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

Example 41 with IMetadata

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

the class MakeLZW method main.

public static void main(String[] args) throws Exception {
    ImageReader reader = new ImageReader();
    ServiceFactory factory = new ServiceFactory();
    OMEXMLService service = factory.getInstance(OMEXMLService.class);
    IMetadata omexmlMeta = service.createOMEXMLMetadata();
    reader.setMetadataStore(omexmlMeta);
    TiffWriter writer = new TiffWriter();
    for (int i = 0; i < args.length; i++) {
        String inFile = args[i];
        String outFile = "lzw-" + inFile;
        System.out.print("Converting " + inFile + " to " + outFile);
        reader.setId(inFile);
        writer.setMetadataRetrieve(omexmlMeta);
        writer.setCompression("LZW");
        writer.setId(outFile);
        int planeCount = reader.getImageCount();
        for (int p = 0; p < planeCount; p++) {
            System.out.print(".");
            byte[] plane = reader.openBytes(p);
            writer.saveBytes(p, plane);
        }
        System.out.println(" [done]");
    }
}

Example 42 with IMetadata

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

the class MultiFileExportExample method main.

public static void main(String[] args) throws FormatException, IOException {
    if (args.length < 2) {
        System.out.println("Usage: java MultiFileExportExample <infile> <output file extension>");
        System.exit(1);
    }
    ImageReader reader = new ImageReader();
    IMetadata metadata;
    try {
        ServiceFactory factory = new ServiceFactory();
        OMEXMLService service = factory.getInstance(OMEXMLService.class);
        metadata = 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(metadata);
    reader.setId(args[0]);
    ImageWriter writer = new ImageWriter();
    writer.setMetadataRetrieve(metadata);
    String baseFile = args[0].substring(0, args[0].lastIndexOf("."));
    writer.setId(baseFile + "_s0_z0" + args[1]);
    for (int series = 0; series < reader.getSeriesCount(); series++) {
        reader.setSeries(series);
        writer.setSeries(series);
        int planesPerFile = reader.getImageCount() / reader.getSizeZ();
        for (int z = 0; z < reader.getSizeZ(); z++) {
            String file = baseFile + "_s" + series + "_z" + z + args[1];
            writer.changeOutputFile(file);
            for (int image = 0; image < planesPerFile; image++) {
                int[] zct = FormatTools.getZCTCoords(reader.getDimensionOrder(), 1, reader.getEffectiveSizeC(), reader.getSizeT(), planesPerFile, image);
                int index = FormatTools.getIndex(reader, z, zct[1], zct[2]);
                writer.saveBytes(image, reader.openBytes(index));
            }
        }
    }
    reader.close();
    writer.close();
}

Example 43 with IMetadata

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

the class PrintLensNA method main.

public static void main(String[] args) throws DependencyException, FormatException, IOException, ServiceException {
    // parse command line arguments
    if (args.length < 1) {
        System.err.println("Usage: java PrintLensNA imageFile");
        System.exit(1);
    }
    String id = args[0];
    // configure reader
    IFormatReader reader = new ImageReader();
    ServiceFactory factory = new ServiceFactory();
    OMEXMLService service = factory.getInstance(OMEXMLService.class);
    IMetadata meta = service.createOMEXMLMetadata();
    reader.setMetadataStore(meta);
    System.out.println("Initializing file: " + id);
    // parse metadata
    reader.setId(id);
    // output metadata values
    int instrumentCount = meta.getInstrumentCount();
    System.out.println("There are " + instrumentCount + " instrument(s) associated with this file");
    for (int i = 0; i < instrumentCount; i++) {
        int objectiveCount = meta.getObjectiveCount(i);
        System.out.println();
        System.out.println("Instrument #" + i + " [" + meta.getInstrumentID(i) + "]: " + objectiveCount + " objective(s) found");
        for (int o = 0; o < objectiveCount; o++) {
            Double lensNA = meta.getObjectiveLensNA(i, o);
            System.out.println("\tObjective #" + o + " [" + meta.getObjectiveID(i, o) + "]: LensNA=" + lensNA);
        }
    }
}

Example 44 with IMetadata

use of loci.formats.meta.IMetadata 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 45 with IMetadata

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