throws FormatException, IOException checkParams(no, buf, x, y, w, h); if (!isFullPlane(x, y, w, h)) { throw new FormatException( "OMEXMLWriter does not yet support saving image tiles."); MetadataRetrieve retrieve = getMetadataRetrieve(); int pixelType = FormatTools.pixelTypeFromString(type); int bytes = FormatTools.getBytesPerPixel(pixelType); int nChannels = getSamplesPerPixel(); int sizeX = retrieve.getPixelsSizeX(series).getValue().intValue(); int sizeY = retrieve.getPixelsSizeY(series).getValue().intValue(); byte[] b = ImageTools.splitChannels(buf, i, nChannels, bytes, false, interleaved); byte[] encodedPix = compress(b);
@Override public void close() throws IOException { if (out != null) { out.writeBytes(xmlFragments.get(xmlFragments.size() - 1)); } if (getMetadataOptions().isValidate()) { try { MetadataRetrieve r = getMetadataRetrieve(); String omexml = service.getOMEXML(r); service.validateOMEXML(omexml); } catch (ServiceException | NullPointerException e) { LOGGER.warn("OMEXMLService unable to create OME-XML metadata object.", e); } } super.close(); xmlFragments = null; service = null; }
@Override public void setId(String id) throws FormatException, IOException { if (id.equals(currentId)) { return; } super.setId(id); MetadataRetrieve retrieve = getMetadataRetrieve(); String xml; try { ServiceFactory factory = new ServiceFactory(); service = factory.getInstance(OMEXMLService.class); xml = service.getOMEXML(retrieve); OMEXMLMetadata noBin = service.createOMEXMLMetadata(xml); service.removeBinData(noBin); OMEXMLMetadataRoot root = (OMEXMLMetadataRoot) noBin.getRoot(); root.setCreator(FormatTools.CREATOR); xml = service.getOMEXML(noBin); } catch (DependencyException de) { throw new MissingLibraryException(OMEXMLServiceImpl.NO_OME_XML_MSG, de); } catch (ServiceException se) { throw new FormatException(se); } xmlFragments = new ArrayList<String>(); currentFragment = "<?xml version=\"1.0\" encoding=\"UTF-8\"?>"; XMLTools.parseXML(xml, new OMEHandler()); xmlFragments.add(currentFragment); }
@Override public void setId(String id) throws FormatException, IOException { if (id.equals(currentId)) { return; } super.setId(id); MetadataRetrieve retrieve = getMetadataRetrieve(); String xml; try { ServiceFactory factory = new ServiceFactory(); service = factory.getInstance(OMEXMLService.class); xml = service.getOMEXML(retrieve); OMEXMLMetadata noBin = service.createOMEXMLMetadata(xml); service.removeBinData(noBin); OMEXMLMetadataRoot root = (OMEXMLMetadataRoot) noBin.getRoot(); root.setCreator(FormatTools.CREATOR); xml = service.getOMEXML(noBin); } catch (DependencyException de) { throw new MissingLibraryException(OMEXMLServiceImpl.NO_OME_XML_MSG, de); } catch (ServiceException se) { throw new FormatException(se); } xmlFragments = new ArrayList<String>(); currentFragment = "<?xml version=\"1.0\" encoding=\"UTF-8\"?>"; XMLTools.parseXML(xml, new OMEHandler()); xmlFragments.add(currentFragment); }
throws FormatException, IOException checkParams(no, buf, x, y, w, h); if (!isFullPlane(x, y, w, h)) { throw new FormatException( "OMEXMLWriter does not yet support saving image tiles."); MetadataRetrieve retrieve = getMetadataRetrieve(); int pixelType = FormatTools.pixelTypeFromString(type); int bytes = FormatTools.getBytesPerPixel(pixelType); int nChannels = getSamplesPerPixel(); int sizeX = retrieve.getPixelsSizeX(series).getValue().intValue(); int sizeY = retrieve.getPixelsSizeY(series).getValue().intValue(); byte[] b = ImageTools.splitChannels(buf, i, nChannels, bytes, false, interleaved); byte[] encodedPix = compress(b);
@Override public void close() throws IOException { if (out != null) { out.writeBytes(xmlFragments.get(xmlFragments.size() - 1)); } if (getMetadataOptions().isValidate()) { try { MetadataRetrieve r = getMetadataRetrieve(); String omexml = service.getOMEXML(r); service.validateOMEXML(omexml); } catch (ServiceException | NullPointerException e) { LOGGER.warn("OMEXMLService unable to create OME-XML metadata object.", e); } } super.close(); xmlFragments = null; service = null; }
MetadataRetrieve r = getMetadataRetrieve(); String type = r.getPixelsType(series).toString(); int pixelType = FormatTools.pixelTypeFromString(type);
MetadataRetrieve r = getMetadataRetrieve(); String type = r.getPixelsType(series).toString(); int pixelType = FormatTools.pixelTypeFromString(type);