Examples with OMEXMLMetadata loci.formats.ome.OMEXMLMetadata used on opensource projects

Example 1 with OMEXMLMetadata

use of loci.formats.ome.OMEXMLMetadata 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 OMEXMLMetadata

use of loci.formats.ome.OMEXMLMetadata 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 3 with OMEXMLMetadata

use of loci.formats.ome.OMEXMLMetadata in project bioformats by openmicroscopy.

the class TrestleReader method initMetadataStore.

/* @see loci.formats.BaseTiffReader#initMetadataStore() */
@Override
protected void initMetadataStore() throws FormatException {
    super.initMetadataStore();
    MetadataStore store = makeFilterMetadata();
    for (int i = 0; i < getSeriesCount(); i++) {
        store.setImageName("Series " + (i + 1), i);
    }
    MetadataLevel level = getMetadataOptions().getMetadataLevel();
    if (level != MetadataLevel.MINIMUM) {
        // will not be stored with the mask dimensions
        if (level != MetadataLevel.NO_OVERLAYS && !(getMetadataStore() instanceof OMEXMLMetadata)) {
            try {
                parseROIs(store);
            } catch (IOException e) {
                LOGGER.debug("Could not parse ROIs", e);
            }
        }
    }
}

Example 4 with OMEXMLMetadata

use of loci.formats.ome.OMEXMLMetadata in project bioformats by openmicroscopy.

the class FakeReaderTest method testTwoPlates.

@Test
public void testTwoPlates() throws Exception {
    Location twoPlates = new FakeImage(mkSubd(wd, "2P.fake")).generateScreen(2, 2, 2, 2, 4);
    reader.setId(twoPlates.getAbsolutePath());
    OMEXMLMetadata metadata = reader.getOmeXmlMetadata();
    int i = reader.getImageCount();
    while (i >= 0) {
        assertEquals(metadata.getChannelCount(i--), reader.getSizeC());
    }
}

Example 5 with OMEXMLMetadata

use of loci.formats.ome.OMEXMLMetadata in project bioformats by openmicroscopy.

the class FileExportSPW method initializeMetadata.

/**
 * Populate the minimum amount of metadata required to export a Plate.
 *
 * @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);
        OMEXMLMetadata meta = service.createOMEXMLMetadata();
        meta.createRoot();
        int plateIndex = 0;
        // count of images
        int series = 0;
        int well = 0;
        // Create Minimal 2x2 Plate
        meta.setPlateID(MetadataTools.createLSID("Plate", 0), 0);
        meta.setPlateRowNamingConvention(NamingConvention.LETTER, 0);
        meta.setPlateColumnNamingConvention(NamingConvention.NUMBER, 0);
        meta.setPlateRows(new PositiveInteger(rows), 0);
        meta.setPlateColumns(new PositiveInteger(cols), 0);
        meta.setPlateName("First test Plate", 0);
        PositiveInteger pwidth = new PositiveInteger(width);
        PositiveInteger pheight = new PositiveInteger(height);
        char rowChar = 'A';
        for (int row = 0; row < rows; row++) {
            for (int column = 0; column < cols; column++) {
                // set up well
                String wellID = MetadataTools.createLSID("Well:", well);
                meta.setWellID(wellID, plateIndex, well);
                meta.setWellRow(new NonNegativeInteger(row), plateIndex, well);
                meta.setWellColumn(new NonNegativeInteger(column), plateIndex, well);
                for (int fov = 0; fov < fovPerWell; fov++) {
                    // Create Image
                    String imageName = rowChar + ":" + Integer.toString(column + 1) + ":FOV:" + Integer.toString(fov + 1);
                    String imageID = MetadataTools.createLSID("Image", well, fov);
                    meta.setImageID(imageID, series);
                    meta.setImageName(imageName, series);
                    String pixelsID = MetadataTools.createLSID("Pixels", row, well, fov);
                    meta.setPixelsID(pixelsID, series);
                    // specify that the pixel data is stored in big-endian format
                    // change 'TRUE' to 'FALSE' to specify little-endian format
                    meta.setPixelsBinDataBigEndian(Boolean.TRUE, series, 0);
                    // specify that the image is stored in ZCT order
                    meta.setPixelsDimensionOrder(DimensionOrder.XYZCT, series);
                    // specify the pixel type of the image
                    meta.setPixelsType(PixelType.fromString(FormatTools.getPixelTypeString(pixelType)), series);
                    // specify the dimensions of the image
                    meta.setPixelsSizeX(pwidth, series);
                    meta.setPixelsSizeY(pheight, series);
                    meta.setPixelsSizeZ(new PositiveInteger(1), series);
                    meta.setPixelsSizeC(new PositiveInteger(1), series);
                    meta.setPixelsSizeT(new PositiveInteger(sizeT), series);
                    // define each channel and specify the number of samples in the
                    // channel the number of samples is 3 for RGB images and 1 otherwise
                    String channelID = MetadataTools.createLSID("Channel", well, fov);
                    meta.setChannelID(channelID, series, 0);
                    meta.setChannelSamplesPerPixel(new PositiveInteger(1), series, 0);
                    // set sample
                    String wellSampleID = MetadataTools.createLSID("WellSample", well, fov);
                    meta.setWellSampleID(wellSampleID, 0, well, fov);
                    // NB sampleIndex here == series ie the image No
                    meta.setWellSampleIndex(new NonNegativeInteger(series), 0, well, fov);
                    meta.setWellSampleImageRef(imageID, 0, well, fov);
                    // add FLIM ModuloAlongT annotation if required
                    // CoreMetadata modlo = createModuloAnn();
                    // meta.addModuloAlong(meta, modlo, series);
                    series++;
                }
                // end of samples
                well++;
            }
            rowChar++;
        }
        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;
}