Installation

Prerequisites

To use the hdf5analysis package, the python framework with version 3.9 or higher is required. For interactive computing, it is highly encouraged to make use of the interactive computing environment Jupyter Notebook.

Anaconda3/Miniforge

A one-stop solution to obtaining python together with the jupyter notebook environment is the Anaconda3 distribution, available on the Anadonda Website. This python distribution also contains important scientific module that do not need to be installed manually, however, the convenience is paid with a lot of disk space. Alternatively, if your organization can not use Anacoda due to licence requirements Miniforge is an alternative, available on the Minforge Website.

Manual Setup

You may proceed to install python for your operating system from the website above. The jupyter notebook environment may conveniently be installed via the pip package manager:

$ pip install notebook

Note, this only installs the minimum requirements to satifsy python and the jupyter notebook. Any other data analysis and scientific packages will need to be installed by hand.

h5analysis package Installation

Install the package from PyPi with the pip package manager. This is the recommended way to obtain a copy for your local machine and will install all required package dependencies.

$ pip install h5analysis

You will need to ffmpeg binaries.

$ conda install ffmpeg

To utilize the xraylarch engine for EXAFS data processing, ensure that the larch python package is installed:

$ pip install h5analysis[EXAFS]

To utilize the pybaselines package for background subtraction, ensure that the python package is properly installed:

$ pip install h5analysis[BASELINE]

Activate widget extensions

In case that certain widgets aren’t rendered properly, make sure to enable the appropriate jupyter extensions

$ jupyter nbextension enable --py widgetsnbextension