Examples with CoreMetadata loci.formats.CoreMetadata used on opensource projects

Example 96 with CoreMetadata

use of loci.formats.CoreMetadata in project bioformats by openmicroscopy.

the class WrapperTest method testCoreMetadata.

@Test(dataProvider = "wrappers")
public void testCoreMetadata(IFormatReader reader) {
    assertNotNull(reader.getCurrentFile());
    List<CoreMetadata> coreList = reader.getCoreMetadataList();
    assertEquals(coreList.size(), reader.getSeriesCount());
    for (int i = 0; i < reader.getSeriesCount(); i++) {
        CoreMetadata core = coreList.get(i);
        reader.setSeries(i);
        assertEquals(core.sizeX, reader.getSizeX());
        assertEquals(core.sizeY, reader.getSizeY());
        assertEquals(core.sizeZ, reader.getSizeZ());
        assertEquals(core.sizeC, reader.getSizeC());
        assertEquals(core.sizeT, reader.getSizeT());
        assertEquals(core.pixelType, reader.getPixelType());
        assertEquals(core.imageCount, reader.getImageCount());
        assertEquals(core.dimensionOrder, reader.getDimensionOrder());
        assertEquals(core.littleEndian, reader.isLittleEndian());
        assertEquals(core.rgb, reader.isRGB());
        assertEquals(core.interleaved, reader.isInterleaved());
        assertEquals(core.indexed, reader.isIndexed());
    }
}

Example 97 with CoreMetadata

use of loci.formats.CoreMetadata in project bioformats by openmicroscopy.

the class FileExportSPW method createModuloAnn.

/**
 * Add ModuloAlong annotation.
 *
 * @param meta
 *          OMEXMLMetadata Object to which Modulo need to be added
 */
private CoreMetadata createModuloAnn() {
    CoreMetadata modlo = new CoreMetadata();
    modlo.moduloT.type = loci.formats.FormatTools.LIFETIME;
    modlo.moduloT.unit = "ps";
    modlo.moduloT.typeDescription = "Gated";
    modlo.moduloT.labels = new String[sizeT];
    for (int i = 0; i < sizeT; i++) {
        modlo.moduloT.labels[i] = Integer.toString(i * 1000);
    }
    return modlo;
}

Example 98 with CoreMetadata

use of loci.formats.CoreMetadata in project bioformats by openmicroscopy.

the class FitsReader method initFile.

// -- Internal FormatReader API methods --
/* @see loci.formats.FormatReader#initFile(String) */
@Override
protected void initFile(String id) throws FormatException, IOException {
    super.initFile(id);
    in = new RandomAccessInputStream(id);
    CoreMetadata m = core.get(0);
    String line = in.readString(LINE_LENGTH);
    if (!line.startsWith("SIMPLE")) {
        throw new FormatException("Unsupported FITS file.");
    }
    String key = "", value = "";
    while (true) {
        line = in.readString(LINE_LENGTH);
        // parse key/value pair
        int ndx = line.indexOf('=');
        int comment = line.indexOf("/", ndx);
        if (comment < 0)
            comment = line.length();
        if (ndx >= 0) {
            key = line.substring(0, ndx).trim();
            value = line.substring(ndx + 1, comment).trim();
        } else
            key = line.trim();
        // image dimensions are only populated by the standard header
        if (key.equals("END") && getSizeX() > 0)
            break;
        if (key.equals("BITPIX")) {
            int bits = Integer.parseInt(value);
            boolean fp = bits < 0;
            boolean signed = bits != 8;
            bits = Math.abs(bits) / 8;
            m.pixelType = FormatTools.pixelTypeFromBytes(bits, signed, fp);
        } else if (key.equals("NAXIS1"))
            m.sizeX = Integer.parseInt(value);
        else if (key.equals("NAXIS2"))
            m.sizeY = Integer.parseInt(value);
        else if (key.equals("NAXIS3"))
            m.sizeZ = Integer.parseInt(value);
        addGlobalMeta(key, value);
    }
    while (in.read() == 0x20) ;
    pixelOffset = in.getFilePointer() - 1;
    m.sizeC = 1;
    m.sizeT = 1;
    if (getSizeZ() == 0)
        m.sizeZ = 1;
    // correct for truncated files
    int planeSize = getSizeX() * getSizeY() * FormatTools.getBytesPerPixel(getPixelType());
    if (DataTools.safeMultiply64(planeSize, getSizeZ()) > (in.length() - pixelOffset)) {
        m.sizeZ = (int) ((in.length() - pixelOffset) / planeSize);
    }
    m.imageCount = m.sizeZ;
    m.rgb = false;
    m.littleEndian = false;
    m.interleaved = false;
    m.dimensionOrder = "XYZCT";
    m.indexed = false;
    m.falseColor = false;
    m.metadataComplete = true;
    MetadataStore store = makeFilterMetadata();
    MetadataTools.populatePixels(store, this);
}

Example 99 with CoreMetadata

use of loci.formats.CoreMetadata in project bioformats by openmicroscopy.

the class IM3Reader method initFile.

/* (non-Javadoc)
   * @see loci.formats.FormatReader#initFile(java.lang.String)
   */
@Override
protected void initFile(String id) throws FormatException, IOException {
    super.initFile(id);
    core.clear();
    IRandomAccess is = Location.getHandle(id, false);
    try {
        is.setOrder(ByteOrder.LITTLE_ENDIAN);
        final int cookie = is.readInt();
        if (cookie != COOKIE) {
            throw new FormatException(String.format("Expected file cookie of %d, but got %d.", COOKIE, cookie));
        }
        long fileLength = is.length();
        while (is.getFilePointer() < fileLength) {
            final IM3Record rec = parseRecord(is);
            if (rec == null) {
                if (is.getFilePointer() > fileLength - 16)
                    break;
                /*
           * # of bytes in chunk.
           */
                @SuppressWarnings("unused") final int chunkLength = is.readInt();
                /*
           * Is always zero? Chunk #?
           */
                @SuppressWarnings("unused") final int unknown = is.readInt();
                /*
           * Is always one? Chunk #?
           */
                @SuppressWarnings("unused") final int unknown1 = is.readInt();
                /*
           * # of records to follow
           */
                @SuppressWarnings("unused") final int nRecords = is.readInt();
            } else {
                if (rec instanceof ContainerRecord) {
                    final ContainerRecord bRec = (ContainerRecord) rec;
                    for (IM3Record subDS : bRec.parseChunks(is)) {
                        if ((subDS instanceof ContainerRecord) && (subDS.name.equals(FIELD_DATA_SET))) {
                            final ContainerRecord bSubDS = (ContainerRecord) subDS;
                            for (IM3Record subSubDS : bSubDS.parseChunks(is)) {
                                if (subSubDS instanceof ContainerRecord) {
                                    final ContainerRecord bDataSet = (ContainerRecord) subSubDS;
                                    dataSets.add(bDataSet);
                                    List<IM3Record> subRecs = bDataSet.parseChunks(is);
                                    final CoreMetadata cm = new CoreMetadata();
                                    cm.dimensionOrder = DimensionOrder.XYCZT.getValue();
                                    cm.littleEndian = true;
                                    // TODO: Detect pixel type
                                    cm.pixelType = FormatTools.UINT16;
                                    for (IM3Record subRec : subRecs) {
                                        if (subRec.name.equals(FIELD_SHAPE) && (subRec instanceof IntIM3Record)) {
                                            final IntIM3Record iRec = (IntIM3Record) subRec;
                                            cm.sizeX = iRec.getEntry(is, 0);
                                            cm.sizeY = iRec.getEntry(is, 1);
                                            cm.sizeC = iRec.getEntry(is, 2);
                                            cm.sizeZ = 1;
                                            cm.sizeT = 1;
                                            cm.imageCount = cm.sizeC;
                                            cm.metadataComplete = true;
                                        }
                                    }
                                    core.add(cm);
                                }
                            }
                        } else if ((subDS instanceof ContainerRecord) && subDS.name.equals(FIELD_SPECTRAL_LIBRARY)) {
                            /*
                 * SpectralLibrary
                 *   (unnamed container record)
                 *       Spectra
                 *           Keys (integers)
                 *           Values
                 *               (unnamed container record for spectrum #1)
                 *               (unnamed container record for spectrum #2)...
                 *
                 */
                            for (IM3Record slContainer : ((ContainerRecord) subDS).parseChunks(is)) {
                                /* unnamed container */
                                if (slContainer instanceof ContainerRecord) {
                                    for (IM3Record slSpectra : ((ContainerRecord) slContainer).parseChunks(is)) {
                                        if ((slSpectra instanceof ContainerRecord) && (slSpectra.name.equals(FIELD_SPECTRA))) {
                                            for (IM3Record slRec : ((ContainerRecord) slSpectra).parseChunks(is)) {
                                                if (slRec.name.equals(FIELD_VALUES) && (slRec instanceof ContainerRecord)) {
                                                    for (IM3Record spectrumRec : ((ContainerRecord) slRec).parseChunks(is)) {
                                                        if (spectrumRec instanceof ContainerRecord) {
                                                            spectra.add(new Spectrum(is, (ContainerRecord) spectrumRec));
                                                        }
                                                    }
                                                }
                                            }
                                        }
                                    }
                                }
                            }
                        }
                    }
                }
                records.add(rec);
            }
        }
    } finally {
        is.close();
    }
    MetadataStore store = makeFilterMetadata();
    MetadataTools.populatePixels(store, this);
}

Example 100 with CoreMetadata

use of loci.formats.CoreMetadata in project bioformats by openmicroscopy.

the class MNGReader method initFile.

// -- Internal FormatReader API methods --
/* @see loci.formats.FormatReader#initFile(String) */
@Override
protected void initFile(String id) throws FormatException, IOException {
    super.initFile(id);
    in = new RandomAccessInputStream(id);
    in.order(false);
    LOGGER.info("Verifying MNG format");
    seriesInfo = new ArrayList<SeriesInfo>();
    seriesInfo.add(new SeriesInfo());
    in.skipBytes(12);
    if (!"MHDR".equals(in.readString(4))) {
        throw new FormatException("Invalid MNG file.");
    }
    LOGGER.info("Reading dimensions");
    in.skipBytes(32);
    final List<Long> stack = new ArrayList<Long>();
    int maxIterations = 0;
    int currentIteration = 0;
    LOGGER.info("Finding image offsets");
    while (in.getFilePointer() < in.length()) {
        int len = in.readInt();
        String code = in.readString(4);
        long fp = in.getFilePointer();
        if (code.equals("IHDR")) {
            seriesInfo.get(0).offsets.add(fp - 8);
        } else if (code.equals("JDAT")) {
            isJNG = true;
            seriesInfo.get(0).offsets.add(fp);
        } else if (code.equals("IEND")) {
            seriesInfo.get(0).lengths.add(fp + len + 4);
        } else if (code.equals("LOOP")) {
            stack.add(fp + len + 4);
            in.skipBytes(1);
            maxIterations = in.readInt();
        } else if (code.equals("ENDL")) {
            long seek = stack.get(stack.size() - 1).longValue();
            if (currentIteration < maxIterations) {
                in.seek(seek);
                currentIteration++;
            } else {
                stack.remove(stack.size() - 1);
                maxIterations = 0;
                currentIteration = 0;
            }
        }
        in.seek(fp + len + 4);
    }
    LOGGER.info("Populating metadata");
    // easiest way to get image dimensions is by opening the first plane
    Hashtable<String, List<Long>> seriesOffsets = new Hashtable<String, List<Long>>();
    Hashtable<String, List<Long>> seriesLengths = new Hashtable<String, List<Long>>();
    SeriesInfo info = seriesInfo.get(0);
    addGlobalMeta("Number of frames", info.offsets.size());
    for (int i = 0; i < info.offsets.size(); i++) {
        long offset = info.offsets.get(i);
        in.seek(offset);
        long end = info.lengths.get(i);
        if (end < offset)
            continue;
        BufferedImage img = readImage(end);
        String data = img.getWidth() + "-" + img.getHeight() + "-" + img.getRaster().getNumBands() + "-" + AWTImageTools.getPixelType(img);
        List<Long> v = seriesOffsets.get(data);
        if (v == null) {
            v = new ArrayList<Long>();
            seriesOffsets.put(data, v);
        }
        v.add(offset);
        v = seriesLengths.get(data);
        if (v == null) {
            v = new ArrayList<Long>();
            seriesLengths.put(data, v);
        }
        v.add(end);
    }
    String[] keys = seriesOffsets.keySet().toArray(new String[0]);
    if (keys.length == 0) {
        throw new FormatException("Pixel data not found.");
    }
    int seriesCount = keys.length;
    core.clear();
    seriesInfo.clear();
    for (int i = 0; i < seriesCount; i++) {
        CoreMetadata ms = new CoreMetadata();
        core.add(ms);
        String[] tokens = keys[i].split("-");
        ms.sizeX = Integer.parseInt(tokens[0]);
        ms.sizeY = Integer.parseInt(tokens[1]);
        ms.sizeC = Integer.parseInt(tokens[2]);
        ms.pixelType = Integer.parseInt(tokens[3]);
        ms.rgb = ms.sizeC > 1;
        ms.sizeZ = 1;
        ms.dimensionOrder = "XYCZT";
        ms.interleaved = false;
        ms.metadataComplete = true;
        ms.indexed = false;
        ms.littleEndian = false;
        ms.falseColor = false;
        SeriesInfo inf = new SeriesInfo();
        inf.offsets = seriesOffsets.get(keys[i]);
        inf.lengths = seriesLengths.get(keys[i]);
        seriesInfo.add(inf);
        ms.imageCount = inf.offsets.size();
        ms.sizeT = ms.imageCount;
    }
    MetadataStore store = makeFilterMetadata();
    MetadataTools.populatePixels(store, this);
    for (int i = 0; i < getSeriesCount(); i++) {
        store.setImageName("Series " + (i + 1), i);
    }
}