[NeXus-committee] Additions to NeXus

Wed May 11 15:41:16 BST 2016

We have defined the stokes parameters for NXmx, but I missed porting that back into NXbeam.

The manual says:

incident_polarisation_stokes[np, 4]: NX_CHAR<http://download.nexusformat.org/sphinx/nxdl-types.html#nx-char>

If there are not np values for each of the np images, it’s either an average or a one-off number. I’m not sure we need two fields.

But getting that into NXbeam was the plan after the acceptance of NXmx. But tracking that is a manual thing and it got dropped.

Tobias

P.S. I “invented” the use of NXbeam in NXsample for NXmx, so my side in that discussion should be obvious.

From: NeXus-committee <nexus-committee-bounces at nexusformat.org<mailto:nexus-committee-bounces at nexusformat.org>> on behalf of Herbert Bernstein <yayahjb at gmail.com<mailto:yayahjb at gmail.com>>
Date: Wednesday, 11 May 2016 at 16:31
To: Benjamin Watts <Benjamin.Watts at psi.ch<mailto:Benjamin.Watts at psi.ch>>
Cc: "nexus-committee at nexusformat.org<mailto:nexus-committee at nexusformat.org>" <nexus-committee at nexusformat.org<mailto:nexus-committee at nexusformat.org>>
Subject: Re: [NeXus-committee] Additions to NeXus

Dear Ben,

  The two-component polarization has been customary in MX work for many years, but you are absolutely right that a full Stokes vector would make the most sense.  I would suggest two versions:

/incident_polarisation_stokes_average=[SVECI,SVECQ,SVECU,SVECV]

     @units="Watts/meter^2"

 /incident_polarisation_stokes=[STOKESI,STOKESQ,STOKESU,STOKESV]

       @units="Watts/meter^2"

So that we can carry frame-by-frame polarization if we have it, or just
the average if we don't.

On Wed, May 11, 2016 at 9:09 AM, Benjamin Watts <benjamin.watts at psi.ch<mailto:benjamin.watts at psi.ch>> wrote:
Hi Everyone,
   I'm going to agree with Eugen that it makes sense for NXbeam to be a child of NXsample as it implies that the beam is described at the position of the sample. If there are multiple sources as Pete described, then they can be differentiated by the name of the NXbeam group being "pump" and "probe".

* It would also be useful to better specify the "polarisation vector" for 'incident_polarization' and 'final_polarization' - I don't understand what this 2-component vector is supposed to be. I would suggest we use a Stokes vector.
* The 'i' and 'j' symbols seems inconsistent on http://download.nexusformat.org/sphinx/classes/base_classes/NXbeam.html Perhaps it is supposed to allow multiple incoming and outgoing beams, but it got messed up along the way.

Cheers,
Ben

On 11/05/16 14:50, Eugen Wintersberger wrote:
Hi Pete

On 05/11/16 13:33, Pete Jemian wrote:

The source is definitely a part of the instrument, not something at the top
level of the experiment (NXentry). Consider the case of a synchrotron X-ray
experiment with a laser pump.  There are two sources to be documented.
They both belong under the description of the pump/probe instrument.

Why should the beam be part of the sample? Makes no sense at all.  The
sample has no beam.  The beam does not describe the sample in any useful
way.  NXbeam documents the state of the beam at some position along the
path from source to detector.  It could go in many places along the optical
path.

Besides the fact that NXbeam is mentioned as a possible child for NXsample
it makes perfect sense there too.
If you have many optical components in your beam path and one is mainly interested in the
beam paramters in front of the sample NXbeam within NXsample would be my
first approach to document these parameters.

regards
  Eugen

Pete
On May 11, 2016 6:17 AM, "Andreas Förster" <andreas.foerster at dectris.com><mailto:andreas.foerster at dectris.com>
wrote:

Dear NeXus folks,

there was a little discussion last week about possible additions to the
NeXus standard (and NXmx) to record beam information relevant for the
estimation of dose.  Herbert proposed a good solution, but the outcome of
this discussion is still pending.

At DECTRIS, we're keen to tell our customers how to record additional
metadata in a NeXus-compliant way.  That's why I'd like to have official
word on the fields below:

Information on the synchrotron should be recorded in an NX_Source group.
Is /entry/source the right place for that?

     /entry/source *NX_SOURCE*
<http://download.nexusformat.org/sphinx/classes/base_classes/NXsource.html><http://download.nexusformat.org/sphinx/classes/base_classes/NXsource.html>

o   *name*: *NX_CHAR*
<http://download.nexusformat.org/sphinx/nxdl-types.html#nx-char><http://download.nexusformat.org/sphinx/nxdl-types.html#nx-char>

§  Name of synchrotron

o   *@short_name*: *NX_CHAR*
<http://download.nexusformat.org/sphinx/nxdl-types.html#nx-char><http://download.nexusformat.org/sphinx/nxdl-types.html#nx-char>

§  short name for source, perhaps the acronym
Data describing the beam as it hits the sample should probably go the
NX_Beam group in /entry/sample/beam.  None of the fields below are
currently defined.  Could these definitions be adopted?

·      /entry/sample/beam *NX_BEAM*
<http://download.nexusformat.org/sphinx/classes/base_classes/NXbeam.html><http://download.nexusformat.org/sphinx/classes/base_classes/NXbeam.html>

o   *name*: *NX_CHAR*
<http://download.nexusformat.org/sphinx/nxdl-types.html#nx-char><http://download.nexusformat.org/sphinx/nxdl-types.html#nx-char>

§  Name of beamline

o   *total_flux/xray_flux*: *NX_FLOAT*
<http://download.nexusformat.org/sphinx/nxdl-types.html#nx-float><http://download.nexusformat.org/sphinx/nxdl-types.html#nx-float> {units=
*NX_RATE* <http://download.nexusformat.org/sphinx/nxdl-types.html#nx-rate><http://download.nexusformat.org/sphinx/nxdl-types.html#nx-rate>
}

§  Beam intensity (example: s-1)

o   *incident_beam_size: **NX_FLOAT*
<http://download.nexusformat.org/sphinx/nxdl-types.html#nx-float><http://download.nexusformat.org/sphinx/nxdl-types.html#nx-float>*[2]*

§  Two-dimensional array of FWHM (if Gaussian) or diameters (if top hat)
of beam

o   *profile*: *NX_CHAR*
<http://download.nexusformat.org/sphinx/nxdl-types.html#nx-char><http://download.nexusformat.org/sphinx/nxdl-types.html#nx-char>

§  Gaussian or top hat

Should the name of the beamline be recorded in beam or in source?  For the
flux (as a rate - in contrast to the already existing flux density field
"flux"), either name is fine by me.

I'm happy to discuss these points during the next NeXus meeting.

Thank you and all best

Andreas

--
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Andreas Förster, Ph.D.
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