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Imagine I have an outer shape and an inner shape (that may overlap like the following picture)

My pic

Is there any algorithm or mathematical property I can use to find a third set of points which will be in the middle of the two?

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    You could plot the locus of points whose distance from the two curves is equal. However, this may require some cleanup where the curves intersect: http://i.stack.imgur.com/mNjBD.png –  Jun 02 '13 at 20:53
  • Are your two sets of points indexed in the same way? That is, do you have Red1, Red2, Red3... and corresponding Green1, Green2, Green3? If so, then the simple averaging (Red1+Green1)/2, (Red2+Green2)/2... may be enough. – ˈjuː.zɚ79365 Jun 04 '13 at 00:53

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