Examples with ServiceFactory loci.common.services.ServiceFactory used on opensource projects

Example 36 with ServiceFactory

use of loci.common.services.ServiceFactory in project bioformats by openmicroscopy.

the class FormatTools method convert.

/**
 * Convenience method for writing all of the images and metadata obtained
 * from the specified IFormatReader into the specified IFormatWriter.
 *
 * It is required that setId(String) be called on the IFormatReader
 * object before it is passed to convert(...).  setMetadataStore(...)
 * should also have been called with an appropriate instance of IMetadata.
 *
 * The setId(String) method must not be called on the IFormatWriter
 * object; this is taken care of internally.  Additionally, the
 * setMetadataRetrieve(...) method in IFormatWriter should not be called.
 *
 * @param input the pre-initialized IFormatReader used for reading data.
 * @param output the uninitialized IFormatWriter used for writing data.
 * @param outputFile the full path name of the output file to be created.
 * @throws FormatException if there is a general problem reading from or
 * writing to one of the files.
 * @throws IOException if there is an I/O-related error.
 */
public static void convert(IFormatReader input, IFormatWriter output, String outputFile) throws FormatException, IOException {
    MetadataStore store = input.getMetadataStore();
    MetadataRetrieve meta = null;
    try {
        ServiceFactory factory = new ServiceFactory();
        OMEXMLService service = factory.getInstance(OMEXMLService.class);
        meta = service.asRetrieve(store);
    } catch (DependencyException de) {
        throw new MissingLibraryException(OMEXMLServiceImpl.NO_OME_XML_MSG, de);
    }
    output.setMetadataRetrieve(meta);
    output.setId(outputFile);
    for (int series = 0; series < input.getSeriesCount(); series++) {
        input.setSeries(series);
        output.setSeries(series);
        byte[] buf = new byte[getPlaneSize(input)];
        for (int image = 0; image < input.getImageCount(); image++) {
            input.openBytes(image, buf);
            output.saveBytes(image, buf);
        }
    }
    input.close();
    output.close();
}

Example 37 with ServiceFactory

use of loci.common.services.ServiceFactory in project bioformats by openmicroscopy.

the class FormatWriterTest method testWriterConsistency.

// -- Tests --
@Test(groups = { "all" }, dataProvider = "getWriterList")
public void testWriterConsistency(IFormatWriter writer) {
    String testName = TestTools.shortClassName(writer) + " " + writer.getCompression() + " testWriterConsistency";
    boolean success = true;
    String msg = null;
    try {
        reader.close();
        ServiceFactory factory = new ServiceFactory();
        OMEXMLService service = factory.getInstance(OMEXMLService.class);
        reader.setMetadataStore(service.createOMEXMLMetadata());
        reader.setId(id);
        int type = reader.getPixelType();
        if (!writer.isSupportedType(type)) {
            success = true;
            result(testName, success, msg);
            return;
        }
        config = configTree.get(id);
        String prefix = id.substring(id.lastIndexOf(File.separator) + 1, id.lastIndexOf("."));
        // will throw an exception
        while (prefix.length() < 3) prefix = "x" + prefix;
        String suffix = "." + writer.getSuffixes()[0];
        File tmpFile = File.createTempFile(prefix, suffix);
        tmpFile.deleteOnExit();
        String convertedFile = tmpFile.getAbsolutePath();
        IMetadata meta = (IMetadata) reader.getMetadataStore();
        writer.close();
        writer.setMetadataRetrieve((MetadataRetrieve) meta);
        // convert the input file
        writer.setId(convertedFile);
        int seriesCount = writer.canDoStacks() ? reader.getSeriesCount() : 1;
        for (int series = 0; series < seriesCount; series++) {
            reader.setSeries(series);
            writer.setSeries(series);
            int imageCount = writer.canDoStacks() ? reader.getImageCount() : 1;
            for (int image = 0; image < imageCount; image++) {
                writer.saveBytes(image, reader.openBytes(image));
            }
        }
        writer.close();
        // verify that the dimensions are accurate
        convertedReader.setId(convertedFile);
        boolean seriesMatch = convertedReader.getSeriesCount() == config.getSeriesCount();
        boolean expectRGB = config.isRGB();
        int expectedCount = config.getSizeZ() * config.getSizeT() * (expectRGB ? 1 : config.getSizeC());
        boolean imageMatch = convertedReader.getImageCount() == expectedCount;
        if (!seriesMatch && writer.canDoStacks()) {
            int totalImages = 0;
            for (int i = 0; i < reader.getSeriesCount(); i++) {
                reader.setSeries(i);
                totalImages += reader.getImageCount();
            }
            reader.setSeries(0);
            if (convertedReader.getImageCount() != totalImages) {
                success = false;
                msg = "Series counts do not match (found " + convertedReader.getSeriesCount() + ", expected " + config.getSeriesCount() + ")";
            } else
                imageMatch = true;
        }
        if (success) {
            for (int series = 0; series < seriesCount; series++) {
                if (series >= convertedReader.getSeriesCount()) {
                    break;
                }
                convertedReader.setSeries(series);
                config.setSeries(series);
                int expectedX = config.getSizeX();
                int expectedY = config.getSizeY();
                expectRGB = config.isRGB();
                if (TestTools.shortClassName(writer).equals("OMEXMLWriter")) {
                    expectRGB = false;
                } else if (TestTools.shortClassName(writer).equals("JPEGWriter")) {
                    expectRGB = expectRGB || config.isIndexed();
                }
                int expectedPixelType = FormatTools.pixelTypeFromString(config.getPixelType());
                expectedCount = config.getSizeZ() * config.getSizeT() * (expectRGB ? 1 : config.getSizeC());
                String expectedMD5 = config.getMD5();
                int x = convertedReader.getSizeX();
                int y = convertedReader.getSizeY();
                int count = convertedReader.getImageCount();
                boolean rgb = convertedReader.isRGB();
                int pixelType = convertedReader.getPixelType();
                boolean isQuicktime = TestTools.shortClassName(writer).equals("QTWriter");
                String md5 = TestTools.md5(convertedReader.openBytes(0));
                if (msg == null)
                    msg = checkMismatch(x, expectedX, series, "X");
                if (msg == null)
                    msg = checkMismatch(y, expectedY, series, "Y");
                if (msg == null && writer.canDoStacks() && !imageMatch) {
                    msg = checkMismatch(count, expectedCount, series, "Image count");
                }
                if (msg == null && !isQuicktime) {
                    msg = checkMismatch(rgb, expectRGB, series, "RGB");
                }
                if (msg == null && !isQuicktime) {
                    msg = checkMismatch(pixelType, expectedPixelType, series, "Pixel type");
                }
                if (msg == null && isLosslessWriter(writer) && config.isRGB() == expectRGB) {
                    msg = checkMismatch(md5, expectedMD5, series, "Pixels hash");
                }
                success = msg == null;
                if (!success)
                    break;
            }
        }
        convertedReader.close();
    } catch (Throwable t) {
        LOGGER.info("", t);
        success = false;
    }
    result(testName, success, msg);
}

Example 38 with ServiceFactory

use of loci.common.services.ServiceFactory in project bioformats by openmicroscopy.

the class Jpeg2000GrindTest method initializeWriter.

/**
 * Initializes the writer.
 * @param output The file where to write the compressed data.
 * @param compression The compression to use.
 * @param bigTiff Pass <code>true</code> to set the <code>bigTiff</code>
 * flag, <code>false</code> otherwise.
 * @throws Exception Thrown if an error occurred.
 */
private void initializeWriter(String output, String compression, boolean bigTiff) throws Exception {
    ServiceFactory sf = new ServiceFactory();
    OMEXMLService service = sf.getInstance(OMEXMLService.class);
    IMetadata metadata = service.createOMEXMLMetadata();
    metadata.setImageID("Image:0", 0);
    metadata.setPixelsID("Pixels:0", 0);
    metadata.setPixelsBinDataBigEndian(true, 0, 0);
    metadata.setPixelsDimensionOrder(DimensionOrder.XYZCT, 0);
    metadata.setPixelsType(ome.xml.model.enums.PixelType.fromString(PIXEL_TYPE), 0);
    metadata.setPixelsSizeX(new PositiveInteger(SIZE_X), 0);
    metadata.setPixelsSizeY(new PositiveInteger(SIZE_Y), 0);
    metadata.setPixelsSizeZ(new PositiveInteger(1), 0);
    metadata.setPixelsSizeC(new PositiveInteger(1), 0);
    metadata.setPixelsSizeT(new PositiveInteger(SIZE_Z * SIZE_C * SIZE_T), 0);
    metadata.setChannelID("Channel:0", 0, 0);
    metadata.setChannelSamplesPerPixel(new PositiveInteger(1), 0, 0);
    writer = new TiffWriter();
    writer.setMetadataRetrieve(metadata);
    writer.setCompression(compression);
    writer.setWriteSequentially(false);
    writer.setInterleaved(true);
    writer.setBigTiff(bigTiff);
    writer.setId(output);
    bytesPerPixel = FormatTools.getBytesPerPixel(PIXEL_TYPE);
}

Example 39 with ServiceFactory

use of loci.common.services.ServiceFactory in project bioformats by openmicroscopy.

the class MetadataConfigurableTest method testSetId.

@Test
public void testSetId() throws FormatException, IOException {
    long t0 = System.currentTimeMillis();
    pixelsOnly.setId(id);
    assertEquals(MetadataLevel.MINIMUM, pixelsOnly.getMetadataOptions().getMetadataLevel());
    long t1 = System.currentTimeMillis();
    all.setId(id);
    assertEquals(MetadataLevel.ALL, all.getMetadataOptions().getMetadataLevel());
    assertFalse(0 == all.getSeriesMetadata().size() + all.getGlobalMetadata().size());
    long t2 = System.currentTimeMillis();
    System.err.println(String.format("Pixels only: %d -- All: %d", t1 - t0, t2 - t1));
    IMetadata metadata = null;
    try {
        ServiceFactory factory = new ServiceFactory();
        OMEXMLService service = factory.getInstance(OMEXMLService.class);
        metadata = service.createOMEXMLMetadata();
        noOverlays.setMetadataStore(metadata);
    } catch (Exception e) {
        throw new FormatException("Cannot initialize OMEXML metadata store");
    }
    noOverlays.setId(id);
    assertEquals(MetadataLevel.NO_OVERLAYS, noOverlays.getMetadataOptions().getMetadataLevel());
    assertEquals(metadata.getROICount(), 0);
}

Example 40 with ServiceFactory

use of loci.common.services.ServiceFactory in project bioformats by openmicroscopy.

the class FileConvert 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
 */
private boolean initialize() {
    Exception exception = null;
    try {
        // 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 ImageWriter();
        writer.setMetadataRetrieve(omexml);
        writer.setInterleaved(reader.isInterleaved());
        writer.setId(outputFile);
    } catch (FormatException e) {
        exception = e;
    } catch (IOException e) {
        exception = e;
    } catch (DependencyException e) {
        exception = e;
    } catch (ServiceException e) {
        exception = e;
    }
    if (exception != null) {
        System.err.println("Failed to initialize files.");
        exception.printStackTrace();
    }
    return exception == null;
}