How can I plot NaN values as a special color with imshow in matplotlib?

Question

I am trying to use imshow in matplotlib to plot data as a heatmap, but some of the values are NaNs. I'd like the NaNs to be rendered as a special color not found in the colormap.

example:

import numpy as np import matplotlib.pyplot as plt f = plt.figure() ax = f.add_subplot(111) a = np.arange(25).reshape((5,5)).astype(float) a[3,:] = np.nan ax.imshow(a, interpolation='nearest') f.canvas.draw() 

The resultant image is unexpectedly all blue (the lowest color in the jet colormap). However, if I do the plotting like this:

ax.imshow(a, interpolation='nearest', vmin=0, vmax=24) 

--then I get something better, but the NaN values are drawn the same color as vmin... Is there a graceful way that I can set NaNs to be drawn with a special color (eg: gray or transparent)?

Answer 1

Hrm, it appears I can use a masked array to do this:

masked_array = np.ma.array (a, mask=np.isnan(a)) cmap = matplotlib.cm.jet cmap.set_bad('white',1.) ax.imshow(masked_array, interpolation='nearest', cmap=cmap) 

This should suffice, though I'm still open to suggestions. :]