Replace Point3D with something which supports arithmetic

[d-perl]

Currently Point3D is a NamedTuple which is sort of fine, but we have to do stuff like:

corrected_centre = Point3D(xray_centre.x - 0.5, xray_centre.y - 0.5, xray_centre.z - 0.5)

instead of being able to just subtract (0.5, 0.5, 0.5).

If we ever need to do more arithmetic with vectors/coordinates then we should replace this with a more robust class, potentially a simple homemade one which can just add/subtract/multiply/divide, but ideally with one from a well-maintained module which supports distances, angles and whatnot, and might be a bit optimised.

[DominicOram]

Use numpy and get rid of names of x, y, z.

[d-perl]

Maybe this is a good issue for @olliesilvester , it's not extremely complicated, but it touches lots of areas of the code, what do you think @DominicOram ?

[DominicOram]

Yep, sounds good