Matplotlib FuncAnimation for scatter plot

Question

I am trying to use the FuncAnimation of Matplotlib to animate the display of one dot per frame of animation.

# modules
#------------------------------------------------------------------------------
import numpy as np
import matplotlib.pyplot as py
from matplotlib import animation

py.close('all') # close all previous plots

# create a random line to plot
#------------------------------------------------------------------------------

x = np.random.rand(40)
y = np.random.rand(40)

py.figure(1)
py.scatter(x, y, s=60)
py.axis([0, 1, 0, 1])
py.show()

# animation of a scatter plot using x, y from above
#------------------------------------------------------------------------------

fig = py.figure(2)
ax = py.axes(xlim=(0, 1), ylim=(0, 1))
scat = ax.scatter([], [], s=60)

def init():
    scat.set_offsets([])
    return scat,

def animate(i):
    scat.set_offsets([x[:i], y[:i]])
    return scat,

anim = animation.FuncAnimation(fig, animate, init_func=init, frames=len(x)+1, 
                               interval=200, blit=False, repeat=False)

Unfortunately, the final animated plot is not the same as original plot. The animated plot also flashes several dots during each frame of animation. Any suggestions on how to correctly animate a scatter plot using the animation package?

Answer 1

The only problem with your example is how you fill the new coordinates in the animate function. set_offsets expects a Nx2 ndarray and you provide a tuple of two 1d arrays.

So just use this:

def animate(i):
    data = np.hstack((x[:i,np.newaxis], y[:i, np.newaxis]))
    scat.set_offsets(data)
    return scat,

And to save the animation you might want to call:

anim.save('animation.mp4')

Answer 2

Disclaimer, I wrote a library to try and make this easy but using ArtistAnimation, called celluloid. You basically write your visualization code as normal and simply take pictures after each frame is drawn. Here's a complete example:

import matplotlib
matplotlib.use('Agg')
import matplotlib.pyplot as plt
import numpy as np
from celluloid import Camera

fig = plt.figure()
camera = Camera(fig)

dots = 40
X, Y = np.random.rand(2, dots)
plt.xlim(X.min(), X.max())
plt.ylim(Y.min(), Y.max())
for x, y in zip(X, Y):
    plt.scatter(x, y)
    camera.snap()
anim = camera.animate(blit=True)
anim.save('dots.gif', writer='imagemagick')