animation plot in matplotlib with double for loop

Question

I would like to create an animation with matplotlib in python. As the animated data is function of two parameter (time, number of bodies) I got an idea to use 2 for loops. The code is below:

import time
import matplotlib as mpl
from matplotlib import pyplot as plt
from matplotlib import pylab as plb

#   set up figure for plotting:
fig = plt.figure()
ax = fig.add_subplot(111)

#    plot limits
ax.set_xlim(-(max(q0) + bodies[-1].L), +(max(q0) + bodies[-1].L))
ax.set_ylim(-(max(q0) + bodies[-1].L), +(max(q0) + bodies[-1].L))

#    colors
colors = ['b', 'g', 'c']


for i_t in range(0, np.shape(t)[1]):    #t is an one column matrix
    for i in range(0, N):
        ax.plot(x_matrix[i_t, i], y_matrix[i_t, i], 's', color=colors[i])
    plt.draw()
plt.show()

The problem is that the code generates me one plot but with all animated points. I would like to have the animation ploted for one time value (counter i_t) and all bodies (counter i) in one window as a movie so the previous plot is erased at the next time step.

I have changed the code you suggested to:

for i_t in range(0, np.shape(t)[1]):
    for i in range(0, N):
        ax.clear()
        ax.plot(x_matrix[i_t, i], y_matrix[i_t, i], 's', color=colors[i])
        plt.pause(0.001)
plt.draw()

But then I get an error:

C:\Python27\lib\site-packages\matplotlib\backend_bases.py:2292: MatplotlibDeprecationWarning: Using default event loop until function specific to this GUI is implemented warnings.warn(str, mplDeprecation)

That isn't so frightening but when running the code the points that would have to be plotted together (counter i) are plotted apart so it looks like blinkig dots (if you know what I mean).

Any suggestions. I think I am close to the solution, but still need the finishig touch for the code to be working. I hope this can be done the way I imagined so I would not have to solve the problem with different approach.

you have to use the show command for every i_t I guess. Keep in mind that you plot all the stuff in exactly one (!) graph with your code. Maybe you should check the matplotlib cookbook for animations: scipy.org/Cookbook/Matplotlib/Animations or if you want a movie, (probably yes), check this: debtechandstuff.blogspot.de/2009/10/… Generally, you have to plot each frame on its own and then make the animation out of it. An animated .gif is rather easy to do. — Faultier
– Faultier, Commented Jun 3, 2013 at 14:37
it will run better if you just replace the data with set_data, rather than blowing the whole axes away every frame. — tacaswell
– tacaswell, Commented Jun 3, 2013 at 19:19

lskrinjar · Accepted Answer · 2013-06-04 19:03:25Z

3

I have solved the problem. The solution is (if anyone will need it):

for i_t in range(0, np.shape(t)[1]):
    ax.clear()
    plt.hold(True)
    #    plot limits
    ax.set_xlim(-(max(q0) + bodies[-1].L), +(max(q0) + bodies[-1].L))
    ax.set_ylim(-(max(q0) + bodies[-1].L), +(max(q0) + bodies[-1].L))
    for i in range(0, N):
        ax.plot(x_matrix[i_t, i], y_matrix[i_t, i], 's', color=colors[0, i])

    plt.pause(0.0001)

I would have posted earlyer, but as a new user I had to wait for 8 hours to answer my own question.

answered Jun 4, 2013 at 19:03

lskrinjar

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2 Comments

praxmon Over a year ago

I tried plt.pause(). The problem is it quits after I complete the plot. How do I avoid this?

lskrinjar Over a year ago

Try changing the value in plt.pause() from 0.0001 to 0.1? Is plt.pause() indented as inner (second) for loop?

Mike Müller · Accepted Answer · 2013-06-03 14:47:53Z

2

Change the last section of your code to this:

for i_t in range(np.shape(t)[1]):    #t is an one column matrix
    for i in range(N):
        ax.clear()
        ax.plot(x_matrix[i_t, i], y_matrix[i_t, i], 's', color=colors[i])
        plt.pause(0.001)
# eof

Adapt the animation speed by changing the number in plt.pause(0.001).

answered Jun 3, 2013 at 14:47

Mike Müller

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