- Ifeffit - millenia.cars.aps.anl.gov

using the mail list archive for mac install
by Joel Brugger SAM 10 Jul '18

10 Jul '18

I ran into the problem that some people seem to have with Demeter on mac while upgrading to High Sierra. I found a fix on this mail list, but 1) I can¹t download Template.pm from the archive (bin file that uncompresses to cpgz file that uncompresses back to a bin file) 2) Matt mentions that he installed 0.9.26 from macports, but I see only 0.9.25 (stable & develop). Sorry for the trivial questions :-) All the best, JOEL [Ifeffit] install for mac error Luke Higgins pmljrh at leeds.ac.uk <mailto:ifeffit%40millenia.cars.aps.anl.gov?Subject=Re:%20Re%3A%20%5BIfeffit %5D%20install%20for%20mac%20error&In-Reply-To=%3CD54C3C92-BBDF-484E-83DA-31D EE99F28A6%40leeds.ac.uk%3E> Tue Apr 3 12:47:31 CDT 2018 * Previous message (by thread): [Ifeffit] install for mac error <http://millenia.cars.aps.anl.gov/pipermail/ifeffit/2018-April/009380.html> * Next message (by thread): [Ifeffit] install for mac error <http://millenia.cars.aps.anl.gov/pipermail/ifeffit/2018-April/009383.html> * Messages sorted by: [ date ] <http://millenia.cars.aps.anl.gov/pipermail/ifeffit/2018-April/date.html#938 2> [ thread ] <http://millenia.cars.aps.anl.gov/pipermail/ifeffit/2018-April/thread.html#9 382> [ subject ] <http://millenia.cars.aps.anl.gov/pipermail/ifeffit/2018-April/subject.html# 9382> [ author ] <http://millenia.cars.aps.anl.gov/pipermail/ifeffit/2018-April/author.html#9 382> Hi All, I see this error too. This is a bit of a bodge job, but if you replace: /opt/local/lib/perl5/vendor_perl/5.26/Text/Template.pm With the attached template.pm from p5.24, it seems to work fine. I¹d just rename the old Template.pm in the same directory, rather than deleting it since another program may end up needing the most recent one. Cheers, Luke From: Ifeffit <ifeffit-bounces at millenia.cars.aps.anl.gov <http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit> > on behalf of Chris Patridge <patridge at buffalo.edu <http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit> > Reply-To: XAFS Analysis using Ifeffit <ifeffit at millenia.cars.aps.anl.gov <http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit> > Date: Tuesday, 3 April 2018 at 19:22 To: XAFS Analysis using Ifeffit <ifeffit at millenia.cars.aps.anl.gov <http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit> > Subject: Re: [Ifeffit] install for mac error Thank you for the input Matt. I am glad to hear that it is not ³user error². I tried it again and I need to correct my earlier statement because Artemis GUI will stay open after the warning however Athena closes/crashes. I will try on a different system. Thanks again, Chris Sent from my iPhone On Apr 3, 2018, at 11:52 AM, Matt Newville <newville at cars.uchicago.edu <http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit> <mailto:newville at cars.uchicago.edu <http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit> >> wrote: Hi Chris, On Mon, Apr 2, 2018 at 4:15 PM, Christopher Patridge <patridge at buffalo.edu <http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit> <mailto:patridge at buffalo.edu <http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit> >> wrote: Hello everyone, I tried to install demeter on my mac (running high Sierra) and it appeared everything went well. However when I run either Athena or Artemis I get an error shown below about Demeter::Templates: showing a error and I am not sure how I can correct this error. Any help would be appreciated. Thanks in advanced, I can confirm this. I just did a fresh install of Macports on 10.13.3 (high sierra). The MacPorts install was not super easy, but once it got to the demeter install, that part went fine. I see the same problem with athena from demeter 0.9.25. I think the warnings about "Demeter::Templates::F" and so forth are meant to be warnings only -- I think they may not be related to the crash of athena. For me, hephaestus gives the same sort of warnings, but runs fine. I can install and run Demeter 0.9.26 (including using Larch as a backend) using Macports, though there are definitely some Mac-specific weirdness. Anyway, I do not believe that "install from source" is a feasible approach for demeter on OSX. I do not know enough about Macports to update the existing package. I don't know that using some other system would be an improvement. We keep seeing problems with demeter on OSX. I'm not sure what the right answer is. Anyone have any suggestions? --Matt _______________________________________________ Ifeffit mailing list Ifeffit at millenia.cars.aps.anl.gov <http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit> <mailto:Ifeffit at millenia.cars.aps.anl.gov <http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit> > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit

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Athena for peak fitting or deconvolution
by Dien.Li＠srnl.doe.gov 09 Jul '18

09 Jul '18

Hi, Bruce I am using the Demeter 9.24 version. I saw in the "main" window the peak fitting and deconvoluting data, but as I clicked, it is not available. Any new update now. Thanks. Dien

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Postdoc position
by Anatoly Frenkel 09 Jul '18

09 Jul '18

Please pass this info along to those who may be interested in this opportunity: There is an opening for a postdoctoral research associate in my group. The postdoc will be stationed in Brookhaven National Laboratory and work as a member of a multi-institution team to develop and apply new methods of operando characterization of catalysts. Expert knowledge of XAFS, strong publication record and strong background in condensed matter physics are required. For inquiries please contact me. Anatoly ------------------------------------------------------------------- Anatoly I. Frenkel Professor Department of Materials Science and Chemical Engineering Stony Brook University Stony Brook, NY 11794, Ph: 631-632-2751 Email: anatoly.frenkel(a)stonybrook.edu <https://mail.bnl.gov/OWA/redir.aspx?C=F6wCGt4adziN6IvpdRQ-rWdgy3Oaoif_x-0yb…> http://you.stonybrook.edu/frenkel Joint Appointment: Chemistry Department, Brookhaven National Laboratory Upton, NY 11973. Ph: 631-344-3013. Group: 631-344-3494 Email: frenkel(a)bnl.gov https://www.bnl.gov/chemistry/bio/FrenkelAnatoly.asp Spokesperson, Synchrotron Catalysis Consortium (SCC) at BNL http://you.stonybrook.edu/scc2 -------------------------------------------------------------------

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Larch 0.9.38
by Matt Newville 08 Jul '18

08 Jul '18

Hi Folks, Version 0.9.38 of Larch has been released and binary installers are now available for Windows, MacOS, and Linux. There have been many minor improvements made in the past several months, particularly for the XAS Viewer application. XAS Viewer is now very close to having feature parity with Athena and Sixpack, with a few things still missing and a few things slightly improved. This should be of particular interest for Mac users, where Athena has proven difficult to install and buggy, and support for Sixpack has also become harder. At this point, XAS Viewer can read data from plain ASCII files or from recent Athena Project files, but does not yet support quite as many different file types as Athena and Sixpack -- help on this would be greatly appreciated! It can do basic group manipulation such as merging, and groups and plot one or more XAFS spectra in various stages of the XAFS normalization process and can save data to Athena Project file or save multiple data sets to CSV files. XAS Viewer has simple dialogs for doing common data correction steps including recalibration, rebinning of QXAFS data (as per a recent discussion), glitch removal, correcting over-absorption, smoothing, and spectral deconvolution. For analysis, XAS Viewer has a notebook panel for pre-edge subtraction and normalization, and one for basic EXAFS processing (background removal and Fourier transforms to chi(R)). Its main emphasis is on visualization and analysis of XANES spectra and so it includes panels dedicated to fitting pre-edge peaks, Linear Combination analysis, and Principal Component Analysis. Though definitely a Graphical User Interface, with forms to guide the novice user, XAS Viewer goes out its way to do all data processing through basic Larch commands that can be viewed, copied, and turned into batch processing scripts. Documentation for all of Larch is a continual work in progress, and docs with screenshots for XAS Viewer is at https://xraypy.github.io/xraylarch/guis/xas_viewer.html Feedback or suggestions on this or any other aspects of Larch are most welcome. Larch can be installed with simple installers for Windows, Mac OSX, Linux which can be found from https://xraypy.github.io/xraylarch/installation.html At the moment, these installers all assume 64-bit operating systems and now are built using Anaconda Python version 3.6. If anyone needs to use Larch with 32-bit Windows please let me know. Support for this will probably be dropped by the end of the calendar year, but I do not know if this is necessary at all at this point. For people using Larch from Python, it can also be installed as a "conda package" for Anaconda Python, as with conda install -c GSECARS xraylarch Currently, packages are available for Python 3.6, and packages for Python 2.7 should be available within a couple days. Please let me know if you have any questions or problems, --Matt

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data after rebinning look worse in k-space than before?
by Ilya Sinev 04 Jul '18

04 Jul '18

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 -- Herr Dr. Ilya Sinev Institute for Experimental Physics IV Faculty of Physics and Astronomy Ruhr-Universität Bochum Universitätsstrasse 150 44801 Bochum, Germany Office: NB 4/134 Phone: +49 234 32 23647 Fax: +49 234 32 14173 e-mail: <mailto:Ilya.Sinev@rub.de> Ilya.Sinev(a)rub.de www.ep4.rub.de

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Fitting Problems in Artemis version 0.9.26
by LIU HUAN 29 Jun '18

29 Jun '18

Dear Dr. Ravel, I want to ask you that when I use the new version "Artemis 0.9.26" I have two problems. (1) The fitting Range was reported to be a error that the Rmin should be larger than the Rkbg value. It makes that the fitting range cannot be smaller than 0.9 (the Rkbg value is 0.9). (2) When Fitting the Debye�CWaller factor (ss) and coordination number (N), although I use "abs()" to make it to be positive, but the fitting results still be negative. But I did not meet these problems in the old version in Artemis 0.8.012. I am wondering that whether could you tell me how to solve these problems. Thank you so much. Sincerely, Huan Huan Liu School of Earth Sciences and Engineering Nanjing University 163 Xianlin Road, Nanjing, Jiangsu, 210023 P. R. China Tel 86-15861809073 Email: huanliu_earth(a)hotmail.com

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Re: [Ifeffit] Ifeffit Digest, Vol 184, Issue 23
by Christopher Chantler 28 Jun '18

28 Jun '18

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(a)unimelb.edu.au<https://owa.unimelb.edu.au/owa/redir.aspx?C=c7BoS0kVVkC1_S95-9x9l5cBu6YTjdA…> chantler(a)me.com<https://owa.unimelb.edu.au/owa/redir.aspx?C=c7BoS0kVVkC1_S95-9x9l5cBu6YTjdA…> http://optics.ph.unimelb.edu.au/~chantler/xrayopt/xrayopt.html<https://owa.unimelb.edu.au/owa/redir.aspx?C=c7BoS0kVVkC1_S95-9x9l5cBu6YTjdA…> http://optics.ph.unimelb.edu.au/~chantler/home.html<https://owa.unimelb.edu.au/owa/redir.aspx?C=c7BoS0kVVkC1_S95-9x9l5cBu6YTjdA…> ________________________________ From: Ifeffit <ifeffit-bounces(a)millenia.cars.aps.anl.gov> on behalf of ifeffit-request(a)millenia.cars.aps.anl.gov <ifeffit-request(a)millenia.cars.aps.anl.gov> Sent: Thursday, 28 June 2018 11:18:33 PM To: ifeffit(a)millenia.cars.aps.anl.gov Subject: Ifeffit Digest, Vol 184, Issue 23 Send Ifeffit mailing list submissions to ifeffit(a)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(a)millenia.cars.aps.anl.gov You can reach the person managing the list at ifeffit-owner(a)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 <mauro.rovezzi(a)esrf.fr> To: ifeffit(a)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(a)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/b9cb5209674bf0c3617b3488a75184d4f84126… 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 <edmund.welter(a)desy.de> To: ifeffit(a)millenia.cars.aps.anl.gov Subject: Re: [Ifeffit] data after rebinning look worse in k-space than before? Message-ID: <c8e72aaf-c53f-df54-30d9-caa6ff45a2fe(a)desy.de> 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 <segre(a)iit.edu > <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(a)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(a)iit.edu <mailto:segre@iit.edu> http://phys.iit.edu/~segre > <http://phys.iit.edu/~segre> segre(a)debian.org > <mailto:segre@debian.org>_______________________________________________ > Ifeffit mailing list > Ifeffit(a)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 > > > > -- > --Matt Newville <newville at http://cars.uchicago.edu > <http://cars.uchicago.edu>> 630-252-0431 > > > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)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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Re: [Ifeffit] Ifeffit Digest, Vol 184, Issue 21
by Christopher Chantler 28 Jun '18

28 Jun '18

Dear all Rebinning is always fraught; I would normally not allow a student to do it... You might be interested in our paper [Schalken, M et al., JSR, 2018] which explicitly avoids rebinning and propagates uncertainty to ifeffit-like [Matt modified] analysis, efeffit. This was an outcome from Q2XAFS. We also include code in supplementary information. Note that this also discusses interpolation and how to preserve information content if that is needed. Best wishes Chris PS looking forward to great discussions at Poland -------------------------------------------------------------------------------------- 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(a)unimelb.edu.au<https://owa.unimelb.edu.au/owa/redir.aspx?C=c7BoS0kVVkC1_S95-9x9l5cBu6YTjdA…> chantler(a)me.com<https://owa.unimelb.edu.au/owa/redir.aspx?C=c7BoS0kVVkC1_S95-9x9l5cBu6YTjdA…> http://optics.ph.unimelb.edu.au/~chantler/xrayopt/xrayopt.html<https://owa.unimelb.edu.au/owa/redir.aspx?C=c7BoS0kVVkC1_S95-9x9l5cBu6YTjdA…> http://optics.ph.unimelb.edu.au/~chantler/home.html<https://owa.unimelb.edu.au/owa/redir.aspx?C=c7BoS0kVVkC1_S95-9x9l5cBu6YTjdA…> ________________________________ From: Ifeffit <ifeffit-bounces(a)millenia.cars.aps.anl.gov> on behalf of ifeffit-request(a)millenia.cars.aps.anl.gov <ifeffit-request(a)millenia.cars.aps.anl.gov> Sent: Thursday, 28 June 2018 4:35 AM To: ifeffit(a)millenia.cars.aps.anl.gov Subject: Ifeffit Digest, Vol 184, Issue 21 Send Ifeffit mailing list submissions to ifeffit(a)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(a)millenia.cars.aps.anl.gov You can reach the person managing the list at ifeffit-owner(a)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? (Matt Newville) 2. Re: data after rebinning look worse in k-space than before? (Carlo Segre) ---------------------------------------------------------------------- Message: 1 Date: Wed, 27 Jun 2018 13:31:44 -0500 From: Matt Newville <newville(a)cars.uchicago.edu> To: Carlo Segre <segre(a)iit.edu>, XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> Subject: Re: [Ifeffit] data after rebinning look worse in k-space than before? Message-ID: <CA+7ESbq--_=qjXALgfZ4Bhg4xcwGJDbby5sSshEwMVB=v_bptA(a)mail.gmail.com> Content-Type: text/plain; charset="utf-8" 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 <segre(a)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(a)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(a)iit.edu http://phys.iit.edu/~segre segre(a)debian.org > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit > -- --Matt Newville <newville at http://cars.uchicago.edu> 630-252-0431

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data after rebinning look worse in k-space than before?
by Ilia Sinev 27 Jun '18

27 Jun '18

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? [image: image.png] Thank you Ilya Sinev -- Dr. Ilya Sinev Institute for Experimental Physics IV Faculty of Physics and Astronomy Ruhr-Universität Bochum Universitätsstrasse 150 44801 Bochum, Germany

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Rank of path and dopant amp
by ABDUL AHAD 23 Jun '18

23 Jun '18

Hi all I have a question regarding the Rank of path. Since the Rank represent the spectral weight of the particular path. So that if i have a dopant say Ca and it shows the rank 60 while the main atoms shows rank 98. So in order to maintain the doping concentration, what i have to do? for half atomic % doping. do i make the amp of these two as amp*0.5 ? or do i first normalized its by rank and then decide the amp percentage ? Thanks

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