Examples with ServiceFactory loci.common.services.ServiceFactory used on opensource projects

Example 81 with ServiceFactory

use of loci.common.services.ServiceFactory 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);
}

Example 82 with ServiceFactory

use of loci.common.services.ServiceFactory in project bioformats by openmicroscopy.

the class OMEXMLWriter method setId.

// -- FormatWriter API methods --
/* @see loci.formats.FormatWriter#setId(String) */
@Override
public void setId(String id) throws FormatException, IOException {
    if (id.equals(currentId)) {
        return;
    }
    super.setId(id);
    MetadataRetrieve retrieve = getMetadataRetrieve();
    String xml;
    try {
        ServiceFactory factory = new ServiceFactory();
        service = factory.getInstance(OMEXMLService.class);
        xml = service.getOMEXML(retrieve);
        OMEXMLMetadata noBin = service.createOMEXMLMetadata(xml);
        service.removeBinData(noBin);
        OMEXMLMetadataRoot root = (OMEXMLMetadataRoot) noBin.getRoot();
        root.setCreator(FormatTools.CREATOR);
        xml = service.getOMEXML(noBin);
    } catch (DependencyException de) {
        throw new MissingLibraryException(OMEXMLServiceImpl.NO_OME_XML_MSG, de);
    } catch (ServiceException se) {
        throw new FormatException(se);
    }
    xmlFragments = new ArrayList<String>();
    currentFragment = "<?xml version=\"1.0\" encoding=\"UTF-8\"?>";
    XMLTools.parseXML(xml, new OMEHandler());
    xmlFragments.add(currentFragment);
}

Example 83 with ServiceFactory

use of loci.common.services.ServiceFactory in project bioformats by openmicroscopy.

the class EightBitLosslessJPEG2000Test method setUp.

@BeforeMethod
public void setUp() throws Exception {
    for (byte v = Byte.MIN_VALUE; v < Byte.MAX_VALUE; v++) {
        int index = v + Byte.MAX_VALUE + 1;
        pixels[index][0] = v;
        String file = index + ".jp2";
        File tempFile = File.createTempFile("test", ".jp2");
        tempFile.deleteOnExit();
        Location.mapId(file, tempFile.getAbsolutePath());
        files.add(file);
        IMetadata metadata;
        try {
            ServiceFactory factory = new ServiceFactory();
            OMEXMLService service = factory.getInstance(OMEXMLService.class);
            metadata = service.createOMEXMLMetadata();
        } catch (DependencyException exc) {
            throw new FormatException("Could not create OME-XML store.", exc);
        } catch (ServiceException exc) {
            throw new FormatException("Could not create OME-XML store.", exc);
        }
        MetadataTools.populateMetadata(metadata, 0, "foo", false, "XYCZT", "uint8", 1, 1, 1, 1, 1, 1);
        IFormatWriter writer = new JPEG2000Writer();
        writer.setMetadataRetrieve(metadata);
        writer.setId(file);
        writer.saveBytes(0, pixels[index]);
        writer.close();
    }
}

Example 84 with ServiceFactory

use of loci.common.services.ServiceFactory in project bioformats by openmicroscopy.

the class OMETiffWriter method getBinaryOnlyOMEXML.

private String getBinaryOnlyOMEXML(String file, String companion, String companionUUID) throws FormatException, IOException, DependencyException, ServiceException {
    ServiceFactory factory = new ServiceFactory();
    OMEXMLService service = factory.getInstance(OMEXMLService.class);
    OMEXMLMetadata meta = service.createOMEXMLMetadata();
    String uuid = "urn:uuid:" + getUUID(new Location(file).getName());
    meta.setUUID(uuid);
    meta.setBinaryOnlyMetadataFile(new Location(companion).getName());
    meta.setBinaryOnlyUUID(companionUUID);
    OMEXMLMetadataRoot root = (OMEXMLMetadataRoot) meta.getRoot();
    root.setCreator(FormatTools.CREATOR);
    return service.getOMEXML(meta);
}

Example 85 with ServiceFactory

use of loci.common.services.ServiceFactory in project bioformats by openmicroscopy.

the class OMETiffWriter method setupServiceAndMetadata.

private void setupServiceAndMetadata() throws DependencyException, ServiceException {
    // extract OME-XML string from metadata object
    MetadataRetrieve retrieve = getMetadataRetrieve();
    ServiceFactory factory = new ServiceFactory();
    service = factory.getInstance(OMEXMLService.class);
    OMEXMLMetadata originalOMEMeta = service.getOMEMetadata(retrieve);
    originalOMEMeta.resolveReferences();
    String omexml = service.getOMEXML(originalOMEMeta);
    omeMeta = service.createOMEXMLMetadata(omexml);
}