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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'
213 lines
6.0 KiB
C
213 lines
6.0 KiB
C
#include <sys/types.h>
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#include <stdlib.h>
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#include <string.h>
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#include <assert.h>
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#include <stdio.h>
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#include <netcdf_filter_build.h>
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#include "xxxx.h"
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/*
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Provide a textual template (not a C++ template)
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from which one can construct a new filter.
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The filter "name is marked with "XXXX" or "xxxx"
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*/
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static htri_t H5Z_can_apply_xxxx(hid_t dcpl_id, hid_t type_id, hid_t space_id);
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static herr_t H5Z_set_local_xxxx)(long long, long long, long long);
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static size_t H5Z_filter_xxxx(unsigned int flags, size_t cd_nelmts,
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const unsigned int cd_values[], size_t nbytes,
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size_t *buf_size, void **buf);
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const H5Z_class2_t H5Z_XXXX[1] = {{
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H5Z_CLASS_T_VERS, /* H5Z_class_t version */
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(H5Z_filter_t)H5Z_FILTER_XXXX, /* Filter id number */
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1, /* encoder_present flag (set to true) */
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1, /* decoder_present flag (set to true) */
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"xxxx", /* Filter name for debugging */
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(H5Z_can_apply_func_t)H5Z_can_apply_xxxx, /* The "can apply" callback | NULL */
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(H5Z_set_local_func_t)H5Z_set_local_xxxx, /* The "set local" callback | NULL */
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(H5Z_func_t)H5Z_filter_xxxx, /* The actual filter function */
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}};
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/* External Discovery Functions */
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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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const void*
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H5PLget_plugin_info(void)
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{
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return H5Z_FILTER_XXXX;
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}
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static htri_t
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H5Z_can_apply_xxxx(hid_t dcpl_id, hid_t type_id, hid_t space_id)
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{
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return 1; /* always applicable */
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}
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static herr_t
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H5Z_set_local_xxxx)(long long, long long, long long)
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{
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return 0; /* always succeed */
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}
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static size_t
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H5Z_filter_xxxx(unsigned int flags, size_t cd_nelmts,
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const unsigned int cd_values[], size_t nbytes,
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size_t *buf_size, void **buf)
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{
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char *outbuf = NULL;
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size_t outbuflen, outdatalen;
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int ret;
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if (flags & H5Z_FLAG_REVERSE) {
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/** Decompress data.
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**
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** This process is troublesome since the size of uncompressed data
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** is unknown, so the low-level interface must be used.
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** Data is decompressed to the output buffer (which is sized
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** for the average case); if it gets full, its size is doubled
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** and decompression continues. This avoids repeatedly trying to
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** decompress the whole block, which could be really inefficient.
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**/
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char *newbuf = NULL;
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size_t newbuflen;
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} else {
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/** Compress data.
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**
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** This is quite simple, since the size of compressed data in the worst
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** case is known and it is not much bigger than the size of uncompressed
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** data. This allows us to use the simplified one-shot interface to
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** compression.
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**/
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unsigned int odatalen; /* maybe not the same size as outdatalen */
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/* Prepare the output buffer. */
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outbuflen = M; /* worst case */
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outbuf = H5allocate_memory(outbuflen,0);
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if (outbuf == NULL) {
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fprintf(stderr, "memory allocation failed for xxxx compression\n");
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goto cleanupAndFail;
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}
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/* Compress data. */
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}
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/* Always replace the input buffer with the output buffer. */
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H5free_memory(*buf);
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*buf = outbuf;
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*buf_size = outbuflen;
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return outdatalen;
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cleanupAndFail:
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if (outbuf)
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H5free_memory(outbuf);
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return 0;
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}
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/**************************************************/
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/* The NCZarr API */
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/* Forward */
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static int NCZ_xxxx_codec_setup(int ncid, int varid, int* nparamsp, unsigned** paramsp);
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static int NCZ_xxxx_codec_shutdown(int nparams, unsigned* params);
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static int NCZ_xxxx_codec_to_hdf5(const char* codec, int* nparamsp, unsigned** paramsp);
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static int NCZ_xxxx_hdf5_to_codec(int nparams, unsigned* params, char** codecp);
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/* Structure for NCZ_PLUGIN_CODEC */
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static NCZ_codec_t NCZ_xxxx_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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"xxxx", /* Standard name/id of the codec */
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H5Z_FILTER_XXXX, /* HDF5 alias for xxxx */
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NCZ_xxxx_codec_to_hdf5,
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NCZ_xxxx_hdf5_to_codec
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NCZ_xxxx_codec_setup,
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NCZ_xxxx_codec_shutdown,
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};
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/* External Export API */
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const void*
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NCZ_get_plugin_info(void)
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{
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return (void*)&NCZ_xxxx_codec;
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}
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/* NCZarr Interface Functions */
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static int
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NCZ_xxxx_codec_setup(int ncid, int varid, int* nparamsp, unsigned** paramsp)
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{
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return NC_NOERR;
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}
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static int
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NCZ_xxxx_codec_shutdown(int nparams, unsigned* params)
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{
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return NC_NOERR;
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}
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static int
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NCZ_xxxx_codec_to_hdf5(const char* codec_json, int* 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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int nparams = 0;
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unsigned* params = NULL;
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struct NCJconst jc;
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if((params = (unsigned*)malloc(sizeof(unsigned)))== NULL)
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{stat = NC_ENOMEM; goto done;}
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/* parse the JSON */
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if((stat = NCJparse(codec_json,0,&jcodec))) 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((stat = NCJdictget(jcodec,"id",&jtmp))) 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_xxxx_codec.codecid)!=0) {stat = NC_EINVAL; goto done;}
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/* Get unsigned integer param */
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if((stat = NCJdictget(jcodec,"param0",&jtmp))) goto done;
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if((stat = NCJcvt(jtmp,NCJ_INT,&jc))) 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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if(nparamsp) *nparamsp = 1;
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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_xxxx_hdf5_to_codec(int nparams, 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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if(nparams == 0 || params == NULL)
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{stat = NC_EINVAL; goto done;}
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snprintf(json,sizeof(json),"{\"id\": \"%s\", \"param0\": \"%u\"}",NCZ_xxxx_codec.codecid,param[0]);
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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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