Refactor Point3f to simply array

[tischi]

The current code contains unnecessary Point3f java objects, which make it overly complicated.
Would be much simpler to have 3D arrays.
For example, code like below could be replaced by loops or even on-liners:

    minx = min(minx, shift.x)
    miny = min(miny, shift.y)
    minz = min(minz, shift.z)