Examples with OMEXMLService loci.formats.services.OMEXMLService used on opensource projects

Example 26 with OMEXMLService

use of loci.formats.services.OMEXMLService in project bioformats by openmicroscopy.

the class FileExport method initializeMetadata.

/**
 * Populate the minimum amount of metadata required to export an image.
 *
 * @param width the width (in pixels) of the image
 * @param height the height (in pixels) of the image
 * @param pixelType the pixel type of the image; @see loci.formats.FormatTools
 */
private IMetadata initializeMetadata(int width, int height, int pixelType) {
    Exception exception = null;
    try {
        // create the OME-XML metadata storage object
        ServiceFactory factory = new ServiceFactory();
        OMEXMLService service = factory.getInstance(OMEXMLService.class);
        IMetadata meta = service.createOMEXMLMetadata();
        meta.createRoot();
        // define each stack of images - this defines a single stack of images
        meta.setImageID("Image:0", 0);
        meta.setPixelsID("Pixels:0", 0);
        // specify that the pixel data is stored in big-endian format
        // change 'TRUE' to 'FALSE' to specify little-endian format
        meta.setPixelsBinDataBigEndian(Boolean.TRUE, 0, 0);
        // specify that the images are stored in ZCT order
        meta.setPixelsDimensionOrder(DimensionOrder.XYZCT, 0);
        // specify that the pixel type of the images
        meta.setPixelsType(PixelType.fromString(FormatTools.getPixelTypeString(pixelType)), 0);
        // specify the dimensions of the images
        meta.setPixelsSizeX(new PositiveInteger(width), 0);
        meta.setPixelsSizeY(new PositiveInteger(height), 0);
        meta.setPixelsSizeZ(new PositiveInteger(1), 0);
        meta.setPixelsSizeC(new PositiveInteger(1), 0);
        meta.setPixelsSizeT(new PositiveInteger(1), 0);
        // define each channel and specify the number of samples in the channel
        // the number of samples is 3 for RGB images and 1 otherwise
        meta.setChannelID("Channel:0:0", 0, 0);
        meta.setChannelSamplesPerPixel(new PositiveInteger(1), 0, 0);
        return meta;
    } catch (DependencyException e) {
        exception = e;
    } catch (ServiceException e) {
        exception = e;
    } catch (EnumerationException e) {
        exception = e;
    }
    System.err.println("Failed to populate OME-XML metadata object.");
    exception.printStackTrace();
    return null;
}

Example 27 with OMEXMLService

use of loci.formats.services.OMEXMLService 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 28 with OMEXMLService

use of loci.formats.services.OMEXMLService 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 29 with OMEXMLService

use of loci.formats.services.OMEXMLService in project bioformats by openmicroscopy.

the class OBFReader method initFile.

@Override
protected void initFile(String id) throws FormatException, IOException {
    super.initFile(id);
    currentInflatedFrame.series = -1;
    currentInflatedFrame.number = -1;
    in = new RandomAccessInputStream(id);
    file_version = getFileVersion(in);
    long stackPosition = in.readLong();
    final int lengthOfDescription = in.readInt();
    final String description = in.readString(lengthOfDescription);
    metadata.put("Description", description);
    if (file_version >= 2) {
        final long meta_data_position = in.readLong();
        final long current_position = in.getFilePointer();
        in.seek(meta_data_position);
        for (String key = readString(); key.length() > 0; key = readString()) {
            if (key.equals("ome_xml")) {
                final String ome_xml = readString();
                try {
                    ServiceFactory factory = new ServiceFactory();
                    OMEXMLService service = factory.getInstance(OMEXMLService.class);
                    if (service.validateOMEXML(ome_xml)) {
                        ome_meta_data = service.createOMEXMLMetadata(ome_xml);
                        for (int image = 0; image != ome_meta_data.getImageCount(); ++image) {
                            if (ome_meta_data.getPixelsBigEndian(image) == null) {
                                ome_meta_data.setPixelsBigEndian(Boolean.FALSE, image);
                            }
                            int channels = ome_meta_data.getChannelCount(image);
                            for (int channel = 0; channel != channels; ++channel) {
                                if (ome_meta_data.getChannelSamplesPerPixel(image, channel) == null) {
                                    ome_meta_data.setChannelSamplesPerPixel(new PositiveInteger(1), image, channel);
                                }
                            }
                        }
                        service.convertMetadata(ome_meta_data, metadataStore);
                        OMEXMLMetadata reference = service.getOMEMetadata(service.asRetrieve(metadataStore));
                        for (int image = 0; image != ome_meta_data.getImageCount(); ++image) {
                            service.addMetadataOnly(reference, image);
                        }
                    }
                } catch (DependencyException exception) {
                    throw new MissingLibraryException(OMEXMLServiceImpl.NO_OME_XML_MSG, exception);
                } catch (ServiceException exception) {
                    throw new FormatException(exception);
                } catch (Exception e) {
                    LOGGER.warn("Could not parse OME-XML metadata", e);
                }
                break;
            } else {
                addGlobalMeta(key, readString());
            }
        }
        in.seek(current_position);
    }
    if (stackPosition != 0) {
        core.clear();
        do {
            stackPosition = initStack(stackPosition);
        } while (stackPosition != 0);
    }
    if (ome_meta_data == null) {
        MetadataTools.populatePixels(metadataStore, this);
        for (int image = 0; image != core.size(); ++image) {
            CoreMetadata meta_data = core.get(image);
            final String name = meta_data.seriesMetadata.get("Name").toString();
            metadataStore.setImageName(name, image);
            @SuppressWarnings("unchecked") final List<Double> lengths = (List<Double>) meta_data.seriesMetadata.get("Lengths");
            if (lengths.size() > 0) {
                double lengthX = Math.abs(lengths.get(0));
                if (lengthX < 0.01) {
                    lengthX *= 1000000;
                }
                if (lengthX > 0) {
                    Length physicalSizeX = FormatTools.getPhysicalSizeX(lengthX / meta_data.sizeX, UNITS.MICROMETER);
                    if (physicalSizeX != null) {
                        metadataStore.setPixelsPhysicalSizeX(physicalSizeX, image);
                    }
                }
            }
            if (lengths.size() > 1) {
                double lengthY = Math.abs(lengths.get(1));
                if (lengthY < 0.01) {
                    lengthY *= 1000000;
                }
                if (lengthY > 0) {
                    Length physicalSizeY = FormatTools.getPhysicalSizeY(lengthY / meta_data.sizeY, UNITS.MICROMETER);
                    if (physicalSizeY != null) {
                        metadataStore.setPixelsPhysicalSizeY(physicalSizeY, image);
                    }
                }
            }
            if (lengths.size() > 2) {
                double lengthZ = Math.abs(lengths.get(2));
                if (lengthZ < 0.01) {
                    lengthZ *= 1000000;
                }
                if (lengthZ > 0) {
                    Length physicalSizeZ = FormatTools.getPhysicalSizeZ(lengthZ / meta_data.sizeZ, UNITS.MICROMETER);
                    if (physicalSizeZ != null) {
                        metadataStore.setPixelsPhysicalSizeZ(physicalSizeZ, image);
                    }
                }
            }
        }
    }
}

Example 30 with OMEXMLService

use of loci.formats.services.OMEXMLService in project bioformats by openmicroscopy.

the class MakeTestOmeTiff method createMetadata.

private IMetadata createMetadata(final String name, final CoreMetadata info) throws DependencyException, ServiceException, EnumerationException {
    final ServiceFactory serviceFactory = new ServiceFactory();
    final OMEXMLService omexmlService = serviceFactory.getInstance(OMEXMLService.class);
    final IMetadata meta = omexmlService.createOMEXMLMetadata();
    MetadataTools.populateMetadata(meta, 0, name, info);
    if (isModulo) {
        meta.setXMLAnnotationID("Annotation:Modulo:0", 0);
        meta.setXMLAnnotationNamespace("openmicroscopy.org/omero/dimension/modulo", 0);
        meta.setXMLAnnotationDescription("For a description of how 6D, 7D, and 8D data is stored using the Modulo extension see https://docs.openmicroscopy.org/latest/ome-model/developers/6d-7d-and-8d-storage.html", 0);
        StringBuilder moduloBlock = new StringBuilder();
        moduloBlock.append("<Modulo namespace=\"http://www.openmicroscopy.org/Schemas/Additions/2011-09\">");
        if (sizeZsub != 1) {
            moduloBlock.append("<ModuloAlongZ Type=\"other\" TypeDescription=\"Example Data Over Z-Plane\" Start=\"0\" Step=\"1\" End=\"");
            moduloBlock.append(sizeZsub);
            moduloBlock.append("\"/>");
        }
        if (sizeTsub != 1) {
            moduloBlock.append("<ModuloAlongT Type=\"other\" TypeDescription=\"Example Data Over Time \" Start=\"0\" Step=\"1\" End=\"");
            moduloBlock.append(sizeTsub);
            moduloBlock.append("\"/>");
        }
        if (sizeCsub != 1) {
            moduloBlock.append("<ModuloAlongC Type=\"other\" TypeDescription=\"Example Data Over Channel\" Start=\"0\" Step=\"1\" End=\"");
            moduloBlock.append(sizeCsub);
            moduloBlock.append("\"/>");
        }
        moduloBlock.append("</Modulo>");
        meta.setXMLAnnotationValue(moduloBlock.toString(), 0);
        meta.setImageAnnotationRef("Annotation:Modulo:0", 0, 0);
    }
    return meta;
}