So the quality of the image changes after you use that fix. It looks like the alpha gets messed up after that.
I have created two images to show the difference. How do I put those images up ?

@WeatherGod : I have mailed you the Images

That isn't a "quality" issue. The question is whether or not the alpha
values should be utilized to indicate depth (which is what the code was
originally supposed to do. In fact, I don't know why your "before" image
doesn't do this. What is your call to scatter?

self.ax = self.fig.gca(projection='3d')
self.ax.scatter(xs, ys, zs, c=c, marker='o', s=20)

ok... in any case, the behavior you had in the past is wrong and it appears that my patch inadvertently fixed it. Perhaps a kwarg could be passed into scatter() to force it to not modify the alpha values?

Cool. Thanks a lot for your help.