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

Example 16 with OMEXMLMetadata

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

the class OMEXMLServiceTest method testOriginalMetadata.

@Test
public void testOriginalMetadata() throws ServiceException {
    OMEXMLMetadata metadata = service.createOMEXMLMetadata();
    service.populateOriginalMetadata(metadata, "testKey", "testValue");
    Hashtable metadataTable = service.getOriginalMetadata(metadata);
    assertEquals(metadataTable.size(), 1);
    assertTrue("testValue".equals(metadataTable.get("testKey")));
    OME root = (OME) metadata.getRoot();
    StructuredAnnotations annotations = root.getStructuredAnnotations();
    assertEquals(annotations.sizeOfXMLAnnotationList(), 1);
    XMLAnnotation xmlAnn = annotations.getXMLAnnotation(0);
    String txt = "<OriginalMetadata><Key>testKey</Key><Value>testValue</Value></OriginalMetadata>";
    assertEquals(txt, xmlAnn.getValue());
    OriginalMetadataAnnotation omAnn = (OriginalMetadataAnnotation) xmlAnn;
    assertEquals("testValue", omAnn.getValueForKey());
}

Example 17 with OMEXMLMetadata

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

the class OMEXMLServiceTest method testIntegerUnitProperty.

/**
 * Test that the XML serialization of integer unit properties does not
 * include a decimal point. In the schema a shape's font size is
 * {@code type="OME:NonNegativeInt"} which in OMERO is mapped to a
 * {@code double}.
 * @throws ServiceException unexpected
 */
@Test
public void testIntegerUnitProperty() throws ServiceException {
    final Length propertyValue = new Length(12.0d, UNITS.POINT);
    final StringBuffer expectedText = new StringBuffer();
    expectedText.append(" FontSize=");
    expectedText.append('"');
    expectedText.append(propertyValue.value().longValue());
    expectedText.append('"');
    final OMEXMLMetadata metadata = service.createOMEXMLMetadata();
    metadata.setROIID("test ROI", 0);
    metadata.setPointID("test point", 0, 0);
    metadata.setPointX(0.0, 0, 0);
    metadata.setPointY(0.0, 0, 0);
    metadata.setPointFontSize(propertyValue, 0, 0);
    final String xml = service.getOMEXML(metadata);
    assertTrue(xml.contains(expectedText));
}

Example 18 with OMEXMLMetadata

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

the class OMEXMLServiceTest method testFloatingPointUnitProperty.

/**
 * Test that the XML serialization of floating point unit properties
 * includes a decimal point. In the schema a shape's stroke width is
 * {@code type="xsd:float"} which in OMERO is mapped to a {@code double}.
 * @throws ServiceException unexpected
 */
@Test
public void testFloatingPointUnitProperty() throws ServiceException {
    final Length propertyValue = new Length(3.0d, UNITS.PIXEL);
    final StringBuffer expectedText = new StringBuffer();
    expectedText.append(" StrokeWidth=");
    expectedText.append('"');
    expectedText.append(propertyValue.value().doubleValue());
    expectedText.append('"');
    final OMEXMLMetadata metadata = service.createOMEXMLMetadata();
    metadata.setROIID("test ROI", 0);
    metadata.setPointID("test point", 0, 0);
    metadata.setPointX(0.0, 0, 0);
    metadata.setPointY(0.0, 0, 0);
    metadata.setPointStrokeWidth(propertyValue, 0, 0);
    final String xml = service.getOMEXML(metadata);
    assertTrue(xml.contains(expectedText));
}

Example 19 with OMEXMLMetadata

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

the class FileWriteSPW method initializeMetadata.

/**
 * Populate the minimum amount of metadata required to export a Plate.
 */
private IMetadata initializeMetadata(int[][] nFovs) {
    Exception exception = null;
    try {
        // create the OME-XML metadata storage object
        ServiceFactory factory = new ServiceFactory();
        service = factory.getInstance(OMEXMLService.class);
        OMEXMLMetadata meta = service.createOMEXMLMetadata();
        // IMetadata meta = service.createOMEXMLMetadata();
        meta.createRoot();
        int plateIndex = 0;
        // count of images
        int series = 0;
        int well = 0;
        meta.setPlateDescription(plateDescription, 0);
        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);
                int nFOV = nFovs[row][column];
                for (int fov = 0; fov < nFOV; fov++) {
                    // Create Image NB numberng in the Name goes from 1->n not 0-> n-1
                    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", 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.setPixelsBigEndian(Boolean.TRUE, series);
                    // 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);
                    if (exposureTimes != null && exposureTimes.length == sizet) {
                        for (int t = 0; t < sizet; t++) {
                            meta.setPlaneTheT(new NonNegativeInteger(t), series, t);
                            meta.setPlaneTheC(new NonNegativeInteger(0), series, t);
                            meta.setPlaneTheZ(new NonNegativeInteger(0), series, t);
                            meta.setPlaneExposureTime(new Time(exposureTimes[t], ome.units.UNITS.SECOND), series, t);
                        }
                    }
                    // add FLIM ModuloAlongT annotation if required
                    if (delays != null) {
                        CoreMetadata modlo = createModuloAnn(meta);
                        service.addModuloAlong(meta, modlo, series);
                    }
                    series++;
                }
                // end of samples
                well++;
            }
            rowChar++;
        }
        expectedImages = new int[series];
        // System.out.println(dump);
        return meta;
    } catch (DependencyException | ServiceException | EnumerationException e) {
        exception = e;
    }
    System.err.println("Failed to populate OME-XML metadata object.");
    return null;
}

Example 20 with OMEXMLMetadata

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

the class OMEXMLReader method initFile.

// -- Internal FormatReader API methods --
/* @see loci.formats.FormatReader#initFile(String) */
@Override
protected void initFile(String id) throws FormatException, IOException {
    super.initFile(id);
    in = new RandomAccessInputStream(id);
    in.setEncoding("ASCII");
    binData = new ArrayList<BinData>();
    binDataOffsets = new ArrayList<Long>();
    compression = new ArrayList<String>();
    DefaultHandler handler = new OMEXMLHandler();
    try {
        RandomAccessInputStream s = new RandomAccessInputStream(id);
        XMLTools.parseXML(s, handler);
        s.close();
    } catch (IOException e) {
        throw new FormatException("Malformed OME-XML", e);
    }
    int lineNumber = 1;
    for (BinData bin : binData) {
        int line = bin.getRow();
        int col = bin.getColumn();
        while (lineNumber < line) {
            in.readLine();
            lineNumber++;
        }
        binDataOffsets.add(in.getFilePointer() + col - 1);
    }
    LOGGER.info("Populating metadata");
    OMEXMLMetadata omexmlMeta;
    OMEXMLService service;
    try {
        ServiceFactory factory = new ServiceFactory();
        service = factory.getInstance(OMEXMLService.class);
        omexmlMeta = service.createOMEXMLMetadata(omexml);
    } catch (DependencyException de) {
        throw new MissingLibraryException(OMEXMLServiceImpl.NO_OME_XML_MSG, de);
    } catch (ServiceException se) {
        throw new FormatException(se);
    }
    hasSPW = omexmlMeta.getPlateCount() > 0;
    // TODO
    // Hashtable originalMetadata = omexmlMeta.getOriginalMetadata();
    // if (originalMetadata != null) metadata = originalMetadata;
    int numDatasets = omexmlMeta.getImageCount();
    int oldSeries = getSeries();
    core.clear();
    for (int i = 0; i < numDatasets; i++) {
        CoreMetadata ms = new CoreMetadata();
        core.add(ms);
        setSeries(i);
        Integer w = omexmlMeta.getPixelsSizeX(i).getValue();
        Integer h = omexmlMeta.getPixelsSizeY(i).getValue();
        Integer t = omexmlMeta.getPixelsSizeT(i).getValue();
        Integer z = omexmlMeta.getPixelsSizeZ(i).getValue();
        Integer c = omexmlMeta.getPixelsSizeC(i).getValue();
        if (w == null || h == null || t == null || z == null | c == null) {
            throw new FormatException("Image dimensions not found");
        }
        Boolean endian = null;
        if (binData.size() > 0) {
            endian = false;
            if (omexmlMeta.getPixelsBigEndian(i) != null) {
                endian = omexmlMeta.getPixelsBigEndian(i).booleanValue();
            } else if (omexmlMeta.getPixelsBinDataCount(i) != 0) {
                endian = omexmlMeta.getPixelsBinDataBigEndian(i, 0).booleanValue();
            }
        }
        String pixType = omexmlMeta.getPixelsType(i).toString();
        ms.dimensionOrder = omexmlMeta.getPixelsDimensionOrder(i).toString();
        ms.sizeX = w.intValue();
        ms.sizeY = h.intValue();
        ms.sizeT = t.intValue();
        ms.sizeZ = z.intValue();
        ms.sizeC = c.intValue();
        ms.imageCount = getSizeZ() * getSizeC() * getSizeT();
        ms.littleEndian = endian == null ? false : !endian.booleanValue();
        ms.rgb = false;
        ms.interleaved = false;
        ms.indexed = false;
        ms.falseColor = true;
        ms.pixelType = FormatTools.pixelTypeFromString(pixType);
        ms.orderCertain = true;
        if (omexmlMeta.getPixelsSignificantBits(i) != null) {
            ms.bitsPerPixel = omexmlMeta.getPixelsSignificantBits(i).getValue();
        }
    }
    setSeries(oldSeries);
    // populate assigned metadata store with the
    // contents of the internal OME-XML metadata object
    MetadataStore store = getMetadataStore();
    service.convertMetadata(omexmlMeta, store);
    MetadataTools.populatePixels(store, this, false, false);
}