/* @see loci.formats.IFormatReader#isThisType(RandomAccessInputStream) */ public boolean isThisType(RandomAccessInputStream stream) throws IOException { final int blockLen = 4; if (!FormatTools.validStream(stream, blockLen, false)) return false; byte[] signature = new byte[blockLen]; stream.read(signature); if (signature[0] != (byte) 0xff || signature[1] != (byte) 0xd8 || signature[2] != (byte) 0xff || ((int) signature[3] & 0xf0) == 0) { return false; } return true; }
private byte[] decodeTile(int no, int row, int col) throws FormatException, IOException { if (tileMap[getCoreIndex()] == null) { return new byte[getTileSize()]; } int[] zct = getZCTCoords(no); TileCoordinate t = new TileCoordinate(nDimensions[getCoreIndex()]); t.coordinate[0] = col; t.coordinate[1] = row; for (String dim : dimensionOrdering.keySet()) { int index = dimensionOrdering.get(dim) + 2; if (dim.equals("Z")) { t.coordinate[index] = zct[0]; } else if (dim.equals("C")) { t.coordinate[index] = zct[1]; } else if (dim.equals("T")) { t.coordinate[index] = zct[2]; } } Integer index = (Integer) tileMap[getCoreIndex()].get(t); if (index == null) { return new byte[getTileSize()]; } Long offset = tileOffsets[getCoreIndex()][index]; RandomAccessInputStream ets = new RandomAccessInputStream(usedFiles[getCoreIndex()]); ets.seek(offset); CodecOptions options = new CodecOptions(); options.interleaved = isInterleaved(); options.littleEndian = isLittleEndian(); int tileSize = getTileSize(); if (tileSize == 0) { tileSize = tileX[getCoreIndex()] * tileY[getCoreIndex()] * 10; } options.maxBytes = (int) (offset + tileSize); byte[] buf = null; long end = index < tileOffsets[getCoreIndex()].length - 1 ? tileOffsets[getCoreIndex()][index + 1] : ets.length(); IFormatReader reader = null; String file = null; switch (compressionType[getCoreIndex()]) { case RAW: buf = new byte[tileSize]; ets.read(buf); break; case JPEG: Codec codec = new JPEGCodec(); buf = codec.decompress(ets, options); break; case JPEG_2000: codec = new JPEG2000Codec(); buf = codec.decompress(ets, options); break; case PNG: file = "tile.png"; reader = new APNGReader(); case BMP: if (reader == null) { file = "tile.bmp"; reader = new BMPReader(); } byte[] b = new byte[(int) (end - offset)]; ets.read(b); Location.mapFile(file, new ByteArrayHandle(b)); reader.setId(file); buf = reader.openBytes(0); Location.mapFile(file, null); break; } if (reader != null) { reader.close(); } ets.close(); return buf; }
/* @see Codec#decompress(RandomAccessInputStream, CodecOptions) */ public byte[] decompress(RandomAccessInputStream in, CodecOptions options) throws FormatException, IOException { if (in == null) throw new IllegalArgumentException("No data to decompress."); // Adapted from LZO for Java, available at // http://www.oberhumer.com/opensource/lzo/ ByteVector dst = new ByteVector(); int t = in.read() & 0xff; int mPos; if (t > 17) { t -= 17; // do dst[op++] = src[ip++]; while (--t > 0); byte[] b = new byte[t]; in.read(b); dst.add(b); t = in.read() & 0xff; // if (t < 16) return; if (t < 16) { return dst.toByteArray(); } } loop: for (; ; t = in.read() & 0xff) { if (t < 16) { if (t == 0) { byte f = in.readByte(); while (f == 0) { t += 255; f = in.readByte(); } t += 15 + (f & 0xff); } t += 3; // do dst[op++] = src[ip++]; while (--t > 0); byte[] b = new byte[t]; in.read(b); dst.add(b); t = in.read() & 0xff; if (t < 16) { mPos = dst.size() - 0x801 - (t >> 2) - ((in.read() & 0xff) << 2); if (mPos < 0) { t = LZO_OVERRUN; break loop; } t = 3; do { dst.add(dst.get(mPos++)); } while (--t > 0); // do dst[op++] = dst[mPos++]; while (--t > 0); in.seek(in.getFilePointer() - 2); t = in.read() & 3; in.skipBytes(1); if (t == 0) continue; // do dst[op++] = src[ip++]; while (--t > 0); b = new byte[t]; in.read(b); dst.add(b); t = in.read() & 0xff; } } for (; ; t = in.read() & 0xff) { if (t >= 64) { mPos = dst.size() - 1 - ((t >> 2) & 7) - ((in.read() & 0xff) << 3); t = (t >> 5) - 1; } else if (t >= 32) { t &= 31; if (t == 0) { byte f = in.readByte(); while (f == 0) { t += 255; f = in.readByte(); } t += 31 + (f & 0xff); } mPos = dst.size() - 1 - ((in.read() & 0xff) >> 2); mPos -= ((in.read() & 0xff) << 6); } else if (t >= 16) { mPos = dst.size() - ((t & 8) << 11); t &= 7; if (t == 0) { byte f = in.readByte(); while (f == 0) { t += 255; f = in.readByte(); } t += 7 + (f & 0xff); } mPos -= ((in.read() & 0xff) >> 2); mPos -= ((in.read() & 0xff) << 6); if (mPos == dst.size()) break loop; mPos -= 0x4000; } else { mPos = dst.size() - 1 - (t >> 2) - ((in.read() & 0xff) << 2); t = 0; } if (mPos < 0) { t = LZO_OVERRUN; break loop; } t += 2; // do dst[op++] = dst[mPos++]; while (--t > 0); do { dst.add(dst.get(mPos++)); } while (--t > 0); in.seek(in.getFilePointer() - 2); t = in.read() & 3; in.skipBytes(1); if (t == 0) break; // do dst[op++] = src[ip++]; while (--t > 0); byte[] b = new byte[t]; in.read(b); dst.add(b); t = 0; } } return dst.toByteArray(); }
/** * The CodecOptions parameter should have the following fields set: {@link CodecOptions#width * width} {@link CodecOptions#height height} * * @see Codec#decompress(RandomAccessInputStream, CodecOptions) */ public byte[] decompress(RandomAccessInputStream in, CodecOptions options) throws FormatException, IOException { if (in == null) throw new IllegalArgumentException("No data to decompress."); if (options == null) options = CodecOptions.getDefaultOptions(); in.skipBytes(8); int plane = options.width * options.height; stride = options.width; int rowInc = stride - 4; short opcode; int nBlocks; int colorA = 0, colorB; int[] color4 = new int[4]; int index, idx; int ta, tb; int blockPtr = 0; rowPtr = pixelPtr = 0; int pixelX, pixelY; int[] pixels = new int[plane]; byte[] rtn = new byte[plane * 3]; while (in.read() != (byte) 0xe1) ; in.skipBytes(3); totalBlocks = ((options.width + 3) / 4) * ((options.height + 3) / 4); while (in.getFilePointer() + 2 < in.length()) { opcode = in.readByte(); nBlocks = (opcode & 0x1f) + 1; if ((opcode & 0x80) == 0) { if (in.getFilePointer() >= in.length()) break; colorA = (opcode << 8) | in.read(); opcode = 0; if (in.getFilePointer() >= in.length()) break; if ((in.read() & 0x80) != 0) { opcode = 0x20; nBlocks = 1; } in.seek(in.getFilePointer() - 1); } switch (opcode & 0xe0) { case 0x80: while (nBlocks-- > 0) { updateBlock(options.width); } break; case 0xa0: if (in.getFilePointer() + 2 >= in.length()) break; colorA = in.readShort(); while (nBlocks-- > 0) { blockPtr = rowPtr + pixelPtr; for (pixelY = 0; pixelY < 4; pixelY++) { for (pixelX = 0; pixelX < 4; pixelX++) { if (blockPtr >= pixels.length) break; pixels[blockPtr] = colorA; short s = (short) (pixels[blockPtr] & 0x7fff); unpack(s, rtn, blockPtr, pixels.length); blockPtr++; } blockPtr += rowInc; } updateBlock(options.width); } break; case 0xc0: case 0x20: if (in.getFilePointer() + 2 >= in.length()) break; if ((opcode & 0xe0) == 0xc0) { colorA = in.readShort(); } colorB = in.readShort(); color4[0] = colorB; color4[1] = 0; color4[2] = 0; color4[3] = colorA; ta = (colorA >> 10) & 0x1f; tb = (colorB >> 10) & 0x1f; color4[1] |= ((11 * ta + 21 * tb) >> 5) << 10; color4[2] |= ((21 * ta + 11 * tb) >> 5) << 10; ta = (colorA >> 5) & 0x1f; tb = (colorB >> 5) & 0x1f; color4[1] |= ((11 * ta + 21 * tb) >> 5) << 5; color4[2] |= ((21 * ta + 11 * tb) >> 5) << 5; ta = colorA & 0x1f; tb = colorB & 0x1f; color4[1] |= (11 * ta + 21 * tb) >> 5; color4[2] |= (21 * ta + 11 * tb) >> 5; while (nBlocks-- > 0) { blockPtr = rowPtr + pixelPtr; for (pixelY = 0; pixelY < 4; pixelY++) { if (in.getFilePointer() >= in.length()) break; index = in.read(); for (pixelX = 0; pixelX < 4; pixelX++) { idx = (index >> (2 * (3 - pixelX))) & 3; if (blockPtr >= pixels.length) break; pixels[blockPtr] = color4[idx]; short s = (short) (pixels[blockPtr] & 0x7fff); unpack(s, rtn, blockPtr, pixels.length); blockPtr++; } blockPtr += rowInc; } updateBlock(options.width); } break; case 0x00: blockPtr = rowPtr + pixelPtr; for (pixelY = 0; pixelY < 4; pixelY++) { for (pixelX = 0; pixelX < 4; pixelX++) { if ((pixelY != 0) || (pixelX != 0)) { if (in.getFilePointer() + 2 >= in.length()) break; colorA = in.readShort(); } if (blockPtr >= pixels.length) break; pixels[blockPtr] = colorA; short s = (short) (pixels[blockPtr] & 0x7fff); unpack(s, rtn, blockPtr, pixels.length); blockPtr++; } blockPtr += rowInc; } updateBlock(options.width); break; } } return rtn; }