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 loci.formats.IFormatReader#openBytes(int, byte[], int, int, int, int) */
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);
int index = no;
for (int i = 0; i < series; i++) {
index += core[i].imageCount;
}
if (index >= binDataOffsets.size()) {
index = binDataOffsets.size() - 1;
}
long offset = binDataOffsets.get(index).longValue();
String compress = compression.get(index);
in.seek(offset);
int depth = FormatTools.getBytesPerPixel(getPixelType());
int planeSize = getSizeX() * getSizeY() * depth;
CodecOptions options = new CodecOptions();
options.width = getSizeX();
options.height = getSizeY();
options.bitsPerSample = depth * 8;
options.channels = getRGBChannelCount();
options.maxBytes = planeSize;
options.littleEndian = isLittleEndian();
options.interleaved = isInterleaved();
byte[] pixels = new Base64Codec().decompress(in, options);
// return a blank plane if no pixel data was stored
if (pixels.length == 0) {
LOGGER.debug("No pixel data for plane #{}", no);
return buf;
}
// TODO: Create a method uncompress to handle all compression methods
if (compress.equals("bzip2")) {
byte[] tempPixels = pixels;
pixels = new byte[tempPixels.length - 2];
System.arraycopy(tempPixels, 2, pixels, 0, pixels.length);
ByteArrayInputStream bais = new ByteArrayInputStream(pixels);
CBZip2InputStream bzip = new CBZip2InputStream(bais);
pixels = new byte[planeSize];
bzip.read(pixels, 0, pixels.length);
tempPixels = null;
bais.close();
bais = null;
bzip = null;
} else if (compress.equals("zlib")) {
pixels = new ZlibCodec().decompress(pixels, options);
} else if (compress.equals("J2K")) {
pixels = new JPEG2000Codec().decompress(pixels, options);
} else if (compress.equals("JPEG")) {
pixels = new JPEGCodec().decompress(pixels, options);
}
for (int row = 0; row < h; row++) {
int off = (row + y) * getSizeX() * depth + x * depth;
System.arraycopy(pixels, off, buf, row * w * depth, w * depth);
}
pixels = null;
return buf;
}