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11fe00ea05
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'
180 lines
5.1 KiB
C
180 lines
5.1 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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/*
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* Programmer: Robb Matzke
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* Friday, August 27, 1999
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*/
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/* Converted to NCZarr support by Dennis Heimbigner 5/1/2021 */
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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 <math.h>
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#include <assert.h>
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#include "netcdf_json.h"
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#include "netcdf.h"
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#include "netcdf_filter.h"
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#include "netcdf_filter_build.h"
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#include "h5misc.h"
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/**************************************************/
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/* NCZarr Filter Objects */
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/* Codec Format
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{
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"id": "test",
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"testcase": "n",
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"byte": "<unsigned int>",
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"ubyte": "<unsigned int>",
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"short": "<unsigned int>",
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"ushort": "<unsigned int>",
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"int": "<unsigned int>",
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"uint": "<unsigned int>",
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"float": "<unsigned int>",
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"double0": "<unsigned int>",
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"double1": "<unsigned int>",
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"int640": "<unsigned int>",
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"int641": "<unsigned int>",
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"uint640": "<unsigned int>",
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"uint641": "<unsigned int>",
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}
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*/
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/* Give unique dict key names for parameters */
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static const char* fields[14] = {
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"testcase",
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"byte",
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"ubyte",
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"short",
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"ushort",
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"int",
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"uint",
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"float",
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"double_0",
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"double_1",
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"int64_0",
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"int64_1",
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"uint64_0",
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"uint64_1"
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};
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/* Forward */
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static int NCZ_misc_codec_to_hdf5(const char* codec, size_t* nparamsp, unsigned** paramsp);
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static int NCZ_misc_hdf5_to_codec(size_t nparams, const unsigned* params, char** codecp);
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/* Structure for NCZ_PLUGIN_CODEC */
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static NCZ_codec_t NCZ_misc_codec = {/* NCZ_codec_t codec fields */
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NCZ_CODEC_CLASS_VER, /* Struct version number */
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NCZ_CODEC_HDF5, /* Struct sort */
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"test", /* Standard name/id of the codec */
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H5Z_FILTER_TEST, /* HDF5 alias for misc */
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NULL, /*NCZ_misc_codec_initialize*/
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NULL, /*NCZ_misc_codec_finalize*/
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NCZ_misc_codec_to_hdf5,
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NCZ_misc_hdf5_to_codec,
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NULL, /*NCZ_misc_modify_parameters*/
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};
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/* External Export API */
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DLLEXPORT
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const void*
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NCZ_get_codec_info(void)
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{
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return (void*)&NCZ_misc_codec;
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}
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/* NCZarr Interface Functions */
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static int
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NCZ_misc_codec_to_hdf5(const char* codec_json, size_t* nparamsp, unsigned** paramsp)
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{
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int stat = NC_NOERR;
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NCjson* jcodec = NULL;
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NCjson* jtmp = NULL;
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size_t i,nparams = 0;
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unsigned* params = NULL;
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/* parse the JSON */
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if(NCJparse(codec_json,0,&jcodec))
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{stat = NC_EFILTER; goto done;}
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if(NCJsort(jcodec) != NCJ_DICT) {stat = NC_EPLUGIN; goto done;}
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/* Verify the codec ID */
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if(NCJdictget(jcodec,"id",&jtmp))
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{stat = NC_EFILTER; goto done;}
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if(jtmp == NULL || !NCJisatomic(jtmp)) {stat = NC_EINVAL; goto done;}
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if(strcmp(NCJstring(jtmp),NCZ_misc_codec.codecid)!=0) {stat = NC_EINVAL; goto done;}
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/* The codec will have (2*14 + 1) +1 = 29 dict entries + id*/
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nparams = (2*14 + 1) + 1;
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if(NCJlength(jcodec) != nparams) {
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fprintf(stderr,"Incorrect no. of codec parameters: need=29 sent=%ld\n",(unsigned long)(nparams-1));
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stat = NC_EINVAL;
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goto done;
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}
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/* Actual # of parameters is 14 (ignoring the testcase number) */
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nparams = 14;
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if((params = (unsigned*)calloc(nparams,sizeof(unsigned)))== NULL)
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{stat = NC_ENOMEM; goto done;}
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for(i=0;i<nparams;i++) {
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struct NCJconst jc;
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if(NCJdictget(jcodec,fields[i],&jtmp))
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{stat = NC_EFILTER; goto done;}
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if(NCJcvt(jtmp,NCJ_INT,&jc))
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{stat = NC_EFILTER; goto done;}
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if(jc.ival < 0 || jc.ival > NC_MAX_UINT) {stat = NC_EINVAL; goto done;}
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params[i] = (unsigned)jc.ival;
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}
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if(nparamsp) *nparamsp = nparams;
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if(paramsp) {*paramsp = params; params = NULL;}
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done:
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if(params) free(params);
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NCJreclaim(jcodec);
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return stat;
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}
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static int
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NCZ_misc_hdf5_to_codec(size_t nparams, const unsigned* params, char** codecp)
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{
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int i,stat = NC_NOERR;
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char json[4096];
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char value[1024];
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if(nparams == 0 || params == NULL)
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{stat = NC_EINVAL; goto done;}
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if(nparams != 14) {
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fprintf(stderr,"Incorrect no. of parameters: need=14 sent=%ld\n",(unsigned long)nparams);
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stat = NC_EINVAL;
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goto done;
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}
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snprintf(json,sizeof(json),"{\"id\": \"%s\"",NCZ_misc_codec.codecid);
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for(i=0;i<14;i++) {
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snprintf(value,sizeof(value),", \"%s\": \"%u\"",fields[i],params[i]);
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strlcat(json,value,sizeof(json));
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}
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strlcat(json,"}",sizeof(json));
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if(codecp) {
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if((*codecp = strdup(json))==NULL) {stat = NC_ENOMEM; goto done;}
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}
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done:
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return stat;
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}
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