(false);
        return;
    } catch (IOException exc) {
        LOGGER.info("", exc);
        wait(false);
        return;
    }
    wait(false);
}

Example 4 with IMetadata

use of loci.formats.meta.IMetadata 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 5 with IMetadata

use of loci.formats.meta.IMetadata 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.");
}