From 1569a9d9fddcbfca22e2fd4a76f3097339a6ff0b Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?V=2E=20Armando=20Sol=C3=A9?= Date: Tue, 15 Dec 2020 17:16:40 +0100 Subject: [PATCH 1/5] Squashed 'src/HDF5Plugin-Zstandard/' content from commit d5afdb5 git-subtree-dir: src/HDF5Plugin-Zstandard git-subtree-split: d5afdb5f04116d5c2d1a869dc9c7c0c72832b143 --- .gitignore | 33 ++++++++ CMakeLists.txt | 31 ++++++++ LICENSE | 201 ++++++++++++++++++++++++++++++++++++++++++++++++ README.md | 36 +++++++++ zstd_h5plugin.c | 81 +++++++++++++++++++ zstd_h5plugin.h | 22 ++++++ 6 files changed, 404 insertions(+) create mode 100644 .gitignore create mode 100644 CMakeLists.txt create mode 100644 LICENSE create mode 100644 README.md create mode 100644 zstd_h5plugin.c create mode 100644 zstd_h5plugin.h diff --git a/.gitignore b/.gitignore new file mode 100644 index 00000000..f805e810 --- /dev/null +++ b/.gitignore @@ -0,0 +1,33 @@ +# Object files +*.o +*.ko +*.obj +*.elf + +# Precompiled Headers +*.gch +*.pch + +# Libraries +*.lib +*.a +*.la +*.lo + +# Shared objects (inc. Windows DLLs) +*.dll +*.so +*.so.* +*.dylib + +# Executables +*.exe +*.out +*.app +*.i*86 +*.x86_64 +*.hex + +# Debug files +*.dSYM/ +*.su diff --git a/CMakeLists.txt b/CMakeLists.txt new file mode 100644 index 00000000..f8a85d7a --- /dev/null +++ b/CMakeLists.txt @@ -0,0 +1,31 @@ +cmake_minimum_required(VERSION 2.8.10) +project(zstd_hdf5) + +# options +set(PLUGIN_INSTALL_PATH "/usr/local/hdf5/lib/plugin" CACHE PATH + "Where to install the dynamic HDF5-plugin") + +# sources +set(SOURCES zstd_h5plugin.c) +set(PLUGIN_SOURCES zstd_h5plugin.c) + +# dependencies +if(MSVC) + # FindHDF5.cmake does not find Windows installations. Try to + # use an environment variable instead until the official "find" + # file can be updated for Windows. + # + # Note that you have to set this environment variable by hand. + file(TO_CMAKE_PATH "$ENV{HDF5_DIR}" HDF5_HINT) + set(HDF5_DIR ${HDF5_HINT} CACHE STRING "Path to HDF5 CMake config directory.") + find_package(HDF5 REQUIRED HINTS ${HDF5_DIR}) +else(MSVC) + find_package(HDF5 REQUIRED) +endif(MSVC) +include_directories(${HDF5_INCLUDE_DIRS}) + +# HDF5 plugin as shared library +add_library(zstd_h5_plugin_shared SHARED ${PLUGIN_SOURCES}) +set_target_properties(zstd_h5_plugin_shared PROPERTIES OUTPUT_NAME H5Zzstd) +target_link_libraries(zstd_h5_plugin_shared zstd ${HDF5_LIBRARIES}) +install(TARGETS zstd_h5_plugin_shared DESTINATION ${PLUGIN_INSTALL_PATH} COMPONENT HDF5_FILTER_DEV) diff --git a/LICENSE b/LICENSE new file mode 100644 index 00000000..8dada3ed --- /dev/null +++ b/LICENSE @@ -0,0 +1,201 @@ + Apache License + Version 2.0, January 2004 + http://www.apache.org/licenses/ + + TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION + + 1. 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It supports an unlimited variety of datatypes, and is +designed for flexible and efficient I/O and for high volume and +complex data. HDF5 is portable and is extensible, allowing +applications to evolve in their use of HDF5. The HDF5 Technology suite +includes tools and applications for managing, manipulating, viewing, +and analyzing data in the HDF5 format. + +https://support.hdfgroup.org/HDF5/ + +--- + +*Zstandard* is a real-time compression algorithm, providing high +compression ratios. It offers a very wide range of compression/speed +trade-off, while being backed by a very fast decoder. + +http://www.zstd.net + +--- + +This repository provides an implementation of Zstandard compression +filter plugin for HDF5 with the assigned filter code 32015. + +--- + +## Build + +This plugin can be built with cmake and installed as shared library to `/usr/local/hdf5/lib/plugin` (or a custom path). + +```bash +cmake . +make +sudo make install +``` diff --git a/zstd_h5plugin.c b/zstd_h5plugin.c new file mode 100644 index 00000000..5a3dfd38 --- /dev/null +++ b/zstd_h5plugin.c @@ -0,0 +1,81 @@ +#include +#include "zstd_h5plugin.h" +#include "zstd.h" + +#define ZSTD_FILTER 32015 + +DLL_EXPORT size_t zstd_filter(unsigned int flags, size_t cd_nelmts, + const unsigned int cd_values[], size_t nbytes, + size_t *buf_size, void **buf) +{ + void *outbuf = NULL; /* Pointer to new output buffer */ + void *inbuf = NULL; /* Pointer to input buffer */ + inbuf = *buf; + + size_t ret_value; + size_t origSize = nbytes; /* Number of bytes for output (compressed) buffer */ + + if (flags & H5Z_FLAG_REVERSE) + { + size_t decompSize = ZSTD_getDecompressedSize(*buf, origSize); + if (NULL == (outbuf = malloc(decompSize))) + goto error; + + decompSize = ZSTD_decompress(outbuf, decompSize, inbuf, origSize); + + free(*buf); + *buf = outbuf; + outbuf = NULL; + ret_value = (size_t)decompSize; + } + else + { + int aggression; + if (cd_nelmts > 0) + aggression = (int)cd_values[0]; + else + aggression = ZSTD_CLEVEL_DEFAULT; + if (aggression < 1 /*ZSTD_minCLevel()*/) + aggression = 1 /*ZSTD_minCLevel()*/; + else if (aggression > ZSTD_maxCLevel()) + aggression = ZSTD_maxCLevel(); + + size_t compSize = ZSTD_compressBound(origSize); + if (NULL == (outbuf = malloc(compSize))) + goto error; + + compSize = ZSTD_compress(outbuf, compSize, inbuf, origSize, aggression); + + free(*buf); + *buf = outbuf; + *buf_size = compSize; + outbuf = NULL; + ret_value = compSize; + } + if (outbuf != NULL) + free(outbuf); + return ret_value; + +error: + return 0; +} + +const H5Z_class_t zstd_H5Filter = +{ + H5Z_CLASS_T_VERS, + (H5Z_filter_t)(ZSTD_FILTER), + 1, 1, + "Zstandard compression: http://www.zstd.net", + NULL, NULL, + (H5Z_func_t)(zstd_filter) +}; + +DLL_EXPORT H5PL_type_t H5PLget_plugin_type(void) +{ + return H5PL_TYPE_FILTER; +} + +DLL_EXPORT const void* H5PLget_plugin_info(void) +{ + return &zstd_H5Filter; +} diff --git a/zstd_h5plugin.h b/zstd_h5plugin.h new file mode 100644 index 00000000..e29c0689 --- /dev/null +++ b/zstd_h5plugin.h @@ -0,0 +1,22 @@ +#include "hdf5.h" + +#if defined(_MSC_VER) + #define DLL_EXPORT __declspec(dllexport) +#else + #define DLL_EXPORT +#endif + +#ifdef __cplusplus +extern "C" { +#endif + +DLL_EXPORT size_t zstd_filter(unsigned int flags, size_t cd_nelmts, + const unsigned int cd_values[], size_t nbytes, + size_t *buf_size, void **buf); + +DLL_EXPORT H5PL_type_t H5PLget_plugin_type(void); +DLL_EXPORT const void* H5PLget_plugin_info(void); + +#ifdef __cplusplus +} +#endif From 82e8de4cb9b902fe4b9c68f57193bac51a56f001 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?V=2E=20Armando=20Sol=C3=A9?= Date: Tue, 15 Dec 2020 17:50:44 +0100 Subject: [PATCH 2/5] Add Zstd plugin. --- hdf5plugin/__init__.py | 6 +++++- setup.py | 20 +++++++++++++++++++- 2 files changed, 24 insertions(+), 2 deletions(-) diff --git a/hdf5plugin/__init__.py b/hdf5plugin/__init__.py index 4c29ec4f..24c1815f 100644 --- a/hdf5plugin/__init__.py +++ b/hdf5plugin/__init__.py @@ -27,7 +27,7 @@ __authors__ = ["V.A. Sole", "H. Payno", "T. Vincent"] __license__ = "MIT" -__date__ = "12/05/2020" +__date__ = "15/05/2020" import ctypes as _ctypes from glob import glob as _glob @@ -70,6 +70,9 @@ ZFP_ID = 32013 """ZFP filter ID""" +ZSTD_ID = 32015 +"""Zstandard filter ID""" + FCIDECOMP_ID = 32018 """FCIDECOMP filter ID""" @@ -77,6 +80,7 @@ 'bshuf': BSHUF_ID, 'lz4': LZ4_ID, 'zfp': ZFP_ID, + 'zstd': ZSTD_ID, 'fcidecomp': FCIDECOMP_ID, } """Mapping of filter name to HDF5 filter ID for available filters""" diff --git a/setup.py b/setup.py index 6d349b08..5ef2fa42 100644 --- a/setup.py +++ b/setup.py @@ -24,7 +24,7 @@ # ###########################################################################*/ __authors__ = ["V.A. Sole", "T. Vincent"] __license__ = "MIT" -__date__ = "12/05/2020" +__date__ = "15/12/2020" from glob import glob @@ -449,6 +449,22 @@ def prefix(directory, files): cpp11=cpp11_kwargs, ) +# HDF5Plugin-Zstandard +zstandard_dir = os.path.join("src", "HDF5Plugin-Zstandard") +zstandard_include_dirs = glob(blosc_dir + 'internal-complibs/zstd*') +zstandard_include_dirs += glob(blosc_dir + 'internal-complibs/zstd*/common') +zstandard_sources = [os.path.join(zstandard_dir, 'zstd_h5plugin.c')] +zstandard_sources += glob(blosc_dir +'internal-complibs/zstd*/*/*.c') +zstandard_depends = [os.path.join(zstandard_dir, 'zstd_h5plugin.h')] +zstandard_depends += glob(blosc_dir +'internal-complibs/zstd*/*/*.h') +zstandard_plugin = HDF5PluginExtension( + "hdf5plugin.plugins.libh5zstd", + sources=zstandard_sources, + depends=zstandard_depends, + include_dirs=zstandard_include_dirs, + define_macros=define_macros, + ) + # lz4 plugin # Source from https://github.com/nexusformat/HDF5-External-Filter-Plugins @@ -545,8 +561,10 @@ def prefix(directory, files): blosc_plugin, fcidecomp_plugin, h5zfp_plugin, + zstandard_plugin, ] + # setup # ########## # From 3e0f552439e96d9105fbc50512c709d2bc327a22 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?V=2E=20Armando=20Sol=C3=A9?= Date: Tue, 15 Dec 2020 18:01:31 +0100 Subject: [PATCH 3/5] Add class. --- hdf5plugin/__init__.py | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/hdf5plugin/__init__.py b/hdf5plugin/__init__.py index 24c1815f..2141aebd 100644 --- a/hdf5plugin/__init__.py +++ b/hdf5plugin/__init__.py @@ -272,6 +272,12 @@ def __init__(self, _logger.info("filter options = %s" % (self.filter_options,)) +class Zstd(_FilterRefClass): + """h5py.Group.create_dataset's compression and compression_opts arguments for using FciDecomp filter. + """ + filter_id = ZSTD_ID + + class FciDecomp(_FilterRefClass): """h5py.Group.create_dataset's compression and compression_opts arguments for using FciDecomp filter. """ From ac4f9bad5062c22e28395d196d00e62a34d1bdba Mon Sep 17 00:00:00 2001 From: Thomas VINCENT Date: Wed, 16 Dec 2020 10:55:21 +0100 Subject: [PATCH 4/5] Add zstd to the test --- hdf5plugin/test.py | 10 ++++++++-- 1 file changed, 8 insertions(+), 2 deletions(-) diff --git a/hdf5plugin/test.py b/hdf5plugin/test.py index 7ad68c47..636fbe0e 100644 --- a/hdf5plugin/test.py +++ b/hdf5plugin/test.py @@ -59,6 +59,7 @@ def _test(self, filter_name, dtype=numpy.int32, lossless=True, **options): "lz4": hdf5plugin.LZ4, "fcidecomp": hdf5plugin.FciDecomp, "zfp": hdf5plugin.Zfp, + "zstd": hdf5plugin.Zstd, }[filter_name](**options) # Write @@ -148,6 +149,11 @@ def testZfp(self): self._test('zfp', dtype=numpy.int32, reversible=True) + def testZstd(self): + """Write/read test with Zstd filter plugin""" + self._test('zstd') + + def suite(): test_suite = unittest.TestSuite() for cls in (TestHDF5PluginRW,): @@ -155,9 +161,9 @@ def suite(): return test_suite -def run_tests(): +def run_tests(*args, **kwargs): """Run test complete test_suite""" - runner = unittest.TextTestRunner() + runner = unittest.TextTestRunner(*args, **kwargs) success = runner.run(suite()).wasSuccessful() print("Test suite " + ("succeeded" if success else "failed")) return success From 5e3eea57aabc7f26ee6163b3247e34277c06ac68 Mon Sep 17 00:00:00 2001 From: Thomas VINCENT Date: Wed, 16 Dec 2020 10:59:28 +0100 Subject: [PATCH 5/5] Update README --- README.rst | 22 +++++++++++++++++++++- 1 file changed, 21 insertions(+), 1 deletion(-) diff --git a/README.rst b/README.rst index 20932e50..c0f35b9b 100644 --- a/README.rst +++ b/README.rst @@ -1,7 +1,7 @@ hdf5plugin ========== -This module provides HDF5 compression filters (namely: blosc, bitshuffle, lz4, FCIDECOMP, ZFP) and registers them to the HDF5 library used by `h5py `_. +This module provides HDF5 compression filters (namely: blosc, bitshuffle, lz4, FCIDECOMP, ZFP, zstd) and registers them to the HDF5 library used by `h5py `_. * Supported operating systems: Linux, Windows, macOS. * Supported versions of Python: >= 3.4 @@ -17,6 +17,7 @@ The HDF5 plugin sources were obtained from: * hdf5-blosc plugin (v1.0.0) and c-blosc (v1.17.0): https://github.com/Blosc/hdf5-blosc and https://github.com/Blosc/c-blosc * FCIDECOMP plugin (v1.0.2) and CharLS (branch 1.x-master SHA1 ID:25160a42fb62e71e4b0ce081f5cb3f8bb73938b5): ftp://ftp.eumetsat.int/pub/OPS/out/test-data/Test-data-for-External-Users/MTG_FCI_Test-Data/FCI_Decompression_Software_V1.0.2/ and https://github.com/team-charls/charls.git * HDF5-ZFP plugin (v1.0.1) and zfp (v0.5.5): https://github.com/LLNL/H5Z-ZFP and https://github.com/LLNL/zfp +* HDF5Plugin-Zstandard (commit d5afdb5) and zstd (v1.4.5): https://github.com/aparamon/HDF5Plugin-Zstandard and https://github.com/Blosc/c-blosc/tree/v1.20.1/internal-complibs/zstd-1.4.5 Installation ------------ @@ -76,6 +77,7 @@ Sample code: - ``FCIDECOMP_ID`` - ``LZ4_ID`` - ``ZFP_ID`` + - ``ZSTD_ID`` * ``FILTERS``: A dictionary mapping provided filters to their ID * ``PLUGINS_PATH``: The directory where the provided filters library are stored. @@ -225,6 +227,23 @@ The following compression modes are supported: f.create_dataset('zfp_expert', data=numpy.random.random(100), **hdf5plugin.Zfp(minbits=1, maxbits=16657, maxprec=64, minexp=-1074)) +Zstd() +****** + +This class returns the compression options to feed into ``h5py.Group.create_dataset`` for using the Zstd filter: + +It can be passed as keyword arguments. + +Sample code: + +.. code-block:: python + + f = h5py.File('test.h5', 'w') + f.create_dataset('zstd', data=numpy.arange(100), + **hdf5plugin.Zstd()) + f.close() + + Dependencies ------------ @@ -265,5 +284,6 @@ Please read the different licenses: * lz4: See `src/LZ4/COPYING `_ * FCIDECOMP: See `src/fcidecomp/LICENSE `_ and `src/charls/src/License.txt `_ * zfp: See `src/H5Z-ZFP/LICENSE `_ and `src/zfp/LICENSE `_ +* zstd: See `src/HDF5Plugin-Zstandard/LICENSE` The HDF5 v1.10.5 headers (and Windows .lib file) used to build the filters are stored for convenience in the repository. The license is available here: `src/hdf5/COPYING `_.