Python matplotlib mask multiple (more than three) values using pcolormesh

Question

I would like to use matplotlibs pcolormesh and mask data (ie indicate with a special color not part of the chosen colormap) for more than 3 types of data in the colormap. As this example shows, it is clear how to do that for three types by using the three functions:

cmap.set_under('yellow')
cmap.set_over('cyan')
cmap.set_bad('blue')

But how can one do this for values that are 'not bad', not under or over a given range, but just deserve special attention eg for indicating the 'best values' (which are within a given range) in the data displayed as colormap. In terms of code: the indices_to_be_masked_with_another_color below shall be colored differently (not using a color from the colormap).

import matplotlib.pyplot as plt
import numpy as np
import copy

np.random.seed(0)
D = np.random.rand(12, 72)
D[4, :] = np.nan
D[6, 6] = np.nan
D[2, :] = np.linspace(0.4, 0.6, D[2, :].size)
D = np.ma.masked_invalid(D)
cmap = copy.copy(plt.get_cmap('bwr'))
cmap.set_bad(color = 'k', alpha = 1.)
cmap.set_under(color = 'cyan')
cmap.set_over(color = 'yellow')
xbin = np.linspace(0, 12, 13)
ybin = np.linspace(-90, 90, 73)

fig = plt.figure()
ax = fig.add_subplot(111)
pl = ax.pcolormesh(xbin, ybin, D.T, cmap = cmap, edgecolors = 'None',
                vmin = 0.1, vmax = 0.9)

indices_to_be_masked_with_another_color = np.where(np.abs(D - 0.5) < 0.1)
# what to do now?

plt.show()

All values in the third column should have a special color, eg green

Answer 1

You can do it with these lines:

import matplotlib.colors as colors

ind = (np.abs(D.T - 0.5) > 0.1)
new_D = np.ma.masked_array(D.T,mask=ind)
greenmap = colors.ListedColormap(['g'])
ax.pcolormesh(xbin,ybin,new_D,cmap=greenmap,edgecolors='None')

First, you don't need to use np.where , but instead create a new mask for those values that you don't want to be green.

Then you create a listed colormap (of just green) to use with pcolormesh

Finally, you use this masked array and new colormap to plot another pcolormesh on top of your other one.