Difference between revisions of "HDF5"
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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. | 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=== | ===Installation=== | ||
| − | # Install | + | # Install HDF5 library |
| − | #* sudo apt-get install libhdf5-dev | + | #* To install the version from the repository: |
| − | #* sudo apt-get install cython | + | #** 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| − | # | + | #* In some cases, the repository version may not work (or be out of date).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 [https://www.hdfgroup.org/HDF5/release/obtainsrc.html#src hdfgroup], and install it by doing: |
| − | #* sudo apt-get install python-setuptools | + | #*# wget http://www.hdfgroup.org/ftp/HDF5/current/src/hdf5-1.8.15-patch1.tar.gz |
| − | #* wget https://pypi.python.org/packages/source/p/pkgconfig/pkgconfig-1.1.0.tar.gz | + | #*# tar xzvf hdf5-1.8.15-patch1.tar.gz |
| − | #* cd d pkgconfig-1.1.0/ | + | #*# cd hdf5-1.8.15-patch1/ |
| − | #* python setup.py install | + | #*# make install |
| + | # If necessary, install dependencies: | ||
| + | ## [http://cython.org/ Cython] (C extensions for Python) | ||
| + | ##* sudo apt-get install cython | ||
| + | ## [https://pypi.python.org/pypi/pkgconfig/1.1.0 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 | ||
# Install the [http://www.h5py.org/ h5py package] ([[Python]] library for HDF5). | # Install the [http://www.h5py.org/ h5py package] ([[Python]] library for HDF5). | ||
## Download and extract tarball (e.g. from [https://pypi.python.org/pypi/h5py]). | ## Download and extract tarball (e.g. from [https://pypi.python.org/pypi/h5py]). | ||
Revision as of 08:31, 5 August 2015
Hierarchical Data Format (HDF) is a portable binary format, meant to be extensible and self-describing.
Contents
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
- 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:
- wget http://www.hdfgroup.org/ftp/HDF5/current/src/hdf5-1.8.15-patch1.tar.gz
- tar xzvf hdf5-1.8.15-patch1.tar.gz
- cd hdf5-1.8.15-patch1/
- make install
- To install the version from the repository:
- If necessary, install dependencies:
- Cython (C extensions for Python)
- sudo apt-get install cython
- 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
- Cython (C extensions for Python)
- Install the h5py package (Python library for HDF5).
- 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
- Setup
- cd h5py
- sudo python setup.py install
- Download and extract tarball (e.g. from [1]).
