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netcdf-c/plugins/H5Zshuffle.c

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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'
2021-09-03 07:04:26 +08:00
/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
* 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. *
* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
#ifdef HAVE_CONFIG_H
#include "config.h"
#endif
#include <stdlib.h>
#include <stdio.h>
#include <string.h>
#include <errno.h>
#include "netcdf_filter_build.h"
#ifndef H5Z_FILTER_SHUFFLE
#define H5Z_FILTER_SHUFFLE 2
#endif
#ifndef H5Z_SHUFFLE_TOTAL_NPARMS
#define H5Z_SHUFFLE_TOTAL_NPARMS 1
#endif
#ifndef H5Z_SHUFFLE_USER_NPARMS
#define H5Z_SHUFFLE_USER_NPARMS 0
#endif
/* Local function prototypes */
#ifdef USE_HDF5
static herr_t H5Z__set_local_shuffle(hid_t dcpl_id, hid_t type_id, hid_t space_id);
#else
#define H5Z__set_local_shuffle NULL
#endif
static size_t H5Z__filter_shuffle(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_SHUFFLE[1] = {{
H5Z_CLASS_T_VERS, /* H5Z_class_t version */
H5Z_FILTER_SHUFFLE, /* Filter id number */
1, /* encoder_present flag (set to true) */
1, /* decoder_present flag (set to true) */
"shuffle", /* Filter name for debugging */
NULL, /* The "can apply" callback */
H5Z__set_local_shuffle, /* The "set local" callback */
H5Z__filter_shuffle, /* 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_SHUFFLE;
}
/* Local macros */
#define H5Z_SHUFFLE_PARM_SIZE 0 /* "Local" parameter for shuffling size */
#ifdef USE_HDF5
/*-------------------------------------------------------------------------
* Function: H5Z__set_local_shuffle
*
* Purpose: Set the "local" dataset parameter for data shuffling to be
* the size of the datatype.
*
* Return: Success: Non-negative
* Failure: Negative
*
* Programmer: Quincey Koziol
* Monday, April 7, 2003
*
*-------------------------------------------------------------------------
*/
static herr_t
H5Z__set_local_shuffle(hid_t dcpl_id, hid_t type_id, hid_t space_id)
{
unsigned flags = 0; /* Filter flags */
unsigned cd_values[H5Z_SHUFFLE_TOTAL_NPARMS]; /* Filter parameters */
herr_t ret_value = 1; /* Return value */
/* Set "local" parameter for this dataset */
if((cd_values[0] = (unsigned)H5Tget_size(type_id)) == 0)
HGOTO_ERROR(H5E_PLINE, H5E_BADTYPE, FAIL, "bad datatype size")
/* Modify the filter's parameters for this dataset */
if(H5Pmodify_filter(dcpl_id, H5Z_FILTER_SHUFFLE, flags, (size_t)H5Z_SHUFFLE_TOTAL_NPARMS, cd_values) < 0)
HGOTO_ERROR(H5E_PLINE, H5E_CANTSET, FAIL, "can't set local shuffle parameters")
done:
return ret_value;
} /* end H5Z__set_local_shuffle() */
#endif
/*-------------------------------------------------------------------------
* Function: H5Z__filter_shuffle
*
* Purpose: Implement an I/O filter which "de-interlaces" a block of data
* by putting all the bytes in a byte-position for each element
* together in the block. For example, for 4-byte elements stored
* as: 012301230123, shuffling will store them as: 000111222333
* Usually, the bytes in each byte position are more related to
* each other and putting them together will increase compression.
*
* Return: Success: Size of buffer filtered
* Failure: 0
*
* Programmer: Kent Yang
* Wednesday, November 13, 2002
*
*-------------------------------------------------------------------------
*/
static size_t
H5Z__filter_shuffle(unsigned flags, size_t cd_nelmts, const unsigned cd_values[],
size_t nbytes, size_t *buf_size, void **buf)
{
void *dest = NULL; /* Buffer to deposit [un]shuffled bytes into */
unsigned char *_src=NULL; /* Alias for source buffer */
unsigned char *_dest=NULL; /* Alias for destination buffer */
unsigned bytesoftype; /* Number of bytes per element */
size_t numofelements; /* Number of elements in buffer */
size_t i; /* Local index variables */
#ifdef NO_DUFFS_DEVICE
size_t j; /* Local index variable */
#endif /* NO_DUFFS_DEVICE */
size_t leftover; /* Extra bytes at end of buffer */
size_t ret_value = 0; /* Return value */
/* Check arguments */
if (cd_nelmts!=H5Z_SHUFFLE_TOTAL_NPARMS || cd_values[H5Z_SHUFFLE_PARM_SIZE]==0)
HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, 0, "invalid shuffle parameters")
/* Get the number of bytes per element from the parameter block */
bytesoftype=cd_values[H5Z_SHUFFLE_PARM_SIZE];
/* Compute the number of elements in buffer */
numofelements=nbytes/bytesoftype;
/* Don't do anything for 1-byte elements, or "fractional" elements */
if(bytesoftype > 1 && numofelements > 1) {
/* Compute the leftover bytes if there are any */
leftover = nbytes%bytesoftype;
/* Allocate the destination buffer */
if (NULL==(dest = H5MM_malloc(nbytes)))
HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, 0, "memory allocation failed for shuffle buffer")
if(flags & H5Z_FLAG_REVERSE) {
/* Get the pointer to the source buffer */
_src =(unsigned char *)(*buf);
/* Input; unshuffle */
for(i=0; i<bytesoftype; i++) {
_dest=((unsigned char *)dest)+i;
#define DUFF_GUTS \
*_dest=*_src++; \
_dest+=bytesoftype;
#ifdef NO_DUFFS_DEVICE
j = numofelements;
while(j > 0) {
DUFF_GUTS;
j--;
} /* end for */
#else /* NO_DUFFS_DEVICE */
{
size_t duffs_index; /* Counting index for Duff's device */
duffs_index = (numofelements + 7) / 8;
switch (numofelements % 8) {
default:
HDassert(0 && "This Should never be executed!");
break;
case 0:
do
{
DUFF_GUTS
H5_ATTR_FALLTHROUGH
case 7:
DUFF_GUTS
H5_ATTR_FALLTHROUGH
case 6:
DUFF_GUTS
H5_ATTR_FALLTHROUGH
case 5:
DUFF_GUTS
H5_ATTR_FALLTHROUGH
case 4:
DUFF_GUTS
H5_ATTR_FALLTHROUGH
case 3:
DUFF_GUTS
H5_ATTR_FALLTHROUGH
case 2:
DUFF_GUTS
H5_ATTR_FALLTHROUGH
case 1:
DUFF_GUTS
} while (--duffs_index > 0);
} /* end switch */
}
#endif /* NO_DUFFS_DEVICE */
#undef DUFF_GUTS
} /* end for */
/* Add leftover to the end of data */
if(leftover>0) {
/* Adjust back to end of shuffled bytes */
_dest -= (bytesoftype - 1); /*lint !e794 _dest is initialized */
H5MM_memcpy((void*)_dest, (void*)_src, leftover);
}
} /* end if */
else {
/* Get the pointer to the destination buffer */
_dest =(unsigned char *)dest;
/* Output; shuffle */
for(i=0; i<bytesoftype; i++) {
_src=((unsigned char *)(*buf))+i;
#define DUFF_GUTS \
*_dest++=*_src; \
_src+=bytesoftype;
#ifdef NO_DUFFS_DEVICE
j = numofelements;
while(j > 0) {
DUFF_GUTS;
j--;
} /* end for */
#else /* NO_DUFFS_DEVICE */
{
size_t duffs_index; /* Counting index for Duff's device */
duffs_index = (numofelements + 7) / 8;
switch (numofelements % 8) {
default:
HDassert(0 && "This Should never be executed!");
break;
case 0:
do
{
DUFF_GUTS
H5_ATTR_FALLTHROUGH
case 7:
DUFF_GUTS
H5_ATTR_FALLTHROUGH
case 6:
DUFF_GUTS
H5_ATTR_FALLTHROUGH
case 5:
DUFF_GUTS
H5_ATTR_FALLTHROUGH
case 4:
DUFF_GUTS
H5_ATTR_FALLTHROUGH
case 3:
DUFF_GUTS
H5_ATTR_FALLTHROUGH
case 2:
DUFF_GUTS
H5_ATTR_FALLTHROUGH
case 1:
DUFF_GUTS
} while (--duffs_index > 0);
} /* end switch */
}
#endif /* NO_DUFFS_DEVICE */
#undef DUFF_GUTS
} /* end for */
/* Add leftover to the end of data */
if(leftover>0) {
/* Adjust back to end of shuffled bytes */
_src -= (bytesoftype - 1); /*lint !e794 _src is initialized */
H5MM_memcpy((void*)_dest, (void*)_src, leftover);
}
} /* end else */
/* Free the input buffer */
H5MM_xfree(*buf);
/* Set the buffer information to return */
*buf = dest;
*buf_size=nbytes;
} /* end else */
/* Set the return value */
ret_value = nbytes;
done:
return ret_value;
}
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