I have an array with np.nan values which I want to plot using pcolor. In principle everything works, but I get a warning I cannot get rid of. Using plt.imshow does not give the warning, but I need to specify the x and y coordinates.
MatplotlibDeprecationWarning: Getting the array from a PolyQuadMesh will return the full array in the future (uncompressed). To get this behavior now set the PolyQuadMesh with a 2D array .set_array(data2d).
import numpy as np
import matplotlib as mpl
import matplotlib.pyplot as plt
x = np.linspace(-2,2,100)
y = np.linspace(-2,2,100)
X, Y = np.meshgrid(x,y)
X[X**2+Y**2>4] = np.nan
Y[X**2+Y**2>4] = np.nan
Z = np.exp(-(X**2+Y**2))
plt.pcolor(Y,X,Z, cmap='viridis')
plt.colorbar()
I use matplotlib v3.9.2 and numpy v1.26.4.
This warning is due to a change in how the internal pcolor logic is structured (changenote here). It is triggered when the colorbar code internally calls get_array on the object returned by pcolor. You can silence the warning by explicitly re-passing your Z array to the set_array method:
pc = plt.pcolor(Y,X,Z, cmap='viridis')
pc.set_array(Z)
plt.colorbar()
Alternatively, you could upgrade your Matplotlib to version 3.10+, since this deprecation is now expired.