pcolormesh with missing values?

Question

I have 3 1-D ndarrays: x, y, z

and the following code:

import numpy as np
import matplotlib.pyplot as plt
import scipy.interpolate as spinterp

## de         


        

Answer 1

Got it. This seems round-about, but this was the solution:

import numpy.ma as ma

Zm = ma.masked_where(np.isnan(Z),Z)
plt.pcolormesh(X,Y,Zm.T)

If the Z matrix contains nan's, it has to be a masked array for pcolormesh, which has to be created with ma.masked_where, or, alternatively,

Zm = ma.array(Z,mask=np.isnan(Z))

Answer 2

A slight improvement on the chosen answer

import numpy.ma as ma
Zm = ma.masked_invalid(Z)
plt.pcolormesh(X, Y, Zm.T)

masked_invalid masks all NaN values, thereby saving the need to specify

mask = np.isnan(Z)

Answer 3

Note that the explicit masking is no longer necessary in matplotlib master as arrays are now masked automatically internally. Will be incorporated into matplotlib >2.1. See my merged pull request https://github.com/matplotlib/matplotlib/pull/5451

So now it's as simple as

plt.pcolormesh(X,Y,Z.T)