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The following example code generates a simple plot, then saves it to 'fig1.pdf', then displays it, then saves it again to 'fig2.pdf'. The first image looks as expected, but the second one is blank (contains a white square). What's actually going on here? The line plt.show() apparently messes something up, but I can't figure out what/how!

import numpy as np
import matplotlib.pyplot as plt
x = np.linspace(-1, 1, 100)
y = x**2
plt.plot(x,y)
plt.savefig('fig1.pdf')
plt.show()
plt.savefig('fig2.pdf')

If you want to save the figure after displaying it, you'll need to hold on to the figure instance. The reason that plt.savefig doesn't work after calling show is that the current figure has been reset.

pyplot keeps track of which figures, axes, etc are "current" (i.e. have not yet been displayed with show) behind-the-scenes. gcf and gca get the current figure and current axes instances, respectively. plt.savefig (and essentially any other pyplot method) just does plt.gcf().savefig(...). In other words, get the current figure instance and call its savefig method. Similarly plt.plot basically does plt.gca().plot(...).

After show is called, the list of "current" figures and axes is empty.

In general, you're better off directly using the figure and axes instances to plot/save/show/etc, rather than using plt.plot, etc, to implicitly get the current figure/axes and plot on it. There's nothing wrong with using pyplot for everything (especially interactively), but it makes it easier to shoot yourself in the foot.

Use pyplot for plt.show() and to generate a figure and an axes object(s), but then use the figure or axes methods directly. (e.g. ax.plot(x, y) instead of plt.plot(x, y), etc) The main advantage of this is that it's explicit. You know what objects you're plotting on, and don't have to reason about what the pyplot state-machine does (though it's not that hard to understand the state-machine interface, either).

As an example of the "recommended" way of doing things, do something like:

import numpy as np
import matplotlib.pyplot as plt

x = np.linspace(-1, 1, 100)
y = x**2

fig, ax = plt.subplots()
ax.plot(x, y)
fig.savefig('fig1.pdf')
plt.show()
fig.savefig('fig2.pdf')

If you'd rather use the pyplot interface for everything, then just grab the figure instance before you call show. For example:

import numpy as np
import matplotlib.pyplot as plt

x = np.linspace(-1, 1, 100)
y = x**2

plt.plot(x, y)
fig = plt.gcf()
fig.savefig('fig1.pdf')
plt.show()
fig.savefig('fig2.pdf')

pyplot.show blocks and destroys the plot upon closing. You can use

plt.show(block=False)

after which the save to fig2.pdf will work or you can plot it again before saving

plt.plot(x,y)
plt.savefig('fig2.pdf')

I had to run plt.cla() and plt.clf() before plotting the second one. Clear current axes and clear current plot, respectively.

If you just want to see the figure before saving, you can call

plt.ion()

before plotting, which starts interactive mode, and shows all figures as they are drawn. This mostly removes the need to call plt.show(). You no longer need to close the figures to continue.

To disable interactive mode again, call plt.ioff().