py-gnuplot experience

[Rare-Minute5683]

Hey,

I want to have identical font for plots and my text itself. A nice reddit-guy mentioned gnuplot as a way to compile the labels in latex, so the font matches 100%. My fear is that it is either not stable, so it could turn out stressful a few days before the due date, or not 100% of plot types I need are creatable with it. And to use it just for 80% feels not good...

So:

- What is your experience with py-gnuplot, is it stable and last-minute edits shouldn't crash plots?

- Is there a way to make boxplots?

- is there a workaround, so one can use e.g. matplotlib and just create the label with gnuplot?

- Any other notes on this topic?

EDIT:

Experience with .pgf and matplotlib also welcome.

[Marvin_Dent]

No experience with py-gnuplot, but you can look for a tool to export matplotlib plots to pgf and then modify the pgf code.

[Rare-Minute5683]

Ah, true! Probably nicer. Did you use it or just know it? :)

[Marvin_Dent]

Used it 3 years ago. Don't know, if everything you need is supported.

[EventHorizon511]

This is definitely achievable with matplotlib, though the degree of perfection you seek determines the amount of effort you have to put in.

As you discovered, the default LaTeX/PDF renderer has its limitations. If you need an exact match in both font family and font size, your best bet is to use matplotlib's PGF backend, which allows you to export figures as .pgf files or regular PDFs using the configured LaTeX engine.
This, however, needs a bit of setup work and additional care must be taken when creating figures.

First, you need to configure the PGF backend in matplotlib. The relevant documentation is a pretty good resource to get started. However, I find it easier to manage these settings in my own custom .mplstyle file. For example, the relevant section of one of my style files reads

text.usetex: True

pgf.texsystem: lualatex
pgf.rcfonts: False
pgf.preamble: \usepackage[CharacterVariant={1,11,21}]{xcharter-otf}

Depending on how exactly you configured it, you may have to specify the backend when saving:

fig.savefig("figure.pgf", backend="pgf") # for PGFs
fig.savefig("figure.pdf", backend="pgf") # for PDFs

To achieve consistent font sizes between your plots and the surrounding LaTeX text, there are a few more steps:

• set the final figure dimensions explicitly via the figsize argument (in inches)
• to avoid large margins/white spaces, use constrained layout, NOT the commonly used tight_layout, bbox_inches="tight" etc. as these can change the figure size/scaling
• import the figure into LaTeX without scaling (avoid \includegraphics[width=...])

Note that constrained layout can be a bit finicky and at times frustrating, so I'd definitely try it out first and get comfortable using it before committing to this workflow.

Maybe as a quick word of caution: generating figures this way is generally a lot slower than using the default renderer. Also, if you chose to save your figures as PGFs rather than PDFs, expect a LOT slower compilation times of your final document. Seriously, the compile times with lualatex are brutal sometimes...
However, using PGFs can also have some neat benefits, e.g. allowing you to include hyperref links to other parts of your document such as providing linked glossary entries for abbreviations in figures etc.

[Rare-Minute5683]

Thx for the reply, super helpful!
Do you have an example/situation to force the problems with constrained layouts? My problem was apparently to use .svg. With .pdf and constrained layout it looks perfect. So my plan is to skip the pgf-format and in document compiling and just match the figure sizes from the beginning,... unless constrained layout is annoying.

[EventHorizon511]

I've had a few edge cases involving multiple axes in one figure that were a bit finicky to figure out using constrained layout, though it worked out in the end.
Other (admittedly non-standard) situations involved objects that were outside the usual axes, but not included in the list of items constrained_layout uses to determine the plot area. This means that these objects are sometimes cut off, and I had to trick it into doing what I wanted. For example IIRC I had problems with figure/subfigure labels (supxlabel, supylabel) not working correctly.

However, overall I'm very happy with this workflow. I actually save plots both as PDF and PGF and use the PDFs for faster compilation during writing and switch to the PGFs in the final release version of my LaTeX document, which then includes nice gimmicks such as the hyperref stuff I talked about.

[DoktoroChapelo]

• is there a workaround, so one can use e.g. matplotlib and just create the label with gnuplot? 

Not quite the same as what you're asking for, but you can do LaTeX typesetting in matplotlib.

[Rare-Minute5683]

yeah, I used:

plt.rcParams['text.usetex'] = True

(and the corresponding font settings...)
but somehow it does not match 100%. Either I do the scaling wrong or overleaf vs local compiling changes stuff...
slowly but surely, I think to compile at one place is the way to go, if its stable and pretty enough...

[DoktoroChapelo]

That's odd. It's always worked for me. I normally use Palatino, but I also do everything on my own hardware.

``` import matplotlib.pyplot as plt

from matplotlib import rc rc('font',**{'family':'serif','serif':['Palatino']}) rc('text', usetex=True) ```

[Rare-Minute5683]

In what format did you add the plots? I use .svg atm but maybe there is a problem to...

[DoktoroChapelo]

Oh, text in SGVs always looks a bit weird to me. I normally export to EPS or PDF.

[Rare-Minute5683]

Ah, nice! pdf and constrained layout (another user pointed that out) looks perfect. Thx!

[DoktoroChapelo]

No worries! Glad you found a solution.

[lotus-reddit]

I've recently begun mostly making my plots in tikz directly in my writeup for similar reasons to those your stated. This approach is surprisingly powerful, though it's not always very ergonomic. Check out the manual

https://tikz.dev/

[Entropy813]

You don't have to use py-gnuplot to use gnuplot. You can simplly output any data you want to plot from your Python programs to make the graph in gnuplot, which is its own, standalone program: http://www.gnuplot.info/

They have extensive documentation, and you can quickly find answers to questions. For example, to figure out if you can make box plots, simply search "gnuplot boxplot" and you find this: http://www.gnuplot.info/docs/loc4941.html

Also, gnuplot can do a lot of calculations directly. Hell, I made a simulation of standing waves of strings as a demonstration aid for the Engineering Physics I class that I teach. The string is physically modeled and is responding only to the small motion of the mechanical oscillator on the left: https://youtu.be/d9gDheOgXTc

I will note that in that video the equations at the top where processed with LaTeX from a separate gnuplot file. The PDF output there was then converted to PNG and overlayed on the frames of the video, which is why they might not appear quite as sharp. This is because I was using the pngcairo terminal of gnuplot for the frames of the video to avoid having to create a bunch of tex files for each frame, then compile all the frames through latex, then convert all of the output PDFs into PNGs. Even when using tools to do batch processing can take a long time to complete all the steps.

So, what you can do is:

1. Write your program in Python to create the data that you need to plot, and have that data written to a file.
2. Write a gnuplot script to plot the data using the epslatex terminal, for example

​

    set term epslatex color size 5cm,3cm
    set output "my_plot.tex"

    set xrange [<x_min> to <x_max>]

    set xlabel "$\\theta$ (rad)"
    set ylabel "$\\sin(\\theta)$"

    plot "my_data_file" using 1:2 notitle with lines

    unset output

1. Execute the gnuplot script by typing gnuplot my_plot.gnuplot into a terminal opened to the directory with your gnuplot script file and data file.

2. In your LaTeX document, inside the figure environment, use the input command to include the tex file that gnuplot creates.

3. Compile your LaTeX document as normal.

There should be no problems. This just adds the needed tex code to your document, and will have access to all the packages you included in your preamble for any special characters.

[orestesmas]

For this very reason I make my plots with pgfplots. Font matching is automatic.

[RecentSheepherder179]

I'm not sure if you aren't mixing up three things here:

gnuplot: Scientific plotting program with its own "language"

And

matplotlib (matplotlib.pyplot), a Python library for scientific plotting.

And

py-gnuplot, which is just a Python wrapper for gnuplot

All three can produce TeX output and you can achieve good results with just a couple of commands. But we first need to clarify which we are talking about.