openPMD-viewer 0.9.0

Visualization tools for openPMD files

openPMD-viewer

Overview

This package contains a set of tools to load and visualize the contents of a set of openPMD files (typically, a timeseries).

The routines of openPMD-viewer can be used in two ways :

• Use the Python API, in order to write a script that loads the data and produces a set of pre-defined plots.

• Use the interactive GUI inside the Jupyter Notebook, in order to interactively visualize the data.

Usage

Tutorials

The notebooks in the folder tutorials/ demonstrate how to use both the API and the interactive GUI. You can view these notebooks online here.

Alternatively, you can even run our tutorials online!

You can also download and run these notebooks on your local computer (when viewing the notebooks with the above link, click on Raw to be able to save them to your local computer). In order to run the notebook on your local computer, please install openPMD-viewer first (see below), as well as wget (pip install wget).

Notebook quick-starter

If you wish to use the interactive GUI, the installation of openPMD-viewer provides a convenient executable which automatically creates a new pre-filled notebook and opens it in a browser. To use this executable, simply type in a regular terminal:

openPMD_notebook

(This executable is installed by default, when installing openPMD-viewer.)

Installation

Installation on a local computer

Installation with conda (recommended)

In order to install openPMD-viewer with conda, please install the Anaconda distribution, and then type

conda install -c rlehe openpmd_viewer

If you are using JupyterLab, please also install the jupyter-matplotlib extension (See installation instructions here).

Installation with pip

If you cannot install openPMD-viewer with conda, the alternative is to use pip. However, you need to first make sure that h5py is installed on your local computer. This can be done for instance by typing pip install h5py, though this may require you to install hdf5 separately.

Once h5py is installed, simply type

pip install openPMD-viewer

In addition, if you wish to use the interactive GUI, please type

pip install jupyter

Installation on a remote scientific cluster

If you wish to install the openPMD-viewer on a remote scientific cluster, please make sure that the packages numpy, scipy and h5py are available in your environment. This is typically done by a set of module load commands (e.g. module load h5py) -- please refer to the documentation of your scientific cluster.

Then type

pip install openPMD-viewer --user

Note: The package jupyter is only required for the interactive GUI and thus it does not need to be installed if you are only using the Python API. For NERSC users, access to Jupyter notebooks is provided when logging to https://ipython.nersc.gov.

Contributing to the openPMD-viewer

We welcome contributions to the code! Please read this page for guidelines on how to contribute.