Just a quick note - the last script in my previous email is wrong. I don't
get the problem in that case, I get it if the arrays are 32-bit:

import matplotlib.pyplot as mpl

import numpy as np

np.random.seed(-12421412)

x = np.random.random(10000).astype(np.float32)
y = np.random.random(10000).astype(np.float32)
c = np.random.random(10000).astype(np.float32)

fig = mpl.figure()
ax = fig.add_subplot(111)
ax.scatter(x,y,c=c,alpha=0.01,cmap=mpl.cm.jet)
fig.canvas.draw()

which explains why there is probably some small numerical inaccuracy in
deciding whether the color value is above the maximum of the range (if the
latter is calculated in 64-bit). However, the question of why alpha gets set
to 1 for color values above the maximum still holds.

Tom
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