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

Example 21 with DependencyException

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

the class FileExport method initializeMetadata.

/**
 * Populate the minimum amount of metadata required to export an image.
 *
 * @param width the width (in pixels) of the image
 * @param height the height (in pixels) of the image
 * @param pixelType the pixel type of the image; @see loci.formats.FormatTools
 */
private IMetadata initializeMetadata(int width, int height, int pixelType) {
    Exception exception = null;
    try {
        // create the OME-XML metadata storage object
        ServiceFactory factory = new ServiceFactory();
        OMEXMLService service = factory.getInstance(OMEXMLService.class);
        IMetadata meta = service.createOMEXMLMetadata();
        meta.createRoot();
        // define each stack of images - this defines a single stack of images
        meta.setImageID("Image:0", 0);
        meta.setPixelsID("Pixels:0", 0);
        // specify that the pixel data is stored in big-endian format
        // change 'TRUE' to 'FALSE' to specify little-endian format
        meta.setPixelsBinDataBigEndian(Boolean.TRUE, 0, 0);
        // specify that the images are stored in ZCT order
        meta.setPixelsDimensionOrder(DimensionOrder.XYZCT, 0);
        // specify that the pixel type of the images
        meta.setPixelsType(PixelType.fromString(FormatTools.getPixelTypeString(pixelType)), 0);
        // specify the dimensions of the images
        meta.setPixelsSizeX(new PositiveInteger(width), 0);
        meta.setPixelsSizeY(new PositiveInteger(height), 0);
        meta.setPixelsSizeZ(new PositiveInteger(1), 0);
        meta.setPixelsSizeC(new PositiveInteger(1), 0);
        meta.setPixelsSizeT(new PositiveInteger(1), 0);
        // define each channel and specify the number of samples in the channel
        // the number of samples is 3 for RGB images and 1 otherwise
        meta.setChannelID("Channel:0:0", 0, 0);
        meta.setChannelSamplesPerPixel(new PositiveInteger(1), 0, 0);
        return meta;
    } catch (DependencyException e) {
        exception = e;
    } catch (ServiceException e) {
        exception = e;
    } catch (EnumerationException e) {
        exception = e;
    }
    System.err.println("Failed to populate OME-XML metadata object.");
    exception.printStackTrace();
    return null;
}

Example 22 with DependencyException

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

the class OBFReader method initFile.

@Override
protected void initFile(String id) throws FormatException, IOException {
    super.initFile(id);
    currentInflatedFrame.series = -1;
    currentInflatedFrame.number = -1;
    in = new RandomAccessInputStream(id);
    file_version = getFileVersion(in);
    long stackPosition = in.readLong();
    final int lengthOfDescription = in.readInt();
    final String description = in.readString(lengthOfDescription);
    metadata.put("Description", description);
    if (file_version >= 2) {
        final long meta_data_position = in.readLong();
        final long current_position = in.getFilePointer();
        in.seek(meta_data_position);
        for (String key = readString(); key.length() > 0; key = readString()) {
            if (key.equals("ome_xml")) {
                final String ome_xml = readString();
                try {
                    ServiceFactory factory = new ServiceFactory();
                    OMEXMLService service = factory.getInstance(OMEXMLService.class);
                    if (service.validateOMEXML(ome_xml)) {
                        ome_meta_data = service.createOMEXMLMetadata(ome_xml);
                        for (int image = 0; image != ome_meta_data.getImageCount(); ++image) {
                            if (ome_meta_data.getPixelsBigEndian(image) == null) {
                                ome_meta_data.setPixelsBigEndian(Boolean.FALSE, image);
                            }
                            int channels = ome_meta_data.getChannelCount(image);
                            for (int channel = 0; channel != channels; ++channel) {
                                if (ome_meta_data.getChannelSamplesPerPixel(image, channel) == null) {
                                    ome_meta_data.setChannelSamplesPerPixel(new PositiveInteger(1), image, channel);
                                }
                            }
                        }
                        service.convertMetadata(ome_meta_data, metadataStore);
                        OMEXMLMetadata reference = service.getOMEMetadata(service.asRetrieve(metadataStore));
                        for (int image = 0; image != ome_meta_data.getImageCount(); ++image) {
                            service.addMetadataOnly(reference, image);
                        }
                    }
                } catch (DependencyException exception) {
                    throw new MissingLibraryException(OMEXMLServiceImpl.NO_OME_XML_MSG, exception);
                } catch (ServiceException exception) {
                    throw new FormatException(exception);
                } catch (Exception e) {
                    LOGGER.warn("Could not parse OME-XML metadata", e);
                }
                break;
            } else {
                addGlobalMeta(key, readString());
            }
        }
        in.seek(current_position);
    }
    if (stackPosition != 0) {
        core.clear();
        do {
            stackPosition = initStack(stackPosition);
        } while (stackPosition != 0);
    }
    if (ome_meta_data == null) {
        MetadataTools.populatePixels(metadataStore, this);
        for (int image = 0; image != core.size(); ++image) {
            CoreMetadata meta_data = core.get(image);
            final String name = meta_data.seriesMetadata.get("Name").toString();
            metadataStore.setImageName(name, image);
            @SuppressWarnings("unchecked") final List<Double> lengths = (List<Double>) meta_data.seriesMetadata.get("Lengths");
            if (lengths.size() > 0) {
                double lengthX = Math.abs(lengths.get(0));
                if (lengthX < 0.01) {
                    lengthX *= 1000000;
                }
                if (lengthX > 0) {
                    Length physicalSizeX = FormatTools.getPhysicalSizeX(lengthX / meta_data.sizeX, UNITS.MICROMETER);
                    if (physicalSizeX != null) {
                        metadataStore.setPixelsPhysicalSizeX(physicalSizeX, image);
                    }
                }
            }
            if (lengths.size() > 1) {
                double lengthY = Math.abs(lengths.get(1));
                if (lengthY < 0.01) {
                    lengthY *= 1000000;
                }
                if (lengthY > 0) {
                    Length physicalSizeY = FormatTools.getPhysicalSizeY(lengthY / meta_data.sizeY, UNITS.MICROMETER);
                    if (physicalSizeY != null) {
                        metadataStore.setPixelsPhysicalSizeY(physicalSizeY, image);
                    }
                }
            }
            if (lengths.size() > 2) {
                double lengthZ = Math.abs(lengths.get(2));
                if (lengthZ < 0.01) {
                    lengthZ *= 1000000;
                }
                if (lengthZ > 0) {
                    Length physicalSizeZ = FormatTools.getPhysicalSizeZ(lengthZ / meta_data.sizeZ, UNITS.MICROMETER);
                    if (physicalSizeZ != null) {
                        metadataStore.setPixelsPhysicalSizeZ(physicalSizeZ, image);
                    }
                }
            }
        }
    }
}

Example 23 with DependencyException

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

the class OMETiffReader method setupService.

private void setupService() throws FormatException {
    try {
        ServiceFactory factory = new ServiceFactory();
        service = factory.getInstance(OMEXMLService.class);
    } catch (DependencyException de) {
        throw new MissingLibraryException(OMEXMLServiceImpl.NO_OME_XML_MSG, de);
    }
}

Example 24 with DependencyException

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

the class OMETiffWriter method close.

// -- IFormatHandler API methods --
/* @see loci.formats.IFormatHandler#close() */
@Override
public void close() throws IOException {
    try {
        if (currentId != null) {
            setupServiceAndMetadata();
            // remove any BinData and old TiffData elements from the OME-XML
            service.removeBinData(omeMeta);
            service.removeTiffData(omeMeta);
            for (int series = 0; series < omeMeta.getImageCount(); series++) {
                setSeries(series);
                populateImage(omeMeta, series);
            }
            String companion = getCompanion();
            String companionUUID = null;
            if (null != companion) {
                String companionXML = getOMEXML(companion);
                PrintWriter out = new PrintWriter(companion, Constants.ENCODING);
                out.println(XMLTools.indentXML(companionXML, true));
                out.close();
                companionUUID = "urn:uuid:" + getUUID(new Location(companion).getName());
            }
            List<String> files = new ArrayList<String>();
            for (String[] s : imageLocations) {
                for (String f : s) {
                    if (!files.contains(f) && f != null) {
                        files.add(f);
                        String xml = null;
                        if (null != companion) {
                            xml = getBinaryOnlyOMEXML(f, companion, companionUUID);
                        } else {
                            xml = getOMEXML(f);
                        }
                        xml = insertWarningComment(xml);
                        if (getMetadataOptions().isValidate()) {
                            service.validateOMEXML(xml);
                        }
                        // write OME-XML to the first IFD's comment
                        saveComment(f, xml);
                    }
                }
            }
        }
    } catch (DependencyException de) {
        throw new RuntimeException(de);
    } catch (ServiceException se) {
        throw new RuntimeException(se);
    } catch (FormatException fe) {
        throw new RuntimeException(fe);
    } catch (IllegalArgumentException iae) {
        throw new RuntimeException(iae);
    } finally {
        super.close();
        boolean canReallyClose = omeMeta == null || ifdCounts.size() == omeMeta.getImageCount();
        if (omeMeta != null && canReallyClose) {
            int omePlaneCount = 0;
            for (int i = 0; i < omeMeta.getImageCount(); i++) {
                int sizeZ = omeMeta.getPixelsSizeZ(i).getValue();
                int sizeC = omeMeta.getPixelsSizeC(i).getValue();
                int sizeT = omeMeta.getPixelsSizeT(i).getValue();
                omePlaneCount += sizeZ * sizeC * sizeT;
            }
            int ifdCount = 0;
            for (String key : ifdCounts.keySet()) {
                ifdCount += ifdCounts.get(key);
            }
            canReallyClose = omePlaneCount == ifdCount;
        }
        if (canReallyClose) {
            imageLocations = null;
            omeMeta = null;
            service = null;
            ifdCounts.clear();
        } else {
            for (String k : ifdCounts.keySet()) ifdCounts.put(k, 0);
        }
    }
}

Example 25 with DependencyException

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

the class ConversionTest method createMetadata.

private IMetadata createMetadata(String pixelType, int rgbChannels, int seriesCount, boolean littleEndian) throws Exception {
    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);
    }
    for (int i = 0; i < seriesCount; i++) {
        MetadataTools.populateMetadata(metadata, i, "image #" + i, littleEndian, "XYCZT", pixelType, WIDTH, HEIGHT, 1, rgbChannels, 1, rgbChannels);
    }
    return metadata;
}