Weighted phase Laplacian formula
A few points.  In your code, some of these render others irrelevant, but they may be relevant in other code you write:


Try to follow PEP8
It should be possible to vectorize ComputePhaseLaplacian.
It is better to loop over rows and columns directly rather than looping over indexes.  You can use enumerate to keep track of the rows and columns.  
You shouldn't flatten, you can index in two dimensions.
Instead of vstack, you should use pad in this case.
You create U and V, then immediately overwrite them.  This is redundant.
You should use ravel instead of flatten since it doesn't make a copy.