Q:

drawing a line on a 3D plot in matplotlib

I have a 3D plot which looks quite similar to this one , but I want to add two lines drawn on the bottom contour plot. I would like the two lines to cross at and point to a particular (x,y) value.
I can draw a line there but it is always beneath the contour plot, despite my numerous attempts. Can anyone help me drawing the line on the contour plot? I am pasting my code below. The line is visible only in the part where it sticks out from the contour.
#!/usr/bin/env python

import sys, re, math
import matplotlib.pyplot as plt
from mpl_toolkits.mplot3d import Axes3D
from matplotlib.collections import LineCollection
from matplotlib import cm
from matplotlib.mlab import griddata
import numpy as np

x = []
y = []
z = []
for i in range(0,628,10) :
  for j in range(0,628,10) :
    x.append(i*0.01)
    y.append(j*0.01)
    z.append(math.sin(x[-1]*y[-1])*20)

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

xi = np.linspace(min(x), max(x))
yi = np.linspace(min(y), max(y))

X, Y = np.meshgrid(xi, yi)
Z = griddata(x, y, z, xi, yi)
ax.autoscale(False)
ax.view_init(elev=30, azim=-140)

surf = ax.plot_surface(X, Y, Z, rstride=1, cstride=1, cmap=cm.cool,
               linewidth=0.1, antialiased=True, shade=True,alpha=0.8)
cset = ax.contourf(X, Y, Z, zdir='z', offset=-100, cmap=cm.cool, cstride=1,
        linewidth=0.1, antialiased=True, shade=True)

ax.set_xlim3d(0, math.pi*2)
ax.set_ylim3d(0, math.pi*2)
ax.set_zlim3d(-100, 20)

xi = [0,6]
yi = [3,3]
l=zip(xi,yi)
lines = LineCollection((l,l),zorder=10000,color='k')
ax.add_collection3d(lines,zs=-90)

plt.show()

A:

Because Axe3D will calculate the zorder attribute for every 3d object by 3d projection. To disable this you can create a FixZorderCollection class and change the 3d line's __class__ attribute. Here is a full example:
import sys, re, math
import matplotlib.pyplot as plt
from mpl_toolkits.mplot3d import Axes3D
from matplotlib.collections import LineCollection
from matplotlib import cm
from matplotlib.mlab import griddata
import numpy as np

x = []
y = []
z = []
for i in range(0,628,10) :
  for j in range(0,628,10) :
    x.append(i*0.01)
    y.append(j*0.01)
    z.append(math.sin(x[-1]*y[-1])*20)

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

xi = np.linspace(min(x), max(x))
yi = np.linspace(min(y), max(y))

X, Y = np.meshgrid(xi, yi)
Z = griddata(x, y, z, xi, yi)
ax.autoscale(False)
ax.view_init(elev=30, azim=-140)

surf = ax.plot_surface(X, Y, Z, rstride=1, cstride=1, cmap=cm.cool,
               linewidth=0.1, antialiased=True, shade=True,alpha=0.8)
cset = ax.contourf(X, Y, Z, zdir='z', offset=-100, cmap=cm.cool, cstride=1,
        linewidth=0.1, antialiased=True, shade=True)

ax.set_xlim3d(0, math.pi*2)
ax.set_ylim3d(0, math.pi*2)
ax.set_zlim3d(-100, 20)

xi = [0,6]
yi = [3,3]
l=zip(xi,yi)
lines = LineCollection((l,l),zorder=1000,color='k',lw=3)
ax.add_collection3d(lines,zs=-90)

from mpl_toolkits.mplot3d.art3d import Line3DCollection

class FixZorderCollection(Line3DCollection):
    _zorder = 1000

    @property
    def zorder(self):
        return self._zorder

    @zorder.setter
    def zorder(self, value):
        pass

ax.collections[-1].__class__ = FixZorderCollection

plt.show()

output:

