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

Example 1 with Image

use of ome.xml.model.Image 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 Image

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

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

the class OMEXMLServiceImpl method removeBinData.

/**
 * @see OMEXMLService#removeBinData(OMEXMLMetadata)
 */
@Override
public void removeBinData(OMEXMLMetadata omexmlMeta) {
    omexmlMeta.resolveReferences();
    OMEXMLMetadataRoot root = (OMEXMLMetadataRoot) omexmlMeta.getRoot();
    List<Image> images = root.copyImageList();
    for (Image img : images) {
        Pixels pix = img.getPixels();
        List<BinData> binData = pix.copyBinDataList();
        for (BinData bin : binData) {
            pix.removeBinData(bin);
        }
        pix.setMetadataOnly(null);
    }
    omexmlMeta.setRoot(root);
}

Example 4 with Image

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

the class InOutCurrentTest method testValidWellSamples.

@Test(dependsOnMethods = { "testValidPlateNode" })
public void testValidWellSamples() {
    Plate plate = ome.getPlate(0);
    Integer wellSampleIndex = 0;
    for (int row = 0; row < plate.getRows().getValue(); row++) {
        for (int col = 0; col < plate.getColumns().getValue(); col++) {
            Well well = plate.getWell(row * plate.getColumns().getValue() + col);
            assertEquals(1, well.sizeOfWellSampleList());
            WellSample sample = well.getWellSample(0);
            assertNotNull(sample);
            assertEquals(String.format("WellSample:%d_%d", row, col), sample.getID());
            assertEquals(wellSampleIndex, sample.getIndex().getValue());
            Image image = sample.getLinkedImage();
            assertNotNull(image);
            assertEquals(IMAGE_ID, image.getID());
            wellSampleIndex++;
        }
    }
}

Example 5 with Image

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

the class ObjectBasedOMEModelMock method makeImage.

private Image makeImage() {
    // Create <Image/>
    Image image = new Image();
    image.setID(InOutCurrentTest.IMAGE_ID);
    ListAnnotation listAnnotation = new ListAnnotation();
    listAnnotation.setID(InOutCurrentTest.IMAGE_LIST_ANNOTATION_ID);
    listAnnotation.setNamespace(InOutCurrentTest.GENERAL_ANNOTATION_NAMESPACE);
    annotations.addListAnnotation(listAnnotation);
    BooleanAnnotation annotation = new BooleanAnnotation();
    annotation.setID(InOutCurrentTest.IMAGE_ANNOTATION_ID);
    annotation.setValue(InOutCurrentTest.IMAGE_ANNOTATION_VALUE);
    annotation.setNamespace(InOutCurrentTest.GENERAL_ANNOTATION_NAMESPACE);
    listAnnotation.linkAnnotation(annotation);
    image.linkAnnotation(listAnnotation);
    annotations.addBooleanAnnotation(annotation);
    // Create <Pixels/>
    Pixels pixels = new Pixels();
    pixels.setID(InOutCurrentTest.PIXELS_ID);
    pixels.setSizeX(new PositiveInteger(InOutCurrentTest.SIZE_X));
    pixels.setSizeY(new PositiveInteger(InOutCurrentTest.SIZE_Y));
    pixels.setSizeZ(new PositiveInteger(InOutCurrentTest.SIZE_Z));
    pixels.setSizeC(new PositiveInteger(InOutCurrentTest.SIZE_C));
    pixels.setSizeT(new PositiveInteger(InOutCurrentTest.SIZE_T));
    pixels.setDimensionOrder(InOutCurrentTest.DIMENSION_ORDER);
    pixels.setType(InOutCurrentTest.PIXEL_TYPE);
    // Create <TiffData/>
    TiffData tiffData = new TiffData();
    // Create <UUID/>
    UUID uuid = new UUID();
    uuid.setValue(InOutCurrentTest.TIFF_DATA_UUID);
    tiffData.setUUID(uuid);
    pixels.addTiffData(tiffData);
    // Create <Channel/> under <Pixels/>
    for (int i = 0; i < InOutCurrentTest.SIZE_C; i++) {
        Channel channel = new Channel();
        channel.setID("Channel:" + i);
        if (i == 0) {
            XMLAnnotation channelAnnotation = new XMLAnnotation();
            channelAnnotation.setID(InOutCurrentTest.CHANNEL_ANNOTATION_ID);
            channelAnnotation.setValue(InOutCurrentTest.CHANNEL_ANNOTATION_VALUE);
            channelAnnotation.setNamespace(InOutCurrentTest.GENERAL_ANNOTATION_NAMESPACE);
            channel.linkAnnotation(channelAnnotation);
            annotations.addXMLAnnotation(channelAnnotation);
        }
        pixels.addChannel(channel);
    }
    // Put <Pixels/> under <Image/>
    image.setPixels(pixels);
    return image;
}