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

Example 26 with ServiceException

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

the class FormatTools method convert.

// -- Conversion convenience methods --
/**
 * Convenience method for converting the specified input file to the
 * specified output file.  The ImageReader and ImageWriter classes are used
 * for input and output, respectively.  To use other IFormatReader or
 * IFormatWriter implementation,
 * @see #convert(IFormatReader, IFormatWriter, String).
 *
 * @param input the full path name of the existing input file
 * @param output the full path name of the output file to be created
 * @throws FormatException if there is a general problem reading from or
 * writing to one of the files.
 * @throws IOException if there is an I/O-related error.
 */
public static void convert(String input, String output) throws FormatException, IOException {
    IFormatReader reader = new ImageReader();
    try {
        ServiceFactory factory = new ServiceFactory();
        OMEXMLService service = factory.getInstance(OMEXMLService.class);
        reader.setMetadataStore(service.createOMEXMLMetadata());
    } catch (DependencyException de) {
        throw new MissingLibraryException(OMEXMLServiceImpl.NO_OME_XML_MSG, de);
    } catch (ServiceException se) {
        throw new FormatException(se);
    }
    reader.setId(input);
    IFormatWriter writer = new ImageWriter();
    convert(reader, writer, output);
}

Example 27 with ServiceException

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

the class MetadataTools method populatePixels.

/**
 * Populates the Pixels element of the given metadata store, using core
 * metadata from the given reader.  If the {@code doPlane} flag is set,
 * then the Plane elements will be populated as well. If the
 * {@code doImageName} flag is set, then the image name will be populated as
 * well.
 *
 * @param store       The metadata store whose Pixels should be populated
 * @param r           The format reader whose core metadata should be used
 * @param doPlane     Specifies whether Plane elements should be populated
 * @param doImageName Specifies whether the Image name should be populated
 */
public static void populatePixels(MetadataStore store, IFormatReader r, boolean doPlane, boolean doImageName) {
    if (store == null || r == null)
        return;
    int oldSeries = r.getSeries();
    for (int i = 0; i < r.getSeriesCount(); i++) {
        r.setSeries(i);
        String imageName = null;
        if (doImageName) {
            Location f = new Location(r.getCurrentFile());
            imageName = f.getName();
            if (r.getSeriesCount() > 1) {
                imageName += " #" + (i + 1);
            }
        }
        String pixelType = FormatTools.getPixelTypeString(r.getPixelType());
        populateMetadata(store, r.getCurrentFile(), i, imageName, r.isLittleEndian(), r.getDimensionOrder(), pixelType, r.getSizeX(), r.getSizeY(), r.getSizeZ(), r.getSizeC(), r.getSizeT(), r.getRGBChannelCount());
        store.setPixelsInterleaved(r.isInterleaved(), i);
        store.setPixelsSignificantBits(new PositiveInteger(r.getBitsPerPixel()), i);
        try {
            OMEXMLService service = new ServiceFactory().getInstance(OMEXMLService.class);
            if (service.isOMEXMLRoot(store.getRoot())) {
                MetadataStore baseStore = r.getMetadataStore();
                if (service.isOMEXMLMetadata(baseStore)) {
                    OMEXMLMetadata omeMeta;
                    try {
                        omeMeta = service.getOMEMetadata(service.asRetrieve(baseStore));
                        if (omeMeta.getTiffDataCount(i) == 0 && omeMeta.getPixelsBinDataCount(i) == 0) {
                            service.addMetadataOnly(omeMeta, i, i == 0);
                        }
                    } catch (ServiceException e) {
                        LOGGER.warn("Failed to add MetadataOnly", e);
                    }
                }
            }
        } catch (DependencyException exc) {
            LOGGER.warn("Failed to add MetadataOnly", exc);
        }
        if (doPlane) {
            for (int q = 0; q < r.getImageCount(); q++) {
                int[] coords = r.getZCTCoords(q);
                store.setPlaneTheZ(new NonNegativeInteger(coords[0]), i, q);
                store.setPlaneTheC(new NonNegativeInteger(coords[1]), i, q);
                store.setPlaneTheT(new NonNegativeInteger(coords[2]), i, q);
            }
        }
    }
    r.setSeries(oldSeries);
}

Example 28 with ServiceException

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

the class OMEXMLServiceImpl method getOMEXML.

/**
 * @see OMEXMLService#getOMEXML(loci.formats.meta.MetadataRetrieve)
 */
@Override
public String getOMEXML(MetadataRetrieve src) throws ServiceException {
    OMEXMLMetadata omexmlMeta = getOMEMetadata(src);
    String xml = omexmlMeta.dumpXML();
    // make sure that the namespace has been set correctly
    // convert XML string to DOM
    Document doc = null;
    Exception exception = null;
    try {
        doc = XMLTools.parseDOM(xml);
    } catch (ParserConfigurationException exc) {
        exception = exc;
    } catch (SAXException exc) {
        exception = exc;
    } catch (IOException exc) {
        exception = exc;
    }
    if (exception != null) {
        LOGGER.info("Malformed OME-XML", exception);
        return null;
    }
    Element root = doc.getDocumentElement();
    root.setAttribute("xmlns", SCHEMA_PATH + getLatestVersion());
    // convert tweaked DOM back to XML string
    try {
        xml = XMLTools.getXML(doc);
    } catch (TransformerConfigurationException exc) {
        exception = exc;
    } catch (TransformerException exc) {
        exception = exc;
    }
    if (exception != null) {
        LOGGER.info("Internal XML conversion error", exception);
        return null;
    }
    return xml;
}

Example 29 with ServiceException

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

the class ImageViewer method actionPerformed.

// -- ActionListener API methods --
/**
 * Handles menu commands.
 */
@Override
public void actionPerformed(ActionEvent e) {
    String cmd = e.getActionCommand();
    if ("open".equals(cmd)) {
        wait(true);
        JFileChooser chooser = GUITools.buildFileChooser(myReader);
        wait(false);
        int rval = chooser.showOpenDialog(this);
        if (rval == JFileChooser.APPROVE_OPTION) {
            final File file = chooser.getSelectedFile();
            if (file != null)
                open(file.getAbsolutePath(), fileReader);
        }
    } else if ("save".equals(cmd)) {
        wait(true);
        JFileChooser chooser = GUITools.buildFileChooser(myWriter);
        wait(false);
        int rval = chooser.showSaveDialog(this);
        if (rval == JFileChooser.APPROVE_OPTION) {
            final File file = chooser.getSelectedFile();
            if (file != null)
                save(file.getAbsolutePath(), fileWriter);
        }
    } else if ("view".equals(cmd)) {
        if (omeMeta != null) {
            XMLWindow metaWindow = new XMLWindow("OME Metadata - " + getTitle());
            metaWindow.setDefaultCloseOperation(XMLWindow.DISPOSE_ON_CLOSE);
            Exception exception = null;
            try {
                MetadataRetrieve retrieve = omexmlService.asRetrieve(omeMeta);
                metaWindow.setXML(omexmlService.getOMEXML(retrieve));
                metaWindow.setVisible(true);
            } catch (ServiceException exc) {
                exception = exc;
            } catch (ParserConfigurationException exc) {
                exception = exc;
            } catch (SAXException exc) {
                exception = exc;
            } catch (IOException exc) {
                exception = exc;
            }
            if (exception != null) {
                LOGGER.info("Cannot display OME metadata", exception);
            }
        }
    } else if ("exit".equals(cmd))
        dispose();
    else if ("fps".equals(cmd)) {
        // HACK - JOptionPane prevents shutdown on dispose
        setDefaultCloseOperation(EXIT_ON_CLOSE);
        String result = JOptionPane.showInputDialog(this, "Animate using space bar. How many frames per second?", "" + fps);
        try {
            fps = Integer.parseInt(result);
        } catch (NumberFormatException exc) {
            LOGGER.debug("Could not parse fps '{}'", fps, exc);
        }
    } else if ("about".equals(cmd)) {
        // HACK - JOptionPane prevents shutdown on dispose
        setDefaultCloseOperation(EXIT_ON_CLOSE);
        String msg = "<html>" + "OME Bio-Formats package for reading and " + "converting biological file formats." + "<br>Copyright (C) 2005 - " + FormatTools.YEAR + " Open Microscopy Environment:" + "<ul>" + "<li>Board of Regents of the University of Wisconsin-Madison</li>" + "<li>Glencoe Software, Inc.</li>" + "<li>University of Dundee</li>" + "</ul>" + "<i>" + FormatTools.URL_BIO_FORMATS + "</i>" + "<br>Version " + FormatTools.VERSION + " (VCS revision " + FormatTools.VCS_REVISION + "), built on " + FormatTools.DATE + "<br><br>See <a href=\"" + "https://docs.openmicroscopy.org/bio-formats/" + FormatTools.VERSION + "/users/index.html\">" + "https://docs.openmicroscopy.org/bio-formats/" + FormatTools.VERSION + "/users/index.html</a>" + "<br>for help with using Bio-Formats.";
        ImageIcon bioFormatsLogo = new ImageIcon(IFormatHandler.class.getResource("bio-formats-logo.png"));
        JOptionPane.showMessageDialog(null, msg, "Bio-Formats", JOptionPane.INFORMATION_MESSAGE, bioFormatsLogo);
    }
}

Example 30 with ServiceException

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

the class ImageViewer method save.

/**
 * Saves the current images to the given destination
 * using the current format writer.
 */
public void save(String id) {
    if (images == null)
        return;
    wait(true);
    try {
        if (omeMeta == null) {
            omeMeta = omexmlService.createOMEXMLMetadata();
            omeMeta.setImageID(MetadataTools.createLSID("Image", 0), 0);
            omeMeta.setPixelsID(MetadataTools.createLSID("Pixels", 0), 0);
            omeMeta.setPixelsBigEndian(false, 0);
            String order = "XYCZT";
            if (in != null)
                order = in.getDimensionOrder();
            omeMeta.setPixelsDimensionOrder((DimensionOrder) new DimensionOrderEnumHandler().getEnumeration(order), 0);
            int type = AWTImageTools.getPixelType(images[0]);
            String pixelType = FormatTools.getPixelTypeString(type);
            omeMeta.setPixelsType((PixelType) new PixelTypeEnumHandler().getEnumeration(pixelType), 0);
            int rgbChannelCount = images[0].getRaster().getNumBands();
            int realChannelCount = sizeC / rgbChannelCount;
            for (int i = 0; i < realChannelCount; i++) {
                omeMeta.setChannelID(MetadataTools.createLSID("Channel", i, 0), 0, i);
                omeMeta.setChannelSamplesPerPixel(new PositiveInteger(rgbChannelCount), 0, i);
            }
            omeMeta.setPixelsSizeX(new PositiveInteger(images[0].getWidth()), 0);
            omeMeta.setPixelsSizeY(new PositiveInteger(images[0].getHeight()), 0);
            omeMeta.setPixelsSizeC(new PositiveInteger(sizeC), 0);
            omeMeta.setPixelsSizeZ(new PositiveInteger(sizeZ), 0);
            omeMeta.setPixelsSizeT(new PositiveInteger(sizeT), 0);
        }
        myWriter.setMetadataRetrieve(omexmlService.asRetrieve(omeMeta));
        myWriter.setId(id);
        boolean stack = myWriter.canDoStacks();
        ProgressMonitor progress = new ProgressMonitor(this, "Saving " + id, null, 0, stack ? images.length : 1);
        if (stack) {
            // save entire stack
            for (int i = 0; i < images.length; i++) {
                progress.setProgress(i);
                boolean canceled = progress.isCanceled();
                myWriter.saveImage(i, images[i]);
                if (canceled)
                    break;
            }
            progress.setProgress(images.length);
        } else {
            // save current image only
            myWriter.savePlane(0, getImage());
            progress.setProgress(1);
        }
        myWriter.close();
    } catch (FormatException exc) {
        LOGGER.info("", exc);
    } catch (IOException exc) {
        LOGGER.info("", exc);
    } catch (ServiceException exc) {
        LOGGER.info("", exc);
    } catch (EnumerationException exc) {
        LOGGER.info("", exc);
    }
    wait(false);
}