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

Example 6 with OMETiffWriter

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

the class OMETiffWriterBigTiffLargeImageWidthTest method testImageWidthWrittenCorrectly.

@Test
public void testImageWidthWrittenCorrectly() throws Exception {
    OMETiffWriter writer = new OMETiffWriter();
    writer.setBigTiff(true);
    writer.setMetadataRetrieve(ms);
    writer.setId(target.getAbsolutePath());
    writer.saveBytes(0, buf, 0, 0, buf.length, 1);
    writer.close();
    TiffReader reader = new TiffReader();
    reader.setId(target.getAbsolutePath());
    assertEquals(SIZE_X, reader.getSizeX());
    assertEquals(SIZE_Y, reader.getSizeY());
}

Example 7 with OMETiffWriter

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

the class OMETiffWriterUnicodeTest method testImageWidthWrittenCorrectly.

@Test
public void testImageWidthWrittenCorrectly() throws Exception {
    OMETiffWriter writer = new OMETiffWriter();
    writer.setMetadataRetrieve(ms);
    writer.setId(target.getAbsolutePath());
    writer.saveBytes(0, buf, 0, 0, buf.length, 1);
    writer.close();
    ImageReader reader = new ImageReader();
    reader.setId(target.getAbsolutePath());
    assertEquals(reader.getFormat(), "OME-TIFF");
    reader.close();
}

Example 8 with OMETiffWriter

use of loci.formats.out.OMETiffWriter 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 9 with OMETiffWriter

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

the class MakeTestOmeTiff method createWriter.

private OMETiffWriter createWriter(final String name, final CoreMetadata info, final String id) throws FormatException, IOException {
    final OMETiffWriter out = new OMETiffWriter();
    try {
        out.setMetadataRetrieve(createMetadata(name, info));
    } catch (final DependencyException e) {
        throw new FormatException(e);
    } catch (final ServiceException e) {
        throw new FormatException(e);
    } catch (final EnumerationException e) {
        throw new FormatException(e);
    }
    ensureNonExisting(id);
    out.setId(id);
    return out;
}

Example 10 with OMETiffWriter

use of loci.formats.out.OMETiffWriter 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);
}