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Re: More thoughts on polarization, divergence, time-stamps in CBF
- To: imgcif-l@bnl.gov
- Subject: Re: More thoughts on polarization, divergence, time-stamps in CBF
- From: "I. David Brown" <idbrown@mcmail.cis.McMaster.CA>
- Date: Fri, 13 Oct 2000 09:50:25 -0400 (EDT)
- In-Reply-To: <Pine.OSF.3.95.1001013120853.511236B-100000@alf1.mrc-lmb.cam.ac.uk>
On Fri, 13 Oct 2000, Harry Powell wrote: > I've been thinking about this problem with the polarization. There is a version of imgCIF/CBF (0.7.0) that has almost completed its review by the Comcifs Dictionary Review Committee and is on the point of being forwarded for official Comcifs approval. The problems of reporting polarization are not trivial and and it would be a mistake to try to slip a poorly thought out set of items into version 0.7.0 before it is sent off for approval. I would recommend that we get version 0.7.0 on the books and treat the addition of polarization and collimation as something to be added once the topic has received the kind of in depth consideration it deserves. Examples of the kind of problems that need to be considered are given below. > However, I'm not at > all sure that collimation and polarization should be combined in one > item anyway. I definitely agree. > For the purpose of > processing diffraction images, it makes good sense to define the plane > explicitly in terms of the incident radiation beam and the raster > direction of the detector with highest precedence (any polarization > correction will be made with reference to the diffraction maximum's > position on the detector). The current version of imgCIF/CBF has a quite precise definition of the axis system to be used in describing the diffraction experiment based on the incident beam and the 'principal axis of the diffractometer'. The second direction is the tricky one to choose because the natural second direction depends on the kind of experiment that is being done. Not all detectors have raster directions. For many diffractometers, the scattering vector is the only direction that makes sense, but this direction is not defined for a 2-dimensional detector just as the raster direction is not defined for a point detector. The current imgCIF/CBF defines all other axes systems (including the rastering directions) in terms of this 'principal axis' system. Since the polarization is a function of the incident beam and not the detector, it would be a gross mistake to define polarization in terms of the detector axes however convenient it may be in some experiments. We should stay with the axis system already defined in imgCIF/CBF. > So, what I'd like to propose is that IUCr scrap its definition of > _diffrn_radiation_polarisn_ratio and use something more sensible, > e.g. the EBI definition, or even Stokes Parameters (which have other > advantages, and I think are very close to what Jim uses). > > At the same time, it makes good sense to get the spelling right > (that's polarize with a "Z" not polareese with an "S"...)! > > It makes sense to have a more flexible arrangement than the current > IUCr category (which doesn't have sub-items) and instead have > something which _does_ use category items, as much of the imgCIF/CBF > stuff does already. I agree. > If we have > > _diffrn_radiation_polarizn > > as a category, then we can have > > _diffrn_radiation_polarizn.ratio > _diffrn_radiation_polarizn.norm > _diffrn_radiation_polarizn.stokes_i > _diffrn_radiation_polarizn.stokes_q > _diffrn_radiation_polarizn.stokes_u > _diffrn_radiation_polarizn.stokes_v In order to proceed further with this idea it is necessary to see the full dictionary definitions. Only then will it be clear whether it makes sense to have the items *.ratio and *.norm etc. The principle is fine, its the details that need to be examined. > So there should be in the core CIF dictionary items like; > > _diffrn_source_divh > _diffrn_source_divv > > Where divh & divv refer to the horizontal and vertical divergences > with respect to the horizontal and vertical (more correct would be to > have them wrt primary and secondary precedence of the) raster > directions of the detector. Horizontal and vertical are horrible conventions. What happens when someone rotates the diffractometer (or source - not perhaps a synchrotron source) by 90 degrees in order to fit it into a tight corner in the beam hall? Again the divergence is a property of the source collimation not the detector and, as pointed out above, not every experiment has a raster axis system. The powder diffraction CIF dictionary has a number of items describing the divergence not only of the beam between the monochromator and the specimen, but between the source and monochromator, the specimen and analyser (analyzer?) and the analys/zer and the detector. These definitions are unsatisfactory as the axis system is defined with respect to the incident and diffracted beams. It is clear that if the core is to contain this kind of information it has to be applicable to all kinds of diffraction experiment (even those we have not yet thought up :-)). > In my discussions with people about imgCIF/CBF, another item has > arisen; unless I'm missing something, there is no "time-stamp" item > for the image. This is certainly useful information which is included > in many current image formats and which I'd like to see in the > CBF. Something like > > _diffrn_scan.date_start > _diffrn_scan.date_end > > using a standard UNIX style date format would be appropriate. I am not sure what the UNIX standard is, but CIF uses the international standard yyyy-mm-ddThh:mm:ss+zz. This can be truncated as necessary. These items would be useful. The next stage is to produce tight definitions in DDL that the rest of us can pull apart. David ***************************************************** Dr.I.David Brown, Professor Emeritus Brockhouse Institute for Materials Research, McMaster University, Hamilton, Ontario, Canada Tel: 1-(905)-525-9140 ext 24710 Fax: 1-(905)-521-2773 idbrown@mcmaster.ca *****************************************************
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