hernando / HighFive

HighFive - Header only C++ HDF5 interface

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

• libhdf5
• (optional) boost >= 1.41

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 interger 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::From on 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

See create_dataset_double.cpp

Write and read a matrix of double float (boost::ublas) to a 2D HDF5 dataset

See boost_ublas_double.cpp

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/ sub-directory for more infos

Compile with HighFive

c++ -o program -I/path/to/highfive/include source.cpp  -lhdf5

Test Compilation

Remember: Compilation is not required. Used only for unit test and examples

mkdir build; pushd build
cmake ../
make
make test

Feature support

• create/read/write file, dataset, group, dataspace.
• automatic memory management / ref counting
• automatic convertion of std::vector and nested std::vector from/to any dataset with basic types
• automatic convertion of std::string to/from variable length string dataset
• selection() / slice support
• parallel Read/Write operations from several nodes with Parallel HDF5
• support HDF5 attributes

Contributors

• Adrien Devresse [e-mail] - Blue Brain Project
• Ali Can Demiralp [e-mail] -
• Fernando Pereira [e-mail] - Blue Brain Project
• Stefan Eilemann [e-mail] - Blue Brain Project
• Tristan Carel [e-mail] - Blue Brain Project
• Wolf Vollprecht [e-mail] - QuantStack

License

Boost Software License 1.0