I am writing a basic Python module which contains a function that plots some data from a Pandas DataFrame. The problem is that I expect users to call this function from both the interactive shell and IPython notebooks. Unfortunately, our interactive shell environment does not have any valid DISPLAY options for matplotlib to use, so I want my function (or the full module) to behave slightly different depending on which environment it is loaded into. (E.g., the default is show the plot without saving in IPython, and save the plot without showing in the shell).
This question gives me a partial answer, in that I can explicitly tell users to write matplotlib.use('Agg') before they ever import my module, but surely there is a more automated backend way to handle this?
You could try checking if you are running into the situation (empty $DISPLAY) and default users to the Agg backend, rather than asking them to do so.
def configure_matplotlib():
import os
if 'DISPLAY' not in os.environ:
if matplotlib.get_backend() != 'Agg':
matplotlib.use('Agg')
import matplotlib
configure_matplotlib()
import matplotlib.pyplot as plt
...
Now matplotlib.use has no effect once pyplot has been imported, but if your users have already done so, they probably have a working configuration anyway.
Related
I have a program that is working fine locally, but I need to use it in CoCalc on the cloud to share with a group. Everything works fine until the end, when I want to create a scatter graph, in standard way. There are a bunch of other specs, but essentially, it's just
plt.scatter(x, y, color = 'blue')
plt.show()
Nothing tricky. But in Cocalc, it tells me "UserWarning: Matplotlib is currently using agg, which is a non-GUI backend, so cannot show the figure."
Here are the imports from the beginning of the file:
import nltk
import pandas as pd
import matplotlib.pyplot as plt
import numpy as np
I've searched for this error and tried the solutions I've found, such as importing tkinter. So, for instance, if I change the headers to
import nltk
import tkinter as tk
import pandas as pd
import matplotlib
matplotlib.use('TkAgg')
import matplotlib.pyplot as plt
import numpy as np
I get a different error: "Cannot load backend 'TkAgg' which requires the 'tk' interactive framework, as 'headless' is currently running."
I've seen instructions about pip installations and such, but a) I'm not sure the installations would make everything work for my group, and b) CoCalc generally has most of the standard packages ready to go, so maybe that's not the problem?
Obviously, I'm not experienced with these issues, so help is much appreciated.
If you're using a Jupyter notebook in CoCalc, then the above will just work fine. Here's an example:
https://cocalc.com/wstein/support/matplotlib-scatter-in-jupyter
If you're writing all of your code as part of a Python program (so, e.g., .py files) and running this from a Terminal, CoCalc will also fully support Tk and this working! However, you have to start a new X11 desktop session in CoCalc by clicking +New --> "Linux Graphical X11 Desktop", then run your Python program from the terminal in the upper left. You'll see any windows that pop up in the main window off to the right.
See https://cocalc.com/wstein/support/scatter-matplotlib-x11
Qt5Agg is necessary to use the mayavi 3D visualization package. I have installed PyQt5 and mayavi using pip in a separate copied conda environment. The default backend then changes from TkAgg to QtAgg. This is a bit weird because in an earlier installation in a different PC the default changed directly to Qt5Agg. I always check the backend using the following commands from the python console :
import matplotlib
matplotlib.get_backend()
Even with the backend being 'QtAgg', I am able to use mayavi from the terminal without any issue but not when I do so in Pycharm. Here I get a non-responsive empty window (image below) :
Image of the non-responsive window
I have been able to get rid of this issue by explicitly using Qt5Agg instead of QtAgg before the plt call :
import matplotlib
matplotlib.use('Qt5Agg')
import matplotlib.pyplot as plt
But I would prefer a better way than using the above in every script that I write. As I had mentioned earlier, I already have mayavi installed and have used it successfully it in Pycharm in a different PC and there the default backend is 'Qt5Agg' and hence there is no need to change the backend explicitly.
Is there anything obvious that I'm overlooking ? Can you please let me know of a way to change the default backend for matplotlib from QtAgg to Qt5Agg after PyQt5 installation using pip ?
Thanks in advance !!
Thanks to #PaulH's comment, I was able to solve the issue. Owing to #mx0's suggestion, I shall now explicitly mention the fix below so that others can also benefit from it.
In a particular conda environment, if matplotlib package is installed, then there will be a 'matplotlibrc' file stored somewhere that defines what the default backend will be whenever matplotlib is imported from that conda environment. The location of this 'matplotlibrc' can be found using the following commands :
import matplotlib
matplotlib.matplotlib_fname()
Please look into the following link if there's any deprecation issue with the above commands :
https://matplotlib.org/stable/tutorials/introductory/customizing.html#customizing-with-matplotlibrc-files
Once the location of the 'matplotlibrc' file is known, open it and simply uncomment one line inside this file. Just change the backend from :
##backend: Agg
to :
backend: Qt5Agg
And that's it. All the plot window troubles in PyCharm will be solved as far as the mayavi 3D visualization package is concerned. For any other use, where a specific backend is necessary, you can also set the default to any other backend of choice.
I want to choose the best IDE for Python programming so I'm testing different softwares but I have problem.
When I try this code blocks on VS Code I don't see any error but the image is not showing
import matplotlib.pyplot as plt
import matplotlib.image as mpimg
image = mpimg.imread('exit-ramp.jpg')
plt.imshow(image)
VS Code
When I try run the same code on PyCharm I see some errors
PyCharm
But when I run the same code on Jupyter Notebook it works. What can I do?
Bro, try that:
import matplotlib.pyplot as plt
import matplotlib.image as mpimg
image = mpimg.imread('exit-ramp.jpg')
plt.imshow(image)
plt.show()
i've made a test in my vscode.
Few weeks ago i used a lot pycharm... but i get some library errors with pandas and pycharm its a little bit heavy.
VSCODE its light and i didnt get any library error that i had with pycharm.
I believe this is a backend problem to be changed in matplotlib. If you start your Python shell whether you are in a bash shell or in vscode, you should use a backend that will show the plot. Otherwise the plt.show() call is required.
So, one solution is to change the backend either manually in you Python shell or when starting the Python shell as explained here below.
Note, however, that I always use the qt5 backend but got the same issue as yours: no plot appears. I changed to the Qt5Agg backend and it worked for me (providing PyQt5 is installed).
So, first solution, you can try to set the backend when starting the Python shell:
ipython --pylab Qt5Agg
You should use a GUI backend amongst the possible backend. If you do not known, try to replace Qt5Agg by auto
The second solution consists in changing the backend manually once in the Python shell:
import matplotlib as plt
plt.use('Qt5Agg')
Right click on your code -> Run current file in interactive window.
Setup:
I have an IPython Notebook I’d like to include in the tutorials section of my docs. I’ve written a .ipynb —> .rst conversion script (using pandoc) that works as follows: the notebook is first converted to a .py file, which is executed as a script, and if the script execution raises no exceptions, an .rst export is triggered and a link to that tutorial is built in the appropriate spot of the docs. That way, the tutorials can be integrated into my docs only under the condition that the code does what the tutorial says it does. This method was developed as a result of the following question: Raise exception if script fails
Ok, so here is the problem. I’d like for some of the .ipynb tutorials to include in-line plots with matplotlib. The way I display plots in an IPython Notebook is using the magic function call:
%matplotlib inline
However, if this command appears in a python executable script, python raises an exception. So none of my tutorials can currently include plots.
Question:
So my question is this: how can I include in-line plots in a Notebook in a way that will not raise an exception when the notebook is exported to a .py file and executed as a script? Or, short of that, any suggestions for another workaround?
Use this instead:
from IPython import get_ipython
ipython = get_ipython()
if ipython:
ipython.magic("matplotlib inline")
Currently, there should be no real need to use %matplotlib inline magic in jupyter. Instead, this should display nicely:
import matplotlib.pyplot as plt
fig, ax = plt.subplot(111)
ax.plot([3,4,2,5])
fig
matplotlib has a config file and IPython has its own. Which one has precedence when it comes to setting things like matplotlib backends?
For example, say my config file for matplotlib says to use a specific backend, but then I modify my IPython startup or config files to use a different one. Which one would be used when I start IPython and import matplotlib?
More generally, what is the right way to set things up so that different profiles use different matplotlib backends or matplotlib configurations?
IPython configuration is used, as IPython itself chooses the matplotlib backend.
For reference, see IPython:core/pylabtools.py:activate_matplotlib and notice how matplotlib.use(backend) is called explicitly.