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libpressio version 0.49.0
Major Changes + Added BitGrooming and DigitRounding compressor plugins. Thanks to Hengzhi Chen for contributing them!
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‎CMakeLists.txt

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cmake_minimum_required(VERSION 3.13 FATAL_ERROR)
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project(libpressio VERSION "0.48.0" LANGUAGES CXX C)
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project(libpressio VERSION "0.49.0" LANGUAGES CXX C)
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#correct was to set a default build type
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# https://blog.kitware.com/cmake-and-the-default-build-type/
@@ -170,6 +170,30 @@ if(LIBPRESSIO_HAS_OPENMP)
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)
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endif()
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option(LIBPRESSIO_HAS_DIGIT_ROUNDING "build the DIGIT ROUNDING plugin" OFF)
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if(LIBPRESSIO_HAS_DIGIT_ROUNDING)
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set(LIBPRESSIO_COMPRESSORS "${LIBPRESSIO_COMPRESSORS} DR")
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find_package(dround REQUIRED)
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find_package(ZLIB REQUIRED)
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target_sources(libpressio
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PRIVATE
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${CMAKE_CURRENT_SOURCE_DIR}/src/plugins/compressors/digit_rounding_plugin.cc
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)
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target_link_libraries(libpressio PRIVATE dround ZLIB::ZLIB)
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endif()
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option(LIBPRESSIO_HAS_BIT_GROOMING "build the BIT GROOMING plugin" OFF)
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if(LIBPRESSIO_HAS_BIT_GROOMING)
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set(LIBPRESSIO_COMPRESSORS "${LIBPRESSIO_COMPRESSORS} BG")
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find_package(bg REQUIRED)
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find_package(ZLIB REQUIRED)
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target_sources(libpressio
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PRIVATE
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${CMAKE_CURRENT_SOURCE_DIR}/src/plugins/compressors/bit_groooming_plugin.cc
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)
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target_link_libraries(libpressio PRIVATE bg ZLIB::ZLIB)
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endif()
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option(LIBPRESSIO_HAS_MGARD "build the MGARD plugin" OFF)
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if(LIBPRESSIO_HAS_MGARD)
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set(LIBPRESSIO_COMPRESSORS "${LIBPRESSIO_COMPRESSORS} mgard")

‎CONTRIBUTORS.md

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@@ -43,6 +43,7 @@ Thanks for you interest in LibPressio! Here are a few things you can do to spee
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The following people have contributed code to LibPressio in alphabetical order:
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+ Robert Underwood
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+ Hengzhi Chen
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# Acknowledgments
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‎docs/PressioOptions.md

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## Compressors
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### bit grooming
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option | type | description
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------------------------|-------------|------------
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`bit_grooming:mode` | int32 | the mode parameter of bit grooming: BITGROOM, BITSHAVE and BITSET.
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`bit_grooming:mode_str` | char* | name of the mode to use. One of : BITGROOM, BITSHAVE and BITSET.
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`bit_grooming:error_control_mode` | int32 | the error control mode of bit grooming: BG_NSD or BG_DSD. BG_NSD stands for number of significant number. BG_DSD stands for number of significant decimal number.
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`bit_grooming:error_control_mode_str` | char* | the error control mode of bit grooming: either NSD or DSD. NSD stands for number of significant number. DSD stands for number of significant decimal number.
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`bit_grooming:n_sig_digits` | int32 | If you set BG_NSD in the error control mode, please set this parameter.
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`bit_grooming:n_sig_decimals` | int32 | If you set BG_DSD in the error control mode, please set this parameter.
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### BLOSC
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BLOSC is a collection of lossless compressors optimized to transfer data more quickly than a direct memory fetch can preform. More information on BLOSC can be found on its [project homepage](https://blosc.org/pages/blosc-in-depth/)
@@ -14,6 +30,16 @@ option | type | description
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`blosc:doshuffle` | int32 | what if any kind of pre-bit shuffling to preform
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`blosc:numinternalthreads` | int32 | number of threads used internally by the library
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### digit rounding
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option | type | description
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------------------------|-------------|------------
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`digit_rounding:prec` | int32 | the prec parameter of digit rounding (a number between 0 and 64)
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### fpzip
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‎src/plugins/compressors/bit_groooming_plugin.cc

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#include <cmath> //for exp and log
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#include <iterator>
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#include <map>
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#include <sstream>
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#include <bg/bg.h>
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#include "libpressio_ext/cpp/data.h" //for access to pressio_data structures
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#include "libpressio_ext/cpp/compressor.h" //for the libpressio_compressor_plugin class
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#include "libpressio_ext/cpp/options.h" // for access to pressio_options
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#include "libpressio_ext/cpp/pressio.h" //for the plugin registries
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#include "pressio_options.h"
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#include "pressio_data.h"
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#include "pressio_compressor.h"
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#include "libpressio_ext/compat/memory.h"
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#define INVALID_TYPE -1
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namespace {
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struct bg_iless {
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bool operator()(std::string lhs, std::string rhs) const {
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std::transform(std::begin(lhs), std::end(lhs), std::begin(lhs), [](unsigned char c){return std::tolower(c);});
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std::transform(std::begin(rhs), std::end(rhs), std::begin(rhs), [](unsigned char c){return std::tolower(c);});
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return lhs < rhs;
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}
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};
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static std::map<std::string, int, bg_iless> const bitgroom_mode_str_to_code {
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{"bitgroom", BITGROOM},
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{"bitshave", BITSHAVE},
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{"bitset", BITSET},
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};
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static std::map<std::string, int, bg_iless> const bitgroom_ec_mode_str_to_code {
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{"nsd", BG_NSD},
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{"dsd", BG_DSD},
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};
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template <class Map>
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std::vector<std::string> bg_keys(Map const& map) {
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std::vector<std::string> keys;
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keys.reserve(map.size());
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std::transform(
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std::begin(map), std::end(map), std::back_inserter(keys),
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[](typename Map::const_reference it) { return it.first; });
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return keys;
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}
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}
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class bit_grooming_plugin: public libpressio_compressor_plugin {
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public:
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bit_grooming_plugin() {
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std::stringstream ss;
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ss << bit_grooming_plugin::major_version() << "." << bit_grooming_plugin::minor_version() << "." << bit_grooming_plugin::patch_version() << "." << bit_grooming_plugin::revision_version();
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bg_version = ss.str();
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};
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struct pressio_options get_options_impl() const override {
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struct pressio_options options;
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set(options, "bit_grooming:mode", bgMode);
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set_type(options, "bit_grooming:mode_str", pressio_option_charptr_type);
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set(options, "bit_grooming:error_control_mode", errorControlMode);
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set_type(options, "bit_grooming:error_control_mode_str", pressio_option_charptr_type);
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set(options, "bit_grooming:n_sig_digits", nun_sig_digits); // number of significant digits
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set(options, "bit_grooming:n_sig_decimals", num_sig_decimals); // number of significant decimal digits
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return options;
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}
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struct pressio_options get_configuration_impl() const override {
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struct pressio_options options;
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set(options, "pressio:thread_safe", static_cast<int>(pressio_thread_safety_multiple));
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set(options, "bit_grooming:mode", bg_keys(bitgroom_mode_str_to_code));
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set(options, "bit_grooming:error_control_mode_mode", bg_keys(bitgroom_ec_mode_str_to_code));
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return options;
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}
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int set_options_impl(struct pressio_options const& options) override {
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get(options, "bit_grooming:mode", &bgMode);
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std::string tmp_mode;
80+
if(get(options, "bit_grooming:mode_str", &tmp_mode) == pressio_options_key_set) {
81+
auto const& it = bitgroom_mode_str_to_code.find(tmp_mode);
82+
if(it != bitgroom_mode_str_to_code.end()) {
83+
bgMode = it->second;
84+
}
85+
}
86+
if(get(options, "bit_grooming:error_control_mode_str", &tmp_mode) == pressio_options_key_set) {
87+
auto const& it = bitgroom_ec_mode_str_to_code.find(tmp_mode);
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if(it != bitgroom_ec_mode_str_to_code.end()) {
89+
errorControlMode = it->second;
90+
}
91+
}
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get(options, "bit_grooming:error_control_mode", &errorControlMode);
93+
get(options, "bit_grooming:n_sig_digits", &nun_sig_digits); // number of significant digits
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get(options, "bit_grooming:n_sig_decimals",
95+
&num_sig_decimals); // number of significant decimal digits
96+
return 0;
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}
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int compress_impl(const pressio_data *input, struct pressio_data* output) override {
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int type = libpressio_type_to_bg_type(pressio_data_dtype(input));
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if(type == INVALID_TYPE) {
102+
return INVALID_TYPE;
103+
}
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105+
size_t nbEle = pressio_data_num_elements(input);
106+
unsigned long outSize;
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void* data = pressio_data_ptr(input, nullptr);
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unsigned char* compressed_data;
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110+
compressed_data = BG_compress_args(type, data, &outSize, bgMode, errorControlMode,
111+
nun_sig_digits, num_sig_decimals, nbEle);
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if(compressed_data == NULL)
114+
{
115+
return set_error(2, "Error when bit grooming is compressing the data");
116+
}
117+
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*output = pressio_data::move(pressio_byte_dtype, compressed_data, 1, &outSize, pressio_data_libc_free_fn, nullptr);
119+
return 0;
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}
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int decompress_impl(const pressio_data *input, struct pressio_data* output) override {
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int type = libpressio_type_to_bg_type(pressio_data_dtype(output));
124+
if(type == INVALID_TYPE) {
125+
return INVALID_TYPE;
126+
}
127+
unsigned char* bytes = (unsigned char*)pressio_data_ptr(input, nullptr);
128+
size_t nbEle = pressio_data_num_elements(output);
129+
size_t byteLength = pressio_data_get_bytes(input);
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void* decompressed_data = BG_decompress(type, bytes, byteLength, nbEle);
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*output = pressio_data::move(pressio_data_dtype(output), decompressed_data, 1, &nbEle, pressio_data_libc_free_fn, nullptr);
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return 0;
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}
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int major_version() const override {
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return BG_VER_MAJOR;
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}
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int minor_version() const override {
142+
return BG_VER_MINOR;
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}
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int patch_version() const override {
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return BG_VER_BUILD;
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}
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int revision_version () const {
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return BG_VER_REVISION;
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}
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const char* version() const override {
152+
return bg_version.c_str();
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}
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const char* prefix() const override {
157+
return "bit_grooming";
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}
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std::shared_ptr<libpressio_compressor_plugin> clone() override {
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return compat::make_unique<bit_grooming_plugin>(*this);
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}
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private:
164+
std::string bg_version;
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int libpressio_type_to_bg_type(pressio_dtype type)
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{
167+
if(type == pressio_float_dtype)
168+
{
169+
return BG_FLOAT;
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}
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else if(type == pressio_double_dtype)
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{
173+
return BG_FLOAT;
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}
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else
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{
177+
set_error(2, "Invalid data type");
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return INVALID_TYPE;
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}
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}
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int bgMode = BITGROOM;
183+
int errorControlMode = BG_NSD;
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int nun_sig_digits = 5;
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int num_sig_decimals = 5;
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};
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static pressio_register compressor_bit_grooming_plugin(compressor_plugins(), "bit_grooming", [](){return compat::make_unique<bit_grooming_plugin>(); });

‎src/plugins/compressors/digit_rounding_plugin.cc

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#include <cmath> //for exp and log
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#include <sstream>
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#include <dr/libdround.h>
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#include "libpressio_ext/cpp/data.h" //for access to pressio_data structures
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#include "libpressio_ext/cpp/compressor.h" //for the libpressio_compressor_plugin class
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#include "libpressio_ext/cpp/options.h" // for access to pressio_options
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#include "libpressio_ext/cpp/pressio.h" //for the plugin registries
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#include "pressio_options.h"
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#include "pressio_data.h"
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#include "pressio_compressor.h"
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#include "libpressio_ext/compat/memory.h"
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#define INVALID_TYPE -1
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class digit_rounding_plugin: public libpressio_compressor_plugin {
16+
public:
17+
digit_rounding_plugin() {
18+
std::stringstream ss;
19+
ss << digit_rounding_plugin::major_version() << "." << digit_rounding_plugin::minor_version() << "." << digit_rounding_plugin::patch_version() << "." << digit_rounding_plugin::revision_version();
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dround_version = ss.str();
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};
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struct pressio_options get_options_impl() const override {
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struct pressio_options options;
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set(options, "digit_rounding:prec", prec);
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return options;
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}
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struct pressio_options get_configuration_impl() const override {
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struct pressio_options options;
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set(options, "pressio:thread_safe", static_cast<int>(pressio_thread_safety_multiple));
31+
return options;
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}
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int set_options_impl(struct pressio_options const& options) override {
35+
get(options, "digit_rounding:prec", &prec);
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return 0;
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}
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int compress_impl(const pressio_data *input, struct pressio_data* output) override {
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int type = libpressio_type_to_dr_type(pressio_data_dtype(input));
42+
if(type == INVALID_TYPE) {
43+
return INVALID_TYPE;
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}
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size_t nbEle = pressio_data_num_elements(input);
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unsigned long outSize;
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void* data = pressio_data_ptr(input, nullptr);
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unsigned char* compressed_data = dround_compress(type, data, nbEle, prec, &outSize);
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*output = pressio_data::move(pressio_byte_dtype, compressed_data, 1, &outSize, pressio_data_libc_free_fn, nullptr);
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return 0;
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}
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int decompress_impl(const pressio_data *input, struct pressio_data* output) override {
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int type = libpressio_type_to_dr_type(pressio_data_dtype(output));
57+
if(type == INVALID_TYPE) {
58+
return INVALID_TYPE;
59+
}
60+
void* bytes = pressio_data_ptr(input, nullptr);
61+
size_t nbEle = pressio_data_num_elements(output);
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size_t outSize = input -> size_in_bytes();
63+
void* decompressed_data = dround_decompress(type, (unsigned char*)bytes, nbEle, static_cast<unsigned long>(outSize));
64+
*output = pressio_data::move(pressio_data_dtype(output), decompressed_data, 1, &nbEle, pressio_data_libc_free_fn, nullptr);
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return 0;
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}
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int major_version() const override {
71+
return DROUND_VER_MAJOR;
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}
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int minor_version() const override {
74+
return DROUND_VER_MINOR;
75+
}
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int patch_version() const override {
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return DROUND_VER_BUILD;
78+
}
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int revision_version () const {
80+
return DROUND_VER_REVISION;
81+
}
82+
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const char* version() const override {
84+
return dround_version.c_str();
85+
}
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const char* prefix() const override {
89+
return "digit_rounding";
90+
}
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std::shared_ptr<libpressio_compressor_plugin> clone() override {
93+
return compat::make_unique<digit_rounding_plugin>(*this);
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}
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private:
96+
int prec;
97+
std::string dround_version;
98+
int libpressio_type_to_dr_type(pressio_dtype type)
99+
{
100+
if(type == pressio_float_dtype)
101+
{
102+
return DIGIT_FLOAT;
103+
}
104+
else if(type == pressio_double_dtype)
105+
{
106+
return DIGIT_DOUBLE;
107+
}
108+
else
109+
{
110+
set_error(2, "Invalid data type");
111+
return INVALID_TYPE;
112+
}
113+
}
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};
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static pressio_register compressor_digit_rounding_plugin(compressor_plugins(), "digit_rounding", [](){return compat::make_unique<digit_rounding_plugin>(); });

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