Aliasing when saving matplotlib filled contour plot to .pdf or .eps

Question

I\'m generating a filed contour plot with the matplotlib.pyplot.contourf() function. The arguments in the call to the function are:

contourf(xvec,xvec,w,leve         


        

Answer 1

I had no idea that contouring in pdf was so bad. You're right, I think the contours are being anti-aliased by the PDF renderers outside of matplotlib. It is for this reason I think you need to be particularly careful which application you use to view the resulting PDF - the best behaviour I have seen is with GIMP, but I'm sure there are plenty of other viewers which perform well.

To fix this problem (when viewing the PDF with GIMP), I was able to "rasterize" the contours produced with matplotlib to avoid the ugly white line problem:

import matplotlib.pyplot as plt
import numpy as np


xs, ys = np.mgrid[0:30, 0:40]
data = (xs - 15) ** 2 + (ys - 20) ** 2 + (np.sin(ys) + 10) ** 2

cs = plt.contourf(xs, ys, data, 60, cmap='jet')

# Rasterize the contour collections
for c in cs.collections:
    c.set_rasterized(True)

plt.savefig('test.pdf')

This produced a contour plot which did not exhibit the problems you've shown.

Another alternative, perhaps better, approach, would be to fool the anti-aliasing by putting coloured lines below the contourf.

import matplotlib.pyplot as plt
import numpy as np


xs, ys = np.mgrid[0:30, 0:40]
data = (xs - 15) ** 2 + (ys - 20) ** 2 + (np.sin(ys) + 10) ** 2

# contour the plot first to remove any AA artifacts
plt.contour(xs, ys, data, 60, cmap='jet', lw=0.1)
cs = plt.contourf(xs, ys, data, 60, cmap='jet')

plt.savefig('test.pdf')

I should note that I don't see these problems if I save the figure as a ".ps" rather than a ".pdf" - perhaps that is a third alternative.

Hope this helps you get the paper looking exactly how you want it.

Answer 2

After using the useful answer by @pelson for a while, I finally found a proper solution to this long-standing problem (currently in Matplotlib 2.0), which does not require multiple calls to contour or rasterizing the figure.

I refer to my original answer here for a more extensive explanation and examples.

In summary, the solution consists of the following lines:

cnt = plt.contourf(x, y, z)

for c in cnt.collections:
    c.set_edgecolor("face")

plt.savefig('test.pdf')