Matplotlib plot_surface transparency artefact

Question

I'm trying to plot a surface in 3D from a set of data which specifies the z-values. I get some weird transparency artefact though, where I can see through the surface, even though I set alpha=1.0.

The artefact is present both when plotting and when saved to file (both as png and pdf):

I have tried changing the line width, and changing the number of strides from 1 to 10 (in the latter case, the surface is not visible though due to too rough resolution).

Q: How can I get rid of this transparency?

Here is my code:

import sys
import numpy as np
import numpy.ma as ma
import matplotlib as mpl
import matplotlib.pyplot as plt
from mpl_toolkits.mplot3d import Axes3D

y_label = r'x'
x_label = r'y'
z_label = r'z'

x_scale = 2.0*np.pi
y_scale = 2.0*np.pi

y_numPoints = 250
x_numPoints = 250

def quasiCrystal(x, y):
    z = 0
    for i in range(0,5):
        z += np.sin(x * np.cos(float(i)*np.pi/5.0) +
                    y * np.sin(float(i)*np.pi/5.0))
    return z

x = np.linspace(-x_scale, x_scale, x_numPoints)
y = np.linspace(-y_scale, y_scale, y_numPoints)
X,Y = np.meshgrid(x,y)

Z = quasiCrystal(X, Y)


f = plt.figure()
ax = f.gca(projection='3d')

surf = ax.plot_surface( X, Y, Z,
                        rstride=5, cstride=5,
                        cmap='seismic',
                        alpha=1,
                        linewidth=0,
                        antialiased=True,
                        vmin=np.min(Z),
                        vmax=np.max(Z)
                      )

ax.set_zlim3d(np.min(Z), np.max(Z))

f.colorbar(surf, label=z_label)

ax.set_xlabel(x_label)
ax.set_ylabel(y_label)
ax.set_zlabel(z_label)

plt.show()

Here is another picture of my actual data where it is easier to see the artefact:

Answer 1

Matplotlib is not a "real" 3D engine. This is a very well known problem and once in a while a similar question to yours appears appears (see this and this). The problem is that the same artefact can originate problems that seem to be different. I believe such is the case for you.

Before going on with my recommendations let me just quote this information from the maplotlib website:

My 3D plot doesn’t look right at certain viewing angles

This is probably the most commonly reported issue with mplot3d. The problem is that – from some viewing angles – a 3D object would appear in front of another object, even though it is physically behind it. This can result in plots that do not look “physically correct.”

Unfortunately, while some work is being done to reduce the occurance of this artifact, it is currently an intractable problem, and can not be fully solved until matplotlib supports 3D graphics rendering at its core.

The problem occurs due to the reduction of 3D data down to 2D + z-order scalar. A single value represents the 3rd dimension for all parts of 3D objects in a collection. Therefore, when the bounding boxes of two collections intersect, it becomes possible for this artifact to occur. Furthermore, the intersection of two 3D objects (such as polygons or patches) can not be rendered properly in matplotlib’s 2D rendering engine.

This problem will likely not be solved until OpenGL support is added to all of the backends (patches are greatly welcomed). Until then, if you need complex 3D scenes, we recommend using MayaVi.

It seems that Mayavi has finally moved on to Python 3, so its certainly a possibility. If you want to stick with matplotlib for this kind of plot my advice is that you work with rstride and cstride values to see which ones produce a plot satisfactory to you.

surf = ax.plot_surface( X, Y, Z,
                        rstride=5, cstride=5,
                        cmap='jet',
                        alpha=1,
                        linewidth=0,
                        antialiased=True,
                        vmin=0,
                        rstride=10,
                        cstride=10,
                        vmax=z_scale
                      )

Other possibility is to try to see if other kinds of 3D plots do better. Check plot_trisurf, contour or contourf. I know its not ideal but in the past I also managed to circumvent other type of artefacts using 3D polygons.

Sorry for not having a more satisfactory answer. Perhaps other SO users have better solutions for this. Best of luck.

Answer 2

I ran into some similar issues and found that they were antialiasing artifacts and could be fixed by setting antialiased=False in plot_surface.