Examples with OMETiffWriter loci.formats.out.OMETiffWriter used on opensource projects

Example 1 with OMETiffWriter

use of loci.formats.out.OMETiffWriter in project bioformats by openmicroscopy.

the class OMETiffWriterTest method testCompanion.

@Test
public void testCompanion() throws Exception {
    Path wd = Files.createTempDirectory(this.getClass().getName());
    File outFile = wd.resolve("test.ome.tif").toFile();
    File cFile = wd.resolve("test.companion.ome").toFile();
    String companion = cFile.getAbsolutePath();
    DynamicMetadataOptions options = new DynamicMetadataOptions();
    options.set(OMETiffWriter.COMPANION_KEY, companion);
    int planeCount = WriterUtilities.SIZE_Z * WriterUtilities.SIZE_C * WriterUtilities.SIZE_T;
    OMETiffWriter cwriter = new OMETiffWriter();
    cwriter.setMetadataOptions(options);
    cwriter.setMetadataRetrieve(metadata);
    cwriter.setId(outFile.getAbsolutePath());
    cwriter.setSeries(0);
    byte[] img = new byte[WriterUtilities.SIZE_X * WriterUtilities.SIZE_Y];
    for (int i = 0; i < planeCount; i++) {
        cwriter.saveBytes(i, img);
    }
    cwriter.close();
    assertTrue(cFile.exists());
    OMETiffReader reader = new OMETiffReader();
    reader.setId(companion);
    assertEquals(reader.getSizeX(), WriterUtilities.SIZE_X);
    assertEquals(reader.getSizeY(), WriterUtilities.SIZE_Y);
    assertEquals(reader.getSizeZ(), WriterUtilities.SIZE_Z);
    assertEquals(reader.getSizeC(), WriterUtilities.SIZE_C);
    assertEquals(reader.getSizeT(), WriterUtilities.SIZE_T);
    reader.close();
    outFile.deleteOnExit();
    cFile.deleteOnExit();
    wd.toFile().deleteOnExit();
}

Example 2 with OMETiffWriter

use of loci.formats.out.OMETiffWriter in project bioformats by openmicroscopy.

the class OverlappedTiledWriter 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 3 with OMETiffWriter

use of loci.formats.out.OMETiffWriter in project bioformats by openmicroscopy.

the class OrthogonalReader method initialiseWriter.

private OMETiffWriter initialiseWriter(String fileName, ImageReader reader) throws Exception {
    ServiceFactory factory = new ServiceFactory();
    OMEXMLService service = factory.getInstance(OMEXMLService.class);
    IMetadata metadata = service.createOMEXMLMetadata();
    MetadataRetrieve mr = (MetadataRetrieve) reader.getMetadataStore();
    Length originalSizeX = mr.getPixelsPhysicalSizeX(0);
    Length originalSizeY = mr.getPixelsPhysicalSizeY(0);
    Length originalSizeZ = mr.getPixelsPhysicalSizeZ(0);
    // Original XY planes
    // XZ planes
    MetadataTools.populateMetadata(metadata, 0, "XZ", reader.isLittleEndian(), reader.getDimensionOrder(), FormatTools.getPixelTypeString(reader.getPixelType()), reader.getSizeX(), reader.getSizeZ(), reader.getSizeY(), 1, 1, 1);
    metadata.setPixelsPhysicalSizeX(originalSizeX, 0);
    metadata.setPixelsPhysicalSizeY(originalSizeZ, 0);
    metadata.setPixelsPhysicalSizeZ(originalSizeY, 0);
    // YZ planes
    MetadataTools.populateMetadata(metadata, 1, "YZ", reader.isLittleEndian(), reader.getDimensionOrder(), FormatTools.getPixelTypeString(reader.getPixelType()), reader.getSizeY(), reader.getSizeZ(), reader.getSizeX(), 1, 1, 1);
    metadata.setPixelsPhysicalSizeX(originalSizeY, 1);
    metadata.setPixelsPhysicalSizeY(originalSizeZ, 1);
    metadata.setPixelsPhysicalSizeZ(originalSizeX, 1);
    OMETiffWriter writer = new OMETiffWriter();
    writer.setMetadataRetrieve(metadata);
    writer.setId(fileName);
    return writer;
}

Example 4 with OMETiffWriter

use of loci.formats.out.OMETiffWriter in project bioformats by openmicroscopy.

the class SimpleTiledWriter 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);
    /* initialize-tiling-writer-example-start */
    // 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);
/* initialize-tiling-writer-example-end */
}

Example 5 with OMETiffWriter

use of loci.formats.out.OMETiffWriter in project bioformats by openmicroscopy.

the class OMETiffWriterTest method setUp.

@BeforeMethod
public void setUp() throws Exception {
    writer = new OMETiffWriter();
    metadata = WriterUtilities.createMetadata();
    for (int i = 0; i < 1024 * 1024; i++) {
        buf[i] = (byte) (i % 255);
    }
}