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https://github.com/Unidata/netcdf-c.git
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126b3f9423
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.
545 lines
16 KiB
C
545 lines
16 KiB
C
/* Copyright 2003-2018, University Corporation for Atmospheric
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* Research. See the COPYRIGHT file for copying and redistribution
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* conditions.
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*/
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/*
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Author: Dennis Heimbigner
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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 <stdio.h>
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#include <string.h>
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#include <assert.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 "netcdf_json.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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#endif
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#define H5Z_FILTER_DEFLATE 1 /*deflation like gzip */
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#define H5Z_FILTER_SHUFFLE 2 /*shuffle the data */
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#define H5Z_FILTER_FLETCHER32 3 /*fletcher32 checksum of EDC */
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/**************************************************/
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/* NCZarr Filter Objects */
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/* Forward */
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static int NCZ_shuffle_codec_to_hdf5(const char* codec, size_t* nparamsp, unsigned** paramsp);
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static int NCZ_shuffle_hdf5_to_codec(size_t nparams, const unsigned* params, char** codecp);
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static int NCZ_shuffle_modify_parameters(int ncid, int varid, size_t* vnparamsp, unsigned** vparamsp, size_t* wnparamsp, unsigned** wparamsp);
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static int NCZ_fletcher32_codec_to_hdf5(const char* codec, size_t* nparamsp, unsigned** paramsp);
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static int NCZ_fletcher32_hdf5_to_codec(size_t nparams, const unsigned* params, char** codecp);
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static int NCZ_fletcher32_modify_parameters(int ncid, int varid, size_t* vnparamsp, unsigned** vparamsp, size_t* wnparamsp, unsigned** wparamsp);
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static int NCZ_deflate_codec_to_hdf5(const char* codec, size_t* nparamsp, unsigned** paramsp);
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static int NCZ_deflate_hdf5_to_codec(size_t nparams, const unsigned* params, char** codecp);
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#ifdef HAVE_SZ
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static int NCZ_szip_codec_to_hdf5(const char* codec, size_t* nparamsp, unsigned** paramsp);
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static int NCZ_szip_hdf5_to_codec(size_t nparams, const unsigned* params, char** codecp);
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static int NCZ_szip_modify_parameters(int ncid, int varid, size_t* vnparamsp, unsigned** vparamsp, size_t* wnparamsp, unsigned** wparamsp);
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#endif
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/**************************************************/
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static NCZ_codec_t NCZ_shuffle_codec = {
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NCZ_CODEC_CLASS_VER, /* Struct version number */
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NCZ_CODEC_HDF5, /* Struct sort */
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"shuffle", /* Standard name/id of the codec */
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H5Z_FILTER_SHUFFLE, /* HDF5 alias for shuffle */
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NULL, /*NCZ_shuffle_codec_initialize*/
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NULL, /*NCZ_shuffle_codec_finalize*/
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NCZ_shuffle_codec_to_hdf5,
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NCZ_shuffle_hdf5_to_codec,
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NCZ_shuffle_modify_parameters,
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};
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static int
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NCZ_shuffle_codec_to_hdf5(const char* codec, size_t* nparamsp, unsigned** paramsp)
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{
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int stat = NC_NOERR;
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/* Ignore any incoming elementsize */
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if(nparamsp) *nparamsp = 0;
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return stat;
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}
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static int
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NCZ_shuffle_hdf5_to_codec(size_t nparams, const unsigned* params, char** codecp)
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{
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int stat = NC_NOERR;
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char json[1024];
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unsigned typesize = 0;
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if(nparams > 0)
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typesize = params[0];
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snprintf(json,sizeof(json),"{\"id\": \"%s\", \"elementsize\": \"%u\"}",NCZ_shuffle_codec.codecid,typesize);
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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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static int
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NCZ_shuffle_modify_parameters(int ncid, int varid, size_t* vnparamsp, unsigned** vparamsp, size_t* wnparamsp, unsigned** wparamsp)
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{
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int stat = NC_NOERR;
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nc_type vtype;
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size_t typesize;
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char vname[NC_MAX_NAME+1];
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unsigned int* params = NULL;
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/* Ignore the visible parameters */
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if(!wnparamsp || !wparamsp) {stat = NC_EINTERNAL; goto done;}
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/* Get variable info */
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if((stat = nc_inq_var(ncid,varid,vname,&vtype,NULL,NULL,NULL))) goto done;
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/* Get the typesize */
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if((stat = nc_inq_type(ncid,vtype,NULL,&typesize))) goto done;
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if((params=(unsigned*)malloc(sizeof(unsigned)))==NULL)
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{stat = NC_ENOMEM; goto done;}
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params[0] = (unsigned)typesize;
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if(wnparamsp) *wnparamsp = 1;
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if(wparamsp) {
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nullfree(*wparamsp);
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*wparamsp = params; params = NULL;
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}
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done:
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nullfree(params);
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return stat;
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}
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#if 0
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static int
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NCZ_shuffle_visible_parameters(int ncid, int varid, size_t nparamsin, const unsigned int* paramsin, size_t* nparamsp, unsigned** paramsp)
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{
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int stat = NC_NOERR;
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unsigned* params = NULL;
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size_t typesize = 0;
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if(!nparamsp || !paramsp) {stat = NC_EINTERNAL; goto done;}
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if(nparamsin > 0)
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typesize = paramsin[0];
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if((params=(unsigned*)malloc(sizeof(unsigned)))==NULL)
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{stat = NC_ENOMEM; goto done;}
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params[0] = (unsigned)typesize;
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/* add the typesize as a new parameter */
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nullfree(*paramsp);
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*paramsp = params; params = NULL;
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*nparamsp = 1;
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done:
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nullfree(params);
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return stat;
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}
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#endif
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/**************************************************/
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static NCZ_codec_t NCZ_fletcher32_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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"fletcher32", /* Standard name/id of the codec */
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H5Z_FILTER_FLETCHER32, /* HDF5 alias for zlib */
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NULL, /*NCZ_fletcher32_codec_initialize*/
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NULL, /*NCZ_fletcher32_codec_finalize*/
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NCZ_fletcher32_codec_to_hdf5,
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NCZ_fletcher32_hdf5_to_codec,
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NCZ_fletcher32_modify_parameters,
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};
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static int
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NCZ_fletcher32_codec_to_hdf5(const char* codec, size_t* nparamsp, unsigned** paramsp)
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{
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int stat = NC_NOERR;
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NC_UNUSED(codec);
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if(!nparamsp || !paramsp) {stat = NC_EINTERNAL; goto done;}
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*nparamsp = 0;
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nullfree(*paramsp);
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*paramsp = NULL;
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done:
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return stat;
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}
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static int
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NCZ_fletcher32_hdf5_to_codec(size_t nparams, const unsigned* params, char** codecp)
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{
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int stat = NC_NOERR;
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char json[1024];
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snprintf(json,sizeof(json),"{\"id\": \"%s\"}",NCZ_fletcher32_codec.codecid);
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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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static int
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NCZ_fletcher32_modify_parameters(int ncid, int varid, size_t* vnparamsp, unsigned** vparamsp, size_t* wnparamsp, unsigned** wparamsp)
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{
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int stat = NC_NOERR;
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/* Ignore the visible parameters */
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if(!wnparamsp || !wparamsp) {stat = NC_EINTERNAL; goto done;}
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*wnparamsp = 0;
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nullfree(*wparamsp);
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*wparamsp = NULL;
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done:
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return stat;
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}
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#if 0
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static int
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NCZ_fletcher32_visible_parameters(int ncid, int varid, size_t nparamsin, const unsigned int* paramsin, size_t* nparamsp, unsigned** paramsp)
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{
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int stat = NC_NOERR;
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if(!nparamsp || !paramsp) {stat = NC_EINTERNAL; goto done;}
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nullfree(*paramsp); *paramsp = NULL;
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*nparamsp = 0;
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done:
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return stat;
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}
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#endif
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/**************************************************/
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static NCZ_codec_t NCZ_zlib_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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"zlib", /* Standard name/id of the codec */
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H5Z_FILTER_DEFLATE, /* HDF5 alias for zlib */
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NULL, /*NCZ_deflate_codec_initialize*/
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NULL, /*NCZ_deflate_codec_finalize*/
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NCZ_deflate_codec_to_hdf5,
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NCZ_deflate_hdf5_to_codec,
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NULL, /*NCZ_deflate_modify_parameters*/
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};
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static int
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NCZ_deflate_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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unsigned* params = NULL;
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struct NCJconst jc;
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if(nparamsp == NULL || paramsp == NULL)
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{stat = NC_EINTERNAL; goto done;}
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if((params = (unsigned*)calloc(1,sizeof(unsigned)))== NULL)
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{stat = NC_ENOMEM; goto done;}
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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_EFILTER; goto done;}
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if(strcmp(NCJstring(jtmp),NCZ_zlib_codec.codecid)!=0) {stat = NC_EINVAL; goto done;}
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/* Get Level */
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if(NCJdictget(jcodec,"level",&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[0] = (unsigned)jc.ival;
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*nparamsp = 1;
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*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_deflate_hdf5_to_codec(size_t nparams, const unsigned* params, char** codecp)
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{
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int stat = NC_NOERR;
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unsigned level = 0;
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char json[1024];
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if(nparams == 0 || params == NULL)
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{stat = NC_EFILTER; goto done;}
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level = params[0];
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snprintf(json,sizeof(json),"{\"id\": \"%s\", \"level\": \"%u\"}",NCZ_zlib_codec.codecid,level);
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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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/**************************************************/
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#ifdef HAVE_SZ
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static NCZ_codec_t NCZ_szip_codec = {
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NCZ_CODEC_CLASS_VER, /* Struct version number */
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NCZ_CODEC_HDF5, /* Struct sort */
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"szip", /* Standard name/id of the codec */
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H5Z_FILTER_SZIP, /* HDF5 alias for szip */
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NULL, /*NCZ_szip_codec_initialize*/
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NULL, /*NCZ_szip_codec_finalize*/
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NCZ_szip_codec_to_hdf5,
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NCZ_szip_hdf5_to_codec,
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NCZ_szip_modify_parameters,
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};
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static int
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NCZ_szip_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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unsigned* params = NULL;
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size_t nparams = 2; /* No. of visible parameters */
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NCjson* json = NULL;
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NCjson* jtmp = NULL;
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struct NCJconst jc = {0,0,0,NULL};
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if(nparamsp == NULL || paramsp == NULL)
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{stat = NC_EINTERNAL; goto done;}
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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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if(NCJparse(codec_json,0,&json))
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{stat = NC_EFILTER; goto done;}
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if(NCJdictget(json,"mask",&jtmp) || jtmp == NULL)
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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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params[H5Z_SZIP_PARM_MASK] = (unsigned)jc.ival;
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jtmp = NULL;
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if(NCJdictget(json,"pixels-per-block",&jtmp) || jtmp == NULL)
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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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params[H5Z_SZIP_PARM_PPB] = (unsigned)jc.ival;
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*nparamsp = nparams;
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*paramsp = params; params = NULL;
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done:
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NCJreclaim(json);
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nullfree(params);
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return stat;
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}
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static int
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NCZ_szip_hdf5_to_codec(size_t nparams, const unsigned* params, char** codecp)
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{
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int stat = NC_NOERR;
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char json[2048];
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snprintf(json,sizeof(json),"{\"id\": \"%s\", \"mask\": %u, \"pixels-per-block\": %u}",
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NCZ_szip_codec.codecid,
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params[H5Z_SZIP_PARM_MASK],
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params[H5Z_SZIP_PARM_PPB]);
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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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static int
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NCZ_szip_modify_parameters(int ncid, int varid, size_t* vnparamsp, unsigned** vparamsp, size_t* wnparamsp, unsigned** wparamsp)
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{
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int i,ret_value = NC_NOERR;
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nc_type vtype;
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size_t typesize, scanline, dtype_precision, npoints;
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int ndims, storage, dtype_order;
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int dimids[NC_MAX_VAR_DIMS];
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char vname[NC_MAX_NAME+1];
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size_t chunklens[NC_MAX_VAR_DIMS];
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unsigned* params = NULL;
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unsigned* vparams = NULL;
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size_t wnparams = 4;
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if(wnparamsp == NULL || wparamsp == NULL)
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{ret_value = NC_EFILTER; goto done;}
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if(vnparamsp == NULL || vparamsp == NULL)
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{ret_value = NC_EFILTER; goto done;}
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if(*vnparamsp > 0 && *vparamsp == NULL)
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{ret_value = NC_EFILTER; goto done;}
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vparams = *vparamsp;
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/* Get variable info */
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if((ret_value = nc_inq_var(ncid,varid,vname,&vtype,&ndims,dimids,NULL))) goto done;
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/* Get the typesize */
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if((ret_value = nc_inq_type(ncid,vtype,NULL,&typesize))) goto done;
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/* Get datatype's precision, in case is less than full bits */
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dtype_precision = typesize*8;
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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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if(ndims == 0) {ret_value = NC_EFILTER; goto done;}
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/* Set "local" parameter for this dataset's "pixels-per-scanline" */
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if((ret_value = nc_inq_dimlen(ncid,dimids[ndims-1],&scanline))) goto done;
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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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/* Compute chunksize */
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if((ret_value = nc_inq_var_chunking(ncid,varid,&storage,chunklens))) goto done;
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if(storage != NC_CHUNKED) {ret_value = NC_EFILTER; goto done;}
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npoints = 1;
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for(i=0;i<ndims;i++) npoints *= chunklens[i];
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/* Get datatype's endianness order */
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if((ret_value = nc_inq_var_endian(ncid,varid,&dtype_order))) goto done;
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if((params = (unsigned*)malloc(wnparams*sizeof(unsigned)))==NULL)
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{ret_value = NC_ENOMEM; goto done;}
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params[H5Z_SZIP_PARM_MASK] = vparams[H5Z_SZIP_PARM_MASK];
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params[H5Z_SZIP_PARM_PPB] = vparams[H5Z_SZIP_PARM_PPB];
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/* Set "local" parameter for this dataset's "bits-per-pixel" */
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params[H5Z_SZIP_PARM_BPP] = dtype_precision;
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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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if(scanline < vparams[H5Z_SZIP_PARM_PPB]) {
|
|
if(npoints < vparams[H5Z_SZIP_PARM_PPB])
|
|
HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "pixels per block greater than total number of elements in the chunk")
|
|
scanline = MIN((vparams[H5Z_SZIP_PARM_PPB] * SZ_MAX_BLOCKS_PER_SCANLINE), npoints);
|
|
} else {
|
|
if(scanline <= SZ_MAX_PIXELS_PER_SCANLINE)
|
|
scanline = MIN((vparams[H5Z_SZIP_PARM_PPB] * SZ_MAX_BLOCKS_PER_SCANLINE), scanline);
|
|
else
|
|
scanline = vparams[H5Z_SZIP_PARM_PPB] * SZ_MAX_BLOCKS_PER_SCANLINE;
|
|
} /* end else */
|
|
/* Assign the final value to the scanline */
|
|
params[H5Z_SZIP_PARM_PPS] = (unsigned)scanline;
|
|
|
|
/* Set the correct mask flags */
|
|
|
|
/* From H5Pdcpl.c#H5Pset_szip */
|
|
params[H5Z_SZIP_PARM_MASK] &= (unsigned)(~H5_SZIP_CHIP_OPTION_MASK);
|
|
params[H5Z_SZIP_PARM_MASK] |= H5_SZIP_ALLOW_K13_OPTION_MASK;
|
|
params[H5Z_SZIP_PARM_MASK] |= H5_SZIP_RAW_OPTION_MASK;
|
|
params[H5Z_SZIP_PARM_MASK] &= (unsigned)(~(H5_SZIP_LSB_OPTION_MASK | H5_SZIP_MSB_OPTION_MASK));
|
|
|
|
/* From H5Zszip.c#H5Z__set_local_szip */
|
|
params[H5Z_SZIP_PARM_MASK] &= (unsigned)(~(H5_SZIP_LSB_OPTION_MASK | H5_SZIP_MSB_OPTION_MASK));
|
|
switch(dtype_order) {
|
|
case NC_ENDIAN_LITTLE: /* Little-endian byte order */
|
|
params[H5Z_SZIP_PARM_MASK] |= H5_SZIP_LSB_OPTION_MASK;
|
|
break;
|
|
case NC_ENDIAN_BIG: /* Big-endian byte order */
|
|
params[H5Z_SZIP_PARM_MASK] |= H5_SZIP_MSB_OPTION_MASK;
|
|
break;
|
|
default:
|
|
HGOTO_ERROR(H5E_PLINE, H5E_BADTYPE, FAIL, "bad datatype endianness order")
|
|
} /* end switch */
|
|
|
|
*wnparamsp = wnparams;
|
|
nullfree(*wparamsp);
|
|
*wparamsp = params; params = NULL;
|
|
|
|
done:
|
|
nullfree(params);
|
|
FUNC_LEAVE_NOAPI(ret_value)
|
|
}
|
|
|
|
#if 0
|
|
static int
|
|
NCZ_szip_visible_parameters(int ncid, int varid, size_t nparamsin, const unsigned int* paramsin, size_t* nparamsp, unsigned** paramsp)
|
|
{
|
|
int stat = NC_NOERR;
|
|
unsigned* params = NULL;
|
|
|
|
if(nparamsp == NULL || paramsp == NULL)
|
|
{stat = NC_EFILTER; goto done;}
|
|
|
|
if((params = (unsigned*)malloc(2*sizeof(unsigned)))==NULL)
|
|
{stat = NC_ENOMEM; goto done;}
|
|
|
|
params[H5Z_SZIP_PARM_MASK] = paramsin[H5Z_SZIP_PARM_MASK];
|
|
params[H5Z_SZIP_PARM_PPB] = paramsin[H5Z_SZIP_PARM_PPB];
|
|
|
|
nullfree(*paramsp);
|
|
*paramsp = params; params = NULL;
|
|
|
|
done:
|
|
nullfree(params);
|
|
return stat;
|
|
}
|
|
#endif
|
|
|
|
#endif /*HAVE_SZ*/
|
|
|
|
/**************************************************/
|
|
|
|
NCZ_codec_t* NCZ_default_codecs[] = {
|
|
&NCZ_shuffle_codec,
|
|
&NCZ_fletcher32_codec,
|
|
&NCZ_zlib_codec,
|
|
#ifdef HAVE_SZ
|
|
&NCZ_szip_codec,
|
|
#endif
|
|
NULL
|
|
};
|
|
|
|
/* External Export API */
|
|
DLLEXPORT
|
|
const void*
|
|
NCZ_codec_info_defaults(void)
|
|
{
|
|
return (void*)&NCZ_default_codecs;
|
|
}
|
|
|