Python color map but with all zero values mapped to black

Question

I have a square array of elements which correspond to lattice sites. Some of the elements are zero and the rest vary between 1 and about 2700. Using imshow and the OrRd colo

Answer 1

The colormaps of Matplotlib have a set_bad and set_under property which can be used for this. This example shows how to use the set_bad

import matplotlib.pyplot as plt
import numpy as np

# make some data
a = np.random.randn(10,10)

# mask some 'bad' data, in your case you would have: data == 0
a = np.ma.masked_where(a < 0.05, a)

cmap = plt.cm.OrRd
cmap.set_bad(color='black')

plt.imshow(a, interpolation='none', cmap=cmap)

To use the set_under variant you have to add the vmin keyword to the plotting command and setting is slightly above zero (but below any other valid value):

cmap.set_under(color='black')    
plt.imshow(a, interpolation='none', cmap=cmap, vmin=0.0000001)