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

Example 26 with RandomAccessInputStream

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

the class I2IReader method initFile.

// -- Internal FormatReader API methods --
/* @see loci.formats.FormatReader#initFile(String) */
@Override
public void initFile(String id) throws FormatException, IOException {
    super.initFile(id);
    in = new RandomAccessInputStream(id);
    CoreMetadata m = core.get(0);
    char pixelType = (char) in.readByte();
    switch(pixelType) {
        case 'I':
            m.pixelType = FormatTools.INT16;
            break;
        case 'R':
            m.pixelType = FormatTools.FLOAT;
            break;
        case 'C':
            throw new FormatException("Complex pixel data not yet supported");
        default:
            throw new FormatException("Invalid pixel type: " + pixelType);
    }
    if ((char) in.readByte() != ' ') {
        throw new FormatException("Expected space after pixel type character");
    }
    m.sizeX = getDimension(in);
    m.sizeY = getDimension(in);
    m.sizeZ = getDimension(in);
    m.littleEndian = (char) in.readByte() != 'B';
    in.order(isLittleEndian());
    short minPixelValue = in.readShort();
    short maxPixelValue = in.readShort();
    short xCoordinate = in.readShort();
    short yCoordinate = in.readShort();
    int n = in.readShort();
    // reserved for future use
    in.skipBytes(33);
    for (int i = 0; i < 15; i++) {
        String history = in.readString(64);
        addGlobalMetaList("Image history", history.trim());
    }
    addGlobalMeta("Minimum intensity value", minPixelValue);
    addGlobalMeta("Maximum intensity value", maxPixelValue);
    addGlobalMeta("Image position X", xCoordinate);
    addGlobalMeta("Image position Y", yCoordinate);
    // needs to be adjusted to reflect the true Z count
    if (n > 0) {
        m.sizeZ /= n;
    }
    // the user defines what the N dimension means
    // in practice, it could be timepoints, channels, etc. but we have no
    // way of knowing based on the file metadata
    m.sizeT = n;
    m.imageCount = getSizeZ() * getSizeT();
    m.sizeC = 1;
    m.rgb = false;
    m.dimensionOrder = "XYZTC";
    MetadataStore store = makeFilterMetadata();
    MetadataTools.populatePixels(store, this);
}

Example 27 with RandomAccessInputStream

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

the class PCIReader method getOptimalTileWidth.

/* @see loci.formats.IFormatReader#getOptimalTileWidth() */
@Override
public int getOptimalTileWidth() {
    FormatTools.assertId(currentId, true, 1);
    String file = imageFiles.get(0);
    try {
        if (poi == null) {
            initPOIService();
        }
        RandomAccessInputStream s = poi.getDocumentStream(file);
        TiffParser tp = new TiffParser(s);
        if (tp.isValidHeader()) {
            IFD ifd = tp.getFirstIFD();
            s.close();
            return (int) ifd.getTileWidth();
        }
        s.close();
    } catch (FormatException e) {
        LOGGER.debug("Could not retrieve tile width", e);
    } catch (IOException e) {
        LOGGER.debug("Could not retrieve tile width", e);
    }
    return super.getOptimalTileWidth();
}

Example 28 with RandomAccessInputStream

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

the class PCIReader 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();
    }
    String file = imageFiles.get(no);
    RandomAccessInputStream s = poi.getDocumentStream(file);
    TiffParser tp = new TiffParser(s);
    if (tp.isValidHeader()) {
        IFD ifd = tp.getFirstIFD();
        tp.getSamples(ifd, buf, x, y, w, h);
    } else {
        s.seek(0);
        readPlane(s, x, y, w, h, buf);
    }
    s.close();
    return buf;
}

Example 29 with RandomAccessInputStream

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

the class PCORAWReader method initFile.

// -- Internal FormatReader API methods --
/* @see loci.formats.FormatReader#initFile(String) */
@Override
protected void initFile(String id) throws FormatException, IOException {
    if (checkSuffix(id, "rec")) {
        paramFile = new Location(id).getAbsolutePath();
        String base = new Location(id).getAbsoluteFile().getAbsolutePath();
        base = base.substring(0, base.lastIndexOf("."));
        id = base + ".pcoraw";
        if (!new Location(id).exists()) {
            throw new FormatException("Could not find image file.");
        }
    }
    super.initFile(id);
    imageFile = new Location(id).getAbsolutePath();
    reader.close();
    reader.setMetadataStore(getMetadataStore());
    reader.setId(id);
    core = reader.getCoreMetadataList();
    metadata = reader.getGlobalMetadata();
    in = new RandomAccessInputStream(id);
    try {
        if (in.length() >= Math.pow(2, 32)) {
            // even though BigTIFF is likely being used, the offsets
            // are still recorded as though only 32 bits are available
            long add = 0;
            long prevOffset = 0;
            for (IFD ifd : reader.ifds) {
                long[] offsets = ifd.getStripOffsets();
                for (int i = 0; i < offsets.length; i++) {
                    offsets[i] += add;
                    if (offsets[i] < prevOffset) {
                        add += 0x100000000L;
                        offsets[i] += 0x100000000L;
                    }
                    prevOffset = offsets[i];
                }
                ifd.put(IFD.STRIP_OFFSETS, offsets);
            }
        }
    } finally {
        in.close();
    }
    if (paramFile == null) {
        String base = imageFile.substring(0, imageFile.lastIndexOf("."));
        base += ".rec";
        if (new Location(base).exists()) {
            paramFile = base;
        }
    }
    MetadataStore store = makeFilterMetadata();
    MetadataTools.populatePixels(store, this, true);
    if (paramFile != null) {
        // parse extra metadata from the parameter file
        store.setInstrumentID(MetadataTools.createLSID("Instrument", 0), 0);
        String detector = MetadataTools.createLSID("Detector", 0, 0);
        store.setDetectorID(detector, 0, 0);
        String[] lines = DataTools.readFile(paramFile).split("\n");
        for (int i = 0; i < lines.length; i++) {
            String line = lines[i];
            int sep = line.indexOf(':');
            if (sep < 0) {
                continue;
            }
            String key = line.substring(0, sep).trim();
            String value = line.substring(sep + 1).trim();
            addGlobalMeta(key, value);
            if (key.equals("Exposure / Delay")) {
                // set the exposure time
                String exp = value.substring(0, value.indexOf(' '));
                Double parsedExp = new Double(exp);
                Time exposure = null;
                if (parsedExp != null) {
                    exposure = new Time(parsedExp / 1000, UNITS.SECOND);
                }
                for (int plane = 0; plane < getImageCount(); plane++) {
                    store.setPlaneExposureTime(exposure, 0, plane);
                }
            } else if (key.equals("Camera serial number")) {
                // set the serial number
                store.setDetectorSerialNumber(value, 0, 0);
            } else if (key.equals("Binning horz./vert.")) {
                store.setDetectorSettingsID(detector, 0, 0);
                value = value.charAt(1) + value;
                value = value.substring(0, 3);
                store.setDetectorSettingsBinning(getBinning(value), 0, 0);
            } else if (key.equals("Comment")) {
                final StringBuilder description = new StringBuilder();
                for (int j = i + 1; j < lines.length; j++) {
                    lines[j] = lines[j].trim();
                    if (lines[j].length() > 0) {
                        description.append(lines[j]);
                        description.append(" ");
                    }
                }
                store.setImageDescription(description.toString().trim(), 0);
                break;
            }
        }
    }
}

Example 30 with RandomAccessInputStream

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

the class PSDReader 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);
    m.littleEndian = false;
    if (!in.readString(4).equals("8BPS")) {
        throw new FormatException("Not a valid Photoshop file.");
    }
    addGlobalMeta("Version", in.readShort());
    // reserved, set to 0
    in.skipBytes(6);
    m.sizeC = in.readShort();
    m.sizeY = in.readInt();
    m.sizeX = in.readInt();
    int bits = in.readShort();
    addGlobalMeta("Bits per pixel", bits);
    m.pixelType = FormatTools.pixelTypeFromBytes(bits / 8, false, false);
    int colorMode = in.readShort();
    String modeString = null;
    switch(colorMode) {
        case 0:
            modeString = "monochrome";
            break;
        case 1:
            modeString = "gray-scale";
            break;
        case 2:
            modeString = "palette color";
            break;
        case 3:
            modeString = "RGB";
            break;
        case 4:
            modeString = "CMYK";
            break;
        case 6:
            modeString = "Duotone";
            break;
        case 7:
            modeString = "Multichannel color";
            break;
        case 8:
            modeString = "Duotone";
            break;
        case 9:
            modeString = "LAB color";
            break;
    }
    addGlobalMeta("Color mode", modeString);
    // read color mode block, if present
    int modeDataLength = in.readInt();
    long fp = in.getFilePointer();
    if (modeDataLength != 0) {
        if (colorMode == 2) {
            lut = new byte[3][256];
            for (int i = 0; i < lut.length; i++) {
                in.read(lut[i]);
            }
        }
        in.seek(fp + modeDataLength);
    }
    // read image resources block
    in.skipBytes(4);
    while (in.readString(4).equals("8BIM")) {
        int tag = in.readShort();
        int read = 1;
        while (in.read() != 0) read++;
        if (read % 2 == 1)
            in.skipBytes(1);
        int size = in.readInt();
        if (size % 2 == 1)
            size++;
        in.skipBytes(size);
    }
    in.seek(in.getFilePointer() - 4);
    int blockLen = in.readInt();
    if (blockLen == 0) {
        offset = in.getFilePointer();
    } else {
        int layerLen = in.readInt();
        int layerCount = in.readShort();
        if (layerCount < 0) {
            throw new FormatException("Vector data is not supported.");
        }
        if (layerLen == 0 && layerCount == 0) {
            in.skipBytes(2);
            int check = in.readShort();
            in.seek(in.getFilePointer() - (check == 0 ? 4 : 2));
        }
        int[] w = new int[layerCount];
        int[] h = new int[layerCount];
        int[] c = new int[layerCount];
        for (int i = 0; i < layerCount; i++) {
            int top = in.readInt();
            int left = in.readInt();
            int bottom = in.readInt();
            int right = in.readInt();
            w[i] = right - left;
            h[i] = bottom - top;
            c[i] = in.readShort();
            in.skipBytes(c[i] * 6 + 12);
            int len = in.readInt();
            if (len % 2 == 1)
                len++;
            in.skipBytes(len);
        }
        // skip over pixel data for each layer
        for (int i = 0; i < layerCount; i++) {
            if (h[i] < 0) {
                continue;
            }
            int[] lens = new int[h[i]];
            for (int cc = 0; cc < c[i]; cc++) {
                boolean compressed = in.readShort() == 1;
                if (!compressed)
                    in.skipBytes(w[i] * h[i]);
                else {
                    for (int y = 0; y < h[i]; y++) {
                        lens[y] = in.readShort();
                    }
                    for (int y = 0; y < h[i]; y++) {
                        in.skipBytes(lens[y]);
                    }
                }
            }
        }
        long start = in.getFilePointer();
        while (in.read() != '8') ;
        in.skipBytes(7);
        if (in.getFilePointer() - start > 1024) {
            in.seek(start);
        }
        int len = in.readInt();
        if ((len % 4) != 0)
            len += 4 - (len % 4);
        if (len > in.length() - in.getFilePointer() || (len & 0xff0000) >> 16 == 1) {
            in.seek(start);
            len = 0;
        }
        in.skipBytes(len);
        String s = in.readString(4);
        while (s.equals("8BIM")) {
            in.skipBytes(4);
            len = in.readInt();
            if ((len % 4) != 0)
                len += 4 - (len % 4);
            in.skipBytes(len);
            s = in.readString(4);
        }
        offset = in.getFilePointer() - 4;
    }
    m.sizeZ = 1;
    m.sizeT = 1;
    m.rgb = modeString.equals("RGB") || modeString.equals("CMYK");
    m.imageCount = getSizeC() / (isRGB() ? 3 : 1);
    m.indexed = modeString.equals("palette color");
    m.falseColor = false;
    m.dimensionOrder = "XYCZT";
    m.interleaved = false;
    m.metadataComplete = true;
    in.seek(offset);
    compressed = in.readShort() == 1;
    lens = new int[getSizeC()][getSizeY()];
    if (compressed) {
        for (int c = 0; c < getSizeC(); c++) {
            for (int row = 0; row < getSizeY(); row++) {
                lens[c][row] = in.readShort();
            }
        }
    }
    offset = in.getFilePointer();
    MetadataStore store = makeFilterMetadata();
    MetadataTools.populatePixels(store, this);
}