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 dependencies
   • sudo apt-get install libhdf5-dev
   • sudo apt-get install cython
2. If necessary, install 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