How to configure FuncAnimation (dynamic plotting from matplotlib.animation) to numpy arrays?

Question

I have some issues with the FuncAnimation fonction of MatPlotLib. I can't configure it to my code... I hope someone could help me !!

This is a diffusion equation, I need to plot it for each step of the time. At each step, the result of the calculation is a numpy array. I manage to plot it in a dynamic way with pyplot.interactive(True) but it is very laggy. I read that FuncAnimation can deal with that problem but I did not manage to have it working with results in lists or arrays.

Here is the code with a classic slow plot :
It produces a vector of vectors (U) wich are ploted after all calculations

import numpy as np
import scipy
from scipy.linalg import solve_banded
from matplotlib import pyplot as plt
import matplotlib.animation as animation


def DrawRecord(U):
    plt.interactive(True)
    plt.figure(1)
    for i in range(0,len(U)):
        plt.clf()
        plt.plot(U[i])
        plt.ylim([0,1])
        plt.draw()

J=350.0 
dt=0.01 
T=3.0 
t=np.arange(dt,T,dt) 
dx=1.0/J 

D=0.005 
c=0.5 
r=0.1 

mu=c*dt/(2.0*dx) 
lambd=D*dt/(dx**2.0) 

K_x=50.0*np.ones(J-1) 
alpha_t=0.5*np.ones(len(t)) 

#initial conditions
u=np.zeros(J) 
u[J/5*1:J/5*2]=1 
U=u

espace=np.linspace(0,1,J) 

#Matrix
A=np.diag(-lambd*np.ones(J-2),1)+np.diag((1+2*lambd)*np.ones(J-1),0)+np.diag(-lambd*np.ones(J-2),-1)  
AA=scipy.linalg.inv(A)


for i in t:

    u[1:J]=scipy.dot(AA,u[1:J]+(r-alpha_t[i/dt])*dt*(u[1:J]-u[1:J]/K_x))
    u[0]=0 
    u[J-1]=0  

    U=np.vstack([U,u])

DrawRecord(U)

And here is my try of making turn the FuncAnimation with the previous code (big fail) :
nb : U contents the arrays of results calculated for each steps

global U

fig = plt.figure()
window = fig.add_subplot(111)
line, = window.plot(list(U[1,:]))

def init():
    line=list(U[1,:])
    return line

def animate(i):
    line.set_ydata(list(U[i,:]))
    return line

anim = animation.FuncAnimation(fig, animate, init_func=init,
                           frames=200, interval=20, blit=True)

plt.show()

That produces a lot of errors ... Maybe someone can set it up for the previous code !
I hope I'm clear (sorry for my english) and thank you for your help.

Answer 1

Your init function isn't right, it should be:

def init():
    line.set_ydata(U[1,:])
    return line

You also don't need to convert the numpy slice to a list.