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

Example 56 with OMEXMLService

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

the class SewTiffs method main.

public static void main(String[] args) throws Exception {
    if (args.length < 2) {
        System.out.println("Usage: java SewTiffs base_name channel_num [time_count]");
        System.exit(1);
    }
    String base = args[0];
    int c = Integer.parseInt(args[1]);
    int num;
    if (args.length < 3) {
        FilePattern fp = new FilePattern(new Location(base + "_C" + c + "_TP1.tiff"));
        int[] count = fp.getCount();
        num = count[count.length - 1];
    } else
        num = Integer.parseInt(args[2]);
    System.out.println("Fixing " + base + "_C" + c + "_TP<1-" + num + ">.tiff");
    TiffReader in = new TiffReader();
    TiffWriter out = new TiffWriter();
    String outId = base + "_C" + c + ".tiff";
    System.out.println("Writing " + outId);
    out.setId(outId);
    System.out.print("   ");
    boolean comment = false;
    for (int t = 0; t < num; t++) {
        String inId = base + "_C" + c + "_TP" + (t + 1) + ".tiff";
        ServiceFactory factory = new ServiceFactory();
        OMEXMLService service = factory.getInstance(OMEXMLService.class);
        IMetadata meta = service.createOMEXMLMetadata();
        in.setMetadataStore(meta);
        in.setId(inId);
        out.setMetadataRetrieve(meta);
        // read first image plane
        byte[] image = in.openBytes(0);
        in.close();
        if (t == 0) {
            // read first IFD
            RandomAccessInputStream ras = new RandomAccessInputStream(inId);
            TiffParser parser = new TiffParser(ras);
            IFD ifd = parser.getFirstIFD();
            ras.close();
            // preserve TIFF comment
            String desc = ifd.getComment();
            if (desc != null) {
                ifd = new IFD();
                ifd.putIFDValue(IFD.IMAGE_DESCRIPTION, desc);
                comment = true;
                out.saveBytes(t, image, ifd);
                System.out.print(".");
                continue;
            }
        }
        // write image plane
        out.saveBytes(t, image);
        // update status
        System.out.print(".");
        if (t % DOTS == DOTS - 1) {
            System.out.println(" " + (t + 1));
            System.out.print("   ");
        }
    }
    System.out.println();
    if (comment)
        System.out.println("OME-TIFF comment saved.");
    else
        System.out.println("No OME-TIFF comment found.");
}

Example 57 with OMEXMLService

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

the class TiledExportExample method main.

public static void main(String[] args) throws Exception {
    if (args.length < 2) {
        System.out.println("Usage: java TiledExportExample <infile> <outfile>");
        System.exit(1);
    }
    ImageReader reader = new ImageReader();
    ImageWriter writer = new ImageWriter();
    IMetadata meta;
    try {
        ServiceFactory factory = new ServiceFactory();
        OMEXMLService service = factory.getInstance(OMEXMLService.class);
        meta = 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(meta);
    reader.setId(args[0]);
    writer.setMetadataRetrieve(meta);
    writer.setId(args[1]);
    for (int series = 0; series < reader.getSeriesCount(); series++) {
        reader.setSeries(series);
        writer.setSeries(series);
        for (int image = 0; image < reader.getImageCount(); image++) {
            for (int row = 0; row < 2; row++) {
                for (int col = 0; col < 2; col++) {
                    int w = reader.getSizeX() / 2;
                    int h = reader.getSizeY() / 2;
                    int x = col * w;
                    int y = row * h;
                    /* debug */
                    System.out.println("[" + x + ", " + y + ", " + w + ", " + h + "]");
                    byte[] buf = reader.openBytes(image, x, y, w, h);
                    writer.saveBytes(image, buf, x, y, w, h);
                }
            }
        }
    }
    reader.close();
    writer.close();
}

Example 58 with OMEXMLService

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

the class WriteRGBMovie 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 20 blank 512x512 image planes
    System.out.println("Creating random image planes...");
    int w = 511, h = 507, numFrames = 20, numChannels = 3;
    int pixelType = FormatTools.UINT8;
    int bpp = FormatTools.getBytesPerPixel(pixelType);
    int planeSize = h * w * numChannels * bpp;
    byte[][] img = new byte[numFrames][planeSize];
    // fill with random data
    for (int t = 0; t < numFrames; t++) {
        for (int i = 0; i < img[t].length; i += numChannels) {
            for (int c = 0; c < numChannels; c++) {
                img[t][i + c] = (byte) (256 * Math.random());
            }
        }
    }
    // create metadata object with 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, numChannels, numFrames, numChannels);
    // write image planes to disk
    System.out.print("Writing planes to '" + id + "'");
    IFormatWriter writer = new ImageWriter();
    writer.setMetadataRetrieve(meta);
    writer.setId(id);
    for (int t = 0; t < numFrames; t++) {
        System.out.print(".");
        writer.saveBytes(t, img[t]);
    }
    writer.close();
    System.out.println("Done.");
}

Example 59 with OMEXMLService

use of loci.formats.services.OMEXMLService in project digilib by robcast.

the class BioFormatsDocuImage method loadImage.

@Override
public void loadImage(ImageInput ii) throws FileOpException {
    logger.debug("loadImage: " + ii);
    this.input = ii;
    reader = new ImageReader();
    try {
        // construct the object that stores OME-XML metadata
        ServiceFactory factory = new ServiceFactory();
        OMEXMLService service = factory.getInstance(OMEXMLService.class);
        meta = service.createOMEXMLMetadata();
        // set up the reader and associate it with the input file
        reader = new ImageReader();
        reader.setMetadataStore(meta);
        reader.setId(ii.getFile().getAbsolutePath());
        BufferedImageReader biReader = BufferedImageReader.makeBufferedImageReader(reader);
        img = biReader.openImage(0);
        logger.debug("image loaded: " + img);
    } catch (FormatException e) {
        throw new FileOpException("Unable to load image format: " + e);
    } catch (IOException e) {
        throw new FileOpException("Unable to load image file: " + e);
    } catch (ServiceException e) {
        // TODO Auto-generated catch block
        e.printStackTrace();
    } catch (DependencyException e) {
        // TODO Auto-generated catch block
        e.printStackTrace();
    }
}