fix: translation must take into account magnification

Otherwise pixel size and translation are into two different reference. Expected reference is the one of EBS-tomo (Bliss) like:

   |
   | z
   |
    ----------->
  /   x - beam
 /
/ y

Notes:

• as x is parallel to the beam magnification will have to effect to it.
• for EDF we don't have information regarding magnification. So this information must be given by the user (by editing the NXtomo output file)