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

Example 36 with DependencyException

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

the class ZeissLSMReader method parseMDB.

/**
 * Parse a .mdb file and return a list of referenced .lsm files.
 */
private String[] parseMDB(String mdbFile) throws FormatException, IOException {
    Location mdb = new Location(mdbFile).getAbsoluteFile();
    Location parent = mdb.getParentFile();
    MDBService mdbService = null;
    try {
        ServiceFactory factory = new ServiceFactory();
        mdbService = factory.getInstance(MDBService.class);
    } catch (DependencyException de) {
        throw new FormatException("MDB Tools Java library not found", de);
    }
    try {
        mdbService.initialize(mdbFile);
    } catch (Exception e) {
        return null;
    }
    Vector<Vector<String[]>> tables = mdbService.parseDatabase();
    mdbService.close();
    final List<String> referencedLSMs = new ArrayList<String>();
    int referenceCount = 0;
    for (Vector<String[]> table : tables) {
        String[] columnNames = table.get(0);
        String tableName = columnNames[0];
        for (int row = 1; row < table.size(); row++) {
            String[] tableRow = table.get(row);
            for (int col = 0; col < tableRow.length; col++) {
                String key = tableName + " " + columnNames[col + 1];
                if (currentId != null) {
                    addGlobalMetaList(key, tableRow[col]);
                }
                if (tableName.equals("Recordings") && columnNames[col + 1] != null && columnNames[col + 1].equals("SampleData")) {
                    String filename = tableRow[col].trim();
                    filename = filename.replace('\\', File.separatorChar);
                    filename = filename.replace('/', File.separatorChar);
                    filename = filename.substring(filename.lastIndexOf(File.separator) + 1);
                    if (filename.length() > 0) {
                        Location file = new Location(parent, filename);
                        if (file.exists()) {
                            referencedLSMs.add(file.getAbsolutePath());
                        }
                    }
                    referenceCount++;
                }
            }
        }
    }
    if (referencedLSMs.size() == referenceCount) {
        return referencedLSMs.toArray(new String[0]);
    }
    String[] fileList = parent.list(true);
    Arrays.sort(fileList);
    for (int i = 0; i < fileList.length; i++) {
        Location f = new Location(fileList[i]);
        if (!f.exists()) {
            f = new Location(parent, fileList[i]);
        }
        String absolutePath = f.getAbsolutePath();
        if (checkSuffix(fileList[i], "mdb") && (!absolutePath.equals(mdbFile) && !fileList[i].equals(mdbFile) && !absolutePath.equals(new Location(mdbFile).getAbsolutePath()))) {
            if (referencedLSMs.size() > 0) {
                return referencedLSMs.toArray(new String[0]);
            }
            break;
        }
    }
    referencedLSMs.clear();
    int mdbCount = 0;
    for (int i = 0; i < fileList.length; i++) {
        String absolutePath = new Location(parent, fileList[i]).getAbsolutePath();
        if (checkSuffix(fileList[i], "lsm")) {
            referencedLSMs.add(absolutePath);
        } else if (checkSuffix(fileList[i], "mdb")) {
            mdbCount++;
        }
    }
    if (mdbCount > 1 || ((referencedLSMs.size() > referenceCount) && mdbCount > 1)) {
        for (int i = 0; i < fileList.length; i++) {
            String absolutePath = new Location(parent, fileList[i]).getAbsolutePath();
            if (checkSuffix(fileList[i], "mdb") && !absolutePath.endsWith(mdbFile)) {
                String[] files = parseMDB(absolutePath);
                for (String f : files) {
                    referencedLSMs.remove(f);
                }
            }
        }
    }
    return referencedLSMs.toArray(new String[0]);
}

Example 37 with DependencyException

use of loci.common.services.DependencyException 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 38 with DependencyException

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

the class MultiFileExportExample method main.

public static void main(String[] args) throws FormatException, IOException {
    if (args.length < 2) {
        System.out.println("Usage: java MultiFileExportExample <infile> <output file extension>");
        System.exit(1);
    }
    ImageReader reader = new ImageReader();
    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);
    }
    reader.setMetadataStore(metadata);
    reader.setId(args[0]);
    ImageWriter writer = new ImageWriter();
    writer.setMetadataRetrieve(metadata);
    String baseFile = args[0].substring(0, args[0].lastIndexOf("."));
    writer.setId(baseFile + "_s0_z0" + args[1]);
    for (int series = 0; series < reader.getSeriesCount(); series++) {
        reader.setSeries(series);
        writer.setSeries(series);
        int planesPerFile = reader.getImageCount() / reader.getSizeZ();
        for (int z = 0; z < reader.getSizeZ(); z++) {
            String file = baseFile + "_s" + series + "_z" + z + args[1];
            writer.changeOutputFile(file);
            for (int image = 0; image < planesPerFile; image++) {
                int[] zct = FormatTools.getZCTCoords(reader.getDimensionOrder(), 1, reader.getEffectiveSizeC(), reader.getSizeT(), planesPerFile, image);
                int index = FormatTools.getIndex(reader, z, zct[1], zct[2]);
                writer.saveBytes(image, reader.openBytes(index));
            }
        }
    }
    reader.close();
    writer.close();
}

Example 39 with DependencyException

use of loci.common.services.DependencyException 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 40 with DependencyException

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