2021-09-03 07:04:26 +08:00
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/*
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Blosc - A blocking, shuffling and lossless compression library
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Copyright (C) 2009-2015 Francesc Alted <francesc@blosc.org>
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Permission is hereby granted, free of charge, to any person obtaining a copy
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of this software and associated documentation files (the "Software"), to deal
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in the Software without restriction, including without limitation the rights
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to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
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copies of the Software, and to permit persons to whom the Software is
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furnished to do so, subject to the following conditions:
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The above copyright notice and this permission notice shall be included in
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all copies or substantial portions of the Software.
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THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
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IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
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FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
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AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
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LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
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OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
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THE SOFTWARE.
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Blosc for HDF5 - An HDF5 filter that uses the Blosc compressor.
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Copyright (C) 2009-2015 Francesc Alted <francesc@blosc.org>
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Permission is hereby granted, free of charge, to any person obtaining a copy
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of this software and associated documentation files (the "Software"), to deal
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in the Software without restriction, including without limitation the rights
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to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
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copies of the Software, and to permit persons to whom the Software is
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furnished to do so, subject to the following conditions:
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The above copyright notice and this permission notice shall be included in
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all copies or substantial portions of the Software.
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THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
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IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
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FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
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AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
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LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
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OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
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THE SOFTWARE.
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Copyright Notice and Statement for the h5py Project
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Copyright (c) 2008 Andrew Collette
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http://h5py.alfven.org
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All rights reserved.
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Redistribution and use in source and binary forms, with or without
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modification, are permitted provided that the following conditions are
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met:
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a. Redistributions of source code must retain the above copyright
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notice, this list of conditions and the following disclaimer.
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b. Redistributions in binary form must reproduce the above copyright
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notice, this list of conditions and the following disclaimer in the
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documentation and/or other materials provided with the
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distribution.
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c. Neither the name of the author nor the names of contributors may
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be used to endorse or promote products derived from this software
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without specific prior written permission.
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THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
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"AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
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LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
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A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
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OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
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SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
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LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
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DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
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THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
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(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
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OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
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*/
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/*
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Copyright (C) 2010-2016 Francesc Alted
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http://blosc.org
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License: MIT (see LICENSE.txt)
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Filter program that allows the use of the Blosc filter in HDF5.
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This is based on the LZF filter interface (http://h5py.alfven.org)
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by Andrew Collette.
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*/
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2022-07-13 05:19:07 +08:00
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/*
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HDF5 Blosc filter takes 7 parameters as follows:
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param[0] -- FILTER_BLOSC_VERSION (ignored)
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param[1] -- BLOSC_VERSION_FORMAT (ignored)
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param[2] -- typesize in bytes
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param[3] -- chunksize in bytes (ignored)
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param[4] -- compression level
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param[5] -- shuffle enabled
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param[6] -- compressor to use
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*/
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2021-09-03 07:04:26 +08:00
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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 <stdio.h>
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#include <string.h>
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#include <errno.h>
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#include "netcdf_filter_build.h"
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#include <netcdf_json.h>
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#include "H5Zblosc.h"
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#ifdef USE_HDF5
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#include <H5Epubgen.h>
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#endif
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2022-07-13 05:19:07 +08:00
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#undef BLOSC_DEBUG
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2021-09-03 07:04:26 +08:00
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2022-07-13 05:19:07 +08:00
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#undef BLOSCCTX
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2021-09-03 07:04:26 +08:00
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static size_t blosc_filter(unsigned flags, size_t cd_nelmts,
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const unsigned cd_values[], size_t nbytes,
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size_t* buf_size, void** buf);
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#ifndef USE_HDF5
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#define blosc_set_local NULL
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#else
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static herr_t blosc_set_local(hid_t dcpl, hid_t type, hid_t space);
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/* Filter setup. Records the following inside the DCPL:
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1. If version information is not present, set slots 0 and 1 to the filter
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revision and Blosc version, respectively.
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2. Compute the type size in bytes and store it in slot 2.
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3. Compute the chunk size in bytes and store it in slot 3.
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*/
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static
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herr_t blosc_set_local(hid_t dcpl, hid_t type, hid_t space)
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{
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2022-07-13 05:19:07 +08:00
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int i,ndims;
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2021-09-03 07:04:26 +08:00
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unsigned int typesize, basetypesize;
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unsigned int bufsize;
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2022-07-13 05:19:07 +08:00
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unsigned int flags = 0;
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size_t nelements = 7;
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unsigned int values[] = {0, 0, 0, 0, 0, 0, 0};
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2021-09-03 07:04:26 +08:00
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hid_t super_type;
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H5T_class_t classt;
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2022-07-13 05:19:07 +08:00
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hsize_t chunkdims[32];
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2021-09-03 07:04:26 +08:00
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2022-07-13 05:19:07 +08:00
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assert(sizeof(hid_t) == 8);
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if(H5Pget_filter_by_id1(dcpl, H5Z_FILTER_BLOSC, &flags, &nelements, values, 0, NULL) < 0) goto failed;
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2021-09-03 07:04:26 +08:00
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2022-07-13 05:19:07 +08:00
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assert(nelements == 7);
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2021-09-03 07:04:26 +08:00
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2022-07-13 05:19:07 +08:00
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#ifdef BLOSC_DEBUG
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fprintf(stderr, "Blosc: initial parameters =(%u) [%u %u %u %u %u %u %u]\n",
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(unsigned)nelements,values[0],values[1],values[2],values[3],values[4],values[5],values[6]); fflush(stderr);
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#endif
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/* Ignore first two slots */
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values[0] = 0; /* FILTER_BLOSC_VERSION*/
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values[1] = 0; /*BLOSC_VERSION_FORMAT*/
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2021-09-03 07:04:26 +08:00
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ndims = H5Pget_chunk(dcpl, 32, chunkdims);
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2022-07-13 05:19:07 +08:00
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if (ndims < 0) goto failed;
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2021-09-03 07:04:26 +08:00
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if (ndims > 32) {
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2022-07-13 05:19:07 +08:00
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fprintf(stderr,"Blosc Filter Error: blosc_set_local: Chunk rank exceeds limit\n");
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goto failed;
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2021-09-03 07:04:26 +08:00
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}
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typesize = H5Tget_size(type);
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2022-07-13 05:19:07 +08:00
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if (typesize == 0) goto failed;
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2021-09-03 07:04:26 +08:00
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/* Get the size of the base type, even for ARRAY types */
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classt = H5Tget_class(type);
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if (classt == H5T_ARRAY) {
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/* Get the array base component */
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super_type = H5Tget_super(type);
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basetypesize = H5Tget_size(super_type);
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/* Release resources */
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H5Tclose(super_type);
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} else {
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basetypesize = typesize;
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}
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/* Limit large typesizes (they are pretty expensive to shuffle
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and, in addition, Blosc does not handle typesizes larger than
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256 bytes). */
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if (basetypesize > BLOSC_MAX_TYPESIZE) basetypesize = 1;
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values[2] = basetypesize;
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2022-07-13 05:19:07 +08:00
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{
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/* Get the size of the chunk */
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bufsize = typesize;
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#ifdef BLOSC_DEBUG
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fprintf(stderr,">>> set_local: |dims|=%d dims=(",(int)ndims);
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for (i = 0; i < ndims; i++) {
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fprintf(stderr,"%s%u",(i==0?"":","),(unsigned)chunkdims[i]);
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}
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fprintf(stderr,")\n");
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#endif
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for (i = 0; i < ndims; i++) {
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bufsize *= chunkdims[i];
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}
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values[3] = bufsize;
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2021-09-03 07:04:26 +08:00
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}
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#ifdef BLOSC_DEBUG
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2022-07-13 05:19:07 +08:00
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fprintf(stderr, "Blosc: working parameters =(%u) [%u %u %u %u %u %u %u]\n",
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(unsigned)nelements,values[0],values[1],values[2],values[3],values[4],values[5],values[6]); fflush(stderr);
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2021-09-03 07:04:26 +08:00
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#endif
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2022-07-13 05:19:07 +08:00
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if(H5Pmodify_filter(dcpl, H5Z_FILTER_BLOSC, flags, nelements, values) < 0) goto failed;
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2021-09-03 07:04:26 +08:00
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return 1;
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2022-07-13 05:19:07 +08:00
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failed:
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return -1;
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2021-09-03 07:04:26 +08:00
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}
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#endif /*USE_HDF5*/
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/* The filter function */
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static
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size_t blosc_filter(unsigned flags, size_t cd_nelmts,
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const unsigned cd_values[], size_t nbytes,
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size_t* buf_size, void** buf)
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{
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void* outbuf = NULL;
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size_t typesize;
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size_t outbuf_size;
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int clevel = 5; /* Compression level default */
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int doshuffle = 1; /* Shuffle default */
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int compcode; /* Blosc compressor */
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int code;
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2021-09-28 08:36:33 +08:00
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const char* compname = "blosclz"; /* The compressor by default */
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2022-07-13 05:19:07 +08:00
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int bloscsize = 0;
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#ifdef BLOSC_DEBUG
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fprintf(stderr, "Blosc: compressor =(%u) [%u %u %u %u %u %u %u]\n",
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(unsigned)cd_nelmts,cd_values[0],cd_values[1],cd_values[2],cd_values[3],cd_values[4],cd_values[5],cd_values[6]); fflush(stderr);
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#endif
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2021-09-03 07:04:26 +08:00
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/* Filter params that are always set */
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typesize = cd_values[2]; /* The datatype size */
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/* Optional params */
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if (cd_nelmts >= 5) {
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clevel = cd_values[4]; /* The compression level */
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}
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if (cd_nelmts >= 6) {
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doshuffle = cd_values[5]; /* BLOSC_SHUFFLE, BLOSC_BITSHUFFLE */
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}
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if (cd_nelmts >= 7) {
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compcode = cd_values[6]; /* The Blosc compressor used */
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code = blosc_compcode_to_compname(compcode, &compname);
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if (code == -1) {
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2022-07-13 05:19:07 +08:00
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fprintf(stderr,"Blosc Filter Error: this Blosc library does not have support for the '%s' compressor\n",compname);
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2021-09-03 07:04:26 +08:00
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goto failed;
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}
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}
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/* We're compressing */
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if (!(flags & H5Z_FLAG_REVERSE)) {
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/* Allocate an output buffer exactly as long as the input data; if
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the result is larger, we simply return 0. The filter is flagged
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as optional, so HDF5 marks the chunk as uncompressed and
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proceeds.
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*/
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outbuf_size = (*buf_size);
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#ifdef BLOSC_DEBUG
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2022-07-13 05:19:07 +08:00
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fprintf(stderr, "Blosc: Compress %zd chunk w/chunksize %zd\n",
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nbytes, outbuf_size);
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2021-09-03 07:04:26 +08:00
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#endif
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outbuf = malloc(outbuf_size);
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if (outbuf == NULL) {
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2022-07-13 05:19:07 +08:00
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fprintf(stderr,"Blosc Filter Error: blosc_filter: Can't allocate compression buffer\n");
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2021-09-03 07:04:26 +08:00
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goto failed;
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}
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#ifdef BLOSCCTX
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2022-07-13 05:19:07 +08:00
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bloscsize = blosc_compress_ctx(clevel, doshuffle, typesize, nbytes, *buf, outbut, nbytes,
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2021-09-03 07:04:26 +08:00
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compname, /*blocksize*/0, /*no. thredds*/0);
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2022-07-13 05:19:07 +08:00
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#else
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blosc_set_compressor(compname);
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bloscsize = blosc_compress(clevel, doshuffle, typesize, nbytes, *buf, outbuf, nbytes);
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2021-09-03 07:04:26 +08:00
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#endif
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2022-07-13 05:19:07 +08:00
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if(bloscsize == 0) {
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fprintf(stderr,"Blosc_FIlter Error: blosc_filter: Buffer is uncompressible.\n");
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goto failed;
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} else if(bloscsize < 0) {
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fprintf(stderr,"Blosc Filter Error: blosc_filter: blosc compression error\n");
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2021-09-03 07:04:26 +08:00
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goto failed;
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}
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2022-07-13 05:19:07 +08:00
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} else { /* We're decompressing */
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2021-09-03 07:04:26 +08:00
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/* declare dummy variables */
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size_t cbytes, blocksize;
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if(outbuf) {
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free(outbuf);
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outbuf = NULL;
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}
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/* Extract the exact outbuf_size from the buffer header.
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*
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* NOTE: the guess value got from "cd_values" corresponds to the
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* uncompressed chunk size but it should not be used in a general
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* cases since other filters in the pipeline can modify the buffere
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* size.
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*/
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blosc_cbuffer_sizes(*buf, &outbuf_size, &cbytes, &blocksize);
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|
#ifdef BLOSC_DEBUG
|
|
|
|
fprintf(stderr, "Blosc: Decompress %zd chunk w/buffer %zd\n", nbytes, outbuf_size);
|
|
|
|
#endif
|
|
|
|
|
|
|
|
outbuf = malloc(outbuf_size);
|
|
|
|
|
|
|
|
if (outbuf == NULL) {
|
2022-07-13 05:19:07 +08:00
|
|
|
fprintf(stderr,"Blosc Filter Error: blosc_filter: can't allocate decompression buffer\n");
|
2021-09-03 07:04:26 +08:00
|
|
|
goto failed;
|
|
|
|
}
|
|
|
|
|
|
|
|
#ifdef BLOSCCTX
|
2022-07-13 05:19:07 +08:00
|
|
|
bloscsize = blosc_decompress_ctx(*buf, outbuf, outbuf_size, /*no. thredds*/0);
|
2021-09-03 07:04:26 +08:00
|
|
|
#else
|
2022-07-13 05:19:07 +08:00
|
|
|
bloscsize = blosc_decompress(*buf, outbuf, outbuf_size);
|
2021-09-03 07:04:26 +08:00
|
|
|
#endif
|
|
|
|
|
2022-07-13 05:19:07 +08:00
|
|
|
if(bloscsize <= 0) { /* decompression failed */
|
|
|
|
fprintf(stderr,"Blosc Filter Error: blosc_filter: blosc decompression error\n");
|
2021-09-03 07:04:26 +08:00
|
|
|
goto failed;
|
|
|
|
} /* if !status */
|
|
|
|
|
|
|
|
} /* compressing vs decompressing */
|
|
|
|
|
2022-07-13 05:19:07 +08:00
|
|
|
{
|
2021-09-03 07:04:26 +08:00
|
|
|
free(*buf);
|
|
|
|
*buf = outbuf;
|
|
|
|
*buf_size = outbuf_size;
|
2022-07-13 05:19:07 +08:00
|
|
|
return bloscsize; /* Size of compressed/decompressed data */
|
2021-09-03 07:04:26 +08:00
|
|
|
}
|
|
|
|
|
2022-07-13 05:19:07 +08:00
|
|
|
failed:
|
2021-09-03 07:04:26 +08:00
|
|
|
free(outbuf);
|
|
|
|
return 0;
|
|
|
|
|
|
|
|
} /* End filter function */
|
|
|
|
|
|
|
|
|
|
|
|
/* HDF5 Plugin Interface */
|
|
|
|
const H5Z_class2_t blosc_H5Filter[1] = {
|
|
|
|
{
|
|
|
|
H5Z_CLASS_T_VERS,
|
Support installation of filters into user-specified location
re: https://github.com/Unidata/netcdf-c/issues/2294
Ed Hartnett suggested that the netcdf library installation process
be extended to install the standard filters into a user specified
location. The user can then set HDF5_PLUGIN_PATH to that location.
This PR provides that capability using:
````
configure option: --with-plugin-dir=<absolute directory path>
cmake option: -DPLUGIN_INSTALL_DIR=<absolute directory path>
````
Currently, the following plugins are always installed, if
available: bzip2, zstd, blosc.
If NCZarr is enabled, then additional plugins are installed:
fletcher32, shuffle, deflate, szip.
Additionally, the necessary codec support is installed
for each of the above filters that is installed.
## Changes:
1. Cleanup handling of built-in bzip2.
2. Add documentation to docs/filters.md
3. Re-factor the NCZarr codec libraries
4. Add a test, although it can only be exercised after
the library is installed, so it cannot be used during
normal testing.
5. Cleanup use of HDF5_PLUGIN_PATH in the filter test cases.
2022-04-30 04:31:55 +08:00
|
|
|
(H5Z_filter_t)(H5Z_FILTER_BLOSC),
|
2021-09-03 07:04:26 +08:00
|
|
|
1, /* encoder_present flag (set to true) */
|
|
|
|
1, /* decoder_present flag (set to true) */
|
|
|
|
"blosc",
|
|
|
|
/* Filter info */
|
|
|
|
NULL, /* The "can apply" callback */
|
|
|
|
(H5Z_set_local_func_t)(blosc_set_local), /* The "set local" callback */
|
|
|
|
(H5Z_func_t)(blosc_filter), /* The filter function */
|
|
|
|
}
|
|
|
|
};
|
|
|
|
|
|
|
|
|
|
|
|
H5PL_type_t H5PLget_plugin_type(void) { return H5PL_TYPE_FILTER; }
|
|
|
|
const void* H5PLget_plugin_info(void) { return blosc_H5Filter; }
|