Check usage of volumes centres and edges, and make explicit their dimensions

[GilesStrong]

Volume.build_edges produces a tensor of corner coordinates for voxels in the volume, and Volume.centres is the centre coordinates of the each voxel. These are in (x,y,z) form. However in many locations in the code, e.g. during volume inference, or returning the voxel layer from volumes, the form is (z,x,y).

• We should check the code to make sure the tensors are permuted or reshaped correctly.
• We should improve the names and APIs to make it clearer to users and devs what shapes are expected/returned.