pythonarraysmatplotlibplotcolor-mapping

Python color map but with all zero values mapped to black


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 colour map, I want all lattice sites greater than 0 to display the corresponding colour but importantly, all sites with value 0 to be displayed as black. I have tried defining a new color map as follows:

colors = [(0,0,0)] + [(pylab.cm.OrRd(i)) for i in range(1,256)] 
new_map = matplotlib.colors.LinearSegmentedColormap.from_list('new_map', colors, N=256)

but the range of values in my array is too large and so a lot of non-zero values get displayed as black.

Many thanks.


Solution

  • 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
    
    # for mpl 3.3 and higher use
    cmap = mpl.cm.get_cmap("OrRd").copy()
    
    cmap.set_bad(color='black')
    
    im = plt.imshow(a, interpolation='none', cmap=cmap)
    

    enter image description here

    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')    
    im = plt.imshow(a, interpolation='none', cmap=cmap, vmin=0.0000001)