Re: [Ifeffit] Ifeffit Digest, Vol 184, Issue 23

Yes all, good points. It would be good to test out a few of these procedures. We have done so in the paper mentioned; but it is correct what Edmund said, we did not start with an /extremely/ fine grid as e.g. from a continuous scan. Also it would be good to process this with uncertainties, whether from repeated measurements or fluorescent pixels. Interesting what might come out. -------------------------------------------------------------------------------------- Christopher Chantler, Professor, FAIP, Fellow American Physical Society Editor-in-Chief, Radiation Physics and Chemistry Chair, International IUCr Commission on XAFS CIT, CCN President, International Radiation Physics Society School of Physics, University of Melbourne Parkville Victoria 3010 Australia +61-3-83445437 FAX +61-3-93474783 chantler@unimelb.edu.auhttps://owa.unimelb.edu.au/owa/redir.aspx?C=c7BoS0kVVkC1_S95-9x9l5cBu6YTjdAITgSrfUpfDAUV5oUH1LFYBcz08w8xvHMJoosZRdagfQM.&URL=mailto%3achantler%40unimelb.edu.au chantler@me.comhttps://owa.unimelb.edu.au/owa/redir.aspx?C=c7BoS0kVVkC1_S95-9x9l5cBu6YTjdAITgSrfUpfDAUV5oUH1LFYBcz08w8xvHMJoosZRdagfQM.&URL=mailto%3achantler%40me.com http://optics.ph.unimelb.edu.au/~chantler/xrayopt/xrayopt.htmlhttps://owa.unimelb.edu.au/owa/redir.aspx?C=c7BoS0kVVkC1_S95-9x9l5cBu6YTjdAITgSrfUpfDAUV5oUH1LFYBcz08w8xvHMJoosZRdagfQM.&URL=http%3a%2f%2foptics.ph.unimelb.edu.au%2f%7echantler%2fxrayopt%2fxrayopt.html http://optics.ph.unimelb.edu.au/~chantler/home.htmlhttps://owa.unimelb.edu.au/owa/redir.aspx?C=c7BoS0kVVkC1_S95-9x9l5cBu6YTjdAITgSrfUpfDAUV5oUH1LFYBcz08w8xvHMJoosZRdagfQM.&URL=http%3a%2f%2foptics.ph.unimelb.edu.au%2f%7echantler%2fhome.html ________________________________ From: Ifeffit on behalf of ifeffit-request@millenia.cars.aps.anl.gov Sent: Thursday, 28 June 2018 11:18:33 PM To: ifeffit@millenia.cars.aps.anl.gov Subject: Ifeffit Digest, Vol 184, Issue 23 Send Ifeffit mailing list submissions to ifeffit@millenia.cars.aps.anl.gov To subscribe or unsubscribe via the World Wide Web, visit http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit or, via email, send a message with subject or body 'help' to ifeffit-request@millenia.cars.aps.anl.gov You can reach the person managing the list at ifeffit-owner@millenia.cars.aps.anl.gov When replying, please edit your Subject line so it is more specific than "Re: Contents of Ifeffit digest..." Today's Topics: 1. Re: data after rebinning look worse in k-space than before? (Mauro Rovezzi) 2. Re: data after rebinning look worse in k-space than before? (Edmund Welter) ---------------------------------------------------------------------- Message: 1 Date: Thu, 28 Jun 2018 07:40:13 +0200 From: Mauro Rovezzi To: ifeffit@millenia.cars.aps.anl.gov Subject: Re: [Ifeffit] data after rebinning look worse in k-space than before? Message-ID: <9eae776b-8047-376e-c826-0927b066a1c8@esrf.eu> Content-Type: text/plain; charset=utf-8; format=flowed Matt, From my experience at the ESRF, many users dealing with XAFS data collected in continuous scan mode (either in angle, energy or time) apply the following workflow: 1) average many scans with PyMca; 2) import them in Athena; PyMca does a linear interpolation using the grid of the first scan in the list: https://github.com/vasole/pymca/blob/b9cb5209674bf0c3617b3488a75184d4f841264... I have never run a study on which merging scheme is the best, but I would recommend using an "histogram-like" approach, as you propose: 1) make a "normal XAFS energy grid"; 2) assign each energy point in the original data to one of these energy bins and take the average of all the points in each bin. This approach is usually employed in ray tracing applications, where the number of rays is huge and one needs to make an histogram for plotting (e.g. ray intensity versus a given variable). Mauro On 2018-06-27 20:31, Matt Newville wrote:

This seems like a good chance to test these procedures out.

My approach for this is to this is to make a "normal XAFS energy grid" of ~5 eV steps, 0.25 eV steps, 0.05 Ang^-1 steps that the downstream processing needs, and then do one of two strategies -- maybe there should be more?: ?a) do a straight interpolation onto this array -- that is probably the "noisy" result. ?b) assign each energy point in the original data to one of these energy bins, and take the average of all the points in each bin.

I'd also like to try using energy-weighted mean (centroid).? Probably most of the data is so finely spaced that this won't make much difference, but it might be a good option.?? It might be able to help compensate for energy jitter, assuming that the recorded energy (probably from an encoder) is more accurate than the requested energy.

It's also interesting to think about doing a Savitzky-Golay smoothing, though that might require knowing if the data points are actually uniform in mono angle or mono energy.? It also makes it easy to over-do the smoothing, and so a little trickier to prevent bad results.

Do you (or anyone else) have any suggestions for how to best re-bin this kind of data?

--Matt

------------------------------ Message: 2 Date: Thu, 28 Jun 2018 15:18:04 +0200 From: Edmund Welter To: ifeffit@millenia.cars.aps.anl.gov Subject: Re: [Ifeffit] data after rebinning look worse in k-space than before? Message-ID: Content-Type: text/plain; charset="utf-8"; Format="flowed" Dear Matt, attached you will find a recent data file which is showing the problem and two plots of the data (A RuO2 powder sample on Scotch tape) in the file. One plot is showing the Chi(k) with and without rebinning the other one just mue(E) with and without rebinning. It seems it is no good to convert previously rebinned data to k-space. the rebinned mue(E) looks okay and the original data converted to k-space does also look ok. I produced the plots with Athena 0.9.24 (I know not the most recent version) under WIN 7 with IFEFFIT as backend. I wasn't able yet to reproduce this on my office desktop using LINUX and the most recent dathena and Larch, because of some trouble with reading the data file... No idea yet, might be worse another thread or might be something stupid on my site. Cheers, Edmund On 27.06.2018 20:31, Matt Newville wrote:

HI Ilya, Edmund, Carlo,

Ilya and/or Carlo: can you post some example unbinned data?? As it turns out, I am adding a rebinning feature in the Larch XAS Viewer GUI that should be ready for a ready-to-try release very soon (for IIT XAFS School and XAFS2018).

This seems like a good chance to test these procedures out.

My approach for this is to this is to make a "normal XAFS energy grid" of ~5 eV steps, 0.25 eV steps, 0.05 Ang^-1 steps that the downstream processing needs, and then do one of two strategies -- maybe there should be more?: ?a) do a straight interpolation onto this array -- that is probably the "noisy" result. ?b) assign each energy point in the original data to one of these energy bins, and take the average of all the points in each bin.

I'd also like to try using energy-weighted mean (centroid).? Probably most of the data is so finely spaced that this won't make much difference, but it might be a good option.?? It might be able to help compensate for energy jitter, assuming that the recorded energy (probably from an encoder) is more accurate than the requested energy.

It's also interesting to think about doing a Savitzky-Golay smoothing, though that might require knowing if the data points are actually uniform in mono angle or mono energy.? It also makes it easy to over-do the smoothing, and so a little trickier to prevent bad results.

Do you (or anyone else) have any suggestions for how to best re-bin this kind of data?

--Matt

On Wed, Jun 27, 2018 at 10:15 AM Carlo Segre mailto:segre@iit.edu> wrote:

Yes, we measure fast and have taken as many as 20000 points.? ?The problem is not in the shifts that you mention.? This is normal and expected.? the problem is specificallly in the rebinning algorithm in Demeter.? It seems to be different than the one in the old Horae package.? I have done a test of this and I attache a coule of figures that show the difference.

I have used 10 continuous scans for this test.? The data were taken at the MRCAT beamline, Sector 10 at the APS.? The data are for the Fe K-edge and there are about 3400 points per scan with a point density of about 0.35 eV/step.? I used both versions of Athena and performed the following steps to give the data groups shown in the plots

new_athena.png ? Fe_new_rebin_merge - (blue) all 10 scans rebinned at input and then ? ? ? ? ? ? ? ? ? ? ? ?merged ? Fe_new_merge? ? ? ?- (red) all 10 scans merged only ? Fe_new_merge_rebin - (green) all 10 scans merged then rebinned

old_athena.png ? Fe_old_rebin_merge - (blue) all 10 scans rebinned at input and then ? ? ? ? ? ? ? ? ? ? ? ?merged ? Fe_old_merge? ? ? ?- (red) all 10 scans merged only ? Fe_old_merge_rebin - (green) all 10 scans merged then rebinned

comp_athena.png ? Fe_old_rebin_merge - (blue) ? Fe_new_rebin_merge - (red)

It is clear that the new Athena (Demeter) is not rebinning the same way as the old one (Horae).? The contrast is particularly evident with the last plot. The new rebinning algorithm is introducing more noise.? For the moment, I recommend only merging and perhaps smoothing if you can tolerate a bit of amplitude reduction.

I have been thinking that it might even be better to have the data acquisition software do the rebinning on the fly so the data does not have to be manipulated in Athena.? I am not sure if this is a good idea yet but I think it would help my users.

Carlo

On Wed, 27 Jun 2018, Edmund Welter wrote:

> Dear Carlo, > > do you also measure as fast as possible in the sense that for two consecutive > scans the points on the energy axis are not at the same positions? This is > what happens at my beamline. The differences are typically very small but > there are differences and one should not just add all the first points and > all the second points and so on because they are not necessarily exactly at > the same energy. Sometimes the beamline computer is doing something else in > parallel (whatever that might be) and the distance between points A and B is > significantly larger than the distance between B and C. > > So, the problem is, at which point does it make sense to merge several > spectra of the same sample? I presume that Athena is taking care of this when > I use it to merge spectra, but it can only do so by interpolating the points > in the spectrum onto a common grid before summing up the spectra. > > The best solution might be to rebin/interpolate the spectra onto a fixed grid > before they are imported into Athena (or any other program), depends on what > Athena is exactly doing when it is rebinning data. > > Another aspect is that Athena is not very happy about 8600 points/spectrum > anyway, at least as long as it using Ifeffit. > > Cheers, > > Edmund > > > > On 27.06.2018 15:14, Carlo Segre wrote: >> >> >> Hi Ilya: >> >> We always take data in this mode at APS Sector 10 and I have also find that >> the rebinning function is not working satisfactorily at this time.? I find >> that for the current version of the software it is better to merge your >> data and let IFEFFIT interpolate to the dk=0.05 grid that it uses. >> >> Carlo >> >> >> On Wed, 27 Jun 2018, Ilya Sinev wrote: >> >>> Hi all, >>> >>> >>> >>> I have a question regarding the chi(k) function isolation and rebinning >>> processes. I have some data recorded in ?quasi channel-cut? modus, i.e. >>> with >>> the mono constantly moving and the data points collected with the highest >>> possible rate. With 180 sec measurement in yields to a spectrum of ca. >>> 8600 >>> point, which obviously needs to be rebinned. The rebinned data, however, >>> does not look good in k-space even if multiple data are merged. Moreover, >>> I >>> have an impression that the raw spectrum in k-space does not have those >>> 8000+ points anymore but significantly less. Is there any reduction of the >>> data points number that is not seen (e.g. as a preparation step for FT)? >>> Since the unbinned data has higher quality, does it then make more sense >>> to >>> keep using it for EXAFS analysis? >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> Thank you >>> >>> Ilya Sinev >>> >>> >>> >>> >> > > _______________________________________________ > Ifeffit mailing list > Ifeffit@millenia.cars.aps.anl.gov mailto:Ifeffit@millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit >

-- Carlo U. Segre -- Duchossois Leadership Professor of Physics Interim Chair, Department of Chemistry Director, Center for Synchrotron Radiation Research and Instrumentation Illinois Institute of Technology Voice: 312.567.3498? ? ? ? ? ? Fax: 312.567.3494 segre@iit.edu mailto:segre@iit.edu http://phys.iit.edu/~segre http://phys.iit.edu/~segre segre@debian.org mailto:segre@debian.org_______________________________________________ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov mailto:Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit

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