Examples with PositiveInteger ome.xml.model.primitives.PositiveInteger used on opensource projects

Example 36 with PositiveInteger

use of ome.xml.model.primitives.PositiveInteger in project bioformats by openmicroscopy.

the class OMETiffWriterUnicodeTest method setUp.

@BeforeClass
public void setUp() throws Exception {
    target = File.createTempFile("OMETiffWriterUnicodeTest", ".ome.tiff");
    ServiceFactory sf = new ServiceFactory();
    OMEXMLService service = sf.getInstance(OMEXMLService.class);
    ms = service.createOMEXMLMetadata();
    ms.setImageID("Image:1", 0);
    ms.setPixelsID("Pixels:1", 0);
    ms.setPixelsDimensionOrder(DimensionOrder.XYZCT, 0);
    ms.setPixelsSizeX(new PositiveInteger(SIZE_X), 0);
    ms.setPixelsSizeY(new PositiveInteger(SIZE_Y), 0);
    ms.setPixelsSizeZ(new PositiveInteger(SIZE_Z), 0);
    ms.setPixelsSizeC(new PositiveInteger(SIZE_C), 0);
    ms.setPixelsSizeT(new PositiveInteger(SIZE_T), 0);
    ms.setPixelsPhysicalSizeX(new Length(10, UNITS.MICROMETER), 0);
    ms.setPixelsPhysicalSizeX(new Length(10, UNITS.MICROMETER), 0);
    ms.setPixelsPhysicalSizeX(new Length(10, UNITS.MICROMETER), 0);
    ms.setPixelsType(PixelType.UINT8, 0);
    ms.setPixelsBinDataBigEndian(true, 0, 0);
    ms.setChannelID("Channel:1", 0, 0);
    ms.setChannelSamplesPerPixel(new PositiveInteger(1), 0, 0);
}

Example 37 with PositiveInteger

use of ome.xml.model.primitives.PositiveInteger in project bioformats by openmicroscopy.

the class IMetadataBasedOMEModelMock method makeImage.

private void makeImage() {
    // Create <Image/>
    store.setImageID(InOutCurrentTest.IMAGE_ID, 0);
    store.setListAnnotationID(InOutCurrentTest.IMAGE_LIST_ANNOTATION_ID, 0);
    store.setListAnnotationNamespace(InOutCurrentTest.GENERAL_ANNOTATION_NAMESPACE, 0);
    store.setBooleanAnnotationID(InOutCurrentTest.IMAGE_ANNOTATION_ID, 0);
    store.setBooleanAnnotationNamespace(InOutCurrentTest.GENERAL_ANNOTATION_NAMESPACE, 0);
    store.setListAnnotationAnnotationRef(InOutCurrentTest.IMAGE_ANNOTATION_ID, 0, 0);
    store.setBooleanAnnotationValue(InOutCurrentTest.IMAGE_ANNOTATION_VALUE, 0);
    store.setBooleanAnnotationNamespace(InOutCurrentTest.GENERAL_ANNOTATION_NAMESPACE, 0);
    store.setBooleanAnnotationValue(InOutCurrentTest.IMAGE_ANNOTATION_VALUE, 0);
    store.setImageAnnotationRef(InOutCurrentTest.IMAGE_LIST_ANNOTATION_ID, 0, 0);
    // Create <Pixels/>
    store.setPixelsID(InOutCurrentTest.PIXELS_ID, 0);
    store.setPixelsSizeX(new PositiveInteger(InOutCurrentTest.SIZE_X), 0);
    store.setPixelsSizeY(new PositiveInteger(InOutCurrentTest.SIZE_Y), 0);
    store.setPixelsSizeZ(new PositiveInteger(InOutCurrentTest.SIZE_Z), 0);
    store.setPixelsSizeC(new PositiveInteger(InOutCurrentTest.SIZE_C), 0);
    store.setPixelsSizeT(new PositiveInteger(InOutCurrentTest.SIZE_T), 0);
    store.setPixelsDimensionOrder(InOutCurrentTest.DIMENSION_ORDER, 0);
    store.setPixelsType(InOutCurrentTest.PIXEL_TYPE, 0);
    store.setUUIDValue(InOutCurrentTest.TIFF_DATA_UUID, 0, 0);
    // Create <Channel/> under <Pixels/>
    store.setXMLAnnotationID(InOutCurrentTest.CHANNEL_ANNOTATION_ID, 0);
    store.setXMLAnnotationNamespace(InOutCurrentTest.GENERAL_ANNOTATION_NAMESPACE, 0);
    store.setXMLAnnotationValue(InOutCurrentTest.CHANNEL_ANNOTATION_VALUE, 0);
    store.setXMLAnnotationNamespace(InOutCurrentTest.GENERAL_ANNOTATION_NAMESPACE, 0);
    for (int i = 0; i < InOutCurrentTest.SIZE_C; i++) {
        store.setChannelID("Channel:" + i, 0, i);
        if (i == 0) {
            store.setChannelAnnotationRef(InOutCurrentTest.CHANNEL_ANNOTATION_ID, 0, i, 0);
        }
    }
}

Example 38 with PositiveInteger

use of ome.xml.model.primitives.PositiveInteger 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 39 with PositiveInteger

use of ome.xml.model.primitives.PositiveInteger in project bioformats by openmicroscopy.

the class OMETiffReader method initFile.

// -- Internal FormatReader API methods --
/* @see loci.formats.FormatReader#initFile(String) */
@Override
protected void initFile(String id) throws FormatException, IOException {
    // normalize file name
    super.initFile(normalizeFilename(null, id));
    id = currentId;
    String dir = new File(id).getParent();
    // parse and populate OME-XML metadata
    String fileName = new Location(id).getAbsoluteFile().getAbsolutePath();
    if (!new File(fileName).exists()) {
        fileName = currentId;
    }
    String xml;
    IFD firstIFD = null;
    boolean companion = false;
    if (checkSuffix(fileName, "companion.ome")) {
        xml = DataTools.readFile(fileName);
        companion = true;
    } else {
        RandomAccessInputStream ras = new RandomAccessInputStream(fileName, 16);
        try {
            TiffParser tp = new TiffParser(ras);
            firstIFD = tp.getFirstIFD();
            xml = firstIFD.getComment();
        } finally {
            ras.close();
        }
    }
    if (service == null)
        setupService();
    try {
        if (meta == null || !metaFile.equals(currentId)) {
            meta = service.createOMEXMLMetadata(xml);
            metaFile = currentId;
        }
        if (companion) {
            String firstTIFF = meta.getUUIDFileName(0, 0);
            initFile(new Location(dir, firstTIFF).getAbsolutePath());
            return;
        }
    } catch (ServiceException se) {
        throw new FormatException(se);
    }
    String metadataPath = null;
    try {
        metadataPath = meta.getBinaryOnlyMetadataFile();
    } catch (NullPointerException e) {
    }
    if (metadataPath != null) {
        // this is a binary-only file
        // overwrite XML with what is in the companion OME-XML file
        Location path = new Location(dir, metadataPath);
        if (path.exists()) {
            metadataFile = path.getAbsolutePath();
            xml = readMetadataFile();
            try {
                meta = service.createOMEXMLMetadata(xml);
            } catch (ServiceException se) {
                throw new FormatException(se);
            } catch (NullPointerException e) {
                metadataFile = null;
                metadataPath = null;
            }
        }
    }
    hasSPW = meta.getPlateCount() > 0;
    for (int i = 0; i < meta.getImageCount(); i++) {
        int sizeC = meta.getPixelsSizeC(i).getValue().intValue();
        service.removeChannels(meta, i, sizeC);
    }
    Hashtable originalMetadata = service.getOriginalMetadata(meta);
    if (originalMetadata != null)
        metadata = originalMetadata;
    LOGGER.trace(xml);
    if (meta.getRoot() == null) {
        throw new FormatException("Could not parse OME-XML from TIFF comment");
    }
    String[] acquiredDates = new String[meta.getImageCount()];
    for (int i = 0; i < acquiredDates.length; i++) {
        Timestamp acquisitionDate = meta.getImageAcquisitionDate(i);
        if (acquisitionDate != null) {
            acquiredDates[i] = acquisitionDate.getValue();
        }
    }
    String currentUUID = meta.getUUID();
    if (!isGroupFiles() && !isSingleFile(currentId)) {
        IFormatReader reader = new MinimalTiffReader();
        reader.setId(currentId);
        core.set(0, reader.getCoreMetadataList().get(0));
        int ifdCount = reader.getImageCount();
        reader.close();
        int maxSeries = 0;
        info = new OMETiffPlane[meta.getImageCount()][];
        ArrayList<Integer> imagesToRemove = new ArrayList<Integer>();
        ArrayList<int[]> cBounds = new ArrayList<int[]>();
        for (int i = 0; i < meta.getImageCount(); i++) {
            int maxZ = 0;
            int maxC = 0;
            int maxT = 0;
            int minZ = Integer.MAX_VALUE;
            int minC = Integer.MAX_VALUE;
            int minT = Integer.MAX_VALUE;
            int sizeZ = meta.getPixelsSizeZ(i).getValue();
            int sizeC = meta.getChannelCount(i);
            int sizeT = meta.getPixelsSizeT(i).getValue();
            String order = meta.getPixelsDimensionOrder(i).getValue();
            int num = sizeZ * sizeC * sizeT;
            CoreMetadata m = i < core.size() ? core.get(i) : new CoreMetadata(core.get(0));
            m.dimensionOrder = order;
            info[i] = new OMETiffPlane[meta.getTiffDataCount(i)];
            int next = 0;
            for (int td = 0; td < meta.getTiffDataCount(i); td++) {
                String uuid = null;
                try {
                    uuid = meta.getUUIDValue(i, td);
                } catch (NullPointerException e) {
                }
                String filename = null;
                try {
                    filename = meta.getUUIDFileName(i, td);
                } catch (NullPointerException e) {
                }
                if ((uuid == null || !uuid.equals(currentUUID)) && (filename == null || !currentId.endsWith(filename))) {
                    // this plane doesn't appear to be in the current file
                    continue;
                }
                if (i > maxSeries) {
                    maxSeries = i;
                }
                NonNegativeInteger ifd = meta.getTiffDataIFD(i, td);
                NonNegativeInteger count = meta.getTiffDataPlaneCount(i, td);
                NonNegativeInteger firstZ = meta.getTiffDataFirstZ(i, td);
                NonNegativeInteger firstC = meta.getTiffDataFirstC(i, td);
                NonNegativeInteger firstT = meta.getTiffDataFirstT(i, td);
                int realCount = count == null ? 1 : count.getValue();
                if (ifd == null && count == null) {
                    realCount = ifdCount;
                }
                for (int q = 0; q < realCount; q++) {
                    OMETiffPlane p = new OMETiffPlane();
                    p.id = currentId;
                    p.ifd = q;
                    if (ifd != null) {
                        p.ifd += ifd.getValue();
                    }
                    p.reader = reader;
                    info[i][next++] = p;
                    int z = firstZ == null ? 0 : firstZ.getValue();
                    int c = firstC == null ? 0 : firstC.getValue();
                    int t = firstT == null ? 0 : firstT.getValue();
                    if (q > 0) {
                        int index = FormatTools.getIndex(order, sizeZ, sizeC, sizeT, num, z, c, t);
                        int[] add = FormatTools.getZCTCoords(order, sizeZ, sizeC, sizeT, num, q);
                        z += add[0];
                        c += add[1];
                        t += add[2];
                    }
                    if (z > maxZ) {
                        maxZ = z;
                    }
                    if (c > maxC) {
                        maxC = c;
                    }
                    if (t > maxT) {
                        maxT = t;
                    }
                    if (z < minZ) {
                        minZ = z;
                    }
                    if (c < minC) {
                        minC = c;
                    }
                    if (t < minT) {
                        minT = t;
                    }
                }
            }
            if (i <= maxSeries) {
                m.sizeZ = (maxZ - minZ) + 1;
                m.sizeC = (maxC - minC) + 1;
                m.sizeT = (maxT - minT) + 1;
                m.imageCount = m.sizeZ * m.sizeC * m.sizeT;
                m.sizeC *= meta.getChannelSamplesPerPixel(i, 0).getValue();
                if (i >= core.size()) {
                    core.add(m);
                }
                cBounds.add(new int[] { minC, maxC });
            } else {
                imagesToRemove.add(i);
            }
        }
        // remove extra Images, Channels, and Planes
        meta.resolveReferences();
        OMEXMLMetadataRoot root = (OMEXMLMetadataRoot) meta.getRoot();
        List<Image> images = root.copyImageList();
        for (int i = imagesToRemove.size() - 1; i >= 0; i--) {
            images.remove(imagesToRemove.get(i));
        }
        for (int i = 0; i < images.size(); i++) {
            Image img = images.get(i);
            Pixels pix = img.getPixels();
            List<Plane> planes = pix.copyPlaneList();
            for (int p = 0; p < planes.size(); p++) {
                Plane plane = planes.get(p);
                if (plane.getTheZ().getValue() >= core.get(i).sizeZ || plane.getTheC().getValue() >= core.get(i).sizeC || plane.getTheT().getValue() >= core.get(i).sizeT) {
                    pix.removePlane(planes.get(p));
                }
            }
            pix.setMetadataOnly(null);
            List<Channel> channels = pix.copyChannelList();
            for (int c = 0; c < channels.size(); c++) {
                if (c < cBounds.get(i)[0] || c > cBounds.get(i)[1]) {
                    pix.removeChannel(channels.get(c));
                }
            }
        }
        meta.setRoot(root);
        service.convertMetadata(meta, metadataStore);
        MetadataTools.populatePixels(metadataStore, this);
        return;
    }
    service.convertMetadata(meta, metadataStore);
    // determine series count from Image and Pixels elements
    int seriesCount = meta.getImageCount();
    core.clear();
    for (int i = 0; i < seriesCount; i++) {
        core.add(new CoreMetadata());
    }
    info = new OMETiffPlane[seriesCount][];
    tileWidth = new int[seriesCount];
    tileHeight = new int[seriesCount];
    // compile list of file/UUID mappings
    Hashtable<String, String> files = new Hashtable<String, String>();
    boolean needSearch = false;
    for (int i = 0; i < seriesCount; i++) {
        int tiffDataCount = meta.getTiffDataCount(i);
        for (int td = 0; td < tiffDataCount; td++) {
            String uuid = null;
            try {
                uuid = meta.getUUIDValue(i, td);
            } catch (NullPointerException e) {
            }
            String filename = null;
            if (uuid == null) {
                // no UUID means that TiffData element refers to this file
                uuid = "";
                filename = id;
            } else {
                filename = meta.getUUIDFileName(i, td);
                if (!new Location(dir, filename).exists())
                    filename = null;
                if (filename == null) {
                    if (uuid.equals(currentUUID) || currentUUID == null) {
                        // UUID references this file
                        filename = id;
                    } else {
                        // will need to search for this UUID
                        filename = "";
                        needSearch = true;
                    }
                } else
                    filename = normalizeFilename(dir, filename);
            }
            String existing = files.get(uuid);
            if (existing == null)
                files.put(uuid, filename);
            else if (!existing.equals(filename)) {
                throw new FormatException("Inconsistent UUID filenames");
            }
        }
    }
    // search for missing filenames
    if (needSearch) {
        Enumeration en = files.keys();
        while (en.hasMoreElements()) {
            String uuid = (String) en.nextElement();
            String filename = files.get(uuid);
            if (filename.equals("")) {
                // to make this work with OME server may be a little tricky?
                throw new FormatException("Unmatched UUID: " + uuid);
            }
        }
    }
    // build list of used files
    Enumeration en = files.keys();
    int numUUIDs = files.size();
    // ensure no duplicate filenames
    HashSet fileSet = new HashSet();
    for (int i = 0; i < numUUIDs; i++) {
        String uuid = (String) en.nextElement();
        String filename = files.get(uuid);
        fileSet.add(filename);
    }
    used = new String[fileSet.size()];
    Iterator iter = fileSet.iterator();
    for (int i = 0; i < used.length; i++) used[i] = (String) iter.next();
    // process TiffData elements
    Hashtable<String, IFormatReader> readers = new Hashtable<String, IFormatReader>();
    boolean adjustedSamples = false;
    for (int i = 0; i < seriesCount; i++) {
        int s = i;
        LOGGER.debug("Image[{}] {", i);
        LOGGER.debug("  id = {}", meta.getImageID(i));
        String order = meta.getPixelsDimensionOrder(i).toString();
        PositiveInteger samplesPerPixel = null;
        if (meta.getChannelCount(i) > 0) {
            samplesPerPixel = meta.getChannelSamplesPerPixel(i, 0);
        }
        int samples = samplesPerPixel == null ? -1 : samplesPerPixel.getValue();
        int tiffSamples = firstIFD.getSamplesPerPixel();
        if (adjustedSamples || (samples != tiffSamples && (i == 0 || samples < 0))) {
            LOGGER.warn("SamplesPerPixel mismatch: OME={}, TIFF={}", samples, tiffSamples);
            samples = tiffSamples;
            adjustedSamples = true;
        } else {
            adjustedSamples = false;
        }
        if (adjustedSamples && meta.getChannelCount(i) <= 1) {
            adjustedSamples = false;
        }
        int effSizeC = meta.getPixelsSizeC(i).getValue().intValue();
        if (!adjustedSamples) {
            effSizeC /= samples;
        }
        if (effSizeC == 0)
            effSizeC = 1;
        if (effSizeC * samples != meta.getPixelsSizeC(i).getValue().intValue()) {
            effSizeC = meta.getPixelsSizeC(i).getValue().intValue();
        }
        int sizeT = meta.getPixelsSizeT(i).getValue().intValue();
        int sizeZ = meta.getPixelsSizeZ(i).getValue().intValue();
        int num = effSizeC * sizeT * sizeZ;
        OMETiffPlane[] planes = new OMETiffPlane[num];
        for (int no = 0; no < num; no++) planes[no] = new OMETiffPlane();
        int tiffDataCount = meta.getTiffDataCount(i);
        Boolean zOneIndexed = null;
        Boolean cOneIndexed = null;
        Boolean tOneIndexed = null;
        for (int td = 0; td < tiffDataCount; td++) {
            NonNegativeInteger firstC = meta.getTiffDataFirstC(i, td);
            NonNegativeInteger firstT = meta.getTiffDataFirstT(i, td);
            NonNegativeInteger firstZ = meta.getTiffDataFirstZ(i, td);
            int c = firstC == null ? 0 : firstC.getValue();
            int t = firstT == null ? 0 : firstT.getValue();
            int z = firstZ == null ? 0 : firstZ.getValue();
            if (c >= effSizeC && cOneIndexed == null) {
                cOneIndexed = true;
            } else if (c == 0) {
                cOneIndexed = false;
            }
            if (z >= sizeZ && zOneIndexed == null) {
                zOneIndexed = true;
            } else if (z == 0) {
                zOneIndexed = false;
            }
            if (t >= sizeT && tOneIndexed == null) {
                tOneIndexed = true;
            } else if (t == 0) {
                tOneIndexed = false;
            }
        }
        for (int td = 0; td < tiffDataCount; td++) {
            LOGGER.debug("    TiffData[{}] {", td);
            // extract TiffData parameters
            String filename = null;
            String uuid = null;
            try {
                filename = meta.getUUIDFileName(i, td);
            } catch (NullPointerException e) {
                LOGGER.debug("Ignoring null UUID object when retrieving filename.");
            }
            try {
                uuid = meta.getUUIDValue(i, td);
            } catch (NullPointerException e) {
                LOGGER.debug("Ignoring null UUID object when retrieving value.");
            }
            NonNegativeInteger tdIFD = meta.getTiffDataIFD(i, td);
            int ifd = tdIFD == null ? 0 : tdIFD.getValue();
            NonNegativeInteger numPlanes = meta.getTiffDataPlaneCount(i, td);
            NonNegativeInteger firstC = meta.getTiffDataFirstC(i, td);
            NonNegativeInteger firstT = meta.getTiffDataFirstT(i, td);
            NonNegativeInteger firstZ = meta.getTiffDataFirstZ(i, td);
            int c = firstC == null ? 0 : firstC.getValue();
            int t = firstT == null ? 0 : firstT.getValue();
            int z = firstZ == null ? 0 : firstZ.getValue();
            // NB: some writers index FirstC, FirstZ and FirstT from 1
            if (cOneIndexed != null && cOneIndexed)
                c--;
            if (zOneIndexed != null && zOneIndexed)
                z--;
            if (tOneIndexed != null && tOneIndexed)
                t--;
            if (z >= sizeZ || c >= effSizeC || t >= sizeT) {
                LOGGER.warn("Found invalid TiffData: Z={}, C={}, T={}", new Object[] { z, c, t });
                break;
            }
            int index = FormatTools.getIndex(order, sizeZ, effSizeC, sizeT, num, z, c, t);
            int count = numPlanes == null ? 1 : numPlanes.getValue();
            if (count == 0) {
                core.set(s, null);
                break;
            }
            // get reader object for this filename
            if (filename == null) {
                if (uuid == null)
                    filename = id;
                else
                    filename = files.get(uuid);
            } else
                filename = normalizeFilename(dir, filename);
            IFormatReader r = readers.get(filename);
            if (r == null) {
                r = new MinimalTiffReader();
                readers.put(filename, r);
            }
            Location file = new Location(filename);
            boolean exists = true;
            if (!file.exists()) {
                // if this is an absolute file name, try using a relative name
                // old versions of OMETiffWriter wrote an absolute path to
                // UUID.FileName, which causes problems if the file is moved to
                // a different directory
                filename = filename.substring(filename.lastIndexOf(File.separator) + 1);
                filename = dir + File.separator + filename;
                if (!new Location(filename).exists()) {
                    filename = currentId;
                    // if only one file is defined, we have to assume that it
                    // corresponds to the current file
                    exists = fileSet.size() == 1;
                }
            }
            // populate plane index -> IFD mapping
            for (int q = 0; q < count; q++) {
                int no = index + q;
                planes[no].reader = r;
                planes[no].id = filename;
                planes[no].ifd = ifd + q;
                planes[no].certain = true;
                planes[no].exists = exists;
                LOGGER.debug("      Plane[{}]: file={}, IFD={}", new Object[] { no, planes[no].id, planes[no].ifd });
            }
            if (numPlanes == null) {
                // unknown number of planes; fill down
                for (int no = index + 1; no < num; no++) {
                    if (planes[no].certain)
                        break;
                    planes[no].reader = r;
                    planes[no].id = filename;
                    planes[no].ifd = planes[no - 1].ifd + 1;
                    planes[no].exists = exists;
                    LOGGER.debug("      Plane[{}]: FILLED", no);
                }
            } else {
                // known number of planes; clear anything subsequently filled
                for (int no = index + count; no < num; no++) {
                    if (planes[no].certain)
                        break;
                    planes[no].reader = null;
                    planes[no].id = null;
                    planes[no].ifd = -1;
                    LOGGER.debug("      Plane[{}]: CLEARED", no);
                }
            }
            LOGGER.debug("    }");
        }
        if (core.get(s) == null)
            continue;
        // verify that all planes are available
        LOGGER.debug("    --------------------------------");
        for (int no = 0; no < num; no++) {
            LOGGER.debug("    Plane[{}]: file={}, IFD={}", new Object[] { no, planes[no].id, planes[no].ifd });
            if (planes[no].reader == null) {
                LOGGER.warn("Image ID '{}': missing plane #{}.  " + "Using TiffReader to determine the number of planes.", meta.getImageID(i), no);
                TiffReader r = new TiffReader();
                r.setId(currentId);
                try {
                    planes = new OMETiffPlane[r.getImageCount()];
                    for (int plane = 0; plane < planes.length; plane++) {
                        planes[plane] = new OMETiffPlane();
                        planes[plane].id = currentId;
                        planes[plane].reader = r;
                        planes[plane].ifd = plane;
                    }
                    num = planes.length;
                } finally {
                    r.close();
                }
            }
        }
        LOGGER.debug("  }");
        // populate core metadata
        CoreMetadata m = core.get(s);
        info[s] = planes;
        try {
            RandomAccessInputStream testFile = new RandomAccessInputStream(info[s][0].id, 16);
            String firstFile = info[s][0].id;
            if (!info[s][0].reader.isThisType(testFile)) {
                LOGGER.warn("{} is not a valid OME-TIFF", info[s][0].id);
                info[s][0].id = currentId;
                info[s][0].exists = false;
            }
            testFile.close();
            for (int plane = 1; plane < info[s].length; plane++) {
                if (info[s][plane].id.equals(firstFile)) {
                    // don't repeat slow type checking if the files are the same
                    if (!info[s][0].exists) {
                        info[s][plane].id = info[s][0].id;
                        info[s][plane].exists = false;
                    }
                    continue;
                }
                testFile = new RandomAccessInputStream(info[s][plane].id, 16);
                if (!info[s][plane].reader.isThisType(testFile)) {
                    LOGGER.warn("{} is not a valid OME-TIFF", info[s][plane].id);
                    info[s][plane].id = info[s][0].id;
                    info[s][plane].exists = false;
                }
                testFile.close();
            }
            info[s][0].reader.setId(info[s][0].id);
            tileWidth[s] = info[s][0].reader.getOptimalTileWidth();
            tileHeight[s] = info[s][0].reader.getOptimalTileHeight();
            m.sizeX = meta.getPixelsSizeX(i).getValue().intValue();
            int tiffWidth = (int) firstIFD.getImageWidth();
            if (m.sizeX != tiffWidth && s == 0) {
                LOGGER.warn("SizeX mismatch: OME={}, TIFF={}", m.sizeX, tiffWidth);
            }
            m.sizeY = meta.getPixelsSizeY(i).getValue().intValue();
            int tiffHeight = (int) firstIFD.getImageLength();
            if (m.sizeY != tiffHeight && s == 0) {
                LOGGER.warn("SizeY mismatch: OME={}, TIFF={}", m.sizeY, tiffHeight);
            }
            m.sizeZ = meta.getPixelsSizeZ(i).getValue().intValue();
            m.sizeC = meta.getPixelsSizeC(i).getValue().intValue();
            m.sizeT = meta.getPixelsSizeT(i).getValue().intValue();
            m.pixelType = FormatTools.pixelTypeFromString(meta.getPixelsType(i).toString());
            int tiffPixelType = firstIFD.getPixelType();
            if (m.pixelType != tiffPixelType && (s == 0 || adjustedSamples)) {
                LOGGER.warn("PixelType mismatch: OME={}, TIFF={}", m.pixelType, tiffPixelType);
                m.pixelType = tiffPixelType;
            }
            m.imageCount = num;
            m.dimensionOrder = meta.getPixelsDimensionOrder(i).toString();
            // hackish workaround for files exported by OMERO that have an
            // incorrect dimension order
            String uuidFileName = "";
            try {
                if (meta.getTiffDataCount(i) > 0) {
                    uuidFileName = meta.getUUIDFileName(i, 0);
                }
            } catch (NullPointerException e) {
            }
            if (meta.getChannelCount(i) > 0 && meta.getChannelName(i, 0) == null && meta.getTiffDataCount(i) > 0 && uuidFileName.indexOf("__omero_export") != -1) {
                m.dimensionOrder = "XYZCT";
            }
            m.orderCertain = true;
            PhotoInterp photo = firstIFD.getPhotometricInterpretation();
            m.rgb = samples > 1 || photo == PhotoInterp.RGB;
            if ((samples != m.sizeC && (samples % m.sizeC) != 0 && (m.sizeC % samples) != 0) || m.sizeC == 1 || adjustedSamples) {
                m.sizeC *= samples;
            }
            if (m.sizeZ * m.sizeT * m.sizeC > m.imageCount && !m.rgb) {
                if (m.sizeZ == m.imageCount) {
                    m.sizeT = 1;
                    m.sizeC = 1;
                } else if (m.sizeT == m.imageCount) {
                    m.sizeZ = 1;
                    m.sizeC = 1;
                } else if (m.sizeC == m.imageCount) {
                    m.sizeT = 1;
                    m.sizeZ = 1;
                }
            }
            if (meta.getPixelsBinDataCount(i) > 1) {
                LOGGER.warn("OME-TIFF Pixels element contains BinData elements! " + "Ignoring.");
            }
            m.littleEndian = firstIFD.isLittleEndian();
            m.interleaved = false;
            m.indexed = photo == PhotoInterp.RGB_PALETTE && firstIFD.getIFDValue(IFD.COLOR_MAP) != null;
            if (m.indexed) {
                m.rgb = false;
            }
            m.falseColor = true;
            m.metadataComplete = true;
            if (meta.getPixelsSignificantBits(i) != null) {
                m.bitsPerPixel = meta.getPixelsSignificantBits(i).getValue();
            }
        } catch (NullPointerException exc) {
            throw new FormatException("Incomplete Pixels metadata", exc);
        }
    }
    // remove null CoreMetadata entries
    ArrayList<CoreMetadata> series = new ArrayList<CoreMetadata>();
    final List<OMETiffPlane[]> planeInfo = new ArrayList<OMETiffPlane[]>();
    for (int i = 0; i < core.size(); i++) {
        if (core.get(i) != null) {
            series.add(core.get(i));
            planeInfo.add(info[i]);
        }
    }
    core = series;
    info = planeInfo.toArray(new OMETiffPlane[0][0]);
    if (getImageCount() == 1) {
        CoreMetadata ms0 = core.get(0);
        ms0.sizeZ = 1;
        if (!ms0.rgb) {
            ms0.sizeC = 1;
        }
        ms0.sizeT = 1;
    }
    for (int i = 0; i < core.size(); i++) {
        CoreMetadata m = core.get(i);
        Modulo z = service.getModuloAlongZ(meta, i);
        if (z != null) {
            m.moduloZ = z;
        }
        Modulo c = service.getModuloAlongC(meta, i);
        if (c != null) {
            m.moduloC = c;
        }
        Modulo t = service.getModuloAlongT(meta, i);
        if (t != null) {
            m.moduloT = t;
        }
    }
    MetadataTools.populatePixels(metadataStore, this, false, false);
    for (int i = 0; i < meta.getImageCount(); i++) {
        // TheT values are not changed
        for (int p = 0; p < meta.getPlaneCount(i); p++) {
            NonNegativeInteger z = meta.getPlaneTheZ(i, p);
            NonNegativeInteger c = meta.getPlaneTheC(i, p);
            NonNegativeInteger t = meta.getPlaneTheT(i, p);
            if (z == null) {
                z = new NonNegativeInteger(0);
                metadataStore.setPlaneTheZ(z, i, p);
            }
            if (c == null) {
                c = new NonNegativeInteger(0);
                metadataStore.setPlaneTheC(c, i, p);
            }
            if (t == null) {
                t = new NonNegativeInteger(0);
                metadataStore.setPlaneTheT(t, i, p);
            }
        }
    }
    for (int i = 0; i < acquiredDates.length; i++) {
        if (acquiredDates[i] != null) {
            metadataStore.setImageAcquisitionDate(new Timestamp(acquiredDates[i]), i);
        }
    }
}

Example 40 with PositiveInteger

use of ome.xml.model.primitives.PositiveInteger in project bioformats by openmicroscopy.

the class MetamorphTiffReader method initFile.

// -- Internal FormatReader API methods --
/* @see loci.formats.FormatReader#initFile(String) */
@Override
protected void initFile(String id) throws FormatException, IOException {
    super.initFile(id);
    List<String> uniqueChannels = new ArrayList<String>();
    final List<Double> uniqueZs = new ArrayList<Double>();
    final List<Length> stageX = new ArrayList<Length>();
    final List<Length> stageY = new ArrayList<Length>();
    CoreMetadata m = core.get(0);
    String filename = id.substring(id.lastIndexOf(File.separator) + 1);
    filename = filename.substring(0, filename.indexOf('.'));
    boolean integerFilename = true;
    try {
        Integer.parseInt(filename);
    } catch (NumberFormatException e) {
        integerFilename = false;
    }
    if (integerFilename && ifds.size() == 1 && ifds.get(0).getIFDIntValue(IFD.NEW_SUBFILE_TYPE) == 2) {
        // look for other files in the dataset
        findTIFFs();
        String stageLabel = null;
        for (String tiff : files) {
            MetamorphHandler handler = new MetamorphHandler();
            parseFile(tiff, handler);
            String label = handler.getStageLabel();
            if (stageLabel == null) {
                stageLabel = label;
            } else if (!label.equals(stageLabel)) {
                break;
            }
            if (!uniqueChannels.contains(handler.getChannelName())) {
                uniqueChannels.add(handler.getChannelName());
            }
            final List<Double> zPositions = handler.getZPositions();
            Double pos = Math.rint(zPositions.get(0));
            if (!uniqueZs.contains(pos)) {
                uniqueZs.add(pos);
            }
        }
        MetamorphHandler handler = new MetamorphHandler();
        parseFile(files[files.length - 1], handler);
        String lastStageLabel = handler.getStageLabel();
        int lastField = getField(lastStageLabel);
        int lastWellRow = getWellRow(lastStageLabel);
        int lastWellColumn = getWellColumn(lastStageLabel);
        int field = getField(stageLabel);
        int fieldRow = getWellRow(stageLabel);
        int fieldColumn = getWellColumn(stageLabel);
        wellCount = lastField - field + 1;
        fieldRowCount = lastWellRow - fieldRow + 1;
        fieldColumnCount = lastWellColumn - fieldColumn + 1;
        m.sizeC = uniqueChannels.size();
        m.sizeZ = uniqueZs.size();
    } else {
        files = new String[] { id };
        wellCount = 1;
        fieldRowCount = 1;
        fieldColumnCount = 1;
        m.sizeC = 0;
    }
    // parse XML comment
    MetamorphHandler handler = new MetamorphHandler(getGlobalMetadata());
    final List<Length> xPositions = new ArrayList<Length>();
    final List<Length> yPositions = new ArrayList<Length>();
    for (IFD ifd : ifds) {
        String xml = XMLTools.sanitizeXML(ifd.getComment());
        XMLTools.parseXML(xml, handler);
        final Length x = handler.getStagePositionX();
        final Length y = handler.getStagePositionY();
        if (xPositions.isEmpty()) {
            xPositions.add(x);
            yPositions.add(y);
        } else {
            final Length previousX = xPositions.get(xPositions.size() - 1);
            final Length previousY = yPositions.get(yPositions.size() - 1);
            final double x1 = x.value(UNITS.REFERENCEFRAME).doubleValue();
            final double x2 = previousX.value(UNITS.REFERENCEFRAME).doubleValue();
            final double y1 = y.value(UNITS.REFERENCEFRAME).doubleValue();
            final double y2 = previousY.value(UNITS.REFERENCEFRAME).doubleValue();
            if (Math.abs(x1 - x2) > 0.21 || Math.abs(y1 - y2) > 0.21) {
                xPositions.add(x);
                yPositions.add(y);
            }
        }
    }
    if (xPositions.size() > 1) {
        fieldRowCount = xPositions.size();
    }
    final List<Integer> wavelengths = handler.getWavelengths();
    final List<Double> zPositions = handler.getZPositions();
    dualCamera = handler.hasDualCamera();
    // calculate axis sizes
    final List<Integer> uniqueC = new ArrayList<Integer>();
    for (Integer c : wavelengths) {
        if (!uniqueC.contains(c)) {
            uniqueC.add(c);
        }
    }
    int effectiveC = uniqueC.size();
    if (effectiveC == 0)
        effectiveC = 1;
    if (getSizeC() == 0)
        m.sizeC = 1;
    int samples = ifds.get(0).getSamplesPerPixel();
    m.sizeC *= effectiveC * samples;
    final List<Double> uniqueZ = new ArrayList<Double>();
    for (Double z : zPositions) {
        if (!uniqueZ.contains(z))
            uniqueZ.add(z);
    }
    if (getSizeZ() == 0)
        m.sizeZ = 1;
    if (uniqueZ.size() > 1)
        m.sizeZ *= uniqueZ.size();
    Double physicalSizeZ = null;
    if (m.sizeZ > 1) {
        Double zRange = zPositions.get(zPositions.size() - 1) - zPositions.get(0);
        physicalSizeZ = Math.abs(zRange);
        physicalSizeZ /= (m.sizeZ - 1);
    }
    int totalPlanes = files.length * ifds.size();
    effectiveC = getSizeC() / samples;
    // account for the multiple actual Z sections
    if (effectiveC * getSizeZ() > totalPlanes && (effectiveC * (getSizeZ() / uniqueC.size()) == totalPlanes || effectiveC == totalPlanes)) {
        if (getSizeZ() >= uniqueC.size()) {
            m.sizeZ /= uniqueC.size();
        } else {
            m.sizeZ = 1;
        }
    }
    m.sizeT = totalPlanes / (wellCount * fieldRowCount * fieldColumnCount * getSizeZ() * effectiveC);
    if (getSizeT() == 0)
        m.sizeT = 1;
    int seriesCount = wellCount * fieldRowCount * fieldColumnCount;
    if (seriesCount > 1 && getSizeZ() > totalPlanes / seriesCount || totalPlanes > getSizeZ() * getSizeT() * effectiveC) {
        m.sizeZ = 1;
        m.sizeT = totalPlanes / (seriesCount * effectiveC);
    }
    m.imageCount = getSizeZ() * getSizeT() * effectiveC;
    if (dualCamera) {
        m.sizeX /= 2;
        m.sizeC *= 2;
        m.imageCount *= 2;
    }
    if (seriesCount > 1) {
        core.clear();
        for (int i = 0; i < seriesCount; i++) {
            core.add(m);
        }
    }
    for (int s = 0; s < wellCount * fieldRowCount * fieldColumnCount; s++) {
        if (files.length > 1) {
            int[] lengths = new int[] { getSizeZ(), getEffectiveSizeC(), fieldColumnCount, fieldRowCount, wellCount, getSizeT() };
            Well well = getWell(s);
            int[] position = new int[] { 0, 0, well.fieldCol, well.fieldRow, well.well, 0 };
            int fileIndex = FormatTools.positionToRaster(lengths, position);
            parseFile(files[fileIndex], handler);
            stageX.add(handler.getStagePositionX());
            stageY.add(handler.getStagePositionY());
        } else {
            stageX.add(xPositions.get(s));
            stageY.add(yPositions.get(s));
        }
    }
    MetadataStore store = makeFilterMetadata();
    MetadataTools.populatePixels(store, this);
    // effectively useless).
    if (wellCount > 1) {
        store.setPlateID(MetadataTools.createLSID("Plate", 0), 0);
        store.setPlateRows(new PositiveInteger(1), 0);
        store.setPlateColumns(new PositiveInteger(wellCount), 0);
        store.setPlateRowNamingConvention(NamingConvention.LETTER, 0);
        store.setPlateColumnNamingConvention(NamingConvention.NUMBER, 0);
        store.setPlateAcquisitionID(MetadataTools.createLSID("PlateAcquisition", 0, 0), 0, 0);
        for (int well = 0; well < wellCount; well++) {
            store.setWellID(MetadataTools.createLSID("Well", 0, well), 0, well);
            store.setWellRow(new NonNegativeInteger(0), 0, well);
            store.setWellColumn(new NonNegativeInteger(well), 0, well);
            for (int row = 0; row < fieldRowCount; row++) {
                for (int col = 0; col < fieldColumnCount; col++) {
                    int field = row * fieldColumnCount + col;
                    String wellSampleID = MetadataTools.createLSID("WellSample", 0, well, field);
                    store.setWellSampleID(wellSampleID, 0, well, field);
                    int seriesIndex = getSeriesIndex(row, col, well);
                    String imageID = MetadataTools.createLSID("Image", seriesIndex);
                    store.setImageID(imageID, seriesIndex);
                    store.setWellSampleImageRef(imageID, 0, well, field);
                    store.setWellSampleIndex(new NonNegativeInteger(seriesIndex), 0, well, field);
                    store.setPlateAcquisitionWellSampleRef(wellSampleID, 0, 0, seriesIndex);
                }
            }
        }
    }
    final List<String> timestamps = handler.getTimestamps();
    final List<Double> exposures = handler.getExposures();
    if (getMetadataOptions().getMetadataLevel() != MetadataLevel.MINIMUM) {
        for (int i = 0; i < timestamps.size(); i++) {
            long timestamp = DateTools.getTime(timestamps.get(i), DATE_FORMAT, ".");
            addGlobalMetaList("timestamp", timestamp);
        }
        for (int i = 0; i < exposures.size(); i++) {
            addGlobalMetaList("exposure time (ms)", exposures.get(i).floatValue() * 1000);
        }
    }
    for (int s = 0; s < seriesCount; s++) {
        setSeries(s);
        Well well = getWell(s);
        String name = handler.getImageName();
        if (seriesCount > 1) {
            name = "Field " + (char) (well.fieldRow + 'A') + (well.fieldCol + 1) + ", Well " + (well.well + 1) + ": " + name;
        }
        store.setImageName(name, s);
        String date = DateTools.formatDate(handler.getDate(), DateTools.ISO8601_FORMAT, ".");
        if (date != null) {
            store.setImageAcquisitionDate(new Timestamp(date), s);
        }
        if (getMetadataOptions().getMetadataLevel() != MetadataLevel.MINIMUM) {
            long startDate = 0;
            if (timestamps.size() > 0) {
                startDate = DateTools.getTime(timestamps.get(0), DATE_FORMAT, ".");
            }
            store.setImageDescription("", s);
            int image = 0;
            for (int c = 0; c < getEffectiveSizeC(); c++) {
                for (int t = 0; t < getSizeT(); t++) {
                    store.setPlaneTheZ(new NonNegativeInteger(0), s, image);
                    store.setPlaneTheC(new NonNegativeInteger(c), s, image);
                    store.setPlaneTheT(new NonNegativeInteger(t), s, image);
                    if (t < timestamps.size()) {
                        String stamp = timestamps.get(t);
                        long ms = DateTools.getTime(stamp, DATE_FORMAT, ".");
                        store.setPlaneDeltaT(new Time((ms - startDate) / 1000.0, UNITS.SECOND), s, image);
                    }
                    int exposureIndex = image;
                    if (dualCamera) {
                        exposureIndex /= getEffectiveSizeC();
                    }
                    if (exposures.size() == 1) {
                        exposureIndex = 0;
                    }
                    if (exposureIndex < exposures.size() && exposures.get(exposureIndex) != null) {
                        store.setPlaneExposureTime(new Time(exposures.get(exposureIndex), UNITS.SECOND), s, image);
                    }
                    if (s < stageX.size()) {
                        store.setPlanePositionX(stageX.get(s), s, image);
                    }
                    if (s < stageY.size()) {
                        store.setPlanePositionY(stageY.get(s), s, image);
                    }
                    image++;
                }
            }
            store.setImagingEnvironmentTemperature(new Temperature(handler.getTemperature(), UNITS.CELSIUS), s);
            Length sizeX = FormatTools.getPhysicalSizeX(handler.getPixelSizeX());
            Length sizeY = FormatTools.getPhysicalSizeY(handler.getPixelSizeY());
            Length sizeZ = physicalSizeZ == null ? null : FormatTools.getPhysicalSizeZ(physicalSizeZ);
            if (sizeX != null) {
                store.setPixelsPhysicalSizeX(sizeX, s);
            }
            if (sizeY != null) {
                store.setPixelsPhysicalSizeY(sizeY, s);
            }
            if (sizeZ != null) {
                store.setPixelsPhysicalSizeZ(sizeZ, s);
            }
            if (uniqueChannels.size() == 0) {
                uniqueChannels = handler.getChannelNames();
            }
            for (int c = 0; c < getEffectiveSizeC(); c++) {
                if (uniqueChannels.size() > c) {
                    store.setChannelName(uniqueChannels.get(c), s, c);
                } else
                    store.setChannelName(handler.getChannelName(), s, c);
                if (c < wavelengths.size()) {
                    store.setChannelEmissionWavelength(FormatTools.getEmissionWavelength(Double.valueOf(wavelengths.get(c))), s, c);
                }
            }
        }
    }
}