How to manipulate figures while a script is running in Python?

Question

Introduction

As I am coming from matlab, I am used to an interactive interface where a script can update figures while it is running. During the processing each figure can be re-sized or even closed. This probably means that each figure is running in its own thread which is obviously not the case with matplotlib.

IPython can imitate the Matlab behavior using the magic command %pylab or %matplotlib which does something that I don't understand yet and which is the very point of my question.

My goal is then to allow standalone Python scripts to work as Matlab does (or as IPython with %matplotlib does). In other words, I would like this script to be executed from the command line. I am expecting a new figure that pop-up every 3 seconds. During the execution I would be able to zoom, resize or even close the figure.

#!/usr/bin/python
import matplotlib.pyplot as plt
import time

def do_some_work(): 
    time.sleep(3)

for i in range(10):
    plt.plot([1,2,3,4])
    plt.show() # this is way too boilerplate, I'd like to avoid it too. 
    do_some_work()

What alternative to %matplotlib I can use to manipulate figures while a script is running in Python (not IPython)?

What solutions I've already investigated?

I currently found 3 way to get a plot show.

1. %pylab / %matplotlib

As tom said, the use of %pylab should be avoided to prevent the namespace to be polluted.

>>> %pylab
>>> plot([1,2,3,4])

This solution is sweet, the plot is non-blocking, there is no need for an additionnal show(), I can still add a grid with grid() afterwards and I can close, resize or zoom on my figure with no additional issues.

Unfortunately the %matplotlib command is only available on IPython.

2. from pylab import * or from matplotlib.pyplot import plt

>>> from pylab import *
>>> plot([1,2,3,4])

Things are quite different here. I need to add the command show() to display my figure which is blocking. I cannot do anything but closing the figure to execute the next command such as grid() which will have no effect since the figure is now closed...

** 3. from pylab import * or from matplotlib.pyplot import plt + ion()** Some suggestions recommend to use the ion() command as follow:

>>> from pylab import *
>>> ion()
>>> plot([1,2,3,4])
>>> draw()
>>> pause(0.0001)

Unfortunately, even if the plot shows, I cannot close the figure manually. I will need to execute close() on the terminal which is not very convenient. Moreover the need for two additional commands such as draw(); pause(0.0001) is not what I am expecting.

Summary

With %pylab, everything is wonderful, but I cannot use it outside of IPython

With from pylab import * followed by a plot, I get a blocking behavior and all the power of IPython is wasted.

from pylab import * followed by ion offers a nice alternative to the previous one, but I have to use the weird pause(0.0001) command that leads to a window that I cannot close manually (I know that the pause is not needed with some backends. I am using WxAgg which is the only one that works well on Cygwin x64.

This question advices to use matplotlib.interactive(True). Unfortunately it does not work and gives the same behavior as ion() does.

Answer 1

Change your do_some_work function to the following and it should work.

def do_some_work(): 
    plt.pause(3)

For interactive backends plt.pause(3) starts the event loop for 3 seconds so that it can process your resize events. Note that the documentation says that it is an experimental function and that for complex animations you should use the animation module.

The, %pylab and %matplotlib magic commands also start an event loop, which is why user interaction with the plots is possible. Alternatively, you can start the event loop with %gui wx, and turn it off with %gui. You can use the IPython.lib.guisupport.is_event_loop_running_wx() function to test if it is running.

The reason for using ion() or ioff() is very well explained in the 'What is interactive mode' page. In principle, user interaction is possible without IPython. However, I could not get the interactive-example from that page to work with the Qt4Agg backend, only with the MacOSX backend (on my Mac). I didn't try with the WX backend.

Edit

I did manage to get the interactive-example to work with the Qt4Agg backend by using PyQt4 instead of PySide (so by setting backend.qt4 : PyQt4 in my ~/.config/matplotlibrc file). I think the example doesn't work with all backends. I submitted an issue here.

Edit 2

I'm afraid I can't think of a way of manipulating the figure while a long calculation is running, without using threads. As you mentioned: Matplotlib doesn't start a thread, and neither does IPython. The %pylab and %matplotlib commands alternate between processing commands from the read-eval-print loop and letting the GUI processing events for a short time. They do this sequentially.

In fact, I'm unable to reproduce your behavior, even with the %matplotlib or %pylab magic. (Just to be clear: in ipython I first call %matplotlib and then %run yourscript.py). The %matplotlib magic puts Matplotlib in interactive-mode, which makes the plt.show() call non-blocking so that the do_some_work function is executed immediately. However, during the time.sleep(3) call, the figure is unresponsive (this becomes even more apparent if I increase the sleeping period). I don't understand how this can work at your end.

Unless I'm wrong you'll have to break up your calculation in smaller parts and use plt.pause (or even better, the animation module) to update the figures.

Answer 2

My advice would be to keep using IPython, since it manages the GUI event loop for you (that's what pylab/pylot does). I tried interactive plotting in a normal interpreter and it worked the way it is expected, even without calling ion() (Debian unstable, Python 3.4.3+, Matplotlib 1.4.2-3.1). If I recall it right, it's a fairly new feature in Matplotlib.

Alternatively, you can also use Matplotlib's animation capabilities to update a plot periodically:

import numpy as np
import matplotlib.pyplot as plt
import matplotlib.animation as animation
import time

plt.ion()

tt = np.linspace(0, 1, 200)
freq = 1  # parameter for sine
t0 = time.time()  # for measuring ellapsed time

fig, ax = plt.subplots()


def draw_func(i):
    """ This function gets called repeated times """ 
    global freq  # needed because freq is changed in this function
    xx = np.sin(2*np.pi*freq*tt)/freq
    ax.set_title("Passed Time: %.1f s, " % (time.time()-t0) +
                 "Parameter i=%d" % i)
    ax.plot(tt, xx, label="$f=%d$ Hz" % freq)
    ax.legend()
    freq += 1


# call draw_func every 3 seconds 1 + 4 times (first time is initialization):
ani = animation.FuncAnimation(fig, draw_func,  np.arange(4), interval=3000,
                              repeat=False)
# plt.show()

Checkout matplotlib.animation.FuncAnimation for details. You'll find further examples in the examples section.