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

Example 6 with ServiceException

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

the class OMEXMLServiceImpl method createRoot.

/**
 * Constructs an OME root node. <b>NOTE:</b> This method is mostly here to
 * ensure type safety of return values as instances of service dependency
 * classes should not leak out of the interface.
 * @param xml String of XML to create the root node from.
 * @return An ome.xml.model.OMEModelObject subclass root node.
 * @throws IOException If there is an error reading from the string.
 * @throws SAXException If there is an error parsing the XML.
 * @throws ParserConfigurationException If there is an error preparing the
 * parsing infrastructure.
 */
private OMEXMLMetadataRoot createRoot(String xml) throws ServiceException {
    try {
        OMEModel model = new OMEModelImpl();
        OMEXMLMetadataRoot ome = new OMEXMLMetadataRoot(XMLTools.parseDOM(xml).getDocumentElement(), model);
        model.resolveReferences();
        return ome;
    } catch (Exception e) {
        throw new ServiceException(e);
    }
}

Example 7 with ServiceException

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

the class ImageViewer method open.

/**
 * Opens the given data source using the current format reader.
 */
public void open(String id) {
    wait(true);
    try {
        // Location f = new Location(id);
        // id = f.getAbsolutePath();
        IMetadata meta = null;
        if (omexmlService != null) {
            try {
                meta = omexmlService.createOMEXMLMetadata();
                myReader.setMetadataStore(meta);
            } catch (ServiceException exc) {
                LOGGER.debug("Could not create OME-XML metadata", exc);
            }
        }
        if (meta == null) {
            LOGGER.info("OME metadata unavailable");
        }
        myReader.setId(id);
        int num = myReader.getImageCount();
        ProgressMonitor progress = new ProgressMonitor(this, "Reading " + id, null, 0, num + 1);
        sizeZ = myReader.getSizeZ();
        sizeT = myReader.getSizeT();
        sizeC = myReader.getEffectiveSizeC();
        // if (myReader.isRGB(id)) sizeC = (sizeC + 2) / 3; // adjust for RGB
        progress.setProgress(1);
        BufferedImage[] img = new BufferedImage[num];
        for (int i = 0; i < num; i++) {
            if (progress.isCanceled())
                break;
            img[i] = myReader.openImage(i);
            if (i == 0)
                setImages(myReader, img);
            progress.setProgress(i + 2);
        }
        myReader.close(true);
    } catch (FormatException exc) {
        LOGGER.info("", exc);
        wait(false);
        return;
    } catch (IOException exc) {
        LOGGER.info("", exc);
        wait(false);
        return;
    }
    wait(false);
}

Example 8 with ServiceException

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

the class PrintROIs method main.

public static void main(String[] args) throws Exception {
    ImageReader reader = new ImageReader();
    IMetadata omexml;
    try {
        ServiceFactory factory = new ServiceFactory();
        OMEXMLService service = factory.getInstance(OMEXMLService.class);
        omexml = 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(omexml);
    reader.setId(args[0]);
    printAllROIs(omexml);
    System.out.println();
    for (int series = 0; series < reader.getSeriesCount(); series++) {
        printSeriesROIs(omexml, series);
    }
    reader.close();
}

Example 9 with ServiceException

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

the class NetCDFServiceImpl method getArray.

/* (non-Javadoc)
   * @see loci.formats.NetCDFService#getArray(java.lang.String, int[], int[])
   */
@Override
public Object getArray(String path, int[] origin, int[] shape) throws ServiceException {
    String groupName = getDirectory(path);
    String variableName = getName(path);
    Group group = getGroup(groupName);
    Variable variable = group.findVariable(variableName);
    try {
        if (origin != null && shape != null) {
            return variable.read(origin, shape).reduce().copyToNDJavaArray();
        }
        return variable.read().copyToNDJavaArray();
    } catch (InvalidRangeException e) {
        throw new ServiceException(e);
    } catch (IOException e) {
        throw new ServiceException(e);
    } catch (NullPointerException e) {
        return null;
    }
}

Example 10 with ServiceException

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

the class CellWorxReader method getReader.

private IFormatReader getReader(String file, boolean omexml) throws FormatException, IOException {
    IFormatReader pnl = new DeltavisionReader();
    if (checkSuffix(file, "tif")) {
        pnl = new MetamorphReader();
    }
    if (omexml) {
        IMetadata metadata;
        try {
            metadata = service.createOMEXMLMetadata();
        } catch (ServiceException exc) {
            throw new FormatException("Could not create OME-XML store.", exc);
        }
        pnl.setMetadataStore(metadata);
    }
    pnl.setId(file);
    return pnl;
}