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Great idea to include the current commit in figures and so on. How about putting it up on GitHub?
Very nice idea, never thought about these color perception issues.
There is a small bug in pmkmp.m with my version of MATLAB (220.127.116.114 (R2013a)). When using the edge colormap and n values around 100 (e.g. 128 or 64) I get
Error using colormap (line 99)
Colormap must have values in [0,1].
I think this is due to interp1 returning negative values under these circumstances.