Post-processing Lethe with PyVista

Lethe has a post-processing module written in Python based on Lethe users specific needs. lethe_pyvista_tools was conceived to optimize the reading and post-treatment of Lethe data using Python.

The module is powered by PyVista, a powerful 3D plotting and mesh analysis tool. It is a pythonic interface to deal with Visualization Toolkit (VTK) data. The module also uses the powerful multiprocessing Python library to increase post-processing speed by running tasks in multiple processors.

Warning

For lethe_pyvista_tools to work, along with Python 3, the following libraries are needed: os, NumPy, PyVista, tqdm, matplotlib, SciPy, and scikit-learn. If any of the modules are missing, use pip to install it by running pip3 install $NAME_OF_THE_MODULE on the terminal. Alternatively, use the requirements.txt file and install them all at once running pip install -r requirements.txt located at contrib/postprocessing/.

Importing lethe_pyvista_tools

There are two ways to have access to lethe_pyvista_tools: you can install the module and have it on your machine just like os, sys, or other PyPi modules; or, you can use it without installing. Here, we explain how to do both.

Installing

Installing lethe_pyvista_tools is very simple. In the contrib/postprocessing of your Lethe version you will find all source files, including setup.py and requirements.txt. Those two files take care of configuring your installation and assuring that everything is set correctly. To install it, navigate to contrib/postprocessing on your terminal and run:

pip3 install .

or

pip install .

Note

If you do not have pip on your machine, run sudo apt install python3-pip.

Tip

Uninstalling lethe_pyvista_tools is exactly like doing so with any other library: pip3 uninstall lethe_pyvista_tools or pip3 uninstall lethe_pyvista_tools.

Importing without installing

In this case, we use the sys module to import it directly from Lethe’s directory into a python session:

import sys
path_to_module = '$LETHE_PATH/contrib/postprocessing/'
sys.path.append(path_to_module)
from lethe_pyvista_tools import *
import matplotlib.pyplot as plt

where sys.path is a list of strings that specifies the search path for modules. Another option is to simply copy the lethe_pyvista_tools.py file to the same folder as the Python post-processing script, and import it as follows:

from lethe_pyvista_tools import *

One third and very convenient way to always import the module without copying it or even adding the sys.path.append(path_to_module) is permanently adding the path to the module (i.e., /contrib/postprocessing/) to your PYTHONPATH.

The * means that we want to import all members of lethe_pyvista_tools.

Using lethe_pyvista_tools

To get quick-started, follow the hand-on Small Scale Rotating Drum Post-processing example. It has a detailed explanation on how to use the module. You can also start with a “raw” template file, check this example file.