dials.refine does not write out the refined orientation of a multi-axis goniometer

[dagewa]

          This code illustrates the problem

>>> from dxtbx.model import ExperimentList
>>> el=ExperimentList.from_file("imported.expt")
>>> gonio=el[0].goniometer
>>> type(gonio)
<class 'dxtbx_model_ext.MultiAxisGoniometer'>
>>> gonio.get_rotation_axis()
(0.0, -1.0, 0.0)
>>> gonio.set_rotation_axis((1,0,0))
>>> gonio.get_rotation_axis()
(1.0, 0.0, 0.0)
>>> el.as_file("modified.expt")
>>> el2=ExperimentList.from_file("modified.expt")
>>> gonio2=el2[0].goniometer
>>> gonio2.get_rotation_axis()
(0.0, -1.0, 0.0)

Clearly set_rotation_axis does not "stick" for a MultiAxisGoniometer (in which case, perhaps it should raise an error). Now I need to figure out how to set the rotation axis in this case. The way dials.refine does it is to modify the setting matrix only. Perhaps that is the correct way?

Originally posted by @dagewa in #2656 (comment)

[dagewa]

summary: dials.refine parameterises the setting matrix of a goniometer. For a multi-axis goniometer, this is not primary information but is derived from definitions of the axes and angles. During refinement, dials.refine appears to modify the model, but once the result is written out these modifications are lost.

NB this is an unsual case - we do not usually refine the orientation of the rotation axis. It just affects those rare situations where we do want to do this