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3ffe7be446
re: Discussion https://github.com/Unidata/netcdf-c/discussions/2214 The primary change is to support so-called "standard filters". A standard filter is one that is defined by the following netcdf-c API: ```` int nc_def_var_XXX(int ncid, int varid, size_t nparams, unsigned* params); int nc_inq_var_XXXX(int ncid, int varid, int* usefilterp, unsigned* params); ```` So for example, zstandard would be a standard filter by defining the functions *nc_def_var_zstandard* and *nc_inq_var_zstandard*. In order to define these functions, we need a new dispatch function: ```` int nc_inq_filter_avail(int ncid, unsigned filterid); ```` This function, combined with the existing filter API can be used to implement arbitrary standard filters using a simple code pattern. Note that I would have preferred that this function return a list of all available filters, but HDF5 does not support that functionality. So this PR implements the dispatch function and implements the following standard functions: + bzip2 + zstandard + blosc Specific test cases are also provided for HDF5 and NCZarr. Over time, other specific standard filters will be defined. ## Primary Changes * Add nc_inq_filter_avail() to netcdf-c API. * Add standard filter implementations to test use of *nc_inq_filter_avail*. * Bump the dispatch table version number and add to all the relevant dispatch tables (libsrc, libsrcp, etc). * Create a program to invoke nc_inq_filter_avail so that it is accessible to shell scripts. * Cleanup szip support to properly support szip when HDF5 is disabled. This involves detecting libsz separately from testing if HDF5 supports szip. * Integrate shuffle and fletcher32 into the existing filter API. This means that, for example, nc_def_var_fletcher32 is now a wrapper around nc_def_var_filter. * Extend the Codec defaulting to allow multiple default shared libraries. ## Misc. Changes * Modify configure.ac/CMakeLists.txt to look for the relevant libraries implementing standard filters. * Modify libnetcdf.settings to list available standard filters (including deflate and szip). * Add CMake test modules to locate libbz2 and libzstd. * Cleanup the HDF5 memory manager function use in the plugins. * remove unused file include//ncfilter.h * remove tests for the HDF5 memory operations e.g. H5allocate_memory. * Add flag to ncdump to force use of _Filter instead of _Deflate or _Shuffle or _Fletcher32. Used for testing.
360 lines
14 KiB
C
360 lines
14 KiB
C
/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
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* Copyright by The HDF Group. *
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* Copyright by the Board of Trustees of the University of Illinois. *
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* All rights reserved. *
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* *
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* This file is part of HDF5. The full HDF5 copyright notice, including *
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* terms governing use, modification, and redistribution, is contained in *
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* the COPYING file, which can be found at the root of the source code *
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* distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases. *
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* If you do not have access to either file, you may request a copy from *
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* help@hdfgroup.org. *
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* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
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#ifdef HAVE_CONFIG_H
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#include "config.h"
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#endif
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#include <stdlib.h>
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#include <string.h>
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#include <math.h>
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#include "netcdf_filter_build.h"
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#ifdef HAVE_SZ
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#include <szlib.h>
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#include "H5Zszip.h"
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/* Local function prototypes */
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static htri_t H5Z___can_apply_szip(hid_t dcpl_id, hid_t type_id, hid_t space_id);
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static herr_t H5Z___set_local_szip(hid_t dcpl_id, hid_t type_id, hid_t space_id);
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static size_t H5Z___filter_szip(unsigned flags, size_t cd_nelmts,
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const unsigned cd_values[], size_t nbytes, size_t *buf_size, void **buf);
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/* This message derives from H5Z */
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H5Z_class2_t H5Z_SZIP[1] = {{
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H5Z_CLASS_T_VERS, /* H5Z_class_t version */
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H5Z_FILTER_SZIP, /* Filter id number */
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1, /* Assume encoder present: check before registering */
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1, /* decoder_present flag (set to true) */
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"szip", /* Filter name for debugging */
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H5Z___can_apply_szip, /* The "can apply" callback */
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H5Z___set_local_szip, /* The "set local" callback */
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H5Z___filter_szip, /* The actual filter function */
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}};
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/*-------------------------------------------------------------------------
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* Function: H5Z___can_apply_szip
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*
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* Purpose: Check the parameters for szip compression for validity and
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* whether they fit a particular dataset.
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*
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* Note: This function currently range-checks for datatypes with
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* 8-bit boundaries (8, 16, 24, etc.). It appears that the szip
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* library can actually handle 1-24, 32 & 64 bit samples. If
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* this becomes important, we should make the checks below more
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* sophisticated and have them check for n-bit datatypes of the
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* correct size, etc. - QAK
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*
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* Return: Success: Non-negative
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* Failure: Negative
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*
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* Programmer: Quincey Koziol
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* Monday, April 7, 2003
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*
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*-------------------------------------------------------------------------
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*/
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static htri_t
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H5Z___can_apply_szip(hid_t H5_ATTR_UNUSED dcpl_id, hid_t type_id, hid_t H5_ATTR_UNUSED space_id)
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{
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htri_t ret_value = TRUE; /* Return value */
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#ifdef USE_HDF5
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unsigned dtype_size; /* Datatype's size (in bits) */
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H5T_order_t dtype_order; /* Datatype's endianness order */
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FUNC_ENTER_STATIC
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/* Get datatype's size, for checking the "bits-per-pixel" */
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if((dtype_size = (8 * H5Tget_size(type_id))) == 0)
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HGOTO_ERROR(H5E_PLINE, H5E_BADTYPE, FAIL, "bad datatype size")
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/* Range check datatype's size */
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if(dtype_size > 32 && dtype_size != 64)
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HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FALSE, "invalid datatype size")
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/* Get datatype's endianness order */
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if((dtype_order = H5Tget_order(type_id)) == H5T_ORDER_ERROR)
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HGOTO_ERROR(H5E_PLINE, H5E_BADTYPE, FAIL, "can't retrieve datatype endianness order")
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/* Range check datatype's endianness order */
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/* (Note: this may not handle non-atomic datatypes well) */
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if(dtype_order != H5T_ORDER_LE && dtype_order != H5T_ORDER_BE)
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HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FALSE, "invalid datatype endianness order")
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done:
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FUNC_LEAVE_NOAPI(ret_value)
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#else /*!USE_HDF5*/
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return ret_value;
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#endif /*USE_HDF5*/
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} /* end H5Z___can_apply_szip() */
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/*-------------------------------------------------------------------------
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* Function: H5Z___set_local_szip
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*
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* Purpose: Set the "local" dataset parameters for szip compression.
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*
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* Return: Success: Non-negative
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* Failure: Negative
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*
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* Programmer: Quincey Koziol
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* Monday, April 7, 2003
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*
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*-------------------------------------------------------------------------
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*/
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static herr_t
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H5Z___set_local_szip(hid_t dcpl_id, hid_t type_id, hid_t space_id)
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{
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herr_t ret_value = SUCCEED; /* Return value */
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#ifdef USE_HDF5
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unsigned flags; /* Filter flags */
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size_t cd_nelmts = H5Z_SZIP_USER_NPARMS; /* Number of filter parameters */
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unsigned cd_values[H5Z_SZIP_TOTAL_NPARMS]; /* Filter parameters */
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hsize_t dims[H5S_MAX_RANK+1]; /* Dataspace (i.e. chunk) dimensions */
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int ndims; /* Number of (chunk) dimensions */
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H5T_order_t dtype_order; /* Datatype's endianness order */
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size_t dtype_size; /* Datatype's size (in bits) */
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size_t dtype_precision; /* Datatype's precision (in bits) */
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size_t dtype_offset; /* Datatype's offset (in bits) */
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hsize_t scanline; /* Size of dataspace's fastest changing dimension */
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FUNC_ENTER_STATIC
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/* Get the filter's current parameters */
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if(H5Pget_filter_by_id1(dcpl_id, H5Z_FILTER_SZIP, &flags, &cd_nelmts, cd_values, 0, NULL) < 0)
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HGOTO_ERROR(H5E_PLINE, H5E_CANTGET, FAIL, "can't get szip parameters")
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/* Get datatype's size, for checking the "bits-per-pixel" */
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if((dtype_size = (8 * H5Tget_size(type_id))) == 0)
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HGOTO_ERROR(H5E_PLINE, H5E_BADTYPE, FAIL, "bad datatype size");
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/* Get datatype's precision, in case is less than full bits */
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if((dtype_precision = H5Tget_precision(type_id)) == 0)
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HGOTO_ERROR(H5E_PLINE, H5E_BADTYPE, FAIL, "bad datatype precision");
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if(dtype_precision < dtype_size) {
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dtype_offset = H5Tget_offset(type_id);
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if(dtype_offset != 0)
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dtype_precision = dtype_size;
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} /* end if */
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if(dtype_precision > 24) {
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if(dtype_precision <= 32)
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dtype_precision = 32;
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else if(dtype_precision <= 64)
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dtype_precision = 64;
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} /* end if */
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/* Set "local" parameter for this dataset's "bits-per-pixel" */
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cd_values[H5Z_SZIP_PARM_BPP] = dtype_precision;
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/* Get dimensions for dataspace */
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if((ndims = H5Sget_simple_extent_dims(space_id, dims, NULL)) < 0)
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HGOTO_ERROR(H5E_PLINE, H5E_CANTGET, FAIL, "unable to get dataspace dimensions")
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/* Set "local" parameter for this dataset's "pixels-per-scanline" */
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/* (Use the chunk's fastest changing dimension size) */
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HDassert(ndims > 0);
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scanline = dims[ndims - 1];
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/* Adjust scanline if it is smaller than number of pixels per block or
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if it is bigger than maximum pixels per scanline, or there are more than
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SZ_MAX_BLOCKS_PER_SCANLINE blocks per scanline */
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/* Check the pixels per block against the 'scanline' size */
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if(scanline < cd_values[H5Z_SZIP_PARM_PPB]) {
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hssize_t npoints; /* Number of points in the dataspace */
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/* Get number of elements for the dataspace; use
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total number of elements in the chunk to define the new 'scanline' size */
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if((npoints = H5Sget_simple_extent_npoints(space_id)) < 0)
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HGOTO_ERROR(H5E_PLINE, H5E_CANTGET, FAIL, "unable to get number of points in the dataspace")
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if(npoints < cd_values[H5Z_SZIP_PARM_PPB])
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HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "pixels per block greater than total number of elements in the chunk")
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scanline = MIN((cd_values[H5Z_SZIP_PARM_PPB] * SZ_MAX_BLOCKS_PER_SCANLINE), npoints);
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}
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else {
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if(scanline <= SZ_MAX_PIXELS_PER_SCANLINE)
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scanline = MIN((cd_values[H5Z_SZIP_PARM_PPB] * SZ_MAX_BLOCKS_PER_SCANLINE), scanline);
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else
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scanline = cd_values[H5Z_SZIP_PARM_PPB] * SZ_MAX_BLOCKS_PER_SCANLINE;
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} /* end else */
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/* Assign the final value to the scanline */
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H5_CHECKED_ASSIGN(cd_values[H5Z_SZIP_PARM_PPS], unsigned, scanline, hsize_t);
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/* Get datatype's endianness order */
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if((dtype_order = H5Tget_order(type_id)) == H5T_ORDER_ERROR)
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HGOTO_ERROR(H5E_PLINE, H5E_BADTYPE, FAIL, "bad datatype endianness order")
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/* Set the correct endianness flag for szip */
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/* (Note: this may not handle non-atomic datatypes well) */
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cd_values[H5Z_SZIP_PARM_MASK] &= ~(H5_SZIP_LSB_OPTION_MASK|H5_SZIP_MSB_OPTION_MASK);
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switch(dtype_order) {
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case H5T_ORDER_LE: /* Little-endian byte order */
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cd_values[H5Z_SZIP_PARM_MASK] |= H5_SZIP_LSB_OPTION_MASK;
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break;
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case H5T_ORDER_BE: /* Big-endian byte order */
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cd_values[H5Z_SZIP_PARM_MASK] |= H5_SZIP_MSB_OPTION_MASK;
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break;
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case H5T_ORDER_ERROR:
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case H5T_ORDER_VAX:
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case H5T_ORDER_MIXED:
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case H5T_ORDER_NONE:
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default:
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HGOTO_ERROR(H5E_PLINE, H5E_BADTYPE, FAIL, "bad datatype endianness order")
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} /* end switch */
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/* Modify the filter's parameters for this dataset */
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if(H5Pmodify_filter(dcpl_id, H5Z_FILTER_SZIP, flags, H5Z_SZIP_TOTAL_NPARMS, cd_values) < 0)
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HGOTO_ERROR(H5E_PLINE, H5E_CANTSET, FAIL, "can't set local szip parameters")
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done:
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FUNC_LEAVE_NOAPI(ret_value)
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#else /*!USE_HDF5*/
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return ret_value;
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#endif /*USE_HDF5*/
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} /* end H5Z___set_local_szip() */
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/*-------------------------------------------------------------------------
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* Function: H5Z___filter_szip
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*
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* Purpose: Implement an I/O filter around the 'rice' algorithm in
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* libsz
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*
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* Return: Success: Size of buffer filtered
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* Failure: 0
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*
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* Programmer: Kent Yang
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* Tuesday, April 1, 2003
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*
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*-------------------------------------------------------------------------
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*/
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static size_t
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H5Z___filter_szip(unsigned flags, size_t cd_nelmts, const unsigned cd_values[],
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size_t nbytes, size_t *buf_size, void **buf)
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{
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size_t ret_value = 0; /* Return value */
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size_t size_out = 0; /* Size of output buffer */
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unsigned char *outbuf = NULL; /* Pointer to new output buffer */
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unsigned char *newbuf = NULL; /* Pointer to input buffer */
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SZ_com_t sz_param; /* szip parameter block */
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FUNC_ENTER_STATIC
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/* Sanity check to make certain that we haven't drifted out of date with
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* the mask options from the szlib.h header */
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HDassert(H5_SZIP_ALLOW_K13_OPTION_MASK==SZ_ALLOW_K13_OPTION_MASK);
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HDassert(H5_SZIP_CHIP_OPTION_MASK==SZ_CHIP_OPTION_MASK);
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HDassert(H5_SZIP_EC_OPTION_MASK==SZ_EC_OPTION_MASK);
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HDassert(H5_SZIP_LSB_OPTION_MASK==SZ_LSB_OPTION_MASK);
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HDassert(H5_SZIP_MSB_OPTION_MASK==SZ_MSB_OPTION_MASK);
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HDassert(H5_SZIP_NN_OPTION_MASK==SZ_NN_OPTION_MASK);
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HDassert(H5_SZIP_RAW_OPTION_MASK==SZ_RAW_OPTION_MASK);
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/* Check arguments */
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if (cd_nelmts!=4)
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HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, 0, "invalid number of filter parameters")
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/* Copy the filter parameters into the szip parameter block */
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H5_CHECKED_ASSIGN(sz_param.options_mask, int, cd_values[H5Z_SZIP_PARM_MASK], unsigned);
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H5_CHECKED_ASSIGN(sz_param.bits_per_pixel, int, cd_values[H5Z_SZIP_PARM_BPP], unsigned);
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H5_CHECKED_ASSIGN(sz_param.pixels_per_block, int, cd_values[H5Z_SZIP_PARM_PPB], unsigned);
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H5_CHECKED_ASSIGN(sz_param.pixels_per_scanline, int, cd_values[H5Z_SZIP_PARM_PPS], unsigned);
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/* Input; uncompress */
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if (flags & H5Z_FLAG_REVERSE) {
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uint32_t stored_nalloc; /* Number of bytes the compressed block will expand into */
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size_t nalloc; /* Number of bytes the compressed block will expand into */
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/* Get the size of the uncompressed buffer */
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newbuf = (unsigned char *)(*buf);
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UINT32DECODE(newbuf,stored_nalloc);
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H5_CHECKED_ASSIGN(nalloc, size_t, stored_nalloc, uint32_t);
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/* Allocate space for the uncompressed buffer */
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if(NULL == (outbuf = (unsigned char *)H5MM_malloc(nalloc)))
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HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, 0, "memory allocation failed for szip decompression")
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/* Decompress the buffer */
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size_out=nalloc;
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if(SZ_BufftoBuffDecompress(outbuf, &size_out, newbuf, nbytes-4, &sz_param) != SZ_OK)
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HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, 0, "szip_filter: decompression failed")
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HDassert(size_out==nalloc);
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/* Free the input buffer */
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H5MM_xfree(*buf);
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/* Set return values */
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*buf = outbuf;
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outbuf = NULL;
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*buf_size = nalloc;
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ret_value = size_out;
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}
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/* Output; compress */
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else {
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unsigned char *dst = NULL; /* Temporary pointer to new output buffer */
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/* Allocate space for the compressed buffer & header (assume data won't get bigger) */
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if(NULL == (dst=outbuf = (unsigned char *)H5MM_malloc(nbytes+4)))
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HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, 0, "unable to allocate szip destination buffer")
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/* Encode the uncompressed length */
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H5_CHECK_OVERFLOW(nbytes,size_t,uint32_t);
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UINT32ENCODE(dst,nbytes);
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/* Compress the buffer */
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size_out = nbytes;
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if(SZ_OK!= SZ_BufftoBuffCompress(dst, &size_out, *buf, nbytes, &sz_param))
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HGOTO_ERROR(H5E_PLINE, H5E_CANTINIT, 0, "overflow")
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HDassert(size_out<=nbytes);
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/* Free the input buffer */
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H5MM_xfree(*buf);
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/* Set return values */
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*buf = outbuf;
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outbuf = NULL;
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*buf_size = nbytes+4;
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ret_value = size_out+4;
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}
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done:
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if(outbuf)
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H5MM_xfree(outbuf);
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FUNC_LEAVE_NOAPI(ret_value)
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}
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/* External Discovery Functions */
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DLLEXPORT
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H5PL_type_t
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H5PLget_plugin_type(void)
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{
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return H5PL_TYPE_FILTER;
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}
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DLLEXPORT
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const void*
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H5PLget_plugin_info(void)
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{
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return H5Z_SZIP;
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}
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#endif /* HAVE_SZ */
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