Matplotlib FuncAnimation slow

Question

I have created a simple animation of a surface binding process using matplotlib's FuncAnimation. The result however is very slow. I suspect it is because I am redrawing all elements at each frame, but I haven't figured out a work-around. Any help appreciated.

import matplotlib
matplotlib.use('TKAgg')      # import proper graphics back-end for Mac OS X


import numpy as np
from matplotlib import pyplot as plt
from matplotlib import animation
from matplotlib.collections import PatchCollection
from random import *

nx = 20     # x size of lattice
ny = 20     # y size of lattice

pAds = 0.01     # adsorption probability per time step
pDes = 0.0075   # desorption probability per time step

tMax = 500     # number of time steps

surface = np.zeros((nx,ny))              # create surface
xc = [0]
yc = [0]


# initialization and time step of simulation

def init():
    # initialize an empty list of circles
    patches = []            # empty array to hold drawable objects
    for x in range(0,nx):
        for y in range(0,ny):
            if(surface[x][y] == 0):
                patches.append(ax_surf.add_patch(plt.Circle((x+0.5,y+0.5),0.45,color='w')))
    lines, = ax_covr.plot([],[])
    patches.append(lines)
    return patches

def animate(i): 
    patches = []            # empty array of circles to be drawn
    for x in range(0,nx):
        for y in range(0,ny):
            if(surface[x][y] == 0):
                if(random() < pAds):
                    surface[x][y] = 1
                    patches.append(ax_surf.add_patch(plt.Circle((x+0.5,y+0.5),0.45,color='b')))
                else:
                    patches.append(ax_surf.add_patch(plt.Circle((x+0.5,y+0.5),0.45,color='w')))
            else:
                if(random()<pDes):
                    surface[x][y] = 0
                    patches.append(ax_surf.add_patch(plt.Circle((x+0.5,y+0.5),0.45,color='w')))
                else:
                    patches.append(ax_surf.add_patch(plt.Circle((x+0.5,y+0.5),0.45,color='b')))
    coverage = np.sum(surface)/(nx*ny)
    xc.append(i)
    yc.append(coverage)
    lines, = ax_covr.plot(xc,yc,'ro',ms=2,lw=0)
    patches.append(lines)
    return patches

# set up figure and animate


fig = plt.figure()
ax_surf = plt.subplot2grid((1, 2), (0, 0))
ax_covr = plt.subplot2grid((1, 2), (0, 1))
ax_surf.set_xlim(0,nx)
ax_surf.set_ylim(0,ny)
ax_covr.set_xlim(0,tMax)
ax_covr.set_ylim(0,1)

ax_surf.set_aspect(1)
ax_surf.axis('off')

ax_covr.set_aspect(tMax)

ax_surf.hold(False)

anim = animation.FuncAnimation(fig, animate, init_func=init, frames=tMax, interval=0, blit=True,repeat=False)
plt.show()

Answer 1

Use patches of previous init / animate call instead of creating new one every time.

Following is the modified version of the code.

patches = []

def init():
    global patches
    if patches:
        # prevent the second call of the init()
        return patches
    # initialize an empty list of circles
    for x in range(nx):
        for y in range(ny):
            if(surface[x][y] == 0):
                patches.append(ax_surf.add_patch(plt.Circle((x+0.5,y+0.5),0.45,color='w')))
    lines, = ax_covr.plot([],[])
    patches.append(lines)
    return patches

def animate(i): 
    global patches
    idx = 0
    for x in range(nx):
        for y in range(ny):
            if surface[x][y] == 0:
                if random() < pAds:
                    surface[x][y] = 1
                    patches[idx] = ax_surf.add_patch(plt.Circle((x+0.5,y+0.5),0.45,color='b'))
            else:
                if(random()<pDes):
                    surface[x][y] = 0
                    patches[idx] = ax_surf.add_patch(plt.Circle((x+0.5,y+0.5),0.45,color='w'))
            idx += 1
    coverage = np.sum(surface)/(nx*ny)
    xc.append(i)
    yc.append(coverage)
    lines, = ax_covr.plot(xc,yc,'ro',ms=2,lw=0)
    patches[idx] = lines
    return patches

NOTE: Used global variable to minimize the modification.