Using matplotlib.animate to animate a contour plot in python

Question

I have a 3D array of data (2 spatial dimensions and 1 time dimension) and I'm trying to produce an animated contour plot using matplotlib.animate. I'm using this link as a basis:

http://jakevdp.github.io/blog/2012/08/18/matplotlib-animation-tutorial/

And here's my attempt:

import numpy as np from matplotlib import pyplot as plt from matplotlib import animation from numpy import array, zeros, linspace, meshgrid from boutdata import collect  # First collect data from files n = collect("n")   #  This is a routine to collect data Nx = n.shape[1] Nz = n.shape[2] Ny = n.shape[3] Nt = n.shape[0]  fig = plt.figure() ax = plt.axes(xlim=(0, 200), ylim=(0, 100)) cont, = ax.contourf([], [], [], 500)  # initialisation function def init():     cont.set_data([],[],[])     return cont,  # animation function def animate(i):      x = linspace(0, 200, Nx)     y = linspace(0, 100, Ny)     x,y = meshgrid(x,y)     z = n[i,:,0,:].T     cont.set_data(x,y,z)     return cont,   anim = animation.FuncAnimation(fig, animate, init_func=init,                            frames=200, interval=20, blit=True)  plt.show() 

But when I do this, I get the following error:

Traceback (most recent call last):   File "showdata.py", line 16, in <module>     cont, = ax.contourf([], [], [], 500)   File "/usr/lib/pymodules/python2.7/matplotlib/axes.py", line 7387, in contourf     return mcontour.QuadContourSet(self, *args, **kwargs)   File "/usr/lib/pymodules/python2.7/matplotlib/contour.py", line 1112, in __init__     ContourSet.__init__(self, ax, *args, **kwargs)   File "/usr/lib/pymodules/python2.7/matplotlib/contour.py", line 703, in __init__     self._process_args(*args, **kwargs)   File "/usr/lib/pymodules/python2.7/matplotlib/contour.py", line 1125, in _process_args     x, y, z = self._contour_args(args, kwargs)   File "/usr/lib/pymodules/python2.7/matplotlib/contour.py", line 1172, in _contour_args     x,y,z = self._check_xyz(args[:3], kwargs)   File "/usr/lib/pymodules/python2.7/matplotlib/contour.py", line 1204, in _check_xyz     raise TypeError("Input z must be a 2D array.") TypeError: Input z must be a 2D array. 

So I've tried replacing all the [] by [[],[]] but this then produces:

Traceback (most recent call last):   File "showdata.py", line 16, in <module>     cont, = ax.contourf([[],[]], [[],[]], [[],[]],500)   File "/usr/lib/pymodules/python2.7/matplotlib/axes.py", line 7387, in contourf     return mcontour.QuadContourSet(self, *args, **kwargs)   File "/usr/lib/pymodules/python2.7/matplotlib/contour.py", line 1112, in __init__     ContourSet.__init__(self, ax, *args, **kwargs)   File "/usr/lib/pymodules/python2.7/matplotlib/contour.py", line 703, in __init__     self._process_args(*args, **kwargs)   File "/usr/lib/pymodules/python2.7/matplotlib/contour.py", line 1125, in _process_args     x, y, z = self._contour_args(args, kwargs)   File "/usr/lib/pymodules/python2.7/matplotlib/contour.py", line 1177, in _contour_args     self.zmax = ma.maximum(z)   File "/usr/lib/python2.7/dist-packages/numpy/ma/core.py", line 5806, in __call__     return self.reduce(a)   File "/usr/lib/python2.7/dist-packages/numpy/ma/core.py", line 5824, in reduce     t = self.ufunc.reduce(target, **kargs) ValueError: zero-size array to maximum.reduce without identity 

Thanks in advance!

Answer 1

Felix Schneider is correct about the animation becoming very slow. His solution of setting ax.collections = [] removes all old (and superseded) "artist"s. A more surgical approach is to only remove the artists involved in the drawing the contours:

for c in cont.collections:     c.remove() 

which is useful in more complicated cases, in lieu of reconstructing the entire figure for each frame. This also works in Rehman Ali's example; instead of clearing the entire figure with clf() the value returned by contourf() is saved and used in the next iteration.

Here is an example code similar to Luke's from Jun 7 '13, demonstrating removing the contours only:

import pylab as plt import numpy import matplotlib.animation as animation #plt.rcParams['animation.ffmpeg_path'] = r"C:\some_path\ffmpeg.exe"   # if necessary  # Generate data for plotting Lx = Ly = 3 Nx = Ny = 11 Nt = 20 x = numpy.linspace(0, Lx, Nx) y = numpy.linspace(0, Ly, Ny) x,y = numpy.meshgrid(x,y) z0 = numpy.exp(-(x-Lx/2)**2-(y-Ly/2)**2)   # 2 dimensional Gaussian  def some_data(i):   # function returns a 2D data array     return z0 * (i/Nt)  fig = plt.figure() ax = plt.axes(xlim=(0, Lx), ylim=(0, Ly), xlabel='x', ylabel='y')  cvals = numpy.linspace(0,1,Nt+1)      # set contour values  cont = plt.contourf(x, y, some_data(0), cvals)    # first image on screen plt.colorbar()  # animation function def animate(i):     global cont     z = some_data(i)     for c in cont.collections:         c.remove()  # removes only the contours, leaves the rest intact     cont = plt.contourf(x, y, z, cvals)     plt.title('t = %i:  %.2f' % (i,z[5,5]))     return cont  anim = animation.FuncAnimation(fig, animate, frames=Nt, repeat=False) anim.save('animation.mp4', writer=animation.FFMpegWriter())