Matplotlib - Tcl_AsyncDelete: async handler deleted by the wrong thread?

By default matplotlib uses TK gui toolkit, when you're rendering an image without using the toolkit (i.e. into a file or a string), matplotlib still instantiates a window that doesn't get displayed, causing all kinds of problems. In order to avoid that, you should use an Agg backend. It can be activated like so --

import matplotlib
matplotlib.use('Agg')
from matplotlib import pyplot

For more information please refer to matplotlib documentation -- http://matplotlib.org/faq/howto_faq.html#matplotlib-in-a-web-application-server

The above (accepted) answer is a solution in a terminal environment. If you debug in an IDE, you still might wanna use 'TkAgg' for displaying data. In order to prevent this issue, apply these two simple rules:

1. everytime you display your data, initiate a new fig = plt.figure()
2. don't close old figures manually (e.g. when using a debug mode)

Example code:

import matplotlib
matplotlib.use('TkAgg')
from matplotlib import pyplot as plt

fig = plt.figure()
plt.plot(data[:,:,:3])
plt.show()

This proves to be the a good intermediate solution under MacOS and PyCharm IDE.