HDF5

Hierarchical Data Format (HDF) is a portable binary format, meant to be extensible and self-describing.

Tools

• hdfview

Reading

In order to read HDF5 files, you will need a suitable library. Here, we describe how to arrange to open compressed HDF5 files in a Python environment.

Installation

1. Install HDF5 library
   • To install the version from the repository:
     • sudo apt-get install libhdf5-dev
   • In some cases, the repository version may not work (or be out of date). In that case, you can manually download the source from hdfgroup, and install it by doing:
     1. wget http://www.hdfgroup.org/ftp/HDF5/current/src/hdf5-1.8.15-patch1.tar.gz
     2. tar xzvf hdf5-1.8.15-patch1.tar.gz
     3. cd hdf5-1.8.15-patch1/
     4. make install
     5. Compilation may take 5-10 minutes. If there are any errors, resolve the dependencies using your package manager.
2. If necessary, install dependencies:
   1. Cython (C extensions for Python)
      • sudo apt-get install cython
   2. python-pkgconfig:
      • sudo apt-get install python-setuptools
      • wget https://pypi.python.org/packages/source/p/pkgconfig/pkgconfig-1.1.0.tar.gz
      • cd d pkgconfig-1.1.0/
      • python setup.py install
3. Install the h5py package (Python library for HDF5).
   1. Download and extract tarball (e.g. from [1]).
      • wget https://pypi.python.org/packages/source/h/h5py/h5py-2.5.0.tar.gz
      • tar xzvf h5py-2.5.0.tar.gz
   2. Setup
      • cd h5py
      • sudo python setup.py install

See Also

• Software
• NeXus data format
• Wikipedia:Hierarchical Data Format
• HDF5 Home Page
• HDF5 File Format Specification Version 2.0