matplotlib surface plot hides scatter points which should be in front

Yet another question about matplotlib 3d surfaces… I have code which adds a scatter point to a matplotlib surface graph.

The problem that I have is that the point always appears behind the surface, regardless of which angle you view it from.

If I cobble an (admittedly ugly) version using 3 short lines to mark the same point, it is visible.

I have turned off the depthshade function, so it isn’t this. Can anybody explain what is going on and how I can correct it? Here is a simplified version of the code:

import pandas as pd
import matplotlib
import matplotlib.pyplot as plt
from mpl_toolkits.mplot3d import Axes3D
import numpy as np

df = pd.DataFrame({10: {10: 1,15: 1,20: 1,25: 1,30: 1,35: 1,40: 1,45: 1,50: 1,55: 1,60: 1,65: 1,70: 1,75: 1,80: 1,85: 1,90: 1},
                   15: {10: 4,15: 1,20: 1,25: 1,30: 1,35: 1,40: 1,45: 1,50: 1,55: 1,60: 1,65: 1,70: 1,75: 1,80: 1,85: 1,90: 1},
                   20: {10: 6,15: 3,20: 1,25: 1,30: 1,35: 1,40: 1,45: 1,50: 1,55: 1,60: 1,65: 1,70: 1,75: 1,80: 1,85: 1,90: 1},
                   25: {10: 7,15: 5,20: 3,25: 1,30: 1,35: 1,40: 1,45: 1,50: 1,55: 1,60: 1,65: 1,70: 1,75: 1,80: 1,85: 1,90: 1},
                   30: {10: 9,15: 6,20: 4,25: 3,30: 1,35: 1,40: 1,45: 1,50: 1,55: 1,60: 1,65: 1,70: 1,75: 1,80: 1,85: 1,90: 1},
                   35: {10: 10,15: 7,20: 5,25: 4,30: 2,35: 1,40: 1,45: 1,50: 1,55: 1,60: 1,65: 1,70: 1,75: 1,80: 1,85: 1,90: 1},
                   40: {10: 11,15: 8,20: 6,25: 4,30: 3,35: 2,40: 1,45: 1,50: 1,55: 1,60: 1,65: 1,70: 1,75: 1,80: 1,85: 1,90: 1},
                   45: {10: 12,15: 9,20: 7,25: 5,30: 4,35: 3,40: 2,45: 1,50: 1,55: 1,60: 1,65: 1,70: 1,75: 1,80: 1,85: 1,90: 1},
                   50: {10: 13,15: 9,20: 7,25: 6,30: 5,35: 4,40: 3,45: 2,50: 1,55: 1,60: 1,65: 1,70: 1,75: 1,80: 1,85: 1,90: 1},
                   55: {10: 14,15: 10,20: 8,25: 7,30: 5,35: 4,40: 3,45: 3,50: 2,55: 1,60: 1,65: 1,70: 1,75: 1,80: 1,85: 1,90: 1},
                   60: {10: 15,15: 11,20: 9,25: 7,30: 6,35: 5,40: 4,45: 3,50: 3,55: 2,60: 1,65: 1,70: 1,75: 1,80: 1,85: 1,90: 1},
                   65: {10: 16,15: 12,20: 9,25: 8,30: 6,35: 5,40: 5,45: 4,50: 3,55: 2,60: 2,65: 1,70: 1,75: 1,80: 1,85: 1,90: 1},
                   70: {10: 17,15: 12,20: 10,25: 8,30: 7,35: 6,40: 5,45: 4,50: 4,55: 3,60: 2,65: 2,70: 1,75: 1,80: 1,85: 1,90: 1},
                   75: {10: 18,15: 13,20: 10,25: 9,30: 7,35: 6,40: 5,45: 5,50: 4,55: 3,60: 3,65: 2,70: 2,75: 1,80: 1,85: 1,90: 1},
                   80: {10: 19,15: 14,20: 11,25: 9,30: 8,35: 7,40: 6,45: 5,50: 4,55: 4,60: 3,65: 3,70: 2,75: 2,80: 1,85: 1,90: 1},
                   85: {10: 21,15: 14,20: 11,25: 10,30: 8,35: 7,40: 6,45: 6,50: 5,55: 4,60: 4,65: 3,70: 3,75: 2,80: 2,85: 1,90: 1},
                   90: {10: 23,15: 15,20: 12,25: 10,30: 9,35: 8,40: 7,45: 6,50: 5,55: 5,60: 4,65: 3,70: 3,75: 3,80: 2,85: 2,90: 1}})




xv, yv = np.meshgrid(df.index, df.columns)
ma = np.nanmax(df.values)
norm = matplotlib.colors.Normalize(vmin = 0, vmax = ma, clip = True)

fig = plt.figure(1)
ax = Axes3D(fig)
surf = ax.plot_surface(yv,xv,df, cmap='viridis_r', linewidth=0.3,
                       alpha = 0.8, edgecolor = 'k', norm=norm)
ax.scatter(25,35,4, c='k', depthshade=False, alpha = 1, s=100)

fig = plt.figure(2)
ax = Axes3D(fig)
surf = ax.plot_surface(yv,xv,df, cmap='viridis_r', linewidth=0.3,
                       alpha = 0.8, edgecolor = 'k', norm=norm)
line1_x = [25,25]
line1_y = [35,35]
line1_z = [3,5]

line2_x = [25,25]
line2_y = [33,37]
line2_z = [4,4]

line3_x = [23,27]
line3_y = [35,35]
line3_z = [4,4]

ax.plot(line1_x, line1_y, line1_z, alpha = 1, linewidth = 1, color='k')
ax.plot(line2_x, line2_y, line2_z, alpha = 1, linewidth = 1, color='k')
ax.plot(line3_x, line3_y, line3_z, alpha = 1, linewidth = 1, color='k')
plt.show()

Answer

OK, so as per the comment by Mr T above, there doesn’t seem to be a direct method of dealing with this. There is however, a workaround for what I’m trying to do (highlight specific points on the surface). Using the matplotlib.patches and mpl_toolkits.mplot3d.art3d modules, it is possible to plot a circle on the graph at the appropriate point, and this appears to be unaffected by the same issue.

The modified code is:

import pandas as pd
import matplotlib
import matplotlib.pyplot as plt
from mpl_toolkits.mplot3d import Axes3D, art3d
from matplotlib.patches import Circle
import numpy as np

df = pd.DataFrame({10: {10: 1,15: 1,20: 1,25: 1,30: 1,35: 1,40: 1,45: 1,50: 1,55: 1,60: 1,65: 1,70: 1,75: 1,80: 1,85: 1,90: 1},
                   15: {10: 4,15: 1,20: 1,25: 1,30: 1,35: 1,40: 1,45: 1,50: 1,55: 1,60: 1,65: 1,70: 1,75: 1,80: 1,85: 1,90: 1},
                   20: {10: 6,15: 3,20: 1,25: 1,30: 1,35: 1,40: 1,45: 1,50: 1,55: 1,60: 1,65: 1,70: 1,75: 1,80: 1,85: 1,90: 1},
                   25: {10: 7,15: 5,20: 3,25: 1,30: 1,35: 1,40: 1,45: 1,50: 1,55: 1,60: 1,65: 1,70: 1,75: 1,80: 1,85: 1,90: 1},
                   30: {10: 9,15: 6,20: 4,25: 3,30: 1,35: 1,40: 1,45: 1,50: 1,55: 1,60: 1,65: 1,70: 1,75: 1,80: 1,85: 1,90: 1},
                   35: {10: 10,15: 7,20: 5,25: 4,30: 2,35: 1,40: 1,45: 1,50: 1,55: 1,60: 1,65: 1,70: 1,75: 1,80: 1,85: 1,90: 1},
                   40: {10: 11,15: 8,20: 6,25: 4,30: 3,35: 2,40: 1,45: 1,50: 1,55: 1,60: 1,65: 1,70: 1,75: 1,80: 1,85: 1,90: 1},
                   45: {10: 12,15: 9,20: 7,25: 5,30: 4,35: 3,40: 2,45: 1,50: 1,55: 1,60: 1,65: 1,70: 1,75: 1,80: 1,85: 1,90: 1},
                   50: {10: 13,15: 9,20: 7,25: 6,30: 5,35: 4,40: 3,45: 2,50: 1,55: 1,60: 1,65: 1,70: 1,75: 1,80: 1,85: 1,90: 1},
                   55: {10: 14,15: 10,20: 8,25: 7,30: 5,35: 4,40: 3,45: 3,50: 2,55: 1,60: 1,65: 1,70: 1,75: 1,80: 1,85: 1,90: 1},
                   60: {10: 15,15: 11,20: 9,25: 7,30: 6,35: 5,40: 4,45: 3,50: 3,55: 2,60: 1,65: 1,70: 1,75: 1,80: 1,85: 1,90: 1},
                   65: {10: 16,15: 12,20: 9,25: 8,30: 6,35: 5,40: 5,45: 4,50: 3,55: 2,60: 2,65: 1,70: 1,75: 1,80: 1,85: 1,90: 1},
                   70: {10: 17,15: 12,20: 10,25: 8,30: 7,35: 6,40: 5,45: 4,50: 4,55: 3,60: 2,65: 2,70: 1,75: 1,80: 1,85: 1,90: 1},
                   75: {10: 18,15: 13,20: 10,25: 9,30: 7,35: 6,40: 5,45: 5,50: 4,55: 3,60: 3,65: 2,70: 2,75: 1,80: 1,85: 1,90: 1},
                   80: {10: 19,15: 14,20: 11,25: 9,30: 8,35: 7,40: 6,45: 5,50: 4,55: 4,60: 3,65: 3,70: 2,75: 2,80: 1,85: 1,90: 1},
                   85: {10: 21,15: 14,20: 11,25: 10,30: 8,35: 7,40: 6,45: 6,50: 5,55: 4,60: 4,65: 3,70: 3,75: 2,80: 2,85: 1,90: 1},
                   90: {10: 23,15: 15,20: 12,25: 10,30: 9,35: 8,40: 7,45: 6,50: 5,55: 5,60: 4,65: 3,70: 3,75: 3,80: 2,85: 2,90: 1}})




xv, yv = np.meshgrid(df.index, df.columns)
ma = np.nanmax(df.values)
norm = matplotlib.colors.Normalize(vmin = 0, vmax = ma, clip = True)

fig = plt.figure(1)
ax = Axes3D(fig)
surf = ax.plot_surface(yv,xv,df, cmap='viridis_r', linewidth=0.3,
                       alpha = 0.8, edgecolor = 'k', norm=norm)

p = Circle((25, 35), 3, ec='k', fc="none")
ax.add_patch(p)
art3d.pathpatch_2d_to_3d(p, z=4, zdir="z")

plt.show()