Examples with OMEXMLService loci.formats.services.OMEXMLService used on opensource projects

Example 51 with OMEXMLService

use of loci.formats.services.OMEXMLService in project bioformats by openmicroscopy.

the class EightBitLosslessJPEG2000Test method setUp.

@BeforeMethod
public void setUp() throws Exception {
    for (byte v = Byte.MIN_VALUE; v < Byte.MAX_VALUE; v++) {
        int index = v + Byte.MAX_VALUE + 1;
        pixels[index][0] = v;
        String file = index + ".jp2";
        File tempFile = File.createTempFile("test", ".jp2");
        tempFile.deleteOnExit();
        Location.mapId(file, tempFile.getAbsolutePath());
        files.add(file);
        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);
        }
        MetadataTools.populateMetadata(metadata, 0, "foo", false, "XYCZT", "uint8", 1, 1, 1, 1, 1, 1);
        IFormatWriter writer = new JPEG2000Writer();
        writer.setMetadataRetrieve(metadata);
        writer.setId(file);
        writer.saveBytes(0, pixels[index]);
        writer.close();
    }
}

Example 52 with OMEXMLService

use of loci.formats.services.OMEXMLService in project bioformats by openmicroscopy.

the class OMETiffWriter method getBinaryOnlyOMEXML.

private String getBinaryOnlyOMEXML(String file, String companion, String companionUUID) throws FormatException, IOException, DependencyException, ServiceException {
    ServiceFactory factory = new ServiceFactory();
    OMEXMLService service = factory.getInstance(OMEXMLService.class);
    OMEXMLMetadata meta = service.createOMEXMLMetadata();
    String uuid = "urn:uuid:" + getUUID(new Location(file).getName());
    meta.setUUID(uuid);
    meta.setBinaryOnlyMetadataFile(new Location(companion).getName());
    meta.setBinaryOnlyUUID(companionUUID);
    OMEXMLMetadataRoot root = (OMEXMLMetadataRoot) meta.getRoot();
    root.setCreator(FormatTools.CREATOR);
    return service.getOMEXML(meta);
}

Example 53 with OMEXMLService

use of loci.formats.services.OMEXMLService in project bioformats by openmicroscopy.

the class LIFReader method initMetadata.

// -- Helper methods --
/**
 * Parses a string of XML and puts the values in a Hashtable.
 */
private void initMetadata(String xml) throws FormatException, IOException {
    try {
        ServiceFactory factory = new ServiceFactory();
        OMEXMLService service = factory.getInstance(OMEXMLService.class);
        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);
    }
    MetadataStore store = makeFilterMetadata();
    // the XML blocks stored in a LIF file are invalid,
    // because they don't have a root node
    xml = "<?xml version=\"1.0\" encoding=\"" + ENCODING + "\"?><LEICA>" + xml + "</LEICA>";
    xml = XMLTools.sanitizeXML(xml);
    LOGGER.trace(xml);
    translateMetadata(getMetadataRoot(xml));
    for (int i = 0; i < imageNames.length; i++) {
        setSeries(i);
        addSeriesMeta("Image name", imageNames[i]);
    }
    setSeries(0);
    // set up mapping to rearrange channels
    // for instance, the green channel may be #0, and the red channel may be #1
    realChannel = new int[tileCount.length][];
    int nextLut = 0;
    for (int i = 0; i < core.size(); i++) {
        int index = getTileIndex(i);
        if (realChannel[index] != null) {
            continue;
        }
        CoreMetadata ms = core.get(i);
        realChannel[index] = new int[ms.sizeC];
        for (int q = 0; q < ms.sizeC; q++) {
            String lut = "";
            if (nextLut < lutNames.size()) {
                lut = lutNames.get(nextLut++).toLowerCase();
            }
            if (!CHANNEL_PRIORITIES.containsKey(lut))
                lut = "";
            realChannel[index][q] = CHANNEL_PRIORITIES.get(lut).intValue();
        }
        int[] sorted = new int[ms.sizeC];
        Arrays.fill(sorted, -1);
        for (int q = 0; q < sorted.length; q++) {
            int min = Integer.MAX_VALUE;
            int minIndex = -1;
            for (int n = 0; n < ms.sizeC; n++) {
                if (realChannel[index][n] < min && !DataTools.containsValue(sorted, n)) {
                    min = realChannel[index][n];
                    minIndex = n;
                }
            }
            sorted[q] = minIndex;
        }
    }
    MetadataTools.populatePixels(store, this, true, false);
    int roiCount = 0;
    for (int i = 0; i < getSeriesCount(); i++) {
        setSeries(i);
        String instrumentID = MetadataTools.createLSID("Instrument", i);
        store.setInstrumentID(instrumentID, i);
        int index = getTileIndex(i);
        store.setMicroscopeModel(microscopeModels[index], i);
        store.setMicroscopeType(getMicroscopeType("Other"), i);
        String objectiveID = MetadataTools.createLSID("Objective", i, 0);
        store.setObjectiveID(objectiveID, i, 0);
        store.setObjectiveLensNA(lensNA[index], i, 0);
        store.setObjectiveSerialNumber(serialNumber[index], i, 0);
        if (magnification[index] != null) {
            store.setObjectiveNominalMagnification(magnification[index], i, 0);
        }
        store.setObjectiveImmersion(getImmersion(immersions[index]), i, 0);
        store.setObjectiveCorrection(getCorrection(corrections[index]), i, 0);
        store.setObjectiveModel(objectiveModels[index], i, 0);
        if (cutIns[index] != null && filterModels[index] != null) {
            int channel = 0;
            if (cutIns[index].size() >= filterModels[index].size() * 2) {
                int diff = cutIns[index].size() - filterModels[index].size();
                for (int q = 0; q < diff; q++) {
                    cutIns[index].remove(filterModels[index].size());
                }
            }
            for (int filter = 0; filter < cutIns[index].size(); filter++) {
                String filterID = MetadataTools.createLSID("Filter", i, filter);
                store.setFilterID(filterID, i, filter);
                if (filterModels[index] != null && filter < filterModels[index].size()) {
                    store.setFilterModel((String) filterModels[index].get(filter), i, filter);
                }
                store.setTransmittanceRangeCutIn((Length) cutIns[index].get(filter), i, filter);
                store.setTransmittanceRangeCutOut((Length) cutOuts[index].get(filter), i, filter);
            }
        }
        final List<Double> lasers = laserWavelength[index];
        final List<Double> laserIntensities = laserIntensity[index];
        final List<Boolean> active = laserActive[index];
        final List<Boolean> frap = laserFrap[index];
        int nextChannel = 0;
        if (lasers != null) {
            int laserIndex = 0;
            while (laserIndex < lasers.size()) {
                if ((Double) lasers.get(laserIndex) == 0) {
                    lasers.remove(laserIndex);
                } else {
                    laserIndex++;
                }
            }
            for (int laser = 0; laser < lasers.size(); laser++) {
                String id = MetadataTools.createLSID("LightSource", i, laser);
                store.setLaserID(id, i, laser);
                store.setLaserType(LaserType.OTHER, i, laser);
                store.setLaserLaserMedium(LaserMedium.OTHER, i, laser);
                Double wavelength = (Double) lasers.get(laser);
                Length wave = FormatTools.getWavelength(wavelength);
                if (wave != null) {
                    store.setLaserWavelength(wave, i, laser);
                }
            }
            Set<Integer> ignoredChannels = new HashSet<Integer>();
            final List<Integer> validIntensities = new ArrayList<Integer>();
            int size = lasers.size();
            int channel = 0;
            Set<Integer> channels = new HashSet<Integer>();
            for (int laser = 0; laser < laserIntensities.size(); laser++) {
                double intensity = (Double) laserIntensities.get(laser);
                channel = laser / size;
                if (intensity < 100) {
                    validIntensities.add(laser);
                    channels.add(channel);
                }
                ignoredChannels.add(channel);
            }
            // remove channels w/o valid intensities
            ignoredChannels.removeAll(channels);
            // remove entries if channel has 2 wavelengths
            // e.g. 30% 458 70% 633
            int s = validIntensities.size();
            int jj;
            Set<Integer> toRemove = new HashSet<Integer>();
            int as = active.size();
            for (int j = 0; j < s; j++) {
                if (j < as && !(Boolean) active.get(j)) {
                    toRemove.add(validIntensities.get(j));
                }
                jj = j + 1;
                if (jj < s) {
                    int v = validIntensities.get(j) / size;
                    int vv = validIntensities.get(jj) / size;
                    if (vv == v) {
                        // do not consider that channel.
                        toRemove.add(validIntensities.get(j));
                        toRemove.add(validIntensities.get(jj));
                        ignoredChannels.add(j);
                    }
                }
            }
            if (toRemove.size() > 0) {
                validIntensities.removeAll(toRemove);
            }
            boolean noNames = true;
            if (channelNames[index] != null) {
                for (String name : channelNames[index]) {
                    if (name != null && !name.equals("")) {
                        noNames = false;
                        break;
                    }
                }
            }
            if (!noNames && frap != null) {
                // only use name for frap.
                for (int k = 0; k < frap.size(); k++) {
                    if (!frap.get(k)) {
                        noNames = true;
                        break;
                    }
                }
            }
            int nextFilter = 0;
            // int nextFilter = cutIns[i].size() - getEffectiveSizeC();
            for (int k = 0; k < validIntensities.size(); k++, nextChannel++) {
                int laserArrayIndex = validIntensities.get(k);
                double intensity = (Double) laserIntensities.get(laserArrayIndex);
                int laser = laserArrayIndex % lasers.size();
                Double wavelength = (Double) lasers.get(laser);
                if (wavelength != 0) {
                    while (ignoredChannels.contains(nextChannel)) {
                        nextChannel++;
                    }
                    while (channelNames != null && nextChannel < getEffectiveSizeC() && channelNames[index] != null && ((channelNames[index][nextChannel] == null || channelNames[index][nextChannel].equals("")) && !noNames)) {
                        nextChannel++;
                    }
                    if (nextChannel < getEffectiveSizeC()) {
                        String id = MetadataTools.createLSID("LightSource", i, laser);
                        store.setChannelLightSourceSettingsID(id, i, nextChannel);
                        store.setChannelLightSourceSettingsAttenuation(new PercentFraction((float) intensity / 100f), i, nextChannel);
                        Length ex = FormatTools.getExcitationWavelength(wavelength);
                        if (ex != null) {
                            store.setChannelExcitationWavelength(ex, i, nextChannel);
                        }
                        if (wavelength > 0) {
                            if (cutIns[index] == null || nextFilter >= cutIns[index].size()) {
                                continue;
                            }
                            Double cutIn = ((Length) cutIns[index].get(nextFilter)).value(UNITS.NANOMETER).doubleValue();
                            while (cutIn - wavelength > 20) {
                                nextFilter++;
                                if (nextFilter < cutIns[index].size()) {
                                    cutIn = ((Length) cutIns[index].get(nextFilter)).value(UNITS.NANOMETER).doubleValue();
                                } else {
                                    break;
                                }
                            }
                            if (nextFilter < cutIns[index].size()) {
                                String fid = MetadataTools.createLSID("Filter", i, nextFilter);
                                // store.setLightPathEmissionFilterRef(fid, i, nextChannel, 0);
                                nextFilter++;
                            }
                        }
                    }
                }
            }
        }
        store.setImageInstrumentRef(instrumentID, i);
        store.setObjectiveSettingsID(objectiveID, i);
        store.setObjectiveSettingsRefractiveIndex(refractiveIndex[index], i);
        store.setImageDescription(descriptions[index], i);
        if (acquiredDate[index] > 0) {
            store.setImageAcquisitionDate(new Timestamp(DateTools.convertDate((long) (acquiredDate[index] * 1000), DateTools.COBOL, DateTools.ISO8601_FORMAT, false)), i);
        }
        store.setImageName(imageNames[index].trim(), i);
        Length sizeX = FormatTools.getPhysicalSizeX(physicalSizeXs.get(index));
        Length sizeY = FormatTools.getPhysicalSizeY(physicalSizeYs.get(index));
        Length sizeZ = FormatTools.getPhysicalSizeZ(zSteps[index]);
        if (sizeX != null) {
            store.setPixelsPhysicalSizeX(sizeX, i);
        }
        if (sizeY != null) {
            store.setPixelsPhysicalSizeY(sizeY, i);
        }
        if (sizeZ != null) {
            store.setPixelsPhysicalSizeZ(sizeZ, i);
        }
        if (tSteps[index] != null) {
            store.setPixelsTimeIncrement(new Time(tSteps[index], UNITS.SECOND), i);
        }
        final List<String> detectors = detectorModels[index];
        if (detectors != null) {
            nextChannel = 0;
            int start = detectors.size() - getEffectiveSizeC();
            if (start < 0) {
                start = 0;
            }
            for (int detector = start; detector < detectors.size(); detector++) {
                int dIndex = detector - start;
                String detectorID = MetadataTools.createLSID("Detector", i, dIndex);
                store.setDetectorID(detectorID, i, dIndex);
                store.setDetectorModel((String) detectors.get(detector), i, dIndex);
                store.setDetectorZoom(zooms[index], i, dIndex);
                store.setDetectorType(DetectorType.PMT, i, dIndex);
                if (activeDetector[index] != null) {
                    int detectorIndex = activeDetector[index].size() - getEffectiveSizeC() + dIndex;
                    if (detectorIndex >= 0 && detectorIndex < activeDetector[index].size() && (Boolean) activeDetector[index].get(detectorIndex) && detectorOffsets[index] != null && nextChannel < detectorOffsets[index].length) {
                        store.setDetectorOffset(detectorOffsets[index][nextChannel++], i, dIndex);
                    }
                }
            }
        }
        final List<Boolean> activeDetectors = activeDetector[index];
        int firstDetector = activeDetectors == null ? 0 : activeDetectors.size() - getEffectiveSizeC();
        int nextDetector = firstDetector;
        int nextFilter = 0;
        int nextFilterDetector = 0;
        if (activeDetectors != null && activeDetectors.size() > cutIns[index].size() && (Boolean) activeDetectors.get(activeDetectors.size() - 1) && (Boolean) activeDetectors.get(activeDetectors.size() - 2)) {
            nextFilterDetector = activeDetectors.size() - cutIns[index].size();
            if (cutIns[index].size() > filterModels[index].size()) {
                nextFilterDetector += filterModels[index].size();
                nextFilter += filterModels[index].size();
            }
        }
        for (int c = 0; c < getEffectiveSizeC(); c++) {
            if (activeDetectors != null) {
                while (nextDetector >= 0 && nextDetector < activeDetectors.size() && !(Boolean) activeDetectors.get(nextDetector)) {
                    nextDetector++;
                }
                if (nextDetector < activeDetectors.size() && detectors != null && nextDetector - firstDetector < detectors.size()) {
                    String detectorID = MetadataTools.createLSID("Detector", i, nextDetector - firstDetector);
                    store.setDetectorSettingsID(detectorID, i, c);
                    nextDetector++;
                    if (detectorOffsets[index] != null && c < detectorOffsets[index].length) {
                        store.setDetectorSettingsOffset(detectorOffsets[index][c], i, c);
                    }
                    if (gains[index] != null) {
                        store.setDetectorSettingsGain(gains[index][c], i, c);
                    }
                }
            }
            if (channelNames[index] != null) {
                store.setChannelName(channelNames[index][c], i, c);
            }
            if (pinholes[index] != null) {
                store.setChannelPinholeSize(new Length(pinholes[index], UNITS.MICROMETER), i, c);
            }
            if (exWaves[index] != null) {
                if (exWaves[index][c] != null && exWaves[index][c] > 1) {
                    Length ex = FormatTools.getExcitationWavelength(exWaves[index][c]);
                    if (ex != null) {
                        store.setChannelExcitationWavelength(ex, i, c);
                    }
                }
            }
            // channel coloring is implicit if the image is stored as RGB
            Color channelColor = getChannelColor(realChannel[index][c]);
            if (!isRGB()) {
                store.setChannelColor(channelColor, i, c);
            }
            if (channelColor.getValue() != -1 && nextFilter >= 0) {
                if (nextDetector - firstDetector != getSizeC() && cutIns[index] != null && nextDetector >= cutIns[index].size()) {
                    while (nextFilterDetector < firstDetector) {
                        String filterID = MetadataTools.createLSID("Filter", i, nextFilter);
                        store.setFilterID(filterID, i, nextFilter);
                        nextFilterDetector++;
                        nextFilter++;
                    }
                }
                while (activeDetectors != null && nextFilterDetector < activeDetectors.size() && !(Boolean) activeDetectors.get(nextFilterDetector)) {
                    String filterID = MetadataTools.createLSID("Filter", i, nextFilter);
                    store.setFilterID(filterID, i, nextFilter);
                    nextFilterDetector++;
                    nextFilter++;
                }
                String filterID = MetadataTools.createLSID("Filter", i, nextFilter);
                store.setFilterID(filterID, i, nextFilter);
                store.setLightPathEmissionFilterRef(filterID, i, c, 0);
                nextFilterDetector++;
                nextFilter++;
            }
        }
        for (int image = 0; image < getImageCount(); image++) {
            Length xPos = posX[index];
            Length yPos = posY[index];
            if (i < fieldPosX.size() && fieldPosX.get(i) != null) {
                xPos = fieldPosX.get(i);
            }
            if (i < fieldPosY.size() && fieldPosY.get(i) != null) {
                yPos = fieldPosY.get(i);
            }
            if (xPos != null) {
                store.setPlanePositionX(xPos, i, image);
            }
            if (yPos != null) {
                store.setPlanePositionY(yPos, i, image);
            }
            store.setPlanePositionZ(posZ[index], i, image);
            if (timestamps[index] != null) {
                if (timestamps[index][image] != null) {
                    double timestamp = timestamps[index][image];
                    if (timestamps[index][0] == acquiredDate[index]) {
                        timestamp -= acquiredDate[index];
                    } else if (timestamp == acquiredDate[index] && image > 0) {
                        timestamp = timestamps[index][0];
                    }
                    store.setPlaneDeltaT(new Time(timestamp, UNITS.SECOND), i, image);
                }
            }
            if (expTimes[index] != null) {
                int c = getZCTCoords(image)[1];
                if (expTimes[index][c] != null) {
                    store.setPlaneExposureTime(new Time(expTimes[index][c], UNITS.SECOND), i, image);
                }
            }
        }
        if (imageROIs[index] != null) {
            for (int roi = 0; roi < imageROIs[index].length; roi++) {
                if (imageROIs[index][roi] != null) {
                    imageROIs[index][roi].storeROI(store, i, roiCount++, roi);
                }
            }
        }
    }
}

Example 54 with OMEXMLService

use of loci.formats.services.OMEXMLService in project bioformats by openmicroscopy.

the class ReadWriteInMemory method main.

public static void main(String[] args) throws DependencyException, FormatException, IOException, ServiceException {
    if (args.length < 1) {
        System.out.println("Please specify a (small) image file.");
        System.exit(1);
    }
    String path = args[0];
    /* file-read-start */
    // read in entire file
    System.out.println("Reading file into memory from disk...");
    File inputFile = new File(path);
    int fileSize = (int) inputFile.length();
    DataInputStream in = new DataInputStream(new FileInputStream(inputFile));
    byte[] inBytes = new byte[fileSize];
    in.readFully(inBytes);
    System.out.println(fileSize + " bytes read.");
    /* file-read-end */
    /* mapping-start */
    // determine input file suffix
    String fileName = inputFile.getName();
    int dot = fileName.lastIndexOf(".");
    String suffix = dot < 0 ? "" : fileName.substring(dot);
    // map input id string to input byte array
    String inId = "inBytes" + suffix;
    Location.mapFile(inId, new ByteArrayHandle(inBytes));
    /* mapping-end */
    // read data from byte array using ImageReader
    System.out.println();
    System.out.println("Reading image data from memory...");
    /* read-start */
    ServiceFactory factory = new ServiceFactory();
    OMEXMLService service = factory.getInstance(OMEXMLService.class);
    IMetadata omeMeta = service.createOMEXMLMetadata();
    ImageReader reader = new ImageReader();
    reader.setMetadataStore(omeMeta);
    reader.setId(inId);
    /* read-end */
    int seriesCount = reader.getSeriesCount();
    int imageCount = reader.getImageCount();
    int sizeX = reader.getSizeX();
    int sizeY = reader.getSizeY();
    int sizeZ = reader.getSizeZ();
    int sizeC = reader.getSizeC();
    int sizeT = reader.getSizeT();
    // output some details
    System.out.println("Series count: " + seriesCount);
    System.out.println("First series:");
    System.out.println("\tImage count = " + imageCount);
    System.out.println("\tSizeX = " + sizeX);
    System.out.println("\tSizeY = " + sizeY);
    System.out.println("\tSizeZ = " + sizeZ);
    System.out.println("\tSizeC = " + sizeC);
    System.out.println("\tSizeT = " + sizeT);
    /* out—mapping-start */
    // map output id string to output byte array
    String outId = fileName + ".ome.tif";
    ByteArrayHandle outputFile = new ByteArrayHandle();
    Location.mapFile(outId, outputFile);
    /* out—mapping-end */
    /* write—init-start */
    // write data to byte array using ImageWriter
    System.out.println();
    System.out.print("Writing planes to destination in memory: ");
    ImageWriter writer = new ImageWriter();
    writer.setMetadataRetrieve(omeMeta);
    writer.setId(outId);
    /* write—init-end */
    /* write-start */
    byte[] plane = null;
    for (int i = 0; i < imageCount; i++) {
        if (plane == null) {
            // allow reader to allocate a new byte array
            plane = reader.openBytes(i);
        } else {
            // reuse previously allocated byte array
            reader.openBytes(i, plane);
        }
        writer.saveBytes(i, plane);
        System.out.print(".");
    }
    reader.close();
    writer.close();
    System.out.println();
    byte[] outBytes = outputFile.getBytes();
    outputFile.close();
    /* write-end */
    /* flush-start */
    // flush output byte array to disk
    System.out.println();
    System.out.println("Flushing image data to disk...");
    File outFile = new File(fileName + ".ome.tif");
    DataOutputStream out = new DataOutputStream(new FileOutputStream(outFile));
    out.write(outBytes);
    out.close();
/* flush-end */
}

Example 55 with OMEXMLService

use of loci.formats.services.OMEXMLService in project bioformats by openmicroscopy.

the class TiledReaderWriter method initialize.

/**
 * Set up the file reader and writer, ensuring that the input file is
 * associated with the reader and the output file is associated with the
 * writer.
 *
 * @return true if the reader and writer were successfully set up, or false
 *   if an error occurred
 * @throws DependencyException thrown if failed to create an OMEXMLService
 * @throws IOException thrown if unable to setup input or output stream for reader or writer
 * @throws FormatException thrown if invalid ID set for reader or writer or invalid tile size set
 * @throws ServiceException thrown if unable to create OME-XML meta data
 */
private void initialize() throws DependencyException, FormatException, IOException, ServiceException {
    // construct the object that stores OME-XML metadata
    ServiceFactory factory = new ServiceFactory();
    OMEXMLService service = factory.getInstance(OMEXMLService.class);
    IMetadata omexml = service.createOMEXMLMetadata();
    // set up the reader and associate it with the input file
    reader = new ImageReader();
    reader.setMetadataStore(omexml);
    reader.setId(inputFile);
    // set up the writer and associate it with the output file
    writer = new OMETiffWriter();
    writer.setMetadataRetrieve(omexml);
    writer.setInterleaved(reader.isInterleaved());
    // set the tile size height and width for writing
    this.tileSizeX = writer.setTileSizeX(tileSizeX);
    this.tileSizeY = writer.setTileSizeY(tileSizeY);
    writer.setId(outputFile);
}