Why is part of my contour plot showing white?

Question

I am using Python's matplotlib.pyplot.contourf to create a contour plot of my data with a color bar. I have done this successfully countless times, even with other layers of the same variable. However, when the values get small (on the order of 1E-12), parts of the contour show up white. The white color does not show up in the color bar either. Does anyone know what causes this and how to fix this? The faulty contour is attached below.

a1 = plt.contourf(np.linspace(1,24,24),np.linspace(1,20,20),np.transpose(data[:,:,15]))
plt.colorbar(a1)
plt.show()

Answer 1

tl;dr

Given the new information, matplotlib couldn't set the right number of levels (see parameters in the documentation) for your data leaving data unplotted. To fix that you need to tell matplotlib to extend the limits with either plt.contourf(..., extend="max") or plt.contourf(..., extend="both")

Extensive answer

There are a few reasons why contourf() is showing white zones with a colormap that doesn't include white.

NaN values

NaN values are never plotted.

Masked data

If you mask data before plotting, it won't appear in the plot. But you should know if you masked your data.

Although, you may have unnoticed mask your data if you use something like Tick locator = LogLocator().

Matplotlib couldn't set the right levels for your data

Sometimes matplotlib doesn't set the right levels, leaving some of your data without plotting.

To fix that you can user plt.contourf(..., extend=EXTENDS) where EXTENDS can be "neither", "both", "min", "max"

Coarse grid

contourf plots whitespace over finite data. Past answers do not correct

Answer 2

One remark, white section in the plot can also occur if the X and Y vectors data points are not equally spaced. In that case best to use function tricontourf().