Examples with IFD loci.formats.tiff.IFD used on opensource projects

Example 26 with IFD

use of loci.formats.tiff.IFD in project bioformats by openmicroscopy.

the class IPWReader method get8BitLookupTable.

/* @see loci.formats.IFormatReader#get8BitLookupTable() */
@Override
public byte[][] get8BitLookupTable() throws FormatException, IOException {
    FormatTools.assertId(currentId, true, 1);
    RandomAccessInputStream stream = poi.getDocumentStream(imageFiles.get(0));
    TiffParser tp = new TiffParser(stream);
    IFD firstIFD = tp.getFirstIFD();
    int[] bits = firstIFD.getBitsPerSample();
    if (bits[0] <= 8) {
        int[] colorMap = tp.getColorMap(firstIFD);
        if (colorMap == null) {
            return null;
        }
        byte[][] table = new byte[3][colorMap.length / 3];
        int next = 0;
        for (int j = 0; j < table.length; j++) {
            for (int i = 0; i < table[0].length; i++) {
                table[j][i] = (byte) (colorMap[next++] >> 8);
            }
        }
        return table;
    }
    return null;
}

Example 27 with IFD

use of loci.formats.tiff.IFD in project bioformats by openmicroscopy.

the class IPWReader method openBytes.

/**
 * @see loci.formats.IFormatReader#openBytes(int, byte[], int, int, int, int)
 */
@Override
public byte[] openBytes(int no, byte[] buf, int x, int y, int w, int h) throws FormatException, IOException {
    FormatTools.checkPlaneParameters(this, no, buf.length, x, y, w, h);
    if (poi == null) {
        initPOIService();
    }
    RandomAccessInputStream stream = poi.getDocumentStream(imageFiles.get(no));
    TiffParser tp = new TiffParser(stream);
    IFD ifd = tp.getFirstIFD();
    tp.getSamples(ifd, buf, x, y, w, h);
    stream.close();
    return buf;
}

Example 28 with IFD

use of loci.formats.tiff.IFD in project bioformats by openmicroscopy.

the class SEQReader method initStandardMetadata.

// -- Internal BaseTiffReader API methods --
/* @see BaseTiffReader#initStandardMetadata() */
@Override
protected void initStandardMetadata() throws FormatException, IOException {
    super.initStandardMetadata();
    CoreMetadata m = core.get(0);
    m.sizeZ = 0;
    m.sizeT = 0;
    MetadataLevel level = getMetadataOptions().getMetadataLevel();
    for (IFD ifd : ifds) {
        if (level != MetadataLevel.MINIMUM) {
            short[] tag1 = (short[]) ifd.getIFDValue(IMAGE_PRO_TAG_1);
            if (tag1 != null) {
                StringBuilder seqId = new StringBuilder();
                for (int i = 0; i < tag1.length; i++) {
                    seqId.append(tag1[i]);
                }
                addGlobalMeta("Image-Pro SEQ ID", seqId.toString());
            }
        }
        int tag2 = ifds.get(0).getIFDIntValue(IMAGE_PRO_TAG_2);
        if (tag2 != -1) {
            // should be one of these for every image plane
            m.sizeZ++;
            addGlobalMeta("Frame Rate", tag2);
        }
        addGlobalMeta("Number of images", getSizeZ());
    }
    if (getSizeZ() == 0)
        m.sizeZ = 1;
    if (getSizeT() == 0)
        m.sizeT = 1;
    if (getSizeZ() == 1 && getSizeT() == 1) {
        m.sizeZ = ifds.size();
    }
    // default values
    addGlobalMeta("frames", getSizeZ());
    addGlobalMeta("channels", super.getSizeC());
    addGlobalMeta("slices", getSizeT());
    // parse the description to get channels, slices and times where applicable
    String descr = ifds.get(0).getComment();
    metadata.remove("Comment");
    if (descr != null) {
        String[] lines = descr.split("\n");
        for (String token : lines) {
            token = token.trim();
            int eq = token.indexOf('=');
            if (eq == -1)
                eq = token.indexOf(':');
            if (eq != -1) {
                String label = token.substring(0, eq);
                String data = token.substring(eq + 1);
                addGlobalMeta(label, data);
                if (label.equals("channels"))
                    m.sizeC = Integer.parseInt(data);
                else if (label.equals("frames")) {
                    m.sizeT = Integer.parseInt(data);
                } else if (label.equals("slices")) {
                    m.sizeZ = Integer.parseInt(data);
                }
            }
        }
    }
    if (isRGB() && getSizeC() != 3)
        m.sizeC *= 3;
    m.dimensionOrder = "XY";
    int maxNdx = 0, max = 0;
    int[] dims = { getSizeZ(), getSizeC(), getSizeT() };
    String[] axes = { "Z", "C", "T" };
    for (int i = 0; i < dims.length; i++) {
        if (dims[i] > max) {
            max = dims[i];
            maxNdx = i;
        }
    }
    m.dimensionOrder += axes[maxNdx];
    if (maxNdx != 1) {
        if (getSizeC() > 1) {
            m.dimensionOrder += 'C';
            m.dimensionOrder += (maxNdx == 0 ? axes[2] : axes[0]);
        } else
            m.dimensionOrder += (maxNdx == 0 ? axes[2] : axes[0]) + "C";
    } else {
        if (getSizeZ() > getSizeT())
            m.dimensionOrder += "ZT";
        else
            m.dimensionOrder += "TZ";
    }
}

Example 29 with IFD

use of loci.formats.tiff.IFD in project bioformats by openmicroscopy.

the class SEQReader method isThisType.

// -- IFormatReader API methods --
/* @see loci.formats.IFormatReader#isThisType(RandomAccessInputStream) */
@Override
public boolean isThisType(RandomAccessInputStream stream) throws IOException {
    TiffParser parser = new TiffParser(stream);
    parser.setDoCaching(false);
    IFD ifd = parser.getFirstIFD();
    if (ifd == null)
        return false;
    parser.fillInIFD(ifd);
    Object tag1 = ifd.get(IMAGE_PRO_TAG_1);
    Object tag3 = ifd.get(IMAGE_PRO_TAG_3);
    return (tag1 != null && (tag1 instanceof short[])) || (tag3 != null && (tag3 instanceof int[]));
}

Example 30 with IFD

use of loci.formats.tiff.IFD in project bioformats by openmicroscopy.

the class EPSReader 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);
    LOGGER.info("Verifying EPS format");
    String line = readLine();
    if (!line.trim().startsWith("%!PS")) {
        // read the TIFF preview
        isTiff = true;
        in.order(true);
        in.seek(20);
        int offset = in.readInt();
        int len = in.readInt();
        byte[] b = new byte[len];
        in.seek(offset);
        in.read(b);
        in = new RandomAccessInputStream(b);
        TiffParser tp = new TiffParser(in);
        ifds = tp.getIFDs();
        IFD firstIFD = ifds.get(0);
        map = tp.getColorMap(firstIFD);
        m.sizeX = (int) firstIFD.getImageWidth();
        m.sizeY = (int) firstIFD.getImageLength();
        m.sizeZ = 1;
        m.sizeT = 1;
        m.sizeC = firstIFD.getSamplesPerPixel();
        if (map != null && getSizeC() == 1) {
            m.sizeC = 3;
        }
        if (getSizeC() == 2)
            m.sizeC = 4;
        m.littleEndian = firstIFD.isLittleEndian();
        m.interleaved = true;
        m.rgb = getSizeC() > 1;
        m.pixelType = firstIFD.getPixelType();
        m.imageCount = 1;
        m.dimensionOrder = "XYCZT";
        m.metadataComplete = true;
        m.indexed = false;
        m.falseColor = false;
        MetadataStore store = makeFilterMetadata();
        MetadataTools.populatePixels(store, this);
        return;
    }
    LOGGER.info("Finding image data");
    binary = false;
    String image = "image";
    int lineNum = 1;
    line = readLine().trim();
    while (line != null && !line.equals("%%EOF")) {
        if (line.endsWith(image)) {
            if (!line.startsWith(image)) {
                if (line.indexOf("colorimage") != -1)
                    m.sizeC = 3;
                String[] t = line.split(" ");
                try {
                    int newX = Integer.parseInt(t[0]);
                    int newY = Integer.parseInt(t[1]);
                    if (t.length > 2 && Integer.parseInt(t[2]) >= 8) {
                        m.sizeX = newX;
                        m.sizeY = newY;
                        start = lineNum;
                    }
                } catch (NumberFormatException exc) {
                    LOGGER.debug("Could not parse image dimensions", exc);
                    if (t.length > 3) {
                        m.sizeC = Integer.parseInt(t[3]);
                    }
                }
            }
            break;
        } else if (line.startsWith("%%")) {
            if (line.startsWith("%%BoundingBox:")) {
                line = line.substring(14).trim();
                String[] t = line.split(" ");
                try {
                    int originX = Integer.parseInt(t[0].trim());
                    int originY = Integer.parseInt(t[1].trim());
                    m.sizeX = Integer.parseInt(t[2].trim()) - originX;
                    m.sizeY = Integer.parseInt(t[3].trim()) - originY;
                    addGlobalMeta("X-coordinate of origin", originX);
                    addGlobalMeta("Y-coordinate of origin", originY);
                } catch (NumberFormatException e) {
                    throw new FormatException("Files without image data are not supported.");
                }
            } else if (line.startsWith("%%BeginBinary")) {
                binary = true;
            } else {
                // parse key/value pairs
                int ndx = line.indexOf(':');
                if (ndx != -1) {
                    String key = line.substring(0, ndx);
                    String value = line.substring(ndx + 1);
                    addGlobalMeta(key, value);
                }
            }
        } else if (line.startsWith("%ImageData:")) {
            line = line.substring(11);
            String[] t = line.split(" ");
            m.sizeX = Integer.parseInt(t[0]);
            m.sizeY = Integer.parseInt(t[1]);
            m.sizeC = Integer.parseInt(t[3]);
            for (int i = 4; i < t.length; i++) {
                image = t[i].trim();
                if (image.length() > 1) {
                    image = image.substring(1, image.length() - 1);
                }
            }
        }
        lineNum++;
        line = readLine().trim();
    }
    LOGGER.info("Populating metadata");
    if (getSizeC() == 0)
        m.sizeC = 1;
    m.sizeZ = 1;
    m.sizeT = 1;
    m.dimensionOrder = "XYCZT";
    m.pixelType = FormatTools.UINT8;
    m.rgb = getSizeC() == 3;
    m.interleaved = true;
    m.littleEndian = true;
    m.imageCount = 1;
    // Populate metadata store
    // The metadata store we're working with.
    MetadataStore store = getMetadataStore();
    MetadataTools.populatePixels(store, this);
}