Examples with OMEXMLMetadataRoot ome.xml.meta.OMEXMLMetadataRoot used on opensource projects

Example 1 with OMEXMLMetadataRoot

use of ome.xml.meta.OMEXMLMetadataRoot in project bioformats by openmicroscopy.

the class OMEXMLServiceImpl method populateOriginalMetadata.

/**
 * @see OMEXMLService#populateOriginalMetadata(loci.formats.ome.OMEXMLMetadata, Hashtable)
 */
@Override
public void populateOriginalMetadata(OMEXMLMetadata omexmlMeta, Hashtable<String, Object> metadata) {
    omexmlMeta.resolveReferences();
    if (metadata.size() == 0) {
        return;
    }
    OMEXMLMetadataRoot root = (OMEXMLMetadataRoot) omexmlMeta.getRoot();
    StructuredAnnotations annotations = root.getStructuredAnnotations();
    if (annotations == null)
        annotations = new StructuredAnnotations();
    int annotationIndex = annotations.sizeOfXMLAnnotationList();
    if (annotationIndex > 0) {
        String lastAnnotationID = omexmlMeta.getXMLAnnotationID(annotationIndex - 1);
        String lastIndex = lastAnnotationID.substring(lastAnnotationID.lastIndexOf(":") + 1);
        try {
            int index = Integer.parseInt(lastIndex);
            while (index >= annotationIndex) {
                annotationIndex++;
            }
        } catch (NumberFormatException e) {
        }
    }
    for (String key : metadata.keySet()) {
        OriginalMetadataAnnotation annotation = new OriginalMetadataAnnotation();
        annotation.setID(MetadataTools.createLSID("Annotation", annotationIndex));
        annotation.setKeyValue(key, metadata.get(key).toString());
        annotations.addXMLAnnotation(annotation);
        annotationIndex++;
    }
    root.setStructuredAnnotations(annotations);
    omexmlMeta.setRoot(root);
}

Example 2 with OMEXMLMetadataRoot

use of ome.xml.meta.OMEXMLMetadataRoot in project bioformats by openmicroscopy.

the class OMEXMLServiceImpl method validateOMEXML.

/**
 * @see OMEXMLService#validateOMEXML(java.lang.String, boolean)
 */
@Override
public boolean validateOMEXML(String xml, boolean pixelsHack) {
    // HACK: Inject a TiffData element beneath any childless Pixels elements.
    if (pixelsHack) {
        // convert XML string to DOM
        Document doc = null;
        Exception exception = null;
        try {
            doc = XMLTools.parseDOM(xml);
        } catch (ParserConfigurationException exc) {
            exception = exc;
        } catch (SAXException exc) {
            exception = exc;
        } catch (IOException exc) {
            exception = exc;
        }
        if (exception != null) {
            LOGGER.info("Malformed OME-XML", exception);
            return false;
        }
        // inject TiffData elements as needed
        NodeList list = doc.getElementsByTagName("Pixels");
        for (int i = 0; i < list.getLength(); i++) {
            Node node = list.item(i);
            NodeList children = node.getChildNodes();
            boolean needsTiffData = true;
            for (int j = 0; j < children.getLength(); j++) {
                Node child = children.item(j);
                String name = child.getLocalName();
                if ("TiffData".equals(name) || "BinData".equals(name)) {
                    needsTiffData = false;
                    break;
                }
            }
            if (needsTiffData) {
                // inject TiffData element
                Node tiffData = doc.createElement("TiffData");
                node.insertBefore(tiffData, node.getFirstChild());
            }
        }
        // convert tweaked DOM back to XML string
        try {
            xml = XMLTools.getXML(doc);
        } catch (TransformerConfigurationException exc) {
            exception = exc;
        } catch (TransformerException exc) {
            exception = exc;
        }
        if (exception != null) {
            LOGGER.info("Internal XML conversion error", exception);
            return false;
        }
    }
    try {
        OMEXMLMetadata omexml = createOMEXMLMetadata(xml);
        OMEXMLMetadataRoot root = (OMEXMLMetadataRoot) omexml.getRoot();
        for (int image = 0; image < root.sizeOfImageList(); image++) {
            Image img = root.getImage(image);
            for (int i = 0; i < img.sizeOfLinkedAnnotationList(); i++) {
                Annotation annotation = img.getLinkedAnnotation(i);
                if (!(annotation instanceof XMLAnnotation)) {
                    continue;
                }
                String annotationXML = ((XMLAnnotation) annotation).getValue();
                Document annotationRoot = XMLTools.parseDOM(annotationXML);
                NodeList nodes = annotationRoot.getElementsByTagName("ModuloAlongZ");
                if (nodes.getLength() > 0) {
                    ((XMLAnnotation) annotation).setValue("");
                }
                nodes = annotationRoot.getElementsByTagName("ModuloAlongC");
                if (nodes.getLength() > 0) {
                    ((XMLAnnotation) annotation).setValue("");
                }
                nodes = annotationRoot.getElementsByTagName("ModuloAlongT");
                if (nodes.getLength() > 0) {
                    ((XMLAnnotation) annotation).setValue("");
                }
            }
        }
        omexml.setRoot(root);
        xml = getOMEXML(omexml);
    } catch (ServiceException | ParserConfigurationException | SAXException | IOException e) {
        LOGGER.warn("Could not remove Modulo annotations", e);
    }
    return XMLTools.validateXML(xml, "OME-XML", SCHEMA_CLASSPATH_READER);
}

Example 3 with OMEXMLMetadataRoot

use of ome.xml.meta.OMEXMLMetadataRoot in project bioformats by openmicroscopy.

the class OMEXMLServiceImpl method createOMEXMLMetadata.

/**
 * @see OMEXMLService#createOMEXMLMetadata(java.lang.String, java.lang.String)
 */
@Override
public OMEXMLMetadata createOMEXMLMetadata(String xml, String version) throws ServiceException {
    if (xml != null) {
        xml = XMLTools.sanitizeXML(xml);
    }
    OMEXMLMetadataRoot ome = xml == null ? null : createRoot(transformToLatestVersion(xml));
    OMEXMLMetadata meta = new OMEXMLMetadataImpl();
    if (ome != null)
        meta.setRoot(ome);
    return meta;
}

Example 4 with OMEXMLMetadataRoot

use of ome.xml.meta.OMEXMLMetadataRoot in project bioformats by openmicroscopy.

the class OMEXMLServiceImpl method populateOriginalMetadata.

/**
 * @see OMEXMLService#populateOriginalMetadata(loci.formats.ome.OMEXMLMetadata, java.lang.String, java.lang.String)
 */
@Override
public void populateOriginalMetadata(OMEXMLMetadata omexmlMeta, String key, String value) {
    omexmlMeta.resolveReferences();
    OMEXMLMetadataRoot root = (OMEXMLMetadataRoot) omexmlMeta.getRoot();
    StructuredAnnotations annotations = root.getStructuredAnnotations();
    if (annotations == null)
        annotations = new StructuredAnnotations();
    int annotationIndex = annotations.sizeOfXMLAnnotationList();
    if (annotationIndex > 0) {
        String lastAnnotationID = omexmlMeta.getXMLAnnotationID(annotationIndex - 1);
        String lastIndex = lastAnnotationID.substring(lastAnnotationID.lastIndexOf(":") + 1);
        try {
            int index = Integer.parseInt(lastIndex);
            while (index >= annotationIndex) {
                annotationIndex++;
            }
        } catch (NumberFormatException e) {
        }
    }
    OriginalMetadataAnnotation annotation = new OriginalMetadataAnnotation();
    annotation.setID(MetadataTools.createLSID("Annotation", annotationIndex));
    annotation.setKeyValue(key, value);
    annotations.addXMLAnnotation(annotation);
    root.setStructuredAnnotations(annotations);
    omexmlMeta.setRoot(root);
}

Example 5 with OMEXMLMetadataRoot

use of ome.xml.meta.OMEXMLMetadataRoot in project bioformats by openmicroscopy.

the class OMEXMLServiceImpl method createRoot.

/**
 * Constructs an OME root node. <b>NOTE:</b> This method is mostly here to
 * ensure type safety of return values as instances of service dependency
 * classes should not leak out of the interface.
 * @param xml String of XML to create the root node from.
 * @return An ome.xml.model.OMEModelObject subclass root node.
 * @throws IOException If there is an error reading from the string.
 * @throws SAXException If there is an error parsing the XML.
 * @throws ParserConfigurationException If there is an error preparing the
 * parsing infrastructure.
 */
private OMEXMLMetadataRoot createRoot(String xml) throws ServiceException {
    try {
        OMEModel model = new OMEModelImpl();
        OMEXMLMetadataRoot ome = new OMEXMLMetadataRoot(XMLTools.parseDOM(xml).getDocumentElement(), model);
        model.resolveReferences();
        return ome;
    } catch (Exception e) {
        throw new ServiceException(e);
    }
}