/** Based on the Bio-Formats PackbitsCodec written by Melissa Linkert. */
public byte[] packBitsUncompress(byte[] input, int expected) {
if (expected == 0) expected = Integer.MAX_VALUE;
ByteVector output = new ByteVector(1024);
int index = 0;
while (output.size() < expected && index < input.length) {
byte n = input[index++];
if (n >= 0) { // 0 <= n <= 127
byte[] b = new byte[n + 1];
for (int i = 0; i < n + 1; i++) b[i] = input[index++];
output.add(b);
b = null;
} else if (n != -128) { // -127 <= n <= -1
int len = -n + 1;
byte inp = input[index++];
for (int i = 0; i < len; i++) output.add(inp);
}
}
return output.toByteArray();
}
/**
* Utility method for decoding an LZW-compressed image strip. Adapted from the TIFF 6.0
* Specification: http://partners.adobe.com/asn/developer/pdfs/tn/TIFF6.pdf (page 61) Author:
* Curtis Rueden (ctrueden at wisc.edu)
*/
public byte[] lzwUncompress(byte[] input) {
if (input == null || input.length == 0) return input;
byte[][] symbolTable = new byte[4096][1];
int bitsToRead = 9;
int nextSymbol = 258;
int code;
int oldCode = -1;
ByteVector out = new ByteVector(8192);
BitBuffer bb = new BitBuffer(input);
byte[] byteBuffer1 = new byte[16];
byte[] byteBuffer2 = new byte[16];
while (out.size() < byteCount) {
code = bb.getBits(bitsToRead);
if (code == EOI_CODE || code == -1) break;
if (code == CLEAR_CODE) {
// initialize symbol table
for (int i = 0; i < 256; i++) symbolTable[i][0] = (byte) i;
nextSymbol = 258;
bitsToRead = 9;
code = bb.getBits(bitsToRead);
if (code == EOI_CODE || code == -1) break;
out.add(symbolTable[code]);
oldCode = code;
} else {
if (code < nextSymbol) {
// code is in table
out.add(symbolTable[code]);
// add string to table
ByteVector symbol = new ByteVector(byteBuffer1);
symbol.add(symbolTable[oldCode]);
symbol.add(symbolTable[code][0]);
symbolTable[nextSymbol] = symbol.toByteArray(); // **
oldCode = code;
nextSymbol++;
} else {
// out of table
ByteVector symbol = new ByteVector(byteBuffer2);
symbol.add(symbolTable[oldCode]);
symbol.add(symbolTable[oldCode][0]);
byte[] outString = symbol.toByteArray();
out.add(outString);
symbolTable[nextSymbol] = outString; // **
oldCode = code;
nextSymbol++;
}
if (nextSymbol == 511) {
bitsToRead = 10;
}
if (nextSymbol == 1023) {
bitsToRead = 11;
}
if (nextSymbol == 2047) {
bitsToRead = 12;
}
}
}
return out.toByteArray();
}