private void writeData(final String name, final CoreMetadata info, final String id, final OMETiffWriter out) throws FormatException, IOException { System.out.print(id); for (int i = 0; i < info.imageCount; i++) { final BufferedImage plane = createPlane(name, info, i); out.saveBytes(i, BufferedImageWriter.toBytes(plane, out)); System.out.print("."); } System.out.println(); out.close(); }
@Override public void setId(String id) throws FormatException, IOException { if (id.equals(currentId)) return; super.setId(id); if (imageLocations == null) { MetadataRetrieve r = getMetadataRetrieve(); imageLocations = new String[r.getImageCount()][]; for (int i=0; i<imageLocations.length; i++) { setSeries(i); imageLocations[i] = new String[planeCount()]; } setSeries(0); } }
@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()); } }
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();
try { if (currentId != null) { setupServiceAndMetadata(); setSeries(series); populateImage(omeMeta, series); String companion = getCompanion(); String companionUUID = null; if (null != companion) { String companionXML = getOMEXML(companion); PrintWriter out = new PrintWriter(companion, Constants.ENCODING); out.println(XMLTools.indentXML(companionXML, true)); out.close(); companionUUID = "urn:uuid:" + getUUID( new Location(companion).getName()); xml = getBinaryOnlyOMEXML(f, companion, companionUUID); } else { xml = getOMEXML(f); xml = insertWarningComment(xml); if (getMetadataOptions().isValidate()) { service.validateOMEXML(xml); saveComment(f, xml);
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; }
@Test public void testGetPlaneCount() throws IOException, FormatException { writer.setMetadataRetrieve(metadata); writer.setSeries(0); assertEquals(WriterUtilities.SIZE_T * WriterUtilities.SIZE_Z * WriterUtilities.SIZE_C, writer.getPlaneCount()); metadata.setPixelsSizeC(new PositiveInteger(4), 0); metadata.setPixelsType(PixelType.INT16, 0); writer.setMetadataRetrieve(metadata); assertEquals(WriterUtilities.SIZE_T * WriterUtilities.SIZE_Z * 4, writer.getPlaneCount()); }
/** * @see loci.formats.IFormatWriter#saveBytes(int, byte[], int, int, int, int) */ @Override public void saveBytes(int no, byte[] buf, int x, int y, int w, int h) throws FormatException, IOException { saveBytes(no, buf, null, x, y, w, h); }
int sizeT = omeMeta.getPixelsSizeT(series).getValue().intValue(); int imageCount = getPlaneCount(); String uuid = "urn:uuid:" + getUUID(filename); omeMeta.setUUIDValue(uuid, series, nextPlane); populateTiffData(omeMeta, zct, ifd, series, nextPlane); ifdCounts.put(filename, ifd + 1); nextPlane++;
@AfterMethod public void tearDown() throws Exception { writer.close(); }
@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); } }
@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(); } }
try { if (currentId != null) { setupServiceAndMetadata(); setSeries(series); populateImage(omeMeta, series); String companion = getCompanion(); String companionUUID = null; if (null != companion) { String companionXML = getOMEXML(companion); PrintWriter out = new PrintWriter(companion, Constants.ENCODING); out.println(XMLTools.indentXML(companionXML, true)); out.close(); companionUUID = "urn:uuid:" + getUUID( new Location(companion).getName()); xml = getBinaryOnlyOMEXML(f, companion, companionUUID); } else { xml = getOMEXML(f); xml = insertWarningComment(xml); if (getMetadataOptions().isValidate()) { service.validateOMEXML(xml); saveComment(f, xml);
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; }
/** * @see loci.formats.IFormatWriter#saveBytes(int, byte[], int, int, int, int) */ @Override public void saveBytes(int no, byte[] buf, int x, int y, int w, int h) throws FormatException, IOException { saveBytes(no, buf, null, x, y, w, h); }
int sizeT = omeMeta.getPixelsSizeT(series).getValue().intValue(); int imageCount = getPlaneCount(); String uuid = "urn:uuid:" + getUUID(filename); omeMeta.setUUIDValue(uuid, series, nextPlane); populateTiffData(omeMeta, zct, ifd, series, nextPlane); ifdCounts.put(filename, ifd + 1); nextPlane++;
reader.setId("OMERO"); writer = new OMETiffWriter(); writer.setMetadataRetrieve(retrieve); writer.setWriteSequentially(true); // ticket:6701 long mSize = getMetadataBytes(reader); long dSize = getDataBytes(reader); ( ( mSize + dSize ) > BIG_TIFF_SIZE ); if (bigtiff) { writer.setBigTiff(true); writer.setId(file.getAbsolutePath()); ifd.put(IFD.TILE_LENGTH, 128); writer.saveBytes(i, plane, ifd); writer.close(); } finally {
private void writeData(final String name, final CoreMetadata info, final String id, final OMETiffWriter out) throws FormatException, IOException { System.out.print(id); for (int i = 0; i < info.imageCount; i++) { final BufferedImage plane = createPlane(name, info, i); out.saveBytes(i, BufferedImageWriter.toBytes(plane, out)); System.out.print("."); } System.out.println(); out.close(); }
@Override public void saveBytes(int no, byte[] buf, IFD ifd, int x, int y, int w, int h) throws FormatException, IOException { if (ifd == null) { ifd = new IFD(); } if (getResolution() > 0) { ifd.put(IFD.NEW_SUBFILE_TYPE, 1); } else { if (!ifd.containsKey(IFD.SUB_IFD)) { ifd.put(IFD.SUB_IFD, (long) 0); } } super.saveBytes(no, buf, ifd, x, y, w, h); }