animation – Brushing Up Science

Concluding a scientific paper with a video

As scientists, we record our findings in perpetuity in PDFs— literally simulations of pieces of paper. It’s time to be more dynamic and invoke a proliferation of media types. We don’t need to get rid of the notion of a paper or stop using a PDF as the version of record. But we do need to complement them with something less static. What follows is an approach I recently took using video.

The final sentence of my latest paper (preprint) steers the reader to a video that stands in place of a Conclusion section. And I’m guessing this video is a much more compelling Conclusion than any possible combination of words.

Here’s the gist of the final paragraph (paraphrased to avoid jargon):

Our simulation was made possible by tuning against measurements from a new instrument. This observation-informed simulation depicts instabilities as they evolve throughout the day. It is best appreciated as an animation (doi.org/10.5281/zenodo.4306935).

The link goes to a copy of the video below:

Elaborate Matplotlib animations

Matplotlib, Python’s primary scientific plotting library, provides tools to make many elaborate plots, graphs, and diagrams. Many of these can be animated, but the process isn’t always intuitive. The hardest part is learning how to animate a simple line plot (here’s my easy way). Beyond that, the steps to creating most animations tend to be similar.

The examples below demonstrate the particular methods needed to animate common types of plot. Here I focus on the key components needed for updating each frame of the animation. The full code for the examples is here. It includes liberal and arbitrary use of sines and cosines so as to produce looping gifs.

Scatter with variable colour, position, and size

scatter

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Matplotlib animations the easy way

Creating animations with Python’s Matplotlib is quick and easy once you know how to do it. However, when learning I found the tutorials and examples online either daunting, overly sophisticated, or lacking explanation. In many cases all I need is a quick-and-dirty script that works, rather than longer code that adheres to best practices.

See here for a follow up post with more elaborate animation examples.

Continue reading “Matplotlib animations the easy way”