Tag: matplotlib

Default colormaps: Are Parula and Viridis really an improvement over Jet?

Jet was a ubiquitous colourmap that slowly fell out of fashion over the last five years. It was the default colourmap for Matlab and Matplotlib (and probably others) until 2015ish. The replacements, Parula and Viridis, respectively, get a lot of love. A quick Google search will present numerous blog posts and articles maligning Jet and promoting the use of these newer colourmaps. It’s an unpopular opinion but, especially now that they are common and overused, I dislike Parula and Viridis as much as I dislike Jet.

parula_viridis

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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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Scientific software skills make up for minimal artistic talent

A computer is a better artist than I am. If I can tell it what to draw, it will produce attractive results. To make a nice schematic, the hardest part is to tell the computer what I want to draw. Fortunately for us so-called left-brain types prevalent throughout the sciences, a familiarity with scientific software can overcome a lack of artistic talent, allow rapid iteration of a design, and even provide creative inspiration.

Invoking my scientific software skills, I am able to produce elegant figures:

shear_rotation_schematic
From Evolution of the velocity structure in the diurnal warm layer

Now, compare that with my initial sketch…

shear_schematic_sketch

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Organise scripts and figures easily with Jupyter Notebooks

Keeping track of scripts used to generate figures is difficult. Before realising that Jupyter Notebooks could solve most of my problems, I would have directories with dozens of scripts with filenames of varying levels of ambiguity. Names that probably meant something to me at the time, but are hardly descriptive months or years later. Names like  ISW_plume_plots.m, new_ISW_model_plots.m, and plot_model_behaviour.m. A certain PhD comic springs to mind.

Regardless of whether its Python, R, Julia, Matlab, or pretty much any other type of code, Jupyter Notebooks solve the problem. For example, I use a single notebook to archive the code for all figures in a paper and, more importantly, I can associate each set of code with the figure it generates. Rather than trying to remember what file I want, I need only remember which figure I want. (I say archive because I much prefer to do the bulk of my exploratory analysis in an editor. Alternatively, JupyterLab may work better for you.)

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To make a good schematic, copy, adapt, and refine

Scientific papers are built by taking existing ideas, applying them in new ways, adapting them to fit new situations, and improving them over time. Yet when it comes to drawing a schematic, many people start from scratch or never even start. Instead, start with an image search, let Inkscape do the hard work, and refine the best parts of other schematics.

I will use a figure of mine as a case study:

channel_schematic
This schematic encapsulates the oceanographic processes that I examine in my PhD. I use it in many presentations, my thesis, and my personal website.

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Vector and raster in one with Matplotlib

Vector images are great, except when they shouldn’t be vector. Figures with intricate detail can actually benefit from being rasterized. This can reduce file size and help the figure load more quickly. Python’s Matplotlib has an option to rasterize certain elements, but it doesn’t always work as simply as expected.

This post describes a function that (i) lets you rasterize any chosen elements when you export the figure and (ii) overcomes problems with the current implementation of rasterizing objects with Matplotlib.

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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.

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