Develop Reference

How do I make a simple plot using Matplotlib?

I am trying to plot a text files with X,Y values(attached inline). I am first converting the text file into 2 array objects XAxis1 and YAxis1. The plot doesn't come out properly. Unable to set the X and Y axis values.
Any help is much appreciated.
(Sample1.txt)XAxis1 : 0.51,0.52,0.53,0.54,0.55,0.56,0.57,0.58,0.59,0.6,0.61,0.62,0.63,0.64,0.65,0.66,0.67,0.68,0.69,0.7
(Sample2.txt)YAxis1:
29.63,30.03,30.94,31.67,33.59,35.09,35.35,35.04,36.71,36.77,36.84,37.45,33.87,31.68,30.98,27.97,29.24,38.52,33.37,27.8
Sorry could not paste the code, some errors..

Some people have downvoted your question, because a google search can solve much bigger problems and this is not very exotic.
See https://matplotlib.org/stable/api/_as_gen/matplotlib.pyplot.plot.html
from matplotlib.pyplot import plot
ax_x = [
0.51,0.52,0.53,0.54,0.55,0.56,0.57,0.58,0.59,0.6,0.61,0.62,0.63,0.64,0.65,0.66,0.67,0.68,0.69,0.7]
ax_y = [
29.63,30.03,30.94,31.67,33.59,35.09,35.35,35.04,36.71,36.77,36.84,37.45,33.87,31.68,30.98,27.97,29.24,38.52,33.37,27.8]
plot(ax_x, ax_y)
In case reading from file is a problem, I recommend saving everything in a useful format.
See https://www.programiz.com/python-programming/json

Matplotlib version of latex command "\ell" looking extra-slanted

I use latex in matplotlib by setting
plt.rcParams.update({'mathtext.fontset': 'stix'})
plt.rcParams.update({'font.family': 'STIXGeneral'})
I am using the letter $\ell$ very often in my research and there is a small detail bothering me. As you can see below, matplotlib renders the symbol with the little loop smaller and the letter more slanted. To me it almost looks like a vertically stretched $e$. I tried using the "\mathrm{\ell}" command instead but it did not change anything.
Is there any way I could get the symbol to look normal?
PS: it looks like stackoverflow is not detecting the math mode $ for some reason. If you know how to fix it (or if I am doing something wrong) please point it out or edit the question. Thanks!

The reason is the font you are using in matplotlib. With the following settings, for example, you get the same letter as in overleaf:
import matplotlib.pyplot as plt
import numpy as np
# Example data
t = np.arange(0.0, 10, 1)
s = np.arange(0.0, 10, 1)
plt.rc('text', usetex=True)
plt.rc('font', family='serif')
plt.xlabel(r'$\ell$', fontsize=30)
plt.ylabel(r'$\ell$', fontsize=30)
plt.plot(t, s)
plt.show()
You get:
However, In Jupyterlab I could not reproduce. It used the overleaf fonts even with your settings.

This proved to be the simplest solution for me. Thanks the others for pointing out the font being the issue.
Rather than
plt.rcParams.update({'mathtext.fontset': 'stix'})
plt.rcParams.update({'font.family': 'STIXGeneral'})
I now write the first line as
plt.rcParams.update({'mathtext.fontset': 'cm'})
which works like charm. This is helpful if you are someone like me not using TeX but just the mathtext matplotlib built-in function.

Latex font in matplotlib - Script-r

In matplotlib, one can easily use latex script to label axes, or write legends or any other text. But is there a way to use new fonts such as 'script-r' in matplotlib? In the following code, I am labelling the axes using latex fonts.
import numpy as np
import matplotlib.pyplot as plt
tmax=10
h=0.01
number_of_realizations=6
for n in range(number_of_realizations):
xpos1=0
xvel1=0
xlist=[]
tlist=[]
t=0
while t<tmax:
xlist.append(xpos1)
tlist.append(t)
xvel1=np.random.normal(loc=0.0, scale=1.0, size=None)
xpos2=xpos1+(h**0.5)*xvel1 # update position at time t
xpos1=xpos2
t=t+h
plt.plot(tlist, xlist)
plt.xlabel(r'$ t$', fontsize=50)
plt.ylabel(r'$r$', fontsize=50)
plt.title('Brownian motion', fontsize=20)
plt.show()
It produces the following figure
But I want 'script-r' in place of normal 'r'.
In latex one has to add the following lines in preamble to render 'script-r'
\DeclareFontFamily{T1}{calligra}{}
\DeclareFontShape{T1}{calligra}{m}{n}{<->s*[2.2]callig15}{}
\DeclareRobustCommand{\sr}{%
\mspace{-2mu}%
\text{\usefont{T1}{calligra}{m}{n}r\/}%
\mspace{2mu}%
}
I don't understand how to do this in matplotlib. Any help is appreciated.

Matplotlib uses it's own hand-rolled (pure Python) implementation of TeX to do all of the math text stuff, so you absolutely cannot assume that what works in standard LaTeX will work with Matplotlib. That being said, here's how you do it:
Install the calligra font so that Matplotlib can see it, then rebuild the font cache.
Lots of other threads deal with how to do this, I'm not going to go into detail, but here's some reference:
Use a font installed in a random spot on your filesystem.
How to install a new font into the Matplotlib managed font cache.
List all fonts currently known to your install of Matplotlib.
Replace one of Matplotlib's TeX font families with your font of choice.
Here's a function I wrote a while ago that reliably does that:
import matplotlib
def setMathtextFont(fontName='Helvetica', texFontFamilies=None):
texFontFamilies = ['it','rm','tt','bf','cal','sf'] if texFontFamilies is None else texFontFamilies
matplotlib.rcParams.update({'mathtext.fontset': 'custom'})
for texFontFamily in texFontFamilies:
matplotlib.rcParams.update({('mathtext.%s' % texFontFamily): fontName})
For you, a good way to use the function would be to replace the font used by \mathcal with calligra:
setMathtextFont('calligra', ['cal'])
Label your plots, for example, r'$\mathcal{foo}$', and the contents of the \math<whatever> macro should show up in the desired font.
Here's how you'd change your label-making code:
plt.ylabel(r'$\mathcal{r}$', fontsize=50)
and that should do it.

matplotlib generated PDF cannot be viewed in acrobat reader

I am plotting data with matplotlib including LaTeX fonts. The pdf created can be displayed by evince, inkscape, GIMP but not by acroread resp. adobe reader. The code prototype works with a lot of figures and only a few plots have this problem.
...
fig = plt.figure(figsize=(10, 6))
ax = fig.add_subplot(111)
savedpi = 250
fileformat = 'pdf'
...
p12,=ax.plot(plimit12-binSize/2.0, mean12, '-', lw=2)
ax.set_yscale('log')
ax.yaxis.set_major_formatter(matplotlib.ticker.ScalarFormatter())
ax.legend([p1, p2, p3, p4, p5, p6, p7, p8, p9, p10, p11, p12], [ "C01", "C02", "C03", "C04", "C05", "C06", "C07", "C08", "C09", "C10", "C11", "C12"],numpoints=1, loc=1, ncol=3)
plt.savefig(savepath+'veloDisp'+'.pdf',dpi=None,format=fileformat)
One of these problematic files is to be fount at http://ubuntuone.com/0kuZIKYeZQyGckE5jonPy6
Did anyone encounter such a problem?
EDIT: Thank you William Denman, in fact opening in evince and printing into pdf works, it can be viewed in acroread as well now. Interestingly, other plots with LaTeX Fonts work from the get go. I do not get any error messages from which I could guess where the problem lies, this is why I asked here in the first place. For now your workaround is fine, thank you. However I would really like to know how this can be avoided generally. As these plots should be part of a publication, I have to think also about those people using Adobe pdf viewers.
EDIT: As suggested, I opened a thread on the MPL developers mailing list, see http://matplotlib.1069221.n5.nabble.com/PDF-not-readable-by-Adobe-PDF-readers-td42580.html
EDIT: Solved by matplotlib developers! The problem was the line
ax.axvline(x=1, c='#000000', lw='2', alpha=0.5)
which contains a string as line width. Should be
ax.axvline(x=1, c='#000000', lw=2, alpha=0.5)
Unfortunately standard pdf backend does not warn about this (yet).

After chasing my own bug in matplotlib I figured out based on this post and the referral the OP makes at matplotlib site that chasing bugs in matplotlib can be done with cairo. pip install cairo. Then on top of all other MPL imports add:
#!/usr/bin/env python
# -*- coding: utf-8 -*-
import ...
import matplotlib
matplotlib.use("cairo")
from matplotlib.backends.backend_pdf import PdfPages
..etc.
otherwise the chase will fail because the backend is already set and loaded....

python latex font xcode

I'm trying to use Matplotlib & Python in Xcode to generate scientific graphics. My boss would like them to be in LaTeX with matching fonts. I know you can modify the fonts in python with something like this:
from matplotlib import rc
rc('font',**{'family':'serif','serif':['Computer Modern Roman']})
rc('text', usetex=True)
Unfortunately, opening or saving the figure with plt.show() or plt.savefig() gives a string of errors, eventually leading to OSError: [Errno 2] No such file or directory.
I know "Google is your friend", but I haven't managed to find anything on how to go about solving this. Any help would be greatly appreciated.

I usually find it easiest to directly specify the font file I'm after. Here's an example:
import matplotlib.pyplot as plt
import matplotlib.font_manager
from numpy import *
# cmunso.otf is a randomly selected font in my tex installation
path = '/usr/local/texlive/2012/texmf-dist/fonts/opentype/public/cm-unicode/cmunso.otf'
f0 = matplotlib.font_manager.FontProperties()
f0.set_file(path)
plt.figure()
plt.xlim(0,1.)
plt.ylim(0,1.)
d = arange(0, 1, .1)
plt.plot(d, d, "ob", label='example')
plt.text(.5, .1, 'text.. abcdef', fontproperties=f0, size=30)
plt.xlabel("x label", fontproperties=f0)
plt.legend(prop=f0, loc=2)
I'm not a font expert, but I think the reason this is easier is that font selection often has a cascading set of defaults for when the way you specify the font doesn't exactly match the way the system does. The file, though, is easy to find and specify exactly (though it's obviously less portable).
Note that for xlabel and text the keyword is fontproperties and for legend it's prop.