numpy - 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

## define data
npoints = 50
xreg = np.linspace(x.min(),x.max(),npoints)
yreg = np.linspace(y.min(),y.max(),npoints)
X,Y = np.meshgrid(xreg,yreg)
Z = spinterp.griddata(np.vstack((x,y)).T,z,(X,Y),
                      method='linear').reshape(X.shape)

## plot
plt.close()
ax = plt.axes()
col = ax.pcolormesh(X,Y,Z.T)
plt.draw()

My plot comes out blank, and I suspect it is because the method='linear' interpolation comes out with nans. I've tried converting to a masked array, but to no avail - plot is still blank. Can you tell me what I am doing wrong? Thanks.

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))