[Nexus] Polarisation

[yayahjb]

For what it is worth, for CBF we have (so far) gone through two 
2-parameter polarization definitions.  The second set (from Harry 
Powell) has proven more useful than the first, and is a possibility to 
consider for the current 2-parameter NXbeam definitions.  However, I 
think Tobias is right that it would make a lot of sense to support the 
four Stokes parameters as well (see  
http://en.wikipedia.org/wiki/Stokes_parameters)
To avoid confusion, I would suggest deprecating

incident_polarization and final_polarization or defauting them to the 
popular Denzo definitions

and having 4 new alternate fields

incident_polarization_Denzo:NX_FLOAT[i,2]  (in the order norm, then ratio)
final_polarization_Denzo:NX_FLOAT[i,2]  (in the order norm, then ratio)
incident_polarization_Stokes:NX_FLOAT[i,4] (in the order I, Q, U, V)
final_polarization_Stokes:NX_FLOAT[i,4] (in the order I, Q, U, V)

The first pair two will make the most sense to a crystallographer and 
the second pair will
make the most sense to a physicist.

I think Tobias is right about transposing the arrays so that the slow 
index is beamline component

The 2-parameter polarizations in CBF are:

The first pair we started with was:

_diffrn_radiation.polarisn_norm
     The angle in degrees, as viewed from the specimen, between the 
perpendicular component of the polarization and the diffraction
_diffrn_radiation_polarisn_ratio.
     Polarization ratio of the diffraction beam incident on the crystal. 
This is the ratio of the perpendicularly polarized to the parallel 
polarized component of the radiation. The perpendicular component forms 
an angle of  _diffrn_radiation.polarisn_norm to the normal to the 
diffraction plane of the sample (i.e. the plane containing the incident 
and reflected beams).


The second pair we got from Harry Powell (who works on mosflm, but who 
was also thinking
of ease of support for all crystallographic data processing) was:

_diffrn_radiation.polarizn_source_norm
     The angle in degrees, as viewed from the specimen, between the 
normal to the polarization plane and the laboratory Y axis as defined in 
the AXIS category.  Note that this is the angle of polarization of the 
source  photons, either directly from a synchrotron beamline or from a 
monochromater.  This differs from the value of 
_diffrn_radiation.polarisn_norm in that _diffrn_radiation.polarisn_norm 
refers to polarization relative to the diffraction plane rather than to 
the laboratory axis system.   In the case of an unpolarized beam, or a 
beam with true circular polarization, in which no single plane of 
polarization can be determined, the plane should be taken as the XZ 
plane and the angle as 0.

_diffrn_radiation.polarizn_source_ratio.
     (Ip-In)/(Ip+In), where Ip is the intensity amplitude squared) of 
the electric vector in the plane of polarization and In is the intensity 
(amplitude squared) of the electric vector in the plane of the normal to 
the plane of polarization.  In the case of an unpolarized beam, or a 
beam with true circular polarization, in which no single plane of 
polarization can be determined, the plane is to be taken as the XZ plane 
and the normal is parallel to the Y axis.   Thus, if there was complete 
polarization in the plane of polarization, the value of  
_diffrn_radiation.polarizn_source_ratio would be 1, and for an 
unpolarized beam _diffrn_radiation.polarizn_source_ratio would have a 
value of 0.
     If the X axis has been chosen to lie in the plane of  polarization, 
this definition will agree with the definition of 'MONOCHROMATOR' in the 
Denzo glossary, and values of near 1 should be expected for a 
bending-magnet source.  However, if the X axis were perpendicular to the 
polarization plane (not a common choice), then the Denzo value would be 
the negative of _diffrn_radiation.polarizn_source_ratio.
See http://www.hkl-xray.com for information on Denzo and Otwinowski & 
Minor (1997).
     This differs both in the choice of ratio and choice of orientation 
from _diffrn_radiation.polarisn_ratio, which,  unlike 
_diffrn_radiation.polarizn_source_ratio, is unbounded.
      Reference: Otwinowski, Z. & Minor, W. (1997). 'Processing of X-ray 
diffraction data collected in oscillation mode.' Methods Enzymol. 276, 
307-326.



On 4/22/13 9:01 AM, Tobias.Richter at diamond.ac.uk wrote:
> Hi all,
>
> I am meeting some unexpected problems recording the polarisation of the incoming beam.
> All I could find is in NXbeam:
>
>        final_polarization:NX_FLOAT[2,j]
>        incident_polarization:NX_FLOAT[2,j]
>
> There is no further clue about either the 2 or what j is. The values are float and units are NX_ANY. Hmm?
>
> In any case I guess I would struggle to record circular polarisation in this scheme. Or is someone up for the challenge to explain that to me.
>
> The most natural feeling thing for someone with a vague optical background (reda: me) would be to use the 4 Stokes parameters.
>
> So I assume I propose to change that 2 to 4 (optionally) in the existing NXbeam.
> I'd prefer a [j,4] (transposed) array for these values.
>
> Leaves the question what j is. There is an i index sprinkled into that class as well, but I am not sure how they are supposed to line up. Any one?
>
> Regards,
>
> Tobias
>
>