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The NetCDF-Java Library is a Java interface to NetCDF files,
as well as to many other types of scientific data formats.
The newest version!
/*
* The Apache Software License, Version 1.1
*
* Copyright (c) 2001-2003 The Apache Software Foundation. All rights
* reserved.
*
* Redistribution and use in source and binary forms, with or without
* modification, are permitted provided that the following conditions
* are met:
*
* 1. Redistributions of source code must retain the above copyright
* notice, this list of conditions and the following disclaimer.
*
* 2. Redistributions in binary form must reproduce the above copyright
* notice, this list of conditions and the following disclaimer in
* the documentation and/or other materials provided with the
* distribution.
*
* 3. The end-user documentation included with the redistribution, if
* any, must include the following acknowlegement:
* "This product includes software developed by the
* Apache Software Foundation (http://www.apache.org/)."
* Alternately, this acknowlegement may appear in the software itself,
* if and wherever such third-party acknowlegements normally appear.
*
* 4. The names "Ant" and "Apache Software
* Foundation" must not be used to endorse or promote products derived
* from this software without prior written permission. For written
* permission, please contact [email protected].
*
* 5. Products derived from this software may not be called "Apache"
* nor may "Apache" appear in their names without prior written
* permission of the Apache Group.
*
* THIS SOFTWARE IS PROVIDED ``AS IS'' AND ANY EXPRESSED OR IMPLIED
* WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
* OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
* DISCLAIMED. IN NO EVENT SHALL THE APACHE SOFTWARE FOUNDATION OR
* ITS CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
* SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
* LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF
* USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
* ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
* OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT
* OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
* SUCH DAMAGE.
* ====================================================================
*
* This software consists of voluntary contributions made by many
* individuals on behalf of the Apache Software Foundation. For more
* information on the Apache Software Foundation, please see
* to whom the Ant project is very grateful for his
* great code.
*/
/*
* There has been further modification of this class by Unidata to
* support setting the inputstream. This saves many extra memory
* allocations when doing lots of uncompressions. The read method
* may throw a BZip2ReadException instead of an IOException because
* the superclass catches and discards IOExceptions.
*/
package ucar.unidata.io.bzip2;
import java.io.InputStream;
import java.io.IOException;
/**
* An input stream that decompresses from the BZip2 format (without the file
* header chars) to be read as any other stream.
*
* @author Keiron Liddle
*/
public class CBZip2InputStream extends InputStream implements BZip2Constants {
private static final int START_BLOCK_STATE = 1;
private static final int RAND_PART_A_STATE = 2;
private static final int RAND_PART_B_STATE = 3;
private static final int RAND_PART_C_STATE = 4;
private static final int NO_RAND_PART_A_STATE = 5;
private static final int NO_RAND_PART_B_STATE = 6;
private static final int NO_RAND_PART_C_STATE = 7;
/*
index of the last char in the block, so
the block size == last + 1.
*/
private int last;
/*
index in zptr[] of original string after sorting.
*/
private int origPtr;
/*
always: in the range 0 .. 9.
The current block size is 100000 * this number.
*/
private int blockSize100k;
private boolean blockRandomised;
private int bsBuff;
private int bsLive;
private CRC mCrc = new CRC();
private boolean[] inUse = new boolean[256];
private int nInUse;
private char[] seqToUnseq = new char[256];
private char[] unseqToSeq = new char[256];
private char[] selector = new char[MAX_SELECTORS];
private char[] selectorMtf = new char[MAX_SELECTORS];
private int[] tt;
private char[] ll8;
/*
freq table collected to save a pass over the data
during decompression.
*/
private int[] unzftab = new int[256];
private int[][] limit = new int[N_GROUPS][MAX_ALPHA_SIZE];
private int[][] base = new int[N_GROUPS][MAX_ALPHA_SIZE];
private int[][] perm = new int[N_GROUPS][MAX_ALPHA_SIZE];
private int[] minLens = new int[N_GROUPS];
private InputStream bsStream;
private boolean streamEnd = false;
private int currentChar = -1;
private int currentState = START_BLOCK_STATE;
private int storedBlockCRC, storedCombinedCRC;
private int computedBlockCRC, computedCombinedCRC;
int i2, count, chPrev, ch2;
int i, tPos;
int rNToGo = 0;
int rTPos = 0;
int j2;
char z;
public CBZip2InputStream() {
}
public CBZip2InputStream(InputStream zStream) {
setStream(zStream);
}
public CBZip2InputStream(InputStream zStream, boolean skip) throws IOException {
if (skip) {
char c = (char) zStream.read();
char c2 = (char) zStream.read();
//System.out.println(c+""+c2);
}
setStream(zStream);
}
/**
* Added 5-30-2006 to allow for resetting of the input used
* by this object. This saves in memory allocation costs
*/
public void setStream(InputStream zStream) {
last=0;
origPtr=0;
blockSize100k=0;
blockRandomised=false;
bsBuff=0;
bsLive=0;
mCrc = new CRC();
nInUse=0;
bsStream=null;
streamEnd = false;
currentChar = -1;
currentState = START_BLOCK_STATE;
storedBlockCRC= storedCombinedCRC=0;
computedBlockCRC= computedCombinedCRC=0;
i2= count= chPrev= ch2=0;
i= tPos=0;
rNToGo = 0;
rTPos = 0;
j2=0;
z=0;
bsSetStream(zStream);
initialize();
initBlock();
setupBlock();
}
/**
* Reads the stream.
* @throws BZip2ReadException if there is a problem. InputStream does
* not throw an IOException, so we throw a RuntimeException.
*/
public int read() {
if (streamEnd) {
return -1;
} else {
int retChar = currentChar;
switch (currentState) {
case START_BLOCK_STATE:
break;
case RAND_PART_A_STATE:
break;
case RAND_PART_B_STATE:
setupRandPartB();
break;
case RAND_PART_C_STATE:
setupRandPartC();
break;
case NO_RAND_PART_A_STATE:
break;
case NO_RAND_PART_B_STATE:
setupNoRandPartB();
break;
case NO_RAND_PART_C_STATE:
setupNoRandPartC();
break;
default:
break;
}
return retChar;
}
}
private void initialize() {
char magic3, magic4;
magic3 = bsGetUChar();
magic4 = bsGetUChar();
if (magic3 != 'h' || magic4 < '1' || magic4 > '9') {
bsFinishedWithStream();
streamEnd = true;
return;
}
setDecompressStructureSizes(magic4 - '0');
computedCombinedCRC = 0;
}
private void initBlock() {
char magic1, magic2, magic3, magic4;
char magic5, magic6;
magic1 = bsGetUChar();
magic2 = bsGetUChar();
magic3 = bsGetUChar();
magic4 = bsGetUChar();
magic5 = bsGetUChar();
magic6 = bsGetUChar();
if (magic1 == 0x17 && magic2 == 0x72 && magic3 == 0x45
&& magic4 == 0x38 && magic5 == 0x50 && magic6 == 0x90) {
complete();
return;
}
if (magic1 != 0x31 || magic2 != 0x41 || magic3 != 0x59
|| magic4 != 0x26 || magic5 != 0x53 || magic6 != 0x59) {
badBlockHeader();
streamEnd = true;
return;
}
storedBlockCRC = bsGetInt32();
if (bsR(1) == 1) {
blockRandomised = true;
} else {
blockRandomised = false;
}
// currBlockNo++;
getAndMoveToFrontDecode();
mCrc.initialiseCRC();
currentState = START_BLOCK_STATE;
}
private void endBlock() {
computedBlockCRC = mCrc.getFinalCRC();
/* A bad CRC is considered a fatal error. */
if (storedBlockCRC != computedBlockCRC) {
// crcError();
cadvise("CRC error: storedBlockCRC != computedBlockCRC");
}
computedCombinedCRC = (computedCombinedCRC << 1)
| (computedCombinedCRC >>> 31);
computedCombinedCRC ^= computedBlockCRC;
}
private void complete() {
storedCombinedCRC = bsGetInt32();
if (storedCombinedCRC != computedCombinedCRC) {
// crcError();
cadvise("CRC error: storedCombinedCRC != computedCombinedCRC");
}
bsFinishedWithStream();
streamEnd = true;
}
private void blockOverrun() {
cadvise("Block Overrun");
}
private void badBlockHeader() {
cadvise("Bad Block Header");
}
private void crcError() {
cadvise();
}
private void bsFinishedWithStream() {
try {
if (this.bsStream != null) {
if (this.bsStream != System.in) {
this.bsStream.close();
this.bsStream = null;
}
}
} catch (IOException ioe) {
//ignore
}
}
private void bsSetStream(InputStream f) {
bsStream = f;
bsLive = 0;
bsBuff = 0;
}
private int bsR(int n) {
int v;
while (bsLive < n) {
int zzi;
char thech = 0;
try {
thech = (char) bsStream.read();
} catch (IOException e) {
compressedStreamEOF();
}
if (thech == -1) {
compressedStreamEOF();
}
zzi = thech;
bsBuff = (bsBuff << 8) | (zzi & 0xff);
bsLive += 8;
}
v = (bsBuff >> (bsLive - n)) & ((1 << n) - 1);
bsLive -= n;
return v;
}
private char bsGetUChar() {
return (char) bsR(8);
}
private int bsGetint() {
int u = 0;
u = (u << 8) | bsR(8);
u = (u << 8) | bsR(8);
u = (u << 8) | bsR(8);
u = (u << 8) | bsR(8);
return u;
}
private int bsGetIntVS(int numBits) {
return bsR(numBits);
}
private int bsGetInt32() {
return bsGetint();
}
private void hbCreateDecodeTables(int[] limit, int[] base,
int[] perm, char[] length,
int minLen, int maxLen, int alphaSize) {
int pp, i, j, vec;
pp = 0;
for (i = minLen; i <= maxLen; i++) {
for (j = 0; j < alphaSize; j++) {
if (length[j] == i) {
perm[pp] = j;
pp++;
}
}
}
for (i = 0; i < MAX_CODE_LEN; i++) {
base[i] = 0;
}
for (i = 0; i < alphaSize; i++) {
base[length[i] + 1]++;
}
for (i = 1; i < MAX_CODE_LEN; i++) {
base[i] += base[i - 1];
}
for (i = 0; i < MAX_CODE_LEN; i++) {
limit[i] = 0;
}
vec = 0;
for (i = minLen; i <= maxLen; i++) {
vec += (base[i + 1] - base[i]);
limit[i] = vec - 1;
vec <<= 1;
}
for (i = minLen + 1; i <= maxLen; i++) {
base[i] = ((limit[i - 1] + 1) << 1) - base[i];
}
}
private void recvDecodingTables() {
char len[][] = new char[N_GROUPS][MAX_ALPHA_SIZE];
int i, j, t, nGroups, nSelectors, alphaSize;
int minLen, maxLen;
boolean[] inUse16 = new boolean[16];
/* Receive the mapping table */
for (i = 0; i < 16; i++) {
if (bsR(1) == 1) {
inUse16[i] = true;
} else {
inUse16[i] = false;
}
}
for (i = 0; i < 256; i++) {
inUse[i] = false;
}
for (i = 0; i < 16; i++) {
if (inUse16[i]) {
for (j = 0; j < 16; j++) {
if (bsR(1) == 1) {
inUse[i * 16 + j] = true;
}
}
}
}
makeMaps();
alphaSize = nInUse + 2;
/* Now the selectors */
nGroups = bsR(3);
nSelectors = bsR(15);
for (i = 0; i < nSelectors; i++) {
j = 0;
while (bsR(1) == 1) {
j++;
}
selectorMtf[i] = (char) j;
}
/* Undo the MTF values for the selectors. */
{
char[] pos = new char[N_GROUPS];
char tmp, v;
for (v = 0; v < nGroups; v++) {
pos[v] = v;
}
for (i = 0; i < nSelectors; i++) {
v = selectorMtf[i];
tmp = pos[v];
while (v > 0) {
pos[v] = pos[v - 1];
v--;
}
pos[0] = tmp;
selector[i] = tmp;
}
}
/* Now the coding tables */
for (t = 0; t < nGroups; t++) {
int curr = bsR(5);
for (i = 0; i < alphaSize; i++) {
while (bsR(1) == 1) {
if (bsR(1) == 0) {
curr++;
} else {
curr--;
}
}
len[t][i] = (char) curr;
}
}
/* Create the Huffman decoding tables */
for (t = 0; t < nGroups; t++) {
minLen = 32;
maxLen = 0;
for (i = 0; i < alphaSize; i++) {
if (len[t][i] > maxLen) {
maxLen = len[t][i];
}
if (len[t][i] < minLen) {
minLen = len[t][i];
}
}
hbCreateDecodeTables(limit[t], base[t], perm[t], len[t], minLen,
maxLen, alphaSize);
minLens[t] = minLen;
}
}
private void getAndMoveToFrontDecode() {
char[] yy = new char[256];
int i, j, nextSym, limitLast;
int EOB, groupNo, groupPos;
limitLast = baseBlockSize * blockSize100k;
origPtr = bsGetIntVS(24);
recvDecodingTables();
EOB = nInUse + 1;
groupNo = -1;
groupPos = 0;
/*
Setting up the unzftab entries here is not strictly
necessary, but it does save having to do it later
in a separate pass, and so saves a block's worth of
cache misses.
*/
for (i = 0; i <= 255; i++) {
unzftab[i] = 0;
}
for (i = 0; i <= 255; i++) {
yy[i] = (char) i;
}
last = -1;
{
int zt, zn, zvec, zj;
if (groupPos == 0) {
groupNo++;
groupPos = G_SIZE;
}
groupPos--;
zt = selector[groupNo];
zn = minLens[zt];
zvec = bsR(zn);
while (zvec > limit[zt][zn]) {
zn++;
{
{
while (bsLive < 1) {
int zzi;
char thech = 0;
try {
thech = (char) bsStream.read();
} catch (IOException e) {
compressedStreamEOF();
}
if (thech == -1) {
compressedStreamEOF();
}
zzi = thech;
bsBuff = (bsBuff << 8) | (zzi & 0xff);
bsLive += 8;
}
}
zj = (bsBuff >> (bsLive - 1)) & 1;
bsLive--;
}
zvec = (zvec << 1) | zj;
}
nextSym = perm[zt][zvec - base[zt][zn]];
}
while (true) {
if (nextSym == EOB) {
break;
}
if (nextSym == RUNA || nextSym == RUNB) {
char ch;
int s = -1;
int N = 1;
do {
if (nextSym == RUNA) {
s = s + (0 + 1) * N;
} else if (nextSym == RUNB) {
s = s + (1 + 1) * N;
}
N = N * 2;
{
int zt, zn, zvec, zj;
if (groupPos == 0) {
groupNo++;
groupPos = G_SIZE;
}
groupPos--;
zt = selector[groupNo];
zn = minLens[zt];
zvec = bsR(zn);
while (zvec > limit[zt][zn]) {
zn++;
{
{
while (bsLive < 1) {
int zzi;
char thech = 0;
try {
thech = (char) bsStream.read();
} catch (IOException e) {
compressedStreamEOF();
}
if (thech == -1) {
compressedStreamEOF();
}
zzi = thech;
bsBuff = (bsBuff << 8) | (zzi & 0xff);
bsLive += 8;
}
}
zj = (bsBuff >> (bsLive - 1)) & 1;
bsLive--;
}
zvec = (zvec << 1) | zj;
}
nextSym = perm[zt][zvec - base[zt][zn]];
}
} while (nextSym == RUNA || nextSym == RUNB);
s++;
ch = seqToUnseq[yy[0]];
unzftab[ch] += s;
while (s > 0) {
last++;
ll8[last] = ch;
s--;
}
if (last >= limitLast) {
blockOverrun();
}
continue;
} else {
char tmp;
last++;
if (last >= limitLast) {
blockOverrun();
}
tmp = yy[nextSym - 1];
unzftab[seqToUnseq[tmp]]++;
ll8[last] = seqToUnseq[tmp];
/*
This loop is hammered during decompression,
hence the unrolling.
for (j = nextSym-1; j > 0; j--) yy[j] = yy[j-1];
*/
j = nextSym - 1;
for (; j > 3; j -= 4) {
yy[j] = yy[j - 1];
yy[j - 1] = yy[j - 2];
yy[j - 2] = yy[j - 3];
yy[j - 3] = yy[j - 4];
}
for (; j > 0; j--) {
yy[j] = yy[j - 1];
}
yy[0] = tmp;
{
int zt, zn, zvec, zj;
if (groupPos == 0) {
groupNo++;
groupPos = G_SIZE;
}
groupPos--;
zt = selector[groupNo];
zn = minLens[zt];
zvec = bsR(zn);
while (zvec > limit[zt][zn]) {
zn++;
{
{
while (bsLive < 1) {
int zzi;
char thech = 0;
try {
thech = (char) bsStream.read();
} catch (IOException e) {
compressedStreamEOF();
}
zzi = thech;
bsBuff = (bsBuff << 8) | (zzi & 0xff);
bsLive += 8;
}
}
zj = (bsBuff >> (bsLive - 1)) & 1;
bsLive--;
}
zvec = (zvec << 1) | zj;
}
nextSym = perm[zt][zvec - base[zt][zn]];
}
continue;
}
}
}
private void setupBlock() {
int[] cftab = new int[257];
char ch;
cftab[0] = 0;
for (i = 1; i <= 256; i++) {
cftab[i] = unzftab[i - 1];
}
for (i = 1; i <= 256; i++) {
cftab[i] += cftab[i - 1];
}
for (i = 0; i <= last; i++) {
ch = ll8[i];
tt[cftab[ch]] = i;
cftab[ch]++;
}
cftab = null;
tPos = tt[origPtr];
count = 0;
i2 = 0;
ch2 = 256; /* not a char and not EOF */
if (blockRandomised) {
rNToGo = 0;
rTPos = 0;
setupRandPartA();
} else {
setupNoRandPartA();
}
}
private void setupRandPartA() {
if (i2 <= last) {
chPrev = ch2;
ch2 = ll8[tPos];
tPos = tt[tPos];
if (rNToGo == 0) {
rNToGo = rNums[rTPos];
rTPos++;
if (rTPos == 512) {
rTPos = 0;
}
}
rNToGo--;
ch2 ^= ((rNToGo == 1) ? 1 : 0);
i2++;
currentChar = ch2;
currentState = RAND_PART_B_STATE;
mCrc.updateCRC(ch2);
} else {
endBlock();
initBlock();
setupBlock();
}
}
private void setupNoRandPartA() {
if (i2 <= last) {
chPrev = ch2;
ch2 = ll8[tPos];
tPos = tt[tPos];
i2++;
currentChar = ch2;
currentState = NO_RAND_PART_B_STATE;
mCrc.updateCRC(ch2);
} else {
endBlock();
initBlock();
setupBlock();
}
}
private void setupRandPartB() {
if (ch2 != chPrev) {
currentState = RAND_PART_A_STATE;
count = 1;
setupRandPartA();
} else {
count++;
if (count >= 4) {
z = ll8[tPos];
tPos = tt[tPos];
if (rNToGo == 0) {
rNToGo = rNums[rTPos];
rTPos++;
if (rTPos == 512) {
rTPos = 0;
}
}
rNToGo--;
z ^= ((rNToGo == 1) ? 1 : 0);
j2 = 0;
currentState = RAND_PART_C_STATE;
setupRandPartC();
} else {
currentState = RAND_PART_A_STATE;
setupRandPartA();
}
}
}
private void setupRandPartC() {
if (j2 < (int) z) {
currentChar = ch2;
mCrc.updateCRC(ch2);
j2++;
} else {
currentState = RAND_PART_A_STATE;
i2++;
count = 0;
setupRandPartA();
}
}
private void setupNoRandPartB() {
if (ch2 != chPrev) {
currentState = NO_RAND_PART_A_STATE;
count = 1;
setupNoRandPartA();
} else {
count++;
if (count >= 4) {
z = ll8[tPos];
tPos = tt[tPos];
currentState = NO_RAND_PART_C_STATE;
j2 = 0;
setupNoRandPartC();
} else {
currentState = NO_RAND_PART_A_STATE;
setupNoRandPartA();
}
}
}
private void setupNoRandPartC() {
if (j2 < (int) z) {
currentChar = ch2;
mCrc.updateCRC(ch2);
j2++;
} else {
currentState = NO_RAND_PART_A_STATE;
i2++;
count = 0;
setupNoRandPartA();
}
}
private void setDecompressStructureSizes(int newSize100k) {
if (!(0 <= newSize100k && newSize100k <= 9 && 0 <= blockSize100k
&& blockSize100k <= 9)) {
// throw new IOException("Invalid block size");
}
blockSize100k = newSize100k;
if (newSize100k == 0) {
return;
}
//Modified 5-30-2006 by unidata to allow for reuse of the ll8 and tt buffers
int n = baseBlockSize * newSize100k;
if (ll8 != null && ll8.length != n) {
ll8 = null;
}
if (tt != null && tt.length != n) {
tt = null;
}
if (ll8 == null) {
ll8 = new char[n];
}
if (tt == null) {
tt = new int[n];
}
}
private void cadvise() {
System.out.println("CRC Error");
//throw new CCoruptionError();
}
private void cadvise(String msg) {
throw new BZip2ReadException(msg);
}
private void compressedStreamEOF() {
cadvise("Compressed Stream EOF");
}
private void makeMaps() {
int i;
nInUse = 0;
for (i = 0; i < 256; i++) {
if (inUse[i]) {
seqToUnseq[nInUse] = (char) i;
unseqToSeq[i] = (char) nInUse;
nInUse++;
}
}
}
}