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

Example 1 with StructuredAnnotations

use of ome.xml.model.StructuredAnnotations 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 StructuredAnnotations

use of ome.xml.model.StructuredAnnotations 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 3 with StructuredAnnotations

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

the class OMEXMLServiceImpl method addModuloAlong.

@Override
public void addModuloAlong(OMEXMLMetadata meta, CoreMetadata core, int imageIdx) {
    meta.resolveReferences();
    if (core.moduloZ.length() == 1 && core.moduloC.length() == 1 && core.moduloT.length() == 1) {
        // nothing to populate
        return;
    }
    OMEXMLMetadataRoot root = (OMEXMLMetadataRoot) meta.getRoot();
    Image image;
    try {
        image = root.getImage(imageIdx);
    } catch (IndexOutOfBoundsException ieeb) {
        // and exiting without doing anything.
        return;
    }
    StructuredAnnotations annotations = root.getStructuredAnnotations();
    if (annotations == null)
        annotations = new StructuredAnnotations();
    int annotationIndex = annotations.sizeOfXMLAnnotationList();
    final Set<String> knownModulos = new HashSet<String>();
    if (annotationIndex > 0) {
        // Check which modulo annotations are already present.
        for (int idx = 0; idx < annotationIndex; idx++) {
            if (ModuloAnnotation.MODULO_NS.equals(meta.getXMLAnnotationNamespace(idx))) {
                // ignore this annotation if it is not linked to the current Image
                boolean ignore = true;
                String xmlID = meta.getXMLAnnotationID(idx);
                for (int link = 0; link < image.sizeOfLinkedAnnotationList(); link++) {
                    if (xmlID.equals(image.getLinkedAnnotation(link).getID())) {
                        ignore = false;
                        break;
                    }
                }
                if (ignore) {
                    continue;
                }
                String value = meta.getXMLAnnotationValue(idx);
                try {
                    Document doc = XMLTools.parseDOM(value);
                    NodeList modulos = doc.getElementsByTagName("Modulo");
                    for (int m = 0; m < modulos.getLength(); m++) {
                        Node modulo = modulos.item(m);
                        NodeList children = modulo.getChildNodes();
                        for (int c = 0; c < children.getLength(); c++) {
                            Node child = children.item(c);
                            String name = child.getNodeName();
                            knownModulos.add(name);
                        }
                    }
                } catch (Exception e) {
                    LOGGER.warn("Could not parse XML from annotation: {}", value, e);
                }
            }
        }
        // Calculate the next annotation ID that should be used.
        String lastAnnotationID = meta.getXMLAnnotationID(annotationIndex - 1);
        String lastIndex = lastAnnotationID.substring(lastAnnotationID.lastIndexOf(":") + 1);
        try {
            int index = Integer.parseInt(lastIndex);
            while (index >= annotationIndex) {
                annotationIndex++;
            }
        } catch (NumberFormatException e) {
        }
    }
    int imageAnnotation = 0;
    if (core.moduloZ.length() > 1 && !knownModulos.contains("ModuloAlongZ")) {
        createModulo(meta, core.moduloZ, annotations, image, imageIdx, annotationIndex, imageAnnotation);
        annotationIndex++;
        imageAnnotation++;
    }
    if (core.moduloC.length() > 1 && !knownModulos.contains("ModuloAlongC")) {
        createModulo(meta, core.moduloC, annotations, image, imageIdx, annotationIndex, imageAnnotation);
        annotationIndex++;
        imageAnnotation++;
    }
    if (core.moduloT.length() > 1 && !knownModulos.contains("ModuloAlongT")) {
        createModulo(meta, core.moduloT, annotations, image, imageIdx, annotationIndex, imageAnnotation);
        annotationIndex++;
        imageAnnotation++;
    }
    root.setStructuredAnnotations(annotations);
    meta.setRoot(root);
}

Example 4 with StructuredAnnotations

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

the class FileWriteSPW method cleanup.

/**
 * Close the file writer.
 */
public void cleanup() {
    // No of planes expected for each image = 1 if not FLIM
    int validPlanes = 1;
    if (delays != null) {
        validPlanes = sizet;
    }
    OMEXMLMetadataRoot root = (OMEXMLMetadataRoot) omexml.getRoot();
    Plate plate = root.getPlate(0);
    StructuredAnnotations anns = root.getStructuredAnnotations();
    ArrayList<Image> invalidImages = new ArrayList<>();
    // if not record those images as being invalid
    for (int i = 0; i < expectedImages.length; i++) {
        if (expectedImages[i] < validPlanes) {
            Image im = root.getImage(i);
            invalidImages.add(im);
            // remove modulo Annotation if FLIM
            if (delays != null) {
                XMLAnnotation ann = (XMLAnnotation) im.getLinkedAnnotation(0);
                anns.removeXMLAnnotation(ann);
            }
        }
    }
    // Now remove all limked wellSnmples and then invalid images
    for (int i = 0; i < invalidImages.size(); i++) {
        Image im = invalidImages.get(i);
        List<WellSample> list = im.copyLinkedWellSampleList();
        if (!list.isEmpty()) {
            WellSample wellSample = im.getLinkedWellSample(0);
            Well well = wellSample.getWell();
            well.removeWellSample(wellSample);
        }
        root.removeImage(im);
    }
    if (writer != null) {
        try {
            writer.close();
        } catch (IOException e) {
            System.err.println("Failed to close file writer.");
        }
    }
}

Example 5 with StructuredAnnotations

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

the class Upgrade201004Test method validateUpgrade.

@Test
public void validateUpgrade() throws ServiceException {
    assertEquals(1, ome.sizeOfImageList());
    // StringAnnotation --> CommentAnnotation
    StructuredAnnotations structuredAnnotations = ome.getStructuredAnnotations();
    assertNotNull(structuredAnnotations);
    assertEquals(1, structuredAnnotations.sizeOfCommentAnnotationList());
    CommentAnnotation commentAnnotation = structuredAnnotations.getCommentAnnotation(0);
    assertEquals("StringAnnotation:0", commentAnnotation.getID());
    assertEquals("Transform", commentAnnotation.getNamespace());
    assertEquals("Foobar", commentAnnotation.getValue());
}