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

Example 46 with OMEXMLService

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

the class PrintTimestamps method main.

public static void main(String[] args) throws Exception {
    // parse command line arguments
    if (args.length < 1) {
        System.err.println("Usage: java PrintTimestamps imageFile [seriesNo]");
        System.exit(1);
    }
    String id = args[0];
    int series = args.length > 1 ? Integer.parseInt(args[1]) : 0;
    // enable debugging
    // FormatReader.debug = true;
    // create OME-XML metadata store of the latest schema version
    ServiceFactory factory = new ServiceFactory();
    OMEXMLService service = factory.getInstance(OMEXMLService.class);
    IMetadata meta = service.createOMEXMLMetadata();
    // or if you want a specific schema version, you can use:
    // IMetadata meta = service.createOMEXMLMetadata(null, "2009-02");
    // meta.createRoot();
    // 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);
    printDimensions(reader);
    printGlobalTiming(meta, series);
    printTimingPerTimepoint(meta, series);
    printTimingPerPlane(meta, series);
}

Example 47 with OMEXMLService

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

the class ConvertToOmeTiff method main.

public static void main(String[] args) throws Exception {
    if (args.length == 0) {
        System.out.println("Usage: java ConvertToOmeTiff file1 file2 ...");
        return;
    }
    ImageReader reader = new ImageReader();
    OMETiffWriter writer = new OMETiffWriter();
    for (int i = 0; i < args.length; i++) {
        String id = args[i];
        int dot = id.lastIndexOf(".");
        String outId = (dot >= 0 ? id.substring(0, dot) : id) + ".ome.tif";
        System.out.print("Converting " + id + " to " + outId + " ");
        // record metadata to OME-XML format
        ServiceFactory factory = new ServiceFactory();
        OMEXMLService service = factory.getInstance(OMEXMLService.class);
        IMetadata omexmlMeta = service.createOMEXMLMetadata();
        reader.setMetadataStore(omexmlMeta);
        reader.setId(id);
        // configure OME-TIFF writer
        writer.setMetadataRetrieve(omexmlMeta);
        writer.setId(outId);
        // writer.setCompression("J2K");
        // write out image planes
        int seriesCount = reader.getSeriesCount();
        for (int s = 0; s < seriesCount; s++) {
            reader.setSeries(s);
            writer.setSeries(s);
            int planeCount = reader.getImageCount();
            for (int p = 0; p < planeCount; p++) {
                byte[] plane = reader.openBytes(p);
                // write plane to output file
                writer.saveBytes(p, plane);
                System.out.print(".");
            }
        }
        writer.close();
        reader.close();
        System.out.println(" [done]");
    }
}

Example 48 with OMEXMLService

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

the class DisplayHandler method displayOMEXML.

/**
 * Displays OME-XML metadata in a tree in its own window.
 */
public XMLWindow displayOMEXML() throws FormatException, IOException {
    if (!options.isShowOMEXML())
        return null;
    XMLWindow metaWindow = null;
    metaWindow = new XMLWindow("OME Metadata - " + process.getIdName());
    Exception exc = null;
    try {
        ServiceFactory factory = new ServiceFactory();
        OMEXMLService service = factory.getInstance(OMEXMLService.class);
        metaWindow.setXML(service.getOMEXML(process.getOMEMetadata()));
        WindowTools.placeWindow(metaWindow);
        metaWindow.setVisible(true);
    } catch (DependencyException e) {
        exc = e;
    } catch (ServiceException e) {
        exc = e;
    } catch (ParserConfigurationException e) {
        exc = e;
    } catch (SAXException e) {
        exc = e;
    }
    if (exc != null)
        throw new FormatException(exc);
    // save reference to OME-XML window
    xmlWindow = metaWindow;
    return metaWindow;
}

Example 49 with OMEXMLService

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

the class ImportProcess method createBaseReader.

/**
 * Initializes an {@link loci.formats.IFormatReader}
 * according to the current configuration.
 */
private void createBaseReader() throws FormatException, IOException {
    if (options.isLocal() || options.isHTTP()) {
        BF.status(options.isQuiet(), "Identifying " + idName);
        imageReader = LociPrefs.makeImageReader();
        baseReader = imageReader.getReader(options.isUsingPatternIds() ? new FilePattern(options.getId()).getFiles()[0] : options.getId());
    } else if (options.isOMERO()) {
        BF.status(options.isQuiet(), "Establishing server connection");
        try {
            ReflectedUniverse r = new ReflectedUniverse();
            r.exec("import loci.ome.io.OmeroReader");
            r.exec("baseReader = new OmeroReader()");
            ClassList<IFormatReader> classes = new ClassList<IFormatReader>(IFormatReader.class);
            r.setVar("classes", classes);
            r.exec("class = baseReader.getClass()");
            r.exec("classes.addClass(class)");
            imageReader = new ImageReader(classes);
            baseReader = imageReader.getReader(options.getId());
        } catch (Exception exc) {
            WindowTools.reportException(exc, options.isQuiet(), "Sorry, there was a problem communicating with the server.");
            cancel();
            return;
        }
    } else {
        WindowTools.reportException(null, options.isQuiet(), "Sorry, there has been an internal error: unknown data source");
        cancel();
        return;
    }
    // attach OME-XML metadata store
    Exception exc = null;
    try {
        ServiceFactory factory = new ServiceFactory();
        OMEXMLService service = factory.getInstance(OMEXMLService.class);
        meta = service.createOMEXMLMetadata();
        omeXML = null;
    } catch (DependencyException de) {
        exc = de;
    } catch (ServiceException se) {
        exc = se;
    }
    if (exc != null) {
        WindowTools.reportException(exc, options.isQuiet(), "Sorry, there was a problem constructing the OME-XML metadata store");
        throw new FormatException(exc);
    }
    baseReader.setMetadataStore(meta);
    BF.status(options.isQuiet(), "");
    DebugTools.enableIJLogging(IJ.debugMode);
}

Example 50 with OMEXMLService

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

the class OMEXMLReader method initFile.

// -- Internal FormatReader API methods --
/* @see loci.formats.FormatReader#initFile(String) */
@Override
protected void initFile(String id) throws FormatException, IOException {
    super.initFile(id);
    in = new RandomAccessInputStream(id);
    in.setEncoding("ASCII");
    binData = new ArrayList<BinData>();
    binDataOffsets = new ArrayList<Long>();
    compression = new ArrayList<String>();
    DefaultHandler handler = new OMEXMLHandler();
    try {
        RandomAccessInputStream s = new RandomAccessInputStream(id);
        XMLTools.parseXML(s, handler);
        s.close();
    } catch (IOException e) {
        throw new FormatException("Malformed OME-XML", e);
    }
    int lineNumber = 1;
    for (BinData bin : binData) {
        int line = bin.getRow();
        int col = bin.getColumn();
        while (lineNumber < line) {
            in.readLine();
            lineNumber++;
        }
        binDataOffsets.add(in.getFilePointer() + col - 1);
    }
    LOGGER.info("Populating metadata");
    OMEXMLMetadata omexmlMeta;
    OMEXMLService service;
    try {
        ServiceFactory factory = new ServiceFactory();
        service = factory.getInstance(OMEXMLService.class);
        omexmlMeta = service.createOMEXMLMetadata(omexml);
    } catch (DependencyException de) {
        throw new MissingLibraryException(OMEXMLServiceImpl.NO_OME_XML_MSG, de);
    } catch (ServiceException se) {
        throw new FormatException(se);
    }
    hasSPW = omexmlMeta.getPlateCount() > 0;
    // TODO
    // Hashtable originalMetadata = omexmlMeta.getOriginalMetadata();
    // if (originalMetadata != null) metadata = originalMetadata;
    int numDatasets = omexmlMeta.getImageCount();
    int oldSeries = getSeries();
    core.clear();
    for (int i = 0; i < numDatasets; i++) {
        CoreMetadata ms = new CoreMetadata();
        core.add(ms);
        setSeries(i);
        Integer w = omexmlMeta.getPixelsSizeX(i).getValue();
        Integer h = omexmlMeta.getPixelsSizeY(i).getValue();
        Integer t = omexmlMeta.getPixelsSizeT(i).getValue();
        Integer z = omexmlMeta.getPixelsSizeZ(i).getValue();
        Integer c = omexmlMeta.getPixelsSizeC(i).getValue();
        if (w == null || h == null || t == null || z == null | c == null) {
            throw new FormatException("Image dimensions not found");
        }
        Boolean endian = null;
        if (binData.size() > 0) {
            endian = false;
            if (omexmlMeta.getPixelsBigEndian(i) != null) {
                endian = omexmlMeta.getPixelsBigEndian(i).booleanValue();
            } else if (omexmlMeta.getPixelsBinDataCount(i) != 0) {
                endian = omexmlMeta.getPixelsBinDataBigEndian(i, 0).booleanValue();
            }
        }
        String pixType = omexmlMeta.getPixelsType(i).toString();
        ms.dimensionOrder = omexmlMeta.getPixelsDimensionOrder(i).toString();
        ms.sizeX = w.intValue();
        ms.sizeY = h.intValue();
        ms.sizeT = t.intValue();
        ms.sizeZ = z.intValue();
        ms.sizeC = c.intValue();
        ms.imageCount = getSizeZ() * getSizeC() * getSizeT();
        ms.littleEndian = endian == null ? false : !endian.booleanValue();
        ms.rgb = false;
        ms.interleaved = false;
        ms.indexed = false;
        ms.falseColor = true;
        ms.pixelType = FormatTools.pixelTypeFromString(pixType);
        ms.orderCertain = true;
        if (omexmlMeta.getPixelsSignificantBits(i) != null) {
            ms.bitsPerPixel = omexmlMeta.getPixelsSignificantBits(i).getValue();
        }
    }
    setSeries(oldSeries);
    // populate assigned metadata store with the
    // contents of the internal OME-XML metadata object
    MetadataStore store = getMetadataStore();
    service.convertMetadata(omexmlMeta, store);
    MetadataTools.populatePixels(store, this, false, false);
}