HighFive - HDF5 header-only C++ Library
Brief
HighFive is a modern C++/C++11 friendly interface for libhdf5.
HighFive supports STL vector/string, Boost::UBLAS and Boost::Multi-array. It handles C++ from/to HDF5 automatic type mapping.
HighFive does not require an additional library and supports both HDF5 thread safety and Parallel HDF5 (contrary to the official hdf5 cpp)
Design
- Simple C++-ish minimalist interface
- No other dependency than libhdf5
- Zero overhead
- Support C++11 ( compatible with C++98 )
Dependencies
- hdf5 (dev)
- hdf5-mpi (optional, opt-in with -DDHIGHFIVE_PARALLEL_HDF5=ON)
- boost >= 1.41 (recommended, opt-out with -DDHIGHFIVE_USE_BOOST=OFF)
- eigen3 (optional, opt-in with -DHIGHFIVE_USE_EIGEN=ON)
- xtensor (optional, opt-in with -DHIGHFIVE_USE_XTENSOR=ON)
CMake integration
HighFive can easily be used by other C++ CMake projects.
Below is a very simple foo project creating a bar C++ program
using HighFive library:
cmake_minimum_required(VERSION 3.0 FATAL_ERROR)
project(foo)
set(CMAKE_CXX_STANDARD 11)
find_package(HighFive 2.1 REQUIRED)
add_executable(bar bar.cpp)
target_link_libraries(bar HighFive)
Usage
Write a std::vector to 1D HDF5 dataset and read it back
using namespace HighFive;
// we create a new hdf5 file
File file("/tmp/new_file.h5", File::ReadWrite, File::Create, File::Truncate);
std::vector<int> data(50, 1);
// let's create a dataset of native integer with the size of the vector 'data'
DataSet dataset = file.createDataSet<int>("/dataset_one", DataSpace::From(data));
// let's write our vector of int to the HDF5 dataset
dataset.write(data);
// read back
std::vector<int> result;
dataset.read(result);
Note: if you can use
DataSpace::Fromon your data, you can combine the create and write into one statement:DataSet dataset = file.createDataSet("/dataset_one", data);This works with
createAttribute, as well.
Write a 2 dimensional C double float array to a 2D HDF5 dataset
Write and read a matrix of double float (boost::ublas) to a 2D HDF5 dataset
Write and read a subset of a 2D double dataset
See select_partial_dataset_cpp11.cpp
Create, write and list HDF5 attributes
See create_attribute_string_integer.cpp
And others
See src/examples/ subdirectory for more info.
Compile with HighFive
c++ -o program -I/path/to/highfive/include source.cpp -lhdf5
H5Easy
For several 'standard' use cases the highfive/H5Easy.hpp interface is available. It allows:
-
Reading/writing in a single line of:
- scalars (to/from an extendible DataSet),
- strings,
- vectors (of standard types),
- Eigen::Matrix (optional, enable CMake option
HIGHFIVE_USE_EIGEN), - xt::xarray and xt::xtensor
(optional, enable CMake optionHIGHFIVE_USE_XTENSOR).
-
Getting in a single line:
- the size of a DataSet,
- the shape of a DataSet.
The general idea is to
#include <highfive/H5Easy.hpp>
int main()
{
H5Easy::File file("example.h5", H5Easy::File::Overwrite);
int A = ...;
H5Easy::dump(file, "/path/to/A", A);
A = H5Easy::load<int>(file, "/path/to/A");
}
whereby the int type of this example can be replaced by any of the above types. See easy_load_dump.cpp for more details.
Note that classes such as
H5Easy::Fileare just short for the regularHighFiveclasses (in this caseHighFive::File). They can thus be used interchangeably.
Test Compilation
Remember: Compilation is not required. Used only for unit test and examples
Unit tests need boost (USE_BOOST).
mkdir build; pushd build
cmake ../
make
make test
Feature support
- create/read/write file, dataset, group, dataspace.
- automatic memory management / ref counting
- automatic conversion of
std::vectorand nestedstd::vectorfrom/to any dataset with basic types - automatic conversion of
std::stringto/from variable length string dataset - selection() / slice support
- parallel Read/Write operations from several nodes with Parallel HDF5
- support HDF5 attributes
Contributors
- Adrien Devresse adrien.devresse@epfl.ch - Blue Brain Project
- Ali Can Demiralp demiralpali@gmail.com -
- Fernando Pereira fernando.pereira@epfl.ch - Blue Brain Project
- Stefan Eilemann stefan.eilemann@epfl.ch - Blue Brain Project
- Tristan Carel tristan.carel@epfl.ch - Blue Brain Project
- Wolf Vollprecht w.vollprecht@gmail.com - QuantStack
- Tom de Geus tom@geus.me - EPFL
- Nicolas Cornu nicolas.cornu@epfl.ch - Blue Brain Project
License
Boost Software License 1.0