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/* |
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Teem: Tools to process and visualize scientific data and images . |
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Copyright (C) 2013, 2012, 2011, 2010, 2009 University of Chicago |
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Copyright (C) 2008, 2007, 2006, 2005 Gordon Kindlmann |
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Copyright (C) 2004, 2003, 2002, 2001, 2000, 1999, 1998 University of Utah |
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This library is free software; you can redistribute it and/or |
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modify it under the terms of the GNU Lesser General Public License |
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(LGPL) as published by the Free Software Foundation; either |
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version 2.1 of the License, or (at your option) any later version. |
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The terms of redistributing and/or modifying this software also |
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include exceptions to the LGPL that facilitate static linking. |
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This library is distributed in the hope that it will be useful, |
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but WITHOUT ANY WARRANTY; without even the implied warranty of |
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MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU |
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Lesser General Public License for more details. |
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You should have received a copy of the GNU Lesser General Public License |
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along with this library; if not, write to Free Software Foundation, Inc., |
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51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA |
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*/ |
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#include "nrrd.h" |
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#include "privateNrrd.h" |
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#if TEEM_BZIP2 |
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#include <bzlib.h> |
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#endif |
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static int |
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_nrrdEncodingBzip2_available(void) { |
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#if TEEM_BZIP2 |
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return AIR_TRUE; |
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#else |
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return AIR_FALSE; |
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#endif |
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} |
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static int |
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_nrrdEncodingBzip2_read(FILE *file, void *_data, size_t elNum, |
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Nrrd *nrrd, NrrdIoState *nio) { |
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static const char me[]="_nrrdEncodingBzip2_read"; |
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#if TEEM_BZIP2 |
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size_t bsize, total_read, block_size; |
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int read, bzerror=BZ_OK; |
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long int bi; |
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char *data; |
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BZFILE* bzfin; |
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bsize = nrrdElementSize(nrrd)*elNum; |
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/* Create the BZFILE* for reading in the gzipped data. */ |
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bzfin = BZ2_bzReadOpen(&bzerror, file, 0, 0, NULL, 0); |
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if (bzerror != BZ_OK) { |
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/* there was a problem */ |
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biffAddf(NRRD, "%s: error opening BZFILE: %s", me, |
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BZ2_bzerror(bzfin, &bzerror)); |
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BZ2_bzReadClose(&bzerror, bzfin); |
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return 1; |
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} |
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/* Here is where we do the byte skipping. */ |
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for(bi=0; bi<nio->byteSkip; bi++) { |
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unsigned char b; |
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/* Check to see if a single byte was able to be read. */ |
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read = BZ2_bzRead(&bzerror, bzfin, &b, 1); |
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if (read != 1 || bzerror != BZ_OK) { |
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biffAddf(NRRD, "%s: hit an error skipping byte %ld of %ld: %s", |
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me, bi, nio->byteSkip, BZ2_bzerror(bzfin, &bzerror)); |
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return 1; |
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} |
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} |
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/* bzip2 can handle data sizes up to INT_MAX, so we can't just |
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pass in the bsize, because it might be too large for an int. |
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Therefore it must be read in chunks if the size is larger |
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than INT_MAX. */ |
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if (bsize <= INT_MAX) { |
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block_size = bsize; |
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} else { |
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block_size = INT_MAX; |
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} |
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/* This counter will help us to make sure that we read as much data |
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as we think we should. */ |
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total_read = 0; |
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/* Pointer to the blocks as we read them. */ |
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data = (char *)_data; |
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/* Ok, now we can begin reading. */ |
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bzerror = BZ_OK; |
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while ((read = BZ2_bzRead(&bzerror, bzfin, data, block_size)) |
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&& (BZ_OK == bzerror || BZ_STREAM_END == bzerror) ) { |
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/* Increment the data pointer to the next available spot. */ |
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data += read; |
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total_read += read; |
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/* We only want to read as much data as we need, so we need to check |
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to make sure that we don't request data that might be there but that |
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we don't want. This will reduce block_size when we get to the last |
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block (which may be smaller than block_size). |
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*/ |
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if (bsize >= total_read |
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&& bsize - total_read < block_size) |
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block_size = bsize - total_read; |
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} |
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if (!( BZ_OK == bzerror || BZ_STREAM_END == bzerror )) { |
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biffAddf(NRRD, "%s: error reading from BZFILE: %s", |
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me, BZ2_bzerror(bzfin, &bzerror)); |
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return 1; |
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} |
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/* Close the BZFILE. */ |
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BZ2_bzReadClose(&bzerror, bzfin); |
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if (BZ_OK != bzerror) { |
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biffAddf(NRRD, "%s: error closing BZFILE: %s", me, |
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BZ2_bzerror(bzfin, &bzerror)); |
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return 1; |
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} |
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/* Check to see if we got out as much as we thought we should. */ |
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if (total_read != bsize) { |
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char stmp1[AIR_STRLEN_SMALL], stmp2[AIR_STRLEN_SMALL]; |
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biffAddf(NRRD, "%s: expected %s bytes but received %s", me, |
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airSprintSize_t(stmp1, bsize), |
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airSprintSize_t(stmp2, total_read)); |
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return 1; |
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} |
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return 0; |
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#else |
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AIR_UNUSED(file); |
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AIR_UNUSED(_data); |
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AIR_UNUSED(elNum); |
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AIR_UNUSED(nrrd); |
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AIR_UNUSED(nio); |
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biffAddf(NRRD, "%s: sorry, this nrrd not compiled with bzip2 enabled", me); |
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return 1; |
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#endif |
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} |
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static int |
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_nrrdEncodingBzip2_write(FILE *file, const void *_data, size_t elNum, |
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const Nrrd *nrrd, NrrdIoState *nio) { |
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static const char me[]="_nrrdEncodingBzip2_write"; |
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#if TEEM_BZIP2 |
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size_t bsize, total_written, block_size; |
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int bs, bzerror=BZ_OK; |
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char *data; |
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BZFILE* bzfout; |
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bsize = nrrdElementSize(nrrd)*elNum; |
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/* Set compression block size. */ |
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if (1 <= nio->bzip2BlockSize && nio->bzip2BlockSize <= 9) { |
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bs = nio->bzip2BlockSize; |
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} else { |
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bs = 9; |
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} |
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/* Open bzfile for writing. Verbosity and work factor are set |
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to default values. */ |
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bzfout = BZ2_bzWriteOpen(&bzerror, file, bs, 0, 0); |
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if (BZ_OK != bzerror) { |
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biffAddf(NRRD, "%s: error opening BZFILE: %s", me, |
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BZ2_bzerror(bzfout, &bzerror)); |
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BZ2_bzWriteClose(&bzerror, bzfout, 0, NULL, NULL); |
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return 1; |
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} |
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/* bzip2 can handle data sizes up to INT_MAX, so we can't just |
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pass in the bsize, because it might be too large for an int. |
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Therefore it must be read in chunks if the bsize is larger |
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than INT_MAX. */ |
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if (bsize <= INT_MAX) { |
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block_size = bsize; |
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} else { |
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block_size = INT_MAX; |
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} |
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/* This counter will help us to make sure that we write as much data |
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as we think we should. */ |
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total_written = 0; |
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/* Pointer to the blocks as we write them. */ |
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data = (char *)_data; |
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/* Ok, now we can begin writing. */ |
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bzerror = BZ_OK; |
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while (bsize - total_written > block_size) { |
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BZ2_bzWrite(&bzerror, bzfout, data, block_size); |
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if (BZ_OK != bzerror) break; |
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/* Increment the data pointer to the next available spot. */ |
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data += block_size; |
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total_written += block_size; |
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} |
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/* write the last (possibly smaller) block when its humungous data; |
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write the whole data when its small */ |
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if (BZ_OK == bzerror) { |
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block_size = bsize >= total_written ? bsize - total_written : 0; |
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BZ2_bzWrite(&bzerror, bzfout, data, block_size); |
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total_written += block_size; |
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} |
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if (BZ_OK != bzerror) { |
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biffAddf(NRRD, "%s: error writing to BZFILE: %s", |
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me, BZ2_bzerror(bzfout, &bzerror)); |
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return 1; |
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} |
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/* Close the BZFILE. */ |
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BZ2_bzWriteClose(&bzerror, bzfout, 0, NULL, NULL); |
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if (BZ_OK != bzerror) { |
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biffAddf(NRRD, "%s: error closing BZFILE: %s", me, |
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BZ2_bzerror(bzfout, &bzerror)); |
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return 1; |
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} |
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/* Check to see if we got out as much as we thought we should. */ |
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if (total_written != bsize) { |
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char stmp1[AIR_STRLEN_SMALL], stmp2[AIR_STRLEN_SMALL]; |
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biffAddf(NRRD, "%s: expected to write %s bytes, but only wrote %s", me, |
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airSprintSize_t(stmp1, bsize), |
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airSprintSize_t(stmp2, total_written)); |
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return 1; |
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} |
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return 0; |
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#else |
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AIR_UNUSED(file); |
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AIR_UNUSED(_data); |
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AIR_UNUSED(elNum); |
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AIR_UNUSED(nrrd); |
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AIR_UNUSED(nio); |
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biffAddf(NRRD, "%s: sorry, this nrrd not compiled with bzip2 enabled", me); |
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return 1; |
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#endif |
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} |
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const NrrdEncoding |
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_nrrdEncodingBzip2 = { |
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"bzip2", /* name */ |
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"raw.bz2", /* suffix */ |
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AIR_TRUE, /* endianMatters */ |
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AIR_TRUE, /* isCompression */ |
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_nrrdEncodingBzip2_available, |
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_nrrdEncodingBzip2_read, |
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_nrrdEncodingBzip2_write |
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}; |
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const NrrdEncoding *const |
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nrrdEncodingBzip2 = &_nrrdEncodingBzip2; |