2D contour plot with NaN regions

[martyngigg]

How do 2D colour-fill plots with NaN regions look in matplolib?

Something like the output of an SofQW calculation would be a good test case.

[quantumsteve]

By default pcolormesh appears to plot NaN as the lowest value in the colormap

import matplotlib.pyplot as plt
import numpy as np

plt.rcParams['image.cmap'] = 'viridis'
plt.rcParams['figure.figsize'] = 10,10

# make these smaller to increase the resolution
dx, dy = 0.15, 0.05

# generate 2 2d grids for the x & y bounds
y, x = np.mgrid[slice(-3, 3 + dy, dy),
                slice(-3, 3 + dx, dx)]
z = (1 - x / 2. + x ** 5 + y ** 3) * np.exp(-x ** 2 - y ** 2)
#z[5,5] = float('nan')
# x and y are bounds, so z should be the value *inside* those bounds.
# Therefore, remove the last value from the z array.
z = z[:-1, :-1]
z_min, z_max = -np.abs(z).max(), np.abs(z).max()

plt.subplot(2, 1, 1)
plt.pcolormesh(x, y, z, vmin=z_min, vmax=z_max)
plt.title('pcolormesh')
# set the limits of the plot to the limits of the data
plt.axis([x.min(), x.max(), y.min(), y.max()])
plt.colorbar()

z[0:10,0:10] = float('NaN')

plt.subplot(2, 1, 2)
plt.pcolormesh(x, y, z, vmin=z_min, vmax=z_max)
plt.title('pcolormesh with NaN')
# set the limits of the plot to the limits of the data
plt.axis([x.min(), x.max(), y.min(), y.max()])
plt.colorbar()

plt.savefig('pcolormesh.png',dpi=400,bbox_inches='tight')

[NickDraper]

The colorbars in matplotlib appear to have specific values for over under and bad (masked). These include alpha to allow the area to be transparent.

From the Mantidplot.Color Docs: http://matplotlib.org/api/colors_api.html?highlight=color#module-matplotlib.colors

set_bad(color='k', alpha=None) Set color to be used for masked values.

set_over(color='k', alpha=None) Set color to be used for high out-of-range values. Requires norm.clip = False

set_under(color='k', alpha=None) Set color to be used for low out-of-range values. Requires norm.clip = False