Examples with MissingLibraryException loci.formats.MissingLibraryException used on opensource projects

Example 11 with MissingLibraryException

use of loci.formats.MissingLibraryException in project bioformats by openmicroscopy.

the class JPEGXRCodec method initialize.

// -- Helper methods --
/**
 * Initializes the JPEG-XR dependency service. This is called at the
 * beginning of the {@link #decompress} method to avoid having the
 * constructor's method definition contain a checked exception.
 *
 * @throws FormatException If there is an error initializing JPEG-XR
 * services.
 */
private void initialize() throws FormatException {
    if (service != null)
        return;
    try {
        ServiceFactory factory = new ServiceFactory();
        service = factory.getInstance(JPEGXRService.class);
    } catch (DependencyException e) {
        throw new MissingLibraryException("JPEG-XR library not available", e);
    }
}

Example 12 with MissingLibraryException

use of loci.formats.MissingLibraryException 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 13 with MissingLibraryException

use of loci.formats.MissingLibraryException 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 14 with MissingLibraryException

use of loci.formats.MissingLibraryException 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 15 with MissingLibraryException

use of loci.formats.MissingLibraryException in project bioformats by openmicroscopy.

the class TiffJAIReader method initFile.

// -- Internal FormatReader API methods --
/* @see loci.formats.FormatReader#initFile(String) */
@Override
protected void initFile(String id) throws FormatException, IOException {
    LOGGER.info("Checking for JAI");
    try {
        r = new ReflectedUniverse();
        r.exec("import javax.media.jai.NullOpImage");
        r.exec("import javax.media.jai.OpImage");
        r.exec("import com.sun.media.jai.codec.FileSeekableStream");
        r.exec("import com.sun.media.jai.codec.ImageDecoder");
        r.exec("import com.sun.media.jai.codec.ImageCodec");
    } catch (ReflectException exc) {
        throw new MissingLibraryException(NO_JAI_MSG, exc);
    }
    super.initFile(id);
    LOGGER.info("Reading movie dimensions");
    // map Location to File or RandomAccessFile, if possible
    IRandomAccess ira = Location.getMappedFile(id);
    if (ira != null) {
        if (ira instanceof FileHandle) {
            FileHandle fh = (FileHandle) ira;
            r.setVar("file", fh.getRandomAccessFile());
        } else {
            throw new FormatException("Unsupported handle type" + ira.getClass().getName());
        }
    } else {
        String mapId = Location.getMappedId(id);
        File file = new File(mapId);
        if (file.exists()) {
            r.setVar("file", file);
        } else
            throw new FileNotFoundException(id);
    }
    r.setVar("tiff", "tiff");
    r.setVar("param", null);
    // create TIFF decoder
    int numPages;
    try {
        r.exec("s = new FileSeekableStream(file)");
        r.exec("dec = ImageCodec.createImageDecoder(tiff, s, param)");
        numPages = ((Integer) r.exec("dec.getNumPages()")).intValue();
    } catch (ReflectException exc) {
        throw new FormatException(exc);
    }
    if (numPages < 0) {
        throw new FormatException("Invalid page count: " + numPages);
    }
    // decode first image plane
    BufferedImage img = openBufferedImage(0);
    if (img == null)
        throw new FormatException("Invalid image stream");
    LOGGER.info("Populating metadata");
    CoreMetadata m = core.get(0);
    m.imageCount = numPages;
    m.sizeX = img.getWidth();
    m.sizeY = img.getHeight();
    m.sizeZ = 1;
    m.sizeC = img.getSampleModel().getNumBands();
    m.sizeT = numPages;
    m.rgb = m.sizeC > 1;
    m.dimensionOrder = "XYCZT";
    m.pixelType = AWTImageTools.getPixelType(img);
    m.interleaved = true;
    m.littleEndian = false;
    m.metadataComplete = true;
    m.indexed = false;
    m.falseColor = false;
    // populate the metadata store
    MetadataStore store = makeFilterMetadata();
    MetadataTools.populatePixels(store, this);
}