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Is there a package out there that can compute the Earth Mover's Distance on two 3D grid inputs? Barring that, is there some example code or algorithm description for computing it efficiently?

A: 

There's an implementation in in OpenCV. There's a section on EMD halfway down.:

http://www.seas.upenn.edu/~bensapp/opencvdocs/ref/opencvref_cv.htm

Scott P