Solved
The problem is that you want to do a matrix operation followed by a vectorized operation. i.e you want to multiply a 3x3 matrix by a 3x1 vector to get a 3x1 vector, and then you want to multiply that 3x1 vector by another 3x1 vector, element by element. You can't make that work by vectorizing it, because then (as Stuart notes) the first operation fails. You also can't make it work by not vectorizing it, because then you get a scalar answer, and the comparison fails. So the only way to do it is a two step process.
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