Favourite Tool/Package of 2020

Introduction

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Working with Discrete Element Method (DEM) usually means that you need to visualise your results somehow after the simulation is complete. This is usually the case with some of the open source codes. If you use a commercial code like EDEM or Rocky, the visualisation aspect is usually taken care for you by the software, but occasionally you may wish to do something that isn’t supported. That’s life in research…

Anyway, that’s where ParaView usually comes in. It’s a hugely powerful open-source data analysis and visualization application. However, it’s built on top of the VTK library and usually requires writing all your data out in a ascii VTK format, which is not always practical.

And that’s where my new favourite Python Library comes in … Hello PyVista.

PyVista

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PyVista is a powerful and flexible library for plotting 3D figures using python. It’s also based on VTK, but implements a higher level API that interfaces through NumPy. PyVista is:

3D plotting made simple and built for large/complex data geometries

I don’t want to write a huge tutorial here because there are lots of great examples on the PyVista website which should help you get started. I’m just going to include my favourite examples here and then let you go explore as you wish.

Examples

This is an interactive example of slicing a 3D dataset (a brain!) using a plane widget, but this is super cool and super easy to use.

# sphinx_gallery_thumbnail_number = 2
import pyvista as pv
from pyvista import examples

vol = examples.download_brain()

p = pv.Plotter()
p.add_mesh_clip_plane(vol)
p.show()

As a DEM user you might be interested in plotting some spheres (particles) and this is also very easy, see this example for 1M spheres which renders in about 10s on my laptop.

import numpy as np
import pyvista as pv
pv.set_plot_theme('dark')

n = 1_000_000
mesh = pv.PolyData(np.random.random((n, 3))*1000)
mesh["radius"] = np.random.rand(n) * 2

# Low resolution geometry
geom = pv.Sphere(theta_resolution=8, phi_resolution=8)

# Progress bar is a new feature on master branch
glyphed = mesh.glyph(scale="radius", geom=geom, progress_bar=True)


p = pv.Plotter(notebook=False)
p.add_mesh(glyphed, smooth_shading=True) # if you want everything mono coloured then add the following argument: color='yellow'
# if you want it to look really nice, add the smooth shading option smooth_shading=True. 
# This will be slower rendering!

p.show()