Examples with Annotation ome.xml.model.Annotation used on opensource projects

Example 1 with Annotation

use of ome.xml.model.Annotation 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 2 with Annotation

use of ome.xml.model.Annotation in project bioformats by openmicroscopy.

the class InOutCurrentTest method testValidInstrumentAnnotation.

@Test(dependsOnMethods = { "testValidInstrumentNode" })
public void testValidInstrumentAnnotation() {
    Annotation n = ome.getInstrument(0).getLinkedAnnotation(0);
    assertNotNull(n);
    assertEquals(INSTRUMENT_ANNOTATION_ID, n.getID());
    assertEquals(n.getNamespace(), GENERAL_ANNOTATION_NAMESPACE);
    assertTrue(n instanceof CommentAnnotation);
    CommentAnnotation string = (CommentAnnotation) n;
    assertEquals(INSTRUMENT_ANNOTATION_VALUE, string.getValue());
}

Example 3 with Annotation

use of ome.xml.model.Annotation in project bioformats by openmicroscopy.

the class InOutCurrentTest method testValidROIAnnotation.

@Test(dependsOnMethods = { "testValidROINode" })
public void testValidROIAnnotation() {
    Annotation n = ome.getROI(0).getLinkedAnnotation(0);
    assertNotNull(n);
    assertEquals(ROI_ANNOTATION_ID, n.getID());
    assertEquals(n.getNamespace(), GENERAL_ANNOTATION_NAMESPACE);
    assertTrue(n instanceof CommentAnnotation);
    CommentAnnotation string = (CommentAnnotation) n;
    assertEquals(ROI_ANNOTATION_VALUE, string.getValue());
}

Example 4 with Annotation

use of ome.xml.model.Annotation in project bioformats by openmicroscopy.

the class InOutCurrentTest method testValidDichroicAnnotation.

@Test(dependsOnMethods = { "testValidDichroicNode" })
public void testValidDichroicAnnotation() {
    Annotation n = ome.getInstrument(0).getDichroic(0).getLinkedAnnotation(0);
    assertNotNull(n);
    assertEquals(DICHROIC_ANNOTATION_ID, n.getID());
    assertEquals(n.getNamespace(), GENERAL_ANNOTATION_NAMESPACE);
    assertTrue(n instanceof CommentAnnotation);
    CommentAnnotation string = (CommentAnnotation) n;
    assertEquals(DICHROIC_ANNOTATION_VALUE, string.getValue());
}

Example 5 with Annotation

use of ome.xml.model.Annotation in project bioformats by openmicroscopy.

the class InOutCurrentTest method testValidImageAnnotation.

@Test(dependsOnMethods = { "testValidImageNode" })
public void testValidImageAnnotation() {
    Annotation n = ome.getImage(0).getLinkedAnnotation(0);
    assertNotNull(n);
    assertEquals(ListAnnotation.class, n.getClass());
    ListAnnotation l = (ListAnnotation) n;
    assertEquals(l.getID(), IMAGE_LIST_ANNOTATION_ID);
    assertEquals(l.getNamespace(), GENERAL_ANNOTATION_NAMESPACE);
    Annotation n2 = l.getLinkedAnnotation(0);
    assertEquals(BooleanAnnotation.class, n2.getClass());
    BooleanAnnotation b = (BooleanAnnotation) n2;
    assertEquals(b.getValue(), IMAGE_ANNOTATION_VALUE);
    assertEquals(b.getNamespace(), GENERAL_ANNOTATION_NAMESPACE);
    assertEquals(b.getID(), IMAGE_ANNOTATION_ID);
}