Examples with RandomAccessInputStream loci.common.RandomAccessInputStream used on opensource projects

Example 41 with RandomAccessInputStream

use of loci.common.RandomAccessInputStream in project bioformats by openmicroscopy.

the class SBIGReader 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);
    Double sizeX = null, sizeY = null;
    String date = null, description = null;
    String[] lines = DataTools.readFile(currentId).split("\n");
    for (String line : lines) {
        line = line.trim();
        int eq = line.indexOf('=');
        if (eq != -1) {
            String key = line.substring(0, eq).trim();
            String value = line.substring(eq + 1).trim();
            addGlobalMeta(key, value);
            if (key.equals("Width")) {
                m.sizeX = Integer.parseInt(value);
            } else if (key.equals("Height")) {
                m.sizeY = Integer.parseInt(value);
            } else if (key.equals("Note")) {
                description = value;
            } else if (key.equals("X_pixel_size")) {
                sizeX = new Double(value) * 1000;
            } else if (key.equals("Y_pixel_size")) {
                sizeY = new Double(value) * 1000;
            } else if (key.equals("Date")) {
                date = value;
            } else if (key.equals("Time")) {
                date += " " + value;
            }
        } else if (line.indexOf("Compressed") != -1) {
            compressed = true;
        } else if (line.equals("End"))
            break;
    }
    m.pixelType = FormatTools.UINT16;
    m.littleEndian = true;
    m.rgb = false;
    m.sizeZ = 1;
    m.sizeC = 1;
    m.sizeT = 1;
    m.imageCount = 1;
    m.dimensionOrder = "XYZCT";
    MetadataStore store = makeFilterMetadata();
    MetadataTools.populatePixels(store, this);
    if (date != null) {
        date = DateTools.formatDate(date, DATE_FORMAT);
        if (date != null) {
            store.setImageAcquisitionDate(new Timestamp(date), 0);
        }
    }
    if (getMetadataOptions().getMetadataLevel() != MetadataLevel.MINIMUM) {
        Length x = FormatTools.getPhysicalSizeX(sizeX);
        Length y = FormatTools.getPhysicalSizeY(sizeY);
        if (x != null) {
            store.setPixelsPhysicalSizeX(x, 0);
        }
        if (y != null) {
            store.setPixelsPhysicalSizeY(y, 0);
        }
        store.setImageDescription(description, 0);
    }
}

Example 42 with RandomAccessInputStream

use of loci.common.RandomAccessInputStream in project bioformats by openmicroscopy.

the class SDTReader 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(true);
    LOGGER.info("Reading header");
    // read file header information
    info = new SDTInfo(in, metadata);
    timeBins = info.timeBins;
    channels = info.channels;
    addGlobalMeta("time bins", timeBins);
    addGlobalMeta("channels", channels);
    double timeBase = 1e9 * info.tacR / info.tacG;
    addGlobalMeta("time base", timeBase);
    LOGGER.info("Populating metadata");
    CoreMetadata m = core.get(0);
    int timepoints = info.timepoints;
    if (timepoints == 0) {
        timepoints = 1;
    }
    m.sizeX = info.width;
    m.sizeY = info.height;
    m.sizeZ = 1;
    m.sizeT = intensity ? timepoints : timeBins * timepoints;
    m.sizeC = channels;
    m.dimensionOrder = "XYZTC";
    m.pixelType = FormatTools.UINT16;
    m.rgb = false;
    m.littleEndian = true;
    m.imageCount = m.sizeZ * m.sizeC * m.sizeT;
    m.indexed = false;
    m.falseColor = false;
    m.metadataComplete = true;
    if (intensity) {
        m.moduloT.parentType = FormatTools.SPECTRA;
    } else {
        m.moduloT.type = FormatTools.LIFETIME;
        m.moduloT.parentType = FormatTools.SPECTRA;
        m.moduloT.typeDescription = "TCSPC";
        m.moduloT.start = 0;
        timeBase *= 1000;
        m.moduloT.step = timeBase / timeBins;
        m.moduloT.end = m.moduloT.step * (m.sizeT - 1);
        m.moduloT.unit = "ps";
    }
    for (int i = 1; i < info.allBlockOffsets.length; i++) {
        CoreMetadata p = new CoreMetadata(m);
        core.add(p);
        int planeSize = m.sizeX * m.sizeY * FormatTools.getBytesPerPixel(m.pixelType);
        if (info.allBlockLengths[i] != planeSize * m.imageCount) {
            if (info.mcstaPoints * planeSize == info.allBlockLengths[i]) {
                p.sizeT = info.mcstaPoints;
                p.moduloT.end = p.moduloT.step * (p.sizeT - 1);
                p.imageCount = p.sizeZ * p.sizeC * p.sizeT;
            }
        }
    }
    // Arbitrarily chosen size limit for buffer
    int sizeThreshold = 512 * 512 * 512;
    // default No of bins in buffer
    blockLength = 2048;
    while (blockLength * m.sizeX * m.sizeY > sizeThreshold) {
        blockLength = blockLength / 2;
    }
    if (blockLength > timeBins) {
        blockLength = timeBins;
    }
    MetadataStore store = makeFilterMetadata();
    MetadataTools.populatePixels(store, this);
}

Example 43 with RandomAccessInputStream

use of loci.common.RandomAccessInputStream in project bioformats by openmicroscopy.

the class SIFReader 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);
    double[] timestamp = null;
    int lineNumber = 1;
    String line = in.readLine();
    int endLine = -1;
    while (endLine < 0 || lineNumber < endLine) {
        lineNumber++;
        if (line.startsWith("Pixel number")) {
            String[] tokens = line.split(" ");
            if (tokens.length > 2) {
                m.sizeC = Integer.parseInt(tokens[2]);
                m.sizeX = Integer.parseInt(tokens[3]);
                m.sizeY = Integer.parseInt(tokens[4]);
                m.sizeZ = Integer.parseInt(tokens[5]);
                m.sizeT = Integer.parseInt(tokens[6]);
                m.imageCount = getSizeZ() * getSizeT() * getSizeC();
                timestamp = new double[getImageCount()];
                endLine = lineNumber;
            }
        } else if (lineNumber < endLine) {
            int index = lineNumber - (endLine - getImageCount()) - 1;
            if (index >= 0) {
                try {
                    timestamp[index] = Double.parseDouble(line.trim());
                } catch (NumberFormatException e) {
                    LOGGER.debug("Could not parse timestamp #" + index, e);
                }
            }
        } else {
            addGlobalMetaList("Line", line.trim());
        }
        line = in.readLine();
        if (endLine > 0 && endLine == lineNumber) {
            String[] tokens = line.split(" ");
            int x1 = Integer.parseInt(tokens[1]);
            int y1 = Integer.parseInt(tokens[2]);
            int x2 = Integer.parseInt(tokens[3]);
            int y2 = Integer.parseInt(tokens[4]);
            int x3 = Integer.parseInt(tokens[5]);
            int y3 = Integer.parseInt(tokens[6]);
            m.sizeX = (int) (Math.abs(x1 - x2) + x3);
            m.sizeY = (int) (Math.abs(y1 - y2) + y3);
            pixelOffset = in.length() - FOOTER_SIZE - (getImageCount() * getSizeX() * getSizeY() * 4);
        }
    }
    m.pixelType = FormatTools.FLOAT;
    m.dimensionOrder = "XYCZT";
    m.littleEndian = true;
    MetadataStore store = makeFilterMetadata();
    MetadataTools.populatePixels(store, this, getMetadataOptions().getMetadataLevel() != MetadataLevel.MINIMUM);
    if (getMetadataOptions().getMetadataLevel() != MetadataLevel.MINIMUM) {
        for (int i = 0; i < getImageCount(); i++) {
            store.setPlaneDeltaT(new Time(timestamp[i], UNITS.SECOND), 0, i);
        }
    }
}

Example 44 with RandomAccessInputStream

use of loci.common.RandomAccessInputStream in project bioformats by openmicroscopy.

the class APNGReader 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 (no == lastImageIndex && lastImage != null && y + h <= lastImageRow) {
        RandomAccessInputStream s = new RandomAccessInputStream(lastImage);
        readPlane(s, x, y, w, h, buf);
        s.close();
        s = null;
        return buf;
    }
    if (no == 0) {
        lastImage = null;
        PNGInputStream stream = new PNGInputStream("IDAT");
        int decodeHeight = y + h;
        if (decodeHeight < getSizeY() && decodeHeight % 8 != 0) {
            decodeHeight += 8 - (decodeHeight % 8);
        }
        lastImage = decode(stream, getSizeX(), decodeHeight);
        stream.close();
        lastImageIndex = 0;
        lastImageRow = y + h;
        RandomAccessInputStream pix = new RandomAccessInputStream(lastImage);
        readPlane(pix, x, y, w, h, buf);
        pix.close();
        pix = null;
        if (y + h < getSizeY()) {
            lastImage = null;
        }
        return buf;
    }
    int[] coords = frameCoordinates.get(no);
    lastImage = openBytes(0);
    lastImageRow = getSizeY();
    PNGInputStream stream = new PNGInputStream("fdAT", no);
    byte[] newImage = decode(stream, coords[2], coords[3]);
    stream.close();
    // paste current image onto first image
    int bpp = FormatTools.getBytesPerPixel(getPixelType());
    int len = coords[2] * bpp;
    int plane = getSizeX() * getSizeY() * bpp;
    int newPlane = len * coords[3];
    if (!isInterleaved()) {
        for (int c = 0; c < getRGBChannelCount(); c++) {
            for (int row = 0; row < coords[3]; row++) {
                System.arraycopy(newImage, c * newPlane + row * len, lastImage, c * plane + (coords[1] + row) * getSizeX() * bpp + coords[0] * bpp, len);
            }
        }
    } else {
        len *= getRGBChannelCount();
        for (int row = 0; row < coords[3]; row++) {
            System.arraycopy(newImage, row * len, lastImage, (coords[1] + row) * getSizeX() * bpp * getRGBChannelCount() + coords[0] * bpp * getRGBChannelCount(), len);
        }
    }
    lastImageIndex = no;
    RandomAccessInputStream pix = new RandomAccessInputStream(lastImage);
    readPlane(pix, x, y, w, h, buf);
    pix.close();
    return buf;
}

Example 45 with RandomAccessInputStream

use of loci.common.RandomAccessInputStream 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);
}