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

Example 56 with IMetadata

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

the class ReadWriteInMemory method main.

public static void main(String[] args) throws DependencyException, FormatException, IOException, ServiceException {
    if (args.length < 1) {
        System.out.println("Please specify a (small) image file.");
        System.exit(1);
    }
    String path = args[0];
    /* file-read-start */
    // read in entire file
    System.out.println("Reading file into memory from disk...");
    File inputFile = new File(path);
    int fileSize = (int) inputFile.length();
    DataInputStream in = new DataInputStream(new FileInputStream(inputFile));
    byte[] inBytes = new byte[fileSize];
    in.readFully(inBytes);
    System.out.println(fileSize + " bytes read.");
    /* file-read-end */
    /* mapping-start */
    // determine input file suffix
    String fileName = inputFile.getName();
    int dot = fileName.lastIndexOf(".");
    String suffix = dot < 0 ? "" : fileName.substring(dot);
    // map input id string to input byte array
    String inId = "inBytes" + suffix;
    Location.mapFile(inId, new ByteArrayHandle(inBytes));
    /* mapping-end */
    // read data from byte array using ImageReader
    System.out.println();
    System.out.println("Reading image data from memory...");
    /* read-start */
    ServiceFactory factory = new ServiceFactory();
    OMEXMLService service = factory.getInstance(OMEXMLService.class);
    IMetadata omeMeta = service.createOMEXMLMetadata();
    ImageReader reader = new ImageReader();
    reader.setMetadataStore(omeMeta);
    reader.setId(inId);
    /* read-end */
    int seriesCount = reader.getSeriesCount();
    int imageCount = reader.getImageCount();
    int sizeX = reader.getSizeX();
    int sizeY = reader.getSizeY();
    int sizeZ = reader.getSizeZ();
    int sizeC = reader.getSizeC();
    int sizeT = reader.getSizeT();
    // output some details
    System.out.println("Series count: " + seriesCount);
    System.out.println("First series:");
    System.out.println("\tImage count = " + imageCount);
    System.out.println("\tSizeX = " + sizeX);
    System.out.println("\tSizeY = " + sizeY);
    System.out.println("\tSizeZ = " + sizeZ);
    System.out.println("\tSizeC = " + sizeC);
    System.out.println("\tSizeT = " + sizeT);
    /* out—mapping-start */
    // map output id string to output byte array
    String outId = fileName + ".ome.tif";
    ByteArrayHandle outputFile = new ByteArrayHandle();
    Location.mapFile(outId, outputFile);
    /* out—mapping-end */
    /* write—init-start */
    // write data to byte array using ImageWriter
    System.out.println();
    System.out.print("Writing planes to destination in memory: ");
    ImageWriter writer = new ImageWriter();
    writer.setMetadataRetrieve(omeMeta);
    writer.setId(outId);
    /* write—init-end */
    /* write-start */
    byte[] plane = null;
    for (int i = 0; i < imageCount; i++) {
        if (plane == null) {
            // allow reader to allocate a new byte array
            plane = reader.openBytes(i);
        } else {
            // reuse previously allocated byte array
            reader.openBytes(i, plane);
        }
        writer.saveBytes(i, plane);
        System.out.print(".");
    }
    reader.close();
    writer.close();
    System.out.println();
    byte[] outBytes = outputFile.getBytes();
    outputFile.close();
    /* write-end */
    /* flush-start */
    // flush output byte array to disk
    System.out.println();
    System.out.println("Flushing image data to disk...");
    File outFile = new File(fileName + ".ome.tif");
    DataOutputStream out = new DataOutputStream(new FileOutputStream(outFile));
    out.write(outBytes);
    out.close();
/* flush-end */
}

Example 57 with IMetadata

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

the class TiledReaderWriter 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 58 with IMetadata

use of loci.formats.meta.IMetadata 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 59 with IMetadata

use of loci.formats.meta.IMetadata 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 60 with IMetadata

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