Deformation array axis ordering

[EShalom]

Within mdreg the deformation array is currently an np.ndarray of shape (x, y, z, d, t) where d is the number of directions for the deformation vector (2 in 2D deformations, 3 in 3D).

Changing to (x, y, z, t, d) may make more sense conceptually, but this would be a breaking change and needs investigation into how feasible adjusting this convention is.