Examples with Box com.sun.media.imageioimpl.plugins.jpeg2000.Box used on opensource projects

Example 11 with Box

use of com.sun.media.imageioimpl.plugins.jpeg2000.Box in project bioformats by openmicroscopy.

the class FileFormatReader method readPaletteBox.

/**
 * This method reads the content of the palette box
 */
public void readPaletteBox(int length) throws IOException {
    // Get current position in file
    int pos = in.getPos();
    int lutSize = in.readShort();
    int numComp = in.readByte();
    compSize = new byte[numComp];
    for (int i = 0; i < numComp; i++) {
        compSize[i] = (byte) in.readByte();
    }
    lut = new byte[numComp][lutSize];
    for (int n = 0; n < lutSize; n++) {
        for (int c = 0; c < numComp; c++) {
            int depth = 1 + (compSize[c] & 0x7F);
            if (depth > 32)
                depth = 32;
            int numBytes = (depth + 7) >> 3;
            int mask = (1 << depth) - 1;
            byte[] buf = new byte[numBytes];
            in.readFully(buf, 0, numBytes);
            int val = 0;
            for (int k = 0; k < numBytes; k++) {
                val = buf[k] + (val << 8);
            }
            lut[c][n] = (byte) val;
        }
    }
    if (metadata != null) {
        metadata.addNode(new PaletteBox(length, compSize, lut));
    }
}

Example 12 with Box

use of com.sun.media.imageioimpl.plugins.jpeg2000.Box in project bioformats by openmicroscopy.

the class FileFormatReader method readChannelDefinitionBox.

/**
 * This method reads the Channel Definition box
 *
 * @exception java.io.IOException If an I/O error ocurred.
 */
public void readChannelDefinitionBox(int length) throws IOException {
    int num = in.readShort();
    channels = new short[num];
    cType = new short[num];
    associations = new short[num];
    for (int i = 0; i < num; i++) {
        channels[i] = in.readShort();
        cType[i] = in.readShort();
        associations[i] = in.readShort();
    }
    if (metadata != null) {
        metadata.addNode(new ChannelDefinitionBox(channels, cType, associations));
    }
}

Example 13 with Box

use of com.sun.media.imageioimpl.plugins.jpeg2000.Box in project bioformats by openmicroscopy.

the class FileFormatReader method readXMLBox.

/**
 * This method reads the contents of the XML box
 */
public void readXMLBox(int length) throws IOException {
    if (metadata != null) {
        byte[] data = new byte[length];
        in.readFully(data, 0, length);
        metadata.addNode(new XMLBox(data));
    }
}

Example 14 with Box

use of com.sun.media.imageioimpl.plugins.jpeg2000.Box in project bioformats by openmicroscopy.

the class FileFormatReader method readFileFormat.

/**
 * This method checks whether the given RandomAccessIO is a valid JP2 file
 * and if so finds the first codestream in the file. Currently, the
 * information in the codestream is not used
 *
 * @exception java.io.IOException If an I/O error ocurred.
 *
 * @exception java.io.EOFException If end of file is reached
 */
public void readFileFormat() throws IOException, EOFException {
    int foundCodeStreamBoxes = 0;
    int box;
    int length;
    long longLength = 0;
    int pos;
    short marker;
    boolean jp2HeaderBoxFound = false;
    boolean lastBoxFound = false;
    try {
        // Go through the randomaccessio and find the first
        // contiguous codestream box. Check also that the File Format is
        // correct
        pos = in.getPos();
        // or if not that the first 2 bytes is the SOC marker
        if (in.readInt() != 0x0000000c || in.readInt() != JP2_SIGNATURE_BOX || in.readInt() != 0x0d0a870a) {
            // Not a JP2 file
            in.seek(pos);
            marker = (short) in.readShort();
            if (// Standard syntax marker found
            marker != Markers.SOC)
                throw new Error("File is neither valid JP2 file nor " + "valid JPEG 2000 codestream");
            in.seek(pos);
            if (codeStreamPos == null)
                codeStreamPos = new Vector();
            codeStreamPos.addElement(new Integer(pos));
            return;
        }
        if (metadata != null)
            metadata.addNode(new SignatureBox());
        // Read all remaining boxes
        while (!lastBoxFound) {
            pos = in.getPos();
            length = in.readInt();
            if ((pos + length) == in.length())
                lastBoxFound = true;
            box = in.readInt();
            if (length == 0) {
                lastBoxFound = true;
                length = in.length() - in.getPos();
            } else if (length == 1) {
                longLength = in.readLong();
                throw new IOException("File too long.");
            } else
                longLength = (long) 0;
            pos = in.getPos();
            length -= 8;
            switch(box) {
                case FILE_TYPE_BOX:
                    readFileTypeBox(length + 8, longLength);
                    break;
                case CONTIGUOUS_CODESTREAM_BOX:
                    if (!jp2HeaderBoxFound)
                        throw new Error("Invalid JP2 file: JP2Header box not " + "found before Contiguous codestream " + "box ");
                    readContiguousCodeStreamBox(length + 8, longLength);
                    break;
                case JP2_HEADER_BOX:
                    if (jp2HeaderBoxFound)
                        throw new Error("Invalid JP2 file: Multiple " + "JP2Header boxes found");
                    readJP2HeaderBox(length + 8);
                    jp2HeaderBoxFound = true;
                    length = 0;
                    break;
                case IMAGE_HEADER_BOX:
                    readImageHeaderBox(length);
                    break;
                case INTELLECTUAL_PROPERTY_BOX:
                    readIntPropertyBox(length);
                    break;
                case XML_BOX:
                    readXMLBox(length);
                    break;
                case UUID_INFO_BOX:
                    length = 0;
                    break;
                case UUID_BOX:
                    readUUIDBox(length);
                    break;
                case UUID_LIST_BOX:
                    readUUIDListBox(length);
                    break;
                case URL_BOX:
                    readURLBox(length);
                    break;
                case PALETTE_BOX:
                    readPaletteBox(length + 8);
                    break;
                case BITS_PER_COMPONENT_BOX:
                    readBitsPerComponentBox(length);
                    break;
                case COMPONENT_MAPPING_BOX:
                    readComponentMappingBox(length);
                    break;
                case COLOUR_SPECIFICATION_BOX:
                    readColourSpecificationBox(length);
                    break;
                case CHANNEL_DEFINITION_BOX:
                    readChannelDefinitionBox(length);
                    break;
                case RESOLUTION_BOX:
                    length = 0;
                    break;
                case CAPTURE_RESOLUTION_BOX:
                case DEFAULT_DISPLAY_RESOLUTION_BOX:
                    readResolutionBox(box, length);
                    break;
                default:
                    if (metadata != null) {
                        byte[] data = new byte[length];
                        in.readFully(data, 0, length);
                        metadata.addNode(new Box(length + 8, box, longLength, data));
                    }
            }
            if (!lastBoxFound)
                in.seek(pos + length);
        }
    } catch (EOFException e) {
        throw new Error("EOF reached before finding Contiguous " + "Codestream Box");
    }
    if (codeStreamPos.size() == 0) {
        // Not a valid JP2 file or codestream
        throw new Error("Invalid JP2 file: Contiguous codestream box " + "missing");
    }
    return;
}

Example 15 with Box

use of com.sun.media.imageioimpl.plugins.jpeg2000.Box in project bioformats by openmicroscopy.

the class FileFormatReader method readUUIDBox.

/**
 * This method reads the contents of the Intellectual property box
 */
public void readUUIDBox(int length) throws IOException {
    if (metadata != null) {
        byte[] data = new byte[length];
        in.readFully(data, 0, length);
        metadata.addNode(new UUIDBox(data));
    }
}