netcdf-c/plugins/H5Zdeflate.c
Dennis Heimbigner 11fe00ea05 Add filter support to NCZarr
Filter support has three goals:

1. Use the existing HDF5 filter implementations,
2. Allow filter metadata to be stored in the NumCodecs metadata format used by Zarr,
3. Allow filters to be used even when HDF5 is disabled

Detailed usage directions are define in docs/filters.md.

For now, the existing filter API is left in place. So filters
are defined using ''nc_def_var_filter'' using the HDF5 style
where the id and parameters are unsigned integers.

This is a big change since filters affect many parts of the code.

In the following, the terms "compressor" and "filter" and "codec" are generally
used synonomously.

### Filter-Related Changes:
* In order to support dynamic loading of shared filter libraries, a new library was added in the libncpoco directory; it helps to isolate dynamic loading across multiple platforms.
* Provide a json parsing library for use by plugins; this is created by merging libdispatch/ncjson.c with include/ncjson.h.
* Add a new _Codecs attribute to allow clients to see what codecs are being used; let ncdump -s print it out.
* Provide special headers to help support compilation of HDF5 filters when HDF5 is not enabled: netcdf_filter_hdf5_build.h and netcdf_filter_build.h.
* Add a number of new test to test the new nczarr filters.
* Let ncgen parse _Codecs attribute, although it is ignored.

### Plugin directory changes:
* Add support for the Blosc compressor; this is essential because it is the most common compressor used in Zarr datasets. This also necessitated adding a CMake FindBlosc.cmake file
* Add NCZarr support for the big-four filters provided by HDF5: shuffle, fletcher32, deflate (zlib), and szip
* Add a Codec defaulter (see docs/filters.md) for the big four filters.
* Make plugins work with windows by properly adding __declspec declaration.

### Misc. Non-Filter Changes
* Replace most uses of USE_NETCDF4 (deprecated) with USE_HDF5.
* Improve support for caching
* More fixes for path conversion code
* Fix misc. memory leaks
* Add new utility -- ncdump/ncpathcvt -- that does more or less the same thing as cygpath.
* Add a number of new test to test the non-filter fixes.
* Update the parsers
* Convert most instances of '#ifdef _MSC_VER' to '#ifdef _WIN32'
2021-09-02 17:04:26 -06:00

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/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
* Copyright by The HDF Group. *
* Copyright by the Board of Trustees of the University of Illinois. *
* All rights reserved. *
* *
* This file is part of HDF5. The full HDF5 copyright notice, including *
* terms governing use, modification, and redistribution, is contained in *
* the COPYING file, which can be found at the root of the source code *
* distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases. *
* If you do not have access to either file, you may request a copy from *
* help@hdfgroup.org. *
* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
/*
* Programmer: Robb Matzke
* Friday, August 27, 1999
*/
#include <stdlib.h>
#include <string.h>
#include <math.h>
#include "netcdf_filter_build.h"
#include <zlib.h>
/* Local function prototypes */
static size_t H5Z__filter_deflate (unsigned flags, size_t cd_nelmts,
const unsigned cd_values[], size_t nbytes, size_t *buf_size, void **buf);
/* This message derives from H5Z */
const H5Z_class2_t H5Z_DEFLATE[1] = {{
H5Z_CLASS_T_VERS, /* H5Z_class_t version */
H5Z_FILTER_DEFLATE, /* Filter id number */
1, /* encoder_present flag (set to true) */
1, /* decoder_present flag (set to true) */
"deflate", /* Filter name for debugging */
NULL, /* The "can apply" callback */
NULL, /* The "set local" callback */
H5Z__filter_deflate, /* The actual filter function */
}};
/* External Discovery Functions */
DLLEXPORT
H5PL_type_t
H5PLget_plugin_type(void)
{
return H5PL_TYPE_FILTER;
}
DLLEXPORT
const void*
H5PLget_plugin_info(void)
{
return H5Z_DEFLATE;
}
#define H5Z_DEFLATE_SIZE_ADJUST(s) (HDceil(((double)(s)) * (double)1.001f) + 12)
/*-------------------------------------------------------------------------
* Function: H5Z__filter_deflate
*
* Purpose: Implement an I/O filter around the 'deflate' algorithm in
* libz
*
* Return: Success: Size of buffer filtered
* Failure: 0
*
* Programmer: Robb Matzke
* Thursday, April 16, 1998
*
*-------------------------------------------------------------------------
*/
static size_t
H5Z__filter_deflate(unsigned flags, size_t cd_nelmts,
const unsigned cd_values[], size_t nbytes,
size_t *buf_size, void **buf)
{
void *outbuf = NULL; /* Pointer to new buffer */
int status; /* Status from zlib operation */
size_t ret_value = 0; /* Return value */
FUNC_ENTER_STATIC
/* Sanity check */
HDassert(*buf_size > 0);
HDassert(buf);
HDassert(*buf);
/* Check arguments */
if (cd_nelmts!=1 || cd_values[0]>9)
HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, 0, "invalid deflate aggression level")
if (flags & H5Z_FLAG_REVERSE) {
/* Input; uncompress */
z_stream z_strm; /* zlib parameters */
size_t nalloc = *buf_size; /* Number of bytes for output (compressed) buffer */
/* Allocate space for the compressed buffer */
if (NULL==(outbuf = H5MM_malloc(nalloc)))
HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, 0, "memory allocation failed for deflate uncompression")
/* Set the uncompression parameters */
HDmemset(&z_strm, 0, sizeof(z_strm));
z_strm.next_in = (Bytef *)*buf;
H5_CHECKED_ASSIGN(z_strm.avail_in, unsigned, nbytes, size_t);
z_strm.next_out = (Bytef *)outbuf;
H5_CHECKED_ASSIGN(z_strm.avail_out, unsigned, nalloc, size_t);
/* Initialize the uncompression routines */
if (Z_OK!=inflateInit(&z_strm))
HGOTO_ERROR(H5E_PLINE, H5E_CANTINIT, 0, "inflateInit() failed")
/* Loop to uncompress the buffer */
do {
/* Uncompress some data */
status = inflate(&z_strm, Z_SYNC_FLUSH);
/* Check if we are done uncompressing data */
if (Z_STREAM_END==status)
break; /*done*/
/* Check for error */
if (Z_OK!=status) {
(void)inflateEnd(&z_strm);
HGOTO_ERROR(H5E_PLINE, H5E_CANTINIT, 0, "inflate() failed")
}
else {
/* If we're not done and just ran out of buffer space, get more */
if(0 == z_strm.avail_out) {
void *new_outbuf; /* Pointer to new output buffer */
/* Allocate a buffer twice as big */
nalloc *= 2;
if(NULL == (new_outbuf = H5MM_realloc(outbuf, nalloc))) {
(void)inflateEnd(&z_strm);
HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, 0, "memory allocation failed for deflate uncompression")
} /* end if */
outbuf = new_outbuf;
/* Update pointers to buffer for next set of uncompressed data */
z_strm.next_out = (unsigned char*)outbuf + z_strm.total_out;
z_strm.avail_out = (uInt)(nalloc - z_strm.total_out);
} /* end if */
} /* end else */
} while(status==Z_OK);
/* Free the input buffer */
H5MM_xfree(*buf);
/* Set return values */
*buf = outbuf;
outbuf = NULL;
*buf_size = nalloc;
ret_value = z_strm.total_out;
/* Finish uncompressing the stream */
(void)inflateEnd(&z_strm);
} /* end if */
else {
/*
* Output; compress but fail if the result would be larger than the
* input. The library doesn't provide in-place compression, so we
* must allocate a separate buffer for the result.
*/
const Bytef *z_src = (const Bytef*)(*buf);
Bytef *z_dst; /*destination buffer */
uLongf z_dst_nbytes = (uLongf)H5Z_DEFLATE_SIZE_ADJUST(nbytes);
uLong z_src_nbytes = (uLong)nbytes;
int aggression; /* Compression aggression setting */
/* Set the compression aggression level */
H5_CHECKED_ASSIGN(aggression, int, cd_values[0], unsigned);
/* Allocate output (compressed) buffer */
if(NULL == (outbuf = H5MM_malloc(z_dst_nbytes)))
HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, 0, "unable to allocate deflate destination buffer")
z_dst = (Bytef *)outbuf;
/* Perform compression from the source to the destination buffer */
status = compress2(z_dst, &z_dst_nbytes, z_src, z_src_nbytes, aggression);
/* Check for various zlib errors */
if(Z_BUF_ERROR == status)
HGOTO_ERROR(H5E_PLINE, H5E_CANTINIT, 0, "overflow")
else if(Z_MEM_ERROR == status)
HGOTO_ERROR(H5E_PLINE, H5E_CANTINIT, 0, "deflate memory error")
else if(Z_OK != status)
HGOTO_ERROR(H5E_PLINE, H5E_CANTINIT, 0, "other deflate error")
/* Successfully uncompressed the buffer */
else {
/* Free the input buffer */
H5MM_xfree(*buf);
/* Set return values */
*buf = outbuf;
outbuf = NULL;
*buf_size = nbytes;
ret_value = z_dst_nbytes;
} /* end else */
} /* end else */
done:
if(outbuf)
H5MM_xfree(outbuf);
FUNC_LEAVE_NOAPI(ret_value)
}