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

Example 71 with ServiceFactory

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

the class PrintTimestamps method main.

public static void main(String[] args) throws Exception {
    // parse command line arguments
    if (args.length < 1) {
        System.err.println("Usage: java PrintTimestamps imageFile [seriesNo]");
        System.exit(1);
    }
    String id = args[0];
    int series = args.length > 1 ? Integer.parseInt(args[1]) : 0;
    // enable debugging
    // FormatReader.debug = true;
    // create OME-XML metadata store of the latest schema version
    ServiceFactory factory = new ServiceFactory();
    OMEXMLService service = factory.getInstance(OMEXMLService.class);
    IMetadata meta = service.createOMEXMLMetadata();
    // or if you want a specific schema version, you can use:
    // IMetadata meta = service.createOMEXMLMetadata(null, "2009-02");
    // meta.createRoot();
    // create format reader
    IFormatReader reader = new ImageReader();
    reader.setMetadataStore(meta);
    // initialize file
    System.out.println("Initializing " + id);
    reader.setId(id);
    int seriesCount = reader.getSeriesCount();
    if (series < seriesCount)
        reader.setSeries(series);
    series = reader.getSeries();
    System.out.println("\tImage series = " + series + " of " + seriesCount);
    printDimensions(reader);
    printGlobalTiming(meta, series);
    printTimingPerTimepoint(meta, series);
    printTimingPerPlane(meta, series);
}

Example 72 with ServiceFactory

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

the class VeecoReader method initFile.

// -- Internal FormatReader API methods --
/* @see loci.formats.FormatReader#initFile(String) */
protected void initFile(String id) throws FormatException, IOException {
    super.initFile(id);
    CoreMetadata m = core.get(0);
    try {
        ServiceFactory factory = new ServiceFactory();
        netcdf = factory.getInstance(NetCDFService.class);
        netcdf.setFile(id);
    } catch (DependencyException e) {
        throw new MissingLibraryException(e);
    }
    Vector<String> variableList = netcdf.getVariableList();
    if (variableList.size() == 0) {
        throw new FormatException("No image data found");
    }
    String imageName = variableList.get(0);
    try {
        image = netcdf.getVariableValue(imageName);
    } catch (ServiceException e) {
        throw new FormatException("Could not retrieve image data", e);
    }
    Hashtable<String, Object> attributes = netcdf.getVariableAttributes(imageName);
    for (String attr : attributes.keySet()) {
        addGlobalMeta(attr, attributes.get(attr));
    }
    if (image instanceof byte[][]) {
        byte[][] byteImage = (byte[][]) image;
        m.sizeX = byteImage[0].length;
        m.sizeY = byteImage.length;
        m.pixelType = FormatTools.INT8;
    } else if (image instanceof short[][]) {
        short[][] shortImage = (short[][]) image;
        m.sizeX = shortImage[0].length;
        m.sizeY = shortImage.length;
        m.pixelType = FormatTools.INT16;
        // set the endianness to use when unpacking pixels
        // NetCDF may not return the pixels with a constant endianness,
        // so this ensures that the reader corrects accordingly (see ticket 12085)
        short nativeMin = 0;
        short nativeMax = 0;
        short swappedMin = 0;
        short swappedMax = 0;
        for (int y = 0; y < shortImage.length; y++) {
            for (int x = 0; x < shortImage[y].length; x++) {
                if (shortImage[y][x] < nativeMin) {
                    nativeMin = shortImage[y][x];
                }
                if (shortImage[y][x] > nativeMax) {
                    nativeMax = shortImage[y][x];
                }
                short swapped = DataTools.swap(shortImage[y][x]);
                if (swapped < swappedMin) {
                    swappedMin = swapped;
                }
                if (swapped > swappedMax) {
                    swappedMax = swapped;
                }
            }
        }
        unpackEndian = nativeMin <= swappedMin && nativeMax >= swappedMax;
    }
    m.sizeZ = 1;
    m.sizeC = 1;
    m.sizeT = 1;
    m.imageCount = m.sizeZ * m.sizeC * m.sizeT;
    m.dimensionOrder = "XYCZT";
    m.littleEndian = false;
    MetadataStore store = makeFilterMetadata();
    MetadataTools.populatePixels(store, this);
}

Example 73 with ServiceFactory

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

the class CellH5Writer 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);
    try {
        ServiceFactory factory = new ServiceFactory();
        jhdf = factory.getInstance(JHDFService.class);
        jhdf.setFileForWrite(id);
    } catch (DependencyException e) {
        throw new MissingLibraryException(JHDFServiceImpl.NO_JHDF_MSG, e);
    }
    MetadataRetrieve retrieve = getMetadataRetrieve();
    int sizeX = retrieve.getPixelsSizeX(0).getValue();
    int sizeY = retrieve.getPixelsSizeY(0).getValue();
    int sizeZ = retrieve.getPixelsSizeZ(0).getValue();
    int sizeC = retrieve.getPixelsSizeC(0).getValue();
    int sizeT = retrieve.getPixelsSizeT(0).getValue();
    int type = FormatTools.pixelTypeFromString(retrieve.getPixelsType(0).toString());
    bpp = FormatTools.getBytesPerPixel(type);
    LOGGER.info("CellH5Writer: Found image with dimensions XYZCT {}x{}x{}x{}x{}, and bits per pixel {}", sizeX, sizeY, sizeZ, sizeC, sizeT, bpp);
    String plate = "PLATE_00";
    String well = "WELL_00";
    int site = 1;
    if (retrieve.getPlateCount() > 0) {
        plate = retrieve.getPlateName(0);
        well = retrieve.getWellExternalIdentifier(0, 0);
        site = retrieve.getWellSampleIndex(0, 0, 0).getValue();
        LOGGER.info("CellH5Writer: Found plate information Plate / Well / Site {} / {} / {}", plate, well, site);
    } else {
        LOGGER.info("CellH5Writer: No plate information found. Using default values...");
    }
    jhdf.createGroup(CellH5Constants.DEFINITION + CellH5Reader.CellH5Constants.OBJECT);
    jhdf.createGroup(CellH5Constants.DEFINITION + CellH5Reader.CellH5Constants.FEATURE);
    jhdf.createGroup(CellH5Constants.DEFINITION + CellH5Reader.CellH5Constants.IMAGE);
    outputPath = String.format("/sample/0/plate/%s/experiment/%s/position/%d/image/channel", plate, well, site);
    jhdf.initIntArray(outputPath, new long[] { sizeC, sizeT, sizeZ, sizeY, sizeX }, bpp);
}

Example 74 with ServiceFactory

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

the class WlzWriter method setId.

// -- FormatWriter API methods --
/* @see loci.formats.FormatWriter#setId(String) */
@Override
public void setId(String id) throws FormatException, IOException {
    super.setId(id);
    try {
        ServiceFactory factory = new ServiceFactory();
        wlz = factory.getInstance(WlzService.class);
    } catch (DependencyException e) {
        throw new FormatException(NO_WLZ_MSG, e);
    }
    if (wlz != null) {
        MetadataRetrieve meta = getMetadataRetrieve();
        MetadataTools.verifyMinimumPopulated(meta, series);
        wlz.open(id, "w");
        String stageLabelName = null;
        try {
            stageLabelName = meta.getStageLabelName(0);
        } catch (NullPointerException e) {
        }
        int oX = 0;
        int oY = 0;
        int oZ = 0;
        if ((stageLabelName != null) && stageLabelName.equals(wlz.getWlzOrgLabelName())) {
            final Length stageX = meta.getStageLabelX(0);
            final Length stageY = meta.getStageLabelY(0);
            final Length stageZ = meta.getStageLabelZ(0);
            oX = (int) Math.rint(stageX.value(UNITS.REFERENCEFRAME).doubleValue());
            oY = (int) Math.rint(stageY.value(UNITS.REFERENCEFRAME).doubleValue());
            oZ = (int) Math.rint(stageZ.value(UNITS.REFERENCEFRAME).doubleValue());
        }
        int nX = meta.getPixelsSizeX(series).getValue().intValue();
        int nY = meta.getPixelsSizeY(series).getValue().intValue();
        int nZ = meta.getPixelsSizeZ(series).getValue().intValue();
        int nC = meta.getPixelsSizeC(series).getValue().intValue();
        int nT = meta.getPixelsSizeT(series).getValue().intValue();
        double vX = 1.0;
        double vY = 1.0;
        double vZ = 1.0;
        if (meta.getPixelsPhysicalSizeX(0) != null) {
            vX = meta.getPixelsPhysicalSizeX(0).value(UNITS.MICROMETER).doubleValue();
        }
        if (meta.getPixelsPhysicalSizeY(0) != null) {
            vY = meta.getPixelsPhysicalSizeY(0).value(UNITS.MICROMETER).doubleValue();
        }
        if (meta.getPixelsPhysicalSizeZ(0) != null) {
            vZ = meta.getPixelsPhysicalSizeZ(0).value(UNITS.MICROMETER).doubleValue();
        }
        int gType = FormatTools.pixelTypeFromString(meta.getPixelsType(series).toString());
        wlz.setupWrite(oX, oY, oZ, nX, nY, nZ, nC, nT, vX, vY, vZ, gType);
    }
}

Example 75 with ServiceFactory

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

the class Upgrade200809Test method setUp.

@BeforeMethod
public void setUp() throws Exception {
    ServiceFactory sf = new ServiceFactory();
    service = sf.getInstance(OMEXMLService.class);
    InputStream s = Upgrade200809Test.class.getResourceAsStream(XML_FILE);
    byte[] b = new byte[s.available()];
    s.read(b);
    s.close();
    xml = new String(b);
    metadata = service.createOMEXMLMetadata(xml);
    ome = (OME) metadata.getRoot();
}