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netcdf-c/libnczarr/zfilter.h

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Add filter support to NCZarr 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'
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/* Copyright 2018-2018 University Corporation for Atmospheric
Research/Unidata. */
/**
* @file This header file containsfilter related macros, types, and prototypes for
* the filter code in libnczarr. This header should not be included in
* code outside libnczarr.
*
* @author Dennis Heimbigner
*/
#ifndef ZFILTER_H
#define ZFILTER_H
/* zfilter.c */
/* Dispatch functions are also in zfilter.c */
/* Filterlist management */
/*Mnemonic*/
#define ENCODING 1
/* list of environment variables to check for plugin roots */
I made a major update to this PR with the following changes: ## Overwriting I think I solved the file overwrite problem by doing light name mangling of the shared library names. With this change the probabilty is very small that installing our filter wrappers in a directory will overwrite code produced by others. ## Default Install Location I have setup the --with-plugin-dir option default to install in the following locations in order of preference 1. If HDF5_PLUGIN_PATH is defined (at build time remember), then the last directory in that path will be where the filter wrapper shared libraries will be installed. 2. Otherwise the default is "/usr/local/hdf5/lib/plugin" (on *nix*) or "%ALLUSERSPROFILE%\\hdf5\\lib\\plugin" for Windows or Mingw. Currently, --with-plugin-dir is disabled by default. I should note that even if I enable it by default, installing netcdf-c will still not run "out of the box" because the hypothetical naive user will not know which compressor libraries need to be pre-installed before netcdf is installed. Nor will that user have any way to find out what needs to be installed.
2022-05-20 12:00:40 +08:00
#define PLUGIN_ENV "HDF5_PLUGIN_PATH"
#define PLUGIN_DIR_UNIX "/usr/local/hdf5/plugin"
#define PLUGIN_DIR_WIN "%s/hdf5/lib/plugin"
#define WIN32_ROOT_ENV "ALLUSERSPROFILE"
Add filter support to NCZarr 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'
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/* Opaque */
struct NCZ_Filter;
int NCZ_filter_initialize(void);
int NCZ_filter_finalize(void);
int NCZ_addfilter(NC_FILE_INFO_T*, NC_VAR_INFO_T* var, unsigned int id, size_t nparams, const unsigned int* params);
int NCZ_filter_setup(NC_VAR_INFO_T* var);
Improve filter installation process to avoid use of an extra shell script re: https://github.com/Unidata/netcdf-c/issues/2338 re: https://github.com/Unidata/netcdf-c/issues/2294 In issue https://github.com/Unidata/netcdf-c/issues/2338, Ed Hartnett suggested a better way to install filters to a user defined location -- for Automake, anyway. This PR implements that suggestion. It turns out to be more complicated than it appears, so there are fair number of changes; mostly to shell scripts. Most of the change is in plugins/Makefile.am. NOTE: this PR still does NOT address the use of HDF5_PLUGIN_PATH as the default; this turns out to be complex when dealing with NCZarr. So this will be addressed in a subsequent post 4.9.0 PR. ## Misc. Changes 1. Record the occurrences of incomplete codecs in libnczarr so that they can be included in _Codecs attribute correctly. This allows users to see what missing filters are referenced in the Zarr file. Primarily affects libnczarr/zfilter.[ch]. Also required creating a new no-effect filter: H5Zunknown.c. 2. Move the unknown filter test to a separate test file. 3. Incorporates PR https://github.com/Unidata/netcdf-c/pull/2343
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int NCZ_filter_freelists(NC_VAR_INFO_T* var);
Add filter support to NCZarr 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'
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int NCZ_codec_freelist(NCZ_VAR_INFO_T* zvar);
int NCZ_applyfilterchain(const NC_FILE_INFO_T*, NC_VAR_INFO_T*, NClist* chain, size_t insize, void* indata, size_t* outlen, void** outdata, int encode);
int NCZ_filter_jsonize(const NC_FILE_INFO_T*, const NC_VAR_INFO_T*, struct NCZ_Filter* filter, struct NCjson**);
Improve filter installation process to avoid use of an extra shell script re: https://github.com/Unidata/netcdf-c/issues/2338 re: https://github.com/Unidata/netcdf-c/issues/2294 In issue https://github.com/Unidata/netcdf-c/issues/2338, Ed Hartnett suggested a better way to install filters to a user defined location -- for Automake, anyway. This PR implements that suggestion. It turns out to be more complicated than it appears, so there are fair number of changes; mostly to shell scripts. Most of the change is in plugins/Makefile.am. NOTE: this PR still does NOT address the use of HDF5_PLUGIN_PATH as the default; this turns out to be complex when dealing with NCZarr. So this will be addressed in a subsequent post 4.9.0 PR. ## Misc. Changes 1. Record the occurrences of incomplete codecs in libnczarr so that they can be included in _Codecs attribute correctly. This allows users to see what missing filters are referenced in the Zarr file. Primarily affects libnczarr/zfilter.[ch]. Also required creating a new no-effect filter: H5Zunknown.c. 2. Move the unknown filter test to a separate test file. 3. Incorporates PR https://github.com/Unidata/netcdf-c/pull/2343
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int NCZ_filter_build(const NC_FILE_INFO_T*, NC_VAR_INFO_T* var, const NCjson* jfilter, int chainindex);
Add filter support to NCZarr 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'
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int NCZ_codec_attr(const NC_VAR_INFO_T* var, size_t* lenp, void* data);
Enhance/Fix filter support re: Discussion https://github.com/Unidata/netcdf-c/discussions/2214 The primary change is to support so-called "standard filters". A standard filter is one that is defined by the following netcdf-c API: ```` int nc_def_var_XXX(int ncid, int varid, size_t nparams, unsigned* params); int nc_inq_var_XXXX(int ncid, int varid, int* usefilterp, unsigned* params); ```` So for example, zstandard would be a standard filter by defining the functions *nc_def_var_zstandard* and *nc_inq_var_zstandard*. In order to define these functions, we need a new dispatch function: ```` int nc_inq_filter_avail(int ncid, unsigned filterid); ```` This function, combined with the existing filter API can be used to implement arbitrary standard filters using a simple code pattern. Note that I would have preferred that this function return a list of all available filters, but HDF5 does not support that functionality. So this PR implements the dispatch function and implements the following standard functions: + bzip2 + zstandard + blosc Specific test cases are also provided for HDF5 and NCZarr. Over time, other specific standard filters will be defined. ## Primary Changes * Add nc_inq_filter_avail() to netcdf-c API. * Add standard filter implementations to test use of *nc_inq_filter_avail*. * Bump the dispatch table version number and add to all the relevant dispatch tables (libsrc, libsrcp, etc). * Create a program to invoke nc_inq_filter_avail so that it is accessible to shell scripts. * Cleanup szip support to properly support szip when HDF5 is disabled. This involves detecting libsz separately from testing if HDF5 supports szip. * Integrate shuffle and fletcher32 into the existing filter API. This means that, for example, nc_def_var_fletcher32 is now a wrapper around nc_def_var_filter. * Extend the Codec defaulting to allow multiple default shared libraries. ## Misc. Changes * Modify configure.ac/CMakeLists.txt to look for the relevant libraries implementing standard filters. * Modify libnetcdf.settings to list available standard filters (including deflate and szip). * Add CMake test modules to locate libbz2 and libzstd. * Cleanup the HDF5 memory manager function use in the plugins. * remove unused file include//ncfilter.h * remove tests for the HDF5 memory operations e.g. H5allocate_memory. * Add flag to ncdump to force use of _Filter instead of _Deflate or _Shuffle or _Fletcher32. Used for testing.
2022-03-15 02:39:37 +08:00
Add filter support to NCZarr 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'
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#endif /*ZFILTER_H*/
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