You have it slightly wrong. You make it sound like there are only 9 focus points. When in fact it can post process focus at any point. It just needs to bundle the pixels (rays) that coincide with a synthetic lens that is focused at that point. The math is easy ... but it is still very important to think of the rays through a thin lens.

It might be helpful to watch this: http://www.youtube.com/watch?v=9H7yx31yslM

You might also want to read about the heterodyning camera. It does the same thing as a plenoptic camera but with a large aperture and a cosine filter.