/* @see loci.formats.IFormatReader#isThisType(String, boolean) */
public boolean isThisType(String name, boolean open) {
if (!open) return false; // not allowed to touch the file system
if (name.equals(METADATA)
|| name.endsWith(File.separator + METADATA)
|| name.equals(XML)
|| name.endsWith(File.separator + XML)) {
final int blockSize = 1048576;
try {
RandomAccessInputStream stream = new RandomAccessInputStream(name);
long length = stream.length();
String data = stream.readString((int) Math.min(blockSize, length));
stream.close();
return length > 0
&& (data.indexOf("Micro-Manager") >= 0 || data.indexOf("micromanager") >= 0);
} catch (IOException e) {
return false;
}
}
try {
Location parent = new Location(name).getAbsoluteFile().getParentFile();
Location metaFile = new Location(parent, METADATA);
RandomAccessInputStream s = new RandomAccessInputStream(name);
boolean validTIFF = isThisType(s);
s.close();
return validTIFF && isThisType(metaFile.getAbsolutePath(), open);
} catch (NullPointerException e) {
} catch (IOException e) {
}
return false;
}
/**
* Constructor RawDataBlockList
*
* @param stream the InputStream from which the data will be read
* @exception IOException on I/O errors, and if an incomplete block is read
*/
public RawDataBlockList(final RandomAccessInputStream stream, int size) throws IOException {
List blocks = new ArrayList();
bigBlockSize = size;
while (true) {
RawDataBlock block = new RawDataBlock(stream, size);
if (block.eof()) {
break;
}
blocks.add(block);
if (size + stream.getFilePointer() > stream.length()) {
break;
}
stream.skipBytes(size);
}
setBlocks((RawDataBlock[]) blocks.toArray(new RawDataBlock[0]));
}
private void readTags(RandomAccessInputStream vsi) throws IOException {
// read the VSI header
long fp = vsi.getFilePointer();
if (fp + 24 >= vsi.length()) {
return;
}
int headerSize = vsi.readShort(); // should always be 24
int version = vsi.readShort(); // always 21321
int volumeVersion = vsi.readInt();
long dataFieldOffset = vsi.readLong();
int flags = vsi.readInt();
vsi.skipBytes(4);
int tagCount = flags & 0xfffffff;
if (fp + dataFieldOffset < 0) {
return;
}
vsi.seek(fp + dataFieldOffset);
if (vsi.getFilePointer() >= vsi.length()) {
return;
}
for (int i = 0; i < tagCount; i++) {
if (vsi.getFilePointer() + 16 >= vsi.length()) {
break;
}
// read the data field
int fieldType = vsi.readInt();
int tag = vsi.readInt();
long nextField = vsi.readInt() & 0xffffffffL;
int dataSize = vsi.readInt();
boolean extraTag = ((fieldType & 0x8000000) >> 27) == 1;
boolean extendedField = ((fieldType & 0x10000000) >> 28) == 1;
boolean inlineData = ((fieldType & 0x40000000) >> 30) == 1;
boolean array = (!inlineData && !extendedField) && ((fieldType & 0x20000000) >> 29) == 1;
boolean newVolume = ((fieldType & 0x80000000) >> 31) == 1;
int realType = fieldType & 0xffffff;
int secondTag = -1;
if (extraTag) {
secondTag = vsi.readInt();
}
if (extendedField && realType == NEW_VOLUME_HEADER) {
if (tag == 2007) {
dimensionTag = secondTag;
inDimensionProperties = true;
}
long endPointer = vsi.getFilePointer() + dataSize;
while (vsi.getFilePointer() < endPointer && vsi.getFilePointer() < vsi.length()) {
long start = vsi.getFilePointer();
readTags(vsi);
long end = vsi.getFilePointer();
if (start == end) {
break;
}
}
if (tag == 2007) {
inDimensionProperties = false;
foundChannelTag = false;
}
}
if (inDimensionProperties) {
if (tag == 2012 && !dimensionOrdering.containsValue(dimensionTag)) {
dimensionOrdering.put("Z", dimensionTag);
} else if ((tag == 2100 || tag == 2027) && !dimensionOrdering.containsValue(dimensionTag)) {
dimensionOrdering.put("T", dimensionTag);
} else if (tag == 2039 && !dimensionOrdering.containsValue(dimensionTag)) {
dimensionOrdering.put("L", dimensionTag);
} else if (tag == 2008
&& foundChannelTag
&& !dimensionOrdering.containsValue(dimensionTag)) {
dimensionOrdering.put("C", dimensionTag);
} else if (tag == 2008) {
foundChannelTag = true;
}
}
if (nextField == 0) {
return;
}
if (fp + nextField < vsi.length() && fp + nextField >= 0) {
vsi.seek(fp + nextField);
} else break;
}
}
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;
}
/**
* 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;
}
