Animation with pcolormesh routine in matplotlib, how do I initialize the data?

Question

I am trying to animate a pcolormesh in matplotlib. I have seen many of the examples using the package animation, most of them using a 1D plot routi

Answer 1

There is an ugly detail you need to take care when using QuadMesh.set_array(). If you intantiate your QuadMesh with X, Y and C you can update the values C by using set_array(). But set_array does not support the same input as the constructor. Reading the source reveals that you need to pass a 1d-array and what is even more puzzling is that depending on the shading setting you might need to cut of your array C.

Edit: There is even a very old bug report about the confusing array size for shading='flat'.

That means:

Using QuadMesh.set_array() with shading = 'flat'

'flat' is default value for shading.

# preperation
import numpy as np
import matplotlib.pyplot as plt
plt.ion()
y = np.linspace(-10, 10, num=1000)
x = np.linspace(-10, 10, num=1000)
X, Y = np.meshgrid(x, y)
C = np.ones((1000, 1000)) * float('nan')

# intantiate empty plot (values = nan)
pcmesh = plt.pcolormesh(X, Y, C, vmin=-100, vmax=100, shading='flat')

# generate some new data
C = X * Y

# necessary for shading='flat'
C = C[:-1, :-1]

# ravel() converts C to a 1d-array
pcmesh.set_array(C.ravel())

# redraw to update plot with new data
plt.draw()

Looks like:

Note that if you omit C = C[:-1, :-1] your will get this broken graphic:

Using QuadMesh.set_array() with shading = 'gouraud'

# preperation (same as for 'flat')
import numpy as np
import matplotlib.pyplot as plt
plt.ion()
y = np.linspace(-10, 10, num=1000)
x = np.linspace(-10, 10, num=1000)
X, Y = np.meshgrid(x, y)
C = np.ones((1000, 1000)) * float('nan')

# intantiate empty plot (values = nan)
pcmesh = plt.pcolormesh(X, Y, C, vmin=-100, vmax=100, shading='gouraud')

# generate some new data
C = X * Y

# here no cut of of last row/column!

# ravel() converts C to a 1d-array
pcmesh.set_array(C.ravel())

# redraw to update plot with new data
plt.draw()

If you cut off the last row/column with shade='gouraud' you will get:

ValueError: total size of new array must be unchanged